WO2005002526A2 - Method and compositions for treatment of viral infections - Google Patents

Abstract

The present invention relates to methods and compositions for the treatment and/or prevention of diseases or disorders associated with viral infection. Accordingly, the nucleotide and amino acid sequences for a human Brd4 protein are provided. Also provided are complexes comprising Brd4 and an E2 protein or a functional equivalent of an E2 protein.

Description

METHODS AND COMPOSITIONS FOR TREATMENT OF VIRAL INFECTIONS

RELATED APPLICATIONS This application claims the benefit of priority to U.S. Provisional Patent Application No. 60/484,417, filed on July 1, 2003, and U.S. Provisional Patent Application No. 60/484,792, filed July 3, 2003, which applications are hereby incorporated by reference in their entirety. BACKGROUND Illnesses resulting from viral infections remain a major problem to be addressed by modern medicine. To date, there is no suitably effective treatment for infection with any known virus. Recently there has been progress towards treatment of several viral diseases, however, these treatments are largely directed at specific viruses or classes of viruses. For example, protease inhibitors targeting the virally-encoded human immunodeficiency virus (HIV) protease have been effective against some strains of HIV, and have been responsible, when used in combination with other anti- viral agents, for a decline in HlV-related deaths in the United States. However, the protease inhibitors are directed to specific viruses or classes of viruses, and are not useful for the treatment of viruses outside of those classes. In addition, there is evidence that strains resistant to these new agents are evolving. It is noted that the virus-specific agents currently being used in developed countries are very expensive, being beyond the means of a great number of infected individuals throughout the world. In addition, the dosage regimens are complex and demand careful attention by physicians and the infected individuals. Because viruses co-opt the host's own normal intracellular metabolic processes for their reproductive needs, a major difficulty in the design of antiviral agents is to make agents that target the virus without toxicity to the host organism. There is a need in the art for antiviral agents that are effective against a broad spectrum of viruses, relatively non-toxic, inexpensive to produce, and simple to administer.

SUMMARY The present disclosure provides methods and compositions for treatment and/or prevention of viral infections. In one aspect, the invention provides isolated Brd4 polypeptides, comprising: (a) an amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95% identity with the amino acid sequence set forth in SEQ ID NO: 2; or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein. In certain embodiments, the Brd4 polypeptides are capable of interacting with an E2 protein or a functional equivalent of an E2 protein. In an exemplary embodiment, the Brd4 polypeptides are capable of interacting with the transactivation domain of an E2 protein or a functional equivalent of an E2 protein. In one embodiment, the invention provides an isolated polypeptide comprising at least 5,

10, 20, 25, 30, 40, 50, or more, consecutive amino acid residues of SEQ ID NO: 2 wherein said polypeptide is capable of disrupting an interaction between a Brd4 protein and an E2 protein or a functional equivalent of an E2 protein. In exemplary embodiments, the invention provides isolated polypeptides comprising at least 5, 10, 20, 25, 30, 40, 50, or more, consecutive amino acid residues of a region of SEQ ID NO: 2 having amino acids 1047-1362 or a region of SEQ ID NO: 2 having amino acids 1224-1362. In one embodiment, a polypeptide comprising amino acid residues 1047-1362 of SEQ ID NO: 2 is provided. In another embodiment, a polypeptide

5 comprising amino acid residues 1224-1362 of SEQ ID NO: 2 is provided. In still other embodiments, the invention provides peptidomimetics based on the sequence set forth in SEQ ID NO: 2 or a fragment thereof. In another embodiment, the invention provides an isolated monoclonal antibody that binds to a polypeptide comprising SEQ ID NO: 2 and does not bind to a polypeptide comprising

LO SEQ ID NO: 4. In another embodiment, the antibody binds specifically to a polypeptide comprising SEQ ID NO: 2. In yet another embodiment, the invention provides an anti-human Brd4 antibody that does not substantially cross-react (e.g., less than 50%, 40%, 30%, 25%, 20%, 15%, 10%, 5%, 2%, 1%, 0.5%), 0.1%), or less cross-reactivity) with a protein which is less than 95% identical to SEQ ID NO: 2. In various embodiments, such antibodies may be single chain

[5 and/or humanized antibodies. In other embodiments, the antibodies of the invention may be formulated in a pharmaceutically acceptable carrier. In one embodiment, the invention provides an antibody that interacts with a portion of a Brd4 protein that interacts with an E2 protein or a functional equivalent of an E2 protein. In another embodiment, the invention provides an antibody that interacts with a region of human Brd4 that comprises amino acid residues 1047-

.0 1362 or residues 1224-1362 of SEQ ID NO: 2. In another aspect, the invention provides an isolated nucleic acid comprising (a) the nucleotide sequence of SEQ ID NO: 1, (b) a nucleotide sequence at least 90% identical to SEQ ID NO: 1, (c) a nucleotide sequence that hybridizes under stringent conditions to SEQ ID NO: 1, or (d) the complement of the nucleotide sequence of (a), (b) or (c). In yet another aspect, the invention provides an isolated nucleic acid comprising a nucleotide sequence encoding a fragment of SEQ ID NO: 2 wherein said fragment comprises at least 5 consecutive amino acid residues and wherein said fragment is capable of disrupting an interaction between a Brd4 protein and an E2 protein or a functional equivalent of an E2 protein. In various embodiments, the nucleic acids described herein may further comprise a transcriptional regulatory sequence operably linked to said nucleotide sequence so as to render said nucleic acid suitable for use in an expression vector. Additionally, the nucleotide sequences described herein may be contained on a vector, such as, for example, an expression vector. In another aspect, the invention provides a host cell comprising a nucleic acid encoding a ι polypeptide comprising (a) an amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95% identity with the amino acid sequence set forth in SEQ ID NO: 2; or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein. In yet another aspect, the invention provides an isolated complex comprising (a) Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide. In one exemplary embodiment, the invention provides a complex comprising (a) an amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95%» identity with the amino acid sequence set forth in SEQ ID NO: 2; or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein. In another exemplary embodiment, the invention provides a complex comprising an E2 protein from a papilloma virus, including a human papilloma virus (HPV) or a non-human animal papillomavirus (such as, for example, a bovine papilloma virus (BPV), a canine papillomavirus, a feline papillomavirus, a monkey papillomavirus, an equine papillomavirus, etc.), or a functional equivalent of an E2 protein from a herpes virus. In another exemplary embodiment, the invention provides a complex comprising a latency-associated nuclear antigen (LANA) protein from a Kaposi sarcoma-associated herpesvirus (KSHV). In another embodiment, the invention provides an isolated antibody that has a higher binding affinity for a complex of claim 24 than for the individual polypeptides of said complex. In an exemplary embodiment, the invention provides an antiobdy that disrupts, or inhibits the formation of, a complex comprising a Brd4 protein and an E2 protein or a functional equivalent of an E2 protein. In another aspect, the invention provides a fusion polypeptide, comprising an amino acid sequence having: (a) the amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95% identity with the amino acid sequence set forth in SEQ ID NO: 2; (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein; or (d) an amino acid sequence having at least five consecutive amino acid residues of SEQ ID NO: 2 wherein said polypeptide is capable of interacting with an E2 protein or a functional equivalent of an E2 protein; fused to a polypeptide selected from the group consisting of: (e) an E2 polypeptide; (f) a functional equivalent of an E2 polypeptide; or (g) a fragment of (e) or (f) that is capable of interacting with a polypeptide of (a), (b), (c), or (d). In another aspect, the invention provides a method for identifying a compound that disrupts a Brd4 protein complex, comprising: (i) providing a reaction mixture comprising (a) Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (ii) contacting the reaction mixture with a test agent; and (iii) determining the effect of the test agent on the formation or stability of a complex comprising (a), (b), (c), or (d), wherein a decrease in the formation or stability of said complex is indicative of a compound that disrupts a Brd4 protein complex. In an exemplary embodiment, the reaction mixture is a cell or cell population which may optionally be infected with a virus or otherwise contain at least a portion of a viral genome. In another aspect, the invention provides a method for identifying modulators of a Brd4 protein complex, comprising: (i) forming a reaction comprising a complex, wherein said complex comprises: (a) Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of

Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of

Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (ii) contacting the reaction mixture with a test agent; and (iii) determining the effect of the test agent on one or more of the following activities: (a) a change in the level of said complex, (b) a change in the activity of said complex, (c) a change in the stability of said complex, (d) a change in the conformation of said complex, (e) a change in the activity of at least one polypeptide of said complex, (f) a change in the conformation of at least one polypeptide of said complex, (g) where the reaction mixture is a whole cell, a change in the intracellular localization of the complex or a component thereof, (h) where the reaction mixture is a whole cell, a change in the transcription level of a gene dependent on the complex, and (i) where the reaction mixture is a whole cell, a change in second messenger levels in the cell. In another aspect, the invention provides a method for identifying a compound that inhibits viral infectivity or proliferation comprising: (i) providing a reaction mixture comprising (a) Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (ii) contacting the reaction mixture with a test agent; and (iii) determining the effect of the test agent on the formation or stability of a complex comprising (a), (b), (c), or (d), wherein a decrease in the formation or stability of said complex is indicative of a compound that inhibits viral infectivity or proliferation. In another aspect, the invention provides a method for treating a subject suffering from a viral related disease or disorder, comprising administering to an animal having said condition a therapeutically effective amount of a polypeptide comprising at least five consecutive amino acids from a region of SEQ ID NO: 2 having amino acids 1224-1362, wherein said polypeptide is capable of binding to an E2 polypeptide or a functional equivalent of an E2 polypeptide. In certain embodiment, the subject may be suffering from a disease or disorder related to an infection of a papillomavirus, herpes virus, Epstein Barr virus, or a Kaposi sarcoma-associated virus. In various embodiments, the methods and compositions described herein may be used to treat any organism which is susceptible to a viral infection, including, for example, plants and animals. In an exemplary embodiment, the methods and compositions described herein may be used to treat a human. In other embodiments, the methods and compositions described herein may be used to treat a livestock animal, such as, for example, a cow, pig, goat or sheep. In another aspect, the invention provides a method for inhibiting Brd4 dependent growth or infectivity of a virus, comprising contacting a virus infected cell with a polypeptide comprising at least five consecutive amino acids from a region of SEQ ID NO: 2 having amino acids 1224-1362, wherein said polypeptide is capable of binding to an E2 polypeptide or a functional equivalent of an E2 polypeptide. The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Patent No: 4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss,

Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.);

Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory

Press, Cold Spring Harbor, N.Y., 1986).

BRIEF DESCRIPTION OF THE DRAWINGS FIGURE 1 shows a representation of an SDS-PAGE electrophoresis of polypeptides that co-purified with E2TA (full length E2 from BPV1) or E2TR (a truncation mutant of E2 missing

the transactivation domain). FIGURE 2 shows the results of an E2TA pull down of endogenous Brd4. FIGURE 3 shows the results of an E2TA pull down of FLAG-MBrd4. FIGURE 4 shows the results of an experiment demonstrating that HPV16E2 interacts with HBrd4. FIGURE 5 shows a schematic of the cloning of Human Brd4 (HBrd4). FIGURE 6 shows the nucleotide sequence of human Brd4 (SEQ ID NO: 1). FIGURE 7 shows an alignment between the amino acid sequences for human Brd4 (SEQ

ID NO: 2) and mouse Brd4 (SEQ ID NO: 4). FIGURE 8 shows the results of experiments carried out to map the E2 binding domain on human Brd4 protein. FIGURE 9 shows the results of an experiment demonstrating that the C-terminal region of human Brd4 protein (amino acids 1047-1362) disrupts the interaction between Brd4 and E2. FIGURE 10 shows the results of an immunofluorescence experiment with C33A-E2TA cells double stained with Brd4 antibody and E2TA antibody. FIGURE 11 shows the results of an immunofluorescence experiment demonstrating that a C-terminal fragment of human Brd4 (amino acids 1134-1362) disrupts the interaction between recombinant GST-E2TA and endogenous human Brd4 protein. FIGURE 12 shows the results of an immunofluorescence experiment demonstrating that a C-terminal fragment of human Brd4 (amino acids 1047-1362) blocks the binding of E2 protein to host mitotic chromosomes. FIGURE 13 shows the results of a chromatin immunoprecipitation (ChIP) experiment demonstrating the interaction between human Brd4 protein and the BPV-1 genome. FIGURE 14 shows the results of a colony formation assay demonstrating that a C- terminal fragment of human Brd4 protein (amino acids 1047-1362) inhibits the transformation of C127 cells by BPV-1. FIGURE 15 shows the results of an experiment demonstrating the colocalization of full- length E2 protein with Brd4 on mitotic chromosomes. FIGURE 16 shows a schematic of the generation of cell lines H2-CTD (H2 cells expressing Brd4-CTD) and H2-V (H2 cells carrying empty vector). FIGURE 17 shows the results of an experiment demonstrating that stable expression of the Brd4 C-terminal domain abrogates association of the BPV-1 genome with host mitotic chromosomes. FIGURE 18 shows a schematic of experiments used to investigate curing of BPV-1 5 infected cells in the presence of Brd4 C-terminal domain. FIGURE 19 shows the results of real-time PCR quantitative analysis of BPV-1 episomes in H2 stable cells passaged at 1 : 100 dilution. FIGURE 20 shows the results of a morphology analysis of H2 cells expressing Brd4 C- terminal domain as compared to H2 cells containing empty vector after 12 passages split at 1:10 10 dilution. FIGURE 21 shows the rate of reversion of H2 cells expressing Brd4 C-terminal domain as compared to the rate of reversion of H2 cells containing empty vector after 9 passages split at 1:10 dilution. FIGURE 22 shows the morphological characteristics of H2 cells expressing Brd4 C- [5 terminal domain (bottom panel) as compared to H2 cells containing empty vector (top panel). FIGURE 23 shows the morphological characteristics of a representative revertant cell line (right panel) as compared to that of a transformed cell line (left panel). FIGURE 24 shows the nucleotide sequence of mouse Brd4 (SEQ ID NO: 3). The nucleotide and amino acid sequences for mouse Brd4 may be found at GenBank accession .0 number NM 020508. DETAILED DESCRIPTION General The papillomavirus E2 protein is a multifunctional viral gene product that has been implicated in viral DNA replication, viral transcription, and regulation of cellular transformation. In addition, E2 protein has been shown to play a critical role in plasmid maintenance by linking the viral genomes to the cellular mitotic chromosomes to ensure their accurate segregation into daughter cells. To identify cellular factors that may play important roles in E2 virus-host cell interactions, we employed a proteomic tandem affinity purification (TAP) approach to systematically analyze cellular proteins that associate with E2 in vivo. Mass spec analysis of the proteins co-purified with E2 has identified the Brd4 protein as a factor that associates with the I viral E2 protein. Using co-immunoprecipitation, we showed that endogenous Brd4 interacts with both human and bovine papillomavirus E2 protein, suggesting a conserved role involving Brd4 in papillomavirus E2 function. Brd4 interacts specifically with the N-terminal transactivation domain of E2, and the E2 binding region on Brd4 has been mapped to its C-terminal region. Immunofluorescent analysis revealed the co-localization of E2 and Brd4 on mitotic chromosomes in human cells. Expression of a truncated C-terminal domain of Brd4 inhibits the interaction of endogenous Brd4 with E2 and also prevents the co-localization of the viral protein and its cellular partner. Co-transfection of this dominant-negative truncation mutant of Brd4 with BPV-1 genome into C127 cells significantly inhibited the transformation efficiency. Taken together, our studies indicate that the cellular protein Brd4 is an important therapeutic target for papillomavirus infections. Definitions For convenience, certain terms employed in the specification, examples, and appended claims are collected here. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to

5 which this invention belongs. The articles "a" and "an" are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element. The terms "activity" or "biological activity" or "bioactivity" or "biological function" of a

.0 polypeptide, which are used herein interchangeably, refer to an effector or antigenic function that is directly or indirectly performed by the polypeptide (whether in its native or denatured conformation), or by any subsequence thereof. Biological activities include, but are not limited to, binding to polypeptides, binding to other proteins or molecules, activity as a DNA binding protein, as a transcription regulator, ability to bind damaged DNA, enzymatic activity, methyl

[5 transferase activity, phosphorylase or kinase activity, conformational changes, changes in intracellular localization, changes in the transcription level of the gene encoding the peptide, changes in second messenger levels, etc. An activity may be modulated by directly affecting the subject polypeptide. Alternatively, a bioactivity may be altered by modulating the level of the polypeptide, such as by modulating expression of the corresponding gene.

-0 The term "antibody" refers to an immunoglobulin, derivatives thereof which maintain specific binding ability, and proteins having a binding domain which is homologous or largely homologous to an immunoglobulin binding domain. These proteins may be derived from natural sources, or partly or wholly synthetically produced. An antibody may be monoclonal or polyclonal. The antibody may be a member of any immunoglobulin class, including any of the human classes: IgG, IgM, IgA, IgD, and IgE. In exemplary embodiments, antibodies used with the methods and compositions described herein are derivatives of the IgG class. The term "antibody fragment" refers to any derivative of an antibody which is less than full-length. In exemplary embodiments, the antibody fragment retains at least a significant portion of the full-length antibody's specific binding ability. Examples of antibody fragments include, but are not limited to, Fab, Fab', F(ab')₂, scFv, Fv, dsFv diabody, and Fd fragments. The antibody fragment may be produced by any means. For instance, the antibody fragment may be enzymatically or chemically produced by fragmentation of an intact antibody, it may be recombinantly produced from a gene encoding the partial antibody sequence, or it may be wholly or partially synthetically produced. The antibody fragment may optionally be a single chain antibody fragment. Alternatively, the fragment may comprise multiple chains which are linked together, for instance, by disulfide linkages. The fragment may also optionally be a multimolecular complex. A functional antibody fragment will typically comprise at least about 50 amino acids and more typically will comprise at least about 200 amino acids. The term "binding" or "interacting", as applied to two molecules, refers to an association, which may be a stable association, between the two molecules, e.g., between a polypeptide of the invention and a binding partner, due to, for example, electrostatic, hydrophobic, ionic and/or hydrogen-bond interactions under physiological conditions. Exemplary interactions include protein-protein, protein-nucleic acid, protein-small molecule, and small molecule-nucleic acid interactions. The term "biological sample" when used in reference to a diagnostic assay is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. The term "Brd4 complex polypeptide" refers to an individual polypeptide that may be present in a Brd4 complex, including Brd4 and polypeptides that may interact with Brd4 either directly or indirectly. In exemplary embodiments, a Brd4 complex polypeptide refers to Brd4, E2, and functional equivalents of E2. In other embodiments, a Brd4 complex polypeptide refers to a fusion protein comprising all or a portion of one or more Brd4 complex polypeptides such as Brd4 and/or E2 (or a functional equivalent thereof). The term "complex", as applied to two moieties, refers to an association between at least two moieties (e.g. chemical or biochemical) that have an affinity for one another. Examples of complexes include associations between antigen/antibodies, lectin/avidin, target polynucleotide/probe oligonucleotide, antibody/anti-antibody, receptor/ligand, enzyme/ligand and the like. "Member of a complex" refers to one moiety of the complex, such as an antigen or ligand. "Protein complex" or "polypeptide complex" refers to a complex comprising at least one polypeptide. In certain exemplary embodiments, a complex refers to a "Bdr4 complex" comprising Brd4 and at least one other molecule. In exemplary embodiments, a Brd4 complex comprises (a) Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide. In one embodiment, the complex comprises (a) an amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95% identity with the amino acid sequence set forth in SEQ ID NO: 2; or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein. In another embodiment, the complex comprises a fragment of Brd4 having residues

5 1047-1362, 1134-1362, or 1224-1362 of SEQ ID NO: 2. In another embodiment, the complex comprises a fragment having at least five consecutive amino acid residues from SEQ ID NO: 2 or a region of SEQ ID NO: 2 having amino acid residues 1047-1362, 1134-1362, or 1224-1362 of SEQ ID NO: 2. The term "E2 polypeptide" is known in the art and refers to a viral protein that

[0 participates in viral replication, viral transcription, and or regulation of cellular transformation. In an exemplary embodiment, an E2 protein is capable of interacting with a Brd4 protein. E2 polypeptides typically are composed of two well-conserved functional domains. The E2 carboxy-terminus generally includes a DNA binding domain that binds as a dimer to the ACCN₆GGT recognition sequence (Andropy et al., Nature, 1987, 325, 70). The E2 amino-

[5 terminus typically features a transcriptional activation domain that regulates viral gene expression and interacts with components of the host cell apparatus. The E2 amino-terminus also interacts with the El protein. These amino-terminal and the carboxy-terminal domains are connected by a hinge region that is dispensable for both replication and transcriptional activation. In exemplary embodiments, E2 proteins in accordance with the invention include, for example,

20 E2 proteins from papillomaviruses, Epstein Barr viruses, and Herpes viruses. Exemplary E2 proteins include, for example, the E2 proteins from bovine papilloma virus 1 (BPV1), human papilloma viruses (HPV) 16, 6b, 11, 18, 31, 1A, and 57 (see e.g., Sakai et al., J. Virology 70: 1602- 1611 (1996) for sequences of a variety of exemplary E2 proteins). The term "functional equivalent of an E2 polypeptide" refers to a viral protein that may share little sequence identity (e.g., less than 80%, 70%, 50%, 40%, 30%, 20%, 10%, or less) or structural similarity to an E2 protein but carries out at least one biological activity similar to that of an E2 protein. For example, a functional equivalent of an E2 protein may participate in viral replication, viral transcription, and/or regulation of cellular transformation. In an exemplary embodiment, a functional equivalent of an E2 protein is capable of interacting with a Brd4 protein. An example of a functional equivalent of an E2 polypeptide is the latency-associated nuclear antigen (LANA) protein from Kaposi sarcoma-associated herpesvirus (KSHV). A "fusion protein" or "fusion polypeptide" refers to a chimeric protein as that term is known in the art and may be constructed using methods known in the art. In many examples of fusion proteins, there are two different polypeptide sequences, and in certain cases, there may be more. The sequences may be linked in frame. A fusion protein may include a domain which is found (albeit in a different protein) in an organism which also expresses the first protein, or it may be an "interspecies", "intergenic", etc. fusion expressed by different kinds of organisms. In various embodiments, the fusion polypeptide may comprise one or more amino acid sequences linked to a first polypeptide. In the case where more than one amino acid sequence is fused to a first polypeptide, the fusion sequences may be multiple copies of the same sequence, or alternatively, may be different amino acid sequences. The fusion polypeptides may be fused to the N-terminus, the C-terminus, or the N- and C-terminus of the first polypeptide. Exemplary fusion proteins include polypeptides comprising a glutathione S-transferase tag (GST-tag), histidine tag (His-tag), an immunoglobulin domain or an immunoglobulin binding domain. Other fusion proteins of the invention include polypeptides comprising all or a portion of a Brd4 polypeptide fused to all or a portion of an E2 polypeptide or a functional equivalent of an E2 polypeptide. The term "gene" refers to a nucleic acid comprising an open reading frame encoding a polypeptide having exon sequences and optionally intron sequences. The term "intron" refers to a DNA sequence present in a given gene which is not translated into protein and is generally found between exons. The "level of expression of a gene in a cell" or "gene expression level" refers to the level of mRNA, as well as pre-mRNA nascent transcript(s), transcript processing intermediates, mature mRNA(s) and degradation products, encoded by the gene in the cell. "Gene construct" refers to a vector, plasmid, viral genome or the like which includes a "coding sequence" for a polypeptide or which is otherwise transcribable to a biologically active RNA (e.g., antisense, decoy, ribozyme, etc), may transfect cells, in certain embodiments mammalian cells, and may cause expression of the coding sequence in cells transfected with the construct. The gene construct may include one or more regulatory elements operably linked to the coding sequence, as well as intronic sequences, poly adenylation sites, origins of replication, marker genes, etc. "Host cell" refers to a cell that may be transduced with a specified transfer vector. The cell is optionally selected from in vitro cells such as those derived from cell culture, ex vivo cells, such as those derived from an organism, and in vivo cells, such as those in an organism. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein. The term "including" is used herein to mean "including but not limited to". "Including" and "including but not limited to" are used interchangeably. An "interaction site" refers to a region on a polypeptide that facilitates the interaction of the polypeptide with a second molecule, such as another polypeptide or a nucleic acid or small molecule. The term "isolated polypeptide" refers to a polypeptide, in certain embodiments prepared from recombinant DNA or RNA, or of synthetic origin, or some combination thereof, which (1) is not associated with proteins that it is normally found with in nature, (2) is isolated from the cell in which it normally occurs, (3) is isolated free of other proteins from the same cellular source, (4) is expressed by a cell from a different species than that in which it is naturally found, or (5) is in a form in which it is not found in nature. The term "isolated nucleic acid" refers to a polynucleotide of genomic, cDNA, or synthetic origin or some' combination there of, which (1) is not associated with the cell in which the "isolated nucleic acid" is found in nature, (2) is operably linked to a polynucleotide to which it is not linked in nature, or (3) is in a form in which it is not found in nature. The terms "label" or "labeled" refer to incorporation or attachment, optionally covalently or non-covalently, of a detectable marker into a molecule, such as a polypeptide. Various methods of labeling polypeptides are known in the art and may be used. Examples of labels for polypeptides include, but are not limited to, the following: radioisotopes, fluorescent labels, heavy atoms, enzymatic labels or reporter genes, chemiluminescent groups, biotinyl groups, predetermined polypeptide epitopes recognized by a secondary reporter (e.g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). Examples and use of such labels are described in more detail below. In some embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance. The term "linker" is art-recognized and refers to a molecule or group of molecules connecting two compounds, such as two polypeptides. The linker may be comprised of a single linking molecule or may comprise a linking molecule and a spacer molecule, intended to separate the linking molecule and the library member by a specific distance. Non-limiting examples of linkers for use in the present invention are described further herein. The term "mammal" is known in the art, and exemplary mammals include humans, primates, bovines, porcines, canines, felines, and rodents (e.g., mice and rats). The term "modulation", when used in reference to a functional property or biological activity or process (e.g., enzyme activity or receptor binding), refers to the capacity to either up regulate (e.g., activate or stimulate), down regulate (e.g., inhibit or suppress) or otherwise change a quality of such property, activity or process. In certain instances, such regulation may be contingent on the occurrence of a specific event, such as activation of a signal transduction pathway, and/or may be manifest only in particular cell types. The term "modulator" refers to a polypeptide, nucleic acid, macromolecule, complex, molecule, small molecule, compound, species or the like (naturally-occurring or non-naturally- occurring), or an extract made from biological materials such as bacteria, plants, fungi, or animal cells or tissues, that may be capable of causing modulation. Modulators may be evaluated for potential activity as inhibitors or activators (directly or indirectly) of a functional property, biological activity or process, or combination of them, (e.g., agonist, partial antagonist, partial agonist, inverse agonist, antagonist, anti-microbial agents, inhibitors of microbial infection or proliferation, and the like) by inclusion in assays. In such assays, many modulators may be screened at one time. The activity of a modulator may be known, unknown or partially known. The term "nucleic acid" refers to a polymeric form of nucleotides, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide. The terms should also be

5 understood to include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs, and, as applicable to the embodiment being described, single-stranded (such as sense or antisense) and double-stranded polynucleotides. The term "operably linked", when describing the relationship between two nucleic acid regions, refers to a juxtaposition wherein the regions are in a relationship permitting them to 10 function in their intended manner. For example, a control sequence "operably linked" to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences, such as when the appropriate molecules (e.g., inducers and polymerases) are bound to the control or regulatory sequence(s). A "patient", "subject" or "host" to be treated by the subject method may mean either a L 5 human or non-human animal. A "peptide nucleic acid" or "PNA" refers to an analogue of a nucleic acid in which the backbone of the molecule is not sugar-phosphate, but rather a peptide or peptidomimetic. A detailed description of PNAs may be found in Nielsen, et al. Curr. Issues Mol. Biol. (1999) 1:89- 104. 20 "Peptidomimetic" refers to a compound containing peptide-like structural elements that is capable of mimicking the biological action (s) of a natural parent polypeptide. "Pharmaceutically-acceptable salts" refers to the relatively non-toxic, inorganic and organic acid addition salts of compounds. "Pharmaceutically acceptable carrier" refers to a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting any supplement or composition, or component thereof, from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be "acceptable" in the sense of being compatible with the other ingredients of the supplement and not injurious to the patient. Some examples of materials which may serve as pharmaceutically acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen- free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21) other non-toxic compatible substances employed in pharmaceutical formulations. The term "phenotype" refers to the entire physical, biochemical, and physiological makeup of a cell, e.g., having any one trait or any group of traits. The term "polypeptide", and the terms "protein" (when containing a single polypeptide chain) and "peptide" which are used interchangeably herein, refers to a polymer of amino acids.

Exemplary polypeptides include gene products, naturally-occurring proteins, homologs, orthologs, paralogs, fragments, and other equivalents, variants and analogs of the foregoing. In certain instances, a protein may comprise two or more polypeptide chains that are associated through covalent or non-covalent interactions. The term "polypeptide of the invention" refers to a Brd4 protein, Brd4 protein fragment, a Brd4 interacting protein, or a fragment of a Brd4 interacting protein. In exemplary embodiments, a Brd4 interacting protein refers to an E2 polypeptide or a functional equivalent thereof. The terms "polypeptide fragment", "fragment", or "truncation polypeptide", when used in reference to a reference polypeptide, refers to a polypeptide in which amino acid residues are deleted as compared to the reference polypeptide itself, but where the remaining amino acid sequence is usually identical to the corresponding positions in the reference polypeptide. Such deletions may occur at the amino-terminus or carboxy-terminus of the reference polypeptide, or alternatively both. Fragments typically are at least 5, 6, 8 or 10 amino acids long, at least 14 amino acids long, at least 20, 30, 40 or 50 amino acids long, at least 75 amino acids long, or at least 100, 150, 200, 300, 500 or more amino acids long. A fragment can retain one or more of the biological activities of the reference polypeptide. The term "purified" refers to an object species that is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition). A "purified fraction" is a composition wherein the object species comprises at least about 50 percent (on a molar basis) of all species present. In making the determination of the purity of a species in solution or dispersion, the solvent or matrix in which the species is dissolved or dispersed is usually not included in such determination; instead, only the species (including the one of interest) dissolved or dispersed are taken into account. Generally, a purified composition will have one species that comprises more than about 85 percent of all species present in the composition, more than about 85%, 90%>, 95%, 99% or more of all species present. The object species may be purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single species. A skilled artisan may purify a polypeptide of the invention using standard techniques for protein purification in light of the teachings herein. Purity of a polypeptide may be determined by a number of methods known to those of skill in the art, including for example, amino-terminal amino acid sequence analysis, gel electrophoresis and mass-spectrometry analysis. "Recombinant protein", "heterologous protein" and "exogenous protein" are used interchangeably to refer to a polypeptide which is produced by recombinant DNA techniques, wherein generally, DNA encoding the polypeptide is inserted into a suitable expression vector which is in turn used to transform a host cell to produce the heterologous protein. That is, the polypeptide is expressed from a heterologous nucleic acid. The term "small molecule" refers to a compound, which has a molecular weight of less than about 5 kD, less than about 2.5 kD, less than about 1.5 kD, or less than about 0.9 kD. Small molecules may be, for example, nucleic acids, peptides, polypeptides, peptide nucleic acids, peptidomimetics, carbohydrates, lipids or other organic (carbon containing) or inorganic molecules. Many pharmaceutical companies have extensive libraries of chemical and/or biological mixtures, often fungal, bacterial, or algal extracts, which can be screened with any of the assays of the invention. The term "small organic molecule" refers to a small molecule that is often identified as being an organic or medicinal compound, and does not include molecules that are exclusively nucleic acids, peptides or polypeptides. A "subject" is essentially any organism, although usually a vertebrate, and most typically a mammal, such as a human or a non-human mammal. The term "specifically hybridizes" refers to detectable and specific nucleic acid binding. Polynucleotides, oligonucleotides and nucleic acids of the invention selectively hybridize to nucleic acid strands under hybridization and wash conditions that minimize appreciable amounts of detectable binding to nonspecific nucleic acids. Stringent conditions may be used to achieve selective hybridization conditions as known in the art and discussed herein. Generally, the nucleic acid sequence homology between the polynucleotides, oligonucleotides, and nucleic acids of the invention and a nucleic acid sequence of interest will be at least 30%, 40%>, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99%, or more. In certain instances, hybridization and washing conditions are performed under stringent conditions according to conventional hybridization procedures and as described further herein. The terms "stringent conditions" or "stringent hybridization conditions" refer to conditions which promote specific hydribization between two complementary polynucleotide strands so as to form a duplex. Stringent conditions may be selected to be about 5°C lower than the thermal melting point (Tm) for a given polynucleotide duplex at a defined ionic strength and pH. The length of the complementary polynucleotide strands and their GC content will determine the Tm of the duplex, and thus the hybridization conditions necessary for obtaining a desired specificity of hybridization. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the a polynucleotide sequence hybridizes to a perfectly matched complementary strand. In certain cases it may be desirable to increase the stringency of the hybridization conditions to be about equal to the Tm for a particular duplex. A variety of techniques for estimating the Tm are available. Typically, G-C base pairs in a duplex are estimated to contribute about 3°C to the Tm, while A-T base pairs are estimated to

contribute about 2°C, up to a theoretical maximum of about 80-100°C. However, more sophisticated models of Tm are available in which G-C stacking interactions, solvent effects, the desired assay temperature and the like are taken into account. For example, probes can be designed to have a dissociation temperature (Td) of approximately 60°C, using the formula: Td = (((((3 x #GC) + (2 x #AT)) x 37) - 562)/#bp) - 5; where #GC, #AT, and #bp are the number of guanine-cytosine base pairs, the number of adenine-thymine base pairs, and the number of total base pairs, respectively, involved in the formation of the duplex. Hybridization may be carried out in 5xSSC, 4xSSC, 3xSSC, 2xSSC, lxSSC or 0.2xSSC for at least about 1 hour, 2 hours, 5 hours, 12 hours, or 24 hours. The temperature of the hybridization may be increased to adjust the stringency of the reaction, for example, from about 25°C (room temperature), to about 45°C, 50°C, 55°C, 60°C, or 65°C. The hybridization reaction may also include another agent affecting the stringency, for example, hybridization conducted in the presence of 50% formamide increases the stringency of hybridization at a defined temperature. The hybridization reaction may be followed by a single wash step, or two or more wash steps, which may be at the same or a different salinity and temperature. For example, the temperature of the wash may be increased to adjust the stringency from about 25°C (room temperature), to about 45°C, 50°C, 55°C, 60°C, 65°C, or higher. The wash step may be conducted in the presence of a detergent, e.g., 0.1 or 0.2% SDS. For example, hybridization may be followed by two wash steps at 65°C each for about 20 minutes in 2xSSC, 0.1% SDS, and optionally two additional wash steps at 65°C each for about 20 minutes in 0.2xSSC, 0.1%SDS. Exemplary stringent hybridization conditions include overnight hybridization at 65°C in a solution comprising, or consisting of, 50% formamide, lOxDenhardt (0.2% Ficoll, 0.2% Polyvinylpyrrolidone, 0.2%> bovine serum albumin) and 200 μg/ml of denatured carrier DNA, e.g., sheared salmon sperm DNA, followed by two wash steps at 65°C each for about 20 minutes in 2xSSC, 0.1% SDS, and two wash steps at 65°C each for about 20 minutes in 0.2xSSC, 0.1%SDS. Hybridization may consist of hybridizing two nucleic acids in solution, or a nucleic acid in solution to a nucleic acid attached to a solid support, e.g., a filter. When one nucleic acid is on a solid support, a prehybridization step may be conducted prior to hybridization. Prehybridization may be carried out for at least about 1 hour, 3 hours or 10 hours in the same solution and at the same temperature as the hybridization solution (without the complementary polynucleotide strand). Appropriate stringency conditions are known to those skilled in the art or may be determined experimentally by the skilled artisan. See, for example, Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-12.3.6; Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y; S. Agrawal (ed.) Methods in Molecular Biology, volume 20; Tijssen (1993) Laboratory Techniques in biochemistry and molecular biology-hybridization with nucleic acid probes, e.g., part I chapter 2 "Overview of principles of hybridization and the strategy of nucleic acid probe assays", Elsevier, New York; and Tibanyenda, N. et al., Eur. J. Biochem. 139:19 (1984) and Ebel, S. et al., Biochem. 31:12083 (1992). The term "test compound" refers to a molecule to be tested by one or more screening method(s) as a putative modulator of a polypeptide of the invention or other biological entity or process. A test compound is usually not known to bind to a target of interest. The term "test compound" is meant to include polypeptides, polynucleotides, carbohydrates, lipids, and small molecules, or mixtures thereof. The term "vector" refers to a nucleic acid capable of transporting another nucleic acid to which it has been linked. One type of vector which may be used herein is an episome, i.e., a nucleic acid capable of extra-chromosomal replication. Other vectors include those capable of autonomous replication and expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA techniques are often in the form of "plasmids" which refer to circular double stranded DNA molecules that, in their vector form are not bound to the chromosome. In the present specification, "plasmid" and "vector" are used interchangeably as the plasmid is the most commonly used form of vector. However, the present dislcosure is intended to include such other forms of expression vectors which serve equivalent functions and which become known in the art subsequently hereto. The term "heteroatom" as used herein means an atom of any element other than carbon or hydrogen. Preferred heteroatoms are boron, nitrogen, oxygen, phosphorus, sulfur and selenium. The term "alkyl" refers to the radical of saturated aliphatic groups, including straight- chain alkyl groups, branched-chain alkyl groups, cycloalkyl (alicyclic) groups, alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups. In preferred embodiments, a straight chain or branched chain alkyl has 30 or fewer carbon atoms in its backbone (e.g., C1-C30 for

straight chain, C3-C30 for branched chain), and more preferably 20 or fewer. Likewise, preferred cycloalkyls have from 3-10 carbon atoms in their ring structure, and more preferably have 5, 6 or 7 carbons in the ring structure. Moreover, the term "alkyl" (or "lower alkyl") as used throughout the specification, examples, and claims is intended to include both "unsubstituted alkyls" and "substituted alkyls", the latter of which refers to alkyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone. Such substituents can include, for example, a halogen, a hydroxyl, a carbonyl (such as a carboxyl, an alkoxycarbonyl, a formyl, or an acyl), a thiocarbonyl (such as a thioester, a thioacetate, or a thioformate), an alkoxyl, a phosphoryl, a phosphonate, a phosphinate, an amino, an amido, an amidine, an imine, a cyano, a nitro, an azido, a sulfhydryl, an alkylthio, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a sulfonyl, a heterocyclyl, an aralkyl, or an aromatic or heteroaromatic moiety. It will be understood by those skilled in the art that the moieties substituted on the hydrocarbon chain can themselves be substituted, if appropriate. For instance, the substituents of a substituted alkyl may include substituted and unsubstituted forms of amino, azido, imino, amido, phosphoryl (including phosphonate and phosphinate), sulfonyl (including sulfate, sulfonamido, sulfamoyl and sulfonate), and silyl groups, as well as ethers, alkylthios, carbonyls (including ketones, aldehydes, carboxylates, and esters), -CF3, -CN and the like. Exemplary substituted alkyls are

described below. Cycloalkyls can be further substituted with alkyls, alkenyls, alkoxys, alkylthios, aminoalkyls, carbonyl-substituted alkyls, -CF3, -CN, and the like. The term "aralkyl", as used herein, refers to an alkyl group substituted with an aryl group

(e.g., an aromatic or heteroaromatic group). The terms "alkenyl" and "alkynyl" refer to unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double or triple bond respectively. Unless the number of carbons is otherwise specified, "lower alkyl" as used herein means an alkyl group, as defined above, but having from one to ten carbons, more preferably from one to six carbon atoms in its backbone structure. Likewise, "lower alkenyl" and "lower alkynyl" have similar chain lengths. Preferred alkyl groups are lower alkyls. In preferred embodiments, a substituent designated herein as alkyl is a lower alkyl. The term "aryl" as used herein includes 5-, 6- and 7-membered single-ring aromatic groups that may include from zero to four heteroatoms, for example, benzene, pyrrole, furan, thiophene, imidazole, oxazole, thiazole, triazole, pyrazole, pyridine, pyrazine, pyridazine and pyrimidine, and the like. Those aryl groups having heteroatoms in the ring structure may also be referred to as "aryl heterocycles" or "heteroaromatics." The aromatic ring can be substituted at one or more ring positions with such substituents as described above, for example, halogen, azide, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, alkoxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, sulfonamido, ketone, aldehyde, ester, heterocyclyl, aromatic or heteroaromatic moieties, -CF3, -

CN, or the like. The term "aryl" also includes polycyclic ring systems having two or more cyclic rings in which two or more carbons are common to two adjoining rings (the rings are "fused rings") wherein at least one of the rings is aromatic, e.g., the other cyclic rings can be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls. The terms "heterocyclyl" or "heterocyclic group" refer to 3- to 10-membered ring structures, more preferably 3- to 7-membered rings, whose ring structures include one to four heteroatoms. Heterocycles can also be polycycles. Heterocyclyl groups include, for example, thiophene, thianthrene, furan, pyran, isobenzofuran, chromene, xanthene, phenoxathiin, pyrrole, imidazole, pyrazole, isothiazole, isoxazole, pyridine, pyrazine, pyrimidine, pyridazine, indolizine, isoindole, indole, indazole, purine, quinolizine, isoquinoline, quinoline, phthalazine, naphthyridine, quinoxaline, quinazoline, cinnoline, pteridine, carbazole, carboline, phenanthridine, acridine, pyrimidine, phenanthroline, phenazine, phenarsazine, phenothiazine, furazan, phenoxazine, pyrrolidine, oxolane, thiolane, oxazole, piperidine, piperazine, morpholine, lactones, lactams such as azetidinones and pyrrolidinones, sultams, sultones, and the like. The heterocyclic ring can be substituted at one or more positions with such substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, -CF3, -CN, or the like.

The terms "polycyclyl" or "polycyclic group" refer to two or more rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls) in which two or more carbons are common to two adjoining rings, e.g., the rings are "fused rings". Rings that are joined through non-adjacent atoms are termed "bridged" rings. Each of the rings of the polycycle can be substituted with such substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, -CF3, -CN, or the like.

The term "carbocycle", as used herein, refers to an aromatic or non-aromatic ring in which each atom of the ring is carbon. As used herein, the term "nitro" means -NO2; the term "halogen" designates -F, -CI, -Br

or -I; the term "sulfhydryl" means -SH; the term "hydroxyl" means -OH; and the term "sulfonyl" means -SO2-.

The terms "amine" and "amino" are art-recognized and refer to both unsubstituted and substituted amines, e.g., a moiety that can be represented by the general formula:

R ^ 10 / ¹⁰ I + -\_R or -f-^R" ⁹ R wherein R9, RI Q and R'10 each independently represent a hydrogen, an alkyl, an alkenyl,

-(CH2)_m-R8, or R9 and Ri Q taken together with the N atom to which they are attached complete

a heterocycle having from 4 to 8 atoms in the ring structure; Rg represents an aryl, a cycloalkyl,

a cycloalkenyl, a heterocycle or a polycycle; and m is zero or an integer in the range of 1 to 8. In preferred embodiments, only one of R9 or Ri Q can be a carbonyl, e.g., R9, Ri Q and the nitrogen

together do not form an imide. In even more preferred embodiments, R9 and RI Q (and

optionally R'10) each independently represent a hydrogen, an alkyl, an alkenyl, or -(CH2)_m-Rg.

Thus, the term "alkylamine" as used herein means an amine group, as defined above, having a substituted or unsubstituted alkyl attached thereto, i.e., at least one of R9 and RJQ is an alkyl

group. The term "acylamino" is art-recognized and refers to a moiety that can be represented by the general formula:

wherein R₉ is as defined above, and R'J represents a hydrogen, an alkyl, an alkenyl or

-(CH2)_m-R8, where m and Rg are as defined above.

The term "amido" is art recognized as an amino-substituted carbonyl and includes a moiety that can be represented by the general formula:

wherein R9, RI Q are as defined above. Preferred embodiments of the amide will not include

imides which may be unstable. The term "alkylthio" refers to an alkyl group, as defined above, having a sulfur radical attached thereto. In preferred embodiments, the "alkylthio" moiety is represented by one of -S- alkyl, -S-alkenyl, -S-alkynyl, and -S-(CH2)_m-Rg, wherein m and Rg are defined above.

Representative alkylthio groups include methylthio, ethyl thio, and the like. The term "carbonyl" is art recognized and includes such moieties as can be represented by the general formula:

O O -U— x-Ru ' °^r__χ L__R, 11 wherein X is a bond or represents an oxygen or a sulfur, and R1 1 represents a hydrogen, an

alkyl, an alkenyl, -(CH2)m~R-8 ^{or a} pharmaceutically acceptable salt, R'ι j represents a

hydrogen, an alkyl, an alkenyl or -(CH2)_m-Rg, where m and Rg are as defined above. Where X

is an oxygen and Ri or R'ι 1 is not hydrogen, the formula represents an "ester". Where X is an

oxygen, and Ri \ is as defined above, the moiety is referred to herein as a carboxyl group, and

particularly when Ri 1 is a hydrogen, the formula represents a "carboxylic acid". Where X is an oxygen, and R'ι \ is hydrogen, the formula represents a "formate". In general, where the oxygen

atom of the above formula is replaced by sulfur, the formula represents a "thiolcarbonyl" group. Where X is a sulfur and R1 1 or R'1 1 is not hydrogen, the formula represents a "thiolester."

Where X is a sulfur and ^ is hydrogen, the formula represents a "thiolcarboxylic acid."

Where X is a sulfur and Ri 1 ' is hydrogen, the formula represents a "thiolformate." On the other

hand, where X is a bond, and R^ 1 is not hydrogen, the above formula represents a "ketone"

group. Where X is a bond, and R^ is hydrogen, the above formula represents an "aldehyde"

group. The terms "alkoxyl" or "alkoxy" as used herein refers to an alkyl group, as defined above, having an oxygen radical attached thereto. Representative alkoxyl groups include methoxy, ethoxy, propyloxy, tert-butoxy and the like. An "ether" is two hydrocarbons covalently linked by an oxygen. Accordingly, the substituent of an alkyl that renders that alkyl an ether is or resembles an alkoxyl, such as can be represented by one of -O-alkyl, -O-alkenyl, -O-alkynyl, -O- (CH2)_m-Rg, where m and Rg are described above. The term "sulfonate" is art recognized and includes a moiety that can be represented by the general formula:

O II S- OR₄₁ II o in which R4 \ is an electron pair, hydrogen, alkyl, cycloalkyl, or aryl.

The term "sulfate" is art recognized and includes a moiety that can be represented by the general formula: O II O— S- OR₄₁ I I 0 in which R4 j is as defined above.

The term "sulfonamido" is art recognized and includes a moiety that can be represented by the general formula:

in which R9 and R'ι 1 are as defined above.

The term "sulfamoyl" is art-recognized and includes a moiety that can be represented by the general formula:

⁰ S-N - II \_R 0 ^K9 in which R9 and Ri Q are as defined above.

The term "sulfonyl", as used herein, refers to a moiety that can be represented by the general formula:

in which R44 is selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl,

cycloalkyl, heterocyclyl, aryl, or heteroaryl. The term "sulfoxido" as used herein, refers to a moiety that can be represented by the general formula: O II

in which R44 is selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl,

cycloalkyl, heterocyclyl, aralkyl, or aryl. A "phosphoryl" can in general be represented by the formula:

Qi ^0R« wherein Q1 represented S or O, and R46 represents hydrogen, a lower alkyl or an aryl. When

used to substitute, e.g., an alkyl, the phosphoryl group of the phosphorylalkyl can be represented by the general formula:

Qi Qi II II Q— P— O Q -P OR₄₆ I , or I OR₄₆ OR₄₆ wherein Q represented S or O, and each R46 independently represents hydrogen, a lower alkyl

or an aryl, Q2 represents O, S or N. When Qi is an S, the phosphoryl moiety is a

"phosphorothioate". A "phosphoramidite" can be represented in the general formula:

O O — Q^P— O — — Q— P — OR₄₆ I or ² | N (R₉ ) R₁₀ N (R₉ ) R₁₀ wherein R9 and Ri Q are as defined above, and Q2 represents O, S or N. A "phosphonamidite" can be represented in the general formula:

wherein R9 and Ri Q are as defined above, Q2 represents O, S or N, and R4g represents a lower

alkyl or an aryl, Q2 represents O, S or N.

A "selenoalkyl" refers to an alkyl group having a substituted seleno group attached thereto. Exemplary "selenoethers" which may be substituted on the alkyl are selected from one of -Se-alkyl, -Se-alkenyl, -Se-alkynyl, and -Se-(CH2)_m-R7, m and R7 being defined above.

Analogous substitutions can be made to alkenyl and alkynyl groups to produce, for example, aminoalkenyls, aminoalkynyls, amidoalkenyls, amidoalkynyls, iminoalkenyls, iminoalkynyls, thioalkenyls, thioalkynyls, carbonyl-substituted alkenyls or alkynyls. As used herein, the definition of each expression, e.g. alkyl, m, n, etc., when it occurs more than once in any structure, is intended to be independent of its definition elsewhere in the same structure. It will be understood that "substitution" or "substituted with" includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, e.g., which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, etc. As used herein, the term "substituted" is contemplated to include all permissible substituents of organic compounds. In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and nonaromatic substituents of organic compounds. Illustrative substituents include, for example, those described herein above. The permissible substituents can be one or more and the same or different for appropriate organic compounds. For purposes of this invention, the heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms. This invention is not intended to be limited in any manner by the permissible substituents of organic compounds. The phrase "protecting group" as used herein means temporary substituents which protect a potentially reactive functional group from undesired chemical transformations. Examples of such protecting groups include esters of carboxylic acids, silyl ethers of alcohols, and acetals and ketals of aldehydes and ketones, respectively. The field of protecting group chemistry has been reviewed (Greene, T.W.; Wuts, P.G.M. Protective Groups in Organic Synthesis, 2" ed.; Wiley: New York, 1991). The term "amino acid residue" is known in the art. In general the abbreviations used herein for designating the amino acids and the protective groups are based on recommendations of the IUPAC-IUB Commission on Biochemical Nomenclature (see Biochemistry (1972) 11:1726-1732). In certain embodiments, the amino acids used in the application of this invention are those naturally occurring amino acids found in proteins, or the naturally occurring anabolic or catabolic products of such amino acids which contain amino and carboxyl groups. Particularly suitable amino acid side chains include side chains selected from those of the following amino acids: glycine, alanine, valine, cysteine, leucine, isoleucine, serine, threonine, methionine, glutamic acid, aspartic acid, glutamine, asparagine, lysine, arginine, proline, histidine, phenylalanine, tyrosine, and tryptophan. The term "amino acid residue" further includes analogs, derivatives and congeners of any specific amino acid referred to herein, as well as C-terminal or N-terminal protected amino acid derivatives (e.g. modified with an N-terminal or C-terminal protecting group). For example, the present invention contemplates the use of amino acid analogs wherein a side chain is lengthened or shortened while still providing a carboxyl, amino or other reactive precursor functional group for cyclization, as well as amino acid analogs having variant side chains with appropriate functional groups). For instance, the subject compound can include an amino acid analog such as, for example, cyanoalanine, canavanine, djenkolic acid, norleucine, 3-phosphoserine, homoserine, dihydroxy-phenylalanine, 5-hydroxytryptophan, 1-methylhistidine, 3- methylhistidine, diaminopimelic acid, ornithine, or diaminobutyric acid. Other naturally occurring amino acid metabolites or precursors having side chains which are suitable herein will be recognized by those skilled in the art and are included in the scope of the present invention. Also included are the (D) and (L) stereoisomers of such amino acids when the structure of the amino acid admits of stereoisomeric forms. The configuration of the amino acids and amino acid residues herein are designated by the appropriate symbols (D), (L) or (DL), furthermore when the configuration is not designated the amino acid or residue can have the configuration (D), (L) or (DL). It will be noted that the structure of some of the compounds of this invention includes asymmetric carbon atoms. It is to be understood accordingly that the isomers arising from such asymmetry are included within the scope of this invention. Such isomers can be obtained in substantially pure form by classical separation techniques and by sterically controlled synthesis. For the purposes of this application, unless expressly noted to the contrary, a named amino acid shall be construed to include both the (D) or (L) stereoisomers. D- and L-α-Amino acids are represented by the following Fischer projections and wedge-and-dash drawings. In the majority of cases, D- and L-amino acids have R- and S-absolute configurations, respectively.

D-α-amino acids L-α-amino acids A "reversed" or "retro" peptide sequence as disclosed herein refers to that part of an overall sequence of covalently-bonded amino acid residues (or analogs or mimetics thereof) wherein the normal carboxyl-to amino direction of peptide bond formation in the amino acid backbone has been reversed such that, reading in the conventional left-to-right direction, the amino portion of the peptide bond precedes (rather than follows) the carbonyl portion. See, generally, Goodman, M. and Chorev, M. Accounts of Chem. Res. 1979, 12, 423. The reversed orientation peptides described herein include (a) those wherein one or more amino-terminal residues are converted to a reversed ("rev") orientation (thus yielding a second "carboxyl terminus" at the left-most portion of the molecule), and (b) those wherein one or more carboxyl-terminal residues are converted to a reversed ("rev") orientation (yielding a second "amino terminus" at the right-most portion of the molecule). A peptide (amide) bond cannot be formed at the interface between a normal orientation residue and a reverse orientation residue. Therefore, certain reversed peptide compounds of the invention can be formed by utilizing an appropriate amino acid mimetic moiety to link the two adjacent portions of the sequences depicted above utilizing a reversed peptide (reversed amide) bond. In case (a) above, a central residue of a diketo compound may conveniently be utilized to link structures with two amide bonds to achieve a peptidomimetic structure. In case (b) above, a central residue of a diamino compound will likewise be useful to link structures with two amide bonds to form a peptidomimetic structure. The reversed direction of bonding in such compounds will generally, in addition, require inversion of the enantiomeric configuration of the reversed amino acid residues in order to maintain a spatial orientation of side chains that is similar to that of the non-reversed peptide. The configuration of amino acids in the reversed portion of the peptides is preferably (D), and the configuration of the non-reversed portion is preferably (L). Opposite or mixed configurations are acceptable when appropriate to optimize a binding activity. I Certain compounds of the present invention may exist in particular geometric or stereoisomeric forms. The present invention contemplates all such compounds, including cis- and traws-isomers, R- and S-enantiomers, diastereomers, (D)-isomers, (L)-isomers, the racemic mixtures thereof, and other mixtures thereof, as falling within the scope of the invention. Additional asymmetric carbon atoms may be present in a substituent such as an alkyl group. All such isomers, as well as mixtures thereof, are intended to be included in this invention. If, for instance, a particular enantiomer of a compound of the present invention is desired, it may be prepared by asymmetric synthesis, or by derivation with a chiral auxiliary, where the resulting diastereomeric mixture is separated and the auxiliary group cleaved to provide the pure desired enantiomers. Alternatively, where the molecule contains a basic functional group, such as amino, or an acidic functional group, such as carboxyl, diastereomeric salts are formed with an appropriate optically-active acid or base, followed by resolution of the diastereomers thus formed by fractional crystallization or chromatographic means well known in the art, and subsequent recovery of the pure enantiomers. Contemplated equivalents of the compounds described herein include compounds which otherwise correspond thereto, and which have the same general properties thereof (e.g. the ability to bind to opioid receptors), wherein one or more simple variations of substituents are made which do not adversely affect the efficacy of the compound in binding to an E2 polypeptide. In general, the compounds of the present invention may be prepared by the methods illustrated in the general reaction schemes as, for example, described below, or by modifications thereof, using readily available starting materials, reagents and conventional synthesis procedures. Thus, the contemplated equivalents include small molecule inhibitors that are capable of disrupting an interaction between a Brd4 polypeptide and an E2 polypeptide or a functional equivalent thereof. In these reactions, it is also possible to make use of variants which are in themselves known, but are not mentioned here. For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 67th Ed., 1986-87, inside cover. Also for purposes of this invention, the term "hydrocarbon" is contemplated to include all permissible compounds having at least one hydrogen and one carbon atom. In a broad aspect, the permissible hydrocarbons include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and nonaromatic organic compounds which can be substituted or unsubstituted.

Polypeptides The present invention makes available in a variety of embodiments soluble, purified and/or isolated forms of human Brd4 polypeptides and complexes comprising human Brd4 polypeptides. In one aspect, the present invention contemplates an isolated polypeptide comprising (a) the amino acid sequence set forth in SEQ ID NO: 2 or an amino acid sequence having residues 1047-1362, 1134-1362, or 1224-1362 of SEQ ID NO: 2, (b) an amino acid sequence of (a) with 1 to about 20 conservative amino acid substitutions, deletions, or additions, (c) an amino acid sequence that is at least 95%> identical to an amino acid sequence of (a), or (d) a functional fragment of a polypeptide having an amino acid sequence set forth in (a), (b) or (c). In an exemplary embodiment, the invention contemplates polypeptides having at least 3, 5, 7, 10, 15, 20, 25, 30, 40, 45, 50, or more consecutive amino acids from SEQ ID NO: 2 or a region of SEQ ID NO: 2 having amino acid residues 1047-1362, 1134-1362, or 1224-1362 of SEQ ID NO: 2. In another aspect, the present invention contemplates a complex comprising (a) human

Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) human Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of human Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of human Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide. In one embodiment, the complex comprises a fragment of Brd4 having residues 1047-1362, 1134-1362, or 1224-1362 of SEQ ID NO: 2. In another embodiment, the complex comprises a fragment having at least five consecutive amino acid residues from SEQ ID NO: 2 or a region of SEQ ID NO: 2 having amino acid residues 1047-1362, 1134-1362, or 1224-1362 of SEQ ID NO: 2. In certain embodiments, a polypeptide of the invention comprises one or more post- translational ^' or chemical modifications modifications. Exemplary modifications include, for example, acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. In another aspect, the present invention contemplates a polypeptide of the invention contained within a syringe (or other device for, e.g., introducing the polypeptide into a subject) or bound to a solid support. Exemplary solid supports include the following: particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates and slides. In certain embodiments, a polypeptide of the invention is a fusion protein containing a domain which increases its solubility and/or facilitates its purification, identification, detection, and/or structural characterization. Exemplary domains, include, for example, glutathione S- transferase (GST), protein A, protein G, calmodulin-binding peptide, thioredoxin, maltose binding protein, HA, myc, poly arginine, poly His, poly His-Asp or FLAG fusion proteins and tags. Additional exemplary domains include domains that alter protein localization in vivo, such as signal peptides, type III secretion system-targeting peptides, transcytosis domains, nuclear localization signals, etc. In various embodiments, a polypeptide of the invention may comprise one or more heterologous fusions. Polypeptides may contain multiple copies of the same fusion domain or may contain fusions to two or more different domains. The fusions may occur at the N-terminus of the polypeptide, at the C-terminus of the polypeptide, or at both the N- and C- terminus of the polypeptide. It is also within the scope of the invention to include linker sequences between a polypeptide of the invention and the fusion domain in order to facilitate construction of the fusion protein or to optimize protein expression or structural constraints of the fusion protein. In another embodiment, the polypeptide may be constructed so as to contain protease cleavage sites between the fusion polypeptide and polypeptide of the invention in order to remove the tag after protein expression or thereafter. Examples of suitable endoproteases, include, for example, Factor Xa and TEV proteases. In another embodiment, a polypeptide of the invention may be modified so that its rate of traversing the cellular membrane is increased. For example, the polypeptide may be fused to a second peptide which promotes "transcytosis," e.g., uptake of the peptide by cells. The peptide may be a portion of the HIV transactivator (TAT) protein, such as the fragment corresponding to residues 37 -62 or 48-60 of TAT, portions which have been observed to be rapidly taken up by a cell in vitro (Green and Loewenstein, (1989) Cell_55: 1179-1188). Alternatively, the internalizing peptide may be derived from the Drosophila antennapedia protein, or homologs thereof. The 60 amino acid long homeodomain of the homeo-protein antennapedia has been demonstrated to translocate through biological membranes and can facilitate the translocation of heterologous polypeptides to which it is coupled. Thus, polypeptides may be fused to a peptide consisting of about amino acids 42-58 of Drosophila antennapedia or shorter fragments for transcytosis (Derossi et al. (1996) J Biol Chem 271:18188-18193; Derossi et al. (1994) J Biol Chem 269:10444-10450; and Perez et al. (1992) J Cell Sci 102:717-722). The transcytosis polypeptide may also be a non-naturally-occurring membrane-translocating sequence (MTS), such as the peptide sequences disclosed in U.S. Patent No. 6,248,558. In still another embodiment, the polypeptides of the invention are labeled to facilitate their detection, purification, and/or structural characterization. Exemplary labels include, for example, isotopic labels, heavy atom labels, and fluorescent labels. In an exemplary embodiment, a polypeptide of the invention is fused to a heterologous polypeptide sequence which produces a detectable fluorescent signal, including, for example, green fluorescent protein (GFP), enhanced green fluorescent protein (EGFP), Renilla Reniformis green fluorescent protein, GFPmut2, GFPuv4, enhanced yellow fluorescent protein (EYFP), enhanced cyan fluorescent protein (ECFP), enhanced blue fluorescent protein (EBFP), citrine and red fluorescent protein from discosoma (dsRED). In other embodiments, the invention provides for polypeptides of the invention immobilized onto a solid surface, including, plates, microtiter plates, slides, beads, particles, spheres, films, strands, precipitates, gels, sheets, tubing, containers, capillaries, pads, slices, etc. The polypeptides of the invention may be immobilized onto a "chip" as part of an array. An array, having a plurality of addresses, may comprise one or more polypeptides of the invention in one or more of those addresses. In one embodiment, the chip comprises one or more polypeptides of the invention as part of an array of mammalian and/or viral polypeptide sequences. In still other embodiments, the invention comprises the polypeptide sequences of the invention in computer readable format. The invention also encompasses a database comprising the polypeptide sequences of the invention. In other embodiments, the invention relates to the polypeptides of the invention contained within a vessels useful for manipulation of the polypeptide sample. For example, the polypeptides of the invention may be contained within a microtiter plate to facilitate detection, screening or purification of the polypeptide. The polypeptides may also be contained within a syringe as a container suitable for administering the polypeptide to a subject in order to generate antibodies or as part of a vaccination regimen. The polypeptides may also be contained within an NMR tube in order to enable characterization by nuclear magnetic resonance techniques. In certain embodiments, polypeptides of the invention may be synthesized chemically, ribosomally in a cell free system, or ribosomally within a cell. Chemical synthesis of polypeptides of the invention may be carried out using a variety of art recognized methods, including stepwise solid phase synthesis, semi-synthesis through the conformationally-assisted re-ligation of peptide fragments, enzymatic ligation of cloned or synthetic peptide segments, and chemical ligation. Native chemical ligation employs a chemoselective reaction of two unprotected peptide segments to produce a transient thioester-linked intermediate. The transient thioester-linked intermediate then spontaneously undergoes a rearrangement to provide the full length ligation product having a native peptide bond at the ligation site. Full length ligation products are chemically identical to proteins produced by cell free synthesis. Full length ligation products may be refolded and/or oxidized, as allowed, to form native disulfide-containing protein molecules, (see e.g., U.S. Patent Nos. 6,184,344 and 6,174,530; and T. W. Muir et al., Curr. Opin. Biotech. (1993): vol. 4, p 420; M. Miller, et al., Science (1989): vol. 246, p 1149; A. Wlodawer, et al., Science (1989): vol. 245, p 616; L. H. Huang, et al., Biochemistry (1991): vol. 30, p 7402; M. Schnolzer, et al., Int. J. Pept. Prot. Res. (1992): vol. 40, p 180-193; K. Rajarathnam, et al., Science (1994): vol. 264, p 90; R. E. Offord, "Chemical Approaches to Protein Engineering", in Protein Design and the Development of New therapeutics and Vaccines, J. B. Hook, G. Poste, Eds., (Plenum Press, New York, 1990) pp. 253-282; C. J. A. Wallace, et al., J. Biol. Chem. (1992): vol. 267, p 3852; L. Abrahmsen, et al., Biochemistry (1991): vol. 30, p 4151; T. K. Chang, et al., Proc. Natl. Acad. Sci. USA (1994) 91: 12544-12548; M. Schnlzer, et al, Science (1992): vol., 3256, p 221; and K. Akaji, et al., Chem. Pharm. Bull. (Tokyo) (1985) 33: 184). In certain embodiments, it may be advantageous to provide naturally-occurring or experimentally-derived homologs of a polypeptide of the invention. Such homologs may function in a limited capacity as a modulator to promote or inhibit a subset of the biological activities of the naturally-occurring form of the polypeptide. Thus, specific biological effects may be elicited by treatment with a homolog of limited function, and with fewer side effects relative to treatment with agonists or antagonists which are directed to all of the biological activities of a polypeptide of the invention. For instance, antagonistic homologs may be generated which interfere with the ability of the wild-type polypeptide of the invention to associate with certain proteins, but which do not substantially interfere with the formation of complexes between the native polypeptide and other cellular proteins. Another aspect of the invention relates to polypeptides derived from the full-length polypeptides of the invention. Isolated peptidyl portions of the subject polypeptides may be obtained by screening polypeptides recombinantly produced from the corresponding fragment of the nucleic acid encoding such polypeptides. In addition, fragments may be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry. For example, proteins may be arbitrarily divided into fragments of desired length with no overlap of the fragments, or may be divided into overlapping fragments of a desired length. The fragments may be produced (recombinantly or by chemical synthesis) and tested to identify those peptidyl fragments having a desired property, for example, the capability of functioning as a modulator of the polypeptides of the invention. In an illustrative embodiment, peptidyl portions of a protein of the invention may be tested for binding activity, as well as inhibitory ability, by expression as, for example, thioredoxin fusion proteins, each of which contains a discrete fragment of a protein of the invention (see, for example, U.S. Patents 5,270,181 and 5,292,646; and PCT publication WO94/ 02502). It is also possible to modify the structure of the subject proteins for such purposes as enhancing therapeutic or prophylactic efficacy, or stability (e.g., ex vivo shelf life, resistance to proteolytic degradation in vivo, etc.). Such modified polypeptides may be produced, for instance, by amino acid substitution, deletion, or addition, which substitutions may consist in whole or part by conservative amino acid substitutions. For instance, it is reasonable to expect that an isolated conservative amino acid substitution, such as replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, will not have a major affect on the biological activity of the resulting molecule. Whether a change in the amino acid sequence of a polypeptide results in a functional homolog may be readily determined by assessing the ability of the variant polypeptide to produce a response similar to that of the wild-type protein. Polypeptides in which more than one replacement has taken place may readily be tested in the same manner. This invention further contemplates a method of generating sets of combinatorial mutants of polypeptides of the invention, as well as truncation mutants, and is especially useful for identifying potential variant sequences (e.g. homologs). The purpose of screening such combinatorial libraries is to generate, for example, homologs which may modulate the activity of a polypeptide of the invention, or alternatively, which possess novel activities altogether. Combinatorially-derived homologs may be generated which have a selective potency relative to a naturally-occurring protein. Such homologs may be used in the development of therapeutics. Likewise, mutagenesis may give rise to homologs which have intracellular half-lives dramatically different than the corresponding wild-type protein. For example, the altered protein may be rendered either more stable or less stable to proteolytic degradation or other cellular process which result in destruction of, or otherwise inactivation of the protein. Such homologs, and the genes which encode them, may be utilized to alter protein expression by modulating the half-life of the protein. As above, such proteins may be used for the development of therapeutics or treatment. In similar fashion, protein homologs may be generated by the present combinatorial approach to act as antagonists, in that they are able to interfere with the activity of the corresponding wild-type protein. In a representative embodiment of this method, the amino acid sequences for a population of protein homologs are aligned, preferably to promote the highest homology possible. Such a population of variants may include, for example, homologs from one or more species, or homologs from the same species but which differ due to mutation. Amino acids which appear at each position of the aligned sequences are selected to create a degenerate set of combinatorial sequences. In certain embodiments, the combinatorial library is produced by way of a degenerate library of genes encoding a library of polypeptides which each include at least a portion of potential protein sequences. For instance, a mixture of synthetic oligonucleotides may be enzymatically ligated into gene sequences such that the degenerate set of potential nucleotide sequences are expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g. for phage display). There are many ways by which the library of potential homologs may be generated from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence may be carried out in an automatic DNA synthesizer, and the synthetic genes may then be ligated into an appropriate vector for expression. One purpose of a degenerate set of genes is to provide, in one mixture, all of the sequences encoding the desired set of potential protein sequences. The synthesis of degenerate oligonucleotides is well known in the art (see for example, Narang, SA (1983) Tetrahedron 39:3; Itakura et al., (1981) Recombinant DNA, Proc. 3rd Cleveland Sympos. Macromolecules, ed. AG Walton, Amsterdam: Elsevier pp. 273-289; Itakura et al., (1984) Annu. Rev. Biochem. 53:323; Itakura et al., (1984) Science 198:1056; Ike et al., (1983) Nucleic Acid Res. 11:477). Such techniques have been employed in the directed evolution of other proteins (see, for example, Scott et al., (1990) Science 249:386-390; Roberts et al., (1992) PNAS USA 89:2429-2433; Devlin et al, (1990) Science 249: 404-406; Cwiria et al, (1990) PNAS USA 87: 6378-6382; as well as U.S. Patent Nos: 5,223,409, 5,198,346, and 5,096,815). Alternatively, other forms of mutagenesis may be utilized to generate a combinatorial library. For example, protein homologs (both agonist and antagonist forms) may be generated and isolated from a library by screening using, for example, alanine scanning mutagenesis and the like (Ruf et al., (1994) Biochemistry 33:1565-1572; Wang et al., (1994) J. Biol. Chem. 269:3095-3099; Balint et al., (1993) Gene 137:109-118; Grodberg et al., (1993) Eur. J. Biochem. 218:597-601; Nagashima et al., (1993) J. Biol. Chem. 268:2888-2892; Lowman et al., (1991) Biochemistry 30:10832-10838; and Cunningham et al., (1989) Science 244:1081-1085), by linker scanning mutagenesis (Gustin et al., (1993) Virology 193:653-660; Brown et al., (1992) Mol. Cell Biol. 12:2644-2652; McKnight et al, (1982) Science 232:316); by saturation mutagenesis (Meyers et al., (1986) Science 232:613); by PCR mutagenesis (Leung et al., (1989) Method Cell Mol Biol 1:11-19); or by random mutagenesis (Miller et al., (1992) A Short Course in Bacterial Genetics, CSHL Press, Cold Spring Harbor, NY; and Greener et al., (1994) Strategies in Mol Biol 7:32-34). Linker scanning mutagenesis, particularly in a combinatorial setting, is an attractive method for identifying truncated forms of proteins that are bioactive. A wide range of techniques are known in the art for screening gene products of combinatorial libraries made by point mutations and truncations, and for screening cDNA libraries for gene products having a certain property. Such techniques will be generally adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of protein homologs. The most widely used techniques for screening large gene libraries typically comprises cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates relatively easy isolation of the vector encoding the gene whose product was detected. Each of the illustrative assays described below are amenable to high throughput analysis as necessary to screen large numbers of degenerate sequences created by combinatorial mutagenesis techniques. In an illustrative embodiment of a screening assay, candidate combinatorial gene products are displayed on the surface of a cell and the ability of particular cells or viral particles to bind to the combinatorial gene product is detected in a "panning assay". For instance, the gene library may be cloned into the gene for a surface membrane protein of a bacterial cell (Ladner et al, WO 88/06630; Fuchs et al., (1991) Bio/Technology 9:1370-1371; and Goward et al., (1992) TIBS 18:136-140), and the resulting fusion protein detected by panning, e.g. using a fluorescently labeled molecule which binds the cell surface protein, e.g. FITC-substrate, to score for potentially functional homologs. Cells may be visually inspected and separated under a fluorescence microscope, or, when the morphology of the cell permits, separated by a fluorescence-activated cell sorter. This method may be used to identify substrates or other polypeptides that can interact with a polypeptide of the invention. In similar fashion, the gene library may be expressed as a fusion protein on the surface of a viral particle. For instance, in the filamentous phage system, foreign peptide sequences may be expressed on the surface of infectious phage, thereby conferring two benefits. First, because these phage may be applied to affinity matrices at very high concentrations, a large number of phage may be screened at one time. Second, because each infectious phage displays the combinatorial gene product on its surface, if a particular phage is recovered from an affinity matrix in low yield, the phage may be amplified by another round of infection. The group of almost identical E. coli filamentous phages Ml 3, fd, and fl are most often used in phage display libraries, as either of the phage gill or gVIII coat proteins may be used to generate fusion proteins without disrupting the ultimate packaging of the viral particle (Ladner et al., PCT publication WO 90/02909; Garrard et al., PCT publication WO 92/09690; Marks et al., (1992) J Biol. Chem. 267:16007-16010; Griffiths et al., (1993) EMBO J. 12:725-734; Clackson et al., (1991) Nature 352:624-628; and Barbas et al., (1992) PNAS USA 89:4457-4461). Other phage coat proteins may be used as appropriate.

Peptides and Peptidomimetics In certain embodiments, the invention provides modified peptides that retain the ability to form a complex with a Brd4 protein, an Ε2 protein, or a functional equivalent of an E2 protein. Such modifications include N-terminal acetylation, glycosylation, biotinylation, etc. Peptides with an N-Terminal D-Amino Acid. The presence of an N-terminal D-amino acid increases the serum stability of a peptide which otherwise contains L-amino acids, because exopeptidases acting on the N-terminal residue cannot utilize a D-amino acid as a substrate (Powell, et al. (1993), cited above). Thus, the amino acid sequences of the peptides with N- terminal D-amino acids are usually identical to the sequences of the L-amino acid peptides except that the N-terminal residue is a D-amino acid. Peptides with a C-Terminal D-Amino Acid. The presence of a C-terminal D-amino acid also stabilizes a peptide, which otherwise contains L-amino acids, because serum exopeptidases acting on the C-terminal residue cannot utilize a D-amino acid as a substrate (Powell, et al. (1993), cited above). Thus, the amino acid sequences of the these peptides are usually identical to the sequences of the L-amino acid peptides except that the C-terminal residue is a D-amino acid. Cyclic Peptides. Cyclic peptides have no free N- or C-termini. Thus, they are not susceptible to proteolysis by exopeptidases, although they are of course susceptible to endopeptidases, which do not cleave at peptide termini. The amino acid sequences of the cyclic peptides may be identical to the sequences of the L-amino acid peptides except that the topology is circular, rather than linear. Peptides with Substitution of Natural Amino Acids by Unnatural Amino Acids. Substitution of unnatural amino acids for natural amino acids can also confer resistance to proteolysis. Such a substitution can, for example, confer resistance to proteolysis by exopeptidases acting on the N-terminus. For example, a serine residue can be substituted by a beta-amino acid isoserine. Such substitutions have been described (Coller, et al. (1993), J. Biol Chem., 268:20741-20743) and these substitutions do not affect biological activity. Furthermore, the synthesis of peptides with unnatural amino acids is routine and known in the art (see, for example, Coller, et al. (1993)). Peptides with N-Terminal or C-Terminal Chemical Groups. An effective approach to confer resistance to peptidases acting on the N-terminal or C-terminal residues of a peptide is to add chemical groups at the peptide termini, such that the modified peptide is no longer a substrate for the peptidase. One such chemical modification is glycosylation of the peptides at either or both termini. Certain chemical modifications, in particular N-terminal glycosylation, have been shown to increase the stability of peptides in human serum (Powell et al. (1993), Pharma. Res., 10: 1268-1273). Other chemical modifications which enhance serum stability include, but are not limited to, the addition of an N-terminal alkyl group, consisting of a lower alkyl of from 1 to 20 carbons, such as an acetyl group, and/or the addition of a C-terminal amide or substituted amide group. Reverse-D Peptides. In another embodiment of this invention the peptides are reverse-D peptides. The term "reverse-D peptide" refers to peptides containing D-amino acids, arranged in a reverse sequence relative to a peptide containing L-amino acids. Thus, the C-terminal residue of an L-amino acid peptide becomes N-terminal for the D-amino acid peptide, and so forth. Reverse-D peptides retain the same tertiary conformation, and therefore the same activity, as the L-amino acid peptides, but are more stable to enzymatic degradation in vitro and in vivo, and thus have greater therapeutic efficacy than the original peptide (Brady and Dodson (1994), Nature, 368: 692-693; Jameson et al. (1994), Nature, 368: 744-746). The peptides of this invention, including the analogs and other modified variants, may generally be prepared following known techniques. Preferably, synthetic production of the peptide of the invention may be according to the solid phase synthetic method. For example, the solid phase synthesis is well understood and is a common method for preparation of peptides, as are a variety of modifications of that technique (Merrifield (1964), J. Am. Chem. Soc, 85: 2149; Stewart and Young (1984), Solid Phase Peptide Synthesis, Pierce Chemical Company, Rockford, IL; Bodansky and Bodanszky (1984), The Practice of Peptide Synthesis, Springer- Verlag, New York; Atherton and Sheppard (1989), Solid Phase Peptide Synthesis: A Practical Approach, IRL Press, New York).

5 Alternatively, peptides of this invention may be prepared in recombinant systems using polynucleotide sequences encoding the peptides. It is understood that a peptide of this invention may contain more than one of the above described modifications within the same peptide. Also included in this invention are pharmaceutically acceptable salt complexes of the peptides of this invention.

[0 The invention also provides for reduction of the subject proteins to generate mimetics, e.g. peptide or non-peptide agents, which are able to mimic binding of the authentic protein to another cellular partner. Such mutagenic techniques as described below, as well as the thioredoxin system, are also particularly useful for mapping the determinants of a protein which participates in a protein-protein interaction with another protein. To illustrate, the critical

L5 residues of a protein which are involved in molecular recognition of a substrate protein may be determined and used to generate peptidomimetics that may bind to the substrate protein. The peptidomimetic may then be used as an inhibitor of the wild-type protein by binding to the substrate and covering up the critical residues needed for interaction with the wild-type protein, thereby preventing interaction of the protein and the substrate. By employing, for example,

20 scanning mutagenesis to map the amino acid residues of a protein which are involved in binding a substrate polypeptide, peptidomimetic compounds may be generated which mimic those residues in binding to the substrate. For instance, non-hydrolyzable peptide analogs of such residues may be generated using benzodiazepine (e.g., see Freidinger et al., in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al., in" Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gamma lactam rings (Garvey et al., in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands,

5 1988), keto-methylene pseudopeptides (Ewenson et al., (1986) J. Med. Chem. 29:295; and Ewenson et al., in Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium) Pierce Chemical Co. Rockland, IL, 1985), β-turn dipeptide cores (Nagai et al., (1985) Tetrahedron Lett 26:647; and Sato et al., (1986) J Chem Soc Perkin Trans 1:1231), and β-aminoalcohols (Gordon et al., (1985) Biochem Biophys Res Commun 126:419; and Dann et al.,

[0 (1986) Biochem Biophys Res Commun 134:71). A peptide mimetic is a molecule that mimics the biological activity of a peptide but is no longer peptidic in chemical nature. By strict definition, a peptidomimetic is a molecule that no longer contains any peptide bonds (that is, amide bonds between amino acids). However, the term peptide mimetic is sometimes used to describe molecules that are no longer completely

L5 peptidic in nature, such as pseudo-peptides, semi-peptides and peptoids. Examples of some peptidomimetics by the broader definition (where part of a peptide is replaced by a structure lacking peptide bonds) are described below. Whether completely or partially non-peptide, peptidomimetics according to this invention provide a spatial arrangement of reactive chemical moieties that closely resembles the three-dimensional arrangement of active groups in the

20 peptide on which the peptidomimetic is based. As a result of this similar active-site geometry, the peptidomimetic has effects on biological systems which are similar to the biological activity of the peptide. The present invention encompasses peptidomimetic compositions which are analogs that mimic the activity of biologically active peptides according to the invention, i.e., the peptidomimetics are capable of disrupting an interaction between a Brd4 polypeptide and an E2 polypeptide or a functional equivalent of an E2 polypeptide. In certain embodiments, the peptidomimetic of the invention may be substantially similar in three-dimensional shape and/or biological activity to the peptides as described herein. Thus peptides described above have utility in the development of such small chemical compounds with similar biological activities and therefore with similar therapeutic utilities. The techniques of developing peptidomimetics are conventional. Thus, peptide bonds can be replaced by non-peptide bonds that allow the peptidomimetic to adopt a similar structure, and therefore biological activity, to the original peptide. Further modifications can also be made by replacing chemical groups of the amino acids with other chemical groups of similar structure. The development of peptidomimetics can be aided by determining the tertiary structure of the original peptide, either free or bound to a binding partner, by NMR spectroscopy, crystallography and/or computer-aided molecular modelling. These techniques aid in the development of novel compositions of higher potency and/or greater bioavailability and/or greater stability than the original peptide (Dean (1994), BioEssays, 16: 683-687; Cohen and Shatzmiller (1993), J. Mol. Graph., 11: 166-173; Wiley and Rich (1993), Med. Res. Rev., 13: 327-384; Moore (1994), Trends Pharmacol. Sci., 15: 124-129; Hruby (1993), Biopolymers, 33: 1073-1082; Bugg et al. (1993), Sci. Am., 269: 92-98, all incorporated herein by reference). Once a potential peptidomimetic compound is identified, it may be synthesized and assayed using the assays described herein to assess its activity. Thus, through use of the methods described herein, the present invention provides compounds exhibiting enhanced therapeutic activity in comparison to the peptides described herein. The peptidomimetic compounds obtained by the above methods, having the biological activity of the above named peptides and similar three dimensional structure, are encompassed by this invention. It will be readily apparent to one skilled in the art that a peptidomimetic can be generated from any of the modified peptides described above or from a peptide bearing more than one of the modifications described above. It will furthermore be apparent that the peptidomimetics of this invention can be further used for the development of even more potent non-peptidic compounds, in addition to their utility as therapeutic compounds. Specific examples of peptidomimetics derived from the peptides described in the previous section are presented below. These examples are illustrative and not limiting in terms of the other or additional modifications. Peptides with a Reduced Isostere Pseudopeptide Bond [Ψ(CH₂NH)]. Proteses act on peptide bonds. It therefore follows that substitution of peptide bonds by pseudopeptide bonds confers resistance to proteolysis. A number of pseudopeptide bonds have been described that in general do not affect peptide structure and biological activity. The reduced isostere pseudopeptide bond is a suitable pseudopeptide bond that is known to enhance stability to enzymatic cleavage with no or little loss of biological activity (Couder, et al. (1993), Int. J. Peptide Protein Res., 41:181-184). Thus, the amino acid sequences of these peptides may be identical to the sequences of the L-amino acid peptides described herein except that one or more of the peptide bonds are replaced by an isostere pseudopeptide bond. Preferably the most N- terminal peptide bond is substituted, since such a substitution would confer resistance to proteolysis by exopeptidases acting on the N-terminus. The synthesis of peptides with one or more reduced isostere pseudopeptide bonds is known in the art (Couder, et al. (1993), cited above). Peptides with a Retro-Inverso Pseudopeptide Bond [Ψ(NHCO)]. To confer resistance to proteolysis, peptide bonds may also be substituted by retro-inverso pseudopeptide bonds (Dalpozzo, et al. (1993), Int. J. Peptide Protein Res., 41:561-566, incorporated herein by reference). According to this modification, the amino acid sequences of the peptides may be identical to the sequences of the L-amino acid peptides described herein except that one or more of the peptide bonds are replaced by a retro-inverso pseudopeptide bond. Preferably the most N- terminal peptide bond is substituted, since such a substitution will confer resistance to proteolysis by exopeptidases acting on the N-terminus. The synthesis of peptides with one or more reduced retro-inverso pseudopeptide bonds is known in the art (Dalpozzo, et al. (1993), cited above). Peptoid Derivatives. Peptoid derivatives of peptides represent another form of modified peptides that retain the important structural determinants for biological activity, yet eliminate the peptide bonds, thereby conferring resistance to proteolysis (Simon, et al., 1992, Proc. Natl. Acad. Sci. USA, 89:9367-9371). Peptoids are oligomers of N-substituted glycines. A number of N- alkyl groups have been described, each corresponding to the side chain of a natural amino acid (Simon, et al. (1992), cited above). In various embodiments, all or a portion of the amino acids may be replaced with the corresponding N-substituted glycine. For example, the N-terminal residue may be the only one that is replaced, or a few amino acids may be replaced by the corresponding N-substituted glycines. Moreover, as is apparent from the present disclosure, mimetopes of the subject Brd4 peptides can be provided. Such peptidomimetics can have such attributes as being non- hydrolyzable (e.g., increased stability against proteases or other physiological conditions which degrade the corresponding peptide), increased specificity and/or potency for inhibition of PV replication, and increased cell permeability for intracellular localization of the peptidomimetic. For illustrative purposes, peptide analogs of the present invention can be generated using, for example, benzodiazepines (e.g., see Freidinger et al. in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gama lactam rings (Garvey et al. in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, pl23), C-7 mimics (Huffman et al. in Peptides: Chemistry and Biologyy, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, p. 105), keto- methylene pseudopeptides (Ewenson et al. (1986) J Med Chem 29:295; and Ewenson et al. in Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium) Pierce

Chemical Co. Rockland, IL, 1985), β-turn dipeptide cores (Nagai et al. (1985) Tetrahedron Lett

26:647; and Sato et al. (1986) J Chem Soc Perkin Trans 1 : 1231), β-aminoalcohols (Gordon et al.

(1985) Biochem Biophys Res Communl26:4l9; and Dann et al. (1986) Biochem Biophys Res Commun 134:71), diaminoketones (Natarajan et al. (1984) Biochem Biophys Res Commun 124:141), and methyleneamino-modifed (Roark et al. in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988, pl34). Also, see generally, Session III: Analytic and synthetic methods, in in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988) In addition to a variety of sidechain replacements which can be carried out to generate the subject Brd4 peptidomimetics, the present invention specifically contemplates the use of conformationally restrained mimics of peptide secondary structure. Numerous surrogates have been developed for the amide bond of peptides. Frequently exploited surrogates for the amide bond include the following groups (i) trans-olefins, (ii) fluoroalkene, (iii) methyleneamino, (iv) phosphonamides, and (v) sulfonamides.

Examples of Surrogates

trans olefin fluoroalkene methyleneamino

phosphonamide sulfonamide Additionally, peptidomimietics based on more substantial modifications of the backbone of the Brd4 peptide can be used. Peptidomimetics which fall in this category include (i) retro- l inverso analogs, and (ii) N-alkyl glycine analogs (so-called peptoids).

Examples of analogs:

retro-inverso N-alkyl glycine Furthermore, the methods of combinatorial chemistry are being brought to bearon the development of new peptidomimetics (see e.g., Gierasch et al., Org. Lett. 5: 621-4 (2003)). For example, one embodiment of a so-called "peptide morphing" strategy focuses on the random generation of a library of peptide analogs that comprise a wide range of peptide bond substitutes.

dipeptide peptide morphing

In an exemplary embodiment, the peptidomimetic can be derived as a retro-inverso analog of the peptide. Such retro-inverso analogs can be made according to the methods known in the art, such as that described by the Sisto et al. U.S. Patent 4,522,752. For example, the illustrated retro- inverso analog can be generated as follows. The geminal diamine corresponding to the N- terminal tryptophan is synthesized by treating a protected tryptophan analog with ammonia under HOBT-DCC coupling conditions to yield the N-Boc amide, and then effecting a Hofmann-type rearrangement with I,I-bis-(trifluoroacetoxy)iodobenzene (TIB), as described in Radhakrishna et al. (1979) J. Org. Chem. 44:1746. The product amine salt is then coupled to a side-chain protected (e.g., as the benzyl ester) N-Fmoc D-lys residue under standard conditions to yield the pseudodipeptide. The Fmoc (fluorenylmethoxycarbonyl) group is removed with piperidine in dimethylformamide, and the resulting amine is trimethylsilylated with bistrimethylsilylacetamide (BSA) before condensation with suitably alkylated, side-chain protected derivative of Meldrum's acid, as described in U.S. Patent 5,061,811 to Pinori et al., to yield the retro-inverso tripeptide analog WKH. The pseudotripeptide is then coupled with with an L-methionine analog under standard conditions to give the protected tetrapeptide analog. The protecting groups are removed to release the product, and the steps repeated to enlogate the tetrapeptide to the full length peptidomimetic. It will be understood that a mixed peptide, e.g. including some normal peptide linkages, will be generated. As a general guide, sites which are most susceptible to proteolysis are typically altered, with less susceptible amide linkages being optional for mimetic switching. The final product, or intermediates thereof, can be purified by HPLC. In another illustrative embodiment, the peptidomimetic can be derived as a retro-enatio analog of the peptide. Retro-enantio analogs such as this can be synthesized commercially available D-amino acids (or analogs thereof) and standard solid- or solution-phase peptide- synthesis techniques. For example, in a preferred solid-phase synthesis method, a suitably amino-protected (t-butyloxycarbonyl, Boc) D-trp residue (or analog thereof) is covalently bound to a solid support such as chloromethyl resin. The resin is washed with dichloromethane (DCM), and the BOC protecting group removed by treatment with TFA in DCM. The resin is washed and neutralized, and the next Boc-protected D-amino acid (D-lys) is introduced by coupling with diisopropylcarbodiimide. The resin is again washed, and the cycle repeated for each of the remaining amino acids in turn (D-his, D-met, etc). When synthesis of the protected retro-enantio peptide is complete, the protecting groups are removed and the peptide cleaved from the solid support by treatment with hydrofluoric acid anisole/dimethyl sulfide/thioanisole. The final product is purified by HPLC to yield the pure retro-enantio analog. In still another illustrative embodiment, trans-olefin derivatives can be made for the subject polypeptide. The trans olefin analog of a Brd4 peptide can be synthesized according to the method of Y.K. Shue et al. (1987) Tetrahedron Letters 28:3225. Referring to the illustrated example, Boc-amino L-Ile is converted to the corresponding -amino aldehyde, which is treated with a vinylcuprate to yield a diastereomeric mixture of alcohols, which are carried on together. The allylic alcohol is acetylated with acetic anhydride in pyridine, and the olefin is cleaved with osmium tetroxide/sodium periodate to yield the aldehyde, which is condensed with the Wittig reagent derived from a protected tyrosine precursor, to yield the allylic acetate. The allylic acetate is selectively hydrolyzed with sodium carbonate in methanol, and the allylic alcohol is treated with triphenylphosphine and carbon tetrabromide to yield the allylic bromide. This compound is reduced with zinc in acetic acid to give the transposed trans olefin as a mixture of diastereomers at the newly-formed center. The diastereomers are separated and the pseudodipeptide is obtained by selective transfer hydrogenolysis to unveil the free carboxylic acid. The pseudodipeptide is then coupled at the C-terminus, according to the above example, with a suitably protected tyrosine residue, and at the N-terminus with a protected alanine residue, by standard techniques, to yield the protected tetrapeptide isostere. The terapeptide is then further condensed with the olefinic tripeptide analog derived by similar means to build up the full peptide. The protecting groups are then removed with strong acid to yield the desired peptide analog, which can be further purified by HPLC. Other pseudodipeptides can be made by the method set forth above merely by substitution of the appropriate starting Boc amino acid and Wittig reagent. Variations in the procedure may be necessary according to the nature of the reagents used, but any such variations will be purely routine and will be obvious to one of skill in the art. It is further possible to couple the pseudodipeptides synthesized by the above method to other pseudodipeptides, to make peptide analogs with several olefinic functionalities in place of amide functionalities. For example, pseudodipeptides corresponding to Met-Arg or Tyr-Lys, etc. could be made and then coupled together by standard techniques to yield an analog of the Brd4 peptide which has alternating olefinic bonds between residues. Still another class of peptidomimetic derivatives include the phosphonate derivatives. The synthesis of such phosphonate derivatives can be adapted from known synthesis schemes. See, for example, Loots et al. in Peptides: Chemistry and Biology, (Escom Science Publishers, Leiden, 1988, p. 118); Petrillo et al. in Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium, Pierce Chemical Co. Rockland, IL, 1985). Many other peptidomimetic structures are known in the art and can be readily adapted for use in the the subject Brd4 peptidomimetics. To illustrate, the Brd4 peptidomimetic may incorporate the l-azabicyclo[4.3.0]nonane surrogate ( see Kim et al. (1997) J. Org. Chem. (52:2847), or an N-acyl piperazic acid (see Xi et al. (1998) J. Am. Chem. Soc. 720:80), or a 2- substituted piperazine moiety as a constrained amino acid analogue (see Williams et al. (1996) L Med. Chem. J : 1345-1348). In still other embodiments, certain amino acid residues can be replaced with aryl and bi-aryl moieties, e.g., monocyclic or bicyclic aromatic or heteroaromatic nucleus, or a biaromatic, aromatic-heteroaromatic, or biheteroaromatic nucleus. The subject Brd4 peptidomimetics can be optimized by, e.g., combinatorial synthesis techniques combined with such high throughput screening as described herein. Moreover, other examples of mimetopes include, but are not limited to, protein-based compounds, carbohydrate-based compounds, lipid-based compounds, nucleic acid-based compounds, natural organic compounds, synthetically derived organic compounds, anti-idiotypic antibodies and/or catalytic antibodies, or fragments thereof. A mimetope can be obtained by, for example, screening libraries of natural and synthetic compounds for compounds capable of inhibiting an interaction between a Brd4 polypeptide and an E2 protein or a functional equivalent thereof. A mimetope can also be obtained, for example, from libraries of natural and synthetic compounds, in particular, chemical or combinatorial libraries (i.e., libraries of compounds that differ in sequence or size but that have the same building blocks). A mimetope can also be obtained by, for example, rational drug design. In a rational drug design procedure, the three- dimensional structure of a compound of the present invention can be analyzed by, for example, nuclear magnetic resonance (NMR) or x-ray crystallography. The three-dimensional structure can then be used to predict structures of potential mimetopes by, for example, computer modelling, the predicted mimetope structures can then be produced by, for example, chemical synthesis, recombinant DNA technology, or by isolating a mimetope from a natural source (e.g., plants, animals, bacteria and fungi).

Nucleic Acids One aspect of the invention pertains to isolated nucleic acids of the invention. For example, the present invention contemplates an isolated nucleic acid comprising (a) the nucleotide sequence of SEQ ID NO: 1, (b) a nucleotide sequence at least 90% identical to SEQ ID NO: 1, (c) a nucleotide sequence that hybridizes under stringent conditions to SEQ ID NO: 1, or (d) the complement of the nucleotide sequence of (a), (b) or (c). In certain embodiments, nucleic acids of the invention may be labeled, with for example, a radioactive, chemiluminescent or fluorescent label. In another aspect, the present invention contemplates an isolated nucleic acid that selectively hybridizes under stringent conditions to at least ten nucleotides of SEQ ID NO: 1, or the complement thereof, which nucleic acid can specifically detect or amplify SEQ ID NO: 1, or the complement thereof. In yet another aspect, the present invention contemplates such an isolated nucleic acid comprising a nucleotide sequence encoding a fragment of SEQ ID NO: 2 at least 5 residues in length. The present invention further contemplates a method of hybridizing an oligonucleotide with a nucleic acid of the invention comprising: (a) providing a single-stranded oligonucleotide at least eight nucleotides in length, the oligonucleotide being complementary to a portion of a nucleic acid of the invention; and (b) contacting the oligonucleotide with a sample comprising a nucleic acid of the acid under conditions that permit hybridization of the oligonucleotide with the nucleic acid of the invention. Isolated nucleic acids which differ from the nucleic acids of the invention due to degeneracy in the genetic code are also within the scope of the invention. For example, a number of amino acids are designated by more than one triplet. Codons that specify the same amino acid, or synonyms (for example, CAU and CAC are synonyms for histidine) may result in "silent" mutations which do not affect the amino acid sequence of the protein. However, it is expected that DNA sequence polymorphisms that do lead to changes in the amino acid sequences of the subject proteins will exist among mammalian cells. One skilled in the art will appreciate that these variations in one or more nucleotides (from less than 1% up to about 3 or 5% or possibly more of the nucleotides) of the nucleic acids encoding a particular protein of the invention may exist among individuals of a given species due to natural allelic variation. Any and all such nucleotide variations and resulting amino acid polymorphisms are within the scope of this invention. Bias in codon choice within genes in a single species appears related to the level of expression of the protein encoded by that gene. Accordingly, the invention encompasses nucleic acid sequences which have been optimized for improved expression in a host cell by altering the frequency of codon usage in the nucleic acid sequence to approach the frequency of preferred codon usage of the host cell. Due to codon degeneracy, it is possible to optimize the nucleotide sequence without affecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleotide sequence that encodes all or a substantial portion of the amino acid sequence set forth in SEQ ID NO: 2 or other polypeptides of the invention. The present invention pertains to nucleic acids encoding human Brd4 proteins and amino acid sequences evolutionarily related to a polypeptide of the invention, wherein "evolutionarily related to", refers to proteins having different amino acid sequences which have arisen naturally (e.g. by allelic variance or by differential splicing), as well as mutational variants of the proteins of the invention which are derived, for example, by combinatorial mutagenesis. Fragments of the polynucleotides of the invention encoding a biologically active portion of the subject polypeptides are also within the scope of the invention. Exemplary fragments are presented in the figures and the Examples. As used herein, a fragment of a nucleic acid of the invention encoding an active portion of a polypeptide of the invention refers to a nucleotide sequence having fewer nucleotides than the nucleotide sequence encoding the full length amino acid sequence of, for example, SEQ ID NO: 2, and which encodes a polypeptide which retains at least a portion of a biological activity of the full-length protein as defined herein, or alternatively, which is functional as a modulator of the biological activity of the full-length protein. For example, such fragments include a polypeptide containing a domain or short peptide fragment of the full-length protein from which the polypeptide is derived that mediates the interaction of the protein with another molecule (e.g., polypeptide, DNA, RNA, etc.). In another embodiment, the present invention contemplates an isolated nucleic acid that encodes a polypeptide having a biological activity of a human Brd4 protein. In an exemplary embodiment, the invention contemplates an isolated nucleic acid that encodes a fragment of human Brd4 that is capable of interacting with a viral E2 protein or a functional equivalent of a viral E2 protein. In another embodiment, the invention contemplates an isolated nucleic acid that encodes a fragment of human Brd4 that is capable of preventing, disrupting, and/or inhibiting an interaction between a human Brd4 protein and a viral E2 protein or a functional equivalent of a viral E2 protein. Nucleic acids within the scope of the invention may also contain linker sequences, modified restriction endonuclease sites and other sequences useful for molecular cloning, expression or purification of such recombinant polypeptides. A nucleic acid encoding a polypeptide of the invention may be obtained from mRNA or genomic DNA from any organism in accordance with protocols described herein, as well as those generally known to those skilled in the art. A cDNA encoding a polypeptide of the invention, for example, may be obtained by isolating total mRNA from an organism, e.g. a bacteria, virus, mammal, etc. Double stranded cDNAs may then be prepared from the total mRNA, and subsequently inserted into a suitable plasmid or bacteriophage vector using any one of a number of known techniques. A gene encoding a polypeptide of the invention may also be cloned using established polymerase chain reaction techniques in accordance with the nucleotide sequence information provided by the invention. In one aspect, the present invention contemplates a method for amplification of a nucleic acid of the invention, or a fragment thereof, comprising: (a) providing a pair of single stranded oligonucleotides, each of which is at least eight nucleotides in length, complementary to sequences of a nucleic acid of the invention, and wherein the sequences to which the oligonucleotides are complementary are at least ten nucleotides apart; and (b) contacting the oligonucleotides with a sample comprising a nucleic acid comprising the nucleic acid of the invention under conditions which permit amplification of the region located between the pair of oligonucleotides, thereby amplifying the nucleic acid. Another aspect of the invention relates to the use of nucleic acids of the invention in "antisense therapy". As used herein, antisense therapy refers to administration or in situ generation of oligonucleotide probes or their derivatives which specifically hybridize or otherwise bind under cellular conditions with the cellular mRNA and/or genomic DNA encoding one of the polypeptides of the invention so as to inhibit expression of that polypeptide, e.g. by inhibiting transcription and/or translation. The binding may be by conventional base pair complementarity, or, for example, in the case of binding to DNA duplexes, through specific interactions in the major groove of the double helix. In general, antisense therapy refers to the range of techniques generally employed in the art, and includes any therapy which relies on specific binding to oligonucleotide sequences. An antisense construct of the present invention may be delivered, for example, as an expression plasmid which, when transcribed in the cell, produces RNA which is complementary to at least a unique portion of the mRNA which encodes a polypeptide of the invention. Alternatively, the antisense construct may be an oligonucleotide probe which is generated ex vivo and which, when introduced into the cell causes inhibition of expression by hybridizing with the mRNA and/or genomic sequences encoding a polypeptide of the invention. Such oligonucleotide probes may be modified oligonucleotides which are resistant to endogenous nucleases, e.g. exonucleases and/or endonucleases, and are therefore stable in vivo. Exemplary nucleic acid molecules for use as antisense oligonucleotides are phosphoramidate, phosphothioate and methylphosphonate analogs of DNA (see also U.S. Patents 5,176,996; 5,264,564; and 5,256,775). Additionally, general approaches to constructing oligomers useful in antisense therapy have been reviewed, for example, by van der Krol et al., (1988) Biotechniques 6:958-976; and Stein et al., (1988) Cancer Res 48:2659-2668. In a further aspect, the invention provides double stranded small interfering RNAs (siRNAs), and methods for administering the same. siRNAs decrease or block gene expression. While not wishing to .be bound by theory, it is generally thought that siRNAs inhibit gene expression by mediating sequence specific mRNA degradation. RNA interference (RNAi) is the process of sequence-specific, posf-transcriptional gene silencing, particularly in animals and plants, initiated by double-stranded RNA (dsRNA) that is homologous in sequence to the silenced gene (Elbashir et al. Nature 2001; 411(6836): 494-8). Accordingly, it is understood that siRNAs and long dsRNAs having substantial sequence identity to all or a portion of SEQ ID NO: 1 may be used to inhibit the expression of a nucleic acid of the invention, and particularly when the polynucleotide is expressed in a mammalian or plant cell. The nucleic acids of the invention may be used as diagnostic reagents to detect the presence or absence of the target DNA or RNA sequences to which they specifically bind, such as for determining the level of expression of a nucleic acid of the invention. In one aspect, the present invention contemplates a method for detecting the presence of a nucleic acid of the invention or a portion thereof in a sample, the method comprising: (a) providing an oligonucleotide at least eight nucleotides in length, the oligonucleotide being complementary to a portion of a nucleic acid of the invention; (b) contacting the oligonucleotide with a sample comprising at least one nucleic acid under conditions that permit hybridization of the oligonucleotide with a nucleic acid comprising a nucleotide sequence complementary thereto; and (c) detecting hybridization of the oligonucleotide to a nucleic acid in the sample, thereby detecting the presence of a nucleic acid of the invention or a portion thereof in the sample. In another aspect, the present invention contemplates a method for detecting the presence of a nucleic acid of the invention or a portion thereof in a sample, the method comprising: (a) providing a pair of single stranded oligonucleotides, each of which is at least eight nucleotides in length, complementary to sequences of a nucleic acid of the invention, and wherein the sequences to which the oligonucleotides are complementary are at least ten nucleotides apart; and (b) contacting the oligonucleotides with a sample comprising at least one nucleic acid under hybridization conditions; (c) amplifying the nucleotide sequence between the two oligonucleotide primers; and (d) detecting the presence of the amplified sequence, thereby detecting the presence of a nucleic acid comprising the nucleic acid of the invention or a portion thereof in the sample. In another aspect of the invention, a nucleic acid of the invention is provided in an expression vector comprising a nucleotide sequence encoding a polypeptide of the invention and operably linked to at least one regulatory sequence. It should be understood that the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to be expressed. The vector's copy number, the ability to control that copy number and the expression of any other protein encoded by the vector, such as antibiotic markers, should be considered. The subject nucleic acids may be used to cause expression and over-expression of a polypeptide of the invention in cells propagated in culture, e.g. to produce proteins or polypeptides, including fusion proteins or polypeptides. This invention pertains to a host cell transfected with a recombinant gene in order to express a polypeptide of the invention. The host cell may be any prokaryotic or eukaryotic cell. For example, a polypeptide of the present invention may be expressed in bacterial cells, such as E. coli, insect cells (baculovirus), yeast, or mammalian cells. In those instances when the host cell is human, it may or may not be in a live subject. Other suitable host cells are known to those skilled in the art. Additionally, the host cell may be supplemented with tRNA molecules not typically found in the host so as to optimize expression of the polypeptide. Other methods suitable for maximizing expression of the polypeptide will be known to those in the art. The present invention further pertains to methods of producing the polypeptides of the invention. For example, a host cell transfected with an expression vector encoding a polypeptide of the invention may be cultured under appropriate conditions to allow expression of the polypeptide to occur. The polypeptide may be secreted and isolated from a mixture of cells and medium containing the polypeptide. Alternatively, the polypeptide may be retained cytoplasmically and the cells harvested, lysed and the protein isolated. A cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art. The polypeptide may be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins, including ion- exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for particular epitopes of a polypeptide of the invention. Thus, a nucleotide sequence encoding all or a selected portion of polypeptide of the invention, may be used to produce a recombinant form of the protein via microbial or eukaryotic cellular processes. Ligating the sequence into a polynucleotide construct, such as an expression vector, and transforming or transfecting into hosts, either eukaryotic (yeast, avian, insect or mammalian) or prokaryotic (bacterial cells), are standard procedures. Similar procedures, or modifications thereof, may be employed to prepare recombinant polypeptides of the invention by microbial means or tissue-culture technology in accord with the subject invention. Expression vehicles for production of a recombinant protein include plasmids and other vectors. For instance, suitable vectors for the expression of a polypeptide of the invention include plasmids of the types: pBR322-derived plasmids, pEMBL-derived plasmids, pEX- derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prokaryotic cells, such as E. coli. A number of vectors exist for the expression of recombinant proteins in yeast. For instance, YEP24, YIP5, YEP51, YEP52, pYES2, and YRP17 are cloning and expression vehicles useful in the introduction of genetic constructs into S. cerevisiae (see, for example, Broach et al., (1983) in Experimental Manipulation of Gene Expression, ed. M. Inouye Academic Press, p. 83). These vectors may replicate in E. coli due the presence of the pBR322 ori, and in S. cerevisiae due to the replication determinant of the yeast 2 micron plasmid. In addition, drug resistance markers such as ampicillin may be used. In certain embodiments, mammalian expression vectors contain both prokaryotic sequences to facilitate the propagation of the vector in bacteria, and one or more eukaryotic transcription units that are expressed in eukaryotic cells. The pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, pko-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells. Some of these vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells. Alternatively, derivatives of viruses such as the bovine papilloma virus (BPV- 1), or Epstein-Barr virus (pHEBo, pREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells. The various methods employed in the preparation of the plasmids and transformation of host organisms are well known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells, as well as general recombinant procedures, see Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press, 1989) Chapters 16 and 17. In some instances, it may be desirable to express the recombinant protein by the use of a baculovirus expression system. Examples of such baculovirus expression systems include pVL-derived vectors (such as pVL1392, pVL1393 and ρVL941), pAcUW-derived vectors (such as pAcUWl), and pBlueBac- derived vectors (such as the β-gal containing pBlueBac III). In another variation, protein production may be achieved using in vitro translation systems. In vitro translation systems are, generally, a translation system which is a cell-free extract containing at least the minimum elements necessary for translation of an RNA molecule into a protein. An in vitro translation system typically comprises at least ribosomes, tRNAs, initiator methionyl-tRNAMet, proteins or complexes involved in translation, e.g., eIF2, eIF3, the cap-binding (CB) complex, comprising the cap-binding protein (CBP) and eukaryotic initiation factor 4F (eIF4F). A variety of in vitro translation systems are well known in the art and include commercially available kits. Examples of in vitro translation systems include eukaryotic lysates, such as rabbit reticulocyte lysates, rabbit oocyte lysates, human cell lysates, insect cell lysates and wheat germ extracts. Lysates are commercially available from manufacturers such as Promega Corp., Madison, Wis.; Stratagene, La Jolla, Calif; Amersham, Arlington Heights, 111.; and GIBCO/BRL, Grand Island, N.Y. In vitro translation systems typically comprise macromolecules, such as enzymes, translation, initiation and elongation factors, chemical reagents, and ribosomes. In addition, an in vitro transcription system may be used. Such systems typically comprise at least an RNA polymerase holoenzyme, ribonucleotides and any necessary transcription initiation, elongation and termination factors. In vitro transcription and translation may be coupled in a one-pot reaction to produce proteins from one or more isolated DNAs. When expression of a carboxy terminal fragment of a polypeptide is desired, i.e. a truncation mutant, it may be necessary to add a start codon (ATG) to the oligonucleotide fragment containing the desired sequence to be expressed. It is well known in the art that a methionine at the N-terminal position may be enzymatically cleaved by the use of the enzyme methionine aminopeptidase (MAP). MAP has been cloned from E. coli (Ben-Bassat et al., (1987) J. Bacteriol. 169:751-757) and Salmonella typhimurium and its in vitro activity has been demonstrated on recombinant proteins (Miller ' et al., (1987) PNAS USA §4:2718-1722). Therefore, removal of an N-terminal methionine, if desired, may be achieved either in vivo by expressing such recombinant polypeptides in a host which produces MAP (e.g., E. coli or CM89 or S. cerevisiae), or in vitro by use of purified MAP (e.g., procedure of Miller et al.). Coding sequences for a polypeptide of interest may be incorporated as a part of a fusion gene including a nucleotide sequence encoding a different polypeptide. The present invention contemplates an isolated nucleic acid comprising a nucleic acid of the invention and at least one heterologous sequence encoding a heterologous peptide linked in frame to the nucleotide sequence of the nucleic acid of the invention so as to encode a fusion protein comprising the heterologous polypeptide. The heterologous polypeptide may be fused to (a) the C-terminus of the polypeptide encoded by the nucleic acid of the invention, (b) the N-terminus of the polypeptide, or (c) the C-terminus and the N-terminus of the polypeptide. In certain instances, the heterologous sequence encodes a polypeptide permitting the detection, isolation, solubilization and/or stabilization of the polypeptide to which it is fused. In still other embodiments, the heterologous sequence encodes a polypeptide selected from the group

78 V consisting of a polyHis tag, myc, HA, GST, protein A, protein G, calmodulin-binding peptide, thioredoxin, maltose-binding protein, poly arginine, poly His-Asp, FLAG, a portion of an immunoglobulin protein, and a transcytosis peptide. Fusion expression systems can be useful when it is desirable to produce an immunogenic fragment of a polypeptide of the invention. For example, the VP6 capsid protein of rotavirus may be used as an immunologic carrier protein for portions of polypeptide, either in the monomeric form or in the form of a viral particle. The nucleic acid sequences corresponding to the portion of a polypeptide of the invention to which antibodies are to be raised may be incorporated into a fusion gene construct which includes coding sequences for a late vaccinia virus structural protein to produce a set of recombinant viruses expressing fusion proteins comprising a portion of the protein as part of the virion. The Hepatitis B surface antigen may also be utilized in this role as well. Similarly, chimeric constructs coding for fusion proteins containing a portion of a polypeptide of the invention and the poliovirus capsid protein may be created to enhance immunogenicity (see, for example, EP Publication NO: 0259149; and Evans et al., (1989) Nature 339:385; Huang et al, (1988) J. Virol. 62:3855; and Schlienger et al., (1992) J. Virol. 66:2). Fusion proteins may facilitate the expression and/or purification of proteins. For example, a polypeptide of the present invention may be generated as a glutathione-S-transferase (GST) fusion protein. Such GST fusion proteins may be used to simplify purification of a polypeptide of the invention, such as through the use of glutathione-derivatized matrices (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al., (N.Y.: John Wiley & Sons, 1991)). In another embodiment, a fusion gene coding for a purification leader sequence, such as a poly-(His)/enterokinase cleavage site sequence at the N-terminus of the desired portion of the recombinant protein, may allow purification of the expressed fusion protein by affinity chromatography using a Ni²⁺ metal resin. The purification leader sequence may then be subsequently removed by treatment with enterokinase to provide the purified protein (e.g., see Hochuli et al, (1987) J. Chromatography 411: 177; and Janknecht et al., PNAS USA 88:8972). Techniques for making fusion genes are well known. Essentially, the joining of various

DNA fragments coding for different polypeptide sequences is performed in accordance with conventional techniques, employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene may be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments may be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which may subsequently be annealed to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al., John Wiley & Sons: 1992). The present invention further contemplates a transgenic non-human animal having cells which harbor a transgene comprising a nucleic acid of the invention. In other embodiments, the invention provides for nucleic acids of the invention immobilized onto a solid surface, including, plates, microtiter plates, slides, beads, particles, spheres, films, strands, precipitates, gels, sheets, tubing, containers, capillaries, pads, slices, etc. The nucleic acids of the invention may be immobilized onto a chip as part of an array. The array may comprise one or more polynucleotides of the invention as described herein. In one embodiment, the chip comprises one or more polynucleotides of the invention as part of an array of mammalian polynucleotide sequences. In still other embodiments, the invention comprises the sequence of a nucleic acid of the invention in computer readable format. The invention also encompasses a database comprising the sequence of a nucleic acid of the invention.

Antibodies Another aspect of the invention pertains to antibodies specifically reactive with a polypeptide of the invention. For example, by using peptides based on a polypeptide of the invention, e.g., having an amino acid sequence of SEQ ID NO: 2 or an immunogenic fragment thereof, antisera or monoclonal antibodies may be made using standard methods. An exemplary immunogenic fragment may contain five, eight, ten or more consecutive amino acid residues of SEQ ID NO: 2. In other embodiments, the invention provides antibodies that bind to complexes containing Brd4, such as complexes comprising Brd4 and an E2 protein or a functional equivalent of an E2 protein. In one embodiment, the present invention provides an isolated antibody that has a higher binding affinity for a Brd4/E2 complex than for the individual complex polypeptides. In another embodiment, the present invention provides an isolated antibody that binds to an interaction site on Brd4, E2 or a functional equivalent of an E2 protein. In still other embodiments, the isolated antibodies of the invention disrupt or stabilize a Brd4/E2 complex. In yet another embodiment, the present invention provides an isolated antibody that binds to a Brd4 polypeptide comprising the amino acid sequence of residues 1047-1362, 1134- 1362, and/or 1224-1362 of Brd4. Another aspect of the invention pertains to antibodies specifically reactive with a Brd4 polypeptide. The term "antibody" as used herein is intended to include fragments thereof which are also specifically reactive with a polypeptide of the invention. Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as is suitable for whole antibodies. For example, F(ab')₂ fragments can be generated by treating

antibody with pepsin. The resulting F(ab')2 fragment can be treated to reduce disulfide bridges

to produce Fab' fragments. The antibody of the present invention is further intended to include bispecific and chimeric molecules, as well as single chain (scFv) antibodies. Also within the scope of the invention are trimeric antibodies, humanized antibodies, human antibodies, and single chain antibodies. All of these modified forms of antibodies as well as fragments of antibodies are intended to be included in the term "antibody". In one aspect, the present invention contemplates a purified antibody that binds specifically to a polypeptide of the invention and which does not substantially cross-react with a protein which is less than about 80%, or less than about 90%, identical to a polypeptide of the invention. In another aspect, the present invention contemplates an array comprising a substrate having a plurality of address, wherein at least one of the addresses has disposed thereon a purified antibody that binds specifically to a polypeptide of the invention. Antibodies may be elicited by methods known in the art. For example, a mammal such as a mouse, a hamster or rabbit may be immunized with an immunogenic form of a polypeptide of the invention (e.g., an antigenic fragment which is capable of eliciting an antibody response). Alternatively, immunization may occur by using a nucleic acid of the acid, which presumably in vivo expresses the polypeptide of the invention giving rise to the immunogenic response observed. Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art. For instance, a peptidyl portion of a polypeptide of the invention may be administered in the presence of adjuvant. The progress of immunization may be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassays may be used with the immunogen as antigen to assess the levels of antibodies. Following immunization, antisera reactive with a polypeptide of the invention may be obtained and, if desired, polyclonal antibodies isolated from the serum. To produce monoclonal antibodies, antibody producing cells (lymphocytes) may be harvested from an immunized animal and fused by standard somatic cell fusion'procedures with immortalizing cells such as myeloma cells to yield hybridoma cells. Such techniques are well known in the art, and include, for example, the hybridoma technique (originally developed by Kohler and Milstein, (1975) Nature, 256: 495-497), as the human B cell hybridoma technique (Kozbar et al., (1983) Immunology Today, 4: 72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., (1985) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. pp. 77-96). Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with the polypeptides of the invention and the monoclonal antibodies isolated. Antibodies directed against the polypeptides of the invention can be used to isolate a polypeptide of the invention by standard techniques, such as affinity chromatography or immunoprecipitation. The antibodies may also be used to facilitate the purification of a Brd4 polypeptide from cells obtained from a patient sample or from a cell culture. In addition, such antibodies are useful to detect the presence of a polypeptide of the invention in cells or tissues to determine the pattern of expression of the polypeptide among various tissues in an organism and/or over the course of normal development. Further, such antibodies can be used to detect protein in situ, in vitro, or in a cell lysate or supernatant, in order to evaluate the abundance and pattern of expression. Also, such antibodies can be used to assess abnormal tissue distribution or abnormal expression during development or progression of a biological condition. Further, the antibodies directed against the polypeptides of the invention can be used to assess expression in disease states, including active stages of the disease or pre-disease states to asses an individual's predisposition toward a disease or disorder. When a disorder is caused by an inappropriate tissue distribution, developmental expression, level of expression of the protein, or expressedprocessed form, the antibody can be prepared against the normal protein. If a disorder is characterized by a specific mutation in the protein, antibodies specific for this mutant protein can be used to assay for the presence of the specific mutant protein. The antibodies directed against the polypeptides of the invention can also be used to assess subcellular localization of Brd4 in the various tissues in an organism. The diagnostic uses can be applied, not only in diagnostic applications, but also in monitoring a treatment modality. Accordingly, where a treatment is ultimately aimed at correcting expression level, aberrant tissue distribution, or developmental expression, antibodies directed against the protein or relevant fragments can be used to monitor therapeutic efficacy. For example, antibodies may be used to monitor the effect of modulators of Brd4 complexes, e.g., when administered to a subject. In particular, antibodies to Brd4 complexes can be used to monitor the level of Brd4 complexes. Additionally, antibodies directed against the polypeptides of the invention are useful in pharmacogenomic analysis. For example, antibodies prepared against polymorphic proteins can be used to identify individuals that require modified treatment modalities. The antibodies are also useful as diagnostic tools, for example, as an immunological marker for aberrant protein which may analyzed by a variety of techniques, including, electrophoretic mobility, isoelectric point, proteolytic digest, and other assays known to those in the art. Antibodies directed against the polypeptides of the invention can be used to selectively block the action of the polypeptides of the invention. Antibodies against a polypeptide of the

5 invention may be employed to treat diseases or disorders related to a viral infection. For example, the present invention contemplates a method for treating a subject suffering from a disease or disorder related to a viral infection, comprising administering to an animal having the condition a therapeutically effective amount of a purified antibody that binds specifically to a polypeptide of the invention.0 The invention also encompasses kits comprising antibodies directed against the polypeptides of the invention for use in detecting the presence of a protein in a biological sample. The kit may comprise one or more of the following: antibodies, such as a labeled or labelable antibody; a compound or agent for detecting protein in a biological sample; means for determining the amount of protein in the sample; means for comparing the amount of protein in

.5 the sample with a standard; and instructions for use. Such a kit can be supplied to detect a single protein or epitope or can be configured to detect one of a multitude of epitopes, such as in an antibody detection array. In one embodiment, antibodies reactive with a polypeptide of the invention are used in the immunological screening of cDNA libraries constructed in expression vectors, such as λgtl 1,

'.0 λgtl8-23, λZAP, and λORF8. Messenger libraries of this type, having coding sequences inserted in the correct reading frame and orientation, can produce fusion proteins. For instance, λgtl 1 will produce fusion proteins whose amino termini consist of β-galactosidase amino acid sequences and whose carboxy termini consist of a foreign polypeptide. Antigenic epitopes of a polypeptide of the invention can then be detected with antibodies, as, for example, reacting nitrocellulose filters lifted from phage infected bacterial plates with an antibody specific for a polypeptide of the invention. Phage scored by this assay can then be isolated from the infected plate. Thus, homologs of a polypeptide of the invention can be detected and cloned from other sources. Antibodies may be employed to isolate or to identify clones expressing the polypeptides to purify the polypeptides by affinity chromatography. In other embodiments, the polypeptides of the invention may be modified so as to increase their immunogenicity. For example, a polypeptide, such as an antigenically or immunologically equivalent derivative, may be associated, for example by conjugation, with an immunogenic carrier protein for example bovine serum albumin (BSA) or keyhole limpet haemocyanin (KLH). Alternatively a multiple antigenic peptide comprising multiple copies of the protein or polypeptide, or an antigenically or immunologically equivalent polypeptide thereof may be sufficiently antigenic to improve immunogenicity so as to obviate the use of a carrier. In other embodiments, the antibodies of the invention, or variants thereof, are modified to make them less immunogenic when administered to a subject. For example, if the subject is human, the antibody may be "humanized"; where the complimentarity determining region(s) of the hybridoma-derived antibody has been transplanted into a human monoclonal antibody, for example as described in Jones, P. et al. (1986), Nature 321, 522-525 or Tempest et al. (1991) Biotechnology 9, 266-273. Also, transgenic mice, or other mammals, may be used to express humanized antibodies. Such humanization may be partial or complete. The use of a nucleic acid of the invention in genetic immunization may employ a suitable delivery method such as direct injection of plasmid DNA into muscles (Wolff et al., Hum Mol Genet 1992, 1:363, Manthorpe et al., Hum. Gene Ther. 1963:4, 419), delivery of DNA complexed with specific protein carriers (Wu et al., J Biol Chem. 1989: 264,16985), coprecipitation of DNA with calcium phosphate (Benvenisty & Reshef, PNAS USA, 1986:83,9551), encapsulation of DNA in various forms of liposomes (Kaneda et al., Science 1989:243,375), particle bombardment (Tang et al., Nature 1992, 356:152, Eisenbrauri et al., DNA Cell Biol 1993, 12:791) and in vivo infection using cloned retroviral vectors (Seeger et al., PNAS USA 1984:81,5849).

Methods of Producing, Identifying, and Isolating Brd4 Complexes In another aspect the invention provides methods of producing, identifying, and isolating a Brd4 complex. Brd4 complexes may be produced by a variety of methods. For example, Brd4 complexes may be naturally-occurring, for instance in a cell infected with a virus (such as, for example, a papillomavirus, herpes virus, epstein barr virus, etc.), or produced in a host cell comprising nucleic acids encoding Brd4 and/or E2 or a functional equivalent thereof, or produced in vitro in a solution comprising Brd4 polypeptides and at an E2 protein or functional equivalent thereof. A variety of materials may be used as the source of potential Brd4 and or E2 polypeptides (or functional equivalents thereof). In one embodiment, a cellular extract or extracellular fluid may be used. The choice of starting material for the extract may be based upon the cell or tissue type or type of fluid that would be expected to contain Brd4 complex polypeptides. Micro-organisms or other organisms are grown in a medium that is appropriate for that organism and can be grown in specific conditions to promote the expression of proteins that may interact with the target protein. Exemplary starting material that may be used to make a suitable extract are: 1) one or more types of tissue derived from an animal, especially a human, 2) cells grown in tissue culture that were derived from an animal, especially a human, 3) microorganisms grown in suspension or non-suspension cultures, 4) virus-infected cells, 5) purified organelles (including, but not restricted to nuclei, mitochondria, membranes, Golgi, endoplasmic reticulum, lysosomes, or peroxisomes) prepared by differential centrifugation or another procedure from animal, especially human, cells, 6) serum or other bodily fluids including, but not limited to, blood, urine, semen, synovial fluid, cerebrospinal fluid, amniotic fluid, lymphatic fluid or interstitial fluid. In other embodiments, a total cell extract may not be the optimal source of Brd4 complex polypeptides. Extracts are prepared by methods known to those of skill in the art. The extracts may be prepared at a low temperature (e.g., 4°C) in order to retard denaturation or degradation of proteins in the extract. The pH of the extract may be adjusted to be appropriate for the body fluid or tissue, cellular, or organellar source that is used for the procedure (e.g. pH 7-8 for cytosolic extracts from mammals, but low pH for lysosomal extracts). The concentration of chaofropic or non-chaotropic salts in the extracting solution may be adjusted so as to extract the appropriate sets of proteins for the procedure. Glycerol may be added to the extract, as it aids in maintaining the stability of many proteins and also reduces background non-specific binding. Both the lysis buffer and column buffer may-contain protease inhibitors to minimize proteolytic degradation of proteins in the extract and to protect the polypeptide. Appropriate co-factors that could potentially interact with the interacting proteins may be added to the extracting solution. One or more nucleases or another reagent may be added to the extract, if appropriate, to prevent protein-protein interactions that are mediated by nucleic acids. Appropriate detergents or other agents may be added to the solution, if desired, to extract membrane proteins from the cells or tissue. A reducing agent (e.g. dithiothreitol or 2-mercaptoethanol or glutathione or other agent) may be added. Trace metals or a chelating agent may be added, if desired, to the extracting solution. Usually, the extract is centrifuged in a centrifuge or ultracentrifuge or filtered to provide a clarified supernatant solution. This supernatant solution may be dialyzed using dialysis tubing, or another kind of device that is standard in the art, against a solution that is similar to, but may not be identical with, the solution that was used to make the extract. The extract is clarified by centrifugation or filtration again immediately prior to its use in affinity chromatography. In some cases, the crude lysate will contain small molecules that can interfere with the affinity chromatography. This can be remedied by precipitating proteins with ammonium sulfate, centrifugation of the precipitate, and re-suspending the proteins in the affinity column buffer followed by dialysis. An additional centrifugation of the sample may be needed to remove any particulate matter prior to application to the affinity columns. In an alternative embodiment, a Brd4 complex polypeptide (e.g., Brd4, E2, or a functional equivalent of an E2 polypeptide) is expressed, optionally in a heterologous cell, and purified and then mixed with a potential Brd4 complex polypeptide or mixture of polypeptides to identify Brd4 complex formation. The potential Brd4 complex polypeptide may be a single purified or semi-purified protein, or a mixture of proteins, including a mixture of purified or semi-purified proteins, a cell lysate, a clarified cell lysate, a semi-purified cell lysate, etc. Typically, it will be desirable to immobilize a Brd4 complex polypeptide or Brd4 complex to facilitate separation of Brd4 complexes from uncomplexed forms of the interacting proteins, as well as to accommodate automation of the assay. The Brd4 complex or Brd4 complex polypeptide, or ligand, riiay be immobilized onto a solid support (e.g., column matrix, microtiter plate, slide, etc.). In certain embodiments, the ligand may be purified. In certain instances, a fusion protein may be provided which adds a domain that permits the ligand to be bound to a support. In various in vitro embodiments, the set of proteins engaged in a protein-protein interaction comprises a cell extract, a clarified cell extract, or a reconstituted protein mixture of at least semi-purified proteins. By semi-purified, it is meant that the proteins utilized in the reconstituted mixture have been previously separated from other cellular or viral proteins. For instance, in contrast to cell lysates, the proteins involved in a protein-protein interaction are present in the mixture to at least about 50% purity relative to all other proteins in the mixture, and more preferably are present in greater, even 90-95%, purity. In certain embodiments of the subject method, the reconstituted protein mixture is derived by mixing highly purified proteins such that the reconstituted mixture substantially lacks other proteins (such as of cellular or viral origin) which might interfere with or otherwise alter the ability to measure activity resulting from the given protein-protein interaction. The present invention contemplates a method for identifying a Brd4 complex or Brd4 complex polypeptide, the method comprising: (a) exposing a sample to a solid substrate coupled to a Brd4 complex or Brd4 complex polypeptide under conditions which promote protein-protein interactions; (b) washing the solid substrate so as to remove any polypeptides interacting non- specifically with the polypeptide or fragment; (c) eluting the polypeptides which specifically interact with the Brd4 complex or Brd4 complex polypeptide; and (d) identifying the interacting protein. The interacting protein may be identified by a number of methods, including mass spectrometry, gel electrophoresis, activity assay, or protein sequencing. In another aspect, the present invention contemplates a method for identifying a protein capable of interacting with Brd4, a Brd4 complex polypeptide, or Brd4 complex, or fragments thereof, the method comprising: (a) subjecting a sample to protein-affinity chromatography on multiple columns, the columns having a Brd4 complex or Brd4 complex polypeptide coupled to the column matrix in varying concentrations, and eluting bound components of the extract from the columns; (b) separating the components to isolate a polypeptide capable of interacting with the Brd4 polypeptide, complex or fragment; and (c) analyzing the interacting protein by mass spectrometry to identify the interacting protein. In certain instances, the foregoing method will use polyacrylamide gel electrophoresis to separate and/or analyze the interacting polypeptides. In another aspect, the present invention contemplates a method for identifying a Brd4 complex or Brd4 complex polypeptide the method comprising: (a) subjecting a cellular extract or extracellular fluid to protein-affinity chromatography on multiple columns, the columns having a Brd4 complex or Brd4 complex polypeptide coupled to the column matrix in varying concentrations, and eluting bound components of the extract from the columns; (b) gel- separating the components to isolate an interacting protein; wherein the interacting protein is observed to vary in amount in direct relation to the concentration of coupled polypeptide or fragment; (c) digesting the interacting protein to give corresponding peptides; (d) analyzing the peptides by MALDI-TOF mass spectrometry or post source decay to determine the peptide masses; and (e) performing correlative database searches with the peptide, or peptide fragment, masses, whereby the interacting protein is identified based on the masses of the peptides or peptide fragments. The foregoing method may include the further step of including the identifies of any interacting proteins into a relational database. In another embodiment, proteins that interact with a Brd4 complex or Brd4 complex polypeptide may be identified using affinity chromatography. In one aspect, for affinity chromatography using a solid support, a Brd4 complex polypeptide may be attached by a variety of means known to those of skill in the art. For example, the polypeptide may be coupled directly (through a covalent linkage) to commercially available pre-activated resins as described in Formosa et al., Methods in Enzymology 1991, 208, 24-45; Sopta et al, J. Biol. Chem. 1985, 260, 10353-60; Archambault et al., Proc. Natl. Acad. Sci. USA 1997, 94, 14300-5. Alternatively, the polypeptide may be tethered to the solid support through high affinity binding interactions. If the polypeptide is expressed fused to a tag, such as GST, the fusion tag can be used to anchor the polypeptide to the matrix support, for example Sepharose beads containing immobilized glutathione. Solid supports that take advantage of these tags are commercially available. The amount of cell extract applied to the column may be important for any embodiment. If too little extract is applied to the column and the interacting protein is present at low concentration, the level of interacting protein retained by the column may be difficult to detect. Conversely, if too much extract is applied to the column, protein may precipitate on the column or competition by abundant interacting proteins for the limited amount of protein ligand may result in a difficulty in detecting minor species. The columns functionalized with a Brd4 complex or Brd4 complex polypeptide are loaded with protein extract from an appropriate source that has been dialyzed against a buffer that is consistent with the nature of the expected interaction. The pH, salt concentrations and the presence or absence of reducing and chelating agents, trace metals, detergents, and co-factors may be adjusted according to the nature of the expected interaction. Most commonly, the pH and the ionic strength are chosen so as to be close to physiological for the source of the extract. The extract is most commonly loaded under gravity onto the columns at a flow rate of about 4-6 column volumes per hour, but this flow rate can be adjusted for particular circumstances in an automated procedure. The volume of the extract that is loaded on the columns can be varied but is most commonly equivalent to about 5 to 10 column volumes. When large volumes of extract are loaded on the columns, there is often an improvement in the signal-to-noise ratio because more protein from the extract is available to bind to the protein ligand, whereas the background binding of proteins from the extract to the solid support saturates with low amounts of extract. A control column may be included that contains the highest concentration of protein ligand, but buffer rather than extract is loaded onto this column. The elutions (eluates) from this column will contain polypeptide that failed to be attached to the column in a covalent manner, but no proteins that are derived from the extract. The columns may be washed with a buffer appropriate to the nature of the interaction being analyzed, usually, but not necessarily, the same as the loading buffer. An elution buffer with an appropriate pH, glycerol, and the presence or absence of reducing agent, chelating agent, cofactors, and detergents are all important considerations. The columns may be washed with anywhere from about 5 to 20 column volumes of each wash buffer to eliminate unbound proteins from the natural extract. The flow rate of the wash is usually adjusted to about 4 to 6 column volumes per hour by using gravity or an automated procedure, but other flow rates are possible in specific circumstances. In order to elute the proteins that have been retained by the column, the interactions between the extract proteins and the column ligand should be disrupted. This is performed by eluting the column with a solution of salt or detergent. Retention of activity by the eluted proteins may require the presence of glycerol and a buffer of appropriate pH, as well as proper choices of ionic strength and the presence or absence of appropriate reducing agent, chelating agent, trace metals, cofactors, detergents, chaofropic agents, and other reagents. If physical identification of the bound proteins is the objective, the elution may be performed sequentially, first with buffer of high ionic strength and then with buffer containing a protein denaturant, most commonly, but not restricted to sodium dodecyl sulfate (SDS), urea, or guanidine hydrochloride. In certain instances, the column is eluted with a protein denaturant, particularly SDS, for example as a 1% SDS solution. Using only the SDS wash, and omitting the salt wash, may result in SDS-gels that have higher resolution (sharper bands with less smearing). Also, using only the SDS wash results in half as many samples to analyze. The volume of the eluting solution may be varied but is normally about 2 to 4 column volumes. For 20 ml columns, the flow rate of the eluting procedures are most commonly about 4 to 6 column volumes per hour, under gravity, but can be varied in an automated procedure. In other embodiments, Brd4 complexes may be isolated using immunoprecipitation. The cells expressing a Brd4 complex polypeptide are lysed under conditions which maintain protein- protein interactions, and Brd4 complexes are isolated. In certain embodiments, it may be desirable to use a tagged version of a Brd4 complex polypeptide in order to facilitate isolation of complexes from the reaction mixture. Suitable tags for immunoprecipitation experiments include HA, myc, FLAG, HIS, GST, protein A, protein G, etc. Immunoprecipitation from a cell lysate or other protein mixture may be carried out using an antibody specific for a Brd4 complex or Brd4 complex polypeptide or using an antibody which recognizes a tag to which a Brd4 complex polypeptide is fused (e.g., anti-HA, anti-myc, anti-FLAG, etc.). Antibodies specific for a variety of tags are known to the skilled artisan and are commercially available from a number of sources. In the case where an complex polypeptide is fused to a His, GST, or protein A/G tag, immunoprecipitation may be carried out using the appropriate affinity resin (e.g., beads functionalized with Ni, glutathione, Fc region of IgG, etc.). Test compounds which modulate a protein-protein interaction involving a Brd4 complex polypeptide may be identified by carrying out the immunoprecipitation reaction in the presence and absence of the test agent and comparing the level and/or activity of the Brd4 complex between the two reactions. The proteins from the extract that were bound to and are eluted from the affinity columns or that are immunoprecipitated may be most easily resolved for identification by an electrophoresis procedure, but this procedure may be modified, replaced by another suitable method, or omitted. Any of the denaturing or non-denaturing electrophoresis procedures that are standard in the art may be used for this purpose, including SDS-PAGE, gradient gels, capillary electrophoresis, and two-dimensional gels with isoelectric focusing in the first dimension and SDS-PAGE in the second. Typically, the individual components in the column eluent are separated by polyacrylamide gel electrophoresis. After electrophoresis, protein bands or spots may be visualized using any number of methods know to those of skill in the art, including staining techniques such as Coomassie blue or silver staining, or some other agent that is standard in the art. Alternatively, autoradiography can be used for visualizing proteins isolated from organisms cultured on media containing a radioactive label, for example ³⁵SO₄ ^2" or ³⁵[S]methionine, that is incorporated into the proteins. The use of radioactively labeled extract allows a distinction to be made between extract proteins that were retained by the column and proteolytic fragments of the ligand that may be released from the column. I Protein bands that are derived from the extract (i.e. it did not elute from the control column that was not loaded with protein from the extract) and bound to an experimental column that contained polypeptide covalently attached to the solid support, and did not bind to a control column that did not contain any polypeptide, may be excised from the stained electrophoretic gel and further characterized. Eluates from the affinity chromatography columns or immunoprecipitates may also be analyzed directly without resolution by electrophoretic methods by proteolytic digestion with a protease in solution, followed by applying the proteolytic digestion products to a reverse phase column and eluting the peptides from the column. To identify the protein interactor by mass spectrometry, it may be desirable to reduce the disulfide bonds of the protein followed by alkylation of the free thiols prior to digestion of the protein with protease. The reduction may be performed by treatment of the gel slice with a reducing agent, for example with dithiothreitol, whereupon, the protein is alkylated by treating the gel slice with a suitable alkylating agent, for example iodoacetamide. Prior to analysis by mass spectrometry, the protein may be chemically or enzymatically digested. The protein sample in the gel slice may be subjected to in-gel digestion. Shevchenko

A. et al., Mass Spectrometric Sequencing of Proteins from Silver Stained Polyacrylamide Gels.

Analytical Chemistry 1996, 58, 850-858. One method of digestion is by treatment with the enzyme trypsin. The resulting peptides are extracted from the gel slice into a buffer. The peptide fragments may be purified, for example by use of chromatography. A solid support that differentially binds the peptides and not the other compounds derived from the gel slice, the protease reaction or the peptide extract may be used. The peptides may be eluted from the solid support into a small volume of a solution that is compatible with mass spectrometry

(e.g. 50% acetonitrile/0.1% trifluoroacetic acid). The preparation of a protein sample from a gel slice that is suitable for mass spectrometry may also be done by an automated procedure. Various mass spectrometers may be used within the present invention. Representative examples include: triple quadrupole mass spectrometers, magnetic sector instruments (magnetic tandem mass spectrometer, JEOL, Peabody, Mass), ionspray mass spectrometers (Bruins et al., Anal Chem. 59:2642-2647, 1987), electrospray mass spectrometers (including tandem, nano- and nano-electrospray tandem) (Fenn et al., Science 246:64-71, 1989), laser desorption time-of-flight mass spectrometers (Karas and Hillenkamp, Anal. Chem. 60:2299-2301, 1988), and a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (Extrel Corp., Pittsburgh, Mass.). MALDI ionization is a technique in which samples of interest, in this case peptides and proteins, are co-crystallized with an acidified matrix. The matrix is typically a small molecule that absorbs at a specific wavelength, generally in the ultraviolet (UV) range, and dissipates the absorbed energy thermally. Typically a pulsed laser beam is used to transfer energy rapidly (i.e., a few ns) to the matrix. This transfer of energy causes the matrix to rapidly dissociate from the MALDI plate surface and results in a plume of matrix and the co-crystallized analytes being transferred into the gas phase. MALDI is considered a "soft-ionization" method that typically results in singly-charged species in the gas phase, most often resulting from a protonation reaction with the matrix. MALDI may be coupled in-line with time of flight (TOF) mass spectrometers. TOF detectors are based on the principle that an analyte moves with a velocity proportional to its mass. Analytes of higher mass move slower than analytes of lower mass and thus reach the detector later than lighter analytes. The present invention contemplates a composition comprising a Brd4 complex polypeptide and a matrix suitable for mass spectrometry. In certain instances, the matrix is a nicotinic acid derivative or a cinnamic acid derivative. MALDI-TOF MS is easily performed with modern mass spectrometers. Typically the samples of interest, in this case peptides or proteins, are mixed with a matrix and spotted onto a polished stainless steel plate (MALDI plate). Commercially available MALDI plates can presently hold up to 1536 samples per plate. Once spotted with sample, the MALDI sample plate is then introduced into the vacuum chamber of a MALDI mass spectrometer. The pulsed laser is then activated and the mass to charge ratios of the analytes are measured utilizing a time of flight detector. A mass spectrum representing the mass to charge ratios of the peptides/proteins is generated. As mentioned above, MALDI can be utilized to measure the mass to charge ratios of both proteins and peptides. In the case of proteins, a mixture of intact protein and matrix are co- crystallized on a MALDI target (Karas, M. and Hillenkamp, F. Anal. Chem. 1988, 60 (20) 2299- 2301). The spectrum resulting from this analysis is employed to determine the molecular weight of a whole protein. This molecular weight can then be compared to the theoretical weight of the protein and utilized in characterizing the analyte of interest, such as whether or not the protein has undergone post-translational modifications (e.g., example phosphorylation). In certain embodiments, MALDI mass spectrometry is used for determination of peptide maps of digested proteins. The peptide masses are measured accurately using a MALDI-TOF or a MALDI-Q-Star mass spectrometer, with detection precision down to the low ppm (parts per million) level. The ensemble of the peptide masses observed in a protein digest, such as a tryptic digest, may be used to search protein/DNA databases in a method called peptide mass fingerprinting. In this approach, protein entries in a database are ranked according to the number of experimental peptide masses that match the predicted trypsin digestion pattern. Commercially available software utilizes a search algorithm that provides a scoring scheme based on the size of the databases, the number of matching peptides, and the different peptides. Depending on the number of peptides observed, the accuracy of the measurement, and the size of the genome of the particular species, unambiguous protein identification may be obtained. Statistical analysis may be performed upon each protein match to determine the validity of the match. Typical constraints include error tolerances within 0.1 Da for monoisotopic peptide masses, cysteines may be alkylated and searched as carboxyamidomethyl modifications, 0 or 1 missed enzyme cleavages, and no methionine oxidations allowed. Identified proteins may be stored automatically in a relational database with software links to SDS-PAGE images and ligand sequences. Often even a partial peptide map is specific enough for identification of the protein. If no protein match is found, a more error-tolerant search can be used, for example using fewer peptides or allowing a larger margin error with respect to mass accuracy. Other mass spectroscopy methods such as tandem mass spectrometry or post source decay may be used to obtain sequence information about proteins that cannot be identified by peptide mass mapping,or to confirm the identity of proteins that are tentatively identified by an error-tolerant peptide mass search. (Griffin et al, Rapid Commun. Mass. Spectrom. 1995, 9,

1546-51). Complex formation between a Brd4 complex polypeptide and a binding partner may be detected by a variety of methods. Modulation of the formation of Brd4 complexes may be quantitated using, for example, detectably labeled proteins such as radiolabeled, fluorescently labeled, or enzymatically labeled polypeptides or binding partners, by immunoassay, or by chromatographic detection. Methods of isolating and identifying Brd4 complexes described in above may be incorporated into the detection methods. Typically, it will be desirable to immobilize a Brd4 complex polypeptide or its binding partner to facilitate separation of Brd4 complexes from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Binding of a Brd4 complex polypeptide to a binding partner may be accomplished in any vessel suitable for containing the reactants. Examples include microtitre plates, test tubes, and micro-centrifuge tubes. In one embodiment, a fusion protein may be provided which adds a domain that allows the protein to be bound to a matrix. For example, glutathione-S-transferase/polypeptide (GST/polypeptide) fusion proteins may be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtitre plates, which are then combined with the binding partner, e.g.

an 35§_ι_ab_eι_e(i binding partner, and the test compound, and the mixture incubated under conditions conducive to complex formation, e.g. at physiological conditions for salt and pH, though slightly more stringent conditions may be desired. Following incubation, the beads are washed to remove any unbound label, and the matrix immobilized and radiolabel determined directly (e.g. beads placed in scintillant), or in the supernatant after the complexes are subsequently dissociated. Alternatively, the complexes may be dissociated from the matrix, separated by SDS-PAGE, and the level of Brd4 complex polypeptide or binding partner found in the bead fraction quantitated from the gel using standard electrophoretic techniques such as described in the appended examples. Other techniques for immobilizing proteins on matrices are also available for use in the subject assay. For instance, either the Brd4 complex polypeptide or its binding partner may be immobilized utilizing conjugation of biotin and streptavidin. For instance, biotinylated polypeptide molecules may be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, IL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). Alternatively, antibodies reactive with the polypeptide may be derivatized to the wells of the plate, and polypeptide trapped in the wells by antibody conjugation. As above, preparations of a binding partner and a test compound are incubated in the polypeptide presenting wells of the plate, and the amount of complex trapped in the well may be quantitated. Exemplary methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the binding partner, or which are reactive with the Brd4 complex polypeptide and compete with the binding partner; as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the binding partner, either intrinsic or extrinsic activity. In the instance of the latter, the enzyme may be chemically conjugated or provided as a fusion protein with the binding partner. To illustrate, the binding partner may be chemically cross-linked or genetically fused with horseradish peroxidase, and the amount of Brd4 complex polypeptide trapped in the Brd4 complex may be assessed with a chromogenic substrate of the enzyme, e.g. 3,3'-diamino-benzadine terahydrochlori.de or 4-chloro-l-napthol. Likewise, a fusion protein comprising the Brd4 complex polypeptide and glutathione-S-transferase may be provided, and Brd4 complex formation quantitated by detecting the GST activity using l-chloro-2,4-dinifrobenzene (Habig et al (1974) J Biol Chem 249:7130). For processes that rely on immunodetection for quantitating one of the Brd4 complex polypeptides trapped in the Brd4 complex, antibodies against the Brd4 complex polypeptide, such as anti-Brd4 or anti-E2 antibodies, may be used. Alternatively, the Brd4 complex polypeptide to be detected in the Brd4 complex may be "epitope-tagged" in the form of a fusion protein that includes, in addition to the polypeptide sequence, a second polypeptide for which antibodies are readily available (e.g. from commercial sources). For instance, the GST fusion proteins described above may also be used for quantification of binding using antibodies against the GST moiety. Other useful epitope tags include myc-epitopes (e.g., see Ellison et al. (1991) J Biol Chem 266:21150-21157) which includes a 10-residue sequence from c-myc, as well as the pFLAG system (International Biotechnologies, Inc.) or the pEZZ-protein A system (Pharmacia, NJ). In certain in vitro embodiments of the present assay, the protein or the set of proteins engaged in a protein-protein, protein-substrate, or protein-nucleic acid interaction comprises a reconstituted protein mixture of at least semi-purified proteins. By semi-purified, it is meant that the proteins utilized in the reconstituted mixture have been previously separated from other cellular or viral proteins. For instance, in contrast to cell lysates, the proteins involved in a protein-substrate, protein-protein or nucleic acid-protein interaction are present in the mixture to at least 50% purity relative to all other proteins in the mixture, and more preferably are present at 90-95% purity. In certain embodiments of the subject method, the reconstituted protein mixture is derived by mixing highly purified proteins such that the reconstituted mixture substantially lacks other proteins (such as of cellular or viral origin) which might interfere with or otherwise alter the ability to measure activity resulting from the given protein-substrate, protein-protein interaction, or nucleic acid-protein interaction. In one embodiment, the use of reconstituted protein mixtures allows more careful control of the protein-substrate, protein-protein, or nucleic acid-protein interaction conditions. Moreover, the system may be derived to favor discovery of modulators of particular intermediate states of the protein-protein interaction. For instance, a reconstituted protein assay may be carried out both in the presence and absence of a candidate agent, thereby allowing detection of a modulator of a given protein-substrate, protein-protein, or nucleic acid-protein interaction. Assaying biological activity resulting from a given protein-substrate, protein-protein or nucleic acid-protein interaction, in the presence and absence of a candidate modulator, may be accomplished in any vessel suitable for containing the reactants. Examples include microtitre plates, test tubes, and micro-centrifuge tubes. Typically, it will be desirable to immobilize one of the Brd4 complex polypeptides to facilitate separation of Brd4 complexes from uncomplexed forms of one of the proteins, as well as to accommodate automation of the assay. In an illustrative embodiment, a fusion protein may be provided which adds a domain that permits the protein to be bound to an insoluble matrix. For example, protein-protein interaction component fusion proteins may be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtitre plates, which are then combined with a potential interacting protein, e.g. an ³⁵S- labeled polypeptide, and the test compound and incubated under conditions conducive to complex formation e.g., at 4oC in a buffer of 2 mM Tris-HCl (pH 8), 1 nM EDTA, 0.5% Nonidet P-40, and 100 mM NaCI. Following incubation, the beads are washed to remove any unbound interacting protein, and the matrix bead-bound radiolabel determined directly (e.g. beads placed in scintillant), or in the supernatant after the complexes are dissociated, e.g. when microtitre plate is used. Alternatively, after washing away unbound protein, the complexes may be dissociated from the matrix, separated by SDS-PAGE gel, and the level of interacting polypeptide found in the matrix-bound fraction quantitated from the gel using standard electrophoretic techniques. In yet another embodiment, a Brd4 complex polypeptide may be used to generate a two- hybrid or interaction trap assay (see also, U.S. Patent NO: 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J Biol Chem 268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; and Iwabuchi et al. (1993) Oncogene 8:1693-1696), for subsequently detecting agents which disrupt binding of the interaction components to one another. In particular, the method makes use of chimeric genes which express hybrid proteins. To illustrate, a first hybrid gene comprises the coding sequence for a DNA-binding domain of a transcriptional activator may be fused in frame to the coding sequence for a "bait" protein, e.g., a Brd4 complex polypeptide of sufficient length to bind to a potential interacting protein. The second hybrid protein encodes a transcriptional activation domain fused in frame to a gene encoding a "fish" protein, e.g., a potential interacting protein of sufficient length to interact with the protein-protein interaction component polypeptide portion of the bait fusion protein. If the bait and fish proteins are able to interact, e.g., form a protein-protein interaction component complex, they bring into close proximity the two domains of the transcriptional activator. This proximity causes transcription of a reporter gene which is operably linked to a transcriptional regulatory site responsive to the transcriptional activator, and expression of the reporter gene may be detected and used to score for the interaction of the bait and fish proteins. The host cell also contains a first chimeric gene which is capable of being expressed in the host cell. The gene encodes a chimeric protein, which comprises (a) a DNA-binding domain that recognizes the responsive element on the reporter gene in the host cell, and (b) a bait protein (e.g., a Brd4 complex polypeptide). A second chimeric gene is also provided which is capable of being expressed in the host cell, and encodes the "fish" fusion protein. In one embodiment, both the first and the second chimeric genes are introduced into the host cell in the form of plasmids. Preferably, however, the first chimeric gene is present in a chromosome of the host cell and the second chimeric gene is introduced into the host cell as part of a plasmid. The DNA-binding domain of the first hybrid protein and the transcriptional activation domain of the second hybrid protein may be derived from transcriptional activators having separable DNA-binding and transcriptional activation domains. For instance, these separate DNA-binding and transcriptional activation domains are known to be found in the yeast GAL4 protein, and are known to be found in the yeast GCN4 and ADR1 proteins. Many other proteins involved in transcription also have separable binding and transcriptional activation domains which make them useful for the present invention, and include, for example, the LexA and VP16 proteins. It will be understood that other (substantially) franscriptionally-inert DNA-binding domains may be used in the subject constructs; such as domains of ACE1, λcl, lac repressor, jun or fos. In another embodiment, the DNA-binding domain and the transcriptional activation domain may be from different proteins. The use of a LexA DNA binding domain provides certain advantages. For example, in yeast, the LexA moiety contains no activation function and has no known affect on transcription of yeast genes. In addition, use of LexA allows control over the sensitivity of the assay to the level of interaction (see, for example, the Brent et al. PCT publication WO94/10300). In certain embodiments, any enzymatic activity associated with the bait or fish proteins is inactivated, e.g., dominant negative or other mutants of a protein-protein¹ interaction component can be used. Continuing with the illustrative example, a Brd4 complex polypeptide of the Brd4 complex , if any, between the bait and fish fusion proteins in the host cell, causes the activation domain to activate transcription of the reporter gene. The method is carried out by introducing the first chimeric gene and the second chimeric gene into the host cell, and subjecting that cell to conditions under which the bait and fish fusion proteins and are expressed in sufficient quantity for the reporter gene to be activated. The formation of a Brd4 complex containing a Brd4 complex polypeptide results in a detectable signal produced by the expression of the reporter gene. In still further embodiments, the Brd4 complex of interest is generated in whole cells, taking advantage of cell culture techniques to support the subject assay. For example, the Brd4 complex of can be constituted in a prokaryotic or eukaryotic cell culture system. Advantages to generating the Brd4 complex in an intact cell includes the ability to screen for modulators of the level or activity of the Brd4 complex which are functional in an environment more closely approximating that which therapeutic use of the modulator would require, including the ability of the agent to gain entry into the cell. Furthermore, certain of the in vivo embodiments of the assay are amenable to high through-put analysis of candidate agents. The Brd4 complexes and Brd4 complex polypeptides can be endogenous to the cell selected to support the assay. Alternatively, some or all of the components can be derived from exogenous sources. For instance, fusion proteins can be introduced into the cell by recombinant techniques (such as through the use of an expression vector), as well as by microinjecting the fusion protein itself or mRNA encoding the fusion protein. Moreover, in the whole cell embodiments of the subject assay, the reporter gene construct can provide, upon expression, a selectable marker. Such embodiments of the subject assay are particularly amenable to high through-put analysis in that proliferation of the cell can provide a simple measure of the protein- protein interaction. The amount of transcription from the reporter gene may be measured using any method known to those of skill in the art to be suitable. For example, specific mRNA expression may be detected using Northern blots or specific protein product may be identified by a characteristic stain, western blots or an intrinsic activity. In certain embodiments, the product of the reporter gene is detected by an intrinsic activity associated with that product. For instance, the reporter gene may encode a gene product that, by enzymatic activity, gives rise to a detection signal based on color, fluorescence, or luminescence.

Identification of Compounds that Modulate Brd4 Complexes Modulators of Brd4 complexes and Brd4 complex polypeptides, may be identified and developed as set forth below and otherwise using techniques and methods known to those of skill in the art. The modulators of the invention may be employed, for instance, to inhibit and treat virus-mediated diseases or disorders. The modulators of the invention may also serve as modulators of virus-mediated diseases or disorders via action on a Brd4 complex polypeptide. The modulators of the invention may elicit a change in any of the activities selected from the group consisting of (a) a change in the level of a Brd4 complex, (b) a change in the activity of a Brd4 complex, (c) a change in the stability of a Brd4 complex, (d) a change in the conformation of a Brd4 complex, (e) a change in the activity of at least one polypeptide contained within a Brd4 complex, (f) a change in the conformation of at least one polypeptide contained within a Brd4 complex, (g) where the reaction mixture is a whole cell, a change in the intracellular localization of a Brd4 complex or a Brd4 complex polypeptide thereof, (h) where the reaction mixture is a whole cell, a change the franscription level of a gene dependent on a Brd4 complex, and (i) where the reaction mixture is a whole cell, a change in second messenger levels in the cell. A number of methods for identifying a molecule which modulates a Brd4 complex or a Brd4 complex polypeptide are known in the art. For example, in one such method, a Brd4 complex or a Brd4 complex polypeptide is contacted with a test compound, and the activity of the Brd4 complex or Brd4 complex polypeptide in the presence of the test compound is determined, wherein a change in the activity of the Brd4 complex or Brd4 complex polypeptide is indicative that the test compound modulates the activity of Brd4 complex or Brd4 complex polypeptide. Compounds to be tested for their ability to act as modulators of Brd4 complexes or Brd4 complex polypeptides can be produced, for example, by bacteria, yeast or other organisms (e.g. natural products), produced chemically (e.g. small molecules, including peptidomimetics), or produced recombinantly. Compounds for use with the above-described methods may be selected from the group of compounds consisting of lipids, carbohydrates, polypeptides, peptidomimetics, peptide-nucleic acids (PNAs), small molecules, natural products, aptamers and polynucleotides. In certain embodiments, the compound is a polynucleotide. In some embodiments, said polynucleotide is an antisense nucleic acid. In other embodiments, said polynucleotide is an siRNA. In certain embodiments, the compound comprises a Brd4 complex polypeptide or polynucleotide encoding a Brd4 complex polypeptide as described above. In certain embodiments, the compound may be a member of a library of compounds. A variety of assay formats will suffice and, in light of the present disclosure, those not expressly described herein will nevertheless be comprehended by one of ordinary skill in the art. Assay formats for Brd4 complex formation or enzymatic activity of a Brd4 complex complex or Brd4 complex polypeptides can be generated in many different forms, and include assays based on cell-free systems, e.g. purified proteins or cell lysates, as well as cell-based assays which utilize intact cells. Simple binding assays can also be used to detect agents which, by disrupting the formation of Brd4 complexes, or the binding of a Brd4 complex or Brd4 complex polypeptide to a substrate, can serve as a modulator. Another example of an assay for a modulator of a Brd4 complex polypeptide is a competitive assay that combines a Brd4 complex polypeptide and a potential modulator with Brd4 complex polypeptides, recombinant molecules that comprise a Brd4 complex, Brd4 complex, natural substrates or ligands, or substrate or ligand mimetics, under appropriate conditions for a competitive inhibition assay. Brd4 complex polypeptides can be labeled, such as by radioactivity or a colorimetric compound, such that the number of molecules of a Brd4 complex polypeptide bound to a binding molecule or converted to product can be determined accurately to assess the effectiveness of the potential modulator. Assays may employ kinetic or thermodynamic methodology using a wide variety of techniques including, but not limited to, microcalorimetry, circular dichroism, capillary zone electrophoresis, nuclear magnetic resonance spectroscopy, fluorescence spectroscopy, and combinations thereof. Assays may also employ any of the methods for isolating, preparing and detecting Brd4 complexes as described above. In many drug screening programs which test libraries of compounds and natural extracts, high throughput assays are desirable in order to maximize the number of compounds surveyed in a given period of time. Assays of the present invention which are performed in cell-free systems, such as may be derived with purified or semi-purified proteins or with lysates, are often preferred as "primary" screens in that they can be generated to permit rapid development and relatively easy detection of an alteration in a molecular target which is mediated by a test compound. Moreover, the effects of cellular toxicity and/or bioavailability of the test compound can be generally ignored in the in vitro system, the assay instead being focused primarily on the effect of the drug on the molecular target as may be manifest in an alteration of binding affinity with other proteins or changes in enzymatic properties of the molecular target. Accordingly, potential modifiers, e.g., modulators of Brd4 complexes may be detected in a cell-free assay generated by constitution of a functional Brd4 complex in a cell lysate. In an alternate format, the assay can be derived as a reconstituted protein mixture which, as described below, offers a number of benefits over lysate-based assays. In certain embodiments, methods for identifying a compound that modulates an virus mediated disease or disorder are provided, comprising: (i) contacting a Brd4 complex with a test compound; and (ii) ι assessing the extent of said virus mediated disease or disorder, wherein a modulation in the extent of said virus mediated disease or disorder in the presence of said test compound indicates that the test compound may be a candidate therapeutic for said virus mediated disease or disorder. For example, the extent of a virus mediated cancer could be evaluated by medical diagnostic techniques known to one of skill in the art, such as, for example, biopsy, early antigen serum titer, serum lactate dehydrogenase levels, immunophenotyping, and the like. In another embodiment, the activity of a Brd4 complex may be determined by examining the level of Brd4 complex that is formed or present in a sample. In another embodiment, the activity of a Brd4 complex or Brd4 complex polypeptide may be determined by assaying for the level of expression of RNA and/or protein molecules. Transcription levels may be determined, for example, using Northern blots, hybridization to an oligonucleotide array or by assaying for the level of a resulting protein product. Translation levels may be determined, for example, using Western blotting or by identifying a detectable signal produced by a protein product (e.g., fluorescence, luminescence, enzymatic activity, etc.). Depending on the particular situation, it may be desirable to detect the level of franscription and/or translation of a single gene or of multiple genes. In other embodiments, the biological activity of a Brd4 complex or Brd4 complex polypeptide can be assessed by monitoring changes in the phenotype of the targeted cell. For example, the detection means can include a reporter gene construct which includes a transcriptional regulatory element that is dependent in some form on the level of a Brd4 complex or Brd4 complex polypeptide. The Brd4 complex can be provided as a fusion protein with a domain that binds to a DNA element of the reporter gene construct. The added domain of the fusion protein can be one which, through its DNA-binding ability, increases or decreases transcription of the reporter gene. Which ever the case may be, its presence in the fusion protein renders it responsive to a Brd4 complex or Brd4 complex polypeptide. Accordingly, the level of expression of the reporter gene will vary with the level of expression of a Brd4 complex or Brd4 complex polypeptide. Moreover, in the whole cell embodiments of the subject assay, the reporter gene construct can provide, upon expression, a selectable marker. A reporter gene includes any gene that expresses a detectable gene product, which may be RNA or protein. Preferred reporter genes are those that are readily detectable. The reporter gene may also be included in the construct in the form of a fusion gene with a gene that includes desired transcriptional regulatory sequences or exhibits other desirable properties. For instance, the product of the reporter gene can be an enzyme which confers resistance to antibiotic or other drug, or an enzyme which complements a deficiency in the host cell (i.e. thymidine kinase or dihydrofolate reductase). To illustrate, the aminoglycoside phosphotransferase encoded by the bacterial transposon gene Tn5 neo can be placed under transcriptional control of a promoter element responsive to the level of a Brd4 complex or Brd4 complex polypeptide present in the cell. Such embodiments of the subject assay are particularly amenable to high through-put analysis in that proliferation of the cell can provide a simple measure of inhibition of the Brd4 complex or Brd4 complex polypeptide.

5 Exemplary Uses The methods and compositions described herein may be used for the treatment or prevention of diseases or disorders associated with a variety of viral infections. The methods and compositions described herein may be used to treat or prevent viral infections (or diseases or disorders associated therewith) in any type of organism that is subject to infection by a virus,

.0 including, for example, animals (e.g., mammals, birds, rodents, amphibians, etc.), plants, and bacteria. Accordingly, the methods and compositions of the invention have utility in wide ranging fields such as, for example, agriculture, livestock, crops, medical treatments, combating bio-terrorism, etc. Examples of disease causing viruses that may be treated in accord with the compositions

L5 and methods described herein include: Papovaviridae (papilloma viruses, polyoma viruses); Herpesviridae (herpes simplex virus (HSV) 1 and 2, varicella zoster virus, cytomegalovirus (CMV), herpes viruses'); Retroviridae (e.g., human immunodeficiency viruses, such as HIV-l (also referred to as HTLV-III, LAV or HTLV-III/LAV, See Ratner, L. et al., Nature, Vol. 313, Pp. 227-284 (1985); Wain Hobson, S. et al, Cell, Vol. 40: Pp. 9-17 (1985)); HJV-2 (See Guyader

20 et al., Nature, Vol. 328, Pp. 662-669 (1987); European Patent Publication No. 0 269 520; Chakraborti et al., Nature, Vol. 328, Pp. 543-547 (1987); and European Patent Application No. 0 655 501); and other isolates, such as HIV-LP (International Publication No. WO 94/00562 entitled "A Novel Human Immunodeficiency Virus"); Picornaviridae (e.g., polio viruses, hepatitis A virus, (Gust, I.D., et al., Intervirology, Vol. 20, Pp. 1-7 (1983); entero viruses, human coxsackie viruses, rhinoviruses, echoviruses); Calciviridae (e.g., strains that cause gastroenteritis); Togaviridae (e.g., equine encephalitis viruses, rubella viruses); Flaviridae (e.g., dengue viruses, encephalitis viruses, yellow fever viruses); Coronaviridae (e.g., coronaviruses); Rhabdoviridae (e.g., vesicular stomatitis viruses, rabies viruses); Filoviridae (e.g., ebola viruses); Paramyxoviridae (e.g., parainfluenza viruses, mumps virus, measles virus, respiratory syncytial virus); Orthomyxoviridae (e.g., influenza viruses); Bungaviridae (e.g., Hantaan viruses, bunga viruses, phleboviruses and Nairo viruses); Arena viridae (hemorrhagic fever viruses); Reoviridae (e.g., reoviruses, orbiviurses and rotaviruses); Birnaviridae; Hepadnaviridae (Hepatitis B virus); Parvoviridae (parvoviruses); Adenoviridae (most adenoviruses); Poxviridae (variola viruses, vaccinia viruses, pox viruses); and Iridoviridae (e.g., African swine fever virus); and unclassified viruses (e.g., the etiological agents of Spongiform encephalopathies, the agent of delta hepatities (thought to be a defective satellite of hepatitis B virus), the agents of non- A, non-B hepatitis (class 1 = internally transmitted; class 2 = parenterally transmitted (i.e., Hepatitis C); Norwalk and related viruses, and astro viruses). Genomic information for over 900 viral species is available from TIGR and/or NCBI, including, for example, information about deltaviruses, retroid viruses, satellites, dsDNA viruses, dsRNA viruses, ssDNA viruses, ssRNA negative-strand viruses, ssRNA positive-strand viruses, unclassified bacteriophages, and other unclassified viruses. In another embodiment, the methods and compositions described herein may be used for combating viral based biological warfare agents. Examples of viral based biological warfare agents, include, for example, fϊloviruses (e.g., ebola or Marburg), arenaviruses (e.g., Lassa and Machupo), hantavirus, smallpox (variola major), hemorrhagic fever virus, Nipah virus, and alphaviruses (e.g., Venezuelan equine encephalitis, eastern equine encephalitis, western equine encephalitis). In another embodiment, the methods and compositions described herein may be used for promoting food freshness and/or combating or preventing food contamination. Examples of viral contaminants that may lead to foodborne illnesses include, for example, hepatitis A, norwalk-like viruses, rotavirus, astroviruses, calciviruses, adenoviruses, and parvoviruses. In other embodiments, it may be desirable to administer or formulate the compositions of the invention in conjunction with other therapeutic agents. Exemplary therapeutic agents include, for example, anti-inflammatory agents, immunosuppressive agents, and/or anti-infective agents (such as for example, antibiotic, antiviral, and/or antifungal compounds, etc.). Exemplary anti-inflammatory drugs include, for example, steroidal (such as, for example, cortisol, aldosterone, prednisone, methylprednisone, triamcinolone, dexamethasone, deoxycorticosterone, and fluorocortisol) and non-steroidal anti-inflammatory drugs (such as, for example, ibuprofen, naproxen, and piroxicam). Exemplary immunosuppressive drugs include, for example, prednisone, azathioprine (Imuran), cyclosporine (Sandimmune, Neoral), rapamycin, antithymocyte globulin, daclizumab, OKT3 and ALG, mycophenolate mofetil (Cellcept) and tacrolimus (Prograf, FK506). Exemplary antibiotics include, for example, sulfa drugs (e.g., sulfanilamide), folic acid analogs (e.g., trimethoprim), beta-lactams (e.g., penacillin, cephalosporins), aminoglycosides (e.g., sfretomycin, kanamycin, neomycin, gentamycin), tetracyclines (e.g., chlorotetracycline, oxytetracycline, and doxycycline), macrolides (e.g., erythromycin, azithromycin, and clarithromycin), lincosamides (e.g., clindamycin), streptogramins (e.g., quinupristin and dalfopristin), fluoroquinolones (e.g., ciprofloxacin, levofloxacin, and moxifloxacin), polypeptides (e.g., polymixins), rifampin, mupirocin, cycloserine, aminocyclitol (e.g., spectinomycin), glycopeptides (e.g., vancomycin), and oxazolidinones (e.g., linezolid). Exemplary antiviral agents include, for example, vidarabine, acyclovir, gancyclovir, valganciclovir, nucleoside-analog reverse transcriptase inhibitors (e.g., ZAT, ddl, ddC, D4T, 3TC), non-nucleoside reverse transcriptase inhibitors (e.g., nevirapine, delavirdine), protease inhibitors (e.g., saquinavir, ritonavir, indinavir, nelfinavir), ribavirin, amantadine, rimantadine, relenza, tamiflu, pleconaril, and interferons. Exemplary antifungal drugs include, for example, polyene antifungals (e.g., amphόtericin and nystatin), imidazole antifungals (ketoconazole and miconazole), triazole antifungals (e.g., fluconazole and itraconazole), flucytosine, griseofulvin, and terbinafine. In exemplary embodiments, the subject method is used to treat a subject who is infected with a human papillomavirus (HPV), particularly a high risk HPV such as HPV-16, HPV-18, HPV-31 and HPV-33. In other preferred embodiments, treatment of low risk HPV conditions, e.g., particular topical treatment of cutaneous or mucosal low risk HPV lesions, is also contemplated. The subject method can be used to inhibit pathological progression of papillomavirus infection, such as preventing or reversing the formation of warts, e.g. Plantar warts (verruca plantaris), common warts (verruca plana), Butcher's common warts, flat warts, genital warts (condyloma acuminatum), or epidermodysplasia verruciformis; as well as treating papillomavirus-infected cells which have become, or are at risk of becoming, fransformed and/or immortalized, e.g. cancerous, e.g. a laryngeal papilloma, a focal epithelial, a cervical carcinoma, or as an adjunct to chemotherapy, radiation, surgical or other therapies for eliminating residual infected or pre-cancerous cells. In vitro and ex vivo uses are also contemplated herein. For example, an inhibitor of Brd4 complex formation, such as a portion of a Brd4 protein or an E2 protein or functional equivalent thereof, may be added to ex vivo or in vitro cells and tissues to, e.g., protect the cells from viral contamination or from spreading of a viral contamination. Cells and tissues treated in this manner may be used, e.g., for administering to a subject, such as in a graft transplant, or for analysis, such as forensic analysis. For example, a biopsy obtained from a subject may be treated as described to prevent contamination or spreading of a viral infection. Inhibitors of Brd4 complexes may also be added to blood in blood banks or to other cells.

Pharmaceutical Compositions Pharmaceutical compositions of this invention include any modulator identified according to the present invention, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier, adjuvant, or vehicle. In an exemplary embodiment, pharmaceutical compositions of the invention will include a peptide or peptidomimetic of Brd4 that is capable of disrupting an interaction between Brd4 and an E2 protein or a functional equivalent of an E2 protein. In another embodiment, pharmaceutical compositions of the invention will include an anti-Brd4 and/or anti-E2 antibody that is capable of disrupting an interaction between a Brd4 protein and an E2 protein or a functional equivalent thereof. In yet another embodiment, the pharmaceutical compositions of the invention will include a nucleic acid encoding a Brd4 polypeptide wherein the polypeptide is capable of disrupting an interaction between a Brd4 protein and an E2 protein or a functional equivalent thereof. The term "pharmaceutically acceptable carrier" refers to a carrier(s) that is "acceptable" in the sense of being compatible with the other ingredients of a composition and not deleterious to the recipient thereof. Methods of making and using such pharmaceutical compositions are also included in the invention. The pharmaceutical compositions of the invention can be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally, or via an implanted reservoir. The term parenteral as used herein includes subcutaneous, intracutaneous, intravenous, intramuscular, infra articular, intrasynovial, intrasternal, infrathecal, infralesional, and intracranial injection or infusion techniques. Dosage levels of between about 0.01 and about 100 mg/kg body weight per day, preferably between about 0.5 and about 75 mg/kg body weight per day of the modulators described herein are useful for the prevention and treatment of disease and conditions, including a disease or disorder related to a viral infection. The amount of active ingredient that may be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration. A typical preparation will contain from about 5% to about 95% active compound (w/w). Alternatively, such preparations contain from about 20% to about 80% active compound. In an exemplary embodiment, the active agent is incorporated into a topical formulation containing a topical carrier that is generally suited to topical drug administration and comprising any such material known in the art. The topical carrier is selected so as to provide the composition in the desired form, e.g., as an ointment, lotion, cream, microemulsion, gel, oil, solution, or the like, and may be comprised of a material of either naturally occurring or synthetic origin. The selected carrier preferably does not adversely affect the active agent or other components of the topical formulation. Examples of suitable topical carriers for use herein include water, alcohols and other nontoxic organic solvents, glycerin, mineral oil, silicone, petroleum jelly, lanolin, fatty acids, vegetable oils, parabens, waxes, and the like. Exemplary formulations herein are colorless, odorless ointments, lotions, creams, microemulsions and gels. Ointments are semisolid preparations which are typically based on petrolatum or other petroleum derivatives. The specific ointment base to be used, as will be appreciated by those skilled in the art, is one that will provide for optimum drug delivery, and, preferably, will provide for other desired characteristics as well, e.g., emolliency or the like. As with other carriers or vehicles, an ointment base should be inert, stable, nonirritating and nonsensitizing. As explained in Remington 's (Remington: The Science and Practice of Pharmacy, Alfonso Genaro, ed. Lippincott, Williams & Wilkins, 20^th edition, 2000) ointment bases may be grouped in four classes: oleaginous bases; emulsifiable bases; emulsion bases; and water-soluble bases. Oleaginous ointment bases include, for example, vegetable oils, fats obtained from animals, and semisolid hydrocarbons obtained from petroleum. Emulsifiable ointment bases, also known as absorbent ointment bases, contain little or no water and include, for example, hydroxystearin sulfate, anhydrous lanolin and hydrophilic petrolatum. Emulsion ointment bases are either water- in-oil (W/O) emulsions or oil-in-water (O/W) emulsions, and include, for example, cetyl alcohol, glyceryl monostearate, lanolin and stearic acid. Preferred water-soluble ointment bases are prepared from polyethylene glycols (PEGs) of varying molecular weight; again, reference may be had to Remington's, supra, for further information. Lotions are preparations to be applied to the skin surface without friction, and are typically liquid or semiliquid preparations in which solid particles, including the active agent, are present in a water or alcohol base. Lotions are usually suspensions of solids, and preferably, for the present purpose, comprise a liquid oily emulsion of the oil-in-water type. Lotions are preferred formulations herein for treating large body areas, because of the ease of applying a more fluid composition. It is generally necessary that the insoluble matter in a lotion be finely divided. Lotions will typically contain suspending agents to produce better dispersions as well as compounds useful for localizing and holding the active agent in contact with the skin, e.g., methylcellulose, sodium carboxymethylcellulose, or the like. A particularly preferred lotion formulation for use in conjunction with the present invention contains propylene glycol mixed with a hydrophilic petrolatum such as that which may be obtained under the trademark Aquaphor™ from Beiersdorf, Inc. (Norwalk, Conn.). Creams containing the active agent are, as known in the art, viscous liquid or semisolid emulsions, either oil-in-water or water-in-oil. Cream bases are water- washable, and contain an oil phase, an emulsifier and an aqueous phase. The oil phase is generally comprised of petrolatum and a fatty alcohol such as cetyl or stearyl alcohol; the aqueous phase usually, although not necessarily, exceeds the oil phase in volume, and generally contains a humectant. The emulsifier in a cream formulation, as explained in Remington 's, supra, is generally a nonionic, anionic, cationic or amphoteric surfactant. Microemulsions are thermodynamically stable, isotropically clear dispersions of two immiscible liquids, such as oil and water, stabilized by an interfacial film of surfactant molecules (Encyclopedia of Pharmaceutical Technology (New York: Marcel Dekker, 1992), volume 9). For the preparation of microemulsions, surfactant (emulsifier), co-surfactant (co-emulsifier), an oil phase and a water phase are necessary. Suitable surfactants include any surfactants that are useful in the preparation of emulsions, e.g., emulsifiers that are typically used in the preparation of creams. The co-surfactant (or "co-emulsifer") is generally selected from the group of polyglycerol derivatives, glycerol derivatives and fatty alcohols. Preferred emulsifier/co- emulsifier combinations are generally although not necessarily selected from the group consisting of: glyceryl monostearate and polyoxyethylene stearate; polyethylene glycol and ethylene glycol palmitostearate; and caprilic and capric triglycerides and oleoyl macrogolglycerides. The water phase includes not only water but also, typically, buffers, 5 glucose, propylene glycol, polyethylene glycols, preferably lower molecular weight polyethylene glycols (e.g., PEG 300 and PEG 400), and/or glycerol, and the like, while the oil phase will generally comprise, for example, fatty acid esters, modified vegetable oils, silicone oils, mixtures of mono- di- and triglycerides, mono- and di-esters of PEG (e.g., oleoyl macrogol glycerides), etc.

.0 Gel formulations are semisolid systems consisting of either suspensions made up of small inorganic particles (two-phase systems) or large organic molecules distributed substantially uniformly throughout a carrier liquid (single phase gels). Single phase gels can be made, for example, by combining the active agent, a carrier liquid and a suitable gelling agent such as fragacanth (at 2 to 5%), sodium alginate (at 2-10%), gelatin (at 2-15%), methylcellulose (at 3-

L5 5%), sodium carboxymethylcellulose (at 2-5%), carbomer (at 0.3-5%) or polyvinyl alcohol (at 10-20%) together and mixing until a characteristic semisolid product is produced. Other suitable gelling agents include methylhydroxycellulose, polyoxyethylene-polyoxypropylene, hydroxyethylcellulose and gelatin. Although gels commonly employ aqueous carrier liquid, alcohols and oils can be used as the carrier liquid as well.

20 Various additives, known to those skilled in the art, may be included in the topical formulations of the invention. Examples of additives include, but are not limited to, solubilizers, skin permeation enhancers, opacifiers, preservatives (e.g., anti-oxidants), gelling agents, buffering agents, surfactants (particularly nonionic and amphoteric surfactants), emulsifiers, emollients, thickening agents, stabilizers, humectants, colorants, fragrance, and the like. Inclusion of solubilizers and/or skin permeation enhancers is particularly preferred, along with emulsifiers, emollients and preservatives. An optimum topical formulation comprises approximately: 2 wt. % to 60 wt. %, preferably 2 wt. % to 50 wt. %>, solubilizer and/or skin 5 permeation enhancer; 2 wt. % to 50 wt. %, preferably 2 wt. % to 20 wt. %, emulsifiers; 2 wt. % to 20 wt. % emollient; and 0.01 to 0.2 wt. % preservative, with the active agent and carrier (e.g., water) making of the remainder of the formulation. A skin permeation enhancer serves to facilitate passage of therapeutic levels of active agent to pass through a reasonably sized area of unbroken skin. Suitable enhancers are well

L0 known in the art and include, for example: lower alkanols such as methanol ethanol and 2- propanol; alkyl methyl sulfoxides such as dimethylsulfoxide (DMSO), decylmethylsulfoxide (C.sub.lO MSO) and tetradecylmethyl sulfboxide; pyrrolidones such as 2-pyrrolidone, N-methyl- 2-pyrrolidone and N-(-hydroxyethyl)pyrrolidone; urea; N,N-diethyl-m-toluamide; C.sub.2 - C.sub.6 alkanediols; miscellaneous solvents such as dimethyl formamide (DMF), N,N-

L5 dimethylacetamide (DMA) and tetrahydrofurfuryl alcohol; and the 1 -substituted azacycloheptan- 2-ones, particularly l-n-dodecylcyclazacycloheptan-2-one (laurocapram; available under the trademark Azone™ from Whitby Research Incorporated, Richmond, Va.). Examples of solubilizers include, but are not limited to, the following: hydrophilic ethers such as diethylene glycol monoethyl ether (ethoxydiglycol, available commercially as

50 Transcutol™) and diethylene glycol monoethyl ether oleate (available commercially as Softcutol ); polyethylene castor oil derivatives such as polyoxy 35 castor oil, polyoxy 40 ¹ hydrogenated castor oil, etc.; polyethylene glycol, particularly lower molecular weight polyethylene glycols such as PEG 300 and PEG 400, and polyethylene glycol derivatives such as PEG-8 caprylic/capric glycerides (available commercially as Labrasol™); alkyl methyl sulfoxides such as DMSO; pyrrolidones such as 2-pyrrolidone and N-methyl-2-pyrrolidone; and DMA. Many solubilizers can also act as absorption enhancers. A single solubilizer may be incorporated into the formulation, or a mixture of solubilizers may be incorporated therein. Suitable emulsifiers and co-emulsifiers include, without limitation, those emulsifiers and co-emulsifiers described with respect to microemulsion formulations. Emollients include, for example, propylene glycol, glycerol, isopropyl myristate, polypropylene glycol-2 (PPG-2) myristyl ether propionate, and the like. Other active agents may also be included in the formulation, e.g., other anti-inflammatory agents, analgesics, antimicrobial agents, antifungal agents, antibiotics, vitamins, antioxidants, and sunblock agents commonly found in sunscreen formulations including, but not limited to, anthranilates, benzophenones (particularly benzophenone-3), camphor derivatives, cinnamates (e.g., octyl methoxycinnamate), dibenzoyl methanes (e.g., butyl methoxydibenzoyl methane), p- aminobenzoic acid (PABA) and derivatives thereof, and salicylates (e.g., octyl salicylate). In the preferred topical formulations of the invention, the active agent is present in an amount in the range of approximately 0.25 wt. % to 75 wt. % of the formulation, preferably in the range of approximately 0.25 wt. % to 30 wt. % of the formulation, more preferably in the range of approximately 0.5 wt. % to 15 wt. % of the formulation, and most preferably in the range of approximately 1.0 wt. % to 10 wt. % of the formulation. In an alternative embodiment, a pharmaceutical formulation is provided for oral or parenteral administration, in which case the formulation comprises a resverafrol-containing microemulsion as described above, but may contain alternative pharmaceutically acceptable carriers, vehicles, additives, etc. particularly suited to oral or parenteral drug administration. Alternatively, a resverafrol-containing microemulsion may be administered orally or parenterally substantially as described above, without modification.

EXEMPLIFICATION The invention now being generally described, it will be more readily understood by reference to the following examples which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the invention in any way. Some DNA viruses, like the papillomavirus and the lymphotropic herpesviruses, which establish persistent or latent infections, must maintain their genomes as stable episomes in dividing cells. Although elaborate mechanisms have been demonstrated for the effective segregation of low-copy-number plasmids in prokaryotes, the mechanisms by which eukaryotic episomal viruses ensure genome maintenance have not been yet fully elaborated. A major obstacle for maintaining plasmids in eukaryotes is presented by the breakdown and reassembly of the nuclear membrane during cell division. Noncovalent association with cellular chromosomes appears to be the principle strategy employed by episomal DNA viruses to ensure that their genomes are enclosed within the new nuclear envelopes and thus maintained in progeny cells. The papillomavirus E2 is a multifunctional viral gene product that has been implicated in viral DNA replication, viral transcription, and regulation of cellular fransformation. In addition, E2 protein has been shown to play a critical role in plasmid maintenance by linking the viral genomes to the cellular mitotic chromosomes to ensure their accurate segregation into daughter cells. However, the cellular factors that mediate E2 and host cell interactions remained largely unknown. To address this question, we employed a proteomic tandem affinity purification (TAP) approach to systematically analyze cellular proteins that associate with E2 in vivo. Mass spec analysis of the proteins co-purified with E2 has identified a cellular factor named Brd4. We cloned the full-length cDNA of the human form Brd4 and studied its role in the E2 functions. Using co-immunoprecipitation, we showed that endogenous Brd4 interacts with both human and bovine papillomavirus E2 protein, suggesting a conserved role involving Brd4 in papillomavirus E2 function. Brd4 interacts specifically with the N-terminal transactivation domain of E2, and the E2 binding region on Brd4 has been mapped to its C-terminal region. Immunofluorescent analysis revealed the co-localization of E2 and Brd4 on mitotic chromosomes in human cells, suggesting that the Brd4 may represent the previously unidentified cellular factor that serves as the receptor of E2 on mitotic chromosomes. Expression of a truncated C-terminal domain of Brd4 inhibits the interaction of endogenous Brd4 with E2 and also prevents the co-localization of the viral protein and its cellular partner on mitotic chromosomes. Co-transfection of this dominant-negative truncation mutant of Brd4 with BPV-1 genome into C 127 cells significantly inhibited the transformation efficiency of BPV- 1. We have further demonstrated that the colocalization of E2 with endogenous Brd4 on host mitotic chromosomes involves the N-terminal transactivation domain of E2. In addition, BPV-1 Fluorescence in Situ Hybridization (FISH) analysis showed that, using the E2 binding domain of Brd4, the C-terminal domain (CTD), as a dominant negative inhibitor, we could abolish the tethering of BPVl DNA to host mitotic chromosomes in BPVl transformed cells. Furthermore, quantitative analysis of viral episome levels in CTD-expressing cells that carry BPV-1 exclusively as episomes revealed a progressive loss of BPV-1 DNA with cell passage. Subcloning and morphology analysis of the H2 cells showed that 66% of the CTD-expressing cells reverted to the flat morphology typical of uninfected cells while a 13% rate of revertance was observed for vector control cells. Taken together, our studies demonstrated that the cellular protein Brd4 plays an important role in tethering the papillomavirus genome to host mitotic chromosome through its interaction with E2 protein and may represent an important therapeutic target for papillomavirus infections.

EXAMPLE 1 Tandem Affinity Purification with E2 Protein To identify cellular factors that may play important roles in viral E2-host cell interactions, a proteomic tandem affinity purification (TAP) approach was employed to systematically analyze cellular proteins that associate with E2 in vivo. The results of this experiment are shown in Figure 1. In this study, BPV E2TA protein (full length E2 from BPVl) was tagged with both FLAG and HA epitopes and stably expressed in the human cells. Since most of E2TA's biological functions have been assigned to its N-terminal transactivation domain, a truncation mutant of E2 missing the transactivation domain, E2TR, was similarly tagged and expressed in cells as a negative control. SDS-PAGE electrophoresis of proteins co- purified with E2-TA or E2-TR identified a major protein that is uniquely present in the E2-TA pull down. Mass spec analysis of this E2-TA specific band has identified a cellular factor called Brd4 (bromodomain-containing protein 4).

EXAMPLE 2 Mouse Brd4 Western Blot ofE2 Co-Immunoprecipitation Brd4 contains two bromodomains (named after Drosophila protein brahma), a conserved sequence motif which may be involved in chromatin targeting. Brd4 was identified as the chromosome 19 target of translocation t(15;19)(ql3;pl3.1), which defines a lethal upper respiratory tract carcinoma in young people (CA French et al., Am. J. Pathology 159(6): 1987- 1992 (2001)). The mouse homologue of Brd4, also called MCAP, has been shown to associate with chromosomes during mitosis and affect G(2)-to-M transition (A Dey et al., Mol. Cell. Biology 20(17): 6537-6549 (2000)). Ectopic expression of mouse Brd4 in NIH 3T3 and HeLa cells inhibits cell cycle progression from G(l) to S (T Maruyama et al., Mol. Cell. Biology 22(18): 6509-6520 (2002)). It has also been shown that, while Brd4 heterozygotes mice display pre- and postnatal growth defects associated with a reduced proliferation rate, mouse embryos nullizygous for Brd4 die shortly after implantation. In primary cell cultures, heterozygous cells also display reduced proliferation rates (D Houzelstein et al., Mol. Cell. Biology 22(11): 3794- 3802 (2002)). These studies have suggested a fundamental role of Brd4 in cellular growth control and cell cycle progression. To confirm the mass spec identification result, we used a rabbit Brd4 antibody (recognizes both human and mouse Brd4) to blot the protein samples co-immunoprecipitated with E2TA or E2TR after tandem FLAG and HA affinity purification. The results of this experiment are shown in Figure 2. The mouse Brd4 western blot detected a major band of ~200Kd and two minor short fragments present in the E2TA pull down sample but not in the E2TR sample. This 200Kd band is the expected full-length product of Brd4 and we believed that the two shorter fragments represent proteolytic-cleavage product of Brd4 since they were also detected in the Coomassie Blue stained gel for the mass spec analysis. The experiment confirmed that endogenous Brd4 specifically interacts with E2TA, but not E2TR, and suggested that the transactivation domain of E2 is critical for this interaction. EXAMPLE 3 E2TA Pull Down ofFLAG-MBrd4 Human C33A cells stably expressing either FLAG-HA-E2TA or FLAG-HA-E2TR were transiently transfected with FLAG tagged mouse Brd4 gene (+ lane) or an empty vector (- lane). The results of this experiment are shown in Figure 3. Both cytoplasmic extract (CE) and nuclear extract (NE) were prepared from the transfected cells and immunoprecipitated (IP) with HA antibody to pull down E2 and associated proteins. The IP samples were analyzed by western blot using a Brd4 antibody. Among all the samples analyzed, only NE from cells expressing FLAG-HA-E2TA showed co-immunoprecipitation of Brd4 proteins (lane 9 and 10). Three bands detected in lane 9 where cells were transfected with only an empty vector corresponded to endogenous Brd4 protein and its cleavage products that co-IP with E2TA. In cells transfected with FLAG tagged mouse Brd4 (FLAG-MBrd4) (lane 10), an additional set of bands migrating at slightly higher position were also detected, suggesting the co-IP of the FLAG tagged MBrd4 with E2TA. These experiments demonstrated that, in addition to the endogenous protein, transfected Brd4 protein also specifically interacts with E2TA through the transactivation domain.

EXAMPLE 4 HPV16E2 Interacts with HBrd4 After confirming the interaction of Brd4 protein with E2TA from BPV genome, we further addressed if Brd4 interacts similarly with human papillomavirus E2 such as HPV16 E2. The results of this experiment are shown in Figure 4. C33A cells were transfected with FLAG- 16E2 (F16) or an empty vector (-). CE and NE prepared from these cells were subjected to FLAG IP to pull down 16E2 and associated proteins. Panel A showed that Brd4 antibody specifically detected a set of bands corresponding to the Brd4 and its proteolytic-cleavage products in the NE obtained from cells transfected with FLAG-16E2 (lane 4). No Brd4 bands were detected in the CE IP (lane 1 and 2), nor was Brd4 immunoprecipitated in the NE of the cells transfected with only an empty vector (lane 3). FLAG and 16E2 antibodies were used in western blot to show the IP of 16E2 protein in cells transfected with FLAG-16E2 (panel B and C, respectively).

EXAMPLE 5 Cloning of Human Brd4 Human Brd4 cDNA was previously not available. The three EST clones we obtained from ATCC IMAGE bank only cover part of the predicted hBrd4 cDNA. The region of nt2000- 2500 contains long repeats of polyA sequence and is therefore missing in all of the cDNA clones. This fragment was obtained from screening a human cDNA library. The full-length human Brd4 cDNA was subsequently constructed by ligating cDNA fragments together. A schematic of the cloning of human Brd4 is shown in Figure 5. The nucleotide sequence for human Brd4 (SEQ ID NO: 1) is shown in Figure 6 and the nucleotide sequence for mouse Brd4 is shown in Figure 24 (SEQ ID NO: 3). An alignment between the amino acid sequences of human Brd4 (SEQ ID NO: 2) and mouse Brd4 (SEQ ID NO: 4) is shown in Figure 7. The alignment was carried out using ClustalV and indicated a percent identity between the human and mouse Brd4 amino acid sequences of 94.6%.

EXAMPLE 6 Mapping of the E2 Binding Domain on Human Brd4 To map the E2 binding domain on human Brd4 protein, the hBrd4 cDNA fragments covering different functional domains of the protein were subcloned into an expression vector driven by T7 promoter. Each fragment was then translated and labeled by S using an in vitro transcription and translation (TNT) kit from Promega. Equal amount of each HBrd4 TNT product was then incubated separately with either GST-E2TA or GST-E2TR that has been immobilized on glutathione resin at 4°C for 4 hours. After wash 4 times with binding buffer, the glutathione beads were eluted with SDS sample buffer. The results of this experiment are shown in Figure 8. Equal amount of eluate from GST-E2TA (lane A) and GST-E2TR (lane R) were resolved on SDS-PAGE gel together with 30%_> of the input sample (lane I). The radioactive bands of the TNT products were detected by autoradiography (panel B). Since full-length Brd4 only binds to E2TA but not E2TR, the later GST fusion protein served as a negative control for this binding experiment. The fragments that showed significantly increased signal in lane A than lane I and had no higher than background signal in lane R were identified as E2-binding fragments. As listed in panel A, all protein fragments containing the C-terminal residues 1047- 1362 were able to specifically bind to E2TA protein, indicating that the E2 binding domain of hBrd4 resides in the 1047-1362 region. We further subcloned the region encoding the C-terminal 300 amino acids of hBrd4 and used the TNT method to express them as approximately 100 aa fragments. By repeating the binding of GST-E2TA or E2-TR as described above, the E2 binding region was mapped to the last 138 amino acids of the hBrd4 protein.

EXAMPLE 7 Disruption of the hBrd4/E2 Interaction We tested if expressing the C-terminal 1047-1362 region of hBrd4 in cells would disrupt the binding of Brd4 and E2. The results of this experiment are shown in Figure 9. C33A cells stably expressing the FLAG-HA-E2TA protein were transiently transfected with either a pCDNA4c plasmid expressing His-Xpress-SV40NLS-HBrd41047-1362 product or an empty vector. 48 hours after transfection, cytoplasmic extract (CE) and nuclear extract (NE) were prepared from these cells and immunoprecipitated with anti-FLAG antibody. As shown in panel A, Brd4 antibody can detect the co-IP of the hBrd4 protein with E2 only in the NE of the cells transfected with an empty vector (lane 4). In lane 5, where the cells were transfected with the

5 His-Xpress-SV40NLS-HBrd41047-1362 plasmid, the Brd4 antibody could no longer detect the bands corresponding to the full-length endogenous Brd4 protein and its proteolytic- cleavage products as shown in lane 4. Since the Brd4 antibody was raised against the last 14 aa of the Brd4 protein, it recognized the over-expressed His-Xpress-SV40NLS-HBrd41047-1362 product instead. This result demonstrated that the C-terminal 1047-1362 product of hBrd4, when

L0 expressed in human cells, could indeed disrupt the binding between E2 and Brd4 through competition effect, thus proving that this fragment can be used efficiently as an inhibitor for the E2-Brd4 binding in vivo. (The same bands of His-Xpress-SV40NLS-HBrd41047-1362 product i were also detected by western blot using an anti-Xpress antibody in both the NE and CE sample, suggesting that the His-Xpress-SV40NLS-HBrd41047-1362 product may leak into CE during

L5 cell lysate fractionation).

EXAMPLE 8 Co-Localization ofBrd4 andE2 on Mitotic Chromosomes C33A-E2TA stable cells were double-stained with Brd4 antibody and E2TA antibody. The cells were also counter stained with DAPI to label nucleus and mitotic chromosome. The 20 results of this experiment is shown in Figure 10. In addition to the overall nucleus staining, the Brd4 antibody detected Brd4 protein present in highly condensed dots in the nucleus. E2 antibody also revealed both the nuclear staining of E2 and the high-density E2 staining dots, which have similar pattern as the Brd4 dots. Strikingly, both Brd4 and E2 staining dots were most distinctively observed on all the mitotic chromosomes. This result provided the first indication that E2TA and Brd4 protein co-localize in the dots on mitotic chromosomes.

EXAMPLE 9 HBrd4 C-terminal Fragment Blocks GST-E2TA Binding to Endogenous hBrd4 To test if hBrd4 c-terminus could prevent the recombinant GST-E2TA protein from binding to endogenous hBrd4 protein, C33A cells were treated with Streptolysin-O to allow entering of large molecules into the cells. The E. coli expressed GST-E2TA was pre-incubated for 15 min at room temperature with or without the recombinant His-HBrd41134-1362 before applying to the cells. After fixation and extraction, the cells were double stained for Brd4 and E2. The results of this experiment are shown in Figure 11. The data showed that, in the absence of His-HBrd41134-1362 (labeled as inhibitor, I), nucleus was stained with both E2 (green) and Brd4 (red) antibody. Pre-incubation of GST-E2TA with the inhibitor completely eliminated the E2 nuclear staining without affecting Brd4 staining. The result demonstrated that His- HBrd41134-1362 can bind to E2 and prevent the nuclear localization of E2TA.

EXAMPLE 10 HBrd4 C-terminal Fragment Blocks E2TA Binding to Mitotic Chromosomes C33A-E2TA stable cells were infected with retrovirus to generate cell line stably expressing His-Xpress-SV40NLS-HBrd41047-1362 or carrying an empty vector as a control. These cells were separately double-stained with Brd4 antibody (red) and E2TA antibody (green). Cells were also counter-stained with DAPI to label the nucleus and mitotic chromosome. The results of this Experiment are shown in Figure 12. In the E2 cells carrying an empty vector, the double-staining showed co-localization of E2 and Brd4 as high-density dots on mitotic chromosomes. Remarkably, in cells expressing His-Xpress-SV40NLS-HBrd41047-1362, the E2 staining was completely excluded from mitotic chromosomes, while the Brd4 staining on mitotic chromosomes was not affected. This result demonstrated that, by inhibiting the E2 and Brd4 interaction, HBrd41047-1362 prevented the tethering of E2 to host mitotic chromosomes.

EXAMPLE 11 Chromatin Immunoprecipitation (CMP) Analysis of the Interaction Between hBrd4 and the BPV-1 Genome C127 cells or C127 cells carrying BPV-1 extrachromosomal genomes ,(also called H2 t cells) were used in this experiment. In addition, to block the Brd4 and E2 interaction, H2 cells were infected with retrovirus to generate cell line stably expressing His-Xpress-SV40NLS- HBrd41047-1362 (H2I cells) or carrying an empty vector as a control (H2V cells). Cells were crosslinked in 1% para-formaldehyde for 10 min at room temperature. The fixed cells were washed in PBS, and chromatin was sonicated to an average DNA length of 600 bp. Chromatin

DNA from 2e7 cells was incubated at 4°C for 4 hr with 5 μg of Brd4 antibody or a control nonimmune normal rabbit IgG or without antibody. For "mock" chromatin IP, IP buffer were used instead of chromatin. Antibody complexes were recovered on Staphylococcus aureus protein A-positive cells, extensively washed with buffers and then eluted from the beads.

Chromatin was de-crosslinked, and DNA was extracted with phenol/chloroform and ethanol precipitated. PCR using a pair of primers specifically amplifying a region of BPV-1 genome was performed to detect the BPV-1 DNA in the CHIP sample. The PCR products were separated by elecfrophoresis in 1.2% agarose gels, detected by ethidium bromide staining, and digitally photographed. The results of this experiment are shown in Figure 13. As shown, in contrast to the background signal shown in "no Ab" or "normal rabbit IgG" IP, the Brd4 antibody was able to specifically pull down BPV-1 genome in H2 cells as well as H2V cells (not in C127 cells because these cells don't have BPV-1 episomes). In cells stably expressing the inhibitor, HBrd41047-1362 (see H2I cells), the amount of IPed BPV-1 as detected by the PCR reduced to background level. This data shows that Brd4 can bind to BPV-1 genome through its interaction with E2. By blocking the E2-Brd4 interaction (with the expressed inhibitor), we can disrupt the tethering of BPV-1 genome by Brd4.

EXAMPLE 12 HBrd41047-1362 Inhibits the Transformation ofC127 Cells by BPV-1 Mouse C127 cells were infected with retro virus to generate cell line stably expressing His-Xpress-SV40NLS-HBrd41047-1362 (C 127+1) or carrying an empty vector as a control (C127+V). C127 and the stable cells were transfected with BPV-1 genome. After 14 days, cell foci were fixed and stained with methylene blue. The results of this experiment are shown in Figure 14. As shown in the figure, BPV-1 induced cellular fransformation was demonstrated by the blue foci formed in the dish. In the presence of stable expression of HBrd41047-1362 (see C127+I cells), the cell foci number was dramatically decreased, suggesting that this molecule can inhibited the transformation potency of the BPV-1 virus genome. The results from three independent fransfections into each cell line are summarized below in Table 1.

Table 1. Summary of Colony Formation Assay.

EXAMPLE 13 Colocalization of E2 With Brd4 on Mitotic Chromosomes Involves the N- terminal Transactivation Domain ofE2 C33A, C33A/E2TA or C33A E2TR stable cells were double-stained with an anti-Brd4 antibody and an anti-BPV-1 E2 antibody. The anti-Brd4 antibody is directed to the N-terminus of the protein. Cells were also counter-stained with DAPI to label the nucleus and mitotic chromosomes. In cells stably expressing E2TA, E2 and Brd4 colocalized in densely staining dots on mitotic chromosomes (Figure 15, middle panels). Remarkably, E2TR (which lacks the N-terminal transactivation domain required for interaction with Brd4, see diagram on the right side of Figure 15) was completely excluded from mitotic chromosomes in metaphase cells while Brd4 remained associated with the mitotic chromosomes (Figure 15, bottom panel). The Brd4 mitotic chromosome localization is similar in cells whether or not there is expression of E2 or E2TR. These results indicate that the colocalization of E2TA with Brd4 in punctate dots on mitotic chromosomes requires the E2 transactivation domain and confirms our biochemical findings that human Brd4 protein specifically interacts with E2TA and not with E2TR. EXAMPLE 14 Stable Expression of the Brd4 C-terminal Domain Abrogates Association of the BPV-1 Genome with Host Mitotic Chromosomes To address the affects of Brd4 C-terminal domain (CTD) on the association of BPV-1 genome with host mitotic chromosome, we used the C127C1H2 cells, which are BPVl fransformed mouse C127 cells that carry BPVl DNA exclusively as episomes. These cells were transduced with retroviruses expressing the dominant negative inhibitor His-Xpress-SV40NLS- hBrd4-CTD or vector alone to generate stable cell lines H2-CTD or H2-V (Figure 16). Stable expression of the Brd4-CTD was verified in the H2 cells by immunofluorescent staining using anti-Xpress antibody and we were able to demonstrate CTD expression in 90-95% of the H2- CTD cells. H2 cells stably expressing Brd4-CTD (H2-CTD) or transduced with an empty retrovirus vector (H2-V) cultured in chamber slides were arrested at metaphase by a 2-hr incubation with Colcemid. Cells were lysed with hypotonic solution (0.56% KC1) and fixed to glass slide using Carnoy's fixative (75% methanol and 25% acetic acid) before hybridization with a BPV-1 probe in Fluorescence in Situ Hybridization (FISH) analysis. The BPV-1 probe was labeled in red. Cells were also counter-stained with DAPI to label the nucleus and mitotic chromosomes (in blue). The FISH result showed that the BPV-1 episomes that were readily detected associated with mitotic chromosomes in the H2-V cells, were undetectable in the H2-CTD cells (Figure 17). The data demonstrated that CTD expressed in the H2 cells completely abolished the association of BPV-1 episomes with mitotic chromosomes. The images shown in Figure 17 are representative of the experiment. For the H2-V cells, in 15 of 15 mitotic spreads, the metaphase chromosomes were positive for BPV-1 DNA by FISH. In contrast, for the H2-CTD cells, all of 15 sets of metaphase chromosomes analyzed were negative for BPV-1 DNA. This result demonstrated that, by blocking the E2/Brd4 interaction using CTD, we could specifically disrupt the association of BPV-1 genome to host mitotic chromosomes in cells stably maintaining viral episomes, confirming that the virus episome-chromosome interaction is mediated by E2 and Brd4.

EXAMPLE 15 Real-time PCR Quantitative Analysis of BPV-1 Episomes in H2 Stable Cells H2 cells were used to investigate whether stable expression of Brd4-CTD could lead to curing of infected cells, e.g., the elimination of viral episomes and morphologic reversion of fransformed cells (Figure 18). H2 cells are mouse C127 cells fransformed by BPV-1 that carry BPV-1 exclusively as episomes. Both vector control cell line H2-V and the Brd4-CTD expressing cell line H2-CTD were grown for the indicated number of passages (e.g., passage 1 = PI) and split at a ratio of either 1:100 or 1:10 in different experiments. Total cellular DNA was extracted from the cultures at each passage and assayed for the quantity of BPV-1 DNA by real time PCR. We also analyzed the cells during the passage for their moφhology and their ability to form colony. To look at the dynamics of viral DNA loss in cell expressing the CTD, we carried out a time course experiment examining the levels of BPV-1 DNA by real-time PCR in CTD expressing H2 cells compared to vector control H2 cells. After retrovirus infection, H2 cells stably expressing Brd4-CTD. (H2-CTD) or transduced with an empty retrovirus vector (H2-V) were cultured for the indicated number of passages and split at a ratio of 1:100. Total cellular DNA was extracted from the cultures at each passage and assayed for the quantity of BPV-1 DNA using a LightCycler (Roche). The concentration of viral DNA in each sample was calculated using the LightCycler Software version 3.5 based on a standard curve generated using known amounts of BPV-1 plasmid DNA. 250 pg of total cellular DNA from passage #1 H2-V cells contains 0.21 pg of BPV-1 and the same amount of total cellular DNA from passage #1 H2- CTD cells contains 0.24 pg of episome. In Figure 19, the BPV-1 DNA content of each culture is 5 presented as a percentage of the BPV-1 DNA from passage 1 of the same cell line. Our result indicate that during the first 2 passages, H2-CTD cells showed similar amounts of BPV-1 DNA as the vector control H2-V cells. Furthermore, by passage 3, the loss of viral DNA could be observed, and with continued passage, the H2-CTD cells, but not the H2-V cells, show progressive loss of BPV-1 DNA. By passage 5, there is a 78% loss of the BPV-1 DNA from the

L0 CTD expressing cells. Figure 20 shows the moφhology of H2-V cells and H2-CTD cells after 12 passages split at 1 : 10 dilution. The H2-V cells (top panel) still maintained the transformed moφhology (narrow and long shape cells with shaφ edge). These transformed cells have lost the contact inhibition and, therefore, can grow to high saturation density. In contrast, the majority of the H2-

L5 CTD cells (bottom panel) were reverted to the flat cellular moφhology typical of uninfected C127 cells. These cells can only grow as monolayer. The high frequency of revertance in the H2-CTD cells after cell passage indicated a loss of resident viral genomes in the cells, confirming the real-time PCR result.

50 EXAMPLE 16 Morphology analysis of CTD expressing H2 cells To calculate the frequency of revertance in the stable cells, the H2-V and H2-CTD cells were cultured for 9 passages at 1: 10 dilution and cloned into 96 well plates. Among the 30 single clones isolated for the H2-V cell line, 4 showed the revertant moφhology. However, 12 out of the 18 single clones isolated from the H2-CTD culture showed the revertant moφhology (Figure 21). The moφhology of the fransformed clone and the revertant clone are shown in Figure 22. The transforming clones have long and narrow shape cells that can grow to high cell density to form colonies (or foci) as shown in the top panel of Figure 22. The revertants have round shape flat-looking cells that can only grow as monolayer due to the contact inhibition (Figure 22, bottom panel). Each type of clones was subcultured. The moφhological characteristics of a representative revertant cell line in comparison to that of a transformed cell line are shown in Figure 23. The results demonstrate that the expression of Brd4 CTD leads to an increased frequency (from 13 > for H2-V cell line to 66% for H2-CTD cell line) of revertance, suggesting a loss of BPV-1 viral genomes in the H2-CTD cells.

EQUIVALENTS The present disclosure provides among other things methods and compositions for the prevention and/or treatment of viral infections. While specific embodiments have been discussed, the above specification is illustrative and not restrictive. Many variations of the methods, compositions, and process disclosed herein will become apparent to those skilled in the art upon review of this specification. The appended claims are not intended to claim all such embodiments and variations, and the full scope of the invention should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations. Unless otherwise indicated, all numbers expressing quantities of ingredients, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term "about." Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained.

INCORPORATION BY REFERENCE All publications and patents mentioned herein, including those items listed below, are hereby incoφorated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incoφorated by reference. In case of conflict, the present application, including any definitions herein, will control. Also incoφorated by reference in their entirety are any polynucleotide and polypeptide sequences which reference an accession number correlating to an enfry in a public database, such as those maintained by The Institute for Genomic Research (TIGR) (www.tigr.org) and/or the National Center for Biotechnology Information (NCBI) (www.ncbi.nlm.nih.gov). Also incoφorated by reference are the following: SC Verma & ES Robertson, FEMS Microbiol Lett 222: 155-63 (2003); N Bastien & AA McBride, Virology 270: 124-134 (2000); MH Skiadopoulos & AA McBride, J. Virology 72: 2079-2088 (1998); C French et al., Am. J. Pathology 159: 1987-1992 (2001); D Houzelstein et al., Mol. Cell. Biol. 22: 3794-3802 (2002); T Maruyama et al., Mol. Cell. Biol. 22: 6509-6520 (2002); A Dey et al, Mol. Cell. Biol. 20:^' 6537-6549 (2000); Sakai et al., J. Virology 70: 1602-1611 (1996); J. Choe, et al., J. Virology 63: 1743-1755 (1989); D. Francis, et al., J. Virology, 74: 2679-2686 (2000); N. Frank et al., J. Virology 69: 6323-6334 (1995); S. Vande Pol et al., J. Virology 66: 2346-2358 (1992); T. Zemlo et al, J. Virology 68: 6787-6793 (1994); Accession No. gi60965 (X02346); Accession No. gi3041739 (P03122); U.S. Patent Nos. 6,573,364, 6,420,118, and 6,399,075; and U.S. Patent Application Publication Nos. 2003/0027768 Al, 2003/0103997 Al, and 2002/0099022 Al.

Claims

WE CLAIM:

1. An isolated polypeptide, comprising: (a) an amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95% identity with the amino acid sequence set forth in SEQ ID NO: 2; or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein.

2. The isolated polypeptide of claim 1, wherein the polypeptide is capable of interacting with an E2 protein or a functional equivalent of an E2 protein.

3. An isolated polypeptide comprising at least five consecutive amino acid residues of SEQ ID NO: 2 wherein said polypeptide is capable of disrupting an interaction between a Brd4 protein and an E2 protein or a functional equivalent of an E2 protein. ₍

4. The isolated polypeptide of claim 3, wherein said polypeptide comprises at least ten consecutive amino acid residues.

5. The isolated polypeptide of claim 3, wherein said polypeptide comprises amino acid residues 1047-1362 of SEQ ID NO: 2.

6. The isolated polypeptide of claim 3, wherein said polypeptide comprises amino acid residues 1224-1362 of SEQ ID NO: 2.

7. A peptidomimetic based on the polypeptide of claim 3.

\

8. The isolated polypeptide of claim 1 which is bound to a solid support.

9. An array comprising a substrate having a plurality of addresses, wherein at least one of the addresses has disposed thereon a polypeptide comprising SEQ ID NO: 2, or a fragment thereof.

10. An isolated monoclonal antibody that binds to a polypeptide comprising SEQ ID NO: 2 and does not bind to a polypeptide comprising SEQ ID NO: 4.

11. The isolated monoclonal antibody of claim 10, wherein the antibody binds specifically to a polypeptide comprising SEQ ID NO: 2.

12. The isolated monoclonal antibody of claim 10, wherein the antibody is a single chain antibody.

13. The isolated monoclonal antibody of claim 10, wherein the antibody is a humanized antibody.

14. The isolated monoclonal antibody of claim 10, wherein the antibody does not substantially cross-react with a protein which is less than 95% identical to SEQ ID NO: 2.

15. A composition comprising a purified antibody that binds specifically to a polypeptide comprising SEQ ID NO: 2 and a pharmaceutically acceptable carrier.

16. An isolated nucleic acid comprising (a) the nucleotide sequence of SEQ ID NO: 1, (b) a nucleotide sequence at least 90% identical to SEQ ID NO: 1, (c) a nucleotide sequence that hybridizes under stringent conditions to SEQ ID NO: 1, or (d) the complement of the nucleotide sequence of (a), (b) or (c).

17. An isolated nucleic acid comprising a nucleotide sequence encoding a fragment of SEQ ID NO: 2 wherein said fragment comprises at least 5 consecutive amino acid residues and wherein said fragment is capable of disrupting an interaction between a Brd4 protein and an E2 protein or a functional equivalent of an E2 protein.

18. The isolated nucleic acid of claim 16 or 17, further comprising a transcriptional regulatory sequence operably linked to said nucleotide sequence so as to render said nucleic acid suitable for use in an expression vector.

19. A vector comprising a nucleic acid according to claim 18.

20. An array comprising a substrate having a plurality of addresses, wherein at least one of the addresses has disposed thereon a capture probe that can specifically bind to a nucleic acid of claim 16.

21. A computer readable medium comprising SEQ ID NO: 1.

22. A computer readable medium on which is stored a database comprising SEQ ID NO: 1.

23. A host cell comprising a recombinant nucleic acid encoding a polypeptide comprising (a) an amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95% identity with the amino acid sequence set forth in SEQ ID NO: 2; or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein.

24. An isolated complex comprising (a) Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide.

25. The complex of claim 24, comprising an E2 protein from a papilloma virus or a heφes virus.

26. The complex of claim 24, comprising: (a) an amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95% identity with the amino acid sequence set forth in SEQ ID NO: 2; or (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein.

27. The complex of claim 24, comprising a polypeptide having SEQ ID NO: 2 and an E2 protein from a papilloma virus or a heφes virus.

28. The complex of claim 24, comprising an E2 protein from a papilloma virus or a heφes virus.

29. The complex of claim 24, comprising a polypeptide having SEQ ID NO: 2 and a latency- associated nuclear antigen (LANA) protein from a Kaposi sarcoma-associated heφesvirus (KSHV).

30. The complex of claim 25, wherein the papillomavirus is a human papillomavirus (HPV).

31. The complex of claim 25, wherein the papillomavirus is a non-human animal papillomavirus.

32. The complex of claim 31, wherein the papillomavirus is a bovine papillomavirus, a canine papillomavirus, monkey papillomavirus, rabbit papillomavirus, equine papillomavirus, or feline papillomavirus.

33. The complex of claim 24, comprising at least five consecutive amino acid residues of SEQ ID NO: 2.

34. The complex of claim 24, wherein at least one of said polypeptides or fragments is recombinantly produced.

35. The complex of claim 34, wherein all of the polypeptides or fragments in said complex are recombinantly produced.

36. The complex of claim 24, wherein at least one polypeptide or fragment is a fusion protein.

37. The complex of claim 36, wherein the at least one polypeptide or fragment is a fusion with at least one or more of the following tags: His, myc, HA, GST, protein A, protein G, calmodulin-binding peptide, thiredoxin, maltose-binding protein, poly arginine, poly His-Asp, FLAG, or a portion of an immunoglobulin protein.

38. The complex of claim 36, wherein at least one polypeptide or fragment is a fusion with at least one or more of the following: green fluorescent protein (GFP), enhanced green fluorescent protein (EGFP), Renilla Reniformis green fluorescent protein, GFPmut2, GFPuv4, enhanced yellow fluorescent protein (EYFP), enhanced cyan fluorescent protein (ECFP), enhanced blue fluorescent protein (EBFP), citrine, or red fluorescent protein from discosoma (dsRED).

39. An isolated antibody that has a higher binding affinity for a complex of claim 24 than for the individual polypeptides of said complex.

40. An isolated antibody that disrupts a complex of claim 24.

41. The isolated antibody of claim 40, wherein the antibody binds a polypeptide comprising amino acid residues 1047-1362 of SEQ ID NO: 2.

42. A fusion polypeptide, comprising an amino acid sequence having: (a) the amino acid sequence set forth in SEQ ID NO: 2; (b) an amino acid sequence having at least 95% identity with the amino acid sequence set forth in SEQ ID NO: 2; (c) an amino acid sequence encoded by a polynucleotide that hybridizes under stringent conditions to the complementary strand of a polynucleotide having SEQ ID NO: 1 and wherein said polypeptide has at least one biological activity of a Brd4 protein; or (d) an amino acid sequence having at least five consecutive amino acid residues of SEQ ID NO: 2 wherein said polypeptide is capable of interacting with an E2 protein or a functional equivalent of an E2 protein; fused to a polypeptide selected from the group consisting of: (e) an E2 polypeptide; (f) a functional equivalent of an E2 polypeptide; or (g) a fragment of (e) or (f) that is capable of interacting with a polypeptide of (a), (b), (c), or (d).

43. A method for identifying a compound that disrupts a Brd4 protein complex, comprising: (i) providing a reaction mixture comprising (a) Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (ii) contacting the reaction mixture with a test agent; and (iii) determining the effect of the test agent on the formation or stability of a complex comprising (a), (b), (c), or (d), wherein a decrease in the formation or stability of said complex is indicative of a compound that disrupts a Brd4 protein complex.

44. The method of claim 43 , wherein the reaction mixture is a cell or cell population.

45. The method of claim 44, wherein the cell or cell population is infected with a virus.

46. The method of claim 45, wherein the cell or cell population is expanded after being contacted with the test agent and wherein a decrease in the number of progeny cells infected with the virus is indicative of a compound that disrupts a Brd4 protein complex.

47. The method of claim 46, wherein the number of progeny cells infected with the virus is determined using a colony formation assay.

48. A method for identifying a compound that inhibits viral infectivity or proliferation comprising: (i) providing a reaction mixture comprising (a) Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; (b) Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (c) a fragment of Brd4 and an E2 polypeptide or a functional equivalent of an E2 polypeptide; or (d) a fragment of Brd4 and a fragment of an E2 polypeptide or a functional equivalent of an E2 polypeptide; (ii) contacting the reaction mixture with a test agent; and (iii) determining the effect of the test agent on the formation or stability of a complex comprising (a), (b), (c), or (d), wherein a decrease in the formation or stability of said complex is indicative of a compound that inhibits viral infectivity or proliferation.

49. A method for identifying a compound that modulates a Brd4 protein complex, comprising: (i) contacting a Brd4 protein, or a fragment thereof, and an E2 polypeptide, or a functional equivalent of an E2 polypeptide, or a fragment thereof, with a test agent under conditions in which the Brd4 protein, or a fragment thereof, and the E2 polypeptide, or a functional equivalent of an E2 polypeptide, or a fragment thereof, interact in the absence of the test agent to form a complex; and (ii) determining the effect of the test agent on the formation or stability of the complex, wherein a decrease or an increase in the formation or stability of said complex in the presence of the test compound relative to the absence of the test compound indicates that the test compound modulates the Brd4 protein complex.

50. A method for treating a subject suffering from a viral related disease or disorder, comprising administering to an animal having said condition a therapeutically effective amount of a polypeptide comprising at least five consecutive amino acids from a region of SEQ ID NO: 2 having amino acids 1224-1362, wherein said polypeptide is capable of binding to an E2 polypeptide or a functional equivalent of an E2 polypeptide.

51. The method of claim 50, wherein the subject is suffering from a disease or disorder related to an infection of a papillomavirus or a heφes virus.

52. The method of claim 50, wherein the subject is a human.

53. The method of claim 50, wherein the subject is a livestock animal.

54. The method of claim 53, wherein the animal is a cow, pig, goat or sheep.

55. The method of claim 50, wherein the subject is a domestic animal.

56. The method of claim 55, wherein the animal is dog or cat.

57. A method for inhibiting Brd4 dependent growth or infectivity of a virus, comprising contacting a virus infected cell with a polypeptide comprising at least five consecutive amino acids from a region of SEQ ID NO: 2 having amino acids 1224-1362, wherein said polypeptide is capable of binding to an E2 polypeptide or a functional equivalent of an E2 polypeptide.