Exploring the binding dynamics of covalent inhibitors within active site of PLpro in SARS-CoV-2
Graphical Abstract
Display Omitted
References
[1]
A. Artese, V. Svicher, G. Costa, R. Salpini, V.C. Di Maio, M. Alkhatib, F.A. Ambrosio, M.M. Santoro, Y.G. Assaraf, S. Alcaro, Current status of antivirals and druggable targets of SARS CoV-2 and other human pathogenic coronaviruses, Drug Resist. Updates 53 (2020).
[2]
I.M. Artika, A.K. Dewantari, A. Wiyatno, Molecular biology of coronaviruses: current knowledge, Heliyon 6 (2020).
[3]
K.M. Backus, B.E. Correia, K.M. Lum, S. Forli, B.D. Horning, G.E. González-Páez, S. Chatterjee, B.R. Lanning, J.R. Teijaro, A.J. Olson, Proteome-wide covalent ligand discovery in native biological systems, Nature 534 (2016) 570–574.
[4]
Y.M. Báez-Santos, S.E.S. John, A.D. Mesecar, The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds, Antivir. Res. 115 (2015) 21–38.
[5]
N. Barretto, D. Jukneliene, K. Ratia, Z. Chen, A.D. Mesecar, S.C. Baker, The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity, J. Virol. 79 (2005) 15189–15198.
[6]
D. Benvenuto, M. Giovanetti, A. Ciccozzi, S. Spoto, S. Angeletti, M. Ciccozzi, The 2019-new coronavirus epidemic: evidence for virus evolution, J. Med. Virol. 92 (2020) 455–459.
[7]
J. Cui, F. Li, Z.-L. Shi, Origin and evolution of pathogenic coronaviruses, Nat. Rev. Microbiol. 17 (2019) 181–192.
[8]
S. De Cesco, J. Kurian, C. Dufresne, A.K. Mittermaier, N. Moitessier, Covalent inhibitors design and discovery, Eur. J. Med. Chem. 138 (2017) 96–114.
[9]
C.P. Delgado, J.B.T. Rocha, L. Orian, M. Bortoli, P.A. Nogara, In silico studies of Mpro and PLpro from SARS-CoV-2 and a new class of cephalosporin drugs containing 1, 2, 4-thiadiazole, Struct. Chem. 33 (2022) 2205–2220.
[10]
S.G. Devaraj, N. Wang, Z. Chen, Z. Chen, M. Tseng, N. Barretto, R. Lin, C.J. Peters, C.-T.K. Tseng, S.C. Baker, Regulation of IRF-3-dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus, J. Biol. Chem. 282 (2007) 32208–32221.
[11]
A.W. Edridge, J. Kaczorowska, A.C. Hoste, M. Bakker, M. Klein, M.F. Jebbink, A. Matser, C.M. Kinsella, P. Rueda, M. Prins, Human coronavirus reinfection dynamics: lessons for SARS-CoV-2, MedRxiv 2020 (2020) 05. 11.20086439.
[12]
Z. Fu, B. Huang, J. Tang, S. Liu, M. Liu, Y. Ye, Z. Liu, Y. Xiong, W. Zhu, D. Cao, The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery, Nat. Commun. 12 (2021) 488.
[13]
X. Gao, B. Qin, P. Chen, K. Zhu, P. Hou, J.A. Wojdyla, M. Wang, S. Cui, Crystal structure of SARS-CoV-2 papain-like protease, Acta Pharm. Sin. B 11 (2021) 237–245.
[14]
S.K. Gayatri, V. Chhabra, H. Kumar, M.E. Sobhia, Identification of prospective covalent inhibitors for SARS-CoV-2 main protease using structure-based approach, J. Biomol. Struct. Dyn. (2022) 1–18.
[15]
S.K. Gayatri, V. Chhabra, H. Kumar, M.E. Sobhia, Identification of prospective covalent inhibitors for SARS-CoV-2 main protease using structure-based approach, J. Biomol. Struct. Dyn. 41 (2023) 7913–7930.
[16]
Y.-S. Han, G.-G. Chang, C.-G. Juo, H.-J. Lee, S.-H. Yeh, J.T.-A. Hsu, X. Chen, Papain-like protease 2 (PLP2) from severe acute respiratory syndrome coronavirus (SARS-CoV): expression, purification, characterization, and inhibition, Biochemistry 44 (2005) 10349–10359.
[17]
B.H. Harcourt, D. Jukneliene, A. Kanjanahaluethai, J. Bechill, K.M. Severson, C.M. Smith, P.A. Rota, S.C. Baker, Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity, J. Virol. 78 (2004) 13600–13612.
[18]
S.A. Hollingsworth, R.O. Dror, Molecular dynamics simulation for all, Neuron 99 (2018) 1129–1143.
[19]
D. Jade, S. Ayyamperumal, V. Tallapaneni, C.M.J. Nanjan, S. Barge, S. Mohan, M.J. Nanjan, Virtual high throughput screening: Potential inhibitors for SARS-CoV-2 PLPRO and 3CLPRO proteases, Eur. J. Pharmacol. 901 (2021).
[20]
G. Kalibaeva, M. Ferrario, G. Ciccotti, Constant pressure-constant temperature molecular dynamics: a correct constrained NPT ensemble using the molecular virial, Mol. Phys. 101 (2003) 765–778.
[21]
S. Khare, C. Gurry, L. Freitas, M.B. Schultz, G. Bach, A. Diallo, N. Akite, J. Ho, R.T. Lee, W. Yeo, GISAID’s role in pandemic response, China CDC Wkly. 3 (2021) 1049.
[22]
H. Kim, D. Hauner, J.A. Laureanti, K. Agustin, S. Raugei, N. Kumar, Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors, Sci. Rep. 12 (2022).
[23]
A. Koirala, Y.J. Joo, A. Khatami, C. Chiu, P.N. Britton, Vaccines for COVID-19: the current state of play, Paediatr. Respir. Rev. 35 (2020) 43–49.
[24]
S.S. Krishna, I. Majumdar, N.V. Grishin, Survey and summary: structural classification of zinc fingers, Nucleic Acids Res. 31 (2003) 532.
[25]
H.A. Lindner, N. Fotouhi-Ardakani, V. Lytvyn, P. Lachance, T. Sulea, R. Ménard, The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme, J. Virol. 79 (2005) 15199–15208.
[26]
R. Lonsdale, R.A. Ward, Structure-based design of targeted covalent inhibitors, Chem. Soc. Rev. 47 (2018) 3816–3830.
[27]
C. Ma, M.D. Sacco, Z. Xia, G. Lambrinidis, J.A. Townsend, Y. Hu, X. Meng, T. Szeto, M. Ba, X. Zhang, Discovery of SARS-CoV-2 papain-like protease inhibitors through a combination of high-throughput screening and a FlipGFP-based reporter assay, ACS Cent. Sci. 7 (2021) 1245–1260.
[28]
F. Madeira, M. Pearce, A.R. Tivey, P. Basutkar, J. Lee, O. Edbali, N. Madhusoodanan, A. Kolesnikov, R. Lopez, Search and sequence analysis tools services from EMBL-EBI in 2022, Nucleic Acids Res. 50 (2022) W276–W279.
[29]
R. Mah, J.R. Thomas, C.M. Shafer, Drug discovery considerations in the development of covalent inhibitors, Bioorg. Med. Chem. Lett. 24 (2014) 33–39.
[30]
Y.A. Malik, Properties of coronavirus and SARS-CoV-2, Malays. J. Pathol. 42 (2020) 3–11.
[31]
J. Osipiuk, S.-A. Azizi, S. Dvorkin, M. Endres, R. Jedrzejczak, K.A. Jones, S. Kang, R.S. Kathayat, Y. Kim, V.G. Lisnyak, Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors, Nat. Commun. 12 (2021) 743.
[32]
A.K. Padhi, S.L. Rath, T. Tripathi, Accelerating COVID-19 research using molecular dynamics simulation, J. Phys. Chem. B 125 (2021) 9078–9091.
[33]
A. Palayew, O. Norgaard, K. Safreed-Harmon, T.H. Andersen, L.N. Rasmussen, J.V. Lazarus, Pandemic publishing poses a new COVID-19 challenge, Nat. Hum. Behav. 4 (2020) 666–669.
[34]
S. Rauch, E. Jasny, K.E. Schmidt, B. Petsch, New vaccine technologies to combat outbreak situations, Front. Immunol. 9 (2018) 1963.
[35]
G.S. Rieder, P.A. Nogara, F.B. Omage, T. Duarte, C.L. Dalla Corte, J.B.T. da Rocha, Computational analysis of the interactions between Ebselen and derivatives with the active site of the main protease from SARS-CoV-2, Comput. Biol. Chem. 107 (2023).
[36]
R.L. Roper, K.E. Rehm, SARS vaccines: where are we?, Expert Rev. Vaccin. 8 (2009) 887–898.
[37]
W. Rut, Z. Lv, M. Zmudzinski, S. Patchett, D. Nayak, S.J. Snipas, F. El Oualid, T.T. Huang, M. Bekes, M. Drag, Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: a framework for anti–COVID-19 drug design, Sci. Adv. 6 (2020) eabd4596.
[38]
B. Sanders, S. Pohkrel, A. Labbe, I. Mathews, C. Cooper, R. Davidson, G. Phillips, K. Weiss, Q. Zhang, H. O’Neill, Research square, Potent Sel. covalent Inhib. papain- Protease SARS-CoV-2 (2021).
[39]
B.C. Sanders, S. Pokhrel, A.D. Labbe, I.I. Mathews, C.J. Cooper, R.B. Davidson, G. Phillips, K.L. Weiss, Q. Zhang, H. O’Neill, Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2, Nat. Commun. 14 (2023) 1733.
[40]
S. Satarker, M. Nampoothiri, Structural proteins in severe acute respiratory syndrome coronavirus-2, Arch. Med. Res. 51 (2020) 482–491.
[41]
D. Schoeman, B.C. Fielding, Coronavirus envelope protein: current knowledge, Virol. J. 16 (2019) 1–22.
[42]
Z. Shen, K. Ratia, L. Cooper, D. Kong, H. Lee, Y. Kwon, Y. Li, S. Alqarni, F. Huang, O. Dubrovskyi, Design of SARS-CoV-2 PLpro inhibitors for COVID-19 antiviral therapy leveraging binding cooperativity, J. Med. Chem. 65 (2021) 2940–2955.
[43]
Z. Shen, K. Ratia, L. Cooper, D. Kong, H. Lee, Y. Kwon, Y. Li, S. Alqarni, F. Huang, O. Dubrovskyi, Potent, novel SARS-CoV-2 PLpro inhibitors block viral replication in monkey and human cell cultures, BioRxiv (2021) 2021.02. 13.431008.
[44]
D. Shin, R. Mukherjee, D. Grewe, D. Bojkova, K. Baek, A. Bhattacharya, L. Schulz, M. Widera, A.R. Mehdipour, G. Tascher, Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity, Nature 587 (2020) 657–662.
[45]
J. Singh, The ascension of targeted covalent inhibitors, J. Med. Chem. 65 (2022) 5886–5901.
[46]
F. Sutanto, M. Konstantinidou, A. Dömling, Covalent inhibitors: a rational approach to drug discovery, RSC Med. Chem. 11 (2020) 876–884.
[47]
H. Tan, Y. Hu, P. Jadhav, B. Tan, J. Wang, Progress and challenges in targeting the SARS-CoV-2 papain-like protease, J. Med. Chem. 65 (2022) 7561–7580.
[48]
B. Tan, X. Zhang, A. Ansari, P. Jadhav, H. Tan, K. Li, A. Chopra, A. Ford, X. Chi, F.X. Ruiz, Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model, Science 383 (2024) 1434–1440.
[49]
Y.-F. Tu, C.-S. Chien, A.A. Yarmishyn, Y.-Y. Lin, Y.-H. Luo, Y.-T. Lin, W.-Y. Lai, D.-M. Yang, S.-J. Chou, Y.-P. Yang, A review of SARS-CoV-2 and the ongoing clinical trials, Int. J. Mol. Sci. 21 (2020) 2657.
[50]
E. Weglarz-Tomczak, J.M. Tomczak, M. Talma, M. Burda-Grabowska, M. Giurg, S. Brul, Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2, Sci. Rep. 11 (2021) 1–10.
[51]
C. Wu, Y. Liu, Y. Yang, P. Zhang, W. Zhong, Y. Wang, Q. Wang, Y. Xu, M. Li, X. Li, Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods, Acta Pharm. Sin. B 10 (2020) 766–788.
[52]
A.A. Yameny, The COVID-19 JN. 1 variant diagnosed in Egypt, J. Med. Life Sci. 5 (2023) 318–321.
Index Terms
- Exploring the binding dynamics of covalent inhibitors within active site of PLpro in SARS-CoV-2
Index terms have been assigned to the content through auto-classification.
Recommendations
Repurposing of FDA-approved drugs as potential inhibitors of the SARS-CoV-2 main protease: Molecular insights into improved therapeutic discovery
AbstractWith numerous infections and fatalities, COVID-19 has wreaked havoc around the globe. The main protease (Mpro), which cleaves the polyprotein to form non-structural proteins, thereby helping in the replication of SARS-CoV-2, appears as an ...
Graphical abstractDisplay Omitted
Highlights- All protease inhibitor, antiviral, and antimalarial FDA-approved drugs were screened against the SARS-CoV-2 main protease.
- 53 drugs exhibited interaction energy with Mpro below −7.0 kcal/mol and their pKi values were predicted.
- ...
Identification of Potential SARS-CoV-2 Main Protease Inhibitors Using Drug Repurposing and Molecular Modeling
Bioinformatics Research and ApplicationsAbstractStructure-based virtual screening of a molecular library of bioactive compounds was carried out to identify potential inhibitors against SARS-CoV-2 main protease (Mpro), an enzyme critically important for mediating viral replication and ...
Drug repurposing against SARS-CoV-2 receptor binding domain using ensemble-based virtual screening and molecular dynamics simulations
AbstractSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused worldwide pandemic and is responsible for millions of worldwide deaths due to -a respiratory disease known as COVID-19. In the search for a cure of COVID-19, drug repurposing ...
Graphical abstractDisplay Omitted
Highlights- RBD of SARS-CoV-2 spike protein shows Conformational plasticity in long MD simulation.
- Top 18 drugs have good docking scores to bind with RBD at the ACE2-RBD interface.
- 16 out of the 18 drugs are obtained from the 3 MD ...
Comments
Please enable JavaScript to view thecomments powered by Disqus.Information & Contributors
Information
Published In
Copyright © 2024.
Publisher
Elsevier Science Publishers B. V.
Netherlands
Publication History
Published: 21 November 2024
Author Tags
Qualifiers
- Research-article
Contributors
Other Metrics
Bibliometrics & Citations
Bibliometrics
Article Metrics
- 0Total Citations
- 0Total Downloads
- Downloads (Last 12 months)0
- Downloads (Last 6 weeks)0
Reflects downloads up to 27 Nov 2024
Other Metrics
Citations
View Options
View options
Login options
Check if you have access through your login credentials or your institution to get full access on this article.
Sign in