Search Results (19)

P21-activated kinase 4 (PAK4) plays a crucial role in the proliferation and metastasis of various cancers. However, developing selective PAK4 inhibitors remains challenging due to the high homology within the PAK family. Therefore, developing highly selective PAK4 inhibitors is critical to overcoming the limitations of existing inhibitors. We analyzed the structural differences in the binding pockets of PAK1 and PAK4 by combining cross-docking and molecular dynamics simulations to identify key binding regions and unique structural features of PAK4. We then performed screening using shape and protein conformation ensembles, followed by a re-evaluation of the docking results with deep-learning-driven GNINA to identify the candidate molecule, STOCK7S-56165. Based on this, we applied a fragment-replacement strategy under electrostatic-surface-matching conditions to obtain Compd 26. This optimization significantly improved electrostatic interactions and reduced binding energy, highlighting its potential for selectivity. Our findings provide a novel approach for developing selective PAK4 inhibitors and lay the theoretical foundation for future anticancer drug design. Full article

This study investigates the transient flow dynamics and pressure interactions within Tesla valve configurations through comprehensive CFD simulations. Tesla valves offer efficient passive fluid control without the need for external power, making them favorable in various applications. Previous observations indicated that Tesla valves effectively reduce the amplitude of pressure transients, prolonging their duration and distributing energy over an extended timeframe. While suggesting a potential role for Tesla valves as pressure dampers during transient events, the specific mechanisms behind this behavior remain unexplored. This research focuses on elucidating the internal dynamics of Tesla valves during transient events, aiming to unravel the processes responsible for the observed attenuation in pressure transients. This study reveals the emergence of “pressure pockets” within Tesla valves, deviating from conventional uniform pressure fronts. These pockets manifest as discrete chambers with varying lengths and volumes, contributing to the non-uniform propagation of pressure throughout the system. This investigation employs advanced CFD simulations as a crucial tool to unravel the governing dynamics of transient flow within Tesla valve configurations. By elucidating underlying fluid dynamics, this study lays the groundwork for future Tesla valve design optimization, holding potential implications for applications where the control of transient flow events is crucial. Full article

Background and objectives: Since the beginning of the 20th century, more than 75% of genetic diversity has been lost. As a result of this homogenization, thousands of cultivated and wild food plants are no longer used, although they have high nutritional value. This work aims to develop recipes for new dishes and bring biodiversity to the plate in a way that consumers desire. Methods: Prototypes of new foods were prepared in the experimental kitchen. Each recipe was blind-tasted, evaluated, and ranked according to its organoleptic quality using a systematic approach. Both independent professional taste experts and lay public representatives were involved in the sensory evaluation of dishes. After the initial sensory evaluation (discrimination and hedonic scoring tests) in Serbia, the following recipes were selected for further evaluation in four other countries—Greece, Hungary, France, and Turkey: Dandelion and Tomato Salad; Buckwheat and Grass Pea Stew with Eggplant; Baked Eggplant and Potato à la Papa Alexie; Lentils as a Starter and Buckwheat Pockets Filled with Walnuts and Dried Fruit. The recipes were tested by 132 lay public representatives and 24 professionals. Results and Discussion: Of the five dishes tested, Buckwheat Pockets Filled with Walnuts and Dried Fruit were the most popular, followed by Baked Eggplant and Potato à la Papa Alexie and Dandelion and Tomato Salad. Although cultural differences and individual preferences play a role, none of the dishes was considered unacceptable or undesirable, and most were rated as likable to very likable. In line with the feedback, the optimization of the recipe design was discussed to optimize the sensory perception of the new dishes and to achieve a stimulating and satisfying taste and smell with appropriate texture and mouthfeel. The sensory evaluation showed that the new dishes offered, based on the underutilized foods studied in this project, were highly recognized and well received by consumers. Finally, a recipe book was created that includes a detailed explanation of the preparation methods and a comprehensive presentation of the relevant nutritional information of the new food dishes. Full article

The expression of the Fasciola hepatica carboxylesterase type B (CestB) gene is known to be induced upon exposure to the anthelmintic triclabendazole (TCBZ), leading to a substantial rise in enzyme-specific activity. Furthermore, the nucleotide sequence of the CestB gene displays variations that can potentially result in radical amino acid substitutions at the ligand binding site. These substitutions hold the potential to impact both the ligand–protein interaction and the catalytic properties of the enzyme. Thus, the objective of our study was to identify novel CestB polymorphisms in TCBZ-resistant parasites and field isolates obtained from a highly endemic region in Central Mexico. Additionally, we aimed to assess these amino acid polymorphisms using 3D modeling against the metabolically oxidized form of the anthelmintic TCBZSOX. Our goal was to observe the formation of TCBZSOX-specific binding pockets that might provide insights into the role of CestB in the mechanism of anthelmintic resistance. We identified polymorphisms in TCBZ-resistant parasites that exhibited three radical amino acid substitutions at positions 147, 215, and 263. These substitutions resulted in the formation of a TCBZSOX-affinity pocket with the potential to bind the anthelmintic drug. Furthermore, our 3D modeling analysis revealed that these amino acid substitutions also influenced the configuration of the CestB catalytic site, leading to alterations in the enzyme’s interaction with chromogenic carboxylic ester substrates and potentially affecting its catalytic properties. However, it is important to note that the TCBZSOX-binding pocket, while significant for drug binding, was located separate from the enzyme’s catalytic site, rendering enzymatic hydrolysis of TCBZSOX impossible. Nonetheless, the observed increased affinity for the anthelmintic may provide an explanation for a drug sequestration type of anthelmintic resistance. These findings lay the groundwork for the future development of a molecular diagnostic tool to identify anthelmintic resistance in F. hepatica. Full article

The cyclic AMP-dependent protein kinase (PKA) plays an essential role in the regulation of many important cellular processes and is dysregulated in several pervasive diseases, including diabetes, cardiovascular disease, and various neurodegenerative disorders. Previous studies suggest that the alpha isoform of the catalytic subunit of PKA (PKA-Cα) is oxidized on C199, both in vitro and in situ. However, the molecular consequences of these modifications on PKA-Cα’s substrate selection remain largely unexplored. C199 is located on the P + 1 loop within PKA-Cα’s active site, suggesting that redox modification may affect its kinase activity. Given the proximity of C199 to the substrate binding pocket, we hypothesized that oxidation could differentially alter PKA-Cα’s activity toward its substrates. To this end, we examined the effects of diamide- and H₂O₂-dependent oxidation on PKA-Cα’s activity toward select peptide and protein substrates using a combination of biochemical (i.e., trans-phosphorylation assays and steady-state kinetics analysis) and biophysical (i.e., surface plasmon resonance and fluorescence polarization assays) strategies. These studies suggest that redox modification of PKA-Cα differentially affects its activity toward different substrates. For instance, we found that diamide-mediated oxidation caused a marked decrease in PKA-Cα’s activity toward some substrates (e.g., Kemptide and CREBtide) while having little effect on others (e.g., Crosstide). In contrast, H₂O₂-dependent oxidation of PKA-Cα led to an increase in its activity toward each of the substrates at relatively low H₂O₂ concentrations, with differential effects at higher peroxide concentrations. Together, these studies offer novel insights into crosstalk between redox- and phosphorylation-dependent signaling pathways mediated by PKA. Likewise, since C199 is highly conserved among AGC kinase family members, they also lay the foundation for future studies designed to elucidate the role of redox-dependent modification of kinase substrate selection in physiological and pathological states. Full article

Schistosomiasis is a neglected tropical disease with high morbidity. Recently, the Schistosoma mansoni phosphodiesterase SmPDE4A was suggested as a putative new drug target. To support SmPDE4A targeted drug discovery, we cloned, isolated, and biochemically characterized the full-length and catalytic domains of SmPDE4A. The enzymatically active catalytic domain was crystallized in the apo-form (PDB code: 6FG5) and in the cAMP- and AMP-bound states (PDB code: 6EZU). The SmPDE4A catalytic domain resembles human PDE4 more than parasite PDEs because it lacks the parasite PDE-specific P-pocket. Purified SmPDE4A proteins (full-length and catalytic domain) were used to profile an in-house library of PDE inhibitors (PDE4NPD toolbox). This screening identified tetrahydrophthalazinones and benzamides as potential hits. The PDE inhibitor NPD-0001 was the most active tetrahydrophthalazinone, whereas the approved human PDE4 inhibitors roflumilast and piclamilast were the most potent benzamides. As a follow-up, 83 benzamide analogs were prepared, but the inhibitory potency of the initial hits was not improved. Finally, NPD-0001 and roflumilast were evaluated in an in vitro anti-S. mansoni assay. Unfortunately, both SmPDE4A inhibitors were not effective in worm killing and only weakly affected the egg-laying at high micromolar concentrations. Consequently, the results with these SmPDE4A inhibitors strongly suggest that SmPDE4A is not a suitable target for anti-schistosomiasis therapy. Full article

Recent global warming has led to increased coastal disturbances through a significant transfer of heat between the land and the ocean surface. The polar regions show excessive temperature changes resulting in massive ice sheet melting. Mid-latitudinal storms pull heat away from the equator towards the poles; therefore, the global sea level is rising, making coastal cities the most vulnerable. In last few decades, rapid urbanization in big cities has drastically changed the land cover and land use due to deforestation, which has led to increased land surface temperatures (LSTs). This eventually leads to urban flooding due to oceanic storm surges frequently created by low pressure over the ocean during summer. This paper considered factors such as drastic unplanned urbanization to analyze coastal cities as the focal point of the generation of heat yielding the annihilation of the natural topography. Urban heat pockets (UHP) were studied for nine megacities, which were selected at an interval of 5° of latitudinal difference in the northern hemisphere (NH) since 70% of densely populated megacities are located in coastal regions. A comparative surface temperature analysis was effectively carried out with the same latitudinal reference for nine mid-sized cities using the derived LST data from Landsat 8. The results provide a comparative classification of surface temperature variations across the coastal cities over the NH. This study infers that the issues pertaining to growing urbanization are very important for analyzing the proportional impact caused by the settlement hierarchy and lays a robust foundation for advanced studies of global warming in coastal urban environments. Full article

The broodiness traits of domestic geese are a bottleneck that prevents the rapid development of the goose industry. To reduce the broodiness of the Zhedong goose and thus improve it, this study hybridized it with the Zi goose, which has almost no broody behavior. Genome resequencing was performed for the purebred Zhedong goose, as well as the F2 and F3 hybrids. The results showed that the F1 hybrids displayed significant heterosis in growth traits, and their body weight was significantly greater than those of the other groups. The F2 hybrids showed significant heterosis in egg-laying traits, and the number of eggs laid was significantly greater than those of the other groups. A total of 7,979,421 single-nucleotide polymorphisms (SNPs) were obtained, and three SNPs were screened. Molecular docking results showed that SNP11 located in the gene NUDT9 altered the structure and affinity of the binding pocket. The results suggested that SNP11 is an SNP related to goose broodiness. In the future, we will use the cage breeding method to sample the same half-sib families to accurately identify SNP markers of growth and reproductive traits. Full article

Leishmania tropica is a tropical parasite causing cutaneous leishmaniasis (CL) in humans. Leishmaniasis is a serious public health threat, affecting an estimated 350 million people in 98 countries. The global rise in antileishmanial drug resistance has triggered the need to explore novel therapeutic strategies against this parasite. In the present study, we utilized the recently available multidrug resistant L. tropica strain proteome data repository to identify alternative therapeutic drug targets based on comparative subtractive proteomic and druggability analyses. Additionally, small drug-like compounds were scanned against novel targets based on virtual screening and ADME profiling. The analysis unveiled 496 essential cellular proteins of L. tropica that were nonhomologous to the human proteome set. The druggability analyses prioritized nine parasite-specific druggable proteins essential for the parasite’s basic cellular survival, growth, and virulence. These prioritized proteins were identified to have appropriate binding pockets to anchor small drug-like compounds. Among these, UDPase and PCNA were prioritized as the top-ranked druggable proteins. The pharmacophore-based virtual screening and ADME profiling predicted MolPort-000-730-162 and MolPort-020-232-354 as the top hit drug-like compounds from the Pharmit resource to inhibit L. tropica UDPase and PCNA, respectively. The alternative drug targets and drug-like molecules predicted in the current study lay the groundwork for developing novel antileishmanial therapies. Full article

Soft soils are commonly located in many regions near seas, oceans, and rivers all over the world. These regions are vital and attractive for population and governments development. Soft soil is classified as problematic soil owing to sustaining low shear strength and high settlement under structures. Constructing structures and/or infrastructures on soft soil is a considerable risk that needs great attention from structural engineers. The bearing capacity of structure foundations on soft soil depends mainly on their undrained shear strength. This soil feature strongly influences the selection of appropriate soil improvement methods. However, determining undrained shear strength is very difficult, costly, and time-consuming, especially for sensitive clay. Consequently, extracting undisturbed samples of sensitive clay faces several difficulties on construction sites. In this research, accurate field-tested data were fed to advanced machine learning models to predict the undrained shear strength of the sensitive clay to save hard effort, time, repeated laboratory testing, and costs. In this context, a dataset of 111 geotechnical testing points were collected based on laboratory and field examinations of the soil’s key features. These features included the water content, liquid limit, dry unit weight, plasticity index, consistency index, void ratio, specific gravity, and pocket penetration shear. Several machine learning algorithms were adopted to provide the soft clay modeling, including the linear, Gaussian process regression, ensemble and regression trees, and the support vector regression. The coefficient of determination was mainly used to assess the performance of each predictive model. The achieved results revealed that the support vector regression model attained the most accurate prediction for soil undrained shear strength. These outcomes lay the groundwork for evaluating soil shear strength characteristics in a practical, fast, and low-cost way. Full article

Getah virus (GETV) is a member of the alphavirus genus, and it infects a variety of animal species, including horses, pigs, cattle, and foxes. Human infection with this virus has also been reported. The structure of GETV has not yet been determined. In this study, we report the cryo-EM structure of GETV at a resolution of 3.5 Å. This structure reveals conformational polymorphism of the envelope glycoproteins E1 and E2 at icosahedral 3-fold and quasi-3-fold axes, which is believed to be a necessary organization in forming a curvature surface of virions. In our density map, three extra densities are identified, one of which is believed a “pocket factor”; the other two are located by domain D of E2, and they may maintain the stability of E1/E2 heterodimers. We also identify three N-glycosylations at E1 N141, E2 N200, and E2 N262, which might be associated with receptor binding and membrane fusion. The resolving of the structure of GETV provides new insights into the structure and assembly of alphaviruses and lays a basis for studying the differences of biology and pathogenicity between arthritogenic and encephalitic alphaviruses. Full article

SMYD3 is a SET-domain-containing methyltransferase that catalyzes the transfer of methyl groups onto lysine residues of substrate proteins. Methylation of MAP3K2 by SMYD3 has been implicated in Ras-driven tumorigenesis, which makes SMYD3 a potential target for cancer therapy. Of all SMYD family proteins, SMYD3 adopt a closed conformation in a crystal structure. Several studies have suggested that the conformational changes between the open and closed forms may regulate the catalytic activity of SMYD3. In this work, we carried out extensive molecular dynamics simulations on a series of complexes with a total of 21 ?s sampling to investigate the conformational changes of SMYD3 and unveil the molecular mechanisms. Based on the C-terminal domain movements, the simulated models could be depicted in three different conformational states: the closed, intermediate and open states. Only in the case that both the methyl donor binding pocket and the target lysine-binding channel had bound species did the simulations show SMYD3 maintaining its conformation in the closed state, indicative of a synergetic effect of the cofactors and target lysine on regulating the conformational change of SMYD3. In addition, we performed analyses in terms of structure and energy to shed light on how the two regions might regulate the C-terminal domain movement. This mechanistic study provided insights into the relationship between the conformational change and the methyltransferase activity of SMYD3. The more complete understanding of the conformational dynamics developed here together with further work may lay a foundation for the rational drug design of SMYD3 inhibitors. Full article

Phosphodiesterase 2 (PDE2) has been regarded as a novel target for the treatment of Alzheimer’s disease (AD). In this study, we obtained (R)-LZ77 as a hit compound with moderate PDE2 inhibitory activity (IC₅₀ = 261.3 nM) using a high-throughput virtual screening method based on molecular dynamics. Then, we designed and synthesized 28 dihydropyranopyrazole derivatives as PDE2 inhibitors. Among them, compound (+)-11h was the most potent PDE2 inhibitor, with an IC₅₀ value of 41.5 nM. The molecular docking of PDE2-(+)-11h reveals that the 4-(trifluoromethyl)benzyl)oxyl side chain of the compound enters the H-pocket and forms strong hydrophobic interactions with L770/L809/F862, which improves inhibitory activity. The above results may provide insight for further structural optimization of highly potent PDE2 inhibitors and may lay the foundation for their use in the treatment of AD. Full article

Aminotransferases are employed as industrial biocatalysts to produce chiral amines with high enantioselectivity and yield. BpTA-1 and BpTA-2 are the only two pyridoxal 5′-phosphate-dependent fold type IV transaminase enzymes in Bacillus altitudinis W3. Herein, we compared the structures and biochemical characteristics of BpTA-1 and BpTA-2 using bioinformatic analysis, circular dichroism spectroscopy, atomic force microscopy and other approaches. BpTA-1 and BpTA-2 are similar overall; both form homodimers and utilize a catalytic lysine. However, there are distinct differences in the substrate cofactor-binding pocket, molecular weight and the proportion of the secondary structure. Both enzymes have the same stereoselectivity but different enzymatic properties. BpTA-2 is more active under partial alkaline and ambient temperature conditions and BpTA-1 is more sensitive to pH and temperature. BpTA-2 as novel enzyme not only fills the building blocks of transaminase but also has broader industrial application potential for (R)-α-phenethylamines than BpTA-1. Structure-function relationships were explored to assess similarities and differences. The findings lay the foundation for modifying these enzymes via protein engineering to enhance their industrial application potential. Full article

Remote sensing evapotranspiration estimation over agricultural areas is increasingly used for irrigation management during the crop growing cycle. Different methodologies based on remote sensing have emerged for the leaf area index (LAI) and the canopy chlorophyll content (CCC) estimation, essential biophysical parameters for crop evapotranspiration monitoring. Using Sentinel-2 (S2) spectral information, this study performed a comparative analysis of empirical (vegetation indices), semi-empirical (CLAIR model with fixed and calibrated extinction coefficient) and artificial neural network S2 products derived from the Sentinel Application Platform Software (SNAP) biophysical processor (ANN S2 products) approaches for the estimation of LAI and CCC. Four independent in situ collected datasets of LAI and CCC, obtained with standard instruments (LAI-2000, SPAD) and a smartphone application (PocketLAI), were used. The ANN S2 products present good statistics for LAI (R² > 0.70, root mean square error (RMSE) < 0.86) and CCC (R² > 0.75, RMSE < 0.68 g/m²) retrievals. The normalized Sentinel-2 LAI index (SeLI) is the index that presents good statistics in each dataset (R² > 0.71, RMSE < 0.78) and for the CCC, the ratio red-edge chlorophyll index (CI_red-edge) (R² > 0.67, RMSE < 0.62 g/m²). Both indices use bands located in the red-edge zone, highlighting the importance of this region. The LAI CLAIR model with a fixed extinction coefficient value produces a R² > 0.63 and a RMSE < 1.47 and calibrating this coefficient for each study area only improves the statistics in two areas (RMSE ≈ 0.70). Finally, this study analyzed the influence of the LAI parameter estimated with the different methodologies in the calculation of crop potential evapotranspiration (ET_c) with the adapted Penman–Monteith (FAO-56 PM), using a multi-temporal dataset. The results were compared with ET_c estimated as the product of the reference evapotranspiration (ET_o) and on the crop coefficient (K_c) derived from FAO table values. In the absence of independent reference ET data, the estimated ET_c with the LAI in situ values were considered as the proxy of the ground-truth. ET_c estimated with the ANN S2 LAI product is the closest to the ET_c values calculated with the LAI in situ (R² > 0.90, RMSE < 0.41 mm/d). Our findings indicate the good validation of ANN S2 LAI and CCC products and their further suitability for the implementation in evapotranspiration retrieval of agricultural areas. Full article