Muhammad Irfan Khawar, Muhammad Arshad, Eric P Achterberg, Deedar Nabi
{"title":"Streamlining Linear Free Energy Relationships of Proteins through Dimensionality Analysis and Linear Modeling.","authors":"Muhammad Irfan Khawar, Muhammad Arshad, Eric P Achterberg, Deedar Nabi","doi":"10.1021/acs.jcim.4c01289","DOIUrl":"10.1021/acs.jcim.4c01289","url":null,"abstract":"<p><p>Linear free energy relationships (LFERs) are pivotal in predicting protein-water partition coefficients, with traditional one-parameter (<i>1p</i>-LFER) models often based on octanol. However, their limited scope has prompted a shift toward the more comprehensive but parameter-intensive Abraham solvation-based poly-parameter (<i>pp</i>-LFER) approach. This study introduces a two-parameter (<i>2p</i>-LFER) model, aiming to balance simplicity and predictive accuracy. We showed that the complex six-dimensional intermolecular interaction space, defined by the six Abraham solute descriptors, can be efficiently simplified into two key dimensions. These dimensions are effectively represented by the octanol-water (log <i>K</i><sub>ow</sub>) and air-water (log <i>K</i><sub>aw</sub>) partition coefficients. Our <i>2p</i>-LFER model, utilizing linear combinations of log <i>K</i><sub>ow</sub> and log <i>K</i><sub>aw</sub>, showed promising results. It accurately predicted structural protein-water (log <i>K</i><sub>pw</sub>) and bovine serum albumin-water (log <i>K</i><sub>BSA</sub>) partition coefficients, with <i>R</i><sup>2</sup> values of 0.878 and 0.760 and root mean squared errors (RMSEs) of 0.334 and 0.422, respectively. Additionally, the <i>2p</i>-LFER model favorably compares with <i>pp</i>-LFER predictions for neutral per- and polyfluoroalkyl substances. In a multiphase partitioning model parametrized with <i>2p</i>-LFER-derived coefficients, we observed close alignment with experimental <i>in vivo</i> and <i>in vitro</i> distribution data for diverse mammalian tissues/organs (<i>n</i> = 137, RMSE = 0.44 log unit) and milk-water partitioning data (<i>n</i> = 108, RMSE = 0.29 log units). The performance of the <i>2p</i>-LFER is comparable to <i>pp</i>-LFER and significantly surpasses <i>1p</i>-LFER. Our findings highlight the utility of the <i>2p</i>-LFER model in estimating chemical partitioning to proteins based on hydrophobicity, volatility, and solubility, offering a viable alternative in scenarios where <i>pp</i>-LFER descriptors are unavailable.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9327-9340"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gergely Zahoránszky-Kőhalmi, Brandon Walker, Nathan Miller, Brett Yang, Dhatri V L Penna, Jessica Maine, Timothy Sheils, Ke Wang, Jennifer King, Hythem Sidky, Sridhar Vuyyuru, Jeyaraman Soundarajan, Samuel G Michael, Alexander G Godfrey, Tudor I Oprea
{"title":"SmartGraph API: Programmatic Knowledge Mining in Network-Pharmacology Setting.","authors":"Gergely Zahoránszky-Kőhalmi, Brandon Walker, Nathan Miller, Brett Yang, Dhatri V L Penna, Jessica Maine, Timothy Sheils, Ke Wang, Jennifer King, Hythem Sidky, Sridhar Vuyyuru, Jeyaraman Soundarajan, Samuel G Michael, Alexander G Godfrey, Tudor I Oprea","doi":"10.1021/acs.jcim.4c00789","DOIUrl":"10.1021/acs.jcim.4c00789","url":null,"abstract":"<p><p>The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows with ease in the network-pharmacology paradigm. However, at the time of its publication we identified the need for the development of an Application Programming Interface (API) that could promote biomedical data integration and hypothesis generation in an automated manner. This need was magnified at the time of the COVID-19 pandemic. This study addresses the absence of such an API. Accordingly, most functionalities of the original platform were implemented within the SmartGraph API. We demonstrate that by using the API it is possible to transform the original semiautomated workflow behind the Neo4COVID19 database to a fully automated one. The availability of the SmartGraph API lends a significant improvement to the programmatic integration of network-pharmacology-oriented knowledge graphs and analytics, as well as predictive functionalities and workflows.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9021-9026"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142778710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploring Extended Warheads toward Developing Cysteine-Targeted Covalent Kinase Inhibitors.","authors":"Zheng Zhao, Philip E Bourne","doi":"10.1021/acs.jcim.4c00890","DOIUrl":"10.1021/acs.jcim.4c00890","url":null,"abstract":"<p><p>In designing covalent kinase inhibitors (CKIs), the inclusion of electrophiles as attacking warheads demands careful choreography, ensuring not only their presence on the scaffold moiety but also their precise interaction with nucleophiles in the binding sites. Given the limited number of known electrophiles, exploring adjacent chemical space to broaden the palette of available electrophiles capable of covalent inhibition is desirable. Here, we systematically analyze the characteristics of warheads and the corresponding adjacent fragments for use in CKI design. We first collect all the released cysteine-targeted CKIs from multiple databases and create one CKI data set containing 16,961 kinase-inhibitor data points from 12,381 unique CKIs covering 146 kinases with accessible cysteines in their binding pockets. Then, we analyze this data set, focusing on the extended warheads (i.e., warheads + adjacent fragments)─including 30 common warheads and 1344 unique adjacent fragments. In so doing, we provide structural insights and delineate chemical properties and patterns in these extended warheads. Notably, we highlight the popular patterns observed within reversible CKIs for the popular warheads cyanoacrylamide and aldehyde. This study provides medicinal chemists with novel insights into extended warheads and a comprehensive source of adjacent fragments, thus guiding the design, synthesis, and optimization of CKIs.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9517-9527"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.","authors":"Apoorva Mathur, Rikhia Ghosh, Ariane Nunes-Alves","doi":"10.1021/acs.jcim.4c01520","DOIUrl":"10.1021/acs.jcim.4c01520","url":null,"abstract":"<p><p>Macromolecular crowding in the cellular cytoplasm can potentially impact diffusion rates of proteins, their intrinsic structural stability, binding of proteins to their corresponding partners as well as biomolecular organization and phase separation. While such intracellular crowding can have a large impact on biomolecular structure and function, the molecular mechanisms and driving forces that determine the effect of crowding on dynamics and conformations of macromolecules are so far not well understood. At a molecular level, computational methods can provide a unique lens to investigate the effect of macromolecular crowding on biomolecular behavior, providing us with a resolution that is challenging to reach with experimental techniques alone. In this review, we focus on the various physics-based and data-driven computational methods developed in the past few years to investigate macromolecular crowding and intracellular protein condensation. We review recent progress in modeling and simulation of biomolecular systems of varying sizes, ranging from single protein molecules to the entire cellular cytoplasm. We further discuss the effects of macromolecular crowding on different phenomena, such as diffusion, protein-ligand binding, and mechanical and viscoelastic properties, such as surface tension of condensates. Finally, we discuss some of the outstanding challenges that we anticipate the community addressing in the next few years in order to investigate biological phenomena in model cellular environments by reproducing <i>in vivo</i> conditions as accurately as possible.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9063-9081"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaohua Wang, Ming Zhang, Xibei Yang, Dong-Jun Yu, Fang Ge
{"title":"GPTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in G Protein-Coupled Receptors.","authors":"Xiaohua Wang, Ming Zhang, Xibei Yang, Dong-Jun Yu, Fang Ge","doi":"10.1021/acs.jcim.4c01999","DOIUrl":"10.1021/acs.jcim.4c01999","url":null,"abstract":"<p><p>Accurately predicting mutations in G protein-coupled receptors (GPCRs) is critical for advancing disease diagnosis and drug discovery. In response to this imperative, GPTrans has emerged as a highly accurate predictor of disease-related mutations in GPCRs. The core innovation of GPTrans resides in the design of a novel feature extraction network, that is capable of integrating features from both wildtype and mutant protein variant sites, utilizing multifeature connections within a transformer framework to ensure comprehensive feature extraction. A key aspect of GPTrans's effectiveness is our introduction of an innovative deep feature integration strategy, which merges embeddings and class tokens from multiple protein language models, including evolutionary scale modeling and ProtTrans, thus shedding light on the biochemical properties of proteins. Leveraging transformer components and a self-attention mechanism, GPTrans captures higher-level representations of protein features. Employing both wildtype and mutation site information for feature fusion not only enriches the predictive feature set but also avoids the common issue of overestimation associated with sequence-based predictions. This approach distinguishes GPTrans, enabling it to significantly outperform existing methods. Our evaluations across diverse GPCR data sets, including ClinVar and MutHTP, demonstrate GPTrans's superior performance, with average AUC values of 0.874 and 0.590 in 10-fold cross-validation. Notably, compared to the AlphaMissense method, GPTrans exhibited a remarkable 38.03% improvement in accuracy when predicting disease-associated mutations in the MutHTP data set. A thorough analysis of the predicted results further validates the model's effectiveness. The source code, data sets, and prediction results for GPTrans are available for academic use at https://github.com/EduardWang/GPTrans.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9626-9642"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qing Liu, Dakuo He, Mengmeng Fan, Jinpeng Wang, Zeyu Cui, Hao Wang, Yan Mi, Ning Li, Qingqi Meng, Yue Hou
{"title":"Prediction and Interpretation Microglia Cytotoxicity by Machine Learning.","authors":"Qing Liu, Dakuo He, Mengmeng Fan, Jinpeng Wang, Zeyu Cui, Hao Wang, Yan Mi, Ning Li, Qingqi Meng, Yue Hou","doi":"10.1021/acs.jcim.4c00366","DOIUrl":"10.1021/acs.jcim.4c00366","url":null,"abstract":"<p><p>Ameliorating microglia-mediated neuroinflammation is a crucial strategy in developing new drugs for neurodegenerative diseases. Plant compounds are an important screening target for the discovery of drugs for the treatment of neurodegenerative diseases. However, due to the spatial complexity of phytochemicals, it becomes particularly important to evaluate the effectiveness of compounds while avoiding the mixing of cytotoxic substances in the early stages of compound screening. Traditional high-throughput screening methods suffer from high cost and low efficiency. A computational model based on machine learning provides a novel avenue for cytotoxicity determination. In this study, a microglia cytotoxicity classifier was developed using a machine learning approach. First, we proposed a data splitting strategy based on the molecule murcko generic scaffold, under this condition, three machine learning approaches were coupled with three kinds of molecular representation methods to construct microglia cytotoxicity classifier, which were then compared and assessed by the predictive accuracy, balanced accuracy, F<sub>1</sub>-score, and Matthews Correlation Coefficient. Then, the recursive feature elimination integrated with support vector machine (RFE-SVC) dimension reduction method was introduced to molecular fingerprints with high dimensions to further improve the model performance. Among all the microglial cytotoxicity classifiers, the SVM coupled with ECFP4 fingerprint after feature selection (ECFP4-RFE-SVM) obtained the most accurate classification for the test set (ACC of 0.99, BA of 0.99, F<sub>1</sub>-score of 0.99, MCC of 0.97). Finally, the Shapley additive explanations (SHAP) method was used in interpreting the microglia cytotoxicity classifier and key substructure smart identified as structural alerts. Experimental results show that ECFP4-RFE-SVM have reliable classification capability for microglia cytotoxicity, and SHAP can not only provide a rational explanation for microglia cytotoxicity predictions, but also offer a guideline for subsequent molecular cytotoxicity modifications.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9306-9326"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Generating Multistate Conformations of P-type ATPases with a Conditional Diffusion Model.","authors":"Jingtian Xu, Yong Wang","doi":"10.1021/acs.jcim.4c01519","DOIUrl":"10.1021/acs.jcim.4c01519","url":null,"abstract":"<p><p>Understanding and predicting the diverse conformational states of membrane proteins is essential for elucidating their biological functions. Despite advancements in computational methods, accurately capturing these complex structural changes remains a significant challenge. Here, we introduce a computational approach to generate diverse and biologically relevant conformations of membrane proteins using a conditional diffusion model. Our approach integrates forward and backward diffusion processes, incorporating state classifiers and additional conditioners to control the generation gradient of conformational states. We specifically targeted the P-type ATPases, a critical family of membrane transporters, and constructed a comprehensive data set through a combination of experimental structures and molecular dynamics simulations. Our model, incorporating a graph neural network with specialized membrane constraints, demonstrates exceptional accuracy in generating a wide range of P-type ATPase conformations associated with different functional states. This approach represents a meaningful step forward in the computational generation of membrane protein conformations using AI and holds promise for studying the dynamics of other membrane proteins.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9227-9239"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Muya Xiong, Tianqing Nie, Zhewen Li, Meiyi Hu, Haixia Su, Hangchen Hu, Yechun Xu, Qiang Shao
{"title":"Potency Prediction of Covalent Inhibitors against SARS-CoV-2 3CL-like Protease and Multiple Mutants by Multiscale Simulations.","authors":"Muya Xiong, Tianqing Nie, Zhewen Li, Meiyi Hu, Haixia Su, Hangchen Hu, Yechun Xu, Qiang Shao","doi":"10.1021/acs.jcim.4c01594","DOIUrl":"10.1021/acs.jcim.4c01594","url":null,"abstract":"<p><p>3-Chymotrypsin-like protease (3CL<sup>pro</sup>) is a prominent target against pathogenic coronaviruses. Expert knowledge of the cysteine-targeted covalent reaction mechanism is crucial to predict the inhibitory potency of approved inhibitors against 3CL<sup>pro</sup>s of SARS-CoV-2 variants and perform structure-based drug design against newly emerging coronaviruses. We carried out an extensive array of classical and hybrid QM/MM molecular dynamics simulations to explore covalent inhibition mechanisms of five well-characterized inhibitors toward SARS-CoV-2 3CL<sup>pro</sup> and its mutants. The calculated binding affinity and reactivity of the inhibitors are highly consistent with experimental data, and the predicted inhibitory potency of the inhibitors against 3CL<sup>pro</sup> with L167F, E166V, or T21I/E166V mutant is in full agreement with IC<sub>50</sub>s determined by the accompanying enzymatic assays. The explored mechanisms unveil the impact of residue mutagenesis on structural dynamics that communicates to change not only noncovalent binding strength but also covalent reaction free energy. Such a change is inhibitor dependent, corresponding to varied levels of drug resistance of these 3CL<sup>pro</sup> mutants against nirmatrelvir and simnotrelvir and no resistance to the <b>11a</b> compound. These results together suggest that the present simulations with a suitable protocol can efficiently evaluate the reactivity and potency of covalent inhibitors along with the elucidated molecular mechanisms of covalent inhibition.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9501-9516"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142737777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"How Good are Current Pocket-Based 3D Generative Models?: The Benchmark Set and Evaluation of Protein Pocket-Based 3D Molecular Generative Models.","authors":"Haoyang Liu, Yifei Qin, Zhangming Niu, Mingyuan Xu, Jiaqiang Wu, Xianglu Xiao, Jinping Lei, Ting Ran, Hongming Chen","doi":"10.1021/acs.jcim.4c01598","DOIUrl":"10.1021/acs.jcim.4c01598","url":null,"abstract":"<p><p>The development of a three-dimensional (3D) molecular generative model based on protein pockets has recently attracted a lot of attention. This type of model aims to achieve the simultaneous generation of molecular graphs and 3D binding conformation under the constraint of protein binding. Various pocket-based generative models have been proposed; however, currently, there is a lack of systematic and objective evaluation metrics for these models. To address this issue, a comprehensive benchmark data set, named POKMOL-3D, is proposed to evaluate protein pocket-based 3D molecular generative models. It includes 32 protein targets together with their known active compounds as a test set to evaluate the versatility of generation models to mimic the real-world scenario. Additionally, a series of two-dimensional (2D) and 3D evaluation metrics with some newly created ones was integrated to assess the quality of generated molecular structures and their binding conformations. It is expected that this work can enhance our comprehension of the effectiveness and weakness of current 3D generative models and stimulate the discussion on challenges and useful guidance for developing the next wave of molecular generative models.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9260-9275"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Kinase-Bench: Comprehensive Benchmarking Tools and Guidance for Achieving Selectivity in Kinase Drug Discovery.","authors":"Tian-Hua Wei, Shuang-Shuang Zhou, Xiao-Long Jing, Jia-Chuan Liu, Meng Sun, Zong-Hao Zhao, Qing-Qing Li, Zi-Xuan Wang, Jin Yang, Yun Zhou, Xue Wang, Cheng-Xiao Ling, Ning Ding, Xin Xue, Yan-Cheng Yu, Xiao-Long Wang, Xiao-Ying Yin, Shan-Liang Sun, Peng Cao, Nian-Guang Li, Zhi-Hao Shi","doi":"10.1021/acs.jcim.4c01830","DOIUrl":"10.1021/acs.jcim.4c01830","url":null,"abstract":"<p><p>Developing selective kinase inhibitors remains a formidable challenge in drug discovery because of the highly conserved structural information on adenosine triphosphate (ATP) binding sites across the kinase family. Tailoring docking protocols to identify promising kinase inhibitor candidates for optimization has long been a substantial obstacle to drug discovery. Therefore, we introduced \"Kinase-Bench,\" a pioneering benchmark suite designed for an advanced virtual screen, to improve the selectivity and efficacy of kinase inhibitors. Our comprehensive data set includes 6875 selective ligands and 422,799 decoys for 75 kinases, using extensive bioactivity and structural data from the ChEMBL database and decoys generated by the Directory of Useful Decoys-Enhanced version. Our benchmarking sets and retrospective case studies were designed to provide useful guidance in discovering selective kinase inhibitors. We employed a Glide High-Throughput Virtual Screen and Standard Precision complemented by three scoring functions and customized protein-ligand interaction filters that target specific kinase residue interactions. These innovations were successfully implemented in our virtual screen efforts targeting JAK1 inhibitors, achieving selectivity against its family member, TYK2. Consequently, we identified novel potential hits: Compound <b>2</b> (JAK1 IC<sub>50</sub>: 980.5 nM, TYK2 IC<sub>50</sub>: 4.5 μM) and the approved pan-AKT inhibitor Capivasertib (JAK1 IC<sub>50</sub>: 275.9 nM, TYK2 IC<sub>50</sub>: 10.9 μM). Using the Kinase-Bench protocol, both compounds demonstrated substantial JAK1 selectivity, making them strong candidates for further investigation. Our pharmaceutical results underscore the utility of tailored virtual screen protocols in identifying selective kinase inhibitors with substantial implications for rational drug design. Kinase-Bench offers a robust toolset for selective kinase drug discovery with the potential to effectively guide future therapeutic strategies effectively.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"9528-9550"},"PeriodicalIF":5.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}