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Ensemble docking based virtual screening of SARS-CoV-2 main protease inhibitors. 基于组合对接的 SARS-CoV-2 主要蛋白酶抑制剂虚拟筛选。
IF 2.8 4区 医学
Molecular Informatics Pub Date : 2024-08-01 Epub Date: 2024-07-08 DOI: 10.1002/minf.202300279
Anastasia D Fomina, Victoria I Uvarova, Liubov I Kozlovskaya, Vladimir A Palyulin, Dmitry I Osolodkin, Aydar A Ishmukhametov
{"title":"Ensemble docking based virtual screening of SARS-CoV-2 main protease inhibitors.","authors":"Anastasia D Fomina, Victoria I Uvarova, Liubov I Kozlovskaya, Vladimir A Palyulin, Dmitry I Osolodkin, Aydar A Ishmukhametov","doi":"10.1002/minf.202300279","DOIUrl":"10.1002/minf.202300279","url":null,"abstract":"<p><p>During the first years of COVID-19 pandemic, X-ray structures of the coronavirus drug targets were acquired at an unprecedented rate, giving hundreds of PDB depositions in less than a year. The main protease (Mpro) of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) is the primary validated target of direct-acting antivirals. The selection of the optimal ensemble of structures of Mpro for the docking-driven virtual screening campaign was thus non-trivial and required a systematic and automated approach. Here we report a semi-automated active site RMSD based procedure of ensemble selection from the SARS-CoV-2 Mpro crystallographic data and virtual screening of its inhibitors. The procedure was compared with other approaches to ensemble selection and validated with the help of hand-picked and peer-reviewed activity-annotated libraries. Prospective virtual screening of non-covalent Mpro inhibitors resulted in a new chemotype of thienopyrimidinone derivatives with experimentally confirmed enzyme inhibition.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":" ","pages":"e202300279"},"PeriodicalIF":2.8,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library. 利用 Molpher 探索化学空间：生成并评估糖皮质激素受体配体库。
IF 2.8 4区 医学
Molecular Informatics Pub Date : 2024-08-01 Epub Date: 2024-07-09 DOI: 10.1002/minf.202300316
M Isabel Agea, Ivan Čmelo, Wim Dehaen, Ya Chen, Johannes Kirchmair, David Sedlák, Petr Bartůněk, Martin Šícho, Daniel Svozil
{"title":"Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library.","authors":"M Isabel Agea, Ivan Čmelo, Wim Dehaen, Ya Chen, Johannes Kirchmair, David Sedlák, Petr Bartůněk, Martin Šícho, Daniel Svozil","doi":"10.1002/minf.202300316","DOIUrl":"10.1002/minf.202300316","url":null,"abstract":"<p><p>Computational exploration of chemical space is crucial in modern cheminformatics research for accelerating the discovery of new biologically active compounds. In this study, we present a detailed analysis of the chemical library of potential glucocorticoid receptor (GR) ligands generated by the molecular generator, Molpher. To generate the targeted GR library and construct the classification models, structures from the ChEMBL database as well as from the internal IMG library, which was experimentally screened for biological activity in the primary luciferase reporter cell assay, were utilized. The composition of the targeted GR ligand library was compared with a reference library that randomly samples chemical space. A random forest model was used to determine the biological activity of ligands, incorporating its applicability domain using conformal prediction. It was demonstrated that the GR library is significantly enriched with GR ligands compared to the random library. Furthermore, a prospective analysis demonstrated that Molpher successfully designed compounds, which were subsequently experimentally confirmed to be active on the GR. A collection of 34 potential new GR ligands was also identified. Moreover, an important contribution of this study is the establishment of a comprehensive workflow for evaluating computationally generated ligands, particularly those with potential activity against targets that are challenging to dock.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":" ","pages":"e202300316"},"PeriodicalIF":2.8,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141559260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Navigating pharmacophore space to identify activity discontinuities: A case study with BCR-ABL. 浏览药理空间以识别活性不连续性：BCR-ABL 案例研究。
IF 2.8 4区 医学
Molecular Informatics Pub Date : 2024-08-01 Epub Date: 2024-07-09 DOI: 10.1002/minf.202400050
Maroua Lejmi, Damien Geslin, Ronan Bureau, Bertrand Cuissart, Ilef Ben Slima, Nida Meddouri, Amel Borgi, Jean-Luc Lamotte, Alban Lepailleur
{"title":"Navigating pharmacophore space to identify activity discontinuities: A case study with BCR-ABL.","authors":"Maroua Lejmi, Damien Geslin, Ronan Bureau, Bertrand Cuissart, Ilef Ben Slima, Nida Meddouri, Amel Borgi, Jean-Luc Lamotte, Alban Lepailleur","doi":"10.1002/minf.202400050","DOIUrl":"10.1002/minf.202400050","url":null,"abstract":"<p><p>The exploration of chemical space is a fundamental aspect of chemoinformatics, particularly when one explores a large compound data set to relate chemical structures with molecular properties. In this study, we extend our previous work on chemical space visualization at the pharmacophoric level. Instead of using conventional binary classification of affinity (active vs inactive), we introduce a refined approach that categorizes compounds into four distinct classes based on their activity levels: super active, very active, active, and inactive. This classification enriches the color scheme applied to pharmacophore space, where the color representation of a pharmacophore hypothesis is driven by the associated compounds. Using the BCR-ABL tyrosine kinase as a case study, we identified intriguing regions corresponding to pharmacophore activity discontinuities, providing valuable insights for structure-activity relationships analysis.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":" ","pages":"e202400050"},"PeriodicalIF":2.8,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141559262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cover Picture: (Mol. Inf. 7/2024) 封面图片：（Mol.Inf. 7/2024）
IF 3.6 4区 医学
Molecular Informatics Pub Date : 2024-07-12 DOI: 10.1002/minf.202480701
{"title":"Cover Picture: (Mol. Inf. 7/2024)","authors":"","doi":"10.1002/minf.202480701","DOIUrl":"https://doi.org/10.1002/minf.202480701","url":null,"abstract":"","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":"243 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141609429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chemoinformatic regression methods and their applicability domain. 化学信息回归方法及其适用领域。
IF 2.8 4区 医学
Molecular Informatics Pub Date : 2024-07-01 Epub Date: 2024-05-28 DOI: 10.1002/minf.202400018
Thomas-Martin Dutschmann, Valerie Schlenker, Knut Baumann
{"title":"Chemoinformatic regression methods and their applicability domain.","authors":"Thomas-Martin Dutschmann, Valerie Schlenker, Knut Baumann","doi":"10.1002/minf.202400018","DOIUrl":"10.1002/minf.202400018","url":null,"abstract":"<p><p>The growing interest in chemoinformatic model uncertainty calls for a summary of the most widely used regression techniques and how to estimate their reliability. Regression models learn a mapping from the space of explanatory variables to the space of continuous output values. Among other limitations, the predictive performance of the model is restricted by the training data used for model fitting. Identification of unusual objects by outlier detection methods can improve model performance. Additionally, proper model evaluation necessitates defining the limitations of the model, often called the applicability domain. Comparable to certain classifiers, some regression techniques come with built-in methods or augmentations to quantify their (un)certainty, while others rely on generic procedures. The theoretical background of their working principles and how to deduce specific and general definitions for their domain of applicability shall be explained.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":" ","pages":"e202400018"},"PeriodicalIF":2.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural analysis of neomycin B and kanamycin A binding Aminoglycosides Modifying Enzymes (AME) and bacterial ribosomal RNA. 新霉素 B 和卡那霉素 A 与氨基糖苷类药物修饰酶 (AME) 和细菌核糖体 RNA 结合的结构分析。
IF 2.8 4区 医学
Molecular Informatics Pub Date : 2024-07-01 Epub Date: 2024-06-10 DOI: 10.1002/minf.202300339
Julia Revillo Imbernon, Jean-Marc Weibel, Eric Ennifar, Gilles Prévost, Esther Kellenberger
{"title":"Structural analysis of neomycin B and kanamycin A binding Aminoglycosides Modifying Enzymes (AME) and bacterial ribosomal RNA.","authors":"Julia Revillo Imbernon, Jean-Marc Weibel, Eric Ennifar, Gilles Prévost, Esther Kellenberger","doi":"10.1002/minf.202300339","DOIUrl":"10.1002/minf.202300339","url":null,"abstract":"<p><p>Aminoglycosides are crucial antibiotics facing challenges from bacterial resistance. This study addresses the importance of aminoglycoside modifying enzymes in the context of escalating resistance. Drawing upon over two decades of structural data in the Protein Data Bank, we focused on two key antibiotics, neomycin B and kanamycin A, to explore how the aminoglycoside structure is exploited by this family of enzymes. A systematic comparison across diverse enzymes and the RNA A-site target identified common characteristics in the recognition mode, while assessing the adaptability of neomycin B and kanamycin A in various environments.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":" ","pages":"e202300339"},"PeriodicalIF":2.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141296441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparing search algorithms on the retrosynthesis problem. 比较逆合成问题的搜索算法。
IF 2.8 4区 医学
Molecular Informatics Pub Date : 2024-07-01 Epub Date: 2024-06-12 DOI: 10.1002/minf.202300259
Milo Roucairol, Tristan Cazenave
{"title":"Comparing search algorithms on the retrosynthesis problem.","authors":"Milo Roucairol, Tristan Cazenave","doi":"10.1002/minf.202300259","DOIUrl":"10.1002/minf.202300259","url":null,"abstract":"<p><p>In this article we try different algorithms, namely Nested Monte Carlo Search and Greedy Best First Search, on AstraZeneca's open source retrosynthetic tool : AiZynthFinder. We compare these algorithms to AiZynthFinder's base Monte Carlo Tree Search on a benchmark selected from the PubChem database and by Bayer's chemists. We show that both Nested Monte Carlo Search and Greedy Best First Search outperform AstraZeneca's Monte Carlo Tree Search, with a slight advantage for Nested Monte Carlo Search while experimenting on a playout heuristic. We also show how the search algorithms are bounded by the quality of the policy network, in order to improve our results the next step is to improve the policy network.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":" ","pages":"e202300259"},"PeriodicalIF":2.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141306331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Best of both worlds: An expansion of the state of the art pKa model with data from three industrial partners 两全其美：利用三个工业合作伙伴提供的数据扩展最先进的 pKa 模型
IF 3.6 4区 医学
Molecular Informatics Pub Date : 2024-06-21 DOI: 10.1002/minf.202400088
Robert Fraczkiewicz, Huy Quoc Nguyen, Newton Wu, Nina Kausch‐Busies, Sergio Grimbs, Kai Sommer, Antonius ter Laak, Judith Günther, Björn Wagner, Michael Reutlinger
{"title":"Best of both worlds: An expansion of the state of the art pKa model with data from three industrial partners","authors":"Robert Fraczkiewicz, Huy Quoc Nguyen, Newton Wu, Nina Kausch‐Busies, Sergio Grimbs, Kai Sommer, Antonius ter Laak, Judith Günther, Björn Wagner, Michael Reutlinger","doi":"10.1002/minf.202400088","DOIUrl":"https://doi.org/10.1002/minf.202400088","url":null,"abstract":"In a unique collaboration between Simulations Plus and several industrial partners, we were able to develop a new version 11.0 of the previously published <jats:italic>in silico</jats:italic> pK<jats:sub>a</jats:sub> model, S+pKa, with considerably improved prediction accuracy. The model's training set was vastly expanded by large amounts of experimental data obtained from F. Hoffmann‐La Roche AG, Genentech Inc., and the Crop Science division of Bayer AG. The previous v7.0 of S+pKa was trained on data from public sources and the Pharmaceutical division of Bayer AG. The model has shown dramatic improvements in predictive accuracy when externally validated on three new contributor compound sets. Less expected was v11.0’s improvement in prediction on new compounds developed at Bayer Pharma after v7.0 was released (2013–2023), even without contributing additional data to v11.0. We illustrate chemical space coverage by chemistries encountered in the five domains, public and industrial, outline model construction, and discuss factors contributing to model's success.","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":"86 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141504470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring drug repositioning possibilities of kinase inhibitors via molecular simulation** 通过分子模拟探索激酶抑制剂药物重新定位的可能性**
IF 3.6 4区 医学
Molecular Informatics Pub Date : 2024-06-21 DOI: 10.1002/minf.202300336
Qing‐Xin Wang, Jiao Cai, Zi‐Jun Chen, Jia‐Chuan Liu, Jing‐Jing Wang, Hai Zhou, Qing‐Qing Li, Zi‐Xuan Wang, Yi‐Bo Wang, Zhen‐Jiang Tong, Jin Yang, Tian‐Hua Wei, Meng‐Yuan Zhang, Yun Zhou, Wei‐Chen Dai, Ning Ding, Xue‐Jiao Leng, Xiao‐Ying Yin, Shan‐Liang Sun, Yan‐Cheng Yu, Nian‐Guang Li, Zhi‐Hao Shi
{"title":"Exploring drug repositioning possibilities of kinase inhibitors via molecular simulation**","authors":"Qing‐Xin Wang, Jiao Cai, Zi‐Jun Chen, Jia‐Chuan Liu, Jing‐Jing Wang, Hai Zhou, Qing‐Qing Li, Zi‐Xuan Wang, Yi‐Bo Wang, Zhen‐Jiang Tong, Jin Yang, Tian‐Hua Wei, Meng‐Yuan Zhang, Yun Zhou, Wei‐Chen Dai, Ning Ding, Xue‐Jiao Leng, Xiao‐Ying Yin, Shan‐Liang Sun, Yan‐Cheng Yu, Nian‐Guang Li, Zhi‐Hao Shi","doi":"10.1002/minf.202300336","DOIUrl":"https://doi.org/10.1002/minf.202300336","url":null,"abstract":"Kinases, a class of enzymes controlling various substrates phosphorylation, are pivotal in both physiological and pathological processes. Although their conserved ATP binding pockets pose challenges for achieving selectivity, this feature offers opportunities for drug repositioning of kinase inhibitors (KIs). This study presents a cost‐effective in silico prediction of KIs drug repositioning via analyzing cross‐docking results. We established the KIs database (278 unique KIs, 1834 bioactivity data points) and kinases database (357 kinase structures categorized by the DFG motif) for carrying out cross‐docking. Comparative analysis of the docking scores and reported experimental bioactivity revealed that the Atypical, TK, and TKL superfamilies are suitable for drug repositioning. Among these kinase superfamilies, Olverematinib, Lapatinib, and Abemaciclib displayed enzymatic activity in our focused AKT‐PI3K‐mTOR pathway with IC<jats:sub>50</jats:sub> values of 3.3, 3.2 and 5.8 μM. Further cell assays showed IC<jats:sub>50</jats:sub> values of 0.2, 1.2 and 0.6 μM in tumor cells. The consistent result between prediction and validation demonstrated that repositioning KIs via <jats:italic>in silico</jats:italic> method is feasible.","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":"27 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141504468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Updating and profiling the natural product‐likeness of Latin American compound libraries 更新和剖析拉丁美洲化合物库的天然产品相似性
IF 3.6 4区 医学
Molecular Informatics Pub Date : 2024-06-21 DOI: 10.1002/minf.202400052
Alejandro Gómez‐García, Ann‐Kathrin Prinz, Daniel A. Acuña Jiménez, William J. Zamora, Haruna L. Barazorda‐Ccahuana, Miguel Á. Chávez‐Fumagalli, Marilia Valli, Adriano D. Andricopulo, Vanderlan da S. Bolzani, Dionisio A. Olmedo, Pablo N. Solís, Marvin J. Núñez, Johny R. Rodríguez Pérez, Hoover A. Valencia Sánchez, Héctor F. Cortés Hernández, Oscar M. Mosquera Martinez, Oliver Koch, José L. Medina‐Franco
{"title":"Updating and profiling the natural product‐likeness of Latin American compound libraries","authors":"Alejandro Gómez‐García, Ann‐Kathrin Prinz, Daniel A. Acuña Jiménez, William J. Zamora, Haruna L. Barazorda‐Ccahuana, Miguel Á. Chávez‐Fumagalli, Marilia Valli, Adriano D. Andricopulo, Vanderlan da S. Bolzani, Dionisio A. Olmedo, Pablo N. Solís, Marvin J. Núñez, Johny R. Rodríguez Pérez, Hoover A. Valencia Sánchez, Héctor F. Cortés Hernández, Oscar M. Mosquera Martinez, Oliver Koch, José L. Medina‐Franco","doi":"10.1002/minf.202400052","DOIUrl":"https://doi.org/10.1002/minf.202400052","url":null,"abstract":"Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product‐likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product‐likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small‐molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141504469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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