Journal of Chemical Information and Modeling 最新文献

{"title":"","authors":"Hemant Goyat, Dalwinder Singh*, Sunaina Paliyal and Shrikant Mantri*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00465","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Regina Ibragimova, Dimitrios Iliadis and Willem Waegeman*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00484","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Hawau Abdulsalam, Mark A. Hix, Livia Philip, Kartikey Singh, Alice R. Walker* and Hien M. Nguyen*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00371","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Zicheng Ma, Chuanliu Fan, Zhicong Wang, Zhenyu Chen, Xiaohan Lin, Yanheng Li, Shihao Feng, Ziqiang Cao*, Jun Zhang* and Yi Qin Gao*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00585","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Le Xiong, Jiahao Xu, Hongbo Yu, Weihua Li, Xinmin Li, Wenxiang Song, Jingwei Zhang, Yun Tang* and Guixia Liu*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c01106","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Ewan R. S. Wallace*, Nathan C. Frey and Joshua A. Rackers*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00586","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Palina Pliushcheuskaya,  and , Georg Künze*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00336","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.","authors":"Oleksandra Herasymenko, Madhushika Silva, Abd Al-Aziz A Abu-Saleh, Ayaz Ahmad, Jesus Alvarado-Huayhuaz, Oscar E A Arce, Roly J Armstrong, Cheryl Arrowsmith, Kelly E Bachta, Hartmut Beck, Denes Berta, Mateusz K Bieniek, Vincent Blay, Albina Bolotokova, Philip E Bourne, Marko Breznik, Peter J Brown, Aaron D G Campbell, Emanuele Carosati, Irene Chau, Daniel J Cole, Ben Cree, Wim Dehaen, Katrin Denzinger, Karina Dos Santos Machado, Ian Dunn, Prasannavenkatesh Durai, Kristina Edfeldt, Aled Edwards, Darren Fayne, Daniel Felfoldi, Kallie Friston, Pegah Ghiabi, Elisa Gibson, Judith Günther, Anders Gunnarsson, Alexander Hillisch, Douglas R Houston, Jan Halborg Jensen, Rachel J Harding, Kate S Harris, Laurent Hoffer, Anders Hogner, Joshua T Horton, Scott Houliston, Judd F Hultquist, Ashley Hutchinson, John J Irwin, Marko Jukič, Shubhangi Kandwal, Andrea Karlova, Vittorio L Katis, Ryan P Kich, Dmitri Kireev, David Koes, Nicole L Inniss, Uta Lessel, Sijie Liu, Peter Loppnau, Wei Lu, Sam Martino, Miles McGibbon, Jens Meiler, Akhila Mettu, Sam Money-Kyrle, Rocco Moretti, Yurii S Moroz, Charuvaka Muvva, Joseph A Newman, Leon Obendorf, Brooks Paige, Amit Pandit, Keunwan Park, Sumera Perveen, Rachael Pirie, Gennady Poda, Mykola Protopopov, Vera Pütter, Federico Ricci, Natalie J Roper, Edina Rosta, Margarita Rzhetskaya, Yogesh Sabnis, Karla J F Satchell, Frederico Schmitt Kremer, Thomas Scott, Almagul Seitova, Casper Steinmann, Valerij Talagayev, Olga O Tarkhanova, Natalie J Tatum, Dakota Treleaven, Adriano Velasque Werhli, W Patrick Walters, Xiaowen Wang, Jude Wells, Geoffrey Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Jixian Zhang, Zheng Zhao, Shuangjia Zheng, Matthieu Schapira","doi":"10.1021/acs.jcim.5c00535","DOIUrl":"10.1021/acs.jcim.5c00535","url":null,"abstract":"<p><p>A critical assessment of computational hit-finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comprised of computational chemists and data scientists used protein structure and data from fragment-screening paired with advanced computational and machine learning methods to each predict up to 100 inhibitory ligands. Across all teams, 1957 compounds were predicted and were subsequently procured from commercial catalogs for biophysical assays. Of these compounds, 0.7% were confirmed to bind to Nsp13 in a surface plasmon resonance assay. The six best-performing computational workflows used fragment growing, active learning, or conventional virtual screening with and without complementary deep-learning scoring functions. Follow-up functional assays resulted in identification of two compound scaffolds that bound Nsp13 with a <i>K</i>_d below 10 μM and inhibited <i>in vitro</i> helicase activity. Overall, CACHE #2 participants were successful in identifying hit compound scaffolds targeting Nsp13, a central component of the coronavirus replication-transcription complex. Computational design strategies recurrently successful across the first two CACHE challenges include linking or growing docked or crystallized fragments and docking small and diverse libraries to train ultrafast machine-learning models. The CACHE #2 competition reveals how crowd-sourcing ligand prediction efforts using a distinct array of approaches followed with critical biophysical assays can result in novel lead compounds to advance drug discovery efforts.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"6884-6898"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332056","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":"","authors":"Wataru Matsuoka*,&nbsp;Ken Hirose,&nbsp;Ren Yamada,&nbsp;Taihei Oki*,&nbsp;Satoru Iwata and Satoshi Maeda*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00815","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Jawad Kamran,&nbsp;Julian Hniopek and Thomas Bocklitz*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"65 13","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00513","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}