{"title":"MacGen: A Web Server for Structure-Based Macrocycle Design.","authors":"Zhihan Zhang, Dongliang Ke, Chengshan Jin, Weiyu Zhou, Xiaolin Pan, Yueqing Zhang, Xingyu Wang, Xudong Xiao, Changge Ji","doi":"10.1021/acs.jcim.4c01576","DOIUrl":null,"url":null,"abstract":"<p><p>Macrocyclization is a critical strategy in rational drug design that can offer several advantages, such as enhancing binding affinity, increasing selectivity, and improving cellular permeability. Herein, we introduce MacGen, a web tool devised for structure-based macrocycle design. MacGen identifies exit vector pairs within a ligand that are suitable for cyclization and finds 3D linkers that can align with the geometric arrangement of these pairs to form macrocycles. To aid in the fast acquisition of appropriate linkers, we have built an indexed 3D linker database that includes linkers of various lengths and categories. MacGen provides comprehensive configurable parameters that enable users to obtain preferred linkers, meeting unique requirements in practical ligand design scenarios. We hope MacGen will serve as a handy tool that can rapidly explore potential macrocycle space. The MacGen server is freely accessible at https://macgen.xundrug.cn.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":""},"PeriodicalIF":5.6000,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.4c01576","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0
Abstract
Macrocyclization is a critical strategy in rational drug design that can offer several advantages, such as enhancing binding affinity, increasing selectivity, and improving cellular permeability. Herein, we introduce MacGen, a web tool devised for structure-based macrocycle design. MacGen identifies exit vector pairs within a ligand that are suitable for cyclization and finds 3D linkers that can align with the geometric arrangement of these pairs to form macrocycles. To aid in the fast acquisition of appropriate linkers, we have built an indexed 3D linker database that includes linkers of various lengths and categories. MacGen provides comprehensive configurable parameters that enable users to obtain preferred linkers, meeting unique requirements in practical ligand design scenarios. We hope MacGen will serve as a handy tool that can rapidly explore potential macrocycle space. The MacGen server is freely accessible at https://macgen.xundrug.cn.
期刊介绍：
The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery.
Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field.
As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
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