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Covalent Docking in Drug Discovery: Scope and Limitations

共价键 药物发现 虚拟筛选 化学 对接(动物) 组合化学 共价结合 电泳剂 计算生物学 计算机科学 纳米技术 材料科学 生物化学 有机化学 生物 医学 护理部 催化作用
作者
Andrea Scarpino,György G. Ferenczy,György M. Keserű
出处
期刊:Current Pharmaceutical Design [Bentham Science]
卷期号:26 (44): 5684-5699 被引量:13
标识
DOI:10.2174/1381612824999201105164942
摘要

Drug discovery efforts for new covalent inhibitors have drastically increased in the last few years. The binding mechanism of covalent compounds entails the formation of a chemical bond between their electrophilic warhead group and the protein of interest. The use of moderately reactive warheads targeting nonconserved nucleophilic residues can improve the affinity and selectivity profiles of covalent binders as compared to their non-covalent analogs. Recent advances have also enabled their use as chemical probes to disclose novel and also less tractable targets. Increasing interest in covalent drug discovery prompted the development of new computational tools, including covalent docking methods, that are available to predict the binding mode and affinity of covalent ligands. These tools integrate conventional non-covalent docking and scoring schemes by modeling the newly formed covalent bond and the interactions occurring at the reaction site. In this review, we provide a thorough analysis of state-of-the-art covalent docking programs by highlighting their main features and current limitations. Focusing on the implemented algorithms, we show the differences in handling the formation of the new covalent bond and their relative impact on the prediction. This analysis provides a comprehensive overview of the current technology and suggests future improvements in computer-aided covalent drug design. Finally, discussing successful retrospective and prospective covalent docking-based virtual screening applications, we intend to identify best practices for the drug discovery community.
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