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Molecules. 2019 Jun 10;24(11). pii: E2183. doi: 10.3390/molecules24112183.

Systematic Studies on the Protocol and Criteria for Selecting a Covalent Docking Tool.

Author information

1
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China. wench7@mail2.sysu.edu.cn.
2
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China. yanx28@mail.sysu.edu.cn.
3
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China. guqiong@mail.sysu.edu.cn.
4
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China. jiewen.du@xtalpi.com.
5
National Supercomputer Center in Guangzhou & School of Data and Computer Science, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China. wudi27@mail.sysu.edu.cn.
6
National Supercomputer Center in Guangzhou & School of Data and Computer Science, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China. yutong.lu@nscc-gz.cn.
7
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China. zhuihao@mail.sysu.edu.cn.
8
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China. junxu@biochemomes.com.

Abstract

With the resurgence of drugs with covalent binding mechanisms, much attention has been paid to docking methods for the discovery of targeted covalent inhibitors. The existence of many available covalent docking tools has inspired development of a systematic and objective procedure and criteria with which to evaluate these programs. In order to find a tool appropriate to studies of a covalently binding system, protocols and criteria are proposed for protein-ligand covalent docking studies. This paper consists of three sections: (1) curating a standard data set to evaluate covalent docking tools objectively; (2) establishing criteria to measure the performance of a tool applied for docking ligands into a complex system; and (3) creating a protocol to evaluate and select covalent binding tools. The protocols were applied to evaluate four covalent docking tools (MOE, GOLD, CovDock, and ICM-Pro) and parameters affecting covalent docking performance were investigated.

KEYWORDS:

chemoinformatics; covalent docking; drug design; molecular modeling; protein binding

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