Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy

对接(动物) 环肽 自动停靠 寻找对接的构象空间 化学 二硫键 蛋白质-配体对接 分子动力学 蛋白质结构 计算生物学 立体化学 计算机科学 组合化学 生物化学 生物 计算化学 虚拟筛选 生物信息学 医学 护理部 基因
作者
Huanyu Tao,Xuejun Zhao,Keqiong Zhang,Ping Lin,Sheng‐You Huang
出处
期刊:Bioinformatics [Oxford University Press]
卷期号:38 (17): 4109-4116 被引量:4
标识
DOI:10.1093/bioinformatics/btac486
摘要

Abstract Motivation Cyclization is a common strategy to enhance the therapeutic potential of peptides. Many cyclic peptide drugs have been approved for clinical use, in which the disulfide-driven cyclic peptide is one of the most prevalent categories. Molecular docking is a powerful computational method to predict the binding modes of molecules. For protein-cyclic peptide docking, a big challenge is considering the flexibility of peptides with conformers constrained by cyclization. Results Integrating our efficient peptide 3D conformation sampling algorithm MODPEP2.0 and knowledge-based scoring function ITScorePP, we have proposed an extended version of our hierarchical peptide docking algorithm, named HPEPDOCK2.0, to predict the binding modes of the peptide cyclized through a disulfide against a protein. Our HPEPDOCK2.0 approach was extensively evaluated on diverse test sets and compared with the state-of-the-art cyclic peptide docking program AutoDock CrankPep (ADCP). On a benchmark dataset of 18 cyclic peptide-protein complexes, HPEPDOCK2.0 obtained a native contact fraction of above 0.5 for 61% of the cases when the top prediction was considered, compared with 39% for ADCP. On a larger test set of 25 cyclic peptide-protein complexes, HPEPDOCK2.0 yielded a success rate of 44% for the top prediction, compared with 20% for ADCP. In addition, HPEPDOCK2.0 was also validated on two other test sets of 10 and 11 complexes with apo and predicted receptor structures, respectively. HPEPDOCK2.0 is computationally efficient and the average running time for docking a cyclic peptide is about 34 min on a single CPU core, compared with 496 min for ADCP. HPEPDOCK2.0 will facilitate the study of the interaction between cyclic peptides and proteins and the development of therapeutic cyclic peptide drugs. Availability and implementation http://huanglab.phys.hust.edu.cn/hpepdock/. Supplementary information Supplementary data are available at Bioinformatics online.
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