通过分子对接、分子动力学模拟和结合自由能计算剖析泛素特异性蛋白酶 7 (USP7) 对映体抑制剂的立体选择性。

IF 3.9 2区 化学 Q2 CHEMISTRY, APPLIED
Yusheng Zhang, Wenwen Dou, Ziqi Zhao, Guozhen Li, Chunlong Li, Xiangyu Chen, Linkai Mou
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引用次数: 0

摘要

泛素特异性蛋白酶 7(USP7)是一种去泛素化酶,是包括前列腺癌和肝癌在内的多种癌症的诱人治疗靶点。将抑制剂的立体化学中心从 S 转变为 R(S-ALM → R-ALM34)可显著提高 USP7 的抑制活性。然而,对映体抑制剂对 USP7 的立体选择性的分子机制仍不清楚。本研究采用分子对接、分子动力学(MD)模拟、分子力学/广义伯恩表面积(MM/GBSA)计算和自由能图谱等方法来揭开这一谜团。MD 模拟显示,与 R-ALM34 对应物相比,S-ALM34 表现出高度的构象灵活性,S-ALM34 结合导致 USP7 的域内运动增强,尤其是 BL1 和 BL2 环以及两个螺旋 α4 和 α5。MM/GBSA 计算表明,R-ALM34 与 USP7 的结合力比 S-ALM34 强 - 4.99 kcal/mol,与实验数据观察到的趋势相似。进一步进行了 MM/GBSA 自由能分解,以区分配体-残基谱。这些分析不仅确定了与 R-ALM34 相互作用的热点残基,还揭示了来自 F409、K420、H456 和 Y514 的疏水相互作用在 R-ALM34 与 USP7 的结合中起着主要的决定作用。这一结果有望揭示能量基础和构象动力学信息,从而有助于设计针对 USP7 的更强效、更具选择性的抑制剂。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Stereo-selectivity of enantiomeric inhibitors to ubiquitin-specific protease 7 (USP7) dissected by molecular docking, molecular dynamics simulations, and binding free energy calculations.

The ubiquitin-specific protease 7 (USP7), as a member of deubiquitination enzymes, represents an attractive therapeutic target for various cancers, including prostate cancer and liver cancer. The change of the inhibitor stereocenter from the S to R stereochemistry (S-ALM → R-ALM34) markedly improved USP7 inhibitory activity. However, the molecular mechanism for the stereo-selectivity of enantiomeric inhibitors to USP7 is still unclear. In this work, molecular docking, molecular dynamics (MD) simulations, molecular mechanics/Generalized-Born surface area (MM/GBSA) calculations, and free energy landscapes were performed to address this mystery. MD simulations revealed that S-ALM34 showed a high degree of conformational flexibility compared to the R-ALM34 counterpart, and S-ALM34 binding led to the enhanced intradomain motions of USP7, especially the BL1 and BL2 loops and the two helices α4 and α5. MM/GBSA calculations showed that the binding strength of R-ALM34 to USP7 was stronger than that of S-ALM34 by - 4.99 kcal/mol, a similar trend observed by experimental data. MM/GBSA free energy decomposition was further performed to differentiate the ligand-residue spectrum. These analyses not only identified the hotspot residues interacting with R-ALM34, but also revealed that the hydrophobic interactions from F409, K420, H456, and Y514 play the major determinants in the binding of R-ALM34 to USP7. This result is anticipated to shed light on energetic basis and conformational dynamics information to aid in the design of more potent and selective inhibitors targeting USP7.

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来源期刊
Molecular Diversity
Molecular Diversity 化学-化学综合
CiteScore
7.30
自引率
7.90%
发文量
219
审稿时长
2.7 months
期刊介绍: Molecular Diversity is a new publication forum for the rapid publication of refereed papers dedicated to describing the development, application and theory of molecular diversity and combinatorial chemistry in basic and applied research and drug discovery. The journal publishes both short and full papers, perspectives, news and reviews dealing with all aspects of the generation of molecular diversity, application of diversity for screening against alternative targets of all types (biological, biophysical, technological), analysis of results obtained and their application in various scientific disciplines/approaches including: combinatorial chemistry and parallel synthesis; small molecule libraries; microwave synthesis; flow synthesis; fluorous synthesis; diversity oriented synthesis (DOS); nanoreactors; click chemistry; multiplex technologies; fragment- and ligand-based design; structure/function/SAR; computational chemistry and molecular design; chemoinformatics; screening techniques and screening interfaces; analytical and purification methods; robotics, automation and miniaturization; targeted libraries; display libraries; peptides and peptoids; proteins; oligonucleotides; carbohydrates; natural diversity; new methods of library formulation and deconvolution; directed evolution, origin of life and recombination; search techniques, landscapes, random chemistry and more;
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