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调节严重急性呼吸综合征冠状病毒2型主要蛋白酶中的质子转移热力学：对催化作用和抑制剂设计的影响

Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design.

作者信息

Zanetti-Polzi Laura, Smith Micholas Dean, Chipot Chris, Gumbart James C, Lynch Diane L, Pavlova Anna, Smith Jeremy C, Daidone Isabella

机构信息

Center S3, CNR Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy.

Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States.

出版信息

ChemRxiv. 2020 Nov 6:13200227. doi: 10.26434/chemrxiv.13200227.v1.

DOI:10.26434/chemrxiv.13200227
PMID:33200115
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7668740/
Abstract

In this comutational work a hybrid quantum mechanics/molecular mechanics approach, the MD-PMM approach, is used to investigate the proton transfer reaction the activates the catalytic activity of SARS-CoV-2 main protease. The proton transfer thermodynamics is investigated for the apo ensyme (i.e., without any bound substrate or inhibitor) and in the presence of a inhibitor, N3, which was previously shown to covalently bind SARS-CoV-2 main protease.

摘要

在这项计算工作中，采用了一种混合量子力学/分子力学方法，即MD-PMM方法，来研究激活SARS-CoV-2主要蛋白酶催化活性的质子转移反应。研究了无辅基酶（即没有任何结合底物或抑制剂）以及存在抑制剂N3时的质子转移热力学，N3此前已被证明能与SARS-CoV-2主要蛋白酶共价结合。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/2b7dc73ab9a0/nihpp-13200227-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/ed90c3bd46b3/nihpp-13200227-f0002.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/8143d487e09c/nihpp-13200227-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/d19fe6d89052/nihpp-13200227-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/2b7dc73ab9a0/nihpp-13200227-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/ed90c3bd46b3/nihpp-13200227-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/0d780cde07ea/nihpp-13200227-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/8143d487e09c/nihpp-13200227-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/d19fe6d89052/nihpp-13200227-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e615/7668740/2b7dc73ab9a0/nihpp-13200227-f0006.jpg

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本文引用的文献

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Chem Sci. 2020 Nov 26;12(4):1513-1527. doi: 10.1039/d0sc04942e. eCollection 2021 Jan 28.
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Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods.运用多尺度方法解析严重急性呼吸综合征冠状病毒2主要蛋白酶机制
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An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 M inhibitor.
一种用于设计不可逆衍生物的自动化流水线鉴定出一种有效的 SARS-CoV-2 M 抑制剂。
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Mechanism of inhibition of SARS-CoV-2 M by peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity.通过量子力学/分子力学模拟解释肽基迈克尔受体对SARS-CoV-2 M的抑制机制以及设计具有可调化学反应性的新衍生物
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Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 M by QM/MM computational methods.通过量子力学/分子力学计算方法揭示新冠病毒M蛋白的蛋白水解分子机制。
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