SARS-CoV-2 25 肽结合物的计算设计。

Computational Design of 25-mer Peptide Binders of SARS-CoV-2.

机构信息

Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.

Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.

出版信息

J Phys Chem B. 2020 Dec 3;124(48):10930-10942. doi: 10.1021/acs.jpcb.0c07890. Epub 2020 Nov 17.

Abstract

SARS-CoV-2 is the novel coronavirus causing the COVID-19 pandemic. To enter human cells, the receptor-binding domain (RBD) of the S1 subunit of SARS-CoV-2 (SARS-CoV-2-RBD) initially binds to the peptidase domain of angiotensin-converting enzyme 2 receptor (ACE2-PD). Using peptides to inhibit SARS-CoV-2-RBD binding to ACE2 is a potential therapeutic solution for COVID-19. A previous study identified a 23-mer peptide (SBP1) that bound to SARS-CoV-2-RBD with comparable to ACE2. We employed computational protein design and molecular dynamics (MD) to design SARS-CoV-2-RBD 25-mer peptide binders (SPB25) with better predicted binding affinity than SBP1. Using residues 21-45 of the α1 helix of ACE2-PD as the template, our strategy is employing Rosetta to enhance SPB25 binding affinity to SARS-CoV-2-RBD and avoid disrupting existing favorable interactions by using residues that have not been reported to form favorable interactions with SARS-CoV-2-RBD as designed positions. Designed peptides with better predicted binding affinities, by Rosetta, than SPB25 were subjected to MD validation. The MD results show that five designed peptides (SPB25, SPB25, SPB25, SPB25, and SPB25) have better predicted binding affinities, by the MM-GBSA method, than SPB25 and SBP1. This study developed an approach to design SARS-CoV-2-RBD peptide binders, and these peptides may be promising candidates as potential SARS-CoV-2 inhibitors.

摘要

SARS-CoV-2 是导致 COVID-19 大流行的新型冠状病毒。SARS-CoV-2 刺突蛋白(S)亚基的受体结合结构域(RBD)最初与血管紧张素转换酶 2 受体(ACE2)的肽酶结构域(PD)结合,从而使病毒进入人体细胞。使用肽类抑制 SARS-CoV-2-RBD 与 ACE2 的结合是治疗 COVID-19 的一种潜在方法。先前的研究确定了一种与 SARS-CoV-2-RBD 结合的 23 肽(SBP1),其与 ACE2 的结合能力相当。我们采用计算蛋白质设计和分子动力学(MD)方法,设计了结合亲和力优于 SBP1 的 SARS-CoV-2-RBD 25 肽结合物(SPB25)。我们的策略是使用 ACE2-PD 的α1 螺旋残基 21-45 作为模板,利用 Rosetta 增强 SPB25 与 SARS-CoV-2-RBD 的结合亲和力,并通过使用未报道与 SARS-CoV-2-RBD 形成有利相互作用的残基作为设计位置,避免破坏现有的有利相互作用。使用 Rosetta 设计的具有更好预测结合亲和力的肽进行 MD 验证。MD 结果表明,与 SPB25 相比,有五个设计的肽(SPB25、SPB25、SPB25、SPB25 和 SPB25)通过 MM-GBSA 方法具有更好的预测结合亲和力。本研究开发了一种设计 SARS-CoV-2-RBD 肽结合物的方法,这些肽可能是作为潜在 SARS-CoV-2 抑制剂的有前途的候选物。

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