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水果菠萝蛋白酶衍生肽可能抑制 SARS-CoV-2 变体与 hACE2 的结合:一种基于计算药理学的方法。

Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach.

机构信息

Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia.

The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia.

出版信息

Molecules. 2022 Jan 1;27(1):260. doi: 10.3390/molecules27010260.

Abstract

Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.

摘要

进入细胞之前,SARS-CoV-2 刺突糖蛋白受体结合域(RBD)与人类血管紧张素转化酶 2(hACE2)受体结合。因此,该 RBD 是开发抗病毒药物的关键靶点。最近的研究发现,RBD 中发生突变的 SARS-CoV-2 变体已在全球范围内传播。本计算机研究的目的是确定一种源自水果菠萝蛋白酶的肽,即 DYGAVNEVK,通过靶向 RBD 内的 hACE 结合位点,抑制各种 SARS-CoV-2 变体进入人体细胞。分子对接分析表明,DYGAVNEVK 与几个关键的 RBD 结合残基相互作用,这些残基负责 RBD 与 hACE2 的黏附。此外,通过均方根偏差(RMSD)、回转半径(Rg)和均方根波动(RMSF)分析以及自由结合能计算,100ns MD 模拟揭示了 DYGAVNEVK 与源自轨迹的 RBD 变体之间的稳定相互作用。总的来说,我们的计算结果表明,DYGAVNEVK 值得进一步研究,作为预防 SARS-CoV-2 的候选药物,因为它与 SARS-CoV-2 变体的 RBD 相互作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0031/8746556/2ab173cadd87/molecules-27-00260-g001.jpg

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