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利用计算方法描绘根多酚对 SARS CoV-2 主要蛋白酶的抑制潜力。

Depicting the inhibitory potential of polyphenols from root against the main protease of SARS CoV-2 using computational approaches.

机构信息

School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.

出版信息

J Biomol Struct Dyn. 2022 Jun;40(9):4110-4121. doi: 10.1080/07391102.2020.1858164. Epub 2020 Dec 9.

Abstract

The pandemic disease COVID-19, caused by SARS CoV-2, has created a global crisis. Presently, researchers across the globe are in a quest to identify/develop drugs or vaccines by targeting different non-structural proteins (Nsps) of SARS CoV-2. One such important drug target is Nsp5/main protease (Mpro) which plays a critical role in the viral replication. This cysteine protease/Mpro of SARS CoV-2 has high sequence similarity with the same protease from SARS CoV-1. Previously, it has been shown experimentally that eight polyphenols derived from the root of show inhibitory effect on the cleavage/catalytic activity of the SARS CoV-1 Mpro. But whether these polyphenols exhibit any inhibitory effect on SARS CoV-2 Mpro is unclear. To explore this possibility, here, we have adopted various computational approaches. Polyphenols that qualified the pharmacological parameters (indigo, sinigrin, hesperetin and daidzein) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected to molecular docking studies. Two of them (sinigrin and hesperetin) were selected by comparing their binding affinities with N3 and lopinavir. Sinigrin and hesperetin interacted with the two most important catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these two Mpro-polyphenol complexes are more stable and experience less conformational fluctuations than Mpro-N3/lopinavir complex. The Mpro-hesperetin complex was more compact and less expanded than Mpro-sinigrin complex. These findings were additionally validated by MM-GBSA analysis. As a whole, our study revealed that these two polyphenols may be potent SARS CoV-2 Mpro inhibitors and may possibly be considered for COVID-19 treatment.

摘要

由 SARS CoV-2 引起的大流行病 COVID-19 造成了全球性危机。目前,全球的研究人员都在努力通过针对 SARS CoV-2 的不同非结构蛋白 (Nsp) 来识别/开发药物或疫苗。其中一个重要的药物靶点是 Nsp5/主要蛋白酶 (Mpro),它在病毒复制中起着关键作用。SARS CoV-2 的这种半胱氨酸蛋白酶/Mpro 与 SARS CoV-1 的相同蛋白酶具有高度的序列相似性。以前的实验表明,从根中提取的 8 种多酚对 SARS CoV-1 Mpro 的切割/催化活性具有抑制作用。但是,这些多酚是否对 SARS CoV-2 Mpro 具有任何抑制作用尚不清楚。为了探索这种可能性,我们在这里采用了各种计算方法。符合药理参数的多酚(靛蓝、芥子油苷、橙皮苷和大豆苷元)和两种著名的 Mpro 抑制剂(N3 和洛匹那韦)进行了分子对接研究。通过比较它们与 N3 和洛匹那韦的结合亲和力,选择了其中两种(芥子油苷和橙皮苷)。芥子油苷和橙皮苷与 Mpro 的两个最重要的催化残基(His41 和 Cys145)相互作用。分子动力学研究进一步表明,这两个 Mpro-多酚复合物比 Mpro-N3/洛匹那韦复合物更稳定,构象波动更小。Mpro-橙皮苷复合物比 Mpro-芥子油苷复合物更紧凑,扩展程度更小。这些发现通过 MM-GBSA 分析得到了进一步验证。总的来说,我们的研究表明,这两种多酚可能是有效的 SARS CoV-2 Mpro 抑制剂,可能会考虑用于 COVID-19 的治疗。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9774/7738210/2b5c78a94bf6/TBSD_A_1858164_UF0001_C.jpg

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