Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins.

IF 4.7 Q2 MATERIALS SCIENCE, BIOMATERIALS ACS Applied Bio Materials Pub Date : 2023-05-01 Epub Date: 2023-06-01 DOI:10.2217/fvl-2022-0184

Abdullah R Alanzi, Mohammad K Parvez, Mohammed S Al-Dosari

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引用次数: 1

Abstract

Aim: Structure-based identification of natural compounds against SARS-CoV-2, Delta and Omicron target proteins.

Materials & methods: Several known antiviral natural compounds were subjected to molecular docking and MD simulation against SARS-CoV-2 Mpro, Helicase and Spike, including Delta and Omicron Spikes.

Results: Of the docked ligands, 20 selected for each complex exhibited overall good binding affinities (-7.79 to -5.06 kcal/mol) with acceptable physiochemistry following Lipinski's rule. Finally, two best ligands from each complex upon simulation showed structural stability and compactness.

Conclusion: Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A were identified as potential inhibitors of SARS-CoV-2 Mpro, Helicase and Spike, while Orientin and Obetrioside also showed good binding affinities with Omicron Spike. Catechin and Neridienone A formed stable complexes with Delta Spike.

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基于结构的SARS-CoV-2天然抑制剂及其Delta和Omicron变体蛋白的虚拟鉴定

目的：基于结构鉴定抗严重急性呼吸系统综合征冠状病毒2型、德尔塔和奥密克戎靶蛋白的天然化合物。材料和方法：对几种已知的抗病毒天然化合物进行分子对接和MD模拟，以对抗严重急性呼吸系统综合征冠状病毒2型Mpro、螺旋酶和Spike，包括德尔塔和奥密克戎Spikes。结果：在对接的配体中，为每个复合物选择的20个显示出总体良好的结合亲和力（-7.79至-5.06 kcal/mol），具有可接受的物理化学性质，遵循利平斯基规则。最后，通过模拟，每个配合物中的两个最佳配体显示出结构稳定性和紧密性。结论：槲皮素-3-乙酰葡糖苷、芦丁、山奈酚、儿茶素、Orientin、Obetrioside和Neridienone A被鉴定为严重急性呼吸系统综合征冠状病毒2型Mpro、螺旋酶和Spike的潜在抑制剂，而Orientin和Obetrioide也显示出与奥密克戎Spike的良好结合亲和力。儿茶素和Neridienone A与三角穗形成稳定的复合物。

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来源期刊

ACS Applied Bio Materials Chemistry-Chemistry (all)

CiteScore

9.40

自引率

2.10%

发文量

464

期刊介绍： ACS Applied Bio Materials is an interdisciplinary journal publishing original research covering all aspects of biomaterials and biointerfaces including and beyond the traditional biosensing, biomedical and therapeutic applications. The journal is devoted to reports of new and original experimental and theoretical research of an applied nature that integrates knowledge in the areas of materials, engineering, physics, bioscience, and chemistry into important bio applications. The journal is specifically interested in work that addresses the relationship between structure and function and assesses the stability and degradation of materials under relevant environmental and biological conditions.