In-silico investigation of phytochemicals from Asparagus racemosus as plausible antiviral agent in COVID-19,Journal of Biomolecular Structure and Dynamics

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In-silico investigation of phytochemicals from Asparagus racemosus as plausible antiviral agent in COVID-19
Journal of Biomolecular Structure and Dynamics ( IF 4.4 ) Pub Date : 2020-06-24 , DOI: 10.1080/07391102.2020.1784289
Rupesh V Chikhale ₁ , Saurabh K Sinha ₂ , Rajesh B Patil ₃ , Satyendra K Prasad ₄ , Anshul Shakya ₅ , Nilambari Gurav ₆ , Rupali Prasad ₄ , Suhas R Dhaswadikar ₄ , Manish Wanjari ₇ , Shailendra S Gurav ₈

Affiliation

Abstract

COVID-19 has ravaged the world and is the greatest of pandemics in human history, in the absence of treatment or vaccine the mortality and morbidity rates are very high. The present investigation was undertaken to screen and identify the potent leads from the Indian Ayurvedic herb, Asparagus racemosus (Willd.) against SARS-CoV-2 using molecular docking and dynamics studies. The docking analysis was performed on the Glide module of Schrödinger suite on two different proteins from SARS-CoV-2 viz. NSP15 Endoribonuclease and spike receptor-binding domain. Asparoside-C, Asparoside-D and Asparoside -F were found to be most effective against both the proteins as confirmed through their docking score and affinity. Further, the 100 ns molecular dynamics study also confirmed the potential of these compounds from reasonably lower root mean square deviations and better stabilization of Asparoside-C and Asparoside-F in spike receptor-binding domain and NSP15 Endoribonuclease respectively. MM-GBSA based binding free energy calculations also suggest the most favourable binding affinities of Asparoside-C and Asparoside-F with binding energies of −62.61 and −55.19 Kcal/mol respectively with spike receptor-binding domain and NSP15 Endoribonuclease.

Highlights
Asparagus racemosus have antiviral potential
Phytochemicals of Shatavari showed promising in-silico docking and MD results
Asparaoside-C and Asparoside-F has good binding with target proteins
Asparagus racemosus holds promise as SARS-COV-2 (S) and (N) proteins inhibitor

Communicated by Ramaswamy H. Sarma

中文翻译：

来自总状芦笋的植物化学物质作为 COVID-19 中合理的抗病毒剂的计算机研究

摘要

COVID-19 肆虐世界，是人类历史上最严重的流行病，在没有治疗或疫苗的情况下，死亡率和发病率非常高。目前的调查是为了筛选和鉴定来自印度阿育吠陀草本芦笋的有效铅(Willd.) 使用分子对接和动力学研究对抗 SARS-CoV-2。对接分析是在 Schrödinger 套件的 Glide 模块上对来自 SARS-CoV-2 即的两种不同蛋白质进行的。NSP15 内切核糖核酸酶和刺突受体结合域。Asparoside-C、Asparoside-D 和 Asparoside-F 被发现对这两种蛋白质最有效，这通过它们的对接评分和亲和力得到证实。此外，100 ns 分子动力学研究还证实了这些化合物的潜力，这些化合物的均方根偏差合理较低，并且天冬氨酸-C 和天冬氨酸-F 分别在刺突受体结合域和 NSP15 内切核糖核酸酶中具有更好的稳定性。基于 MM-GBSA 的结合自由能计算还表明天冬氨酸苷-C 和天冬氨酸苷-F 的最有利的结合亲和力，结合能为 -62。