In-silico  investigation of phytochemicals from  Asparagus racemosus  as plausible antiviral agent in COVID-19

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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

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A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou, Xing-Lou Yang, Xian-Guang Wang … (2020)

Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1–4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5–7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.

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Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV

Xiuyuan Ou, Yan Liu, Xiaobo Lei … (2020)

Since 2002, beta coronaviruses (CoV) have caused three zoonotic outbreaks, SARS-CoV in 2002–2003, MERS-CoV in 2012, and the newly emerged SARS-CoV-2 in late 2019. However, little is currently known about the biology of SARS-CoV-2. Here, using SARS-CoV-2 S protein pseudovirus system, we confirm that human angiotensin converting enzyme 2 (hACE2) is the receptor for SARS-CoV-2, find that SARS-CoV-2 enters 293/hACE2 cells mainly through endocytosis, that PIKfyve, TPC2, and cathepsin L are critical for entry, and that SARS-CoV-2 S protein is less stable than SARS-CoV S. Polyclonal anti-SARS S1 antibodies T62 inhibit entry of SARS-CoV S but not SARS-CoV-2 S pseudovirions. Further studies using recovered SARS and COVID-19 patients’ sera show limited cross-neutralization, suggesting that recovery from one infection might not protect against the other. Our results present potential targets for development of drugs and vaccines for SARS-CoV-2.

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Identification of natural compounds with antiviral activities against SARS-associated coronavirus

Shi-you Li, Cong Chen, Hai-qing ZHANG … (2005)

More than 200 Chinese medicinal herb extracts were screened for antiviral activities against Severe Acute Respiratory Syndrome-associated coronavirus (SARS-CoV) using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt (MTS) assay for virus-induced cytopathic effect (CPE). Four of these extracts showed moderate to potent antiviral activities against SARS-CoV with 50% effective concentration (EC50) ranging from 2.4 ± 0.2 to 88.2 ± 7.7 μg/ml. Out of the four, Lycoris radiata was most potent. To identify the active component, L. radiata extract was subjected to further fractionation, purification, and CPE/MTS assays. This process led to the identification of a single substance lycorine as an anti-SARS-CoV component with an EC50 value of 15.7 ± 1.2 nM. This compound has a CC50 value of 14980.0 ± 912.0 nM in cytotoxicity assay and a selective index (SI) greater than 900. The results suggested that four herbal extracts and the compound lycorine are candidates for the development of new anti-SARS-CoV drugs in the treatment of SARS.

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Author and article information

Journal

Journal ID (nlm-ta): J Biomol Struct Dyn

Journal ID (iso-abbrev): J. Biomol. Struct. Dyn

Journal ID (publisher-id): TBSD

Journal ID (publisher-id): tbsd20

Title: Journal of Biomolecular Structure & Dynamics

Publisher: Taylor & Francis

ISSN (Print): 0739-1102

ISSN (Electronic): 1538-0254

Publication date Collection: 2020

Publication date (Electronic): 24 June 2020

Pages: 1-15

Affiliations

[a ]School of Pharmacy, University of East Anglia , Norwich, UK;

[b ]Department of Pharmaceutical Sciences, Mohanlal Shukhadia University , Udaipur, India;

[c ]Sinhgad Technical Education Society’s, Smt. Kashibai Navale College of Pharmacy , Pune, India;

[d ]Department of Pharmaceutical Sciences, R.T.M. University , Nagpur, India;

[e ]Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University , Dibrugarh, India;

[f ]PES’s Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa University , Goa, India;

[g ]Regional Ayurveda Research Institute for Drug Development , Aamkho, Gwalior, India;

[h ]Department of Pharmacognosy, Goa College of Pharmacy, Goa University , Goa, India

Author notes

Supplemental data for this article can be accessed online at https://doi.org/10.1080/07391102.2020.1784289.

CONTACT Shailendra S. Gurav shailendra.gurav@ 123456nic.in Goa College of Pharmacy, Department of Pharmacognosy and Phytochemistry, Goa University , Goa 403 001, India