Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease

6Citations
Citations of this article
12Readers
Mendeley users who have this article in their library.

Abstract

To fight against the devastating coronavirus disease 2019 (COVID-19), identifying robust anti-SARS-CoV-2 therapeutics from all possible directions is necessary. To contribute to this effort, we selected a human metabolites database containing waters and lipid-soluble metabolites to screen against the 3-chymotrypsin-like proteases (3CLpro) protein of SARS-CoV-2. The top 8 hits from virtual screening displayed a docking score varying between ~ − 11 and ~ − 14 kcal/mol. Molecular dynamics simulations complement the virtual screening study in conjunction with the molecular mechanics generalized Born surface area (MM/GBSA) scheme. Our analyses revealed that (HMDB0132640) has the best glide docking score, − 14.06 kcal/mol, and MM-GBSA binding free energy, − 18.08 kcal/mol. The other three lead molecules are also selected along with the top molecule through a critical inspection of their pharmacokinetic properties. HMDB0132640 displayed a better binding affinity than the other three compounds (HMDB0127868, HMDB0134119, and HMDB0125821) due to increased favorable contributions from the intermolecular electrostatic and van der Waals interactions. Further, we have investigated the ligand-induced structural dynamics of the main protease. Overall, we have identified new compounds that can serve as potential leads for developing novel antiviral drugs against SARS-CoV-2 and elucidated molecular mechanisms of their binding to the main protease. Graphical abstract: Identification of probable hits from human metabolites against SARS-CoV-2 using integrated computational approaches-Missed against MS[Figure not available: see fulltext.].

References Powered by Scopus

Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems

25116Citations
N/AReaders
Get full text

Development and testing of a general Amber force field

15074Citations
N/AReaders
Get full text

A new coronavirus associated with human respiratory disease in China

8314Citations
N/AReaders
Get full text

Cited by Powered by Scopus

Plant derived active compounds of ayurvedic neurological formulation, Saraswatharishta as a potential dual leucine zipper kinase inhibitor: an in-silico study

5Citations
N/AReaders
Get full text

Exploring the Binding Effects of Natural Products and Antihypertensive Drugs on SARS-CoV-2: An In Silico Investigation of Main Protease and Spike Protein

5Citations
N/AReaders
Get full text

4″-Alkyl EGCG Derivatives Induce Cytoprotective Autophagy Response by Inhibiting EGFR in Glioblastoma Cells

2Citations
N/AReaders
Get full text

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Cite

CITATION STYLE

APA

Roy, R., Sk, M. F., Tanwar, O., & Kar, P. (2023). Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease. Molecular Diversity, 27(4), 1587–1602. https://doi.org/10.1007/s11030-022-10513-6

Readers' Seniority

Tooltip

PhD / Post grad / Masters / Doc 3

38%

Lecturer / Post doc 2

25%

Researcher 2

25%

Professor / Associate Prof. 1

13%

Readers' Discipline

Tooltip

Chemistry 3

43%

Biochemistry, Genetics and Molecular Bi... 2

29%

Chemical Engineering 1

14%

Pharmacology, Toxicology and Pharmaceut... 1

14%

Article Metrics

Tooltip
Mentions
News Mentions: 1
Social Media
Shares, Likes & Comments: 15

Save time finding and organizing research with Mendeley

Sign up for free