Identification of novel inhibitors of SARS‐CoV‐2 main protease (Mpro) from Withania sp. by molecular docking and molecular dynamics simulation

• Published in: Journal of computational chemistry Vol. 42; no. 26; pp. 1861 - 1872
• Main Authors: Verma, Surjeet, Patel, Chirag N., Chandra, Muktesh
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 05-10-2021; Wiley Subscription Services, Inc
• Subjects: Affinity; Binding energy; Bonding strength; Chymotrypsin; Coronavirus 3C Proteases - antagonists & inhibitors; Coronavirus 3C Proteases - metabolism; COVID-19; COVID-19 Drug Treatment; docking, molecular dynamics simulation; Drug Discovery; Free energy; Herbal medicine; Humans; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Mpro; pharmacokinetics; Protease; Protease Inhibitors - chemistry; Protease Inhibitors - pharmacology; SARS-CoV-2 - drug effects; SARS-CoV-2 - enzymology; SARS‐CoV‐2; Screening; Severe acute respiratory syndrome coronavirus 2; Simulation; Target recognition; Viral diseases; virtual screening, withanolides; Withania - chemistry; COVID-19; pharmacokinetics; SARS-CoV-2; Mpro; docking, molecular dynamics simulation; virtual screening, withanolides
• ISSN: 0192-8651; 1096-987X; 1096-987X
• DOI: 10.1002/jcc.26717

Since December 2019, coronavirus disease (COVID‐19) has claimed the lives of millions of people across the globe. To date, no medicine is available for the responsible virus SARS‐CoV‐2. 3CLpro, that is, 3‐chymotrypsin‐like protease, the main protease (Mpro), has an important role in cleaving pp1a and pp1ab polyproteins. This Mpro serves as an important target in drug designing against COVID‐19. Herein, the study includes the investigation, screening, and identification of potent leads from (Withania sps.), against SARS‐CoV‐2, using virtual screening, molecular docking, and molecular dynamics (MD) simulations. Seventy‐three natural compounds from this important medicinal plant were screened. The Binding affinity was used to identify the most probable target to inhibit the Mpro, compounds 27‐hydroxywithanolide F (W32, −11.5 kcal/mol), withanolide A (W56, −11.4 kcal/mol), and withacoagulin H (W30, −11.1 kcal/mol) showed highest binding energy. Lipinski's rule, followed by drug‐likability and likeness screening, resulted in 36 molecules. Further, MD simulation of 50 ns predicted withacoagulin H possessing strong binding affinity and hydrogen‐bonding interactions with the active site. The binding free energy calculation showed the most negative energy of withacoagulin H (−63.463 KJ/mol) compared to other selected compounds. The study also compared the bonding energy of already reported repurposed and newly synthesized drugs. Further, absorption, distribution, metabolism, and excretion predictions were made to found a good balance of potency. Hence the following screened compounds from Withania sps. could serve as the potential leads for drug development against COVID‐19.