Computational guided drug repurposing for targeting 2′-O-ribose methyltransferase of SARS-CoV-2

• Published in: Life sciences (1973) Vol. 259; p. 118169
• Main Authors: Sharma, Kedar, Morla, Sudhir, Goyal, Arun, Kumar, Sachin
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Inc 15.10.2020; Elsevier BV
• Subjects: 2-O-methyltransferase; active sites; Amino acid sequence; amino acid sequences; Antiviral agents; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Betacoronavirus - drug effects; Betacoronavirus - enzymology; Cardiac glycosides; class; Computational Biology - methods; Computer applications; Coronavirus Infections - drug therapy; Coronavirus Infections - virology; Coronaviruses; COVID-19; Drug Repositioning - methods; Drugs; Emergency medical services; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; family; FDA approved drugs; genome; Genomes; Global health; Glycosides; Humans; Immune system; Immunosuppressive agents; medicine; Methylation; Methylation - drug effects; Methyltransferase; methyltransferases; Methyltransferases - antagonists & inhibitors; Methyltransferases - chemistry; Methyltransferases - metabolism; Methyltransferases - ultrastructure; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Molecular Targeted Therapy; pandemic; Pandemics; Pneumonia, Viral - drug therapy; Pneumonia, Viral - virology; Protein folding; Protein structure; Proteins; Public health; Quality assessment; Quality control; Repurposing; Ribose; RNA; SARS-CoV-2; Sequence Homology, Amino Acid; Severe acute respiratory syndrome coronavirus 2; Simulation analysis; simulation models; Steroid hormones; Steroids; Viral diseases; Virtual screening; Virtual screening; SARS-CoV-2; Repurposing; 2-O-methyltransferase; FDA approved drugs
• ISSN: 0024-3205; 1879-0631; 1879-0631
• DOI: 10.1016/j.lfs.2020.118169

The recent outbreak of pandemic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led the world towards a global health emergency. Currently, no proper medicine or effective treatment strategies are available; therefore, repurposing of FDA approved drugs may play an important role in overcoming the situation. The SARS-CoV-2 genome encodes for 2-O-methyltransferase (2′OMTase), which plays a key role in methylation of viral RNA for evading host immune system. In the present study, the protein sequence of 2′OMTase of SARS-CoV-2 was analyzed, and its structure was modeled by a comparative modeling approach and validated. The library of 3000 drugs was screened against the active site of 2′OMTase followed by re-docking analysis. The apo and ligand-bound 2′OMTase were further validated and analyzed by using molecular dynamics simulation. The modeled structure displayed the conserved characteristic fold of class I MTase family. The quality assessment analysis by SAVES server reveals that the modeled structure follows protein folding rules and of excellent quality. The docking analysis displayed that the active site of 2′OMTase accommodates an array of drugs, which includes alkaloids, antivirals, cardiac glycosides, anticancer, steroids, and other drugs. The redocking and MD simulation analysis of the best 5 FDA approved drugs reveals that these drugs form a stable conformation with the 2′OMTase. The results suggested that these drugs may be used as potential inhibitors for 2′OMTase for combating the SARS-CoV-2 infection.