Abstract
The 2019-novel coronavirus (nCoV) has caused a global health crisis by causing coronavirus disease-19 (COVID-19) pandemic in the human population. The unavailability of specific vaccines and anti-viral drug for nCoV, science demands sincere efforts in the field of drug design and discovery for COVID-19. The novel coronavirus main protease (SARS-CoV-2 Mpro) play a crucial role during the disease propagation, and hence SARS-CoV-2 Mpro represents as a drug target for the drug discovery. Herein, we have applied bioinformatics approach for screening of chemical compounds from Indian spices as potent inhibitors of SARS-CoV-2 main protease (PDBID: 6Y84). The structure files of Indian spices chemical compounds were taken from PubChem database or Zinc database and screened by molecular docking, by using AutoDock-4.2, MGLTools-1.5.6, Raccoon virtual screening tools. Top 04 hits based on their highest binding affinity were analyzed. Carnosol exhibited highest binding affinity -8.2 Kcal/mol and strong and stable interactions with the amino acid residues present on the active site of SARS-CoV-2 Mpro. Arjunglucoside-I (-7.88 Kcal/mol) and Rosmanol (-7.99 Kcal/mol) also showed a strong and stable binding affinity with favourable ADME properties. These compounds on MD simulations for 50 ns shows strong hydrogen-bonding interactions with the protein active site and remains stable inside the active site. Our virtual screening results suggest that these small chemical molecules can be used as potential inhibitors against SARS-CoV-2 Mpro and may have an anti-viral effect on nCoV. However, further validation and investigation of these inhibitors against SARS-CoV-2 main protease are needed to claim their candidacy for clinical trials.Communicated by Ramaswamy H. Sarma.
Keywords: ADME; Novel coronavirus (nCoV); bioinformatics; corona virus disease-2019 (COVID-19); molecular docking; novel coronavirus main protease (SARS-CoV-2 Mpro).
【저자키워드】 bioinformatics, molecular docking, ADME, Novel coronavirus (nCoV), corona virus disease-2019 (COVID-19), novel coronavirus main protease (SARS-CoV-2 Mpro)., 【초록키워드】 COVID-19, coronavirus disease, Zinc, Corona virus, Vaccine, coronavirus, pandemic, Drug discovery, drug design, bioinformatics, molecular docking, clinical trials, Virtual screening, protease, virus, database, SARS-CoV-2 main protease, MD simulations, ZINC database, ADME, binding affinity, MD simulation, Health crisis, Novel coronavirus, Anti-viral, MPro, SARS-CoV-2 Mpro, Protein, Health, Coronavirus disease-19, drug target, molecular, novel, inhibitor, anti-viral drug, Amino acid, AutoDock, Interaction, chemical compounds, human population, active site, hydrogen, Carnosol, inhibitors of SARS-CoV-2, highest binding affinity, Compound, effort, nCoV, amino acid residues, these compounds, unavailability, PubChem database, amino acid residue, approach, raccoon, analyzed, caused, the disease, applied, screened, exhibited, can be used, hydrogen-bonding interaction, 【제목키워드】 identification, Compound,