Abstract
SARS-CoV-2 or Coronavirus disease 19 (COVID-19) is a rapidly spreading, highly contagious, and sometimes fatal disease for which drug discovery and vaccine development are critical. SARS-CoV-2 papain-like protease (PL pro ) was used to virtually screen 1697 clinical FDA-approved drugs. Among the top results expected to bind with SARS-CoV-2 PL pro strongly were three cell protectives and antioxidants (NAD+, quercitrin, and oxiglutatione), three antivirals (ritonavir, moroxydine, and zanamivir), two antimicrobials (doripenem and sulfaguanidine), two anticancer drugs, three benzimidazole anthelmintics, one antacid (famotidine), three anti-hypertensive ACE receptor blockers (candesartan, losartan, and valsartan) and other miscellaneous systemically or topically acting drugs. The binding patterns of these drugs were superior to the previously identified SARS CoV PL pro inhibitor, 6-mercaptopurine (6-MP), suggesting a potential for repurposing these drugs to treat COVID-19. The objective of drug repurposing is the rapid relocation of safe and approved drugs by bypassing the lengthy pharmacokinetic, toxicity, and preclinical phases. The ten drugs with the highest estimated docking scores with favorable pharmacokinetics were subjected to molecular dynamics (MD) simulations followed by molecular mechanics/generalized Born surface area (MM/GBSA) binding energy calculations. Phenformin, quercetin, and ritonavir all demonstrated prospective binding affinities for COVID-19 PL pro over 50 ns MD simulations, with binding energy values of -56.6, -40.9, and -37.6 kcal/mol, respectively. Energetic and structural analyses showed phenformin was more stable than quercetin and ritonavir. The list of the drugs provided herein constitutes a primer for clinical application in COVID-19 patients and guidance for further antiviral studies.Communicated by Ramaswamy H. Sarma.
Keywords: COVID-19; PLpro; SARS-CoV-2; molecular dynamics; protease.
【저자키워드】 COVID-19, SARS-CoV-2, molecular dynamics, Protease., PLPro, 【초록키워드】 coronavirus disease, Drug repurposing, Vaccine development, coronavirus, Drug discovery, Famotidine, Antiviral, Ritonavir, drugs, quercetin, Toxicity, drug, valsartan, molecular dynamics, protease, FDA-approved drugs, antioxidant, antimicrobial, anticancer drugs, MD simulations, binding affinity, binding energy, Papain-like protease, antioxidants, receptor, molecular, coronavirus disease 19, PLPro, inhibitor, Critical, Guidance, COVID-19 patients, Protective, pharmacokinetic, ACE, losartan, COVID-19 patient, Safe, followed by, binding affinities, surface area, candesartan, approved drug, NAD+, Phenformin, doripenem, SARS CoV, 6-mercaptopurine, mercaptopurine, Papain, treat, list, primer, blocker, docking score, contagious, fatal disease, Antacid, binding patterns, moroxydine, Cell, benzimidazole, oxiglutatione, quercitrin, sulfaguanidine, zanamivir, highest, was used, provided, demonstrated, analysis, expected, systemically, acting, binding pattern, bypassing, 【제목키워드】 antivirals, Antibiotics, repurposing, Papain-like protease, Protective, Cell,