Molecular insights to the binding interactions of APNS containing HIV-protease inhibitors against SARS-CoV-2 Mpro: an in silico approach towards drug repurposing

Abstract

SARS-CoV-2 Mpro is one of the most vital enzymes of the new coronavirus-2 (SARS-CoV-2) and is a crucial target for drug discovery. Unfortunately, there is not any potential drugs available to combat the action of SARS-CoV-2 Mpro. Based on the reports HIV-protease inhibitors can be applied against the SARS by targeting the SARS-CoV-1 Mpro, we have chosen few clinically trialed experimental and allophenylnorstatine (APNS) containing HIV-protease inhibitors (JE-2147, JE-533, KNI-227, KNI-272 & KNI-1931), to examine their binding affinities with SARS-CoV-2 Mpro and to assess their potential to check for a possible drug candidate against the protease. Here, we have chosen a methodology to understand the binding mechanism of these five inhibitors to SARS-CoV-2 Mpro by merging molecular docking, molecular dynamics (MD) simulation and MM-PBSA based free energy calculations. Our estimations disclose that JE-2147 is highly effective (ΔG Bind = −28.31 kcal/mol) due to an increased favorable van der Waals (ΔE vdw) interactions and decreased solvation (ΔG solv) energies between the inhibitor and viral protease. JE-2147 shows a higher level of interactions as compared to JE-533 (−6.85 kcal/mol), KNI-227 (−18.36 kcal/mol), KNI-272 (−15.69 kcal/mol) and KNI-1931 (−21.59 kcal/mol) against SARS-CoV-2 Mpro. Binding contributions of important residues (His41, Met49, Cys145, His164, Met165, Glu166, Pro168, Gln189, etc.) from the active site or near the active site regions with ≥1.0 kcal/mol suggest a potent binding of the inhibitors. It is anticipated that the current study of binding interactions of these APNS containing inhibitors can pitch some valuable insights to design the significantly effective anti-SARS-CoV-2 Mpro drugs. Communicated by Ramaswamy H. Sarma