Ligand-based virtual screening to discover potential inhibitors of SARS-CoV-2 main protease

Abstract

The main protease (M^pro, also known as 3CL^pro), a pivotal enzyme of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been considered a prime target for drug development due to its crucial role in viral replication and transcription. Importantly, a high degree of conservation in more than 13 million SARS-CoV-2 sequences affords M^pro as a promising target for antiviral therapy to impede the genetic evolution of SARS-CoV-2. In this work, ∼16 million compounds from various small molecule databases were screened using ligand-based virtual screening (LBVS) with boceprevir as the reference compound to identify new small molecule inhibitors of M^pro. Boceprevir [hepatitis C virus (HCV) drug] has been repurposed as a drug candidate against M^pro activity (IC₅₀ = 4.13 ± 0.61 μM). The lead compounds exhibiting higher binding affinities (−9.9 to −8.0 kcal mol⁻¹) than boceprevir (−7.5 kcal mol⁻¹) were identified from a library of 850 compounds using molecular docking. Furthermore, molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) analysis depicted ChEMBL144205 (C3), ZINC000091755358 (C5), and ZINC000092066113 (C9) with binding affinities of −65.2 ± 6.5, −66.1 ± 7.1, and −67.3 ± 5.8 kcal mol⁻¹, respectively, as high-affinity binders to M^pro. The identified compounds displayed a favourable drug-likeness profile without violating Lipinski's rule of five. Molecular dynamics (MD) simulations revealed the higher structural stability and reduced residue-level fluctuations in M^pro upon binding of C3, C5, and C9 as compared to apo–M^pro and M^pro–boceprevir. Notably, conformational clustering and FEL analyses depicted hydrogen bond interactions of C3 with Thr26, oxyanion hole residues (Asn142 and Gly143), the catalytic residue (Cys145), and Glu166 of M^pro, suggesting its strong binding affinity and potential inhibitory effect. The integrated computational methodology employed in this work identified promising lead compounds against M^pro activity, which warrants further experimental validation to develop them as antiviral agents against SARS-CoV-2.