Molecular Modelling, Synthesis, and In-Vitro Assay to Identify Potential Antiviral Peptides Targeting the 3-Chymotrypsin-Like Protease of SARS-CoV-2

Chymotrypsin-like cysteine protease, also known as main protease (3CLpro/Mpro) of SARS-CoV-2, is highly conserved among various coronaviruses. Hence, therapeutics targeting the main protease are likely to show broad-spectrum activity. Peptides are a promising avenue for antiviral therapeutics as they are capable of offering a sustainable strategy to combat infectious diseases. In this work, we screened clinically proven antimicrobial peptides against the cysteine protease of SARS-CoV-2 using state-of-the-art cheminformatics methods including docking and dynamics simulation, statistical analysis, and structure-activity relationship studies. From the molecular docking investigation, three peptides were chosen which showed the high binding affinities [DRAMP18152 (∆G = − 56.56 kcal/mol), DRAMP18160 (∆G = − 59.9 kcal/mol), DRAMP20773 (∆G = − 56.2 kcal/mol)] and active interactions with His41 and Cys145 residues. Molecular dynamics simulation was employed over 250 ns on these three peptide-Mpro complexes. The MD simulation results reflect the high inhibitory potential of DRAMP18152, DRAMP18160, and DRAMP20773 against Mpro. These three peptides were synthesized using standard solid phase peptide synthesis. Purity (> 90%) and identity of the peptides were established by liquid chromatography and electrospray ionization-mass spectrometry. FRET-based protease assay was conducted for these three top candidates in which only DRAMP18160 showed the inhibition efficiency with an estimated 50% inhibitory concentrations of 59 µM with low cytotoxicity. These results suggest that pursuing further development of peptide-based inhibitors for antiviral applications may be a fruitful endeavor and yield novel antiviral therapeutics. Graphical Abstract: [Figure not available: see fulltext.]