Effects of π–π Stapling on the Inhibitory Activity of Antimicrobial Peptides Against SARS-CoV-2 Mpro
Primary Investigator (PI) Name
Mohammad Halim
Department
CSM – Chemistry and Biochemistry
Abstract
Peptide-based therapeutics offer high potency and site selectivity but are often limited by poor bioavailability due to enzymatic degradation and short circulating half-lives. To address these challenges, peptide analogues are typically designed with enhanced structural stability through cyclization or the incorporation of bulky hydrocarbons. However, π–π stapling, exploits side-chain interactions by substituting specific amino acids with α-methyl-L-phenylalanine residues and prevents the need for additional covalent bonds. The methyl group at the α-carbon restricts side-chain flexibility, promoting π–π interactions between aromatic rings and stabilizing α-helical conformations. This increased conformational rigidity enhances the overall stability of the peptide backbone. In this study, the antimicrobial peptides TLPL3 and DRAMP03064 were selected for their reported inhibitory activity against the main protease (Mpro) of SARS-CoV-2, a positive-sense RNA virus composed of 16 nonstructural, 4 structural, and 9 accessory proteins. Viral replication relies on Mpro, which cleaves nonstructural polyproteins into functional units essential for replication and transcription. All peptides were synthesized using automated Fmoc solid-phase peptide synthesis (SPPS) and cleaved from the resin with 95% trifluoroacetic acid. Inhibitory activity was assessed using a selected ion monitoring (SIM)-based LC-MS assay to determine the half-maximal inhibitory concentration (IC₅₀). Results revealed markedly reduced inhibition efficiencies in the stapled analogues compared to their linear counterparts, with DRAMP03064 exhibiting the most significant decrease in activity (IC₅₀ shifting from 430 nM to 38 nM).
Disciplines
Amino Acids, Peptides, and Proteins | Biochemistry | Enzymes and Coenzymes
Effects of π–π Stapling on the Inhibitory Activity of Antimicrobial Peptides Against SARS-CoV-2 Mpro
Peptide-based therapeutics offer high potency and site selectivity but are often limited by poor bioavailability due to enzymatic degradation and short circulating half-lives. To address these challenges, peptide analogues are typically designed with enhanced structural stability through cyclization or the incorporation of bulky hydrocarbons. However, π–π stapling, exploits side-chain interactions by substituting specific amino acids with α-methyl-L-phenylalanine residues and prevents the need for additional covalent bonds. The methyl group at the α-carbon restricts side-chain flexibility, promoting π–π interactions between aromatic rings and stabilizing α-helical conformations. This increased conformational rigidity enhances the overall stability of the peptide backbone. In this study, the antimicrobial peptides TLPL3 and DRAMP03064 were selected for their reported inhibitory activity against the main protease (Mpro) of SARS-CoV-2, a positive-sense RNA virus composed of 16 nonstructural, 4 structural, and 9 accessory proteins. Viral replication relies on Mpro, which cleaves nonstructural polyproteins into functional units essential for replication and transcription. All peptides were synthesized using automated Fmoc solid-phase peptide synthesis (SPPS) and cleaved from the resin with 95% trifluoroacetic acid. Inhibitory activity was assessed using a selected ion monitoring (SIM)-based LC-MS assay to determine the half-maximal inhibitory concentration (IC₅₀). Results revealed markedly reduced inhibition efficiencies in the stapled analogues compared to their linear counterparts, with DRAMP03064 exhibiting the most significant decrease in activity (IC₅₀ shifting from 430 nM to 38 nM).