Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments

Recent efforts in drug development against influenza A virus (IAV) M2 proton channel S31N mutant resulted in conjugates of amantadine linked with aryl head heterocycles. To understand the mechanism of drug resistance, we chose a representative M2-S31N inhibitor, compound 3, as a chemical probe to identify resistant mutants. To increase the possibility of identifying novel resistant mutants, serial viral passage experiments were performed with multiple strains of H1N1 and H3N2 viruses in different cell lines. This approach not only identified M2 mutations around the drug-binding site, including the pore-lining residues (V27A, V27F, N31S, and G34E) and an interhelical residue (I32N), but also a new allosteric mutation (R45H), in addition to L46P previously identified, located at the C-terminus of M2 that is more than 10 Å away from the drug-binding site. The effects of each mutation were next investigated using electrophysiology, recombinant viruses, and molecular dynamics (MD) simulations. The reduced sensitivity in channel blockage correlated with increased drug resistance in antiviral assays using recombinant viruses. The MD simulations show that the V27A, V27F, G34E, and R45H mutations increase the diameter and hydration state of the pore in complex with compound 3. The Molecular Mechanics Generalized Born (MM-GBSA) calculations result in more positive binding free energies for the complexes of resistant M2 (V27A, V27F, G34E, R45H) with compound 3 compared to the stable complexes (S31N and I32N). Overall, this is the first systematic study of the drug resistance mechanism of M2-S31N channel blockers using multiple viruses in different cell lines.