In silico study on pH-based alanine scanning of Phylloseptin-2 helps determine potential mutant sites for futuristic therapeutic analogues

Analogues of Phylloseptins (PS), membranolytic antimicrobial peptides (AMPs), could replace antibiotics and combat growing multi-drug resistance in urinary tract infections. This study identifies potential mutant sites in a PS scaffold for generation of its analogues, using in silico alanine scanning mutagenesis. Initially, a PS scaffold from native peptides-PS1, PS2 and PS3, is identified using pH-based secondary structure (SS) profiles and conformational free energies after a 20 ns molecular dynamics (MD) simulation at 310 K. PS2 is identified as structurally stable scaffold. Further, alanine scanning is carried out for 17 amino acid residues, at varying pH for 10 ns MD simulation at 310 K to identify structurally and functionally significant and non-significant amino acids in PS2. H-bond occupancy and polar surface area are used as structural and functional parameters in the study. The statistical significance is determined using paired t-tests,using confidence interval of 90%. It was found that the amino acids viz., Leu (4), Val (16) and His (17), were structurally and functionally non-significant (P > .1). Thus, the positions of these aforementioned amino acids in addition to amino acids viz., Ala (8) and Ala (11), can be used as potential mutant sites for generation of therapeutic analogues of PS2.