Design of Highly Specific Antimicrobial Peptides Targeting the BamA Protein of Candidatus Liberibacter Asiaticus

Candidatus Liberibacter asiaticus (CLas) is a putative causative agent of Huanglongbing (citrus greening). The unculturable nature of CLas poses a significant challenge in discovering drugs against citrus greening. This study presents a novel in silico technique to design peptides with a high affinity toward the β-barrel assembly machinery A (BamA) protein, a critical outer membrane component of CLas vital for bacterial functionality. The technique used in this study is based on identifying the strongest binding amino acids at different sites in BamA and linking them using peptide linkers. Initially, amino acid probes that can emulate amino acid activity in peptide form were docked using Schrodinger Glide on the target domain of BamA. Docking results of amino acid probes showed three closely located clusters on BamA. Peptides were designed by selecting the strongest binding probes in each cluster and linking them using short peptide linkers. Initially, 15 peptides were designed, and based on molecular docking, molecular dynamics simulations, and BioLayer Interferometry, three peptides with a high affinity toward BamA were identified. Two of the peptides effectively inhibited Rhizobium grahamii, a CLas surrogate, in in vitro assays, suggesting potential antimicrobial activity against CLas.