Rational design of peptides with antimicrobial activity against the pathogenic bacterium Pseudomonas aeruginosa

TUMAS IN; MIGUEL V; MONTI MR

Congreso; XLIX Reunión Anual Sociedad Argentina de Biofísica; 2021

The Gram-negative bacterium Pseudomonas aeruginosa (PA) is an opportunistic pathogencapable of producing different infections. It has a marked tendency to acquire resistanceto antibiotics for clinical use. It is among the main bacteria with priority for thedevelopment of new antimicrobials, according to the WHO.We propose as a new strategy the in silico development of peptides whose mechanism ofaction consists of interrupting protein-protein interactions (PPI) vital for PA. With thispurpose, we have focused on the node proteins that participate in fundamental processesfor the survival of the bacteria.The periplasmic protein TolB was chosen as a target, since it participates in the divisionand transport of other proteins through the PA membrane. Its essential role has beendemonstrated in the literature and there are several crystalline structures of its homologuein E.coli alone (1C5K and 1CRZ) or interacting with one of its interaction pairs, such asPAL protein (2HQS and 2W8B) and colicin fragments ( 2IVZ, 3IAX and 4JML).We generated a TolB model of PA using MODELLER and a multi-template homologymodeling approach. This model was used to build four different TOLB-partners complexesusing PAL, and three colicines as partners, resulting in 4 different protein-proteinstructures. These complexes were used as starting points for 30 ns molecular dynamicssimulations (DM) in order to evaluate if the complex remains stable. Also, we determinedthe energy contribution of the residues of the ligands in the interaction with TolB usingGROMACS. We found that the complexes showed low RMSD values and high affinityenergies demonstrating that PAL and the colicins fragments can interact with TolB of PA.Finally, we designed various 10 amino acid length peptides that mimics the interaction ofPAL and colicins using the residues that showed the stronger affinity with TolB of PA andwe performed a virtual screening of them by docking using the Autodock CrankPepprogram.