Rational design of peptides with antimicrobial activity against the pathogenic bacterium Pseudomonas aeruginosaRational design of peptides against Pseudomonas aeruginosa TolB-PAL interaction

TUMAS IN; MIGUEL V; MONTI MR

Congreso; L Reunión Anual Sociedad Argentina de Biofísica; 2022

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.In this work, we have focused on the periplasmic protein TolB. It participates in thedivision and transport of other proteins through the PA membrane. Its essential role hasbeen demonstrated in the literature and there are several crystalline structures of itshomologue in E.coli alone (1C5K and 1CRZ) or interacting with one of its interaction pairs,such as PAL protein (2HQS and 2W8B) and colicin fragments (2IVZ, 3IAX and 4JML). Wepropose as a strategy the in silico development of peptides whose mechanism of actionconsists of interrupting TolB-PAL interaction.We generated a TolB model of PA with MODELLER using 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-protein andprotein-peptide structures. These complexes were used as starting points for 30 nsmolecular dynamics simulations (MD) in order to evaluate complexes stability. Also, wedetermined the total interaction energy and energetic contribution of the residues of theligands in the interaction with TolB using GROMACS and gmx_MMPBSA. Complexesshowed low RMSD values and high affinity energies. We selected the PAL and colicinresidues that have the highest interaction energy with TolB.We were able to design several peptides of 10 to 16 amino acid length that mimicked theinteraction of PAL and colicins combining the residues that showed the stronger affinitywith TolB of PA and we evaluated its performance with MDs and interaction energyanalysis.