Rational design of peptides against Pseudomonas aeruginosa TolB-PAL interaction

TUMAS IGNACIO NICOLAS; MIGUEL VIRGINIA; MONTI MARIELA ROXANA

Rosario

Congreso; L Reunión Anual de la Sociedad Argentina de Biofísica; 2022

Sociedad argentina de biofísica

The Gram-negative bacterium Pseudomonas aeruginosa (PA) is an opportunistic pathogen capable of producing different infections. It has a marked tendency to acquire resistance to antibiotics for clinical use. It is among the main bacteria with priority for the development of new antimicrobials, according to the WHO.In this work, we have focused on the periplasmic protein TolB. It participates in the division and transport of other proteins through the PA membrane. Its essential role has been demonstrated in the literature and there are several crystalline structures of its homologue 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). We propose as a strategy the in silico development of peptides whose mechanism of action consists of interrupting TolB-PAL interaction. We generated a TolB model of PA with MODELLER using a multi-template homology modeling approach. This model was used to build four different TOLB-partners complexes using PAL, and three colicines as partners, resulting in 4 different protein-protein and protein-peptide structures. These complexes were used as starting points for 30 ns molecular dynamics simulations (MD) in order to evaluate complexes stability. Also, we determined the total interaction energy and energetic contribution of the residues of the ligands in the interaction with TolB using GROMACS and gmx_MMPBSA. Complexes showed low RMSD values and high affinity energies. We selected the PAL and colicin residues that have the highest interaction energy with TolB.We were able to design several peptides of 10 to 16 amino acid length that mimicked the interaction of PAL and colicins combining the residues that showed the stronger affinity with TolB of PA and we evaluated its performance with MDs and interaction energy analysis.