Rational design of peptides against the Pseudomonas aeruginosa TolB-PAL interaction

TUMAS IGNACIO; MIGUEL VIRGINIA; MONTI MARIELA R

Congreso; XVIII Reunión Anual de SAMIGE; 2023

eudomonas aeruginosa (PA) is an opportunistic pathogen capable of producing infections in immunocompromised patients. This Gram-negative bacterium has a marked tendency to acquire resistance to antibiotics for clinical use. Thus, according to the WHO, it is among the main bacteria with priority for the development of new antimicrobials.In this work, we have focused on the periplasmic protein TolB as a potential antimicrobial target. It participates in the division and transport of other proteins through the PA outer membrane. TolB essentiality has been demonstrated and there are several crystalline structures of its homologue in Escherichia coli alone or interacting with one of its interaction pairs, such as PAL protein and colicin fragments. We propose as a strategy for the development of TolB inhibitors, the in silico design of peptides whose mechanism of action consists of interrupting TolB interaction with partners. With this aim, we generated a TolB 3D model of PA TolB using the MODELLER software, employing a multi-template homology modeling approach. Subsequently, the model was meticulously compared with the model produced by AlphaFold, a state-of-the-art protein structure prediction tool. This comparative analysis was conducted to ensure the absence of significant discrepancies between the two models, thus reinforcing the accuracy and reliability of our constructed TolB model. The TolB model was used to build four different TOLB-partners complexes using PAL protein, and the three colicin fragments 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. Using this information, 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. Finally, we evaluated its performance with MDs and interaction energy analysis