In silico analysis of mutations in penicillin binding protein 3 (PBP3) that are associated with pan beta lactam resistance in pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa remains one of the major opportunistic pathogens causing severe life threatening infections. The infections include; bacteremia, pneumonia, septicemia among others in immunocompromised patients. Many of P.aeruginosa infections have developed antibiotic resistance and this has made it classified as one of the six most problematic bacterial pathogens worldwide. The cell membrane contains Penicillin Binding Protein 3 which are target proteins for Beta Lactam Drugs. The study was aimed at analyzing mutations in Penicillin Binding Protein 3 that are associated with pan beta lactam resistance in P.aeruginosa. It was done through Molecular Docking and structural interaction analysis of both the wild type and mutated PBP3 proteins. Seven co-crystalized PBP3 3D structures with the following PDB identification numbers 6UN1, 6UN3, 9FZO, 6R3X, 3PBR, 6I1E and 3OCL were downloaded from PDB. The proteins were cleaned using Pymol and the ligands obtained were re-docked to both the wild type and mutated proteins using Autodock vina. The following known mutations F533L (Joshi et al., 2024), A244T, V465G, P527S (Clark et al., 2019) , R504C, A539T, G63C and G63D (Glen & Lamont et al., 2021) were introduced in each of the proteins using MODELLER. The mutated proteins were the docked to their respective ligands and the binding energies were obtained. The best poses were re-scored using X-Score function for validation of the docking energies. The 2D structures were analyzed using Ligplot while the 3D structures were analyzed with Pymol. The results were as follows; the wild type PBP3 proteins had lower binding energies as compared to the mutated PBP3 proteins. But binding energies alone is not ideal to conclude on protein ligand interaction, number of hydrogen bonds and amino acid residues were also analyzed. There was a reduction in the number of hydrogen bonds and the number of amino acid residues that involved in the protein ligand interaction in the mutated proteins. For example variant 3PBR_V465G had a higher binding energy of -6.9 (kcal/mol) and Delta-G value of 1.4 (kcal/mol) with only three hydrogen bonds lower than the wild type 3PBR with six hydrogen bonds. This revealed that the wild type PBP3 had a stable interaction with beta lactams and the mutated proteins had a less stable interaction with beta lactams. This led to a reduction in binding affinities between the drugs and the mutated PBP3 protein hence confirming that mutations in PBP3 of P.aeruginosa have an impact on drug interaction.