Docking and MD Simulations of various antibiotic molecules with several proteins associated with strains of Pseudomonas aeruginosa

We made 3D models of a few protein sequences associated with the pathogen Pseudomonas aeruginosa using the Swiss Model server. We picked the model with the best GMQE score, usually 0.9 or higher. Considering both the initial and most recent generations of antibiotics, the compounds levofloxacin (CID: 149096), ciprofloxacin (CID: 2764), norfloxacin (CID: 4539), and nalidixic acid (CID: 4421) (representing fluoroquinolones); mezlocillin (CID: 656511), and penicillin (CID: 5904) (representing β-lactams); as well as tobramycin (CID: 36294), neomycin (CID: 8378), and streptomycin (CID: 19649) (representing aminoglycosides) were sourced from PubChem and utilized as ligands in molecular docking studies with the protein models. The utilization of AutoDock Vina was conducted programmatically, while the preparatory steps were executed employing AutoDock tools. The protonation of the ligands was conducted utilizing pertinent modules within Rdkit.Chem. The results of the subsequent Molecular Dynamics simulations are presented in separate datasets as follows: Protein-Ligand MD Simulation Matrices The molecular dynamics data blocks below are categorized by protein system target classes. Table 1: DD-Transpeptidase (PBP) & Aminonucleotidyltransferase (AMINO) Protein Target (Mutation Year) Penicillin (PEN) Mezlocillin (MEZ) Streptomycin (STEP) Tobramycin (TOB) Neomycin (NEO) DD-Transpeptidase (PBP) (1999) 10.5281/zenodo.15453082 10.5281/zenodo.20525266 DD-Transpeptidase (PBP) (2015) 10.5281/zenodo.20508660 10.5281/zenodo.20525266 DD-Transpeptidase (PBP) (2018) 10.5281/zenodo.15475468 10.5281/zenodo.15478359 Aminonucleotidyltransferase (AMINO) (2012) 10.5281/zenodo.15448121 10.5281/zenodo.20505063 10.5281/zenodo.20505063 Aminonucleotidyltransferase (AMINO) (2016) 10.5281/zenodo.15448121 10.5281/zenodo.15448121 10.5281/zenodo.20505063 Table 2: DNA Gyrase (gyrA) & Topoisomerase IV (parC) Protein Target (Mutation Year) Nalidixic Acid (NDX) Levofloxacin (LEV) Norfloxacin (NOR) Ciprofloxacin (CIP) DNA gyrase subunit A (gyrA) (1996) 10.5281/zenodo.15511963 10.5281/zenodo.20506501 10.5281/zenodo.20508714 DNA gyrase subunit A (gyrA) (2007) 10.5281/zenodo.20508270 10.5281/zenodo.20506501 10.5281/zenodo.20508714 DNA gyrase subunit A (gyrA) (2018) 10.5281/zenodo.15511963 10.5281/zenodo.15494004 10.5281/zenodo.20525266 DNA topoisomerase IV subunit C (parC) (1999) 10.5281/zenodo.15515342 10.5281/zenodo.20588597 10.5281/zenodo.20553013 DNA topoisomerase IV subunit C (parC) (2007) 10.5281/zenodo.20566938 10.5281/zenodo.20588611 10.5281/zenodo.20553440 DNA topoisomerase IV subunit C (parC) (2014) 10.5281/zenodo.20566955 10.5281/zenodo.20588615 10.5281/zenodo.20553454 DNA topoisomerase IV subunit C (parC) (2015) 10.5281/zenodo.20566974 10.5281/zenodo.20588626 10.5281/zenodo.20553480 DNA topoisomerase IV subunit C (parC) (2018) 10.5281/zenodo.15515342 10.5281/zenodo.15494004 10.5281/zenodo.20553520