In silico and in vitro study of some antibiotics against clinical Pseudomonas arruginosa

In this study, Pseudomonas aeruginosa was identified in 89 of the samples isolated from 100 patients with various infections, after biochemical and cultural tests, including VITEK BioMerieux. In addition, commercial antibiotics have been discussed as antibacterial agents against Pseudomonas aeruginosa. The design and drafting of antibiotics was carried out in Silico with computational methodologies. The 3D (3D) structural model of the DNA topoisomerase enzyme of Pseudomonas aeruginosa was created as the target protein by homology modeling method and the active site was visualized. All 3D information of the active site of the target protein was used to examine five antibiotics (ciprofloxacin, ceftazidime, gentamicin, amikacin, and penicillin). Accordingly, it was determined that the ciprofloxacin molecule had the highest binding score (-53.1 kcal/mol) with the active site of the target protein. In addition, the ceftazidime binding score is-32.5 kcal/mol, the gentamicin binding score is -7.7 kcal/mol, and the Amikacin binding score is. It was found as -1.3 kcal/mol. Meanwhile, the penicillin molecule showed the lowest binding score with the target protein of 71.2 kcal/mol. Only two of the five antibiotics (ciprofloxacin, ceftazidime) showed the highest level of antibacterial activity at a concentration of 16 µg/mL, while gentamicin and amikacin showed moderate activity at a concentration of 32 µg/mL. The compound penicillin showed no antibacterial activity against clinical Pseudomonas aeruginosa.