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Molecular docking analysis and determination of minimum inhibition concentration of VIM-38/R228S

Azer Ozad Duzgun, Aysegul Saral

Objective: The aim of this study was to determine the effects of residues at 228th positions of VIM-38 on minimum inhibition concentration (MIC) and molecular docking analysis.

Materials and Methods: blaVIM-38 gene was cloned into expression vector pET100/D-TOPO. Then pET100/D-TOPO-VIM-38 was used to generate the R228S mutation by site-directed mutagenesis. The mutant was transformed into E. coli Dh5α. Changes in the activity of mutation R228S was determined by E-test. Molecular docking analysis of the binding affinity of meropenem and imipenem with VIM-38 and VIM-38 R228S was performed using AutoDock Vina_1_1_2.

Results: According to E-test results, pET100/D-TOPO-VIM-38 and pET100/D-TOPO-VIM-38/ R228S have same MIC value for amoxicillin, ticarcillin/clavulanic acid, ampicillin and ticarcillin. It was determined decrease in pET100/D-TOPO-VIM-38/ R228S of MIC for aztreonam, amikacin and cefixine. There are 3-fold deference in MIC between pET100/D-TOPO-VIM-38 and pET100/D-TOPO-VIM-38/ R228S for cefoxitin. pET100/D-TOPO-VIM-38 has 0.5 μg/ml and pET100/D-TOPO-VIM-38/ R228S has 0.125 μg/m for imipenem, we observed 4-fold deference. Also, there is about 170-fold deference between pET100/D-TOPO-VIM-38 (16 μg/ml) and pET100/D-TOPO-VIM-38/ R228S (0.094 μg/ml) for meropenem. VIM-38 and VIM-38 R228S have very close to the negative low free energies of binding of the meropenem and imipenem.

Conclusion: These results showed that substitution (R228S) slightly have effect on enzyme activity.