Interaction of dihydrofolate reductase and aminoglycoside adenyltransferase enzyme from Klebsiella pneumoniae multidrug resistant strain DF12SA with clindamycin: a molecular modelling and docking study

Klebsiella pneumoniae strain DF12SA (HQ114261) was isolated from diabetic foot wounds. The strain showed resistance against ampicillin, kanamycin, gentamicin, streptomycin, spectinomycin, trimethoprim, tetracycline, meropenem, amikacin, piperacillin/tazobactam, augmentin, co-trimoxazole, carbapenems, penicillins and cefoperazone, and was sensitive to clindamycin. Molecular characterization of the multidrug-resistance phenotype revealed the presence of a class 1 integron containing two genes, a dihydrofolate reductase (DHFR) (PF00186), which confers resistance to trimethoprim; and aminoglycoside adenyltransferase (AadA) (PF01909), which confers resistance to streptomycin and spectinomycin. A class 1 integron in K. pneumoniae containing these two genes was present in eight (18.18 %) out of 44 different diabetic foot ulcer (DFU) patients. Hence, there is a need to develop therapeutics that inhibit growth of multidrug resistant K. pneumoniae in DFU patients and still achieve amputation control. Am attempt was made to create a 3D model and find a suitable inhibitor using an in silico study. Rational drug design/testing requires crystal structures for DHFR and AadA. However, the structures of DHFR and AadA from K. pneumoniae are not available. Modelling was performed using Swiss Model Server and Discovery Studio 3.1. The PDBSum server was used to check stereo chemical properties using Ramachandran plot analysis of modeled structures. Clindamycin was found to be suitable inhibitor of DHFR and AadA. A DockingServer based on Autodock & Mopac was used for docking calculations. The amino acid residues Ser³², Ile⁴⁶, Glu⁵³, Gln⁵⁴, Phe⁵⁷, Thr⁷², Met⁷⁶, Val⁷⁸, Leu⁷⁹, Ser¹²², Tyr¹²⁸, Ile¹⁵¹ in case of DHFR and Phe³⁴, Asp⁶⁰, Arg⁶³, Gln⁶⁴, Leu⁶⁸, Glu⁸⁷, Thr⁸⁹, Val⁹⁰ for AadA were found to be responsible for positioning clindamycin into the active site. The study identifies amino acid residues crucial to ‘DHFR and AadA -drug’ and ‘DHFR and AadA -inhibitor’ interactions that might be useful in the ongoing search for a versatile DHFR and AadA -inhibitor.