Insights into the antibiotic resistance and inhibition mechanism of aminoglycoside phosphotransferase from Bacillus cereus: In silico and in vitro perspective

Because of the lack of structural studies on aminoglycoside phosphotransferase (APH) from prevalent volatile human pathogen Bacillus cereus, aminoglycoside resistance therapeutics research remains elusive. Hence, in this computational study, we have performed homology modeling, molecular docking, molecular dynamics (MD), and principal component analysis studies on APH from B. cereus. The structure of APH was predicted by homology modeling using MODELLER 9v12 and validated for its stereochemical qualities. Sequence analysis study of the template (Protein Data Bank ID: 3TDW) and APH from B. cereus sensu lato group showed exact matching of active‐site residues. The mechanism of substrate and inhibitor binding to APH was studied using molecular docking, which identified GTP as the more preferred substrate, whereas ZINC71575479 as the most effective inhibitor. The active‐site residues, ARG41, TYR90, ASP195, and ASP215 at nucleotide triphosphate–binding cavity of APH were found to be involved in binding with substrate and inhibitor. Molecular dynamics simulation study of APH in apo form and bound form confirmed the stability and effective binding of GTP and ZINC71575479 in a dynamic state. Molecular mechanics Poisson‐Boltzmann surface area calculations revealed energetic contributions of active‐site residues of APH in binding with GTP and ZINC71575479. The principal component analysis revealed the internal global motion of APH in apo and complex form. Furthermore, experimental studies on APH from B. cereus ATCC 10876 validated the in silico findings for its inhibition. Thus, this study provides more information on structure‐function relationships of APH from B. cereus and open avenues for designing effective strategies to overcome antibiotic resistance. Structure elucidation of aminoglycoside phosphotransferase (APH) from Bacillus cereus helped to unveil the catalytic cleft for substrate and inhibitor binding. Molecular dynamics simulation insubordinate with the principal component analysis helped to understand the internal global motion of APH in the presence of most preferred substrate GTP and most potent inhibitor ZINC71575479. The structure‐function relationship of APH significantly explored from our study not just relates to B. cereus but also to different organisms from B. cereus sensu lato group.