DOI: 10.4103/bbrj.bbrj_56_26 ISSN: 2588-9834

Molecular Conservation Analysis and Structure-Based Evaluation of the GyrB ATPase Pocket as a Potential Target for SPR719 in Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

Hawraa Natiq Kabroot Al-Fatlawy
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Abstract

Background:

Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a major clinical challenge due to the accumulation of multiple antimicrobial resistance mechanisms. DNA gyrase subunit B ( gyrB ) has emerged as an attractive antibacterial target.

Methods:

A total of 314 clinical specimens; 54 K. pneumoniae isolates were identified, including 41 multidrug-resistant (MDR) carbapenem-resistant strains (75.9%). Antimicrobial susceptibility testing and polymerase chain reaction-based molecular screening were performed, followed by sequencing and phylogenetic analysis of the gyrB gene, including submission of a representative clinical isolates to deoxyribonucleic acid Data Bank of Japan (Accession No. LC918550).

Results:

CRKP isolates exhibited extensive multidrug resistance (41MDR isolates) associated with a complex resistance gene profile including blaIMP (100%), blaNDM-1 ( 36.5%), blaOXA-48-like (26.8%), blaKPC (12.19%), blaCTX-M (100%), blaSHV (100%), and the Class 1 integron integrase gene int1 ( 100%). Housekeeping genes (gyrB, 16 S ribosomal DNA [16S rDNA]) were detected in all isolates. Structural modeling revealed a high-quality and reliable gyrB structure, with 97.42% of residues located with favored regions of the Ramachandran plot. Molecular docking predicted favorable and preferential binding of SPR719 to a conserved Adenosine triphosphatase (ATPase) pocket of gyrB with a high binding affinity (−9.8 kcal/mol), involving several conserved residues within the ATPase pocket. Molecular dynamics (MD) simulation of the apo-gyrB protein demonstrated structural stability, compactness, and dynamic equilibrium throughout the 25 ns simulation period, with Root mean square fluctuation (RMDS) values stability after approximately 6–8 ns under physiological conditions.

Conclusions:

The principal contribution of this study lies in integrating clinical resistance profiling with gyrB sequence-based conservation analysis and structural modeling, molecular docking and MD simulations in CRKP clinical isolates. The findings demonstrated that the gyrB ATPase pocket remains highly conserved despite the widespread presence of Carbapenemase and Extended spectrum β-lactamases resistance determinants. Structural modeling revealed a high-quality GyrB structure, while molecular docking indicated favorable binding of SPR719 within the ATPase pocket. MD simulations further supported the structural stability and conformational integrity of the modeled gyrB protein under physiological conditions. Collectively, these findings provide a molecular framework for future experiment investigations of GyrB-targeted therapeutic strategies against multidrug-resistant K. pneumoniae .

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