Comparative and Subtractive Genomics Analysis of Multidrug-Resistant Klebsiella pneumoniae Strains for Novel Target...

The rapid rise of multidrug-resistant (MDR) Klebsiella pneumoniae has created a major global health challenge due to the limited availability of conserved therapeutic targets effective across diverse resistant strains. In this study, an integrative computational target-discovery and drug-repurposing framework was applied to six clinically relevant K. pneumoniae strains. Comparative genomic analysis identified 3012 conserved genes, which were subsequently filtered to nine essential, non-host homologous proteins. Among these, three conserved cytoplasmic proteins (accD, cpxR, and mraZ) were prioritized for functional analysis, with acetyl-CoA carboxylase subunit beta (accD) emerging as the most promising therapeutic target based on sequence conservation, predicted essentiality, subcellular localization, and pathway association. Structural assessment supported the reliability of the predicted accD model, whereas consensus binding-site analysis identified key residues suitable for ligand interaction. Virtual screening of FDA-approved drugs followed by molecular docking identified several compounds with favorable binding profiles toward accD. Subsequent molecular dynamics simulations, including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), hydrogen-bond occupancy, principal component analysis (PCA), and PCA-based free energy landscape (FEL) analyses, consistently identified tenapanor, micafungin, deferoxamine, and cobicistat as the most stable protein-ligand complexes, with tenapanor exhibiting the most favorable overall structural and thermodynamic stability profile. These findings identify accD as a promising therapeutic target in MDR K. pneumoniae and suggest several FDA-approved compounds as potential candidates for drug repurposing. Although experimental validation is needed to confirm their biological activity and therapeutic potential, this study demonstrates the potential of integrating comparative genomics with molecular dynamics analyses to support antimicrobial target identification and drug repurposing against MDR bacterial pathogens.