Characterization of Druggable Genome and the Identification of the Putative Drug Targets in the Multi-drug Resistant Klebsiella pneumoniae

Abstract

Characterization of the drugabble genome of gram negative, multidrug resistant Klebsiella pneumoniae subsp. pneumoniae HS11286 by the ‘subtractive’ channel of genome mining brought forth 16 putative targets of therapeutic potential. With the focus of the study centred on ‘drug’ target identification, LpxC, a Zn+2 dependant cytoplasmic metalloprotein of lipopolysaccharide biosynthesis pathway was selected as the most promising candidate. Primary sequence analysis followed by 3D structure elucidation of the protein led to the detection of topology of KpLpxC distinct from its orthologous counterparts in other bacterial species. Molecular docking protocol recognized compound 106, a uridine based LpxC inhibitory compound as the ligand best able to fit the binding pocket with the GoldScore of 67.53. The KpLpxC docked complex of this compound was scrutinized in order to determine the nature of molecular interactions governing the energetically favourable fit of the inhibitor in receptor’s active site. In addition to the Zn+2 interacting catalytic triad of HIS 8, HIS 167 and ASP 171; THR 120 and LYS 168 were identified as hydrogen bond forming residues and SER 4 and ILE 32 were found to be involved in van der waals interactions. Molecular dynamics simulations of compound 106-KpLpxC complex were performed in order to determine the time dependant behaviour of docked system. Simulations of the undocked system were carried out to determine ligand induced changes in protein conformation. Thirty two nanosecond simulation analysis of docked KpLpxC revealed an alternate binding pattern of ligand in the active site. Comparison with undocked system demonstrated ligand induced conformational changes in the hydrophobic channel of KpLpxC. This behaviour of the ligand demonstrated its inhibitory potential by rendering the channel unstable for substrate binding. The coordination dynamics of the Zn+2cofactor were subjected to the environment of the protein; for instance in docked system Zn+2 maintained its preference for 6 fold coordination throughout the simulation time period. The undocked system however showed an interesting transition from 6 fold to 5 fold coordination over the simulation of twelve nanoseconds. Key findings of the study can be employed to guide the design of targeted KpLpxC inhibitory drugs.