All-atoms molecular dynamics study to screen potent efflux pump inhibitors against KpnE protein of Klebsiella pneumoniae

Abstract

The Small Multidrug Resistance efflux pump protein KpnE, plays a pivotal role in multi-drug resistance in Klebsiella pneumoniae. Despite well-documented study of its close homolog, EmrE, from Escherichia coli, the mechanism of drug binding to KpnE remains obscure due to the absence of a high-resolution experimental structure. Herein, we exclusively elucidate its structure-function mechanism and report some of the potent inhibitors through drug repurposing. We used molecular dynamics simulation to develop a dimeric structure of KpnE and explore its dynamics in lipid-mimetic bilayers. Our study identified both semi-open and open conformations of KpnE, highlighting its importance in transport process. Electrostatic surface potential map suggests a considerable degree of similarity between KpnE and EmrE at the binding cleft, mostly occupied by negatively charged residues. We identify key amino acids Glu14, Trp63 and Tyr44, indispensable for ligand recognition. Molecular docking and binding free energy calculations recognizes potential inhibitors like acarbose, rutin and labetalol. Further validations are needed to confirm the therapeutic role of these compounds. Altogether, our membrane dynamics study uncovers the crucial charged patches, lipid-binding sites and flexible loop that could potentiate substrate recognition, transport mechanism and pave the way for development of novel inhibitors against K. pneumoniae.

Communicated by Ramaswamy H. Sarma

Keywords:

• Klebsiella pneumoniae
• molecular docking simulation
• lipid bilayers
• drug repurposing

Acknowledgement

The author would like to thank Director, ICMR-RMRC, Bhubaneswar, Odisha for providing necessary technical support to carry out this work. We would also thankful to the President of the SOA, University and the Dean of the Centre for providing the essential support to carry out the present work.

Authors’ contribution

SDe: Conceptualization, formal analysis, investigation, methodology, visualization, writing-original draft, review & editing; MR: Methodology, visualization, formal analysis, review & editing; SP: Resources and supervision; MKS: Data analysis; BD: Supervision, conceptualization, investigation, visualization, methodology, formal analysis, review & editing; ES: Supervision, review and editing; all the authors have gone through the manuscript and approved it.

Disclosure statement

The authors have no conflict of interest to declare.

Additional information

Funding

The financial support of ICMR (AMR/Fellowship/13/2019/ECD-II) for the present work is highly appreciated.