Repurposing Rifaximin against Klebsiella pneumoniae via Targeting of Transcription Anti-termination Protein RfaH for Novel Antimicrobial Development

Abstract

Anti-termination protein RfaH plays a crucial role in promoting virulence across various Gram-negative pathogens, including Klebsiella pneumoniae (KP). RfaH directly interacts with RNA-polymerase and ribosomes, which in turn facilitates the activation of operons associated with capsule, cell wall, and pilus biosynthesis. This study aimed to investigate the repurposing potential of rifaximin, a well-established antibiotic, against KP by strategically targeting RfaH, a pivotal anti-terminator protein in transcription. Fluorescence studies observed an excellent binding affinity between rifaximin and RfaH (Ka = 7.38 x 106M−1). Intriguingly, rifaximin treatment causes a significant reduction in capsule production in KP when compared to untreated controls, elucidating its inhibitory influence on RfaH activity. The minimum inhibitory concentration for Rifaximin was calculated as 100µM and a minimum bactericidal concentration of 200µM against KP (ATCC 700603 strain). Docking and MD simulation studies provided detailed atomic insights into the Rifaximin binding to RfaH and structural dynamics of the RfaH-Rifaximin complex. These multifaceted findings collectively investigated the potential of rifaximin as a repurposed antibiotic against KP. Finally, a strong interaction of RfaH with rifaximin and subsequent inhibition of the growth of KP provides a novel avenue for antimicrobial development for addressing the persistent global challenge of antibiotic-resistant infections.