Elucidating the Antimycobacterial Mechanism of Action of Decoquinate Derivative RMB041 Using Metabolomics

Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), still remains one of the leading causes of death from a single infectious agent worldwide. The high prevalence of this disease is mostly ascribed to the rapid development of drug resistance to the current anti-TB drugs, exacerbated by lack of patient adherence due to drug toxicity. The aforementioned highlights the urgent need for new anti-TB compounds with different antimycobacterial mechanisms of action to those currently being used. An N-alkyl quinolone; decoquinate derivative RMB041, has recently shown promising antimicrobial activity against Mtb, while also exhibiting low cytotoxicity and excellent pharmacokinetic characteristics. Its exact mechanism of action, however, is still unknown. Considering this, we used GCxGC-TOFMS and well described metabolomic approaches to analyze and compare the metabolic alterations of Mtb treated with decoquinate derivative RMB041 by comparison to non-treated Mtb controls. The most significantly altered pathways in Mtb treated with this drug include fatty acid metabolism, amino acid metabolism, glycerol metabolism, and the urea cycle. These changes support previous findings suggesting this drug acts primarily on the cell wall and secondarily on the DNA metabolism of Mtb. Additionally, we identified metabolic changes suggesting inhibition of protein synthesis and a state of dormancy.

Keywords: GCxGC-TOFMS; Mycobacterium tuberculosis; decoquinate derivative RMB041; mechanism of action; metabolomics; tuberculosis.

Figure 1

PCA scores plot obtained from GCxGC-TOFMS whole metabolome analysis of Mtb samples in the presence and absence of DQ derivative RMB041.

Figure 2

Venn diagram illustrating the multi-statistical approach for selecting the metabolites that best describe the variation detected in the metabolome of Mtb cultured with and without DQ derivative RMB041.

Figure 3

Metabolomic pathway map of DQ derivative RMB041-treated Mtb. The metabolite markers best describing the variation in the metabolome compared to that of untreated Mtb are represented with up or down arrows, indicating elevated or reduced concentrations, respectively. The dotted lines represent flux of amino acids from nucleotide degradation into the central carbon metabolism. Metabolites that are incorporated into the cell wall are indicated in italic.