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.

In SilicoDrug Discovery Strategies Identified ADMET Properties of Decoquinate RMB041 and Its Potential Drug Targets against Mycobacterium tuberculosis

“…Beteck, Seldon ( 13 ) and colleagues established that decoquinate RMB041 primarily acts on the cell wall and, second, inhibits DNA synthesis. Our findings during an earlier metabolomic investigation confirmed this and also suggested that decoquinate RMB041 inhibits protein synthesis, and pathways associated with M. tuberculosis in the nonreplicating state ( 11 ). In the current study, we examined each drug target to better understand the perturbations caused by decoquinate RMB041 and explore the cellular response by which M. tuberculosis counteracts these, such as those leading to the metabolomic changes revealed in our previous investigation and will be discussed below.…”

“…In this study, the KEGG database BRITE hierarchy files annotated 10 of the 12 targets, of which all are involved in M. tuberculosis energy metabolism, protein synthesis, fatty acid synthesis, cell wall synthesis, TCA cycle activity, and/or amino acid synthesis. All of the aforementioned pathways were found to be altered in our previous study ( 11 ), possibly indicating the imbuing of adaptions by M. tuberculosis in an attempt to counteract or adapt to the disruption of the primary drug targets identified in this study. Correlations of M. tuberculosis genes have been extensively studied and are still barely understood.…”

“…Decoquinate RMB041 (see structure in Fig. 1 ) is an inexpensive compound with promising in vitro antimycobacterial activity ( 11 , 12 ), and some good in vitro ADMET (absorption, distribution, metabolism, elimination, and toxicity) properties ( 13 ). To identify and characterize decoquinate RMB041’s hit targets, we combined several functions offered by a variety of software and online web servers; reverse pharmacophore docking, also known as target fishing, by PharmMapper ( 14 ), prioritization of targets by TDR Targets, identification of correlated proteins by TBDB, mapping of coexpressed proteins by STRING, annotation of metabolomic pathways by KEGG, virtual screening with Discovery Studio (DS) Visualizer, and docking with AutoDock Vina.…”

Dissecting Host-Pathogen Interactions in TB Using Systems-Based Omic Approaches

“…The mode-of-action of BDQ is complex and has been investigated by multiple research demonstrating that BDQ induces Mtb's glycolytic and gluconeogenic metabolic dependencies and that pyruvate phosphate dikinase (PPDK) is a vulnerable metabolic target (62). Knoll et al (63) measured metabolite markers involved in TCA cycle metabolism, cell wall and DNA synthesis with GCxGC-TOF-MS in Mtb grown with and without ciprofloxacin, (a quinolone potent against drug resistance TB) to identify mechanism of action and Mtb's adaptation to antimicrobials (63). Comparison of drug resistant and drug susceptible metabolic profiles showed proline and isoleucine levels significantly reduced in drug resistant strains (64).…”

“…Knoll et al. ( 63 ) measured metabolite markers involved in TCA cycle metabolism, cell wall and DNA synthesis with GCxGC-TOF-MS in Mtb grown with and without ciprofloxacin, (a quinolone potent against drug resistance TB) to identify mechanism of action and Mtb’s adaptation to antimicrobials ( 63 ). Comparison of drug resistant and drug susceptible metabolic profiles showed proline and isoleucine levels significantly reduced in drug resistant strains ( 64 ).…”