N -methylation of a bactericidal compound as a resistance mechanism in Mycobacterium tuberculosis

Abstract

The rising incidence of antimicrobial resistance (AMR) makes it imperative to understand the underlying mechanisms. Mycobacterium tuberculosis (Mtb) is the single leading cause of death from a bacterial pathogen and estimated to be the leading cause of death from AMR. A pyrido-benzimidazole, 14, was reported to have potent bactericidal activity against Mtb. Here, we isolated multiple Mtb clones resistant to 14. Each had mutations in the putative DNA-binding and dimerization domains of rv2887, a gene encoding a transcriptional repressor of the MarR family. The mutations in Rv2887 led to markedly increased expression of rv0560c. We characterized Rv0560c as an S-adenosyl-L-methionine-dependent methyltransferase that N-methylates 14, abolishing its mycobactericidal activity. An Mtb strain lacking rv0560c became resistant to 14 by mutating decaprenylphosphoryl-β-d-ribose 2-oxidase (DprE1), an essential enzyme in arabinogalactan synthesis; 14 proved to be a nanomolar inhibitor of DprE1, and methylation of 14 by Rv0560c abrogated this activity. Thus, 14 joins a growing list of DprE1 inhibitors that are potently mycobactericidal. Bacterial methylation of an antibacterial agent, 14, catalyzed by Rv0560c of Mtb, is a previously unreported mechanism of AMR.

Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome

“…In contrast, transcriptome-based approaches, while biologically broader in scope, report on the response, rather than direct impact, of a given compound, and thus make it hard to identify targets beyond the pathway level, or in comparison to a compendium of previously characterized reference compounds [52]. Whole genome sequencing of drug-resistant clones, though uniquely powerful for their organism-wide scope, is similarly associated with complex isolation procedures and the not infrequent discovery of secondary resistance genes involved in drug-activation, drug efflux and associated DNA transcription, while missing the primary target [53–55]. Existing technologies have thus left key gaps in the compound-based pipeline.…”

“…Within this context, metabolomics have helped to identify N-methylation as a mechanism of drug resistance [55]. …”

“…Such an integrated approach that offers a simultaneous readout for both the pharmacokinetics and pharmacodynamics properties of a compound would be particularly useful for drugs that are metabolically inactivated [55], or activated [53,67]. The thiophenecarboxamide derivative 7947882, for example, requires activation by the monooxygenase EthA to inhibit the CTP synthetase PyrG, which then leads to decreased CTP levels and characteristic downstream effects on the metabolome [67].…”

Impact of Early-Life Antibiotic Use on Gut Microbiota of Infants

“…And worse still, abuse and misuse of antibiotics make antibiotic resistance give birth to the 'super bacteria' [57,58]. In one study on Mycobacterium tuberculosis, the causative agent of tuberculosis, Warrier et al [59] have discovered a novel bacterial drug resistance, antibiotic inactivation via N-methylation. Nevertheless, it is not clear whether this new drug resistance mechanism is widely present in bacteria, and how to inhibit bacterial drug resistance [58,59].…”

“…In one study on Mycobacterium tuberculosis, the causative agent of tuberculosis, Warrier et al [59] have discovered a novel bacterial drug resistance, antibiotic inactivation via N-methylation. Nevertheless, it is not clear whether this new drug resistance mechanism is widely present in bacteria, and how to inhibit bacterial drug resistance [58,59]. Currently, the UN General Assembly High-Level Meeting of Heads of State discussed sustainable access to effective antimicrobials in September, 2016. International scientists advocated awareness about lack of access to antibiotics and drug resistance [60].…”