N-methylation of a bactericidal compound as a resistance mechanism inMycobacterium 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 ofrv2887, a gene encoding a transcriptional repressor of the MarR family. The mutations in Rv2887 led to markedly increased expression ofrv0560c.We characterized Rv0560c as anS-adenosyl-L-methionine-dependent methyltransferase thatN-methylates 14, abolishing its mycobactericidal activity. An Mtb strain lackingrv0560cbecame 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.