Identification of cell wall synthesis inhibitors active against Mycobacterium tuberculosis by competitive activity-based protein profiling

Abstract

The identification and validation of a small molecule's targets is a major bottleneck in the discovery process for tuberculosis antibiotics. Activity-based protein profiling (ABPP) is an efficient tool for determining a small molecule's targets within complex proteomes. However, how target inhibition relates to biological activity is often left unexplored. Here, we study the effects of 1,2,3-triazole ureas on Mycobacterium tuberculosis (Mtb). After screening $200 compounds, we focus on 4 compounds that form a structure-activity series. The compound with negligible activity reveals targets, the inhibition of which is functionally less relevant for Mtb growth and viability, an aspect not addressed in other ABPP studies. Biochemistry, computational docking, and morphological analysis confirms that active compounds preferentially inhibit serine hydrolases with cell wall and lipid metabolism functions and that disruption of the cell wall underlies biological activity. Our findings show that ABPP identifies the targets most likely relevant to a compound's antibacterial activity.

Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis

“…Here, we report the synthesis of two new analogues of CyC 17 containing a terminal alkyne function (i.e. CyC yne ) and describe their use for the direct capture of target proteins in a living M. tb culture using a direct click-chemistry ABPP approach (CC-ABPP) [17][18][19][20]. Since HsaD appeared also as a target of these new CyC yne probes, and given its potential as therapeutic target [21], we further explore and validate, through a combination of biochemical and structural approaches, the specificities of HsaD inhibition by the CyC analogues.…”

Chemoproteomic identification of a dipeptidyl peptidase 4 (DPP4) homolog in Bacteroides thetaiotaomicron important for envelope integrity and fitness

“…Studied extensively in mammalian systems, they play roles in proteolysis, metabolism, and cell signaling 17 , all of which likely affect the fitness of gut commensals in complex communities. Human serine hydrolases have been targeted with several FDA-approved therapeutics to treat diseases such as type 2 diabetes 18 , and recent efforts have identified serine hydrolases as novel drug targets for bacterial pathogens such as Mycobacterium tuberculosis [19][20][21][22][23] . However, little is known about the diversity of serine hydrolases in phylogenetically diverse gut commensal bacteria and their roles in interspecies communication and competition.…”

Chemoproteomic identification of a dipeptidyl peptidase 4 (DPP4) homolog in Bacteroides thetaiotaomicron important for envelope integrity and fitness

“…Studied extensively in mammalian systems, they play roles in proteolysis, metabolism, and cell signaling 17 , all of which likely affect the tness of gut commensals in complex communities. Human serine hydrolases have been targeted with several FDA-approved therapeutics to treat diseases such as type 2 diabetes 18 , and recent efforts have identi ed serine hydrolases as novel drug targets for bacterial pathogens such as Mycobacterium tuberculosis [19][20][21][22][23] . However, little is known about the diversity of serine hydrolases in phylogenetically diverse gut commensal bacteria and their roles in interspecies communication and competition.…”