Essential metabolites of Mycobacterium tuberculosis and their mimics

Abstract

An organism requires a range of biomolecules for its growth. By definition, these are essential molecules which constitute the basic metabolic requirements of an organism. A small organic molecule with chemical similarity to that of an essential metabolite may bind to the enzyme that catalyzes its production and inhibit it, likely resulting in the stasis or death of the organism. Here, we report a high-throughput approach for identifying essential metabolites of an organism using genetic and biochemical approaches and then implement computational approaches to identify metabolite mimics. We generated and genotyped 5,126 Mycobacterium tuberculosis mutants and performed a statistical analysis to determine putative essential genes. The essential molecules of M. tuberculosis were classified as products of enzymes that are encoded by genes in this list. Although incomplete, as many enzymes of M. tuberculosis have yet to be identified and characterized, this is the first report of a large number of essential molecules of the organism. We identified essential metabolites of three distinct metabolic pathways in M. tuberculosis and selected molecules with chemical similarity using cheminformatics strategies that illustrate a variety of different pharmacophores. Our approach is aimed at systematic identification of essential molecules and their mimics as a blueprint for development of effective chemical probes of M. tuberculosis metabolism, with the ultimate goal of seeking drugs that can kill this pathogen. As an illustration of this approach, we report that compounds JFD01307SC and l-methionine-S-sulfoximine, which share chemical similarity with an essential molecule of M. tuberculosis, inhibited the growth of this organism at micromolar concentrations.

FIG 1

Schematic for identification of essential molecules and their mimics. The genome of an organism is mutagenized to saturation, and nonessential genes whose loss does not compromise the ability of an organism to proliferate are identified. The genes whose loss could not be tolerated are essential and code for essential proteins that have structural or regulatory functions or are enzymes. The metabolite(s) that is produced by an essential enzyme is determined, and its molecular mimic(s) with pharmacological potential is identified using cheminformatics. These mimics may bind to the essential enzyme, inhibit its function, and eventually kill the organism.

FIG 2

(A) Genes and metabolites that comprise the pathway for the biosynthesis of the building blocks of peptidoglycan in M. tuberculosis; (B) composite of 23 genes of M. tuberculosis of the peptidoglycan biosynthesis pathway (right) and a depiction of random loci with identical sizes and TA densities. The arrows show the number of transposon insertions that each locus was able to sustain.