Predictive modeling targets thymidylate synthase ThyX in Mycobacterium tuberculosis

Abstract

There is an urgent need to identify new treatments for tuberculosis (TB), a major infectious disease caused by Mycobacterium tuberculosis (Mtb), which results in 1.5 million deaths each year. We have targeted two essential enzymes in this organism that are promising for antibacterial therapy and reported to be inhibited by naphthoquinones. ThyX is an essential thymidylate synthase that is mechanistically and structurally unrelated to the human enzyme. DNA gyrase is a DNA topoisomerase present in bacteria and plants but not animals. The current study set out to understand the structure-activity relationships of these targets in Mtb using a combination of cheminformatics and in vitro screening. Here, we report the identification of new Mtb ThyX inhibitors, 2-chloro-3-(4-methanesulfonylpiperazin-1-yl)-1,4-dihydronaphthalene-1,4-dione) and idebenone, which show modest whole-cell activity and appear to act, at least in part, by targeting ThyX in Mtb.

Synthesis and Structure–Activity Relationship Studies of Benzo[b][1,4]oxazin‐3(4H)‐one Analogues as Inhibitors of Mycobacterial Thymidylate Synthase X

“…Mycobacterial ThyX NADPH oxidase assay : M. tuberculosis ThyX was produced and purified as described . The synthesized compounds were screened using a NADPH oxidation assay for M. tuberculosis ThyX activity in 96‐well plates . To determine IC 50 values of compounds 22 g , 27 , 28 , 29 d , 45 c , 48 and 52 , the reaction mixture (100 μL) contained 50 m m HEPES pH7.5, 1 m m MgCl 2 , 12 μ m FAD, 0.5 % glycerol, 0.05 % Triton X‐100, 0.5 mg mL −1 BSA, 3 μ m dUMP, 2.5 % DMSO, a range of concentrations (ranging from 40 n m to 20 μ m ) of each testing compound and 0.5 μ m of purified Mtb ThyX.…”

Use of artificial intelligence in infectious diseases

“…Their data clearly suggest that Bayesian models constructed with data generated by different laboratories in various mouse models can have predictive value and can be used in conjunction with other datasets for the selection of the most-fit antimicrobial compound. The same mathematical approaches can be performed either on a very specific target for potential drugs (Djaout et al, 2016) or for a more systematic analysis such as performed for the known inhibitors of fructose bisphosphate aldolase, an enzyme central to the glycolysis pathway in M. tuberculosis, in short, an essential player in the bacteria metabolism (Tiwari et al, 2016). Naïve Bayes, random forest, and C4.5 J48 algorithms were used with an approach to improve models by avoiding over fitting and generating faster and cost-effective models.…”

Collaborative drug discovery for More Medicines for Tuberculosis (MM4TB)

“…DNA gyrase is a DNA topoisomerase present in bacteria and plants but not animals [30]. A combination of cheminformatics (pharmacophore and similarity searching) and in vitro screening was able to identify several new M. tuberculosis ThyX inhibitors (one of which is a drug, idebenone, in Phase III clinical trials for a rare disease) with modest whole-cell activity; and at the same time we were able to show the differences in SAR, with ThyX being much more permissive than GyrB [31]. …”