Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments

Abstract

Tuberculosis (TB) is one of the main causes of death from a single pathological agent, Mycobacterium tuberculosis ( Mtb ). In addition, the emergence of drug-resistant TB strains has exacerbated even further the treatment outcome of TB patients. It is thus needed the search for new therapeutic strategies to improve the current treatment and to circumvent the resistance mechanisms of Mtb . The shikimate kinase (SK) is the fifth enzyme of the shikimate pathway, which is essential for the survival of Mtb . The shikimate pathway is absent in humans, thereby indicating SK as an attractive target for the development of anti-TB drugs. In this work, a combination of in silico and in vitro techniques was used to identify potential inhibitors for SK from Mtb ( Mt SK). All compounds of our in-house database (Centro de Pesquisas em Biologia Molecular e Funcional, CPBMF) were submitted to in silico toxicity analysis to evaluate the risk of hepatotoxicity. Docking experiments were performed to identify the potential inhibitors of Mt SK according to the predicted binding energy. In vitro inhibitory activity of Mt SK-catalyzed chemical reaction at a single compound concentration was assessed. Minimum inhibitory concentration values for in vitro growth of pan-sensitive Mtb H37Rv strain were also determined. The mixed approach implemented in this work was able to identify five compounds that inhibit both Mt SK and the in vitro growth of Mtb . Supplementary Information The online version contains supplementary material available at 10.1007/s10822-022-00495-w.

Toxicological Profiling of Potential Shikimate Kinase Inhibitors Against Mycobacterium tuberculosis

“…Energy minimisation of the macromolecule was then carried out with Chimera software. 24 The macromolecule was then submitted to CASTp (http://sts.bioe.uic.edu/castp/index.html?1bxw) for the prediction of the active site of the enzyme, and the final processed file of the macromolecule 2IYQ was used for the molecular docking analyses.…”

“…It had a crystallographic resolution of 1.8 Å and was complexed with shikimic acid and ADP. 24 The macromolecule was then processed by using the Discovery Studio tool. The addition of H atoms was carried out and was followed by the equitable distribution of respective charges of the amino acid groups across the structure of the macromolecule.…”