Computational Approaches to Identify Molecules Binding to <i>Mycobacterium tuberculosis</i> KasA
Ana C. Puhl, Thomas R. Lane, Patricia A. Vignaux, Kimberley M. Zorn, Glenn C. Capodagli, Matthew B. Neiditch, Joel S. Freundlich, Sean Ekins
Abstract
Tuberculosis is caused by Mycobacterium tuberculosis (Mtb) and is a deadly disease resulting in the deaths of approximately 1.5 million people with 10 million infections reported in 2018. Recently, a key condensation step in the synthesis of mycolic acids was shown to require β-ketoacyl-ACP synthase (KasA). A crystal structure of KasA with the small molecule DG167 was recently described, which provided a starting point for using computational structure-based approaches to identify additional molecules binding to this protein. We now describe structure-based pharmacophores, docking and machine learning studies with Assay Central as a computational tool for the identification of small molecules targeting KasA. We then tested these compounds using nanoscale differential scanning fluorimetry and microscale thermophoresis. Of note, we identified several molecules including the Food and Drug Administration (FDA)-approved drugs sildenafil and flubendazole with Kd values between 30–40 μM. This may provide additional starting points for further optimization.