Identification of a small molecule that inhibits Pks13 with anti-tuberculosis activity

ABSTRACT The persistent spread of multidrug-resistant and extensively drug-resistant tuberculosis (TB) necessitates the development of novel anti-TB agents characterized by high efficacy and innovative mechanisms of action. Polyketide synthase 13 (Pks13), a vital protein in the mycolic acid biosynthetic pathway, serves as a valuable target for TB therapy due to its exclusive presence in the genus Mycobacterium . This study identified a compound, B-AP15, that potently inhibited the activity of the Pks13 thioesterase domain (Pks13-TE), giving an IC 50 of 22.48 μM. The binding interaction between B-AP15 and Pks13-TE was corroborated via surface plasmon resonance (SPR) analysis and molecular docking. Furthermore, site-directed mutagenesis, SPR analysis, and inhibitory activity assays of mutant enzymes revealed that residues H1664 and Q1633 likely serve as key binding residues for the interaction between B-AP15 and Pks13-TE. Additionally, B-AP15 exerted an inhibitory effect on Mycobacterium tuberculosis and potential intracellular anti-TB efficacy in macrophages similar to that of first-line anti-TB drugs. The higher minimum inhibitory concentration of B-AP15 for M. marinum strain overexpressing Pks13 confirmed that Pks13 is likely the target of this compound. Collectively, this study identified a Pks13 inhibitor, B-AP15, which exhibits considerable potential as a lead compound for anti-TB therapy. IMPORTANCE The spread of drug-resistant tuberculosis (TB) urgently requires new anti-TB drugs with novel mechanisms. Pks13, a key enzyme in the mycolic acid biosynthetic pathway, is an attractive therapeutic target. We identified B-AP15 as a potent Pks13 inhibitor with a distinct scaffold from previously reported Pks13 inhibitors. B-AP15 directly binds Pks13 and exhibits in vitro and intracellular anti-TB activity comparable to first-line anti-TB drugs, with promising activity especially against drug-resistant Mycobacterium tuberculosis . This study provides a promising lead compound for developing anti-TB agents.