Research advances in M. Tuberculosis polyketide synthase 13 inhibitors / 药学学报

Polyketide synthase 13 (Pks13) performs a critical role in the final assembly step of mycolic acid synthesis in Mycobacterium tuberculosis. The inhibition of Pks13 can influence the biosynthesis of mycolic acid, which leads to Mycobacterium tuberculosis cell death. Researchers have discovered Pks13 inhibitors with five chemical scaffolds as antituberculosis agents. Herein, we summarize recent advances in the study of Pks13 inhibitors including the process of discovery, the mechanism of action and structure-activity relationships.

Identification of polyketide synthase 13 inhibitor: Pharmacophore-based virtual screening and molecular dynamics simulation

Polyketide synthase 13 (Pks13) is one of prominent targets to treat Mycobacterium tuberculosis (Mtb). In the presentstudy, pharmacophore features for Pks13, including two hydrogen bond donors, one hydrogen bond acceptor, and onehydrophobic feature, were built using a novel Pks13 inhibitor, TAM16. The pharmacophore features were then usedto perform virtual screening on ZINC database to identify small molecules of Pks13 inhibitors. The obtained virtualhits of 107 small molecules were subjected to molecular docking studies employing iDock software to reveal theirbinding orientation to Pks13. Furthermore, four best hits, each bound to Pks13, were submitted to 40-ns moleculardynamics simulation to explore their conformational changes throughout simulation. The result showed that all hitcompounds, i.e., Lig79/ZINC09281113, Lig94/ZINC09584070, Lig95/ZINC09209668, and Lig97/ZINC09216165,have better stabilities than that of TAM16 as indicated by their lower values of root-mean-square-deviation and rootmean-square-fluctuation. In a similar way, prediction of binding free energy using molecular mechanics Poisson–Boltzmann Surface Area method showed that all hit compounds have lower binding free energies than that of TAM16,indicating their potential as novel compounds of Pks13 inhibitors.