Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis

Antibiotic-resistant bacterial pathogens pose an urgent healthcare threat, prompting a demand for new medicines. We report the mode of action of the natural ansamycin antibiotic kanglemycin A (KglA). KglA binds bacterial RNA polymerase at the rifampicin-binding pocket but maintains potency against RNA polymerases containing rifampicin-resistant mutations. KglA has antibiotic activity against rifampicin-resistant Gram-positive bacteria and multidrug-resistant Mycobacterium tuberculosis (MDR-M. tuberculosis). The X-ray crystal structures of KglA with the Escherichia coli RNA polymerase holoenzyme and Thermus thermophilus RNA polymerase-promoter complex reveal an altered—compared with rifampicin—conformation of KglA within the rifampicin-binding pocket. Unique deoxysugar and succinate ansa bridge substituents make additional contacts with a separate, hydrophobic pocket of RNA polymerase and preclude the formation of initial dinucleotides, respectively. Previous ansa-chain modifications in the rifamycin series have proven unsuccessful. Thus, KglA represents a key starting point for the development of a new class of ansa-chain derivatized ansamycins to tackle rifampicin resistance. [Display omitted] •Rifamycin kanglemycin A (KglA) inhibits rifampicin-resistant RNA polymerases (RNAPs)•KglA’s extra groups improve binding to RNAP and block first dinucleotide formation•KglA is effective against multidrug-resistant M. tuberculosis Resistance to rifamycins, inhibitors of bacterial RNA polymerase used for treatment of tuberculosis, is increasing. Mosaei et al. report an analog of the rifamycins, kanglemycin A, that inhibits rifampicin-resistant RNA polymerases and is effective against multidrug-resistant M. tuberculosis, and they describe its mechanism of action.