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

Abstract

SummaryAntibiotic-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.

Evolving MRSA: High-level β-lactam resistance in Staphylococcus aureus is associated with RNA Polymerase alterations and fine tuning of gene expression

“…B) The three-dimensional structure of E . coli RNAP holoenzyme was used to map the rpoB and rpoC mutations [ 67 ]. The two subunits β (red) and β’ (blue) are shown as molecular surface.…”

Repositioning rifamycins for Mycobacterium abscessus lung disease

“…An analysis of soil metagenomes also revealed that soil bacteria have evolved great diversity in their rifamycin biosynthetic machinery, suggesting an untapped source of rifamycin congeners [110]. For example, the rifamycin congener kanglemycin A inhibits bacterial RNA polymerases via a mechanism that is distinct from rifampicin and retains potency against rifampicin-resistant mycobacteria [110,111].…”

Actinomycete-Derived Polyketides as a Source of Antibiotics and Lead Structures for the Development of New Antimicrobial Drugs

“…The reason for the higher MIC of Gram-negatives is most likely due to a reduced penetration of the rifamycins through the outer membranes of Gram-negatives [258]. The rifamycins remain the first-line treatment of tuberculosis (TB) caused by M. tuberculosis and for treatment of non-tuberculous mycobacterial infections [105,119,244]. Collectively, the rifamycins interact with the bacterial DNA-dependent RNAP whereby transcription is blocked.…”

“…Based on the crystal structure of the RNAP-promoter complex of Thermus thermophiles with kanglemycin A, it became evident that the sugar (β-O-3,4-O,O -methylene digitoxose) and acid (2,2-dimethyl succinic acid) moieties on the ansa bridge in the molecule increase the binding surface of the antibiotic with the RNAP. Furthermore, the additional interaction of the sugar group of kanglemycin A was hypothesized to limit the frequency of resistance development as this would require two simultaneous mutations in the binding pocket of the RNAP [119,120]. Although kanglemycin A (Table 1) itself has not been introduced to the clinics, its discovery might open up for future structural derivatisation efforts in which the ansa bridge might prove to be a valuable "target" for generating new synthetic ansamycin antibiotics with improved bioactivities.…”