DNA-Dependent Binding of Nargenicin to DnaE1 Inhibits Replication in Mycobacterium tuberculosis

Abstract

Natural products provide a rich source of potential antimicrobials for treating infectious diseases for which drug resistance has emerged. Foremost among these diseases is tuberculosis. Assessment of the antimycobacterial activity of nargenicin, a natural product that targets the replicative DNA polymerase of Staphylococcus aureus , revealed that it is a bactericidal genotoxin that induces a DNA damage response in Mycobacterium tuberculosis ( Mtb ) and inhibits growth by blocking the replicative DNA polymerase, DnaE1. Cryo-electron microscopy revealed that binding of nargenicin to Mtb DnaE1 requires the DNA substrate such that nargenicin is wedged between the terminal base pair and the polymerase and occupies the position of both the incoming nucleotide and templating base. Comparative analysis across three bacterial species suggests that the activity of nargenicin is partly attributable to the DNA binding affinity of the replicative polymerase. This work has laid the foundation for target-led drug discovery efforts focused on Mtb DnaE1.

Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutation of Staphylococcus aureus DNA Polymerase PolC

“…Compared to viral and bacteriophage replicative DNA polymerases, mechanistic studies of cellular replicative polymerases have lagged behind. Among the cellular replicative polymerases, the bacterial C-family polymerases have been particularly challenging to study, largely because of weak binding to DNA and the unique catalytic cycle of the enzyme, but the available structures of several essential C-family polymerases (7,8,(31)(32)(33)(34)(35)(36) and our transientstate kinetic characterization of S. aureus PolC (16,17,24) provide the framework needed for a mechanistic structure-function approach to developing antibiotics targeting bacterial DNA replication.…”

“Upcycling” known molecules and targets for drug-resistant TB

“…As deeply reviewed by Reiche et al (2017), the DNA replication machinery is encoded by essential mycobacterial genes. Thus, other replication inhibitors are being explored including compounds targeting topoisomerase I (Sandhaus et al, 2016;Ekins et al, 2017), DNA polymerase complex (by Nargenicin, targeting DnaE1) (Chengalroyen et al, 2022) or Griselymicin (DnaN) as described above. Whether or not these molecules targeting machinery other than the fluoroquinolone targeti.e.…”

An in silico analysis: Deciphering the role of differential expressed genes in tuberculosis in response to bedaquiline antibiotic drug

“…During host infection, the increase of DNA gene expression directly contributes to mutation leads to DNA damage induced by immunemediated reactive oxygen and nitrogen intermediates. Especially, ATP genes may play an essential role in the emergence of mutants that are better suited to surviving during infection and drug resistance evolution in this organism [29]. The bacteria tend to reduce cellular ATP consumption while increasing the capacity of ATP-generating pathways, which adds to bacterial survival in the face of antibiotic stress.…”