9IAF

Crystal structure of Arr in complex with Rifampicin and Chr-16

This is a non-PDB format compatible entry.

Summary for 9IAF

• Entry DOI: 10.2210/pdb9iaf/pdb
• Descriptor: Rifampin ADP-ribosyl transferase, 2-amino-6-chloro-3-phenyl-1H-quinolin-4-one, RIFAMPICIN, ... (5 entities in total)
• Functional Keywords: adp-ribosyltransferase, complex, inhibitor, rifampicin, transferase
• Biological source: Mycolicibacterium smegmatis
• Total number of polymer chains: 1
• Total formula weight: 17035.65

Authors

Alaviuhkola, J.,Abdulmajeed, S.,Lehtio, L. (deposition date: 2025-02-10, release date: 2025-12-17, Last modification date: 2026-07-01)

Primary citation

Alaviuhkola, J.,Abdulmajeed, S.,Sowa, S.T.,Paakkonen, J.,Lehtio, L.
Discovery of Inhibitors for Bacterial Arr Enzymes ADP-Ribosylating and Inactivating Rifamycin Antibiotics.
Acs Chem.Biol., 20:1584-1593, 2025

PubMed Abstract: ADP-ribosylation is an enzymatic process where an ADP-ribose moiety is transferred from NAD to an acceptor molecule. While ADP-ribosylation is well-established as a post-translational modification of proteins, rifamycin antibiotics are its only known small-molecule targets. ADP-ribosylation of rifampicin was first identified in , whose Arr enzyme transfers the ADP-ribose moiety to the 23-hydroxy group of rifampicin preventing its interaction with the bacterial RNA polymerase thereby inactivating the antibiotic. Arr homologues are widely spread among bacterial species and present in several pathogenic species often associated with mobile genetic elements. Inhibition of Arr enzymes offers a promising strategy to overcome ADP-ribosylation mediated rifamycin resistance. We developed a high-throughput activity assay which was applied to screen an in-house library of human ADP-ribosyltransferase-targeted compounds. We identified 15 inhibitors with IC values below 5 μM against four Arr enzymes from , , , and . The observed overall selectivity of the hit compounds over the other homologues indicated structural differences between the proteins. We crystallized and Arr enzymes, the former in complex with its most potent hit compound with an IC value of 1.3 μM. We observed structural differences in the NAD binding pockets of the two Arr homologues explaining the selectivity. Although the Arr inhibitors did not sensitize to rifampicin in a growth inhibition assay, the structural information and the collection of inhibitors provide a foundation for rational modifications and further development of the compounds.

PubMed: 40509881
DOI: 10.1021/acschembio.5c00164

Experimental method

X-RAY DIFFRACTION (2.2 Å)