10PX

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with benzoxaborole derivative of azithromycin (AZI-BB2), mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.45A resolution

This is a non-PDB format compatible entry.

Summary for 10PX

• Entry DOI: 10.2210/pdb10px/pdb
• Descriptor: 23S Ribosomal RNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (62 entities in total)
• Functional Keywords: macrolides, azithromycin, benzoxaboroles, ribosome, translation, inhibition, antibiotic, drug resistance
• Biological source: Escherichia coli; More
• Total number of polymer chains: 112
• Total formula weight: 4572995.02

Authors

Chen, C.-W.,Volynkina, I.A.,Bortyazh, M.O.,Tereshchenkov, A.G.,Karakchieva, A.O.,Lukianov, D.A.,Komarova, E.S.,Tupikin, A.E.,Skvortsov, D.A.,Tevyashova, A.N.,Tikhomirov, A.S.,Tashlitsky, V.N.,Kabilov, M.R.,Shchekotikhin, A.E.,Dontsova, O.A.,Sergiev, P.V.,Polikanov, Y.S. (deposition date: 2026-02-01, release date: 2026-03-11, Last modification date: 2026-04-08)

Primary citation

Volynkina, I.A.,Bortyazh, M.O.,Chen, C.-W.,Tereshchenkov, A.G.,Karakchieva, A.O.,Lukianov, D.A.,Komarova, E.S.,Tupikin, A.E.,Skvortsov, D.A.,Tevyashova, A.N.,Tikhomirov, A.S.,Tashlitsky, V.N.,Kabilov, M.R.,Shchekotikhin, A.E.,Dontsova, O.A.,Polikanov, Y.S.,Sergiev, P.V.
Benzoxaborole-modified azithromycins inhibit translation without inducing ermC expression.
Antimicrob.Agents Chemother., :e0153925-e0153925, 2026

PubMed Abstract: The rapid increase in antimicrobial resistance underscores the urgent need for new antibacterial agents. One promising strategy involves designing novel compounds through targeted chemical modifications of existing antibiotics. Azithromycin (AZI), a widely used macrolide, has served as a versatile scaffold for developing numerous antibacterial candidates. However, the mechanistic consequences of such modifications remain largely unexplored. Here, we characterize the activity and mechanism of action of three AZI-benzoxaborole (AZI-BB) conjugates. We show that these compounds inhibit bacterial translation and remain active against a model strain carrying an inducible operon, which confers resistance to macrolide antibiotics. Unlike erythromycin, these derivatives, along with AZI itself, exhibit minimal induction of ErmC expression. Structural analysis reveals that the benzoxaborole moiety of AZI-BB2 forms additional interactions with nucleotides C2441 and C2586 of 23S rRNA, likely contributing to premature ribosome stalling at the regulatory sequence and thereby preventing ErmC expression. Furthermore, high-throughput toeprinting analysis combined with deep sequencing (Toe-seq) demonstrates that AZI-BB2 exhibits reduced sequence specificity for canonical macrolide-sensitive stalling motifs. Altogether, these findings demonstrate that targeted chemical modification of AZI can reshape its context-specific interaction with the ribosome and attenuate the induction of macrolide resistance mechanisms.

PubMed: 41874376
DOI: 10.1128/aac.01539-25

Experimental method

X-RAY DIFFRACTION (2.45 Å)