7SZK

Cryo-EM structure of 27a bound to E. coli RNAP and rrnBP1 promoter complex

Summary for 7SZK

• Entry DOI: 10.2210/pdb7szk/pdb
• EMDB information: 25570 25571
• Descriptor: DNA-directed RNA polymerase subunit alpha, ZINC ION, DNA-directed RNA polymerase subunit beta, ... (10 entities in total)
• Functional Keywords: transcription, antibiotics, rifamycin, transferase-dna-antibiotic complex, transferase/dna/antibiotic
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 8
• Total formula weight: 500650.54

Authors

Shin, Y.,Murakami, K.S. (deposition date: 2021-11-28, release date: 2022-07-13, Last modification date: 2024-02-28)

Primary citation

Rajeswaran, W.,Ashkar, S.R.,Lee, P.H.,Yeomans, L.,Shin, Y.,Franzblau, S.G.,Murakami, K.S.,Showalter, H.D.,Garcia, G.A.
Optimization of Benzoxazinorifamycins to Improve Mycobacterium tuberculosis RNA Polymerase Inhibition and Treatment of Tuberculosis.
Acs Infect Dis., 8:1422-1438, 2022

PubMed Abstract: Rifampin (RMP), a very potent inhibitor of the (MTB) RNA polymerase (RNAP), remains a keystone in the treatment of tuberculosis since its introduction in 1965. However, rifamycins suffer from serious drawbacks, including 3- to 9-month treatment times, Cyp450 induction (particularly problematic for HIV-MTB coinfection), and resistant mutations within RNAP that yield RIF-resistant (RIF) MTB strains. There is a clear and pressing need for improved TB therapies. We have utilized a structure-based drug design approach to synthesize and test novel benzoxazinorifamycins (bxRIF), congeners of the clinical candidate rifalazil. Our goal is to gain binding interactions that will compensate for the loss of RIF-binding affinity to the (RIF) MTB RNAP and couple those with substitutions that we have previously found that essentially eliminate Cyp450 induction. Herein, we report a systematic exploration of 42 substituted bxRIFs that have yielded an analogue () that has an excellent in vitro activity (MTB RNAP inhibition, MIC, MBC), enhanced (∼30-fold > RMP) activity against RIF MTB RNAP, negligible hPXR activation, good mouse pharmacokinetics, and excellent activity with no observable adverse effects in an acute mouse TB model. In a time-kill study, has a 7 day MBC that is ∼10-fold more potent than RMP. These results suggest that may exhibit a faster kill rate than RMP, which could possibly reduce the clinical treatment time. Our synthetic protocol enabled the synthesis of ∼2 g of at >95% purity in 3 months, demonstrating the feasibility of scale-up synthesis of bxRIFs for preclinical and clinical studies.

PubMed: 35772744
DOI: 10.1021/acsinfecdis.1c00636

Experimental method

ELECTRON MICROSCOPY (2.94 Å)