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TitleMolecular insights into de novo small-molecule recognition by an intron RNA structure.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 122, Issue 19, Page e2502425122, Year 2025
Publish dateMay 13, 2025
AuthorsTianshuo Liu / Ling Xu / Kevin Chung / Luke J Sisto / Jimin Hwang / Chengxin Zhang / Michael C Van Zandt / Anna Marie Pyle /
PubMed AbstractDespite the promise of vastly expanding the druggable genome, rational design of RNA-targeting ligands remains challenging as it requires the rapid identification of hits and visualization of the ...Despite the promise of vastly expanding the druggable genome, rational design of RNA-targeting ligands remains challenging as it requires the rapid identification of hits and visualization of the resulting cocomplexes for guiding optimization. Here, we leveraged high-throughput screening, medicinal chemistry, and structural biology to identify a de novo splicing inhibitor against a large and highly folded fungal group I intron. High-resolution cryoEM structures of the intron in different liganded states not only reveal molecular interactions that rationalize experimental structure-activity relationship but also shed light on a unique strategy whereby RNA-associated metal ions and RNA conformation exhibit exceptional plasticity in response to small-molecule binding. This study reveals general principles that govern RNA-ligand recognition, the interplay between chemical bonding specificity, and dynamic responses within an RNA target.
External linksProc Natl Acad Sci U S A / PubMed:40339124 / PubMed Central
MethodsEM (single particle)
Resolution2.43 - 3.1 Å
Structure data

48538

9mqs

EMDB-48538, PDB-9mqs:
CryoEM Structure of the Candida albicans Group I Intron-GMP Complex
Method: EM (single particle) / Resolution: 3.1 Å

48539

9mqt

EMDB-48539, PDB-9mqt:
CryoEM Structure of the Candida albicans Group I Intron-Compound 11 Complex under Magnesium Condition
Method: EM (single particle) / Resolution: 2.43 Å

48540

9mqu

EMDB-48540, PDB-9mqu:
CryoEM Structure of the Candida albicans Group I Intron-Compound 11 Complex under Calcium Condition
Method: EM (single particle) / Resolution: 2.59 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE

ChemComp-HOH:
WATER

PDB-1bnu:
CARBONIC ANHYDRASE II INHIBITOR

ChemComp-MG:
Unknown entry

Source
  • candida albicans (yeast)
KeywordsRNA / Intron / Group I / Splicing

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