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Structure paper

TitleContext-dependent translation inhibition as a cancer therapeutic modality.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateFeb 24, 2026
AuthorsPaige D Diamond / Paul V Sauer / Mikael Holm / Canessa J Swanson-Swett / Lucas Ferguson / Natalie M Bratset / Grant W Wienker / Justin Seiwert Sim / Hailey K Adams / Lillian Kenner / Margot Meyers / David Gygi / Zef A Könst / Sogole Sami Bahmanyar / Lawrence G Hamann / Anthony P Schuller /
PubMed AbstractRecent work has demonstrated that some bacterial antibiotics that inhibit protein synthesis by binding the peptidyl transferase center (PTC) of the ribosome act in a context-dependent manner, ...Recent work has demonstrated that some bacterial antibiotics that inhibit protein synthesis by binding the peptidyl transferase center (PTC) of the ribosome act in a context-dependent manner, inhibiting translation elongation only at specific amino acids. However, this phenomenon has yet to be documented for compounds that inhibit the PTC of the human ribosome. Here, we use structure-based design to guide the synthesis of such PTC-binding, context-dependent inhibitors of the human ribosome, termed interdictors. In the PTC, these compounds preferentially interact with nascent protein residues that exhibit complementary physiochemical properties to the moieties of the small molecule, causing structural rearrangements in both the nascent polypeptide chain and ribosomal RNA. Further, the compounds differentially impact ribosome surveillance pathways, including the ribotoxic stress response. Finally, we confirm their anti-tumor activity after oral dosing in a mouse xenograft model of triple-negative breast cancer. Together, our data establish targeting oncogenic dependency factors through context-dependent inhibition of translation as a potential small molecule therapeutic modality for historically difficult to address cancers.
External linksNat Commun / PubMed:41735331 / PubMed Central
MethodsEM (single particle)
Resolution1.9 - 2.2 Å
Structure data

70083

9o3v

EMDB-70083, PDB-9o3v:
Human 80S ribosome stalled on MYC nascent chain
Method: EM (single particle) / Resolution: 2.2 Å

70084

9o3w

EMDB-70084, PDB-9o3w:
Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
Method: EM (single particle) / Resolution: 1.9 Å

70086

9o3y

EMDB-70086, PDB-9o3y:
Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chain
Method: EM (single particle) / Resolution: 2.2 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-SPD:
SPERMIDINE

ChemComp-PUT:
1,4-DIAMINOBUTANE

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

PDB-1b75:
SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN L25 FROM ESCHERICHIA COLI

PDB-1b76:
GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP

Source
  • homo sapiens (human)
KeywordsTRANSLATION / translation inhibitor / interdictor / ribosome / cryogenic-electron microscopy (cryo-EM) / ribotoxic stress response / cancer / MYC

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