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TitleStructure-based design of Sec61 translocon targeting prodrugs minimize off-target toxicity.
Journal, issue, pagesCell Chem Biol, Vol. 33, Issue 6, Page 823-836.e21, Year 2026
Publish dateJun 18, 2026
AuthorsQingqing Hao / Laurie Wang / Hui Pan / Xihui Xiao / Wenyan Dong / Wencong Pan / Jingjing Sun / Wu Su / Lijing Fang / Eunyong Park / Guiyang Yao /
PubMed AbstractCoibamide A (CbA) is a cyclic depsipeptide that inhibits the function of the Sec61 translocon and exhibits significant antitumor activity. However, its broad Sec61 inhibition results in non-selective ...Coibamide A (CbA) is a cyclic depsipeptide that inhibits the function of the Sec61 translocon and exhibits significant antitumor activity. However, its broad Sec61 inhibition results in non-selective cytotoxicity, limiting therapeutic applications. To elucidate the molecular mechanism of CbA-mediated Sec61 blockade and enable rational prodrug design, we determined the cryo-EM structure of human Sec61 bound to CbA at 3.1 Å resolution. The structure reveals that CbA adopts a distinctive lasso-like conformation and occupies the lateral gate of Sec61, a binding site shared with other Sec61 inhibitors, while forming a particularly more expansive set of interactions with the lateral gate. Guided by these structural insights, we conducted structure-activity relationship studies and developed prodrug strategies that modulate CbA's antitumor activity through the controlled perturbation of intramolecular and protein hydrogen bonding interactions. Together, these results establish a structure-guided strategy for prodrug design of CbA and demonstrate the general applicability of backbone-caging to enhance the tolerability of Sec61 inhibitors.
External linksCell Chem Biol / PubMed:42263680
MethodsEM (single particle)
Resolution3.1 Å
Structure data

73558

9yws

EMDB-73558, PDB-9yws:
Human Sec61 complex bound to coibamide A
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-CLR:
CHOLESTEROL

Source
  • homo sapiens (human)
  • leptolyngbya sp. (bacteria)
KeywordsPROTEIN TRANSPORT / Sec61 / Coibamide / Endoplasmic reticulum / depsipeptide

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