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Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site

Martin L Rennie1, Connor Arkinson1, Viduth K Chaugule1

  • 1Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.

Science Advances
|September 28, 2022
PubMed

Insights

Researchers uncovered the binding mode of USP1 inhibitors, revealing how ML323 disrupts the enzyme’s structure to inhibit its function in DNA repair, crucial for cancer therapy.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Oncology

Background:

  • DNA damage repair is vital for genomic stability and often impaired in cancers.
  • Ubiquitin-specific protease 1 (USP1) is a key deubiquitinase in DNA repair pathways and a cancer drug target.
  • The binding mechanism of existing USP1 inhibitors remains unknown.

Purpose of the Study:

  • To elucidate the binding mode of the USP1 inhibitor ML323 using structural biology techniques.
  • To understand the structural basis for USP1 inhibition by ML323.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) was employed to determine the structure of the USP1-ML323 complex.
  • High-resolution structures (2.5 Å) were obtained for USP1 with and without the inhibitor ML323.

Main Results:

  • An unusual binding mode for ML323 was identified, disrupting USP1's hydrophobic core.
  • Inhibitor binding induced conformational changes in USP1's secondary structure.
  • These rearrangements led to subtle active site modifications, explaining the inhibition mechanism.

Conclusions:

  • The determined structures reveal the mechanism of USP1 inhibition by ML323.
  • These findings provide a structural foundation for developing novel, structure-based USP1 inhibitors for cancer treatment.

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