Fragment-based discovery of TopBP1 inhibitors integrated with AI-driven molecular docking

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• DNA topoisomerase IIβ-binding protein 1 (TopBP1) is implicated in key oncogenic pathways driving cancer.
• Understanding TopBP1 inhibitor mechanisms is crucial but hindered by a lack of structural data.

Purpose of the Study:

• To identify and characterize small-molecule inhibitors of TopBP1 using fragment-based screening.
• To elucidate the binding modes of identified inhibitors for structure-based drug design.

Main Methods:

• Fragment-based screening was used to identify ligands for the TopBP1 BRCT7-8 domain.
• Nuclear magnetic resonance (NMR) chemical shift perturbations determined binding affinities and sites.
• Deep learning model Chai-1 predicted binding models.
• X-ray crystallography confirmed the binding mode of adamantane acetic acid (ADA).

Main Results:

• Four small-molecule ligands (adamantane acetic acid, zaltoprofen, diclofenac sodium, and quinine) were identified.
• NMR indicated that ADA, zaltoprofen, and diclofenac sodium bind to the same site, while quinine binds to a distinct site.
• Crystal structure confirmed ADA as an orthosteric inhibitor, competing with the native substrate BACH1.
• Quinine is proposed as a potential allosteric inhibitor.

Conclusions:

• This study identifies novel orthosteric (ADA) and potential allosteric (quinine) inhibitors of TopBP1.
• The findings provide a foundation for developing more potent TopBP1 inhibitors for cancer therapy.
• Structural insights facilitate future structure-based drug design targeting TopBP1.