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Updated: Jul 20, 2026

Genetically-encoded Molecular Probes to Study G Protein-coupled Receptors
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Epitope-guided selection of CXCR4-targeting antibodies using AlphaFold3 for GPCR modulation and cancer therapy

Srimathi Venkataraman1, Yi-Chuan Li2, Zi-Wei Hung3

  • 1Graduate Institute of Biological Science and Technology, China Medical University Taichung 406040, Taiwan.

American Journal of Cancer Research
|June 16, 2025
PubMed

Insights

Researchers identified key interaction sites on G protein-coupled receptors (GPCRs) using AlphaFold3. This led to the development of antibodies that block signaling and target cancer cells expressing CXC chemokine receptor 4 (CXCR4).

Area of Science:

  • Structural biology and pharmacology
  • GPCR signaling and antibody therapeutics

Background:

  • G protein-coupled receptors (GPCRs) are crucial cell surface receptors involved in signal transduction.
  • GPCR dysregulation is linked to various diseases, including cancer, inflammation, and metabolic disorders, making them therapeutic targets.
  • Structural elucidation of GPCR-ligand interactions is challenging but vital for drug development.

Purpose of the Study:

  • To predict GPCR-ligand interaction sites using AlphaFold3.
  • To develop novel antibodies targeting CXC chemokine receptor 4 (CXCR4) for therapeutic intervention.
  • To evaluate the efficacy of developed antibodies in blocking CXCR4 signaling and mediating anti-cancer effects.

Main Methods:

  • Utilized AlphaFold3 for predicting interaction sites between ligands and GPCRs, focusing on CXCR4.
  • Employed an epitope-guided approach to select antibodies from a combinatorial library targeting CXCR4.
  • Assessed antibody efficacy in blocking CXCL12 signaling in reporter cell lines and mediating antibody-dependent cellular cytotoxicity (ADCC) in cancer cell lines.

Main Results:

  • AlphaFold3 successfully predicted crucial interaction sites, identifying the extracellular loop 2 (ECL2) as critical for CXCL12-CXCR4 binding.
  • Two antibodies, C5 and F4, were identified that effectively inhibit CXCL12-CXCR4 signaling.
  • These antibodies demonstrated significant antibody-dependent cellular cytotoxicity against acute T cell leukemia and B cell lymphoma cell lines.

Conclusions:

  • The study presents a novel epitope-guided strategy for developing therapeutic antibodies against GPCRs.
  • The identified antibodies (C5 and F4) show potential for treating CXCR4-expressing cancers.
  • This approach offers a promising avenue for developing treatments for diseases associated with GPCR dysfunction.
Keywords:
AlphaFold3CXCL12CXCR4GPCRantibodyphage display

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