Modeling the P2X7 receptor: a comparative analysis of conventional methods and AlphaFold

Area of Science:

• Structural biology
• Computational chemistry
• Pharmacology

Background:

• The P2X7 receptor is a key target for treating inflammation, pain, and neurodegeneration.
• Currently, no drugs targeting P2X7 are approved for clinical use.
• Limited availability of crystallized human P2X7 (hP2X7) structures hinders drug discovery.

Purpose of the Study:

• To evaluate the structural accuracy of hP2X7 models generated by homology modeling and AlphaFold.
• To assess the suitability of these models for structure-based drug discovery efforts.
• To compare AlphaFold 2 (AF2) and AlphaFold 3 (AF3) against conventional modeling techniques.

Main Methods:

• Modeled hP2X7 using SWISS-MODEL (homology) and AlphaFold 2 (AF2) and AlphaFold 3 (AF3).
• Assessed model confidence at ligand-binding sites.
• Performed docking simulations with ATP and JNJ47965567 to evaluate ligand-receptor interactions.

Main Results:

• AF2 and AF3 models showed high prediction confidence (scores > 0.82).
• AlphaFold models primarily generated closed-state conformations, limiting open-state modeling.
• Docking simulations indicated AF2 and homology models captured key interactions at orthosteric and allosteric sites.

Conclusions:

• AF2 produced high-confidence hP2X7 models with significant potential for virtual screening (VS).
• While AF3 modeled protein-ligand complexes, AF2 demonstrated superior ligand-binding potential for VS.
• Traditional modeling remains essential for refining flexible or poorly resolved protein regions, accelerating P2X7 antagonist discovery.