Efficient screening and evaluation of MRGPRX2 antagonists based on AlphaFold 3

Activation of MRGPRX2 directly induces mast cell activation, which is closely related to various allergic inflammatory diseases and could serve as a therapeutic target. However, MRGPRX2 small molecule antagonist drugs have not yet been launched. Virtual screening based on protein structure is an efficient approach for the discovery of small molecule drugs. Nevertheless, the current virtual prediction based on known MRGPRX2 PDB structures is not satisfactory due to the lack of crystallization under inhibitory configuration. In this study, AlphaFold 3 was applied to predict the structure of MRGPRX2 and then used for a Bioactive Compound Library virtual screening using Schrodinger software. The top 30 compounds with the highest scores among 23,562 compounds were selected and validated for their inhibitory effect against Ca²⁺ influx in MRGPRX2-overexpressing HEK293 cells and mast cell degranulation. Further in vivo study indicated that HCH6-1 had a competent cure effect on MRGPRX2-related atopic dermatitis. In addition, cell membrane chromatography (CMC) was also applied to verify the binding characteristic between MRGPRX2 and HCH6-1. Overall, our research demonstrated the use of AlphaFold 3 for protein structure prediction and virtual screening and discovered a novel small molecule MRGPRX2 antagonist.