Multi-omics analyses, cell experiments, and network pharmacology tools identified key proteins and candidate drugs for alopecia areata treatment.

PURPOSE: Alopecia Areata (AA) is an inflammatory non-cicatricial alopecia with a high prevalence. Some patients with AA show an inferior response to treatment. To find key proteins in AA, Genome-wide association study data from three cohorts were analyzed using Mendelian randomization (MR) method. PATIENTS AND METHODS: The gene expression of the identified proteins was further evaluated and compared between AA and healthy samples from two single-cell RNA datasets (GSE212447 and GSE233906). A cell model was also built to validate the findings. Autodock Vina and GROMACS, were also employed to search for ingredients from traditional Chinese medicine(TCM) that interacted with the identified protein. RESULTS: Three proteins, DEFB1, HGFAC, and CYB5D2, were identified as potential drug targets. The altered gene expression in lesional samples of AA patients was consistent with the promoting or protective effects of identified proteins on the disease. The overexpression of risk factor DEFB1 upregulated the RNA and protein expression of MICA in HaCaT cells. The TCM ingredient cimigenol was found to interact with DEFB1 via molecular docking, and molecular dynamics simulations confirmed the stability of this interaction. CONCLUSION: DEFB1 is a potential drug target with promising prospects for the development of novel drugs for treating AA. The TCM ingredient, cimigenol, is a promising drug for AA treatment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12014-025-09544-6.