Structure-based computational analysis of quercetin and withaferin A as prolactin receptor inhibitors for male breast cancer therapy

Male breast cancer (MBC) is a rare malignancy that is frequently diagnosed at advanced stages and managed using therapeutic strategies largely extrapolated from female breast cancer despite important biological differences. Notably, prolactin receptor (PRLR) expression has been reported in approximately 60% of male breast carcinomas compared with only approximately 20% of benign gynecomastia specimens, highlighting aberrant PRL–PRLR signaling as a potentially relevant molecular feature of MBC. PRLR activates JAK/STAT, PI3K–Akt, and MAPK signaling pathways involved in tumor-cell proliferation and survival, providing a strong rationale for exploring PRLR-directed therapeutic strategies in MBC. This study therefore employed computer-aided drug design (CADD) to identify plant-derived phytochemicals as potential PRLR inhibitors. The PRLR crystal structure (PDB ID: 4I18) was retrieved and validated (3.24 Å resolution, ERRAT score 79.78, 98.8% of evaluated residues in favored or allowed Ramachandran regions). Protein–protein interaction analysis and KEGG pathway mapping confirmed PRLR’s central role in oncogenic signaling. Eighteen phytochemicals were screened via AutoDock Vina and HDOCK; withaferin A (AutoDock Vina: –8.8 kcal/mol; HDOCK score: –226.80, confidence score: 0.8229) and quercetin (AutoDock Vina: –8.7 kcal/mol; HDOCK score: –199.25, confidence score: 0.7281) emerged as top binders. Interaction analysis revealed quercetin forming multiple hydrogen bonds (ASN60: 2.15 Å, SER112: 2.73 Å) and π–π stacking with TRP23 (3.83 Å, 4.53 Å), while withaferin A engaged hydrophobic contacts (ILE55: 4.26 Å; TYR117: 5.15 Å, 5.19 Å) and key hydrogen bonds (SER57: 1.96 Å; LEU47: 2.47 Å). Integrated docking and 500-ns MD simulations identified withaferin A and quercetin as stable predicted PRLR binders, with withaferin A showing superior pose persistence and interaction energy, warranting experimental validation. Pharmacophore mapping showed quercetin’s balanced polar-aromatic profile (3 aromatic rings, 5 donors, 6 acceptors, 3 hydrophobic regions) versus withaferin A’s hydrophobic-rich profile (2 donors, 5 acceptors, 8 hydrophobic regions). DFT analysis yielded small HOMO–LUMO gaps for quercetin (0.16436 eV) and withaferin A (0.18065 eV), indicating high reactivity. ADMET predictions indicated good gastrointestinal absorption, non–BBB permeation, and zero Lipinski violations for both, with bioavailability scores of 0.55; quercetin exhibited a cleaner toxicity profile than withaferin A, which showed AMES mutagenicity and hERG inhibition risks. In conclusion, Quercetin showed greater early conformational adjustment before converging toward a stable bound pose, whereas withaferin A maintained closer and more persistent proximity to the predicted binding pocket and exhibited stronger van der Waals stabilization, together indicating greater predicted dynamic stability of the PRLR–withaferin A complex.