Systematic Investigation of Tumor Immune Microenvironment Modulation by Cynomorium songaricum Against Breast Cancer Through Integrated Chemomics, Network Pharmacology and Molecular Docking

<b>Background/Objectives</b>: Breast cancer remains a leading cause of cancer-related mortality in women, with therapeutic resistance frequently arising from tumor heterogeneity and an immunosuppressive tumor immune microenvironment (TIME). While <i>Cynomorium songaricum</i> Rupr. (CS) has been used traditionally in Chinese medicine and exhibits preliminary anti-tumor activity, its bioactive constituents and precise mechanisms against breast cancer remain to be elucidated. <b>Methods</b>: The chemical constituents of CS were systematically profiled using ultra-high-performance liquid chromatography coupled with Q Exactive Orbitrap mass spectrometry (UHPLC-Q-Exactive Orbitrap MS/MS). Network pharmacology and functional enrichment analyses were performed to identify immuno-related targets and pathways, followed by molecular docking to prioritize component-target pairs. Molecular dynamics (MD) simulations were conducted to validate the stability of a representative docked complex and to characterize binding stability, interaction persistence, molecular mechanics/(Poisson-Boltzmann) surface area (MM/(P)BSA) energetics, and principal component analysis (PCA)-based conformational landscapes. <b>Results</b>: We identified 1100 compounds, of which 84 satisfied the in silico drug-likeness criteria, including 12 phenylpropanoids, 4 terpenes, 35 flavonoids, 2 quinones, 1 phenol, 3 alkaloids, and other phytochemicals. Network pharmacology analysis revealed 776 overlapping targets associated with both breast cancer and immune regulation. Functional enrichment analysis underscored significant involvement in immune-related pathways, and molecular docking studies supported high-affinity interactions between the components and their targets. MD analyses further supported a stable bound ensemble for the representative SRC-Tomentogenin complex during the equilibrated window, with persistent pocket occupancy, consistent interaction signatures, favorable MM/(P)BSA binding energetics, and a concentrated low-energy basin on the PCA-based free energy landscape. <b>Conclusions</b>: These findings elucidate the chemical basis of CS and uncover its immunomodulatory mechanism against breast cancer, offering a foundation for developing CS-based immunotherapeutic strategies and supporting multi-target drug discovery from traditional medicines.