Integrated Transcriptomic and Molecular Docking Analysis Prioritizes TLR۴/MD-۲ as a Therapeutic Target and Identifies Candidate Small-Molecule Modulators for Skin Ageing

Background: Skin inflammageing is characterized by chronic, low-grade inflammation that contributes to progressive deterioration of skin structure and function during ageing. Increasing evidence implicates persistent activation of the Toll-like receptor ۴ (TLR۴)/myeloid differentiation factor-۲ (MD-۲) complex in senescence-associated inflammatory signaling, making this pathway an attractive therapeutic target. However, transcriptomics-guided identification of natural modulators targeting the TLR۴/MD-۲ complex remains limited. Methods: An integrated transcriptomic and structure-based computational workflow was applied. RNA-sequencing data from primary human dermal fibroblasts obtained from young and aged donors were analyzed to identify differentially expressed genes (DEGs). Significant DEGs were validated using the CellAge database and the SAUL_SEN_MAYO senescence signature, followed by protein–protein interaction analysis using STRING. TLR۴ was prioritized based on transcriptomic evidence, biological relevance, and structural suitability for molecular docking. Docking simulations against the human TLR۴/MD-۲ complex (PDB ID: ۳FXI) were performed using AutoDock Vina in PyRx, and the docking protocol was validated by redocking the co-crystallized ligand. Results: Nineteen significant DEGs distinguished aged from young dermal fibroblasts. Integration with senescence-related resources identified TLR۴ as a senescence-associated candidate gene, supporting its prioritization for docking. Redocking reproduced the crystallographic binding pose within the MD-۲ hydrophobic pocket with an RMSD of ۲.۰۵۹ Å, confirming docking reliability. All tested compounds occupied the MD-۲ hydrophobic pocket with favorable predicted binding affinities. Celastrol showed the strongest predicted affinity (−۹.۸ kcal/mol), followed by Lupeol (−۹.۵ kcal/mol), Bakuchiol (−۸.۱ kcal/mol), and Resveratrol (−۷.۷ kcal/mol), all exceeding the reference inhibitor TLR۴-IN-C۳۴ (−۶.۴ kcal/mol). Conclusion: This integrated transcriptomic and structure-based analysis identifies TLR۴ as a biologically relevant therapeutic target in skin inflammageing and highlights Celastrol and Lupeol as promising natural modulators of the TLR۴/MD-۲ complex. These findings provide a robust rationale for future experimental validation of TLR۴-targeted interventions for age-associated skin inflammation.

کلیدواژه ها:

Skin ageing ، ageing ، RNA sequencing ، TLR۴ ، transcriptomics ، bioinformatics