In Silico Discovery and Preliminary In Vitro Evaluation of a SETDB1-Related Candidate Compound Associated with Early Osteogenic Effects

Background/Objectives: Osteoporosis remains a clinically important metabolic bone disorder with limited bone-forming therapeutic options. SET domain bifurcated protein 1 (SETDB1) is involved in osteogenic epigenetic regulation, but small-molecule discovery guided by SETDB1-associated structural regions remains limited. This study aimed to identify a candidate compound with in silico relevance to a SETDB1-associated ligand-bound pocket and assess its association with early osteogenic readouts. Methods: A computational–experimental workflow was used, including hierarchical molecular docking, MM-GBSA rescoring, ADMET-based prioritization, redocking validation, molecular dynamics simulations, and preliminary in vitro evaluation in MC3T3-E1 cells. Compound 271 (C271) was selected based on structure-based screening results and predicted developability-related properties. Cytocompatibility, alkaline phosphatase (ALP) activity and staining, selected molecular markers, and SETDB1–H3 molecular dynamics behavior were evaluated. Results: Redocking reproduced the reference binding mode, and molecular dynamics simulations indicated that C271 maintained a relatively persistent conformation around the predicted SETDB1-associated pocket. Comparative SETDB1–H3 simulations showed altered H3 dynamics and SETDB1–H3 contact patterns in the C271-containing system. In cell-based assays, C271 showed no appreciable cytotoxicity within the tested concentration range and was associated with increased ALP activity and staining. C271 treatment was accompanied by higher global H3K9me3 and Runx2 levels, whereas SETDB1 protein abundance remained largely unchanged. Conclusions: C271 was identified as a computationally prioritized SETDB1-related candidate compound associated with early osteogenic-associated cellular responses. The evidence supports computational plausibility and cell-level association, but does not establish direct SETDB1 engagement, SETDB1 enzymatic modulation, SETDB1-dependent causality, or late-stage osteogenic maturation/mineralization. Given the single-compound evaluation, further target-engagement, enzymatic, and functional studies are needed.