Long-Term Enoxaparin Use and Osteoporosis Risk: A Real-World Cohort Study with Integrative Computational and Network Toxicology Approaches

Background Enoxaparin sodium is a widely used low-molecular-weight heparin for thromboprophylaxis and anticoagulation. Although it is generally considered to have a lower skeletal toxicity profile than unfractionated heparin, emerging evidence suggests that prolonged exposure may adversely affect bone metabolism. However, robust real-world evidence and mechanistic insights linking long-term enoxaparin use to osteoporosis remain limited. Methods We conducted a large retrospective cohort study using the Medical Information Mart for Intensive Care IV (MIMIC-IV) database, including 23,852 adult patients with documented enoxaparin exposure and complete follow-up. The association between enoxaparin exposure duration and osteoporosis risk was evaluated using multivariable logistic regression, subgroup analyses, restricted cubic spline modeling, and causal mediation analysis. To explore potential molecular mechanisms, we integrated network toxicology, transcriptomic analysis, weighted gene co-expression network analysis (WGCNA), machine learning–based feature selection, and molecular docking. Results Prolonged enoxaparin exposure was significantly associated with an increased risk of osteoporosis in a duration-dependent and nonlinear manner. Patients exposed for more than 90 days had a much higher risk of osteoporosis compared to those exposed for less than 15 days. This risk remained strong even after demographic factors, clinical covariates, and dosing intensity were taken into account. Restricted cubic spline analysis confirmed a significant nonlinear exposure–response relationship. Mediation analyses indicated that dosing frequency and daily dose partially mediated this association, while exposure duration remained the predominant driver. Network toxicology and enrichment analyses implicated oxidative stress, inflammatory signaling, apoptosis, and osteoclast differentiation pathways. Integrative WGCNA and machine learning identified CDK16 and VHL as core regulatory genes. Molecular docking demonstrated stable binding affinities between enoxaparin and both targets, supporting their potential involvement in enoxaparin-associated bone dysregulation. Conclusion Long-term enoxaparin use is associated with an increased risk of osteoporosis, exhibiting clear duration-dependent and nonlinear characteristics. Integrating real-world epidemiologic evidence with systems-level network toxicology highlights CDK16- and VHL-centered pathways as potential mechanistic mediators.