Integrative transcriptomic and molecular dynamics simulations analysis identifies IL6 as a therapeutic hub gene in inflammatory arthritis.

Abstract

Inflammatory arthritis, encompassing autoimmune-driven rheumatoid arthritis (RA) and degenerative osteoarthritis (OA), is characterized by progressive joint destruction, cartilage deterioration, and persistent synovial inflammation. With serious systemic complications, such as cardiovascular and pulmonary involvement, it continues to rank among the world's leading causes of disability. Heterogeneity in therapeutic outcomes highlights the significance for new biomarkers and precision-based therapeutics, even though the pathophysiology of RA is known to involve genetic predisposition, environmental triggers, and dysregulated immune responses. The integrative transcriptomic study of synovial tissue (GSE55235) led to the identification of 177 differentially expressed genes (83 up-regulated and 94 down-regulated) in inflammatory arthritis, where the functional enrichment pointed out a powerful induction of neutrophils-mediated inflammation, cytokines' signaling, remodeling of extracellular matrix, and NF-κB, chemokines, and complement cascades. In the light of network topology, IL6 gene was determined to be the key hub gene under the regulatory influence of PTGS2, JUN, MYC, and CXCL8 and controlled by STAT3, CEBPD, and MAPK14/CDK kinases. IL-6 encoded protein is a four helix bundle cytokine that does not have an active site but has a protein-protein interaction (PPI) interface for interacting with the receptor. Herein, we targeted the region of IL-6 that interacts with IL-6R binding interface. Thus, drug-gene interactions highlighted the FDA-approved drug candidates, where levofloxacin anhydrous exhibited the strongest binding affinity towards the IL-6 target (-7.0 kcal/mol), superior to nelfinavir (-6.8 kcal/mol), and surpassing vitamin A palmitate and metronidazole. This was followed by a 100 nanoseconds of molecular dynamics simulation which results in stable trajectories with levofloxacin having an RMSD (~1.2-1.4 Å), RMSF (~0.15-0.20 Å), radius of gyration (~20.4 Å), and B-factor values indicating high dynamic stability and interaction with the receptor-binding interface of IL-6, while metronidazole showed the highest deviations and flexibility and was chosen as a negative control. Both MMPBSA and MMGBSA calculations showed high binding energies and also highlighting the van der Waals and electrostatic interactions as the main thermodynamic contributors to IL-6 binding. Results inferred that levofloxacin remains an ideal therapeutic lead with favorable computational drug-binding properties and retained stability when bound to IL-6 during molecular dynamics simulation. This makes levofloxacin one of the top choices for future experimentation against inflammatory arthritis. However, such findings will serve as a basis for the design of more specific inhibitors to cope with cytokine storm among patients with serious inflammatory arthritis will structure a pathway for an experimentalist.