AUTHOR(S): Mr. Jagdish S. Belekar*, Mr. Avdhut K. Dukandar, Ms. Sanika S. kokane, Ms. Shruti A. Ambale, Ms.Vaishnavi P. Atigre.
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Abstract:
Dysregulated cytokine signalling via the Janus kinase (JAK)–signal transducer and activator of transcription (STAT) pathway is the main cause of rheumatoid arthritis (RA), a chronic autoimmune disease marked by ongoing synovial inflammation and joint damage. JAK1 is a prospective therapeutic target because it is one of the JAK family members that is essential in mediating pro-inflammatory responses. In order to find new JAK1 inhibitors among FDA-approved medications, the current work used a computational drug repurposing strategy that combined molecular docking and virtual screening based on Morgan fingerprints. Nineteen structurally comparable candidates were obtained from the DrugBank database using tofacitinib as a reference molecule. The anticancer medication Ribociclib had the highest binding affinity (–9.1 kcal/mol) against JAK1, outperforming Tofacitinib (–8.8 kcal/mol), according to docking tests conducted using CB-Dock2. Strong target engagement was confirmed by interaction analysis, which showed robust hydrogen bonding and hydrophobic interactions with important active site residues such as Leu959, Glu966, and Asp1003. The PDB-REDO model refinement enhanced structural precision, boosting the trustworthiness of docking results. Additionally, Ribociclib's pharmacokinetic profile as a systemically active medication is consistent with its strong gastrointestinal absorption and restricted blood–brain barrier permeability, according to the BOILED-Egg model analysis. All of these results point to Ribociclib as a viable repurposing option for JAK1 inhibition in rheumatoid arthritis, deserving of additional in vitro and in vivo validation to investigate its safety and therapeutic efficacy in inflammatory conditions.
Keywords:
Clogged pores, inflammation, synthetic & herbal treatments, bacterial infection.
Introduction:
The chronic, systemic autoimmune disease known as rheumatoid arthritis (RA) mostly affects synovial joints, causing inflammation, bone erosion, and cartilage degradation1. It is typified by gradual joint deformity, pannus development, and chronic synovitis, which eventually lead to pain, stiffness, and loss of function2. Approximately 1% of people worldwide suffer from RA, which is a leading cause of disability globally and more common in women than in men3. In addition to joint involvement, RA is linked to systemic consequences such anaemia, lung fibrosis, and cardiovascular disease, all of which drastically lower the quality of life and life expectancy of those who are affected4.
Environmental factors, immune dysregulation, and genetic vulnerability interact intricately in the pathogenesis of RA5. Tumour necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and interleukin-1β (IL-1β) are pro-inflammatory cytokines released by activated T cells, B cells, and macrophages that promote inflammation and tissue destruction6. The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway is essential to this inflammatory signalling because it sends cytokine-mediated signals to the nucleus and controls the expression of genes linked to inflammatory responses and immune activation7.
JAK1 is one of the four members of the JAK family (JAK1, JAK2, JAK3, and TYK2) that is especially important for the spread of inflammatory cytokine signalling8. JAK1 inhibition is a desirable target for RA therapy since it has been demonstrated to lower the synthesis of inflammatory mediators and inhibit immune cell activation9. JAK inhibitors that are currently on the market, such as tofacitinib, baricitinib, and upadacitinib, have shown clinical effectiveness in managing the symptoms of RA10. However, side effects, expensive treatment costs, and long-term safety concerns frequently restrict their use, highlighting the need for new and better options.
One effective method for finding novel therapeutic applications for already-approved medications is drug repurposing, sometimes referred to as drug repositioning11. Because the pharmacokinetic and toxicity profiles of these drugs are already well established, this strategy lowers development time, expense, and risk. By forecasting chemical interactions at the target level, computational techniques like molecular fingerprinting, virtual screening, and molecular docking have sped up the process of finding repurposing candidates in recent years.
Antineoplastic, antiproliferative, and anti-inflammatory qualities are demonstrated by ribociclib, a selective cyclin-dependent kinase (CDK4/6) inhibitor that has been authorised for the treatment of breast cancer12. It was thought that Ribociclib would also inhibit JAK1, providing therapeutic potential in RA, given the structural closeness between kinase domains.
This work identified new JAK1 inhibitors for RA using a computational drug repurposing strategy that combined molecular docking and virtual screening based on Morgan fingerprints. The lead molecule was Tofacitinib, while Ribociclib was the best-scoring contender, outperforming Tofacitinib (–8.8 kcal/mol) with a binding affinity of –9.1 kcal/mol. According to these results, ribociclib may be a viable repurposing option for JAK1 inhibition in RA, which calls for more experimental verification.
Disease Selection: Rheumatoid Arthritis (RA)
The study's target illness is rheumatoid arthritis (RA), a chronic inflammatory disease that causes cartilage degradation, bone erosion, and disability due to persistent inflammation of the synovial joints13. About 1% of people worldwide suffer from RA, which is primarily a female condition. It is linked to extra-articular consequences such pulmonary fibrosis and cardiovascular disease14. Cytokines such as IL-6, TNF-α, and IFN-γ, which mainly signal via the Janus kinase (JAK)–signal transducer and activator of transcription (STAT) pathway, are responsible for the dysregulated immunological activation that underlies the pathophysiology of RA15.
A key player in the pathogenesis of RA, JAK1 is a vital modulator of pro-inflammatory cytokine signalling among the JAK family16. JAK1 inhibition is a useful therapeutic approach since it inhibits several cytokine-driven inflammatory pathways. JAK1 was chosen as the primary target for this structure-and ligand-based therapeutic repurposing study due to its verified molecular target, well-characterized signalling mechanism, and clinical significance17.
Selection of FDA-Approved Lead Compound: Tofacitinib
Because of its proven effectiveness in treating RA, tofacitinib, a small molecule JAK inhibitor that has FDA approval, was chosen as the study's lead medication. By specifically blocking JAK1 and JAK3, it alters the cytokine signalling that triggers immunological and inflammatory reactions. For computational similarity-based drug screening, the compound's established mechanism of action, clinically verified pharmacokinetics, and safety profile serve as a trustworthy benchmark. The receptor model was the crystal structure of JAK1 coupled to a ligand (PDB ID:3EYG).
The availability of experimental and structural data that support precise ligand-based virtual screening and molecular docking validation further supported the selection of tofacitinib as a reference ligand.
Ligand-Based Drug Repurposing (Morgan Fingerprinting)18
For ligand-based drug repurposing, the DrugBank database was used, with an emphasis on FDA-approved medications. Using Tofacitinib as the reference ligand, a virtual screening method based on Morgan fingerprints was used. Tanimoto similarity coefficients between compounds can be calculated thanks to Morgan fingerprints, which encode the molecular structure by taking into account atom habitats within a specified radius.
Because of its effectiveness and precision in discovering compounds that share substructural similarities with known inhibitors, this approach was chosen. For additional investigation, compounds with a Tanimoto similarity score of ≥ 0.7 were shortlisted as possible hits. Out of the 19 structurally similar medications found in the database, the FDA-approved anticancer medication Ribociclib has the highest similarity score to Tofacitinib.
Binding Interaction and Validation
Based on interaction profiles and binding affinity (kcal/mol), the docking results were examined. Protein–ligand interactions, such as hydrogen bonding, hydrophobic contacts, and π–π stacking interactions, were visualised using Discovery Studio Visualiser19.
Ribociclib had the highest binding affinity (–9.1 kcal/mol) among the 19 tested drugs, outperforming Tofacitinib (–8.8 kcal/mol). Ribociclib's significant binding potential within the JAK1 active pocket was confirmed by the interaction study, which showed that it interacted with important active site residues like Leu959, Glu966, and Asp1003.
Molecular Docking Studies20
CB-Dock2, a sophisticated web-based docking platform that uses AutoDock Vina to estimate binding affinities and interaction poses between ligands and target proteins, was used to perform molecular docking simulations. Based on the ideal cavity score and anticipated binding energy, CB-Dock2 automatically selects the top five possible binding cavities and produces docking data.
The Protein Data Bank (PDB) provided the crystal structure of human Janus Kinase 1 (JAK1) (PDB ID: 3EYG). Water molecules were eliminated, polar hydrogens were added, and the active site surrounding the co-crystallized ligand was defined in order to prepare the structure before docking. In the pathogenesis of rheumatoid arthritis (RA), this location is the ATP-binding pocket that activates the JAK-STAT pathway.
The reference ligand was the lead chemical, Tofacitinib, a JAK inhibitor for RA that has FDA approval. In order to evaluate comparative affinities, a total of 19 structurally comparable FDA-approved medications found using Morgan fingerprint-based virtual screening were also docked with JAK1. The CB-Dock2 platform, which offers an effective interface for ligand-protein interaction analysis, was chosen due to its accuracy in identifying the binding pocket and dependability in determining Vina scores.
Binding affinity (kcal/mol), cavity size, and Vina score were used to assess the docking results; stronger binding interactions were indicated by lower (more negative) energy values. In contrast to Tofacitinib (-8.8 kcal/mol), the anticancer medication Ribociclib showed the highest binding affinity (-9.1 kcal/mol), suggesting a possibly stronger and more stable binding to JAK1. To find important hydrogen bonds, hydrophobic contacts, and electrostatic interactions that contribute to complex stability, docking poses were visualised using Discovery Studio Visualiser.
Data Analysis
The Morgan fingerprint Tanimoto similarity scores and binding energies of the docked compounds were used to rank them. Key amino acid residues involved in ligand stabilisation inside the JAK1 active site were identified by analysing interaction patterns. To determine the stability and dependability of docking, parameters such RMSD, hydrogen bond formation, and contact type were examined.
Multiple stabilising contacts with important JAK1 residues, such as Lys908, Glu966, and Asp939, were shown by ribociclib, a CDK4/6 inhibitor with well-established anticancer effects. This suggested robust binding and possible inhibitory efficacy. Through pharmacological repurposing, this implies that Ribociclib may alter the JAK-STAT signalling system, providing therapeutic benefits in rheumatoid arthritis.
Statistical and Computational Tools
Descriptive statistical techniques were used to examine the connection between binding energies and molecular similarity scores. Matplotlib and Seaborn were used for data visualisation and correlation charting, while Python (version 3.10) modules like RDKit were used for fingerprint generation and similarity index computation. The combination of structure-based (CB-Dock2 docking) and ligand-based (Morgan fingerprinting) screening methods provide a thorough evaluation for finding new medication repurposing candidates that target JAK1 in rheumatoid arthritis.
References
1. Jahid M, Khan KU, Ahmed RS. Overview of rheumatoid arthritis and scientific understanding of the disease. Mediterranean journal of rheumatology. 2023;34(3):284-91.
2. Papadogianni P, Lambrou GI. Rheumatoid Arthritis and Pannus. Journal of Research & Practice on the Musculoskeletal System (JRPMS). 2023 Jun 1;7(2).
3. Finckh A, Gilbert B, Hodkinson B, Bae SC, Thomas R, Deane KD, Alpizar-Rodriguez D, Lauper K. Global epidemiology of rheumatoid arthritis. Nature Reviews Rheumatology. 2022 Oct;18(10):591-602.
4. Wu D, Luo Y, Li T, Zhao X, Lv T, Fang G, Ou P, Li H, Luo X, Huang A, Pang Y. Systemic complications of rheumatoid arthritis: focus on pathogenesis and treatment. Frontiers in Immunology. 2022 Dec 22;13:1051082.
5. Arleevskaya M, Takha E, Petrov S, Kazarian G, Renaudineau Y, Brooks W, Larionova R, Korovina M, Valeeva A, Shuralev E, Mukminov M. Interplay of environmental, individual and genetic factors in rheumatoid arthritis provocation. International Journal of Molecular Sciences. 2022 Jul 23;23(15):8140.
6. Habanjar O, Bingula R, Decombat C, Diab-Assaf M, Caldefie-Chezet F, Delort L. Crosstalk of inflammatory cytokines within the breast tumor microenvironment. International journal of molecular sciences. 2023 Feb 16;24(4):4002.
7. Xiong Y, Song X, Sheng X, Wu J, Chang X, Ren T, Cao J, Cheng T, Wang M. A review of Janus kinase/signal transducer and activator of transcription signaling and cytokines in the pain mechanism of rheumatoid arthritis. European Journal of Inflammation. 2023 Aug 16;21:1721727X231197498.
8. Lv Y, Qi J, Babon JJ, Cao L, Fan G, Lang J, Zhang J, Mi P, Kobe B, Wang F. The JAK-STAT pathway: from structural biology to cytokine engineering. Signal transduction and targeted therapy. 2024 Aug 21;9(1):221.
9. Ding Q, Hu W, Wang R, Yang Q, Zhu M, Li M, Cai J, Rose P, Mao J, Zhu YZ. Signaling pathways in rheumatoid arthritis: implications for targeted therapy. Signal transduction and targeted therapy. 2023 Feb 17;8(1):68.
10. Harrington R, Harkins P, Conway R. Janus kinase inhibitors in rheumatoid arthritis: an update on the efficacy and safety of tofacitinib, baricitinib and upadacitinib. Journal of Clinical Medicine. 2023 Oct 23;12(20):6690.
11. Kulkarni VS, Alagarsamy V, Solomon VR, Jose PA, Murugesan S. Drug repurposing: an effective tool in modern drug discovery. Russian journal of bioorganic chemistry. 2023 Apr;49(2):157-66.
12. Elakkiya MR, Krishnasreya M, Tharani S, Arun M, Vijayalakshmi L, Lim J, Ghfar AA, Chithradevi B. Targeting CDK4/6 in Cancer: Molecular Docking and Cytotoxic Evaluation of Thottea siliquosa Root Extract. Biomedicines. 2025 Jul;13(7):1658.
13. Hasan AA, Khudhur HR, Hameed AK. Rheumatic autoimmune diseases (focus on RA): prevalence, types, causes and diagnosis. Karbala Journal of Pharmaceutical Sciences. 2022 Jan 1;1(20).
14. Misra DP. Clinical manifestations of rheumatoid arthritis, including comorbidities, complications, and long-term follow-up. Best Practice & Research Clinical Rheumatology. 2025 Mar 1;39(1):102020.
15. Ding Q, Hu W, Wang R, Yang Q, Zhu M, Li M, Cai J, Rose P, Mao J, Zhu YZ. Signaling pathways in rheumatoid arthritis: implications for targeted therapy. Signal transduction and targeted therapy. 2023 Feb 17;8(1):68.
16. Yu Z, Liu J, Chen L, Xie J. Role of Interleukin-6 in Rheumatoid Arthritis-Associated Interstitial Lung Disease: Focus on the JAK/STAT Pathway and Macrophage Polarization. Journal of Inflammation Research. 2025 Dec 31:10953-67.
17. Enni MA, Maraj MA. IN SILICO DRUG REPURPOSING FOR INFLAMMATORY DISEASES: A SYSTEMATIC REVIEW OF MOLECULAR DOCKING AND VIRTUAL SCREENING STUDIES. American Journal of Advanced Technology and Engineering Solutions. 2022 Dec 29;2(04):35-64.
18. Bacilieri M, Moro S. Ligand-based drug design methodologies in drug discovery process: an overview. Current drug discovery technologies. 2006 Sep 1;3(3):155-65.
19. Owoloye AJ, Ligali FC, Enejoh OA, Musa AZ, Aina O, Idowu ET, Oyebola KM. Molecular docking, simulation and binding free energy analysis of small molecules as Pf HT1 inhibitors. PloS one. 2022 Aug 26;17(8):e0268269.
20. Jakhar R, Dangi M, Khichi A, Chhillar AK. Relevance of molecular docking studies in drug designing. Current Bioinformatics. 2020 May 1;15(4):270-8.
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