Abstract

This study utilised computational analysis to investigate the therapeutic potential of phloroglucinol against rheumatoid arthritis (RA).  The Differentially expressed genes were identified from the GEO dataset GSE1919 and RA-associated targets were retrieved from the Comparative Toxicogenomics Database (CTD). By comparing these datasets, we identified 17 overlapping targets using a Venn diagram.  Then, the top five genes are identified using Cytoscape and CytoHubba plugin. Gene Ontology and KEGG pathway enrichment analyses revealed involvement of these targets in inflammatory signalling.  The ADME analysis through the QikProp module demonstrated favourable pharmacokinetic properties, including a molecular weight of 126.112 Da, QPlogPo/w of -0.020, oral bioavailability of 70.508% and no violation of Lipinski's Rule of Five. The molecular docking analysis indicated moderate binding affinities with key inflammatory proteins such as IL6 (-3.583) IL-10 (-2.735), IL-1β (-3.764), ICAM1 (-2.890), and TNF-α. (-4.568). The phloroglucinol-TNF-α complex was subjected to 500 ns molecular dynamics simulation, which confirmed structural stability as evidenced by RMSD values and preserved secondary structure throughout the simulation. These findings identify phloroglucinol as a promising natural small-molecule with TNF-α as its primary molecular target.

Keywords

Rheumatoid Arthritis, Phloroglucinol, Network Pharmacology, Molecular Docking, Molecular Dynamics Simulation, TNF-Α, Anti-Inflammatory,

Downloads

Download data is not yet available.

References

  1. M. Jahid, K.U. Khan, R.S. Ahmed, Overview of Rheumatoid Arthritis and Scientific Understanding of the Disease. Mediterranean Journal of Rheumatology, 34(3), (2023) 284–291. https://doi.org/10.31138/mjr.20230801.oo
  2. Y. Velmurugan, S.R. Natarajan, N. Chakkarapani, S. Jayaraman, H. Madhukar, R. Venkatachalam, In Silico and in Vitro Studies for the Identification of Small Molecular Inhibitors from Euphorbia Hirta Linn for Rheumatoid Arthritis: Targeting TNF-Α-Mediated Inflammation. Molecular Diversity, 29(2), (2025) 1189-1206. https://doi.org/10.1007/s11030-024-10900-1
  3. A.K. Pandarathodiyil, K.H. Shree, B. Sivapathasundharam, R. Ramadoss, Salivary Biomarker Profile in Rheumatoid Arthritis and its Interlinkage in Oral Manifestations: A Comprehensive Review. Journal of Oral and Maxillofacial Pathology, 29(1), (2025) 117-126. https://doi.org/10.4103/jomfp.jomfp_23_24
  4. L. Caliogna, M. Berni, C. Torriani, M.E. Mancuso, M.N.D. Di Minno, A.M. Brancato, E. Jannelli, M. Mosconi, G. Pasta, Pathogenesis of osteoarthritis, rheumatoid arthritis, and hemophilic arthropathy: The role of angiogenesis. Haemophilia, 30(6), (2024) 1256-1264. https://doi.org/10.1111/hae.15097
  5. Y.H. Gonfa, F.B. Tessema, A. Bachheti, N. Rai, M.G. Tadesse, A. Nasser Singab, K.K. Chaubey, R.K. Bachheti, Anti-Inflammatory Activity of Phytochemicals from Medicinal Plants and their Nanoparticles: A review. Current Research in Biotechnology, 6, (2023) 100152. https://doi.org/10.1016/j.crbiot.2023.100152
  6. H.A. Saleh, M.H. Yousef, A. Abdelnaser, The Anti-Inflammatory Properties of Phytochemicals and Their Effects on Epigenetic Mechanisms Involved in TLR4/NF-/kB-Mediated Inflammation. Frontiers in Immunology, 12, (2021)606069. https://doi.org/10.3389/fimmu.2021.606069
  7. R.T. Polez, M.A. Ajiboye, M. Osterberg, M.M. Horn, Chitosan Hydrogels Enriched with Bioactive Phloroglucinol for Controlled Drug Diffusion and Potential Wound Healing. International Journal of Biological Macromolecules, 265, (2024) 130808. https://doi.org/10.1016/j.ijbiomac.2024.130808
  8. B. Pradhan, R. Nayak, P.P. Bhuyan, S. Patra, C. Behera, S. Sahoo, J.S. Ki, A. Quarta, A. Ragusa, M. Jena, Algal Phlorotannins as Novel Antibacterial Agents with Reference to the Antioxidant Modulation: Current Advances and Future Directions. Marine Drugs, 20(6), (2022) 403. https://doi.org/10.3390/md20060403
  9. X. Huang, J. Yang, R. Zhang, L. Ye, M. Li, W. Chen, Phloroglucinol Derivative Carbomer Hydrogel Accelerates MRSA-Infected Wounds Healing. International Journal of Molecular Sciences, 23(15), (2022) 8682. https://doi.org/10.3390/ijms23158682
  10. S. Muthu, M. Lakshmikanthan, E. Edward-Sam, M. Subramanian, L. Govindan, A.B.M. Patcha, K. Krishnan, N. Duraisamy, S. Jeyaperumal, A.T. Aziz, Encapsulation of Phloroglucinol from Rosenvingea Intricata Macroalgae with Zinc Oxide Nanoparticles against A549 Lung Cancer Cells. Pharmaceutics, 16(10), (2024) 1300. https://doi.org/10.3390/pharmaceutics16101300
  11. M.M. Kim, S.K. Kim, Effect of Phloroglucinol on Oxidative Stress and Inflammation. Food Chemical Toxicology, 48(10), (2010) 2925–33. https://doi.org/10.1016/j.fct.2010.07.029
  12. A. Mieszkowska, L. Martocq, A. Koptyug, M.A. Surmeneva, R.A. Surmenev, J. Naderi, M. Muchova, K.A. Gurzawska-Comis, T.E. Douglas, Anti-Inflammatory and Osteogenic Effect of Phloroglucinol-Enriched Whey Protein Isolate Fibrillar Coating on Ti-6Al-4V Alloy. Polymers, 17(11), (2025) 1514. https://doi.org/10.3390/polym17111514
  13. Y. Gao, Y. Zhang, X. Liu, Rheumatoid Arthritis: Pathogenesis and Therapeutic Advances. MedComm, 5(3), (2024) e509. https://doi.org/10.1002/mco2.509
  14. H.M.U. Rana, H. Nisar, J. Prajapati, D. Goswami, R. Rawat, V. Eyupoglu, S. Shahid, A. Javaid, W. Nisar, Integrative Bioinformatic Analysis to Identify Potential Phytochemical Candidates for Glioblastoma. Heliyon, 10(24), (2024). https://doi.org/10.1016/j.heliyon.2024.e40744
  15. M.K. Gatasheh, S.R. Natarajan, R. Krishnamoorthy, T.S. Alsulami, P. Rajagopal, C.P. Palanisamy, V.P. Veeraraghavan, S. Jayaraman, Molecular Analysis to Identify Novel Potential Biomarkers as Drug Targets in Colorectal Cancer Therapy: An Integrated Bioinformatics Analysis. Molecular & Cellular Oncology, 11(1), (2024.) 2326699. https://doi.org/10.1080/23723556.2024.2326699
  16. Y. Chen, H. Li, L. Lai, Q. Feng, J. Shen, Identification of Common Differentially Expressed Genes and Potential Therapeutic Targets in Ulcerative Colitis and Rheumatoid Arthritis. Frontiers in Genetics, 11, (2020) 572194. https://doi.org/10.3389/fgene.2020.572194
  17. Y. Velmurugan, N. Chakkarapani, S.R. Natarajan, S. Jayaraman, H. Madhukar, R. Venkatachalam, PPI Networking, In-Vitro Expression Analysis, Virtual Screening, DFT, and Molecular Dynamics for Identifying Natural TNF-Α Inhibitors for Rheumatoid Arthritis. Molecular diversity, (2025) 1-20. https://doi.org/10.1007/s11030-025-11158-x
  18. R. Roy, M.F. Sk, N.A. Jonniya, S. Poddar, P. Kar, Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies. Journal of Biomolecular Structure and Dynamics, 40(14), (2022) 6556-6568. https://doi.org/10.1080/07391102.2021.1897680
  19. Y. Velmurugan, S.R. Natarajan, N. Chakkarapani, S. Jayaraman, H. Madhukar, and R. Venkatachalam, In Silico and in Vitro Studies for the Identification of Small Molecular Inhibitors from Euphorbia Hirta Linn for Rheumatoid Arthritis: Targeting TNF-Α-Mediated Inflammation. Molecular Diversity, 29(2), (2025) 1189-1206. https://doi.org/10.1007/s11030-024-10900-1
  20. S. Manandhar, R. Sankhe, K. Priya, G. Hari, B.H. Kumar, C.H. Mehta, U.Y. Nayak, K.S.R. Pai, Molecular Dynamics and Structure-Based Virtual Screening and Identification of Natural Compounds as Wnt Signaling Modulators: Possible Therapeutics for Alzheimer’s Disease. Molecular Diversity, 26(5), (2022) 2793-2811. https://doi.org/10.1007/s11030-022-10395-8
  21. S.R. Natarajan, R. Krishnamoorthy, M.A. Alshuniaber, T.S. Alsulami, M.K. Gatasheh, P. Rajagopal, C.P. Palanisamy, R. Govindan, V.P. Veeraraghavan, S. Jayaraman, ABCE1 Facilitates Tumour Progression Via Aerobic Glycolysis and Inhibits Cell Death in Human Colorectal Cancer Cells through the P53 Signalling Pathway. Scientific Reports, 15(1), (2025) 24674. https://doi.org/10.1038/s41598-025-92436-4
  22. A. Eswaran, S.R. Natarajan, S. Jayaraman, J.M. Khan, S. Jasmine, V.P. Veeraraghavan, Jervine-Induced Suppression of Triple-Negative Breast Cancer (TNBC) Cells Growth through the Regulation of Wnt Signaling Pathway-An In-Silico and In-Vitro Approach. Journal of Computer-Aided Molecular Design, 40(1), (2026) 57. https://doi.org/10.1007/s10822-025-00754-6
  23. P. Balhara, S. Sharma, N. Vasudeva, Unraveling the chemistry, Pharmacological Activities, and Medicinal Utilization of Phloroglucinol: A Comprehensive Review. Pharmacological Research-Natural Products, (2025) 100421.https://doi.org/10.1016/j.prenap.2025.100421
  24. K. Krishnamoorthy, S.R. Natarajan, V.P. Veeraraghavan, S. Jayaraman, Blueberry Extract and its Bioactive Compounds Mitigate Oxidative Stress and Suppress Human Lung Cancer Cell (A549) Growth by Modulating the Expression of P53/EGFR/STAT3/IL6‐Mediated Signaling Molecules. Cell Biochemistry and Function, 42(4), (2024) e4027. https://doi.org/10.1002/cbf.4027
  25. C. Luxenburg, S. Winograd-Katz, L. Addadi, B. Geiger, Involvement of Actin Polymerization in Podosome Dynamics. Journal of cell science, 125(7), (2012) 1666-1672. https://doi.org/10.1242/jcs.075903
  26. M.M. Postema, N.E. Grega-Larson, L.M. Meenderink, M.J. Tyska, PACSIN2-Dependent Apical Endocytosis Regulates the Morphology of Epithelial Microvilli. Molecular biology of the cell, 30(19), (2019) 2515-2526. https://doi.org/10.1091/mbc.E19-06-0352
  27. D. Fu, Z. Hu, X. Xu, X. Dai, Z. Liu, Key Signal Transduction Pathways and Crosstalk in Cancer: Biological and Therapeutic Opportunities. Translational oncology, 26, (2022) 101510. https://doi.org/10.1016/j.tranon.2022.101510
  28. G. Ramarajyam, R. Murugan, S. Rajendiran, Network Pharmacology and Bioinformatics Illuminates Punicalagin's Pharmacological Mechanisms Countering Drug Resistance in Hepatocellular Carcinoma, Human Gene, 42, (2024) 201328. https://doi.org/10.1016/j.humgen.2024.201328
  29. Q. Li, C. Kang, Mechanisms of Action for Small Molecules Revealed by Structural Biology in Drug Discovery. International Journal of Molecular Sciences, 21(15), (2020) 5262. https://doi.org/10.3390/ijms21155262
  30. M. Markovic, S. Ben-Shabat, A. Aponick, E.M. Zimmermann, A. Dahan, Lipids and Lipid-Processing Pathways in Drug Delivery and Therapeutics. International Journal of Molecular Sciences, 21(9), (2020) 3248. https://doi.org/10.3390/ijms21093248
  31. J. Kim, J. Won Choi, H. Jeong Kim, B. Kim, Y. Kim, E. Hwejin Lee, R. Kim, J. Kim, J. Park, Y. Jeong, J.H. Park, Phloroglucinol Derivatives Exert Anti‐Inflammatory Effects and Attenuate Cognitive Impairment in LPS‐Induced Mouse Model. ChemMedChem, 19(17), (2024) e202400056. https://doi.org/10.1002/cmdc.202400056
  32. P.M. Swamy, P.H. Somashekar, S.A. Shivamurthy, S. Shadakshari, M. Puttaswamappa, N.S. Shanthappa, Design, Synthesis, and Insilico Evaluation of 2-Aminothiazole Derivatives as Potential Mtor and EGFR Inhibitors. Discover Molecules, 2(1), (2025) 31. https://doi.org/10.1007/s44345-025-00039-3
  33. P.P. Pal, A.S. Begum, S.A. Basha, H. Araya, Y. Fujimoto, New Natural Pro-Inflammatory Cytokines (TNF-Α, IL-6 And IL-1β) and Inos Inhibitors Identified from Penicillium Polonicum through in Vitro and in Vivo Studies. International Immunopharmacology, 117, (2023) 109940. https://doi.org/10.1016/j.intimp.2023.109940
  34. N.J. Basha, K.T. Akshay, R.M. Mohan, M. Javeed, O.M. Sharma, Synthesis, Molecular Docking, Drug Likeness, In Silico Toxicity and DFT Studies of Small Molecules as P53-MDM2 Interaction and COX-2 Dual Inhibitors. Journal of Molecular Structure, 1322, (2025) 140393. https://doi.org/10.1016/j.molstruc.2024.140393
  35. S.K. Maurya, R. Mishra, Molecular Docking Studies of Natural Immunomodulators Indicate their Interactions with the CD40L of CD40/CD40L Pathway and CSF1R Kinase Domain of Microglia. Journal of Molecular Modeling, 28(4), (2022) 101. https://doi.org/10.1007/s00894-022-05084-0
  36. M. Taylor, J. Ho, MM/GBSA Prediction of Relative Binding Affinities of Carbonic Anhydrase Inhibitors: Effect of Atomic Charges and Comparison with Autodock4Zn. Journal of Computer-Aided Molecular Design, 37(4), (2023) 167-182. https://doi.org/10.1007/s10822-023-00499-0
  37. H. Zhou, J. Zhou, Y. Lu, H. Luo, W. Hu, J. Xie, X. Wu, B. Li, S. Fan, Y. Chen, F. Zhang, Naringin Alleviates Knee Osteoarthritis by Targeting TNF-α and PTGS2: An Integrated Network Pharmacology, Molecular Simulation, and Experimental Validation Study. International Journal of Molecular Sciences, 27(4), (2026) 1812. https://doi.org/10.3390/ijms27041812
  38. S. Butala, L. Castelo-Soccio, R. Seshadri, E.L. Simpson, J.J. O’Shea, T. Bieber, A.S. Paller, Biologic Versus Small Molecule Therapy for Treating Moderate to Severe Atopic Dermatitis: Clinical Considerations. The Journal of Allergy and Clinical Immunology: In Practice, 11(5), (2023) 1361-1373. https://doi.org/10.1016/j.jaip.2023.03.011
  39. S. Xue, Y. He, L. Pei, H. Xu, Progress of Biologics and Small Molecule Drugs in the Treatment of Hidradenitis Suppurativa. The Journal of Dermatology, 52(9), (2025) 1337-1350. https://doi.org/10.1111/1346-8138.17874
  40. D. Ramirez, J Caballero, Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for their Protein Target. International journal of molecular sciences, 17(4), (2016) 525. https://doi.org/10.3390/ijms17040525
  41. S. Shams, J. M. Martinez, J. R. D. Dawson, J. Flores, M. Gabriel, G. Garcia, A. Guevara, K. Murray, N. Pacifici, M. V. Vargas, T. Voelker, J. W. Hell, J. F. Ashouri, The Therapeutic Landscape of Rheumatoid Arthritis: Current State and Future Directions. Frontiers in Pharmacology, 12, (2021) 680043. https://doi.org/10.3389/fphar.2021.680043
  42. D. Boyenle, T. I. Adelusi, A. T. Ogunlana, R. A. Oluwabusola, N. O. Ibrahim, A. Tolulope, O. S. Okikiola, B. L. Adetunji, I. O. Abioye, A. K. Oyedele, Consensus Scoring-Based Virtual Screening and Molecular Dynamics Simulation of Some TNF-alpha Inhibitors. Informatics in Medicine Unlocked, 28, (2021) 100833. https://doi.org/10.1016/j.imu.2021.100833
  43. Z. Su, Y. Wu, Computational Simulations of TNF Receptor Oligomerization on Plasma Membrane. Proteins Structure Function and Bioinformatics, 88(5), (2019) 698–709. https://doi.org/10.1002/prot.25854
  44. D. S. Chan, H. Lee, F. Yang, C. Che, C. C. L. Wong, R. Abagyan, C. Leung, D. Ma, Structure-Based Discovery of Natural-Product-like TNF-α Inhibitors. Angewandte Chemie International Edition, 49(16), (2010) 2860–2864. https://doi.org/10.1002/anie.200907360
  45. S. Liang, J. Dai, S. Hou, L. Su, D. Zhang, H. Guo, Structural Basis for Treating Tumor Necrosis Factor α (TNFα)-Associated Diseases with the Therapeutic Antibody Infliximab. Journal of Biological Chemistry, 288, (2013) 13799–13807. https://doi.org/10.1074/jbc.M112.433961
  46. S. Yang, S. Kar, Protracted Molecular Dynamics and Secondary Structure Introspection to Identify Dual-Target Inhibitors Of Nipah Virus Exerting approved Small Molecules Repurposing. Scientific Reports, 14(1), (2024) 3696. https://doi.org/10.1038/s41598-024-54281-9
  47. S. Kubik, When molecules meet in water—Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water. ChemistryOpen, 11(4), (2022) e202200028. https://doi.org/10.1002/open.202200028
  48. D. Chen, N. Oezguen, P. Urvil, C. Ferguson, S. M. Dann, T. C. Savidge, Regulation of Protein-Ligand Binding Affinity by Hydrogen Bond Pairing. Science Advances, 2(3), (2016) e1501240. https://doi.org/10.1126/sciadv.1501240
  49. Y. Voynikov, Phloroglucinol α-pyrones from Helichrysum: A review on Structural Diversity, plant Distribution and Isolation. Plants, 14(22), (2025) 3460. https://doi.org/10.3390/plants14223460
  50. G. Jeyaraj, B. Yang, K. Sathishkumar, S. Chokkakula, B. O. Almutairi, W. Xie, Pharmacogenomic and in Silico Identification of Isoform-Selective AKT Inhibitors from Pithecellobium dulce for precision Cancer Therapy. Frontiers in Pharmacology, 16, (2026) 1744408. https://doi.org/10.3389/fphar.2025.1744408
  51. Y. Velmurugan, S. R. Natarajan, N. Chakkarapani, S. Jayaraman, H. Madhukar, R. Venkatachalam, In silico and in Vitro Studies for the Identification of Small Molecular Inhibitors from Euphorbia Hirta Linn for Rheumatoid Arthritis: Targeting TNF-α-Mediated Inflammation. Molecular Diversity, 29(2), (2024) 1189–1206. https://doi.org/10.1007/s11030-024-10900-1
  52. A. Saleem, I. Gul, A. Hassan, J. M. Muneeb, M. Khan, A. A. Malik, B. S. Kumar, S. Singh, In Silico Molecular Docking and Molecular Dynamics Simulation Studies of Potential Inhibitors of Canine Lysyl Oxidase. Heliyon, 12(1), (2025) e44425. https://doi.org/10.1016/j.heliyon.2025.e44425
  53. S. Varalakshmi, P. Vijayalakshmi, V. Rajendran, Advancement of an (in vitro/ex vivo) Hybrid Model Framework to Forecast Polyviral Lung Disease Outcomes. Journal of Investigative Medicine, (2025) 10815589251382266. https://doi.org/10.1177/10815589251382266