66
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Immunomodulatory and anticytokine therapeutic potential of three Indian spices constituents and its hyaluronic acid conjugates for prevention and post COVID-19 complications: a computational modeling approach

Received 09 Oct 2023, Accepted 19 Jan 2024, Published online: 06 Mar 2024

References

  • Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D., & Zardecki, C. (2002). The protein data bank. Acta Crystallographica. Section D, Biological Crystallography, 58(Pt 6 No 1), 899–907. https://doi.org/10.1107/S0907444902003451
  • Oso, B. J., Adeoye, A. O., & Olaoye, I. F. (2022). Pharmacoinformatics and hypothetical studies on allicin, curcumin, and gingerol as potential candidates against COVID-19-associated proteases. Journal of Biomolecular Structure & Dynamics, 40(1), 389–400. https://doi.org/10.1080/07391102.2020.1813630
  • Abodunrin, O. P., Onifade, O. F., & Adegboyega, A. E. (2022). Therapeutic capability of five active compounds in typical African medicinal plants against main proteases of SARS-CoV-2 by computational approach. Informatics in Medicine Unlocked, 31, 100964. https://doi.org/10.1016/j.imu.2022.100964
  • Aleem, A., Akbar Samad, A. B., & Vaqar, S. (2023). Emerging Variants of SARS-CoV-2 and Novel Therapeutics Against Coronavirus (COVID-19). In StatPearls. StatPearls Publishing.
  • Amalraj, A., Pius, A., Gopi, S., & Gopi, S. (2016). Biological activities of curcuminoids, other biomolecules from turmeric and their derivatives - A review. Journal of Traditional and Complementary Medicine, 7(2), 205–233. https://doi.org/10.1016/j.jtcme.2016.05.005
  • Baroroh, U., Si, S., Biotek, M., Muscifa, Z. S., Destiarani, W., Rohmatullah, F. G., & Yusuf, M. (2023). Molecular interaction analysis and visualization of protein-ligand docking using Biovia Discovery Studio Visualizer. Indonesian Journal of Computational Biology, 2 (1), 22. https://doi.org/10.24198/ijcb.v2i1.46322
  • Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation] [Paper presentation]. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC’06, November. https://doi.org/10.1145/1188455.1188544
  • Chen, C. Y., Kao, C. L., & Liu, C. M. (2018). The cancer prevention, anti-inflammatory and anti-oxidation of bioactive phytochemicals targeting the TLR4 signaling pathway. International Journal of Molecular Sciences, 19(9), 2729. https://doi.org/10.3390/ijms19092729
  • Douglas, E. V., Pires, T. L., & Blundell, D. B. (2015). Ascher.2-15.pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. 2015. https://doi.org/10.1021/acs.jmedchem.5b00104
  • Fadaka, A. O., Sibuyi, N. R. S., Madiehe, A. M., & Meyer, M. (2022). Computational insight of dexamethasone against potential targets of SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 40(2), 875–885. https://doi.org/10.1080/07391102.2020.1819880
  • Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A., Bloino, J., Janesko, B. G., Gomperts, R., Mennucci, B., Hratchian, H. P., Ortiz, J. V., … Fox, D. J, Gaussian 09, Revision A.02. (2016). Gaussian, Inc., Wallingford CT,
  • Genheden, S., & Ryde, U. (2015). Ulf the MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. 67. https://doi.org/10.1517/17460441.2015.1032936
  • Jayabal, D., Jayanthi, S., Thirumalaisamy, R., Karthika, R., & Iqbal, M. N. (2023a). Comparative anti-Diabetic potential of phytocompounds from Dr. Duke’s phytochemical and ethnobotanical database and standard antidiabetic drugs against diabetes hyperglycemic target proteins: An in silico validation. Journal of Biomolecular Structure & Dynamics, 41(24), 15137–15149. https://doi.org/10.1080/07391102.2023.2187231
  • Jayabal, D., Jayanthi, S., Thirumalaisamy, R., & Shimu, M. S. S. (2023b). Molecular insights of anti-diabetic compounds and its hyaluronic acid conjugates against aldose reductase enzyme through molecular modeling and simulations study-a novel treatment option for inflammatory diabetes. Journal of Molecular Modeling, 29(8), 238. https://doi.org/10.1007/s00894-023-05616-2
  • Jyotirmayee, B., & Mahalik, G. (2022). A review on selected pharmacological activities of Curcuma longa L. International Journal of Food Properties, 25(1), 1377–1398. https://doi.org/10.1080/10942912.2022.2082464
  • Kiyama, R. (2020). Nutritional implications of ginger: Chemistry, biological activities and signaling pathways. The Journal of Nutritional Biochemistry, 86, 108486. https://doi.org/10.1016/j.jnutbio.2020.108486
  • Kowalczyk, A., Przychodna, M., Sopata, S., Bodalska, A., & Fecka, I. (2020). Thymol and thyme essential oil-new insights into selected therapeutic applications. Molecules (Basel, Switzerland), 25(18), 4125. https://doi.org/10.3390/molecules25184125
  • Liu, M., Wang, T., Zhou, Y., Zhao, Y., Zhang, Y., & Li, J. (2020). Potential role of ACE2 in coronavirus disease 2019 (COVID-19) prevention and management. Journal of Translational Internal Medicine, 8(1), 9–19. https://doi.org/10.2478/jtim-2020-0003
  • Mani, S. T., Rathinavel, T., Ammashi, S., & Nasir Iqbal, M. (2023). Polycyclic aromatic bioactive compounds from Eclipta alba and its anticancer potential against breast cancer target proteins: An antibreast cancer intervention through in silico and in vitro validations. Polycyclic Aromatic Compounds, 43, 1–30. https://doi.org/10.1080/10406638.2023.2233661
  • Nasir Iqbal, M., Vinoth, S., Sasikanth, V., & Rathinavel, T. (2023). Molecular insights of marine algal polycyclic aromatic compounds as promising anti-viral agents for targeting SARS-CoV-2 proteins – An in silico validation. Polycyclic Aromatic Compounds, 43, 1–24. https://doi.org/10.1080/10406638.2023.2210728
  • Noor, H., Ikram, A., Rathinavel, T., Kumarasamy, S., Nasir Iqbal, M., & Bashir, Z. (2022). Immunomodulatory and anti-cytokine therapeutic potential of curcumin and its derivatives for treating COVID-19 - a computational modeling. Journal of Biomolecular Structure & Dynamics, 40(13), 5769–5784. https://doi.org/10.1080/07391102.2021.1873190
  • Rai, H., Barik, A., Singh, Y. P., Suresh, A., Singh, L., Singh, G., Nayak, U. Y., Dubey, V. K., & Modi, G. (2021). Molecular docking, binding mode analysis, molecular dynamics, and prediction of ADMET/toxicity properties of selective potential antiviral agents against SARS-CoV-2 main protease: An effort toward drug repurposing to combat COVID-19. Molecular Diversity, 25(3), 1905–1927. https://doi.org/10.1007/s11030-021-10188-5
  • Rajagopal, K., Varakumar, P., Baliwada, A., & Byran, G. (2020). Activity of phytochemical constituents of Curcuma longa (turmeric) and Andrographis paniculata against coronavirus (COVID-19): An in silico approach. Future Journal of Pharmaceutical Sciences, 6(1), 104. https://doi.org/10.1186/s43094-020-00126-x
  • Rajamanickam, K., Rathinavel, T., Periyannan, V., Ammashi, S., Marimuthu, S., & Nasir Iqbal, M. (2023). Molecular insight of phytocompounds from Indian spices and its hyaluronic acid conjugates to block SARS-CoV-2 viral entry. Journal of Biomolecular Structure & Dynamics, 41(15), 7386–7405. https://doi.org/10.1080/07391102.2022.2121757
  • Ramakrishna, K., Sairam, M., Syed, C. S., John, K. S., & Audipudi, A. V. (2022). In-silico molecular docking of dichlooroflavan from Zingiber officinale and Allicin from Allium satinum against Mpro a drug target of SARS COV-2. Journal of Advanced Scientific Research, 13(03), 172–180. https://doi.org/10.55218/JASR.202213327
  • Rathinavel, T., Meganathan, B., Kumarasamy, S., Ammashi, S., Thangaswamy, S., Ragunathan, Y., & Palanisamy, S. (2021). Potential COVID-19 drug from natural phenolic compounds through In Silico virtual screening approach. Biointerface Research in Applied Chemistry, 11 (3), 10161–10173. volume https://doi.org/10.33263/BRIAC113.1016110173
  • Rathinavel, T., Palanisamy, M., Palanisamy, S., Subramanian, A., & Thangaswamy, S. (2020). Phytochemical 6-Gingerol – A promising Drug of choice for COVID-19. International Journal of Advanced Science and Engineering, 06(04), 1482–1489. 1482 https://doi.org/10.29294/IJASE.6.4.2020.1482-1489
  • Rudrapal, M., Gogoi, N., Chetia, D., Khan, J., Banwas, S., Alshehri, B., Alaidarous, M. A., Laddha, U. D., Khairnar, S. J., & Walode, S. G. (2022). Repurposing of phytomedicine-derived bioactive compounds with promising anti-SARS-CoV-2 potential:Molecular docking,MD simulation and drug-likeness/ADMET studies. Saudi Journal of Biological Sciences, 29(4), 2432–2446. https://doi.org/10.1016/j.sjbs.2021.12.018
  • Sahoo, C. R., Paidesetty, S. K., & Padhy, R. N. (2021). The recent development of thymol derivative as a promising pharmacological scaffold. Drug Development Research, 82(8), 1079–1095. https://doi.org/10.1002/ddr.21848
  • Salehi, B., Mishra, A. P., Shukla, I., Sharifi-Rad, M., Contreras, M. D. M., Segura-Carretero, A., Fathi, H., Nasrabadi, N. N., Kobarfard, F., & Sharifi-Rad, J. (2018). Thymol, thyme, and other plant sources: Health and potential uses. Phytotherapy Research, 32(9), 1688–1706. https://doi.org/10.1002/ptr.6109
  • Sankar, M., Ramachandran, B., Pandi, B., Mutharasappan, N., Ramasamy, V., Prabu, P. G., Shanmugaraj, G., Wang, Y., Muniyandai, B., Rathinasamy, S., Chandrasekaran, B., Bayan, M. F., Jeyaraman, J., Halliah, G. P., & Ebenezer, S. K. (2021). In silico screening of natural phytocompounds towards identification of potential lead compounds to treat COVID-19. Frontiers in Molecular Biosciences, 8, 637122. https://doi.org/10.3389/fmolb.2021.637122
  • Seadawy, M. G. (2020). Natural compounds (thymol, carvacrol, hesperidine, and thymoquinone). Against SARS-CoV-2 Strain Isolated from Egyptian Patients, , 11(07), 1-10. https://doi.org/10.21203/rs.3.rs-101405/v1
  • Selvaraj, V., Rathinavel, T., Ammashi, S., & Nasir Iqbal, M. (2022). Polyphenolic phytochemicals exhibit promising SARS-COV-2 papain like protease (PLpro) inhibition validated through a computational approach. Polycyclic Aromatic Compounds, 43(6), 5545–5566. https://doi.org/10.1080/10406638.2022.2103578
  • Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. https://doi.org/10.1021/ct900587b
  • Sindhu, M. S.,Poonkothai, M., &Thirumalaisamy, R. (2022). Phenolic and terpene compounds from Plectranthus amboinicus (Lour.) Spreng. Act as promising hepatic anticancer agents screened through in silico and in vitro approaches. South African Journal of Botany, 149, 145–159. https://doi.org/10.1016/j.sajb.2022.06.001
  • Srinivasan, R., Kamalanathan, D., Rathinavel, T., Iqbal, M. N., & Shanmugam, G. (2023). Anti-cancer potentials of aervine validated through in silico molecular docking, dynamics simulations, pharmacokinetic prediction and in vitro assessment of caspase – 3 in SW480 cell line. Molecular Simulation, 49(8), 799–815. https://doi.org/10.1080/08927022.2023.2193646
  • Tallei, T. E., Tumilaar, S. G., Niode, N. J., Kepel, B. J., Idroes, R., Effendi, Y., Sakib, S. A., Emran, T. B. (2020). Potential of plant bioactive compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) glycoprotein inhibitors: A molecular docking study. Scientifica, 2020Volume 2020, 6307457. https://doi.org/10.1155/2020/6307457
  • Thirumalaisamy, R., Aroulmoji, V., Iqbal, M. N., Deepa, M., Sivasankar, C., Khan, R., & Selvankumar, T. (2021a). Molecular insights of hyaluronic acid-hydroxychloroquine conjugate as a promising drug in targeting SARS-CoV-2 viral proteins. Journal of Molecular Structure, 1238, 130457. https://doi.org/10.1016/j.molstruc.2021.130457
  • Thirumalaisamy, R., Aroulmoji, V., Iqbal, M. N., Saride, S., Bhuvaneswari, M., Deepa, M., Sivasankar, C., & Khan, R. (2021b). Molecular insights of hyaluronic acid - ethambutol and hyaluronic acid - isoniazid drug conjugates act as promising novel drugs for the treatment of tuberculosis. Journal of Biomolecular Structure & Dynamics, 41(8), 3562–3573. https://doi.org/10.1080/07391102.2022.2051748
  • Thirumalaisamy, R., Bhuvaneswari, M., Haritha, S., Jeevarathna, S., Janani, K., & Suresh, K. (2022a). Curcumin, naringenin and resveratrol from natural plant products hold promising solutions for modern world diseases – A recent review. South African Journal of Botany, 151, 567–580. https://doi.org/10.1016/j.sajb.2022.06.027
  • Thirumalaisamy, R., Selvankumar, T., Subramanian, A., & Suresh, K. (2022b). Virtual screening of COVID-19 drug from three indian traditional medicinal plants through in silico approach. Research Journal of Biotechnology, 15, 24–140.
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
  • Weininger, D. (1988). SMILES, a chemical language and information system: 1: Introduction to methodology and encoding rules. Journal of Chemical Information and Computer Sciences, 28(1), 31–36. https://doi.org/10.1021/ci00057a005
  • Wijaya, R. M., Hafidzhah, M. A., Kharisma, V. D., Ansori, A. N. M., & Parikesit, A. A. (2021). COVID-19 in silico drug with zingiber officinale natural product compound library targeting the Mpro protein. Makara Journal of Science, 25 (3), 1-15. https://doi.org/10.7454/mss.v25i3.1244

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.