COMPUTATIONAL INSIGHTS INTO PROTEIN-LIGAND INTERACTIONS OF SEMI-SYNTHETIC DERIVATIVES OBTAINED FROM HERBAL PLANTS
Main Article Content
Keywords
Herbal products, In-vitro, In-vivo, Bio-active chemical, In-silico research, Specific binding site, Drug development, Drug discovery
Abstract
Natural or Herbal products have long been used, especially in developed countries, to cure a wide range of illnesses. In developed countries, the most natural product-based drug development initiatives employ crude extracts in in-vitro or in-vivo tests. Isolating active principles for structural elucidation investigations is a limited effort. It is well known that the process of finding and developing a new medicine is difficult and requires a significant investment of time and money. The production of herbal pharmaceuticals has been too difficult thus far due to the complex and multi-targeted components found in herbal medicinal resources, as well as their bio-active chemical base and modes of action. These issues require thorough, methodical investigation. To pinpoint the precise target of the medication or drugs, in-silico research is conducted. which locates a medication for the specific binding site; to get a conforming outcome, animal testing can be conducted at the end of the process. Structural data is essential in the modern era of drug development and discovery. By using molecular docking or structural information of molecules, we can identify their safety, efficacy or potency
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2. B. David, J.L. Wolfender, D.A. Dias, The pharmaceutical industry and natural products: historical status and new trends, Phytochem. Rev. 14 (2) (2015) 299–315, doi:10.1007/s11101-014-9367-z.
3. E. Oppong, C. Agyare, Y. Duah, B. Mbeah, A. Asase, J. Sarkodie, H. Nettey, F. Adu, P. Boatema, B. Agyarkwa, P. Amoateng, I. Asiedu-gyekye, A. Nyarko, Ethnomedicinal survey and mutagenic studies of plants used in Accra metropolis, Ghana, J. Ethnopharmacol. (2019) 112309 July, doi: 10.1016/j.jep.2019.112309.
4. M.J. Bapela, J.J.M. Meyer, M. Kaiser, In vitro antiplasmodial screening of ethnopharmacologically selected South African plant species used for the treatment of malaria, J. Ethnopharmacol. 156 (2014) 370–373, doi:10.1016/j.jep.2014.09.017.
5. I. Henneh, R. Akrofi, E. Ameyaw, D. Konja, G. Owusu, B. Abane, J. Acquah-Mills, F. Edzeameh, F. Tayman, Stem bark extract of sterculia setigera delile exhibits anti-inflammatory properties through membrane stabilization, inhibition of protein denaturation and prostaglandin E2 activity, J. Pharm. Res. Int. 22 (5) (2018) 1–11, doi:10.9734/jpri/2018/42030.
6. IT. Henneh, E.O. Ameyaw, R.P. Biney, F.A. Armah, E. Obese, D. Konjah, E. Teye, M. Ekor, Ziziphus abyssinica hydro-ethanolic root bark extract attenuates acute inflammation possibly through membrane stabilization and inhibition of protein denaturation and neutrophil degranulation L'extrait d'écorce de racine hydro-éthanolique de Ziziphus abys, West Afr. J. Pharm. 29 (2) (2018) 81-94.
7. G.Komlaga, S.Cojean,M.Beniddir, R. Dicksona, P. Champy, M. Lincoln, K. Mensah, S. Suyyagh-Albouz, J. Jato, P. Loiseau, The Antimalarial Potential of Three Ghanaian Medicinal Plants. 1, (2015) 4. doi:10.21767/2472-0151.10004.
8. M. Omrani, M. Bayati, P. Mehrbod, Natural products as inhibitors of COVID-19 main protease-A virtual screening by molecular docking(2020). https:// doi.org/10.21203/rs.3.rs-57351/v1.
9. E. Oppong Bekoe, C. Agyare, Y.D. Boakye, B.M. Baiden, A. Asase, J. Sarkodie, H. Nettey, F. Adu, P.B. Otu, B. Agyarkwa, P. Amoateng, I. Asiedu-Gyekye, A. Nyarko, Ethnomedicinal survey and mutagenic studies of plants used in accra metropolis, Ghana, J. Ethnopharmacol. 248 (2020) 112309, doi: 10. 1016/j.jep.2019.112309.
10. Isaac Asiamah, Samuel Asiamah Obir, Woasiedem Tamekloe, Francis Ackah Armah, Lawrence Sheringham Borquaye. Applications of molecular docking in natural products-based drug discovery. Scientific African (2023). doi.org/10.1016/j.sciaf.2023.e01593.
11. C. Guerrero-Perilla, F.A. Bernal, E.D. Coy-Barrera, Molecular docking study of naturally-occurring compounds as inhibitors of N-myristoyl transferase towards antifungal agents discovery, Rev. Colomb. Cienc. Quím. Farm 44 (2) (2015) 162-178.
12. A.C. Pilon, M. Valli, A.C. Dametto, M. Emili, F. Pinto, R.T. Freire, I. Castro-Gamboa, A.D. Andricopulo, V.S. Bolzani, NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity, Sci. Rep. 7 (1) (2017) 1–12 2017 7:1, doi:10.1038/s41598-017-07451-x.
13. Monisha M, Mishra AK, Ramesh NV, Pillai KU, Vineeth PK. In-silico studies in herbal drugs: A review. J Ayu Herb Med 2018;4(1):43-47.
14. Gaba M, Gaba P, Singh S. An Overview On Molecular Docking. International journal of drug development & research. 2(2),219-231.
15. Agu PC, Afiukwa CA, Orji OU, Ezeh EM, Ofoke IH, Ogbu CO, Ugwuja EI, Aja PM. Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in disease management. Sci Rep. 2023 Aug 17;13(1):13398. doi: 10.1038/s41598-023-40160-2. PMID: 37592012; PMCID: PMC10435576.
16. Hong C, Cao J, Wu C-F, et al. The Chinese herbal formula Free and Easy Wanderer ameliorates oxidative stress through KEAP1-NRF2/HO-1 pathway. Sci Rep. 2017; 7(1):11551. doi:10.1038/s41598-017-10443-6.
17. Yi F, Sun L, Xu L-J, et al. In silico Approach for Anti-Thrombosis Drug Discovery: P2Y1R Structure-Based TCMs Screening. Front Pharmacol. 2016; 7:531. doi:10.3389/fphar.2016.00531.
18. Luo G, Lu F, Qiao L, Chen X, Li G, Zhang Y. Discovery of Potential Inhibitors of Aldosterone Synthase from Chinese Herbs Using Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Simulation Studies. Biomed Res Int. 2016; 2016:4182595. doi:10.1155/2016/4182595.
19. Kuok C-F, Hoi S-O, Hoi C-F, et al. Synergistic antibacterial effects of herbal extracts and antibiotics on methicillin-resistant Staphylococcus aureus: A computational and experimental study. Exp Biol Med (Maywood). 2017;242(7):731-743. doi:10.1177/1535370216689828.
20. Shukla KL, Gund TM, Meshnick SR. Molecular modeling studies of the artemisinin (qinghaosu)-hemin interaction: docking between the antimalarial agent and its putative receptor. J Mol Graph 1995;13(4):215-222. http://www.ncbi.nlm.nih.gov/pubmed/8527414. Accessed January 19, 2018.
21. Qiao L-S, Zhang X-B, Jiang L, Zhang Y-L, Li G-Y. Identification of potential ACAT-2 selective inhibitors using pharmacophore, SVM and SVR from Chinese herbs. Mol Divers. 2016; 20(4):933-944. doi:10.1007/s11030-016-9684-9.
22. Zheng Y, Wu J, Feng X, et al. In silico Analysis and Experimental Validation of Lignan Extracts from Kadsura longipedunculata for Potential 5-HT1AR Agonists. Taylor P, ed. PLoS One. 2015; 10(6):e0130055. doi:10.1371/journal.pone.0130055.
23. Mohd Fauzi F, John CM, Karunanidhi A, et al. Understanding the mode-of_action of Cassia auriculata via in silico and in vivo studies towards validating it as a long term therapy for type II diabetes. J Ethnopharmacol 2017; 197:61-72. doi:10.1016/j.jep.2016.07.058.
24. Alugolu V, Rentala S, Komarraju AL, Parimi UD. Docking studies of piperine-iron conjugate with human CYP450 3A4. Bioinformation. 2013; 9(7):334-338. doi:10.6026/97320630009334.
25. Tomy MJ, Sharanya CS, Dileep K V, et al. Derivatives form better lipoxygenase inhibitors than piperine: in vitro and in silico study. Chem Biol Drug Des. 2015; 85(6):715-721. doi:10.1111/cbdd.12455.
26. Seo E-J, Saeed M, Law BYK, et al. Pharmacogenomics of Scopoletin in Tumor Cells. Molecules. 2016; 21(4):496. doi:10.3390/molecules21040496.
27. Seniya C, Yadav A, Khan GJ, Sah NK. In-silico Studies Show Potent Inhibition of HIV-1 Reverse Transcriptase Activity by a Herbal Drug. IEEE/ACM Trans Comput Biol Bioinforma. 2015; 12(6):1355-1364. doi:10.1109/TCBB.2015.2415771.
28. Mathew S, Faheem M, Al-Malki AL, Kumosani TA, Qadri I. In silico inhibition of GABARAP activity using antiepileptic medicinal derived compounds. Bioinformation. 2015; 11(4):189-195. doi:10.6026/97320630011189.
29. Chaudhri KK, Mishra N. A review on Molecular Docking: Novel Tool for drug discovery. SciMedcentral. 4(3),1029.
30. Khemnar MD, Galave VB, Kulkarni VC, Menkundale AC, Otari KV. A review on Molecular Docking. International research journal of pure & applied chemistry. 22(3), 60-68.
31. Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Molecular docking and structure-based drug design strategies. Molecules. 2015 Jul 22;20(7):13384-421. doi: 10.3390/molecules200713384. PMID: 26205061; PMCID: PMC6332083.
32. Chen G, Seukep AJ, Guo M. Recent Advances in Molecular Docking for the Research and Discovery of Potential Marine Drugs. Mar Drugs. 2020 Oct 30;18(11):545. doi: 10.3390/md18110545. PMID: 33143025; PMCID: PMC7692358.
33. Xue R, Fang Z, Zhang M, et al. TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2012;41:D1089–95. https://doi.org/10.1093/nar/gks1100.
34. Ntie-Kang F, Zofou D, Babiaka SB, et al. AfroDb: a select highly potent and diverse natural product library from African medicinal plants. PLoS One. 2013;8:e78085. https://doi.org/10.1371/journal.pone.0078085.
35. Mohanraj K, Karthikeyan BS, Vivek-Ananth RP, et al. IMPPAT: a curated database of Indianmedicinal plants, phytochemistry and therapeutics. Sci Rep. 2018 Mar 12;8(1):4329. https://doi.org/10.1038/s41598-018-22631-z.
36. Kim S, Thiessen PA, Bolton EE, et al. PubChem substance and compound databases. Nucleic Acids Res. 2016;44:D1202–13. https://doi.org/10.1093/nar/gkv951.
37. Afendi FM, Okada T, Yamazaki M, et al. KNApSAcK family databases: integrated metabolite–plant species databases for multifaceted plant research. Plant Cell Physiol. 2012;53:e1. https://doi.org/10.1093/pcp/pcr165.
38. Pathania S, Ramakrishnan SM, Bagler G. Phytochemica: a platform to explore phytochemicals of medicinal plants. Database J Biol Databases Curation. 2015;2015:bav075. https://doi.org/10.1093/database/bav075.
39. Wang Y, Hu J-S, Lin H-Q, et al. Herbalog: a tool for target-based identification of herbal drug efficacy through molecular docking. Phytomedicine. 2016;23:1469–74. https://doi.org/10.1016/j.phymed.2016.08.008.
40. Surabhi, Singh BK, Computer Aided Drug Design: An Overview, Journal of Drug Delivery and Therapeutics. 2018; 8(5):504-509. doi.org/10.22270/jddt.v8i5.1894.
41. Bender, B.J., Gahbauer, S., Luttens, A. et al. A practical guide to large-scale docking. Nat Protoc 16, 4799–4832 (2021).
42. Guedes IA, de Magalhães CS, Dardenne LE. Receptor–ligand molecular docking. Biophysical reviews. 2014; 6(1):75-87.
43. Sharp, K. A., Friedman, R. A., Misra, V., Hecht, J. & Honig, B. Salt effects on polyelectrolyte-ligand binding: comparison of Poisson–Boltzmann, and limiting law/counterion binding models. Biopolymers 36, 245–262 (1995).
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Dec 11, 2024
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Keyur Patel, Dr. Neha Tiwari, & Dr. Pragnesh Patani. (2024). COMPUTATIONAL INSIGHTS INTO PROTEIN-LIGAND INTERACTIONS OF SEMI-SYNTHETIC DERIVATIVES OBTAINED FROM HERBAL PLANTS. Journal of Population Therapeutics and Clinical Pharmacology, 31(11), 1157-1164. https://doi.org/10.53555/y29c2338
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Author Biographies
Keyur Patel
Khyati College of Pharmacy, Palodia, Ahmedabad
Dr. Neha Tiwari
Khyati College of Pharmacy, Palodia, Ahmedabad
Dr. Pragnesh Patani
Khyati College of Pharmacy, Palodia, Ahmedabad
How to Cite
Keyur Patel, Dr. Neha Tiwari, & Dr. Pragnesh Patani. (2024). COMPUTATIONAL INSIGHTS INTO PROTEIN-LIGAND INTERACTIONS OF SEMI-SYNTHETIC DERIVATIVES OBTAINED FROM HERBAL PLANTS. Journal of Population Therapeutics and Clinical Pharmacology, 31(11), 1157-1164. https://doi.org/10.53555/y29c2338