Interaction of Coumarin, Daphnetin, Fraxetin from Natural Materials with Carbanoic anhydrase II in Inhibiting Glaucoma

Rismi Verawati; Fajri Ikhsan; Okta Suryani

doi:10.31938/jsn.v14i4.735

Interaction of Coumarin, Daphnetin, Fraxetin from Natural Materials with Carbanoic anhydrase II in Inhibiting Glaucoma

Authors

Rismi Verawati Universitas Negeri Padang
Fajri Ikhsan Universitas Negeri Padang
Okta Suryani Universitas Negeri Padang

DOI:

https://doi.org/10.31938/jsn.v14i4.735

Keywords:

Molecular Docking, Coumarin, Daphnetin, Fraxetin, Carbanoic anhydrase II, Osteopetrosis

Abstract

This article explores the interaction of Coumarin compounds and their derivatives obtained from natural extracts with Carbonic anhydrase II protein in inhibiting Glaucoma computationally. This research method includes modeling using software such as Pymol, Pyrx, Protein Plus, and Lipinski Rule of Five. The results showed Binding Affinity and RMSD of Coumarin, Daphnetin, and Fraxetin compounds with Carbonic anhydrase II with strong interaction. Protein Plus analysis was used to visualize the interaction that occurred between the compound and the Carbonic anhydrase II protein, in addition to the Lipinski Rule of Five test results, which showed results that were in accordance with the rules and met the drug criteria. These results indicate that Coumarin, Daphnetin, and Fraxetin compounds as Carbonic anhydrase II inhibitors have the potential to inhibit glaucoma. Daphnetin compound is the best inhibitor seen from the Binding Affinity value of -6.9, -5.8, and -5.5, as well as the results of Daphnetin's Lipinski Rule of Five data. However, further research is needed to validate this computational study.

Downloads

Download data is not yet available.

References

Aini, N. S., Kharisma, V. D., Widyananda, M. H., Murtadlo, A. A. A., Probojati, R. T., Turista, D. D. R., Tamam, M. B., Jakhmola, V., Novaliendry, D., Mandeli, R. S., Oktavia, B., Albari, M. T., Al Aziz, S., Ghifari, M. R., Suryani, O., Azhari, P., Ghifari, M. A., Purnamasari, D., Samala, A. D., … Zainul, R. (2022). Bioactive Compounds from Purslane (Portulaca oleracea L.) and Star Anise (Illicium verum Hook) as SARS-CoV-2 Antiviral Agent via Dual Inhibitor Mechanism: In Silico Approach. Pharmacognosy Journal, 14(4), 352–357. https://doi.org/10.5530/pj.2022.14.106

Chen, X., Li, H., Tian, L., Li, Q., Luo, J., & Zhang, Y. (2020). Analysis of the Physicochemical Properties of Acaricides Based on Lipinski’s Rule of Five. Journal of Computational Biology, 27(9). https://doi.org/10.1089/cmb.2019.0323

Faridah, A., Verawati, R., Oktavia, B., Ghufron, M., Purnamasari, D., Ghifari, M. R., Rosalina, L., Azhari, P., Zainul, R., Kharisma, V. D., Jakhmola, V., Rebezov, M., & Ansori, A. N. M. (2023). Study on the Inhibition of Sinensetin Extract from Cat’s Whiskers Plant (Orthosiphon aristatus) on ATP Binding Cassette Sub-Family G Member 2 in Uric Acid. Pharmacognosy Journal, 15(4), 506–511. https://doi.org/10.5530/pj.2023.15.110

Fitriani, I. N., Utami, W., Zikri, A. T., & Santoso, P. (2020). In Silico Approach of Potential Phytochemical Inhibitor from Moringa oleifera, Cocos nucifera, Allium cepa, Psidium guajava, and Eucalyptus globulus for the treatment of COVID-19 by Molecular Docking. In ResearchSquare. https://doi.org/10.21203/rs.3.rs-42747

Ige, M., & Liu, J. (2020). Herbal medicines in glaucoma treatment. In Yale Journal of Biology and Medicine (Vol. 93, Issue 2).

Ivanovi?, V., Ran?i?, M., Arsi?, B., & Pavlovi?, A. (2017). Lipinski ’ s rule of five , famous extensions and famous exceptions Lipinski rule of five. 3(1), 171–177.

Khsiba, A., Nasr, S., Hamzaoui, L., Mahmoudi, M., Mohamed, A. Ben, Yaakoubi, M., Medhioub, M., & Azouz, M. M. (2022). Osteopetrosis: a rare case of portal hypertension. Future Science OA, 8(8). https://doi.org/10.2144/fsoa-2022-0028

Komari, N., Hadi, S., & Suhartono, E. (2020). Pemodelan Protein dengan Homology Modeling menggunakan SWISS-MODEL. Jurnal Jejaring Matematika Dan Sains, 2(2), 65–70. https://doi.org/10.36873/jjms.2020.v2.i2.408

Lam, W. W. T., & Siu, S. W. I. (2017). PyMOL mControl: Manipulating molecular visualization with mobile devices. Biochemistry and Molecular Biology Education, 45(1). https://doi.org/10.1002/bmb.20987

Lomelino, C. L., & McKenna, R. (2019). Carbonic anhydrase II in complex with carboxylic acid-based inhibitors. Acta Crystallographica Section F: Structural Biology Communications, 75. https://doi.org/10.1107/S2053230X18018344

Matos, M. J., Santana, L., Uriarte, E., Abreu, O. A., Molina, E., & Yordi, E. G. (2015). Coumarins — An Important Class of Phytochemicals. In Phytochemicals - Isolation, Characterisation and Role in Human Health. https://doi.org/10.5772/59982

Michels, T. C., & Ivan, O. (2023). Glaucoma: Diagnosis and Management. American Family Physician, 107(3). https://doi.org/10.1111/j.1442-9071.2006.01326.x

Nur, M. S., Yudiandani, R. E., & Solikah, A. N. (2022). Potensi Senyawa Chromodoris sebagai Pengikat ReseptorSARS-CoV-2 secara In Silico. Sains Dan Matematika, 7(2), 70–76.

O’Herin, C. B., Moriuchi, Y. W., Bemis, T. A., Kohlbrand, A. J., Burkart, M. D., & Cohen, S. M. (2023). Development of Human Carbonic Anhydrase II Heterobifunctional Degraders. Journal of Medicinal Chemistry, 66(4). https://doi.org/10.1021/acs.jmedchem.2c01843

Patel, H., & Kukol, A. (2021). Integrating molecular modelling methods to advance influenza A virus drug discovery. In Drug Discovery Today (Vol. 26, Issue 2). https://doi.org/10.1016/j.drudis.2020.11.014

Pratama, A. B., Herowati, R., & Ansory, H. M. (2021). Studi Docking Molekuler Senyawa Dalam Minyak Atsiri Pala (Myristica fragrans H.) Dan Senyawa Turunan Miristisin Terhadap Target Terapi Kanker Kulit. Majalah Farmaseutik, 17(2), 233. https://doi.org/10.22146/farmaseutik.v17i2.59297

Ramayanti, K., Riza, H., & Fajriaty, I. (2015). Molecular Docking of Drymaritin, Triptonine A and Triptonine B Compounds Against HIV Enzymes. Jurnal Mahasiswa Farmasi Fakultas Kedokteran UNTAN, 3(1).

Ren, S., Xing, Y., Wang, C., Jiang, F., Liu, G., Li, Z., Jiang, T., Zhu, Y., & Piao, D. (2020). Fraxetin inhibits the growth of colon adenocarcinoma cells via the Janus kinase 2/signal transducer and activator of transcription 3 signalling pathway. International Journal of Biochemistry and Cell Biology, 125(February), 105777. https://doi.org/10.1016/j.biocel.2020.105777

Rosalina, L., Purnamasari, D., Verawati, R., Suryani, O., Ghifari, M. A., Lubis, A. P., Zainul, R., Mandeli, R. S., Kharisma, V. D., Jakhmola, V., Rebezov, M., & Ansori, A. N. M. (2023). In Silico Study on the Inhibition of Sitogluside from Clove Plant (Syzygium aromaticum) on Interleukin 2 in B and T Cell Proliferation. Pharmacognosy Journal, 15(4), 575–580. https://doi.org/10.5530/pj.2023.15.122

Rosignoli, S., & Paiardini, A. (2022). Boosting the Full Potential of PyMOL with Structural Biology Plugins. Biomolecules, 12(12). https://doi.org/10.3390/biom12121764

Schöning-Stierand, K., Diedrich, K., Fährrolfes, R., Flachsenberg, F., Meyder, A., Nittinger, E., Steinegger, R., & Rarey, M. (2020). ProteinsPlus: Interactive analysis of protein–ligand binding interfaces. Nucleic Acids Research, 48(W1), W48–W53. https://doi.org/10.1093/NAR/GKAA235

Scolnick, L. R., Clements, A. M., Liao, J., Crenshaw, L., Hellberg, M., May, J., Dean, T. R., & Christianson, D. W. (1997). Novel binding mode of hydroxamate inhibitors to human carbonic anhydrase II. Journal of the American Chemical Society, 119(4). https://doi.org/10.1021/ja963832z

Singh, D. K., Cheema, H. S., Saxena, A., Jyotshana, Singh, S., Darokar, M. P., Bawankule, D. U., Shanker, K., & Luqman, S. (2017). Fraxetin and ethyl acetate extract from Lawsonia inermis L. ameliorate oxidative stress in P. berghei infected mice by augmenting antioxidant defence system. Phytomedicine, 36. https://doi.org/10.1016/j.phymed.2017.09.012

Stanzione, F., Giangreco, I., & Cole, J. C. (2021). Use of molecular docking computational tools in drug discovery. In Progress in Medicinal Chemistry (Vol. 60). https://doi.org/10.1016/bs.pmch.2021.01.004

Sunadi, Aziz, S. Al, Fitri, F., Sari, D. P., Ghifari, M. R., Verawati, R., Yessirita, N., Illiandri, O., Mandeli, R. S., Purnamasari, D., Azhari, P., Zainul, R., Kharisma, V. D., Jakhmola, V., Rebezov, M., & Ansori, A. N. M. (2023). Hepatitis E Inhibited by Rosmarinic Acid Extract from Clove Plant (Syzygium Aromaricum) through Computational Analysis. Pharmacognosy Journal, 15(4), 518–523. https://doi.org/10.5530/pj.2023.15.112

Thada, R., Chockalingam, S., Dhandapani, R. K., & Panchamoorthy, R. (2013). Extraction and quantitation of coumarin from cinnamon and its effect on enzymatic browning in fresh apple juice: A bioinformatics approach to illuminate its antibrowning activity. Journal of Agricultural and Food Chemistry, 61(22), 5385–5390. https://doi.org/10.1021/jf4009789

Tijjani, H., Olatunde, A., Adegunloye, A. P., & Ishola, A. A. (2022). In silico insight into the interaction of 4-aminoquinolines with selected SARS-CoV-2 structural and nonstructural proteins. In Coronavirus Drug Discovery: Druggable Targets and In Silico Update: Volume 3. https://doi.org/10.1016/B978-0-323-95578-2.00001-7

Tisnadjaja, D., Irawan, H., Ekawati, N., Bustanussalam, B., & Simanjuntak, P. (2020). Potency of Cinnamomum burmannii as Antioxidant and ? Glucosidase Inhibitor and Their Relation to Trans-Cinamaldehyde and Coumarin Contents. Jurnal Fitofarmaka Indonesia, 7(3), 20–25. https://doi.org/10.33096/jffi.v7i3.639

Vitiello, L., Capasso, L., Cembalo, G., De Pascale, I., Imparato, R., & De Bernardo, M. (2023). Herbal and Natural Treatments for the Management of the Glaucoma: An Update. In BioMed Research International (Vol. 2023). https://doi.org/10.1155/2023/3105251

Wróblewska-?uczka, P., Grabarska, A., Góralczyk, A., Marz?da, P., & ?uszczki, J. J. (2023). Fraxetin Interacts Additively with Cisplatin and Mitoxantrone, Antagonistically with Docetaxel in Various Human Melanoma Cell Lines—An Isobolographic Analysis. International Journal of Molecular Sciences, 24(1). https://doi.org/10.3390/ijms24010212

Xia, Y., Chen, C., Liu, Y., Ge, G., Dou, T., & Wang, P. (2018). Synthesis and structure-activity relationship of daphnetin derivatives as potent antioxidant agents. Molecules, 23(10). https://doi.org/10.3390/molecules23102476

Yuan, S., Chan, H. C. S., & Hu, Z. (2017). Using PyMOL as a platform for computational drug design. Wiley Interdisciplinary Reviews: Computational Molecular Science, 7(2). https://doi.org/10.1002/wcms.1298

Zainul, R., Verawati, R., Sukma Rita, R., Ranuharja, F., Ghufron, M., Samala, A. D., Satriawan, H., Ghifari, M. R., Purnamasari, D., Mandeli, R. S., Lubis, A. P., Kharisma, V. D., Jakhmola, V., Rebezov, M., & Ansori, A. N. M. (2023). Computational Evaluation of the Potential of Salicylate Compound from Syzygium aromaticum on Carbonic Anhydrase I as a Gastric Acid Stimulant. Pharmacognosy Journal, 15(4), 489–493. https://doi.org/10.5530/pj.2023.15.107