Interaksi Molekuler Senyawa D-Manitol (Kulit Kopi) terhadap PLPro

Yohanes Bare, Frederiksen Novenrius Sini Timba, Maria Marcelina Dua Nurak, Dewi Ratih Tirto Sari, Marsiana Coo Mogi

Abstract


Perkembangan virus dalam proses replikasi menjadi target dalam menghambat siklus hidup virus. Protein yang memiliki peran dalam replikasi adalah PLPro. Terapi PLPro dilakukan dengan memanfaatkan limbah kopi yang diprediski memilki bioaktif D-manitol dengan sifat farmakologis. Tujuan penelitian ini adalah mengalisis potensi senyawa D-manitol yang terkandung dalam kulit kopisebagai kandidat terapi corona melalui penghambatan PLPro. Metode penelitian Ligan D-manitol (CID: 88038555) sedangkan Protein Papain like protease (PLPro) (PDB ID 6w9c), sebagai target protein anti-coronavirus diunduh struktur tiga dimensinya di Protein Data Bank. Selanjutnya struktur protein dipreparasi protein atau ligan, docking, visualisasi mengikuiti penelitian. Hasil docking senyawa dan protein menggunakan program PyMol versi 2.2. analisis docking dilakukan dengan mengeksplorasi interaksi kompleks baik 3D dan 2d, jenis ikatan, jumlah interaksi. Analisis menggunakkan program Discovery Studio ver 21.1.1.). Senyawa D-manitol memiliki potensi sebagai salah satu terapi covid-19 melalui penghambatan PLPro sehingga menyebabkan terhambatnya replikasi virus corona. Potensi ini didukung dengan adanya energi ikatan yang terbentuk sehingga meningkatkan stabilitas ikatan sebesar -156 Kj/mol. Penelitian lanjutan perlu dilakukan untuk konfirmasi terhadap aktivitas D-manitol sebagai terapi virus.


Keywords


D-manitol, kulit kopi, PLPro, virus corona

References


S. Jo, S. Kim, D. Y. Kim, M.-S. Kim, and D. H. Shin, “Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro,” Journal of Enzyme Inhibition and Medicinal Chemistry, vol. 35, no. 1, pp. 1539–1544, Jan. 2020, doi: 10.1080/14756366.2020.1801672.

Y.-W. Zhou et al., “Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies,” Sig Transduct Target Ther, vol. 6, no. 1, p. 317, Dec. 2021, doi: 10.1038/s41392-021-00733-x.

R. Alexpandi, J. F. De Mesquita, S. K. Pandian, and A. V. Ravi, “Quinolines-Based SARS-CoV-2 3CLpro and RdRp Inhibitors and Spike-RBD-ACE2 Inhibitor for Drug-Repurposing Against COVID-19: An in silico Analysis,” Front. Microbiol., vol. 11, p. 1796, Jul. 2020, doi: 10.3389/fmicb.2020.01796.

M. Bahun et al., “Inhibition of the SARS-CoV-2 3CL(pro) main protease by plant polyphenols,” Food Chem, vol. 373, no. Pt B, pp. 131594–131594, Mar. 2022, doi: 10.1016/j.foodchem.2021.131594.

Y. Bare, F. N. S. Timba, M. M. D. Nurak, and M. C. Mogi, “Eksplorasi Senyawa Kulit Kopi sebagai Anti Covid-19 Melalui Penghambatan 3C-Like Protease,” jpm, vol. 12, no. 2, pp. 127–133, Jun. 2022, doi: 10.37630/jpm.v12i2.563.

Y. Bare, F. N. S. Timba, S. H. J. Putra, M. A. Y. Nirmalasari, D. R. T. Sari, and M. M. Taek, “KAJIAN SENYAWA HEXOSE DAN MALIC ACID SEBAGAI INHIBITOR PAPAIN LIKE PROTEASE (PLPro) CORONA VIRUS,” JURNAL BIOSENSE, vol. 05, no. 01, p. 10, 2022, doi: https://doi.org/10.36526/biosense.v5i01.1997.

M. K. Bohn, A. Hall, L. Sepiashvili, B. Jung, S. Steele, and K. Adeli, “Pathophysiology of COVID-19: Mechanisms Underlying Disease Severity and Progression,” Physiology, vol. 35, no. 5, pp. 288–301, Sep. 2020, doi: 10.1152/physiol.00019.2020.

H. Ouassou et al., “The Pathogenesis of Coronavirus Disease 2019 (COVID-19): Evaluation and Prevention,” Journal of Immunology Research, vol. 2020, pp. 1–7, Jul. 2020, doi: 10.1155/2020/1357983.

T. Tang, M. Bidon, J. A. Jaimes, G. R. Whittaker, and S. Daniel, “Coronavirus membrane fusion mechanism offers a potential target for antiviral development,” Antiviral Research, vol. 178, p. 104792, Jun. 2020, doi: 10.1016/j.antiviral.2020.104792.

T. Klemm et al., “Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2,” The EMBO Journal, vol. 39, no. 18, p. e106275, Sep. 2020, doi: 10.15252/embj.2020106275.

S. Hall et al., “A review of the bioactivity of coffee, caffeine and key coffee constituents on inflammatory responses linked to depression,” Food Research International, vol. 76, pp. 626–636, Oct. 2015, doi: 10.1016/j.foodres.2015.07.027.

C. Somporn, A. Kamtuo, P. Theerakulpisut, and S. Siriamornpun, “Effects of roasting degree on radical scavenging activity, phenolics and volatile compounds of Arabica coffee beans (Coffea arabica L. cv. Catimor): Roasting degree on radical-scavenging activity,” International Journal of Food Science & Technology, vol. 46, no. 11, pp. 2287–2296, Nov. 2011, doi: 10.1111/j.1365-2621.2011.02748.x.

A. Duangjai, N. Suphrom, J. Wungrath, A. Ontawong, N. Nuengchamnong, and A. Yosboonruang, “Comparison of antioxidant, antimicrobial activities and chemical profiles of three coffee (Coffea arabica L.) pulp aqueous extracts,” Integrative Medicine Research, vol. 5, no. 4, pp. 324–331, Dec. 2016, doi: 10.1016/j.imr.2016.09.001.

Y. Bare and D. R. T. Sari, “Pengembangan Lembar Kerja Mahasiswa (LKM) Berbasis Inkuiri Pada Materi Interaksi Molekuler,” BioEdUIN, vol. 11, no. 1, p. 8, 2021, doi: https://doi.org/10.15575/bioeduin.v11i1.12077.

Y. Gao et al., “Structure of the RNA-dependent RNA polymerase from COVID-19 virus,” Science, vol. 368, no. 6492, pp. 779–782, May 2020, doi: 10.1126/science.abb7498.

T. Singhal, “A Review of Coronavirus Disease-2019 (COVID-19),” Indian J Pediatr, vol. 87, no. 4, pp. 281–286, Apr. 2020, doi: 10.1007/s12098-020-03263-6.

J. R. Clasman, R. K. Everett, K. Srinivasan, and A. D. Mesecar, “Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease,” Antiviral Research, vol. 174, p. 104661, Feb. 2020, doi: 10.1016/j.antiviral.2019.104661.

T. N. Elfi, Y. N. Bunga, and Y. Bare, “Studi Aktivitas Biologi Secara In Silico Senyawa Nonivamide Dan Nordihydrocapsaicin Sebagai Anti Inflamasi,” florea, vol. 8, no. 2, p. 82, Nov. 2021, doi: 10.25273/florea.v8i2.9983.

G. C. Krisnamurti, Y. Bare, M. Amin, and C. N. Primiani, “Combination of Curcumin from Curcuma longa and Procyanidin from Tamarindus indica in Inhibiting Cyclooxygenases for Primary Dysmenorrhea Therapy: In silico study,” Biointerface Res Appl Chem, vol. 11, no. 1, pp. 7460–7467, Jun. 2020, doi: 10.33263/BRIAC111.74607467.

G. C. Krisnamurti, D. R. T. Sari, and Y. Bare, “Capsaicinoids from Capsicum annuum as an Alternative FabH Inhibitor of Mycobacterium Tuberculosis: In Silico Study,” Makara Journal Of Science, vol. 25, no. 4, p. 9, 2021, doi: 10.7454/mss.v25i4.1248.

Y. Bare, “Interaction Phloroglucinol as inflammation therapy through Cyclooxygenase-2 (COX-2) gene inhibition,” JINTO, vol. 8, no. 1, pp. 14–21, Mar. 2022, doi: 10.36733/medicamento.v8i1.3162.

M. N. E. Lele, N. I. Ahmad, and Y. Bare, “Molecular Interaction Analysis of Homodihydrocapsaicin as COX-2 Inhibitor,” spibio, vol. 3, no. 2, p. 36, Jun. 2022, doi: 10.55241/spibio.v3i2.63.

M. M. D. Nurak, M. A. Lute, M. N. Eci, and Y. Bare, “Potential of Sechium edule as Hypertensive Therapy: In Silico Study,” spibio, vol. 3, no. 2, p. 10, Jun. 2022, doi: 10.55241/spibio.v3i2.60.

D. R. T. Sari, F. Lailiyah, and Y. Bare, “Studi Komparasi Sappanon A dan Sappanon B terhadap Penambatan Protein Tyrosin Phospatase 1B,” spibio, vol. 3, no. 2, p. 48, Jun. 2022, doi: 10.55241/spibio.v3i2.65.

W. O. Ujiana, L. E. C. Meak, M. F. Hiko, and Y. Bare, “Potential of Triterpenoid Compounds in Sauropus androgynus L Merr as In Silico Inhibitor of Obesity,” spibio, vol. 3, no. 2, p. 43, Jun. 2022, doi: 10.55241/spibio.v3i2.64.

Y. Bare, “ANALISIS SENYAWA FITOSTEROL Cymbopogon citratus dan Curcuma longa SEBAGAI ANTIALZHEIMER,” Biopendix: Jurnal Biologi, Pendidikan dan terapan, vol. 7, no. 2, pp. 53–159, 2021, doi: https://doi.org/10.30598/biopendixvol7issue2page153-159.




DOI: http://dx.doi.org/10.55241/spibio.v3i3.79

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