KAJIAN SENYAWA HEXOSE DAN MALIC ACID SEBAGAI INHIBITOR PAPAIN LIKE PROTEASE (PLPro) CORONA VIRUS
Keywords:
coffee pulp, hexose, malic acid, PLpro, SARSCoV-2
Abstract
Papain-like protease is a SARSCOV-2 protease that functions for ubiquitination in host cells. Caffeine compounds have been widely reported to have antioxidant, anti-inflammatory, antidiabetic, and antiobesity activities. However, hexose and malic acid compounds in coffee rind as potential inhibitors of the papain-like protease SARSCOV2 have not been reported. This study investigated the potential of malic acid and hexose compounds as PLPro inhibitor agents in inhibiting SARSCOV2 ubiquitination. In silico studies were used to identify the potential of the two compounds by interacting hexose and malic acid compounds with papain-like protease (PLPro) proteins with the Molegro virtual Docker 5 program. Next, the ligand-protein complex visualization was done with discovery studio version 5.0. hexose and malic acid compounds showed interactions with papain-like protease proteins on several active site residues. The interactions showed inhibition of ubiquitination and stimulation of interferon in host cells. The two compound complexes – PLPro protein showed hydrophobic interactions, hydrogen bonds, and van der Waals forces, which contributed to the formation of bond energy and strong bonds between compounds and proteins. In this study, it was concluded that hexose and malic acid compounds have the potential to act as inhibitors of papain-like protease (PLPro) protein.
References
Ahmad, N. I., Bunga, Y. N., & Bare, Y. (2019). Etnobotani Tanaman Cabai Merah Keriting (Capsicum Annum L.) Di Desa Waiwuring, Kecamatan Witihama Kabupaten Flores Timur. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 2(2), 10. http://dx.doi.org/10.55241/spibio.v2i2.46
Alexpandi, R., De Mesquita, J. F., Pandian, S. K., & Ravi, A. V. (2020). Quinolines-Based SARS-CoV-2 3CLpro and RdRp Inhibitors and Spike-RBD-ACE2 Inhibitor for Drug-Repurposing Against COVID-19: An in silico Analysis. Frontiers in Microbiology, 11, 1796. https://doi.org/10.3389/fmicb.2020.01796
Ballesteros, L. F., Ramirez, M. J., Orrego, C. E., Teixeira, J. A., & Mussatto, S. I. (2017). Encapsulation of antioxidant phenolic compounds extracted from spent coffee grounds by freeze-drying and spray-drying using different coating materials. Food Chemistry, 237, 623–631. https://doi.org/10.1016/j.foodchem.2017.05.142
Bare, Y. (2022). Interaction Phloroglucinol as inflammation therapy through Cyclooxygenase-2 (COX-2) gene inhibition. Jurnal Ilmiah Medicamento, 8(1), 14–21. https://doi.org/10.36733/medicamento.v8i1.3162
Bare, Y., Helvina, M., Elizabeth, A., & Sari, D. R. T. (2019). Potensi Asam kafeat pada Kopi sebagai Simultan Gen Peroxixme Proliferator-Activated Receptor Gamma (PPAR-γ): Studi In Silico. Jurnal Saintek Lahan Kering, 2(2), 52–53. https://doi.org/10.32938/slk.v2i2.866
Bare, Y., Timba, F. N. S., Nurak, M. M. D., & Mogi, M. C. (2022). Eksplorasi Senyawa Kulit Kopi sebagai Anti Covid-19 Melalui Penghambatan 3C-Like Protease. JURNAL PENDIDIKAN MIPA, 12(2), 127–133. https://doi.org/10.37630/jpm.v12i2.563
Clasman, J. R., Everett, R. K., Srinivasan, K., & Mesecar, A. D. (2020). Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease. Antiviral Research, 174, 104661. https://doi.org/10.1016/j.antiviral.2019.104661
Duangjai, A., Suphrom, N., Wungrath, J., Ontawong, A., Nuengchamnong, N., & Yosboonruang, A. (2016). Comparison of antioxidant, antimicrobial activities and chemical profiles of three coffee (Coffea arabica L.) pulp aqueous extracts. Integrative Medicine Research, 5(4), 324–331. https://doi.org/10.1016/j.imr.2016.09.001
Elfi, T. N., Bunga, Y. N., & Bare, Y. (2021). Studi Aktivitas Biologi Secara In Silico Senyawa Nonivamide Dan Nordihydrocapsaicin Sebagai Anti Inflamasi. Florea : Jurnal Biologi dan Pembelajarannya, 8(2), 82. https://doi.org/10.25273/florea.v8i2.9983
Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science, 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
Klemm, T., Ebert, G., Calleja, D. J., Allison, C. C., Richardson, L. W., Bernardini, J. P., Lu, B. G., Kuchel, N. W., Grohmann, C., Shibata, Y., Gan, Z. Y., Cooney, J. P., Doerflinger, M., Au, A. E., Blackmore, T. R., van der Heden van Noort, G. J., Geurink, P. P., Ovaa, H., Newman, J., … Komander, D. (2020). Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. The EMBO Journal, 39(18), e106275. https://doi.org/10.15252/embj.2020106275
Krisnamurti, G. C., Bare, Y., Amin, M., & Primiani, C. N. (2020). Combination of Curcumin from Curcuma longa and Procyanidin from Tamarindus indica in Inhibiting Cyclooxygenases for Primary Dysmenorrhea Therapy: In silico study. Biointerface Research in Applied Chemistry, 11(1), 7460–7467. https://doi.org/10.33263/BRIAC111.74607467
Krisnamurti, G. C., Sari, D. R. T., & Bare, Y. (2021). Capsaicinoids from Capsicum annuum as an Alternative FabH Inhibitor of Mycobacterium Tuberculosis: In Silico Study. Makara Journal Of Science, 25(4), 9. https://doi.org/10.7454/mss.v25i4.1248
Lele, M. N. E., Ahmad, N. I., & Bare, Y. (2022). Molecular Interaction Analysis of Homodihydrocapsaicin as COX-2 Inhibitor. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), 36. https://doi.org/10.55241/spibio.v3i2.63
Li D, Luan J, Zhang L. (2020) Molecular docking of potential SARS-CoV-2 papain-like protease inhibitors. Biochem Biophys Res Commun. 2021 Jan 29;538:72-79. doi: 10.1016/j.bbrc.2020.11.083.
Nurak, M. M. D., Lute, M. A., Eci, M. N., & Bare, Y. (2022). Potential of Sechium edule as Hypertensive Therapy: In Silico Study. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), 10. https://doi.org/10.55241/spibio.v3i2.60
Sanders B, Pohkrel S, Labbe A, Mathews I, Cooper C, Davidson R, Phillips G, Weiss K, Zhang Q, O'Neill H, Kaur M, Ferrins L, Schmidt J, Reichard W, Surendranathan S, Kumaran D, Andi B, Babnigg G, Moriarty N, Adams P, Joachimiak A, Jonsson C, Wakatsuki S, Galanie S, Head M, Parks J. (2021) Potent and Selective Covalent Inhibitors of the Papain-like Protease from SARS-CoV-2. Res Sq [Preprint]. Oct 8:rs.3.rs-906621. doi: 10.21203/rs.3.rs-906621/v1.
Sari, D. R. T., Krisnamurti, G. C., & Bare, Y. (2022). Pemetaan Bioaktivitas Senyawa Metabolit Sekunder Pada Kayu Secang (Caesalpinia sappan) Secara In Silico. 7(1), 8.
Sari, D. R. T., Lailiyah, F., & Bare, Y. (2022). Studi Komparasi Sappanon A dan Sappanon B terhadap Penambatan Protein Tyrosin Phospatase 1B. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), 48. https://doi.org/10.55241/spibio.v3i2.65
Shin, D., Mukherjee, R., Grewe, D., Bojkova, D., Baek, K., Bhattacharya, A., Schulz, L., Widera, M., Mehdipour, A. R., Tascher, G., Geurink, P. P., Wilhelm, A., van der Heden van Noort, G. J., Ovaa, H., Müller, S., Knobeloch, K.-P., Rajalingam, K., Schulman, B. A., Cinatl, J., … Dikic, I. (2020). Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature, 587(7835), 657–662. https://doi.org/10.1038/s41586-020-2601-5
Singhal, T. (2020). A Review of Coronavirus Disease-2019 (COVID-19). The Indian Journal of Pediatrics, 87(4), 281–286. https://doi.org/10.1007/s12098-020-03263-6
Stasiulewicz A, Maksymiuk AW, Nguyen ML, Bełza B, Sulkowska JI. (2021). SARS-CoV-2 Papain-Like Protease Potential Inhibitors-In Silico Quantitative Assessment. Int J Mol Sci. Apr 12;22(8):3957. doi: 10.3390/ijms22083957.
Ujiana, W. O., Meak, L. E. C., Hiko, M. F., & Bare, Y. (2022). Potential of Triterpenoid Compounds in Sauropus androgynus L Merr as In Silico Inhibitor of Obesity. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), 43. https://doi.org/10.55241/spibio.v3i2.64
Vincentius, A., & Bare, Y. (2022). Pemetaan Bioaktivitas Senyawa pada Kantung Tinta Cumi-cumi (Loligo vulgaris) Secara In Silico. Jurnal Ilmiah Wahana Pendidikan, 8(2), 09–16. https://doi.org/10.5281/ZENODO.5971402
Alexpandi, R., De Mesquita, J. F., Pandian, S. K., & Ravi, A. V. (2020). Quinolines-Based SARS-CoV-2 3CLpro and RdRp Inhibitors and Spike-RBD-ACE2 Inhibitor for Drug-Repurposing Against COVID-19: An in silico Analysis. Frontiers in Microbiology, 11, 1796. https://doi.org/10.3389/fmicb.2020.01796
Ballesteros, L. F., Ramirez, M. J., Orrego, C. E., Teixeira, J. A., & Mussatto, S. I. (2017). Encapsulation of antioxidant phenolic compounds extracted from spent coffee grounds by freeze-drying and spray-drying using different coating materials. Food Chemistry, 237, 623–631. https://doi.org/10.1016/j.foodchem.2017.05.142
Bare, Y. (2022). Interaction Phloroglucinol as inflammation therapy through Cyclooxygenase-2 (COX-2) gene inhibition. Jurnal Ilmiah Medicamento, 8(1), 14–21. https://doi.org/10.36733/medicamento.v8i1.3162
Bare, Y., Helvina, M., Elizabeth, A., & Sari, D. R. T. (2019). Potensi Asam kafeat pada Kopi sebagai Simultan Gen Peroxixme Proliferator-Activated Receptor Gamma (PPAR-γ): Studi In Silico. Jurnal Saintek Lahan Kering, 2(2), 52–53. https://doi.org/10.32938/slk.v2i2.866
Bare, Y., Timba, F. N. S., Nurak, M. M. D., & Mogi, M. C. (2022). Eksplorasi Senyawa Kulit Kopi sebagai Anti Covid-19 Melalui Penghambatan 3C-Like Protease. JURNAL PENDIDIKAN MIPA, 12(2), 127–133. https://doi.org/10.37630/jpm.v12i2.563
Clasman, J. R., Everett, R. K., Srinivasan, K., & Mesecar, A. D. (2020). Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease. Antiviral Research, 174, 104661. https://doi.org/10.1016/j.antiviral.2019.104661
Duangjai, A., Suphrom, N., Wungrath, J., Ontawong, A., Nuengchamnong, N., & Yosboonruang, A. (2016). Comparison of antioxidant, antimicrobial activities and chemical profiles of three coffee (Coffea arabica L.) pulp aqueous extracts. Integrative Medicine Research, 5(4), 324–331. https://doi.org/10.1016/j.imr.2016.09.001
Elfi, T. N., Bunga, Y. N., & Bare, Y. (2021). Studi Aktivitas Biologi Secara In Silico Senyawa Nonivamide Dan Nordihydrocapsaicin Sebagai Anti Inflamasi. Florea : Jurnal Biologi dan Pembelajarannya, 8(2), 82. https://doi.org/10.25273/florea.v8i2.9983
Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science, 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
Klemm, T., Ebert, G., Calleja, D. J., Allison, C. C., Richardson, L. W., Bernardini, J. P., Lu, B. G., Kuchel, N. W., Grohmann, C., Shibata, Y., Gan, Z. Y., Cooney, J. P., Doerflinger, M., Au, A. E., Blackmore, T. R., van der Heden van Noort, G. J., Geurink, P. P., Ovaa, H., Newman, J., … Komander, D. (2020). Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. The EMBO Journal, 39(18), e106275. https://doi.org/10.15252/embj.2020106275
Krisnamurti, G. C., Bare, Y., Amin, M., & Primiani, C. N. (2020). Combination of Curcumin from Curcuma longa and Procyanidin from Tamarindus indica in Inhibiting Cyclooxygenases for Primary Dysmenorrhea Therapy: In silico study. Biointerface Research in Applied Chemistry, 11(1), 7460–7467. https://doi.org/10.33263/BRIAC111.74607467
Krisnamurti, G. C., Sari, D. R. T., & Bare, Y. (2021). Capsaicinoids from Capsicum annuum as an Alternative FabH Inhibitor of Mycobacterium Tuberculosis: In Silico Study. Makara Journal Of Science, 25(4), 9. https://doi.org/10.7454/mss.v25i4.1248
Lele, M. N. E., Ahmad, N. I., & Bare, Y. (2022). Molecular Interaction Analysis of Homodihydrocapsaicin as COX-2 Inhibitor. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), 36. https://doi.org/10.55241/spibio.v3i2.63
Li D, Luan J, Zhang L. (2020) Molecular docking of potential SARS-CoV-2 papain-like protease inhibitors. Biochem Biophys Res Commun. 2021 Jan 29;538:72-79. doi: 10.1016/j.bbrc.2020.11.083.
Nurak, M. M. D., Lute, M. A., Eci, M. N., & Bare, Y. (2022). Potential of Sechium edule as Hypertensive Therapy: In Silico Study. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), 10. https://doi.org/10.55241/spibio.v3i2.60
Sanders B, Pohkrel S, Labbe A, Mathews I, Cooper C, Davidson R, Phillips G, Weiss K, Zhang Q, O'Neill H, Kaur M, Ferrins L, Schmidt J, Reichard W, Surendranathan S, Kumaran D, Andi B, Babnigg G, Moriarty N, Adams P, Joachimiak A, Jonsson C, Wakatsuki S, Galanie S, Head M, Parks J. (2021) Potent and Selective Covalent Inhibitors of the Papain-like Protease from SARS-CoV-2. Res Sq [Preprint]. Oct 8:rs.3.rs-906621. doi: 10.21203/rs.3.rs-906621/v1.
Sari, D. R. T., Krisnamurti, G. C., & Bare, Y. (2022). Pemetaan Bioaktivitas Senyawa Metabolit Sekunder Pada Kayu Secang (Caesalpinia sappan) Secara In Silico. 7(1), 8.
Sari, D. R. T., Lailiyah, F., & Bare, Y. (2022). Studi Komparasi Sappanon A dan Sappanon B terhadap Penambatan Protein Tyrosin Phospatase 1B. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), 48. https://doi.org/10.55241/spibio.v3i2.65
Shin, D., Mukherjee, R., Grewe, D., Bojkova, D., Baek, K., Bhattacharya, A., Schulz, L., Widera, M., Mehdipour, A. R., Tascher, G., Geurink, P. P., Wilhelm, A., van der Heden van Noort, G. J., Ovaa, H., Müller, S., Knobeloch, K.-P., Rajalingam, K., Schulman, B. A., Cinatl, J., … Dikic, I. (2020). Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature, 587(7835), 657–662. https://doi.org/10.1038/s41586-020-2601-5
Singhal, T. (2020). A Review of Coronavirus Disease-2019 (COVID-19). The Indian Journal of Pediatrics, 87(4), 281–286. https://doi.org/10.1007/s12098-020-03263-6
Stasiulewicz A, Maksymiuk AW, Nguyen ML, Bełza B, Sulkowska JI. (2021). SARS-CoV-2 Papain-Like Protease Potential Inhibitors-In Silico Quantitative Assessment. Int J Mol Sci. Apr 12;22(8):3957. doi: 10.3390/ijms22083957.
Ujiana, W. O., Meak, L. E. C., Hiko, M. F., & Bare, Y. (2022). Potential of Triterpenoid Compounds in Sauropus androgynus L Merr as In Silico Inhibitor of Obesity. Spizaetus: Jurnal Biologi dan Pendidikan Biologi, 3(2), 43. https://doi.org/10.55241/spibio.v3i2.64
Vincentius, A., & Bare, Y. (2022). Pemetaan Bioaktivitas Senyawa pada Kantung Tinta Cumi-cumi (Loligo vulgaris) Secara In Silico. Jurnal Ilmiah Wahana Pendidikan, 8(2), 09–16. https://doi.org/10.5281/ZENODO.5971402
Published
2022-06-20
How to Cite
BareY., TimbaF. N. S., PutraS. H. J., NirmalasariM. A. Y., SariD. R. T., & TaekM. M. (2022). KAJIAN SENYAWA HEXOSE DAN MALIC ACID SEBAGAI INHIBITOR PAPAIN LIKE PROTEASE (PLPro) CORONA VIRUS. JURNAL BIOSENSE, 5(01), 128-137. https://doi.org/10.36526/biosense.v5i01.1997
Section
Artikel
