Analisis Docking Molekuler Ligand Fitokimia terhadap Protein 1ND2 Rhinovirus Molecular Docking Analysis of Phytochemical Ligands Against Rhinovirus 1ND2 Protein
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Abstract
Although rhinovirus has a high prevalence worldwide, the development of antiviral agents specific to this virus remains limited. This study aims to evaluate phytochemical compounds from Indonesian medicinal plants as potential antiviral candidates against rhinovirus. This study used a quantitative in silico approach through molecular docking using MOE 2022 to analyze the interactions between 13 ligands and the target protein 1ND2. The results showed that tannin (-10.2962), cowanol (-8.9288), and zanthoxylin (-7.4879) had the best binding affinities compared with the other ligands. These findings indicate that phytochemical compounds have the potential to be developed as plant-based antiviral agent candidates. This study contributes to the development of ethnobotany-based drug discovery research and provides an initial basis for further experimental validation. Thus, the exploration of phytochemical compounds from Indonesian medicinal plants has important implications for the development of antiviral therapeutic candidates that are more specific to rhinovirus.
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References
Abdelrahman, A. H. M., Mekhemer, G. A. H., Sidhom, P. A., El-Tayeb, M. A., Khan, S., & Ibrahim, M. A. A. (2025). Exploration of African natural products as VP35 inhibitors to combat Marburg virus infection: Molecular docking, molecular dynamics, and quantum mechanical computations. PLOS ONE, 20(10), Article e0334160. https://doi.org/10.1371/journal.pone.0334160
Abiri, R., Abdul-Hamid, H., Sytar, O., Abiri, R., de Almeida, E. B., Sharma, S. K., Bulgakov, V. P., Arroo, R. R. J., & Malik, S. (2021). A brief overview of potential treatments for viral diseases using natural plant compounds: The case of SARS-CoV. Molecules, 26(13), Article 3868. https://doi.org/10.3390/molecules26133868
Al Balawi, A. N., Eldiasty, J. G., Mosallam, S. A. E. R., El-Alosey, A. R., & Elmetwalli, A. (2024). Assessing multi-target antiviral and antioxidant activities of natural compounds against SARS-CoV-2: An integrated in vitro and in silico study. Bioresources and Bioprocessing, 11(1), Article 109. https://doi.org/10.1186/s40643-024-00822-z
Alsahag, M. (2025). Computational discovery of natural inhibitors targeting enterovirus D68 3C protease using molecular docking pharmacokinetics and dynamics simulations. Scientific Reports, 15(1), Article 13476. https://doi.org/10.1038/s41598-025-95163-y
Azeem, M., Mustafa, G., Ahmed, S., Mushtaq, A., Arshad, M., Usama, M., & Farooq, M. (2024). Structure based screening and molecular docking with dynamic simulation of natural secondary metabolites to target RNA-dependent RNA polymerase of five different retroviruses. PLOS ONE, 19(8), Article e0307615. https://doi.org/10.1371/journal.pone.0307615
Boswell, Z., Verga, J. U., Mackle, J., Guerrero-Vazquez, K., Thomas, O. P., Cray, J., Wolf, B. J., Choo, Y. M., Croot, P., Hamann, M. T., & Hardiman, G. (2023). In-silico approaches for the screening and discovery of broad-spectrum marine natural product antiviral agents against coronaviruses. Infection and Drug Resistance, 16, 2321–2338. https://doi.org/10.2147/IDR.S395203
Cañedo-Figueroa, D. M., Calderón-Sandate, D. N., Hernández-Castillo, J., Huerta-Garza, M. J., Hernández-Rodríguez, X., Velázquez-Cervantes, M. A., Barrera-Aveleida, G. B., Trujillo-Paez, J. V., Lira-Hernández, F. I., Marquez-Reyna, B. A., León-Juárez, M., García-Herrera, A. C., Osuna-Ramos, J. F., & De Jesús-González, L. A. (2025). Natural compounds with antiviral activity against clinically relevant RNA viruses: Advances of the last decade. Biomolecules, 15(10), Article 1467. https://doi.org/10.3390/biom15101467
Diakou, I., Papakonstantinou, E., Papageorgiou, L., Pierouli, K., Dragoumani, K., Spandidos, D. A., Bacopoulou, F., Chrousos, G. P., Eliopoulos, E., & Vlachakis, D. (2022). Novel computational pipelines in antiviral structure-based drug design. Biomedical Reports, 17(6), Article 88. https://doi.org/10.3892/br.2022.1580
Khanum, A., Bibi, Y., Khan, I., Mustafa, G., Attia, K. A., Mohammed, A. A., Yang, S. H., & Qayyum, A. (2024). Molecular docking of bioactive compounds extracted and purified from selected medicinal plant species against COVID-19 proteins and in vitro evaluation. Scientific Reports, 14(1), Article 3944. https://doi.org/10.1038/s41598-024-54470-6
Maitra, S., Rajak, J., Ghoshal, A., Roy, B., Ghosh, S., Mitra, A. K., Kumer, A., & Dhara, B. (2025). Rhinovirus, an age-old problem yet to be solved: A comprehensive review discussing modern therapeutics. Health Science Reports, 8(8), Article e70922. https://doi.org/10.1002/hsr2.70922
Melk, M. M., & El-Sayed, A. F. (2024). Phytochemical profiling, antiviral activities, molecular docking, and dynamic simulations of selected Ruellia species extracts. Scientific Reports, 14(1), Article 15962. https://doi.org/10.1038/s41598-024-65387-5
Mohanty, S. S., Sahoo, C. R., Paidesetty, S. K., & Padhy, R. N. (2023). Role of phytocompounds as the potential anti-viral agent: An overview. Naunyn-Schmiedeberg’s Archives of Pharmacology, 396(10), 2311–2329. https://doi.org/10.1007/s00210-023-02517-2
Musarra-Pizzo, M., Pennisi, R., Ben-Amor, I., Mandalari, G., & Sciortino, M. T. (2021). Antiviral activity exerted by natural products against human viruses. Viruses, 13(5), Article 828. https://doi.org/10.3390/v13050828
Onyango, O. H. (2023). In silico models for anti-COVID-19 drug discovery: A systematic review. Advances in Pharmacological and Pharmaceutical Sciences, 2023, Article 4562974. https://doi.org/10.1155/2023/4562974
Ponticelli, M., Bellone, M. L., Parisi, V., Iannuzzi, A., Braca, A., de Tommasi, N., Russo, D., Sileo, A., Quaranta, P., Freer, G., Pistello, M., & Milella, L. (2023). Specialized metabolites from plants as a source of new multi-target antiviral drugs: A systematic review. Phytochemistry Reviews, 22(3), 615–693. https://doi.org/10.1007/s11101-023-09855-2
Purohit, P., Sahoo, S., Panda, M., Sahoo, P. S., & Meher, B. R. (2022). Targeting the DENV NS2B-NS3 protease with active antiviral phytocompounds: Structure-based virtual screening, molecular docking and molecular dynamics simulation studies. Journal of Molecular Modeling, 28(11), Article 341. https://doi.org/10.1007/s00894-022-05355-w
Saha, O., Siddiquee, N. H., Akter, R., Sarker, N., Bristi, U. P., Sultana, K. F., Remon, S. L. R., Sultana, A., Shishir, T. A., Rahaman, M. M., Ahmed, F., Hossen, F., Amin, M. R., & Akter, M. S. (2024). Antiviral activity, pharmacoinformatics, molecular docking, and dynamics studies of Azadirachta indica against Nipah virus by targeting envelope glycoprotein: Emerging strategies for developing antiviral treatment. Bioinformatics and Biology Insights, 18. https://doi.org/10.1177/11779322241264145
Samy, A., Hassan, A., Hegazi, N. M., Farid, M., & Elshafei, M. (2024). Network pharmacology, molecular docking, and dynamics analyses to predict the antiviral activity of ginger constituents against coronavirus infection. Scientific Reports, 14(1), Article 13335. https://doi.org/10.1038/s41598-024-60721-3
Singh, D., Mittal, N., Mittal, P., Tiwari, N., Khan, S. U. D., Ali, M. A. M., Chaudhary, A. A., & Siddiqui, M. H. (2024). In silico molecular screening of bioactive natural compounds of rosemary essential oil and extracts for pharmacological potentials against rhinoviruses. Scientific Reports, 14(1), Article 17121. https://doi.org/10.1038/s41598-024-68450-3
Trischitta, P., Tamburello, M. P., Venuti, A., & Pennisi, R. (2024). Pseudovirus-based systems for screening natural antiviral agents: A comprehensive review. International Journal of Molecular Sciences, 25(10), Article 5188. https://doi.org/10.3390/ijms25105188






















