Email this article 
Bioinformatics Analysis of Quercetin and Morin Bioactivity from Morinda citrifolia L. Targeting Streptococcus mutans Virulence Factors In Dental Caries Cases
Abstract
Dental caries remains one of the most neglected oral diseases, particularly among populations living far from healthcare services. Its pathogenesis is largely triggered by poor oral hygiene and the activity of Streptococcus mutans. The use of synthetic antimicrobial agents often leads to prolonged side effects and a higher risk of antibiotic resistance. As an alternative, Morinda citrifolia L. extract shows high potential due to its good public acceptance, minimal side effects, and proven in vitro efficacy in inhibiting S. mutans growth. This study aimed to investigate the bioactivity factors of S. mutans in relation to specific components of Morinda citrifolia L. as an alternative therapeutic agent for dental caries using a bioinformatics-based approach. A descriptive-exploratory bioinformatics method was employed using computational analysis. The bacterial FASTA sequence of Streptococcus mutans UA159 was retrieved from the National Center for Biotechnology Information (NCBI) database and analyzed using several software tools, including STITCH v5.0, VICMPred, VirulentPred, BepiPred v1.0, MHC I and MHC II BindingPred, and PSORTb v3.0. The analysis revealed notable interactions in bioactivity between S. mutans proteins and the phytocompounds quercetin and morin. Seven virulent proteins PknB, SMU_1806, SMU_1213c, SMU_922, SMU_906, SMU_525, and SMU_1078c, contribute to cellular process, metabolism, virulence factors, and information & storage. Five proteins were identified in the cytoplasmic membrane, one in cell wall, and also cytoplasm. Quercetin and morin demonstrated strong antibacterial potential against S. mutans through interactions with virulent proteins. PknB, SMU_906, and SMU_1078c stand out in epitope T cell analysis with high affinity, demonstrating the ability to provoke an adaptive immune system response. Location complexity of 5’-nucleotide enzyme targeted by strategic antimicrobials leads to bacterial mortality.
Keywords
Full Text:
PDFReferences
Akhtar, A. A., & Turner, D. P. (2022). The role of bacterial ATP-binding cassette (ABC) transporters in pathogenesis and virulence: Therapeutic and vaccine potential. Microbial Pathogenesis, 171. https://doi.org/10.1016/j.micpath.2022.105734
Ayunda, M. N., Zulharmita, Azizah, Z., & Rivai, H. (2020). Review of Phytochemical and Pharmacological Activities of Noni (Morinda citrifolia L.). Scholars Academic Journal of Pharmacy, 9(12), 340–346. https://doi.org/10.36347/sajp.2020.v09i12.003
Bonsack, M., Hoppe, S., Winter, J., Tichy, D., Zeller, C., Küpper, M. D., Schitter, E. C., Blatnik, R., & Riemer, A. B. (2019). Performance Evaluation of MHC Class-I Binding Prediction Tools Based on an Experimentally Validated MHC–Peptide Binding Data Set. Cancer Immunology Research, 7(5), 719–736. https://doi.org/10.1158/2326-6066.CIR-18-0584
Capistrano Costa, N. T., de Souza Pereira, A. M., Silva, C. C., Souza, E. de O., de Oliveira, B. C., Ferreira, L. F. G. R., Hernandes, M. Z., & Pereira, V. R. A. (2024). Exploring Bioinformatics Solutions for Improved Leishmaniasis Diagnostic Tools: A Review. Molecules, 29(22), 5259. https://doi.org/10.3390/molecules29225259
Denzer, L., Schroten, H., & Schwerk, C. (2020). From Gene to Protein—How Bacterial Virulence Factors Manipulate Host Gene Expression During Infection. International Journal of Molecular Sciences, 21(10), 3730. https://doi.org/10.3390/ijms21103730
Faisal, A., & Arhasy, F. (2025). The Role of Bioinformatics in the Discovery of Traditional Indonesian Medicines for the Treatment of Metabolic Syndrome. Publication of the International Journal and Academic Research, 1(2), 86–93. https://doi.org/10.63222/pijar.v1i2.19
Fajri Ahmad, F., Junita, N., & Nur Aini Yusuf, S. (2022). Formulasi Dan Uji Aktivitas Antibakteri Sediaan Obat Kumur Ekstrak Etanol Daun Mengkudu (Morinda citrifolia L.) terhadap Bakteri Streptococcus mutans (Vol. 1, Issue 2). Desember.
Galanis, K. A., Nastou, K. C., Papandreou, N. C., Petichakis, G. N., Pigis, D. G., & Iconomidou, V. A. (2021). Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface. International Journal of Molecular Sciences, 22(6), 3210. https://doi.org/10.3390/ijms22063210
Garg, A., & Gupta, D. (2008). VirulentPred: a SVM-based prediction method for virulent proteins in bacterial pathogens. BMC Bioinformatics, 9(1), 62. https://doi.org/10.1186/1471-2105-9-62
Green, E. R., & Mecsas, J. (2016). Bacterial Secretion Systems: An Overview. Microbiology Spectrum, 4(1). https://doi.org/10.1128/microbiolspec.vmbf-0012-2015
Hamidinia, M., Gu, Y., Ser, Z., Brzostek, J., Tay, N. Q., Yap, J., Chua, Y. L., Lim, Y. T., Wood, K. J., Vathsala, A., Sobota, R. M., MacAry, P. A., & Gascoigne, N. R. J. (2025). Occlusion of TCR binding to HLA-A*11:01 by a non-pathogenic human alloantibody. Cellular and Molecular Life Sciences, 82(1). https://doi.org/10.1007/s00018-025-05614-y
Hamka, N. R. Q. P., Jelita, H., & Kahanjak, D. N. (2024). Hubungan Lama Penyakit Ginjal Kronis dengan Kejadian Karies Gigi. Barigas: Jurnal Riset Mahasiswa, 2(1). https://doi.org/10.37304/barigas.v2i1.10445
Kandasamy, P., Gyimesi, G., Kanai, Y., & Hediger, M. A. (2018). Amino acid transporters revisited: New views in health and disease. In Trends in Biochemical Sciences (Vol. 43, Issue 10, pp. 752–789). Elsevier Ltd. https://doi.org/10.1016/j.tibs.2018.05.003
Kashyap, D., Khan, A., & Lahare, B. (2020). Pathogenic Protein Identification and Localization Prediction in Pseudomonas fuscovaginae: A Study on Sheath Brown Rot in Rice. XXIX, 150–160. https://doi.org/10.53555/03276716.2020.20
KEMENKES RI. (2024). Survei Kesehatan Indonesia.
Kementerian Pertanian Republik Indonesia. (2024). Angka Tetap Hortikultura Tahun 2023.
Kumkar, S. N., Kamble, E. E., Chavan, N. S., Dhotre, D. P., & Pardesi, K. R. (2022). Diversity of resistant determinants, virulence factors, and mobile genetic elements in Acinetobacter baumannii from India: A comprehensive in silico genome analysis. Frontiers in Cellular and Infection Microbiology, 12. https://doi.org/10.3389/fcimb.2022.997897
Lemos, J. A., Palmer, S. R., Zeng, L., Wen, Z. T., Kajfasz, J. K., Freires, I. A., Abranches, J., & Brady, L. J. (2019). The Biology of Streptococcus mutans. Microbiology Spectrum, 7(1). https://doi.org/10.1128/microbiolspec.GPP3-0051-2018
Lyon, P. (2015). The cognitive cell: Bacterial behavior reconsidered. In Frontiers in Microbiology (Vol. 6, Issue MAR). Frontiers Media S.A. https://doi.org/10.3389/fmicb.2015.00264
Matsumoto-Nakano, M. (2018). Role of Streptococcus mutans surface proteins for biofilm formation. In Japanese Dental Science Review (Vol. 54, Issue 1, pp. 22–29). Elsevier Ltd. https://doi.org/10.1016/j.jdsr.2017.08.002
Nagarajan, S. N., Lenoir, C., & Grangeasse, C. (2022). Recent advances in bacterial signaling by serine/threonine protein kinases. In Trends in Microbiology (Vol. 30, Issue 6, pp. 553–566). Elsevier Ltd. https://doi.org/10.1016/j.tim.2021.11.005
Nagasawa, R., Ito, T., Yamamoto, C., Unoki, M., Obana, N., Nomura, N., & Toyofuku, M. (2025). Membrane vesicle production via cell-to-cell communication-induced autolysis in Streptococcus mutans. Microbiology Spectrum, 13(7). https://doi.org/10.1128/spectrum.00334-25
Nawan, N., Handayani, S., & Toemon, A. I. (2025). Bioinformatic Analysis of Dihomo-?-linolenic Acid (DGLA) Targeting Virulence Factors in Bacteria Causing Infectious Diseases. Iranian Journal of Medical Microbiology, 19(1), 12–28. https://doi.org/10.30699/ijmm.19.1.12
Nawan, N., Priskila, H., Shinta, H. E., Septi Handayani, & Ravenalla Abdurahman. (2023). Quality of the peat water and its association with public health problems in the community of the Danau Tundai area. Jurnal Kedokteran Dan Kesehatan Indonesia, 163–171. https://doi.org/10.20885/jkki.vol14.iss2.art7
Noviana, R., Fajrina, A., Eriadi, A., & Asra, R. (2021). Antimicrobial Activity of Morinda citrifolia L. Asian Journal of Pharmaceutical Research and Development, 9(1), 141–148. https://doi.org/10.22270/ajprd.v9i1.924
Raychaudhuri, S. (2010). Recent advances in the genetics of rheumatoid arthritis. Current Opinion in Rheumatology, 22(2), 109–118. https://doi.org/10.1097/BOR.0b013e328336474d
Schooch, C. (2020). NCBI Taxonomy: a comprehensive update on curation, resources and tools. In Database (Oxford).
Soesilawati, P. (2020). Imunogenetik Karies Gigi. Airlangga University Press.
Suratri, M. A. L., Jovina, T. A., & Notohartojo, I. T. (2018). Hubungan Kejadian Karies Gigi dengan Konsumsi Air Minum pada Masyarakat di Indonesia. Media Penelitian Dan Pengembangan Kesehatan, 28(3), 211–218. https://doi.org/10.22435/mpk.v28i3.254
Szklarczyk, D., Santos, A., von Mering, C., Jensen, L. J., Bork, P., & Kuhn, M. (2016). STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data. Nucleic Acids Research, 44(D1), D380–D384. https://doi.org/10.1093/nar/gkv1277
Tadros, D. M., Racle, J., & Gfeller, D. (2025). Predicting MHC-I ligands across alleles and species: how far can we go? Genome Medicine, 17(1). https://doi.org/10.1186/s13073-025-01450-8
Wardana, R. D., Savira, M., Anggraini, D., Amalia, A. S., & Nurulita, Y. (2024). Deteksi Mekanisme Efflux Pump Pada Resistensi Bakteri Staphylococcus haemolyticus, Sampel Pus Klinis Rumah Sakit Pekanbaru. Chimica et Natura Acta, 12(3), 182–192. https://doi.org/10.24198/cna.v12.n3.52038
Yaneva, Z., Beev, G., Rusenova, N., Ivanova, D., Tzanova, M., Stoeva, D., & Toneva, M. (2022). Antimicrobial Potential of Conjugated Lignin/Morin/Chitosan Combinations as a Function of System Complexity. Antibiotics, 11(5), 650. https://doi.org/10.3390/antibiotics11050650
You, Y.-O. (2019). Virulence genes of Streptococcus mutans and dental caries. International Journal of Oral Biology, 44(2), 31–36. https://doi.org/10.11620/IJOB.2019.44.2.31
Zhang, Y.-H., Huang, F., Li, J., Shen, W., Chen, L., Feng, K., Huang, T., & Cai, Y.-D. (2024). Identification of Protein–Protein Interaction Associated Functions Based on Gene Ontology. The Protein Journal, 43(3), 477–486. https://doi.org/10.1007/s10930-024-10180-6
DOI: https://doi.org/10.14421/biomedich.2026.151.535-553
Refbacks
- There are currently no refbacks.
Copyright (c) 2026 Astrid Ekklesia Saputri, Rian Ka Praja, Agnes Frethernety, Oktaviani Naulita Turnip, Ysrafil
Biology, Medicine, & Natural Product Chemistry |
|
