Bioinformatics approach to enhance the undergraduate biology students’ understanding of plant terpenoid
DOI:
https://doi.org/10.22219/jpbi.v10i2.33884Keywords:
bioinformatics, medicinal plants, biology undergraduate student profileAbstract
Plant metabolite compounds have been applied on plant cellular metabolism, produces organic and inorganic compounds, primary and secondary bioactive molecules, such as glucose, amino acids, fat acids, alkaloids, flavonoids, and terpenoids. Undergraduate biology students learn about the plant terpenoid assisted by bioinformatics to store, manage, and interpret the molecular information about these compounds. This research aims to observe the students’ understanding of terpenoid through implementing bioinformatics approach. Besides, to investigate how practice the bioinformatics technology in learning terpenoid may impact students' comprehension of plant metabolism domain and their acquisition of bioinformatics inquiry skills. Bioinformatics is a computational database that relies on digital repositories of molecular biology informations. Data analysis was in the form of quantitative and qualitative descriptive using module learning resources based on terpenoid research and assisted by bioinformatics. The results indicate that students’ comprehension of learning and understanding terpenoid has improved, identification and analysis processes of article reviews showed that students were able to discuss and interpret research finding in silico bioinformatics using molecular docking procedures. Assessment of bioinformatics skills showed that all undergraduate biology students could follow the direct instructions well, answer the questions, practice the dry-lab experimental, and formulate the conclusion correctly.
Downloads
References
Abbas, F., Ke, Y., Yu, R., Yue, Y., Amanullah, S., Jahangir, M. M., & Fan, Y. (2017). Volatile terpenoids: Multiple functions, biosynthesis, modulation and manipulation by genetic engineering. Planta, 246(5), 803–816. https://doi.org/10.1007/s00425-017-2749-x
Ahmed, A. U. (2011). An overview of inflammation: Mechanism and consequences. Frontiers in Biology, 6(4), 274. https://doi.org/10.1007/s11515-011-1123-9
Babar, M. M., Zaidi, N.-S. S., Pothineni, V. R., Ali, Z., Faisal, S., Hakeem, K. R., & Gul, A. (2017). Application of bioinformatics and system biology in medicinal plant studies. In K. R. Hakeem, A. Malik, F. Vardar-Sukan, & M. Ozturk (Eds.), Plant Bioinformatics (pp. 375–393). Springer International Publishing. https://doi.org/10.1007/978-3-319-67156-7_15
Bain, S. A., Meagher, T. R., & Barker, D. (2022). Design, delivery and evaluation of a bioinformatics education workshop for 13-16-year-olds. Journal of Biological Education, 56(5), 570–580. https://doi.org/10.1080/00219266.2020.1858932
Branco, I., & Choupina, A. (2021). Bioinformatics: New tools and applications in life science and personalized medicine. Applied Microbiology and Biotechnology, 105(3), 937–951. https://doi.org/10.1007/s00253-020-11056-2
Chapman, B. S., Christmann, J. L., & Thatcher, E. F. (2006). Bioinformatics for undergraduates: Steps toward a quantitative bioscience curriculum. Biochemistry and Molecular Biology Education, 34(3), 180–186. https://doi.org/10.1002/bmb.2006.49403403180
Cheng, A.-X., Lou, Y.-G., Mao, Y.-B., Lu, S., Wang, L.-J., & Chen, X.-Y. (2007). Plant terpenoids: Biosynthesis and ecological functions. Journal of Integrative Plant Biology, 49(2), 179–186. https://doi.org/10.1111/j.1744-7909.2007.00395.x
Chhabra, R. (2021). Pathological inflammation and various mechanisms of apoptosis. European Journal of Experimental Biology, 11(4).
Courdavault, V., O’Connor, S. E., Jensen, M. K., & Papon, N. (2021). Metabolic engineering for plant natural products biosynthesis: New procedures, concrete achievements and remaining limits. Natural Product Reports, 38(12), 2145–2153. https://doi.org/10.1039/D0NP00092B
Cruz, J. V., Giuliatti, S., Alves, L. B., Silva, R. C., Ferreira, E. F. B., Kimani, N. M., Silva, C. H. T. P., Souza, J. S. N. de, Espejo-Román, J. M., & Santos, C. B. R. (2022). Identification of novel potential cyclooxygenase-2 inhibitors using ligand- and structure-based virtual screening approaches. Journal of Biomolecular Structure and Dynamics, 40(12), 5386–5408. https://doi.org/10.1080/07391102.2020.1871413
Dinsdale, E., Elgin, S. C. R., Grandgenett, N., Morgan, W., Rosenwald, A., Tapprich, W., Triplett, E. W., & Pauley, M. A. (2015). NIBLSE: A network for integrating bioinformatics into life sciences education. CBE—Life Sciences Education, 14(4), le3. https://doi.org/10.1187/cbe.15-06-0123
Frank, A., & Groll, M. (2017). The methylerythritol phosphate pathway to isoprenoids. Chemical Reviews, 117(8), 5675–5703. https://doi.org/10.1021/acs.chemrev.6b00537
Giofrè, S. V., Napoli, E., Iraci, N., Speciale, A., Cimino, F., Muscarà, C., Molonia, M. S., Ruberto, G., & Saija, A. (2021). Interaction of selected terpenoids with two SARS-CoV-2 key therapeutic targets: An in silico study through molecular docking and dynamics simulations. Computers in Biology and Medicine, 134, 104538. https://doi.org/10.1016/j.compbiomed.2021.104538
Gogoi, B., Chowdhury, P., Goswami, N., Gogoi, N., Naiya, T., Chetia, P., Mahanta, S., Chetia, D., Tanti, B., Borah, P., & Handique, P. J. (2021). Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation. Molecular Diversity, 25(3), 1963–1977. https://doi.org/10.1007/s11030-021-10211-9
Gomez-Casati, D. F., Busi, M. V., Barchiesi, J., Peralta, D. A., Hedin, N., & Bhadauria, V. (2018). Applications of bioinformatics to plant biotechnology. Current Issues in Molecular Biology, 89–104. https://doi.org/10.21775/cimb.027.089
Greten, F. R., & Grivennikov, S. I. (2019). Inflammation and cancer: Triggers, mechanisms, and consequences. Immunity, 51(1), 27–41. https://doi.org/10.1016/j.immuni.2019.06.025
Gualdani, R., Cavalluzzi, M., Lentini, G., & Habtemariam, S. (2016). The chemistry and pharmacology of citrus limonoids. Molecules, 21(11), 1530. https://doi.org/10.3390/molecules21111530
Joshi, T., Sharma, P., Joshi, T., & Chandra, S. (2020). In silico screening of anti-inflammatory compounds from Lichen by targeting cyclooxygenase-2. Journal of Biomolecular Structure and Dynamics, 38(12), 3544–3562. https://doi.org/10.1080/07391102.2019.1664328
Khater, S., Anand, S., & Mohanty, D. (2016). In silico methods for linking genes and secondary metabolites: The way forward. Synthetic and Systems Biotechnology, 1(2), 80–88. https://doi.org/10.1016/j.synbio.2016.03.001
Liang, X., Zhu, W., Lv, Z., & Zou, Q. (2019). Molecular computing and bioinformatics. Molecules, 24(13), 1–7. https://doi.org/10.3390/molecules24132358
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4–17. https://doi.org/10.1016/j.addr.2012.09.019
Ludwiczuk, A., Skalicka-Woźniak, K., & Georgiev, M. I. (2017). Terpenoids. In Pharmacognosy (pp. 233–266). Elsevier. https://doi.org/10.1016/B978-0-12-802104-0.00011-1
Madden, J. C., Enoch, S. J., Paini, A., & Cronin, M. T. D. (2020). A review of in silico tools as alternatives to animal testing: Principles, resources and applications. Alternatives to Laboratory Animals, 48(4), 146–172. https://doi.org/10.1177/0261192920965977
Mahmud, S., Biswas, S., Paul, G. K., Mita, M. A., Promi, M. M., Afrose, S., Hasan, Md. R., Zaman, S., Uddin, Md. S., Dhama, K., Emran, T. B., Saleh, Md. A., & Simal-Gandara, J. (2021). Plant-based phytochemical screening by targeting main protease of SARS-CoV-2 to design effective potent inhibitors. Biology, 10(7), 589. https://doi.org/10.3390/biology10070589
Martins, A., Fonseca, M. J., Lemos, M., Lencastre, L., & Tavares, F. (2020). bioinformatics-based activities in high school: Fostering students’ literacy, interest, and attitudes on gene regulation, genomics, and evolution. Frontiers in Microbiology, 11, 578099. https://doi.org/10.3389/fmicb.2020.578099
Moradi, M., Golmohammadi, R., Najafi, A., Moosazadeh Moghaddam, M., Fasihi-Ramandi, M., & Mirnejad, R. (2022). A contemporary review on the important role of in silico approaches for managing different aspects of COVID-19 crisis. Informatics in Medicine Unlocked, 28, 100862. https://doi.org/10.1016/j.imu.2022.100862
Osman, K., Hiong, L. C., Vebrianto, R., & Omar, Z. (2020). 21 st century biology: An interdisciplinary approach of biology, technology, engineering and mathematics education. Procedia - Social and Behavioral Sciences, 102(Ifee 2012), 188–194. https://doi.org/10.1016/j.sbspro.2013.10.732
Ren, H., Shi, C., & Zhao, H. (2020). Computational tools for discovering and engineering natural product biosynthetic pathways. iScience, 23(1), 100795. https://doi.org/10.1016/j.isci.2019.100795
Robinson, G. E., Banks, J. A., Padilla, D. K., Burggren, W. W., Cohen, C. S., Delwiche, C. F., Funk, V., Hoekstra, H. E., Jarvis, E. D., Johnson, L., Martindale, M. Q., del Rio, C. M., Medina, M., Salt, D. E., Sinha, S., Specht, C., Strange, K., Strassmann, J. E., Swalla, B. J., & Tomanek, L. (2010). Empowering 21st century biology. BioScience, 60(11), 923–930. https://doi.org/10.1525/bio.2010.60.11.8
Sadeghi, M., Miroliaei, M., Fateminasab, F., & Moradi, M. (2022). Screening cyclooxygenase-2 inhibitors from Allium sativum L. compounds: In silico approach. Journal of Molecular Modeling, 28(1), 24. https://doi.org/10.1007/s00894-021-05016-4
Sayres, M. A., Hauser, C., Sierk, M., Robic, S., Rosenwald, A. G., Smith, T. M., Triplett, E. W., Williams, J. J., Dinsdale, E., Morgan, W. R., Burnette, J. M., Donovan, S. S., Drew, J. C., Elgin, S. C. R., Fowlks, E. R., Galindo-Gonzalez, S., Goodman, A. L., Grandgenett, N. F., Goller, C. C., … Pauley, M. A. (2018). Bioinformatics core competencies for undergraduate life sciences education. PLOS ONE, 13(6), e0196878. https://doi.org/10.1371/journal.pone.0196878
Sharma, V., & Sarkar, I. N. (2013). Bioinformatics opportunities for identification and study of medicinal plants. Briefings in Bioinformatics, 14(2), 238–250. https://doi.org/10.1093/bib/bbs021
Taidi, L., Maurady, A., & Britel, M. R. (2022). Molecular docking study and molecular dynamic simulation of human cyclooxygenase-2 (COX-2) with selected eutypoids. Journal of Biomolecular Structure and Dynamics, 40(3), 1189–1204. https://doi.org/10.1080/07391102.2020.1823884
Tan, Y. C., Kumar, A. U., Wong, Y. P., & Ling, A. P. K. (2022). Bioinformatics approaches and applications in plant biotechnology. Journal of Genetic Engineering and Biotechnology, 20(1), 106. https://doi.org/10.1186/s43141-022-00394-5
Toby, I., Williams, J., Lu, G., Cai, C., Crandall, K. A., Dinsdale, E. A., Drew, J., Edgington, N. P., Goller, C. C., Grandgenett, N. F., Grant, B. J., Hauser, C., Johnson, K. A., Jones, C. J., Jue, N. K., Jungck, J. R., Kerby, J., Kleinschmit, A. J., Miller, K. G., … Robic, S. (2022). Making change sustainable: Network for integrating bioinformatics into life sciences education (niblse) meeting review. CourseSource, 9. https://doi.org/10.24918/cs.2022.10
Tractenberg, R. E., Lindvall, J. M., Attwood, T. K., & Via, A. (2019). The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training. PLOS ONE, 14(11), e0225256. https://doi.org/10.1371/journal.pone.0225256
Umar, H. I., Siraj, B., Ajayi, A., Jimoh, T. O., & Chukwuemeka, P. O. (2021). Molecular docking studies of some selected gallic acid derivatives against five non-structural proteins of novel coronavirus. Journal of Genetic Engineering and Biotechnology, 19(1), 16. https://doi.org/10.1186/s43141-021-00120-7
Vardhan, S., & Sahoo, S. K. (2020). In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19. Computers in Biology and Medicine, 124, 103936. https://doi.org/10.1016/j.compbiomed.2020.103936
Vinay, C. M., Udayamanoharan, S. K., Prabhu Basrur, N., Paul, B., & Rai, P. S. (2021). Current analytical technologies and bioinformatic resources for plant metabolomics data. Plant Biotechnology Reports, 15(5), 561–572. https://doi.org/10.1007/s11816-021-00703-3
Wilson Sayres, M. A., Hauser, C., Sierk, M., Robic, S., Rosenwald, A. G., Smith, T. M., Triplett, E. W., Williams, J. J., Dinsdale, E., Morgan, W. R., Burnette, J. M., Donovan, S. S., Drew, J. C., Elgin, S. C. R., Fowlks, E. R., Galindo-Gonzalez, S., Goodman, A. L., Grandgenett, N. F., Goller, C. C., … Pauley, M. A. (2018). Bioinformatics core competencies for undergraduate life sciences education. PLOS ONE, 13(6), e0196878. https://doi.org/10.1371/journal.pone.0196878
Xiao, Q., Mu, X., Liu, J., Li, B., Liu, H., Zhang, B., & Xiao, P. (2022). Plant metabolomics: A new strategy and tool for quality evaluation of Chinese medicinal materials. Chinese Medicine, 17(1), 45. https://doi.org/10.1186/s13020-022-00601-y
Yi, F., Li, L., Xu, L., Meng, H., Dong, Y., Liu, H., & Xiao, P. (2018). In silico approach in reveal traditional medicine plants pharmacological material basis. Chinese Medicine, 13(1), 33. https://doi.org/10.1186/s13020-018-0190-0
Zhang, X., Wu, F., Yang, N., Zhan, X., Liao, J., Mai, S., & Huang, Z. (2022). In silico methods for identification of potential therapeutic targets. Interdisciplinary Sciences: Computational Life Sciences, 14(2), 285–310. https://doi.org/10.1007/s12539-021-00491-y
Downloads
Published
Issue
Section
License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Authors who publish with JPBI (Jurnal Pendidikan Biologi Indonesia) agree to the following terms:
- For all articles published in JPBI, copyright is retained by the authors. Authors give permission to the publisher to announce the work with conditions. When the manuscript is accepted for publication, the authors agree to automatic transfer of the publishing right to the publisher.
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution-ShareAlike 4.0 International License that allows others to share the work with an acknowledgment of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
