Main Article Content

Abstract

Microbial resistance to antibiotics is a growing global problem, and new antibacterial agents are needed to overcome this. One of the bacteria with a high level of resistance is Staphylococcus aureus. Herbal compounds are an alternative as a source of new antibacterial agents. Molecular docking can be used in screening herbal compounds that can become new antibacterial agents against Staphylococcus aureus. Virtual screening was conducted using Ligandscout, and molecular docking was conducted via Autodock. LigPlot was used to analyze the interaction between hit compounds to the protein target, and finally, the pharmacokinetic characteristics were assessed in SWISSADME and ADMETsar programs. From 1377 compounds in the Indonesian Herbal Database, 12 hit compounds have an affinity to the target protein ftsZ of Staphylococcus aureus. Further analysis of the interaction with target protein and pharmacokinetics properties considers Alpha Santalol a compound with good potential for further development as an antibacterial agent against Staphylococcus aureus. However, in vitro and in vivo study is needed to validate this result.

Keywords

molecular docking herbal compound antibacterial Staphylococcus aureus

Article Details

How to Cite
1.
Monica MD, Erlina L, Fadilah F, Paramita RI. Molecular Docking of ftsZ Protein of Staphylococcus aureus to Indonesian Herbal Compound. EKSAKTA [Internet]. 2024Mar.30 [cited 2024Nov.21];25(01):1-13. Available from: https://eksakta.ppj.unp.ac.id/index.php/eksakta/article/view/431

References

  1. Chokshi, A., Sifri, Z., Cennimo, D., & Horng, H. (2019). Global contributors to antibiotic resistance. Journal of global infectious diseases, 11(1), 36.
  2. Gajdács, M., & Albericio, F. (2019). Antibiotic resistance: from the bench to patients. Antibiotics, 8(3), 129.
  3. Ribeiro da Cunha, B., Fonseca, L. P., & Calado, C. R. (2019). Antibiotic discovery: where have we come from, where do we go?. Antibiotics, 8(2), 45.
  4. Murray, C. J., Ikuta, K. S., Sharara, F., Swetschinski, L., Aguilar, G. R., Gray, A., ... & Tasak, N. (2022). Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet, 399(10325), 629-655.
  5. D’Andrea, M. M., Fraziano, M., Thaller, M. C., & Rossolini, G. M. (2019). The urgent need for novel antimicrobial agents and strategies to fight antibiotic resistance. Antibiotics, 8(4), 254.
  6. Durand, G. A., Raoult, D., & Dubourg, G. (2019). Antibiotic discovery: history, methods and perspectives. International journal of antimicrobial agents, 53(4), 371-382.
  7. Guo, Y., Song, G., Sun, M., Wang, J., & Wang, Y. (2020). Prevalence and therapies of antibiotic-resistance in Staphylococcus aureus. Frontiers in cellular and infection microbiology, 10, 107.
  8. Mancuso, G., Midiri, A., Gerace, E., & Biondo, C. (2021). Bacterial antibiotic resistance: The most critical pathogens. Pathogens, 10(10), 1310.
  9. Khameneh, B., Eskin, N. M., Iranshahy, M., & Fazly Bazzaz, B. S. (2021). Phytochemicals: a promising weapon in the arsenal against antibiotic-resistant bacteria. Antibiotics, 10(9), 1044.
  10. Nazir, A., Malik, K., Qamar, H., Basit, M. H., Liaqat, A., Shahid, M., ... & Sadia, H. (2020). 9. A review: Use of plant extracts and their phytochemical constituents to control antibiotic resistance in S. aureus. Pure and Applied Biology (PAB), 9(1), 720-727.
  11. Audah, K. A. (2019). Drug discovery: a biodiversity perspective. Nanotechnology: Applications in energy, drug and food, 249-265.
  12. Sanka, I., Kusuma, A. B., Martha, F., Hendrawan, A., Pramanda, I. T., Wicaksono, A., ... & Widyaningrum, A. R. (2023). Synthetic biology in Indonesia: Potential and projection in a country with mega biodiversity. Biotechnology Notes, 4, 41-48.
  13. Torres, P. H., Sodero, A. C., Jofily, P., & Silva-Jr, F. P. (2019). Key topics in molecular docking for drug design. International journal of molecular sciences, 20(18), 4574.
  14. R. Jakhar, M. Dangi Hooda, A. Khichi, and A. Chhillar, “Relevance of Molecular Docking Studies in Drug Designing,” Curr. Bioinform., vol.
  15. Anand, U., Jacobo-Herrera, N., Altemimi, A., & Lakhssassi, N. (2019). A comprehensive review on medicinal plants as antimicrobial therapeutics: potential avenues of biocompatible drug discovery. Metabolites, 9(11), 258.
  16. Schaller, D., Šribar, D., Noonan, T., Deng, L., Nguyen, T. N., Pach, S., ... & Wolber, G. (2020). Next generation 3D pharmacophore modeling. Wiley Interdisciplinary Reviews: Computational Molecular Science, 10(4), e1468.
  17. Barrows, J. M., & Goley, E. D. (2021). FtsZ dynamics in bacterial division: what, how, and why?. Current opinion in cell biology, 68, 163-172.
  18. Syahdi, R. R., Iqbal, J. T., Munim, A., & Yanuar, A. (2019). HerbalDB 2.0: Optimization of construction of three-dimensional chemical compound structures to update Indonesian medicinal plant database. Pharmacognosy Journal, 11(6).
  19. Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings. Journal of chemical information and modeling, 61(8), 3891-3898.
  20. DeChancie, J., & Houk, K. N. (2007). The origins of femtomolar protein− ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin−(strept) avidin binding site. Journal of the American Chemical Society, 129(17), 5419-5429.
  21. Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific reports, 7(1), 42717.
  22. Sucharitha, P., Reddy, K. R., Satyanarayana, S. V., & Garg, T. (2022). Absorption, distribution, metabolism, excretion, and toxicity assessment of drugs using computational tools. In Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV2 Infection (pp. 335-355). Academic Press.
  23. Ramírez, D., & Caballero, J. (2018). Is it reliable to take the molecular docking top scoring position as the best solution without considering available structural data?. Molecules, 23(5), 1038.
  24. Aggarwal, R., & Koes, D. R. (2020). Learning rmsd to improve protein-ligand scoring and pose selection.
  25. Maia, E. H. B., Campos, V. A., dos Reis Santos, B., Costa, M. S., Lima, I. G., Greco, S. J., ... & Taranto, A. G. (2017). Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets. Journal of molecular modeling, 23, 1-11.
  26. Maia, E. H. B., Assis, L. C., De Oliveira, T. A., Da Silva, A. M., & Taranto, A. G. (2020). Structure-based virtual screening: from classical to artificial intelligence. Frontiers in chemistry, 8, 343.
  27. Prawiningrum, A. F., Paramita, R. I., & Erlina, L. (2022). Pharmacophore-Based Virtual Screening from Indonesian Herbal Database to Find Putative Selective Estrogen Receptor Degraders. Indonesian Journal of Medical Chemistry and Bioinformatics, 1(1), 1.
  28. Wang, W., Gan, N., Sun, Q., Wu, D., Gan, R., Zhang, M., ... & Li, H. (2019). Study on the interaction of ertugliflozin with human serum albumin in vitro by multispectroscopic methods, molecular docking, and molecular dynamics simulation. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 219, 83-90.
  29. Moussa, N., Hassan, A., & Gharaghani, S. (2021). Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors. Heliyon, 7(4).
  30. Heinzelmann, G., & Gilson, M. K. (2021). Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation. Scientific reports, 11(1), 1116.
  31. Cournia, Z., Allen, B., & Sherman, W. (2017). Relative binding free energy calculations in drug discovery: recent advances and practical considerations. Journal of chemical information and modeling, 57(12), 2911-2937.
  32. Pakpahan, M. T., Saito, H., Kawaguchi, K., & Nagao, H. Binding Free Energy of Protein-Ligand by Combining Docking and MD Simulation: A Comparison of Calculation Methods.
  33. Gurung, A. B., Bhattacharjee, A., & Ali, M. A. (2016). Exploring the physicochemical profile and the binding patterns of selected novel anticancer Himalayan plant derived active compounds with macromolecular targets. Informatics in Medicine Unlocked, 5, 1-14.
  34. Kataria, R., & Khatkar, A. (2019). Molecular docking, synthesis, kinetics study, structure–activity relationship and ADMET analysis of morin analogous as Helicobacter pylori urease inhibitors. BMC chemistry, 13(1), 1-17.
  35. Lobo, S. (2020). Is there enough focus on lipophilicity in drug discovery?. Expert opinion on drug discovery, 15(3), 261-263.
  36. Guan, L., Yang, H., Cai, Y., Sun, L., Di, P., Li, W., ... & Tang, Y. (2019). ADMET-score–a comprehensive scoring function for evaluation of chemical drug-likeness. Medchemcomm, 10(1), 148-157.
  37. Vastag, G., Apostolov, S., & Matijević, B. (2018). Prediction of lipophilicity and pharmacokinetics of chloroacetamides by chemometric approach. Iranian journal of pharmaceutical research: IJPR, 17(1), 100.
  38. Bommareddy, A., Brozena, S., Steigerwalt, J., Landis, T., Hughes, S., Mabry, E., ... & Dwivedi, C. (2019). Medicinal properties of alpha-santalol, a naturally occurring constituent of sandalwood oil. Natural product research, 33(4), 527-543.
  39. Mohankumar, A., Kalaiselvi, D., Thiruppathi, G., Muthusaravanan, S., Nivitha, S., Levenson, C., ... & Sundararaj, P. (2020). α-and β-santalols delay aging in Caenorhabditis elegans via preventing oxidative stress and protein aggregation. ACS omega, 5(50), 32641-32654.
  40. Jirovetz, L., Buchbauer, G., Denkova, Z., Stoyanova, A., Murgov, I., Gearon, V., ... & Geissler, M. (2006). Comparative study on the antimicrobial activities of different sandalwood essential oils of various origin. Flavour and fragrance journal, 21(3), 465-468.
  41. Klūga, A., Terentjeva, M., Vukovic, N. L., & Kačániová, M. (2021). Antimicrobial activity and chemical composition of essential oils against pathogenic microorganisms of freshwater fish. Plants, 10(7), 1265.

Most read articles by the same author(s)