Analisis Uji In Silico Senyawa Bioaktif Daun Kirinyuh (Chromolaena odorata L.) terhadap PBP1 Bakteri Staphylococcus aureus
DOI:
https://doi.org/10.31004/joecy.v6i1.8532Abstract
ABSTRACT
Resistance to β-lactam antibiotics is caused by alterations in penicillin-binding proteins (PBPs). PBP1 of Staphylococcus aureus is a transpeptidase protein involved in bacterial cell wall biosynthesis. Several studies have reported that extracts of Chromolaena odorata L. exhibit inhibitory activity against Staphylococcus aureus in vitro. This study aimed to predict the inhibitory potential of bioactive compounds from kirinyuh leaves against the PBP1 protein of Staphylococcus aureus. This study using an in silico approach with the aid of VegaZZ, PyRx, Discovery Studio, SwissADME, and ToxTree software. The compounds 7-angeloylretronecine, 9-angeloylretroene, rinderine, intermedine, rinderine N-oxide, intermedine N-oxide, 4’,5,6,7-tetramethoxyflavone, odoratin, isosakuranetin, quercetin, luteolin, apigenin, acacetin, sinencetin, quercetagetin, chlorogenic acid, p-coumaric acid, p-hydroxybenzoic acid, protocatechuic acid, and vanillic acid were able to bind to the PBP1 protein with ΔG values ranging from −5.3 to −8.1 kcal/mol and RMSD values of 0.543–2.157 Å. These interactions involved residues SER A:314, SER A:349, and ASN A:370, which are identical to the interaction residues of the native ligand oxacillin. The compounds 7-angeloylretronecine and 9-angeloylretroene, p-coumaric acid and vanillic acid fulfilled Lipinski’s Rule of Five and demonstrated favorable pharmacokinetic properties. The compounds p-hydroxybenzoic acid, protocatechuic acid, p-coumaric acid, and vanillic acid met the Cramer rules.
Keywords: ADME, Chromolaena, Docking, PBP1, Staphylococcus
References
Agu, P. C., Afiukwa, C. A., Orji, O. U., Ezeh, E. M., Ofoke, I. H., Ogbu, C. O., Ugwuja, E. I., & Aja,
P. M. (2023). Molecular docking as a tool for the discovery of molecular targets of
nutraceuticals in diseases management. Scientific Reports, 13(1).
https://doi.org/10.1038/s41598-023-40160-2
Burley, S. K., Berman, H. M., Duarte, J. M., Feng, Z., Flatt, J. W., Hudson, B. P., Lowe, R., Peisach,
E., Piehl, D. W., Rose, Y., Sali, A., Sekharan, M., Shao, C., Vallat, B., Voigt, M., Westbrook,
J. D., Young, J. Y., & Zardecki, C. (2022). Protein Data Bank: A Comprehensive Review
of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and
Students. In Biomolecules (Vol. 12, Number 10). MDPI.
https://doi.org/10.3390/biom12101425
Carlson, E. E., Sparks, N., & Diwakar, S. (2025). Decoding the Penicillin-Binding Proteins with
Activity-Based Probes. Accounts of Chemical Research, 58(11), 1754–1763.
https://doi.org/10.1021/acs.accounts.5c00113
Ciupei, D., Colişar, A., Leopold, L., Stănilă, A., & Diaconeasa, Z. M. (2024). Polyphenols: From
Classification to Therapeutic Potential and Bioavailability. In Foods (Vol. 13, Number 24).
Multidisciplinary Digital Publishing Institute (MDPI).
https://doi.org/10.3390/foods13244131
Fakih, T. M., & Dewi, M. L. (2020). Studi Interaksi Molekuler Aktivitas Antimikroba Peptida Bioaktif
terhadap Staphylococcus aureus Secara In silico. Jurnal Farmasi Dan Ilmu Kefarmasian
Indonesia, 7(2), 93. http://www.rcsb.org/pdb
Fitriawati, A., & Nordeka, M. O. (2024). Physical Quality Test And Optimization of Kirinyuh Leaf
Ethanol Extract Cream (Chromolaena odorata L.) Using Simplex Lattice Design Method.
Ambassador Pharma Journal (Jurnal Duta Farma), 4(1), 209–217.
Harahap, N. D., Dalimunthe, A., & Bangun, H. (2023). Antibacterial Activity of Tekelan Leaf Ethanol
Extract (Chromolaena odorata (L.) R. M. King and H. Rob) against of Staphylococcus
aureus bacteria. International Journal of Basic & Clinical Pharmacology, 13(1), 36–41.
https://doi.org/10.18203/2319-2003.ijbcp20233823
Korkut, A., Özkaya Gül, S., Aydemir, E., Er, H., & Odabaş Köse, E. (2025). Cinnamic Acid
Compounds (p-Coumaric, Ferulic, and p-Methoxycinnamic Acid) as Effective
Antibacterial Agents Against Colistin-Resistant Acinetobacter baumannii. Antibiotics, 14(1).
https://doi.org/10.3390/antibiotics14010071
Listyani, T. A., Addawiyyah, M., Raharjo, D., & Chyang, P. J. (2024). Docking and Structural
Modification of Flavonoid Derivative Compounds as Cycloxygenas-2 Enzyme Inhibitors.
Indonesian Journal of Global Health Research, 7(1), 311–322.
https://doi.org/10.37287/ijghr.v7i1.4041
Miebs, G., Mielniczuk, A., Kadziński, M., & Bachorz, R. A. (2024). Beyond the Arbitrariness of Drug-
Likeness Rules: Rough Set Theory and Decision Rules in the Service of Drug Design.
Applied Sciences (Switzerland), 14(21). https://doi.org/10.3390/app14219966
Mora-Ochomogo, M., & Lohans, C. T. (2021). β-Lactam antibiotic targets and resistance mechanisms:
From covalent inhibitors to substrates. In RSC Medicinal Chemistry (Vol. 12, Number 10,
pp. 1623–1639). Royal Society of Chemistry. https://doi.org/10.1039/d1md00200g
Murray, C. J., Ikuta, K. S., Sharara, F., Swetschinski, L., Robles Aguilar, G., Gray, A., Han, C.,
Bisignano, C., Rao, P., Wool, E., Johnson, S. C., Browne, A. J., Chipeta, M. G., Fell, F.,
Hackett, S., Haines-Woodhouse, G., Kashef Hamadani, B. H., Kumaran, E. A. P.,
McManigal, B., … Naghavi, M. (2022). Global burden of bacterial antimicrobial resistance
in 2019: a systematic analysis. The Lancet, 399(10325), 629–655.
https://doi.org/10.1016/S0140-6736(21)02724-0
Nhlapho, S., Nyathi, M., Ngwenya, B., Dube, T., Telukdarie, A., Munien, I., Vermeulen, A., & Chude -
Okonkwo, U. (2024). Druggability of Pharmaceutical Compounds Using Lipinski Rules
with Machine Learning. Sciences of Pharmacy, 3(4), 177–192.
https://doi.org/10.58920/sciphar0304264
Odhiambo, D. O., Omosa, L. K., Njagi, E. C., Kithure, J. G., & Wekesa, E. N. (2025). In-silico
pharmacokinetics ADME/Tox analysis of phytochemicals from genus Dracaena for their
therapeutic potential. Scientific African, 29. https://doi.org/10.1016/j.sciaf.2025.e02796
Ramadhani, F. A., Prastika, M. F., Fikriyah, N., Isnaeni, & Diyah, N. W. (2024). Molecular Docking
of Flavonoids from Extract of Roselle (Hibiscus sabdariffa L.) Calyx on PBP2a as the Basis
for Antibacterial Activity Against Methicillin Resistant Staphylococcus aureus. Science and
Technology Indonesia, 9(2), 487–493. https://doi.org/10.26554/sti.2024.9.2.487-493
Santhosh, C. R., Chinnam, S., Ananthnag, G. S., Oduselu, G. O., Chidambaram, K., Kerru, N.,
Kottam, N., & Madhu, G. M. (2025). Design, synthesis, crystal structure of novel
hydrazone analogues as SARS-CoV-2 potent inhibitors: MD simulations, MM-GBSA,
docking and ADMET studies. Royal Society Open Science, 12(7).
https://doi.org/10.1098/rsos.250373
Teuku Husni, T. R., Darmawi, D., Azwar, A., & Jamil, K. F. (2023). Bioactive phytoconstituents of
ethanolic extract from Chromolaena odorata leaves interact with vascular endothelial
growth factor and cyclooxygenase-2: A molecular docking study. Journal of Advanced
Pharmaceutical Technology and Research, 14(1), 29–33.
https://doi.org/10.4103/japtr.japtr_520_22
Wacnik, K., Rao, V. A., Chen, X., Lafage, L., Pazos, M., Booth, S., Vollmer, W., Hobbs, J. K., Lewis,
R. J., & Foster, S. J. (2022). Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus
Has Multiple Essential Functions in Cell Division. MBio, 13(4).
https://doi.org/10.1128/mbio.00669-22
Wei, J., Khan, K. ur R., Ahmad, M., Tabassum, S., Dilshad, R., & Basit, A. (2025). Phenolic
Quantification, In Vitro Biological Activities and In Silico Studies of Ultrasound Assisted
Extract of Pleurospermum candollei to Evaluate its Functional Food Potential. Natural
Product Communications, 20(9). https://doi.org/10.1177/1934578X251378072
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