DOI: https://doi.org/10.14710/jksa.25.12.427-435

Interaction Mechanism of Inhibition of Palmitic Acid and α Selinene Targeting FabH and FabI Enzymes in Escherichia coli: In Silico Study

Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University, Jl. Prof. Soedarto, SH., Tembalang, Semarang, Indonesia

Received: 13 Oct 2022; Revised: 24 Nov 2022; Accepted: 20 Dec 2022; Published: 31 Dec 2022.
Open Access Copyright 2022 Jurnal Kimia Sains dan Aplikasi under http://creativecommons.org/licenses/by-sa/4.0.

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Abstract
Investigation studies of the interaction mechanism of palmitic acid and α-selinene in inhibiting FabH and FabI enzymes have been studied using an in silico approach. FabH (Beta-Ketoacyl-ACP Synthase III) and FabI (Enoyl-acyl carrier protein reductase) enzymes are two enzymes that are targets for the inhibition of candidate antibacterial compounds. This study aimed to determine the strongest candidate between palmitic acid and α-selinene as an antibacterial agent for Escherichia coli. The method used in this study is a random and directed molecular docking method using the Autodock Vina program, which is integrated into PyRx 0.8 software. The results of the molecular docking simulation include the pattern and strength of interaction between the ligand and the FabI and FabH enzymes. The interaction pattern includes the cluster pattern, the ligand poses on the protein surface, and the interaction strength based on the binding affinity value. Based on the results of random docking simulation data analysis, it was shown that the majority of α-selinene occupied the position of cluster 1 of the FabI enzyme and palmitic acid in cluster 2 of the FabH enzyme. Based on the binding affinity value, palmitic acid has a weaker interaction strength on the FabH enzyme (-5.7 kcal/mol) than on the FabI enzyme (-7.1 kcal/mol). The interaction strength of α-selinene on the FabI enzyme (-7.3 kcal/mol) was stronger than that of the FabH enzyme (-6.9 kcal/mol). The interaction strength of α-selinene in both FabI and FabH enzymes was greater than that of palmitic acid. α-selinene is projected to have a better potential as an antibacterial agent against Escherichia coli than palmitic acid based on its greater interaction strength.
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Keywords: Palmitic acid; α-selinene; enzyme; in silico; FabH; FabI
Funding: Universitas Diponegoro

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Section: Research Articles
Language : EN
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  1. Filomena Nazzaro, Florinda Fratianni, Laura De Martino, Raffaele Coppola, Vincenzo De Feo, Effect of essential oils on pathogenic bacteria, Pharmaceuticals, 6, 12, (2013), 1451-1474 https://doi.org/10.3390/ph6121451
  2. Tânia A. T. Gomes, Waldir P. Elias, Isabel C. A. Scaletsky, Beatriz E. C. Guth, Juliana F. Rodrigues, Roxane M. F. Piazza, Luís C. S. Ferreira, Marina B. Martinez, Diarrheagenic Escherichia coli, Brazilian Journal of Microbiology, 47, (2016), 3-30 https://doi.org/10.1016/j.bjm.2016.10.015
  3. Sónia Ramos, Vanessa Silva, Maria de Lurdes Enes Dapkevicius, Manuela Caniça, María Teresa Tejedor-Junco, Gilberto Igrejas, Patrícia Poeta, Escherichia coli as Commensal and Pathogenic Bacteria among Food-Producing Animals: Health Implications of Extended Spectrum β-Lactamase (ESBL) Production, Animals, 10, 12, (2020), 2239 https://doi.org/10.3390/ani10122239
  4. Michael J. Pelczar, E.C.S. Chan, Dasar-dasar mikrobiologi, Jilid 1 ed., R.S. Hadioetomo, T. Imas, S.S. Tjotrosomo, S.L. Angka, UI Press, Jakarta, 1988
  5. Veronica W. Rowlett, Venkata K. P. S. Mallampalli, Anja Karlstaedt, William Dowhan, Heinrich Taegtmeyer, William Margolin, Heidi Vitrac, Impact of Membrane Phospholipid Alterations in Escherichia coli on Cellular Function and Bacterial Stress Adaptation, Journal of Bacteriology, 199, 13, (2017), e00849-00816 https://doi.org/10.1128/JB.00849-16
  6. Enrique Rojas, Julie A. Theriot, Kerwyn Casey Huang, Response of Escherichia coli growth rate to osmotic shock, Proceedings of the National Academy of Sciences, 111, 21, (2014), 7807-7812 https://doi.org/10.1073/pnas.1402591111
  7. David C. McKinney, Charles J. Eyermann, Rong-Fang Gu, Jun Hu, Steven L. Kazmirski, Sushmita D. Lahiri, Andrew R. McKenzie, Adam B. Shapiro, Gloria Breault, Antibacterial FabH inhibitors with mode of action validated in Haemophilus influenzae by in vitro resistance mutation mapping, ACS Infectious Diseases, 2, 7, (2016), 456-464 https://doi.org/10.1021/acsinfecdis.6b00053
  8. Chang Ji Zheng, Jung-Sung Yoo, Tae-Gyu Lee, Hee-Young Cho, Young-Ho Kim, Won-Gon Kim, Fatty acid synthesis is a target for antibacterial activity of unsaturated fatty acids, FEBS Letters, 579, 23, (2005), 5157-5162 https://doi.org/10.1016/j.febslet.2005.08.028
  9. Giancarlo Casillas-Vargas, Carlimar Ocasio-Malavé, Solymar Medina, Christian Morales-Guzmán, René García Del Valle, Néstor M. Carballeira, David J. Sanabria-Ríos, Antibacterial fatty acids: An update of possible mechanisms of action and implications in the development of the next-generation of antibacterial agents, Progress in Lipid Research, 82, (2021), 101093 https://doi.org/10.1016/j.plipres.2021.101093
  10. Tita Rialita, Winiati Pudji Rahayu, Lilis Nuraida, Budi Nurtama, Aktivitas antimikroba minyak esensial jahe merah (Zingiber officinale var. Rubrum) dan lengkuas merah (Alpinia purpurata K. Schum) terhadap bakteri patogen dan perusak pangan, Agritech, 35, 1, (2015), 43-52 https://doi.org/10.22146/agritech.9418
  11. Patrezia Dyah Ayu Paminto Putri, Studi In Silico Senyawa Ekstrak Etil Asetat Dari Daun Bandotan (Ageratum Conyzoides L.) sebagai Antibakteri Melalui Mekanisme Inhibisi Enzim FabI, Departemen Kimia, Universitas Diponegoro, Semarang, 2019
  12. Sanjay S. Khandekar, Robert A. Daines, John T. Lonsdale, Bacterial β-ketoacyl-acyl carrier protein synthases as targets for antibacterial agents, Current Protein and Peptide Science, 4, 1, (2003), 21-29 http://dx.doi.org/10.2174/1389203033380377
  13. Khasanah, Skrining In Silico Potensi Essential oil Lengkuas Merah (Alpinia purpurata K. Schum) sebagai Obat Antibakteri melalui Mekanisme Inhibisi Enzim β-ketoacyl-ACP synthase III (FabH) Bakteri Escherichia coli dan Enterococcus faecalis, 2017
  14. Vincent B. Chen, W Bryan Arendall, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson, David C. Richardson, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallographica Section D: Biological Crystallography, 66, 1, (2010), 12-21 https://doi.org/10.1107/S0907444909042073
  15. Christopher A. Lipinski, Franco Lombardo, Beryl W. Dominy, Paul J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Advanced Drug Delivery Reviews, 23, 1-3, (1997), 3-25 https://doi.org/10.1016/S0169-409X(00)00129-0

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