| Title: | Effectiveness of Bioactive Compound as Antibacterial and Anti-Quorum Sensing Agent from Myrmecodia pendans: An In Silico Study |
| Author(s): | Satari MH; Apriyanti E; Dharsono HDA; Nurdin D; Gartika M; Kurnia D; |
| Address: | "Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung 40132, Indonesia. Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia. Department of Conservative Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Bandung 40132, Indonesia. Department of Pediatric Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Bandung 40132, Indonesia" |
| DOI: | 10.3390/molecules26092465 |
| ISSN/ISBN: | 1420-3049 (Electronic) 1420-3049 (Linking) |
| Abstract: | "BACKGROUND: antibiotic resistance encourages the development of new therapies, or the discovery of novel antibacterial agents. Previous research revealed that Myrmecodia pendans (Sarang Semut) contain potential antibacterial agents. However, specific proteins inhibited by them have not yet been identified as either proteins targeted by antibiotics or proteins that have a role in the quorum-sensing system. This study aims to investigate and predict the action mode of antibacterial compounds with specific proteins by following the molecular docking approach. METHODS: butein (1), biflavonoid (2), 3''-methoxyepicatechin-3-O-epicatechin (3), 2-dodecyl-4-hydroxylbenzaldehyde (4), 2-dodecyl-4-hydroxylbenzaldehyde (5), pomolic acid (6), betulin (7), and sitosterol-(6'-O-tridecanoil)-3-O-beta-D-glucopyranoside (8) from M. pendans act as the ligand. Antibiotics or substrates in each protein were used as a positive control. To screen the bioactivity of compounds, ligands were analyzed by Prediction of Activity Spectra for Substances (PASS) program. They were docked with 12 proteins by AutoDock Vina in the PyRx 0.8 software application. Those proteins are penicillin-binding protein (PBP), MurB, Sortase A (SrtA), deoxyribonucleic acid (DNA) gyrase, ribonucleic acid (RNA) polymerase, ribosomal protein, Cytolysin M (ClyM), FsrB, gelatinase binding-activating pheromone (GBAP), and PgrX retrieved from UniProt. The docking results were analyzed by the ProteinsPlus and Discovery Studio software applications. RESULTS: most compounds have Pa value over 0.5 against proteins in the cell wall. In nearly all proteins, biflavonoid (2) has the strongest binding affinity. However, compound 2 binds only three residues, so that 2 is the non-competitive inhibitor. CONCLUSION: compound 2 can be a lead compound for an antibacterial agent in each pathway" |
| Keywords: | Anti-Bacterial Agents/*pharmacology Molecular Docking Simulation Quorum Sensing/drug effects Rubiaceae/*chemistry Myrmecodia pendans anti-bacteria molecular docking protein quorum sensing; |
| Notes: | "MedlineSatari, Mieke Hemiawati Apriyanti, Eti Dharsono, Hendra Dian Adhita Nurdin, Denny Gartika, Meirina Kurnia, Dikdik eng Switzerland 2021/05/01 Molecules. 2021 Apr 23; 26(9):2465. doi: 10.3390/molecules26092465" |
