The aim of this work is to isolate antibacterial compounds from Sarang Semut (Myrmecodia pendans) and to evaluate their antibacterial activity against pathogenic oral bacteria of Enterococcus faecalis ATCC 29212 and inhibitory activity against MurA enzyme. The antibacterial compounds from Sarang Semut were isolated by a bioactivity-guided separation method with various solvents and combination of column chromatography on normal and reverse phases. The compounds with concentrations of 1000 and 5000 ppm were assessed against E. faecalis ATCC 29212 by agar well diffusion method, with chlorhexidine and fosfomicyn being used as positive controls. Two antibacterial compounds isolated from Sarang Semut were identified as two new flavonoids derivates of 1 (10 mg) and 2 (4 mg). Then, both compounds were tested for antibacterial activities against E. faecalis to find inhibition zones, MIC and MBC values, and it was found that their inhibition zones values of compounds 1 and 2 were 8.15 and 8.05 mm at 1000 ppm and 8.62 and 8.55 mm at 5000 ppm, respectively, while their MIC and MBC were 156 and 625 ppm for 1 and 625 and 2500 ppm for 2, respectively. In inhibitory murA enzyme activity assay, compounds 1 and 2 were shown to inhibit the enzyme activity by IC50 values of 21.7 and151.3 ppm. The study demonstrated that ethyl acetate fraction of Sarang Semut contained antibacterial flavonoids as active constituents that showed activity against E. faecalis. These results proved the plant's potential in herbal medicine and the development of new antibacterial agent for pathogenic dental caries.

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-β-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.

Background: Increasing the resistance issue has become the reason for the development of new antibacterial in crucial condition. Many ways are tracked to determine the most effective antibacterial agent. Some proteins that are a key role in bacteria metabolism are targeted including MurA in cell wall biosynthesis and gelatinase biosynthesis-activating pheromone (GBAP) in Fsr Quorum Sensing (QS) system. Objective: The objective of this research is the analysis of compounds 1-4 from M. pendans as antibacterial and anti-QS activity trough protein inhibition by in silico study; focus on the structure-activity relationships, to appraise their role as an antibacterial and anti-QS agent in the molecular level. Method: Both activities of M. pendans compounds (1-4) were analyzed by in silico, comparing to Fosfomycin, Ambuic acid, Quercetin, and Taxifolin as a standard. Chemical structures of M. pendans compounds were converted using an online program molview. The compounds were docked to MurA, GBAP, gelatinase and serine protease using Autodock Vina in Pyrx 0.8 followed PYMOL to visualization and proteis.plus program to analyze of the complex. Results: All compounds from M. pendans bound on MurA, GBAP, gelatinase and serine protease except compound 2. This biflavonoid did not attach to MurA and serine protease yet is the favorable ligand for GBAP and gelatinase with the binding affinity of -6.9 and -9.4 Kcal/mol respectively. Meanwhile, for MurA and serine protease, compound 4 is the highest of bonding energy with values of -8.7 and -6.4 Kcal/mol before quercetin (MurA, -8.9 Kcal/mol) and taxifolin (serine protease, -6.6 Kcal/mol). Conclusion: Based on the data, biflavonoid acts better as anti-QS than an inhibitor of MurA enzyme while the others can be acted into both of them either therapeutic agent of anti-QS or antibacterial agent of MurA inhibitor.

Background: Dental diseases are generally caused by oral bacteria such as Enterococcus faecalis, Streptococcus mutans, and Streptococcus sanguinis. These bacteria have resistance to synthetic drugs; thus, it is required to discover new antibacterial agents. Sarang Semut (Myrmecodia pendans) has been empirically used as a medicinal plant to treat various conditions, including those caused by pathogenic bacteria. Objective: The present study was aimed to investigate the antibacterial activity of Sarang Semut extracts against E. faecalis, S. mutans, and S. sanguinis. Materials and Methods: Sarang Semut was extracted with several solvents to yield n-hexane, ethyl acetate, methanol, and water extracts. Each extract and combination were adjusted for assay with chlorhexidine, fosfomycin, and quercetin and used as positive controls. Results: The n-hexane extract showed activity with inhibition zone values of 7.15 and 10.45 ppm against E. faecalis and S. mutans at 1%, respectively. All combination extracts could inhibit the growth of E. faecalis and S. sanguinis. The synergistic effects resulting from the combination of extract-fosfomycin were also presented in this evaluation, with the strongest shown by water-fosfomycin against S. mutans, with inhibition zones of 28.5 mm at 1%. Conclusion: Sarang Semut extracts demonstrated antibacterial activity against oral pathogenic bacteria. These results offer alternative natural sources for the new antibacterial drug candidate.

Background: The MurA enzyme, enolpyruvyl UDP-N-acetylglucosamine transferase, is one of the targeted proteins by antibiotics for effective treatment of diseases provided by pathogenic bacteria. It plays a key role in the cell wall biosynthesis of Gram-positive bacteria such as Enterococcus faecalis. Butein is a flavonoid that showed antioxidant and anticancer activities, but recently it is a promising antibacterial agent and reported can inhibit E. faecelis, Eschericia coli, and Mycobacterium tuberculosis. It was isolated from medicinal plants, including Sarang Semut (Myrmecodia pendans). However, the molecular mechanism of butein inhibits bacteria that is no clear. Objective: This study aims to predict the molecular action of the butein against MurA, catalyzing the first step of peptidoglycan biosynthesis. Material and Methods: Butein isolation used a combinational separation technique and characterization using spectroscopic methods. Then, in silico method used was virtual screening using programs including Autodock Vina in PyRx, protein. plus, and ligplots. Butein and UDP-N-acetylglucosamine (UNAG as a positive control) act as ligand were subject binding to 3KQJ MurA as protein. To evaluate in vitro antibacterial activity, we used the Kirby-Bauer method. Results: Butein from M. pendans is a potential compound to inhibit the MurA with binding affinity - 7.6 kcal.mol-1. It is lower than UNAG but higher than Fosfomycin as a MurA inhibitor. Butein attaches to MurA in the same position as UNAG so that it concludes that both is a competitive inhibitor. Meanwhile, in vitro study showed that butein inhibits the E. faecalis growth with inhibit zone of 8.37 mm at 1 mg/ml. Conclusions: Butein as a potent antibacterial agent through blocking MurA enzyme in cell wall formation.