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-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.
Highlights
Infectious disease leads to sickness, including infection caused by bacteria [1]
Strategic pathways that can be inhibited by antibacterial agents, especially in Grampositive bacteria, are in the step of the cell wall, protein, ribonucleic acid (RNA), and deoxyribonucleic acid(DNA) synthesis
The MurB enzyme contributes to the first step of peptidoglycan synthesis, while penicillin-binding proteins (PBPs) play a role in the final step of cell wall biosynthesis [4,5]
Summary
Antibiotic resistance intensifies the difficulty to deal with pathogenic bacteria, and the development of new therapy or the discovery of novel antibacterial agents plays a vital role to counteract this [3]. Strategic pathways that can be inhibited by antibacterial agents, especially in Grampositive bacteria, are in the step of the cell wall, protein, ribonucleic acid (RNA), and deoxyribonucleic acid(DNA) synthesis. The processes of their syntheses involve many proteins that support them. The MurB enzyme contributes to the first step of peptidoglycan synthesis, while penicillin-binding proteins (PBPs) play a role in the final step of cell wall biosynthesis [4,5]. The Sortase A (SrtA) enzyme, a protein anchored to the cell wall, is an important agent for virulence and biofilm formation [6]
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