Bioinformatic approach of propolis as an inhibitor of peptidoglycan glycosyltransferase to improve antibacterial agent: An in-silico study

Background: In Indonesia, the prevalence of dental and oral problems is still high at 57.6% in 2018, especially periodontitis at 74.1%. Peptidoglycan is an essential component of the bacterial cell wall. Peptidoglycan glycosyltransferase (PGT) is a protein target that plays a role in transferring lipid disaccharides II to growing glycan chains for bacterial cell wall synthesis. Propolis is a natural ingredient produced by bees and has anti-inflammatory, antibacterial, antiviral and antioxidant properties so that it has the potential to be a natural mouthwash ingredient. One of the antibacterial properties of propolis is to be able to kill and reduce the number of bacteria that cause periodontitis. Purpose: This study aims to investigate the potential of a specific compound of propolis as an inhibitor of protein peptidoglycan glycosyltransferase through bonding interactions. Methods: The method used is an in-silico test in molecular docking with computational software, namely Molegro virtual docker and Discovery Studio visualizer. Results: This study showed the types of bonds between the four compounds, and chlorhexidine as a control showed similar types of bonds, including hydrogen bonds, hydrophobic interactions and unfavourable bonds. The binding energy values of each of the five compounds were pinocembrin -222.166 kJ/mol, hesperetin -230.144 kJ/mol, chrysin -219.45 kJ/mol, caffeic acid phenethyl ester -266.64 kJ/mol and chlorhexidine -362.71 kJ/mol. Conclusion: Caffeic acid phenethyl ester (CAPE) is the most significant potential as an inhibitor of protein peptidoglycan glycosyltransferase and chlorhexidine has the highest binding affinity than the four propolis compounds, followed by caffeic acid phenethyl ester in propolis in silico.

Unipolar Peptidoglycan Synthesis in the Rhizobiales Requires an Essential Class A Penicillin-Binding Protein

While the structure and function of the bacterial cell wall are well conserved, the mechanisms responsible for cell wall biosynthesis during elongation are variable. It is increasingly clear that rod-shaped bacteria use a diverse array of growth strategies with distinct spatial zones of cell wall biosynthesis, including lateral elongation, unipolar growth, bipolar elongation, and medial elongation.

Peptidoglycan Deacetylases in Bacterial Cell Wall Remodeling and Pathogenesis

: The bacterial cell wall peptidoglycan (PG) is a dynamic structure that is constantly synthesized, re-modeled and degraded during bacterial division and growth. Post-synthetic modifications modulate the action of endogenous autolysis during PG lysis and remodeling for growth and sporulation, but also they are a mechanism used by pathogenic bacteria to evade the host innate immune system. Modifica-tions of the glycan backbone are limited to the C-2 amine and the C-6 hydroxyl moieties of either Glc-NAc or MurNAc residues. This paper reviews the functional roles and properties of peptidoglycan de-N-acetylases (distinct PG GlcNAc and MurNAc deacetylases) and recent progress through genetic stud-ies and biochemical characterization to elucidate their mechanism of action, 3D structures, substrate specificities and biological functions. Since they are virulence factors in pathogenic bacteria, peptidogly-can deacetylases are potential targets for the design of novel antimicrobial agents.

MurA escape mutations uncouple peptidoglycan biosynthesis from PrkA signaling

Gram-positive bacteria are protected by a thick mesh of peptidoglycan (PG) completely engulfing their cells. This PG network is the main component of the bacterial cell wall, it provides rigidity and acts as foundation for the attachment of other surface molecules. Biosynthesis of PG consumes a high amount of cellular resources and therefore requires careful adjustments to environmental conditions.An important switch in the control of PG biosynthesis of Listeria monocytogenes, a Gram-positive pathogen with a high infection fatality rate, is the serine/threonine protein kinase PrkA. A key substrate of this kinase is the small cytosolic protein ReoM. We have shown previously that ReoM phosphorylation regulates PG formation through control of MurA stability. MurA catalyzes the first step in PG biosynthesis and the current model suggests that phosphorylated ReoM prevents MurA degradation by the ClpCP protease. In contrast, conditions leading to ReoM dephosphorylation stimulate MurA degradation. How ReoM controls degradation of MurA and potential other substrates is not understood. Also, the individual contribution of the ∼20 other known PrkA targets to PG biosynthesis regulation is unknown.We here present murA mutants which escape proteolytic degradation. The release of MurA from ClpCP-dependent proteolysis was able to constitutively activate PG biosynthesis and further enhances the intrinsic cephalosporin resistance of L. monocytogenes. This activation required the RodA3/PBP B3 transglycosylase/transpeptidase pair as additional effectors of the PrkA signaling route. One murA escape mutation not only fully rescued an otherwise non-viable prkA mutant during growth in batch culture and inside macrophages but also overcompensated cephalosporin hypersensitivity. Our data collectively indicate that the main purpose of PrkA-mediated signaling in L. monocytogenes is control of MurA stability during extra- and intracellular growth. These findings have important implications for the understanding of PG biosynthesis regulation and β-lactam resistance of L. monocytogenes and related Gram-positive bacteria.Author SummaryPeptidoglycan (PG) is the main component of the bacterial cell wall and many of the PG synthesizing enzymes are antibiotic targets. We previously have discovered a new signaling route controlling PG production in the human pathogen Listeria monocytogenes. This route also determines the intrinsic resistance of L. monocytogenes against cephalosporins, a group of β-lactam antibiotics. Signaling involves PrkA, a membrane-embedded protein kinase, that is activated during cell wall stress to phosphorylate its target ReoM. Depending on its phosphorylation, ReoM activates or inactivates PG production by controlling the proteolytic stability of MurA, which catalyzes the first step in PG biosynthesis. MurA degradation depends on the ClpCP protease and we here have isolated murA mutations that escape this degradation. Using these mutants, we could show that regulation of PG biosynthesis through control of MurA stability is the primary purpose of PrkA-mediated signaling in L. monocytogenes. Further experiments identified the transglycosylase RodA and the transpeptidase PBP B3 as additional effectors of PrkA signaling. Our results suggest that both proteins act together to translate the signals received by PrkA into intensification of PG biosynthesis. These findings shed new light on the regulation of PG biosynthesis in Gram-positive bacteria with intrinsic β-lactam resistance.

Specific bacterial cell wall components influence the stability of Coxsackievirus B3

Enteric viruses infect the mammalian gastrointestinal tract and lead to significant morbidity and mortality worldwide. Data indicate that enteric viruses can utilize intestinal bacteria to promote viral replication and pathogenesis. However, the precise interactions between enteric viruses and bacteria are unknown. Here we examined the interaction between bacteria and Coxsackievirus B3, an enteric virus from the picornavirus family. We found that bacteria enhance the infectivity of Coxsackievirus B3 (CVB3) in vitro . Notably, specific bacteria are required as Gram-negative Salmonella enterica , but not Escherichia coli , enhanced CVB3 infectivity and stability. Investigating the cell wall components of both S. enterica and E. coli revealed that structures in the O-antigen or core of lipopolysaccharide, a major component of the Gram-negative bacterial cell wall, were required for S. enterica to enhance CVB3. To determine if these requirements were necessary for similar enteric viruses, we investigated if S. enterica and E. coli enhanced infectivity of poliovirus, another enteric virus in the picornavirus family. We found that while E. coli did not enhance the infectivity of CVB3, E. coli enhanced poliovirus infectivity. Overall, these data indicate that distinct bacteria enhance CVB3 infectivity and stability, and specific enteric viruses may have differing requirements for their interactions with specific bacterial species. Importance Previous data indicate that several enteric viruses utilize bacteria to promote intestinal infection and viral stability. Here we show that specific bacteria and bacterial cell wall components are required to enhance infectivity and stability of Coxsackievirus B3 in vitro . These requirements are likely enteric virus-specific as the bacteria for CVB3 differs from poliovirus, a closely related virus. Therefore, these data indicate that specific bacteria and their cell wall components dictate the interaction with various enteric viruses in distinct mechanisms.