Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme A synthase from the crotonase fold superfamily

Phytochemical and antibacterial properties of calyces Hibiscus sabdariffa L.: an in vitro and in silico multitarget-mediated antibacterial study

BACKGROUND

Multidrug-resistant (MDR) bacteria pose a significant threat to human health worldwide by increasing the harmful impact of traditional synthetic antibiotics. Traditional medicinal plants have bioactive metabolites that can significantly modulate the growth rate, cell survival, and pathogenicity of antibiotic-resistant bacteria. Hibiscus sabdariffa L., known as Roselle or Karkade, belongs to the Malvaceae family. It is well-known for its edible aromatic red/purple calyces and is extensively utilized in the food industry and pharmacological applications. H. sabdariffa calyx bioactive phytocompounds have potent therapeutic activities such as antimicrobial, antidiabetic, antiobesity, antioxidant, anti-inflammatory, and anticancer properties.

METHODS

This study utilized gas chromatography-mass spectrometry (GC-MS) analysis to determine the volatile aromatic compounds that found in the hydroethanolic extract of Hibiscus sabdariffa calyces. The purpose was to verify the antibacterial properties of Roselle calyces against selective MDR clinical bacterial isolates, including A. baumanii, E. coli, K. pneumoniae, and P. aeruginosa.

RESULTS

The GC-MS spectrum profile revealed the presence of twenty-seven volatile organic components, including organic fatty acid derivatives, ester compounds, sugar derivatives, and terpene components. The major GC-MS fractionations and the main active chemical compositions of the hydroethanolic extract of H. sabdariffa flowers were (E)-10-Octadecenoic acid methyl ester (59.23%), 8,11-Octadecadienoic acid, methyl ester (11.51%), Butanedioic acid, 3-hydroxy-2,2-dimethyl-, diethyl ester (6.22%), Diethyl succinate/Butanedioic acid, diethyl ester (2.35%), and Heptadecanoic acid, 16-methyl-, methyl ester/Methyl isostearate (2.31%). The hydroethanolic extract of H. sabdariffa dried calyces demonstrated potent antibacterial properties (zones diameter of inhibition growth, MIC, MBC, and MBC/MIC) against selective MDR clinical bacterial isolates, such as A. baumanii, E. coli, K. pneumoniae, and P. aeruginosa, as determined by the phytochemical screening (TAC, TFC, and TPC) and antioxidant activity (DPPH). The surface morphological characteristics of the treated A. baumanii, E. coli, K. pneumoniae, and P. aeruginosa clinical isolates have been affected in comparison to the untreated forms by the hydroethanolic extract of H. sabdariffa calyces, as determined by scanning electron microscopy (SEM). In silico predictive investigation revealed that the volatile aromatic components of the hydroethanolic extract of Roselle calyces exhibited significant scoring functions, binding affinities, and non-covalent intermolecular interactions with the MenB lyase and DNA gyrase targets of E. coli. These interactions significantly enhanced the activities of the volatile aromatic components against the bacterial pathogenicity, cell survival, growth, and differentiation of selective MDR clinical bacterial isolates.

CONCLUSIONS

According to the in vitro and in silico findings, the hydroethanolic extract of H. sabdariffa calyces has shown potentials as an effective antioxidant and antibacterial treatment. It contains volatile aromatic compounds that can modulate selective MDR Gram-negative clinical bacterial isolates.

Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation

The biosynthesis of plumbagin is known to occur via the acetate polymalonate pathway; however there are several intermediary steps that remain unidentified that leads to its synthesis. The study identifies enzyme naphthoate synthase to catalyze the cyclization of O-malonyl benzoyl CoA to form an intermediate that is acted upon by thioesterase before the reaction proceeds to form plumbagin. Two possible structures were predicted for this intermediate using quantum mechanics studies. A total of 60 ns molecular dynamics simulations revealed the most probable intermediate structure of the predicted two.

Identification and evaluation of quercetin as a potential inhibitor of naphthoate synthase from Enterococcus faecalis

Enterococcus faecalis is a gram-positive, rod-shape bacteria responsible for around 65% to 80% of all enterococcal nosocomial infections. It is multidrug resistant (MDR) bacterium resistant to most of the first-line antibiotics. Due to the emergence of MDR strains, there is an urgent need to find novel targets to develop new antibacterial drugs against E. faecalis. In this regard, we have identified naphthoate synthase (1,4-dihydroxy-2-naphthoyl-CoA synthase, EC: 4.1.3.36; DHNS) as an anti-E. faecalis target, as it is an essential enzyme for menaquinone (vitamin K₂ ) synthetic pathway in the bacterium. Thus, inhibiting naphtholate synthase may consequently inhibit the bacteria's growth. In this regard, we report here cloning, expression, purification, and preliminary structural studies of naphthoate synthase along with in silico modeling, molecular dynamic simulation of the model and docking studies of naphthoate synthase with quercetin, a plant alkaloid. Biochemical studies have indicated quercetin, a plant flavonoid as the potential lead compound to inhibit catalytic activity of EfDHNS. Quercetin binding has also been validated by spectrofluorimetric studies in order to confirm the bindings of the ligand compound with EfDHNS at ultralow concentrations. Reported studies may provide a base for structure-based drug development of antimicrobial compounds against E. faecalis.

A Methyl 4-Oxo-4-phenylbut-2-enoate with in Vivo Activity against MRSA that Inhibits MenB in the Bacterial Menaquinone Biosynthesis Pathway

4-Oxo-4-phenyl-but-2-enoates inhibit MenB, the 1,4-dihydroxyl-2-naphthoyl-CoA synthase in the bacterial menaquinone (MK) biosynthesis pathway, through the formation of an adduct with coenzyme A (CoA). Here, we show that the corresponding methyl butenoates have MIC values as low as 0.35-0.75 µg/mL against drug sensitive and resistant strains of Staphylococcus aureus. Mode of action studies on the most potent compound, methyl 4-(4-chlorophenyl)-4-oxobut-2-enoate (1), reveal that 1 is converted into the corresponding CoA adduct in S. aureus cells, and that this adduct binds to the S. aureus MenB (saMenB) with a K_d value of 2 µM. The antibacterial spectrum of 1 is limited to bacteria that utilize MK for respiration, and the activity of 1 can be complemented with exogenous MK or menadione. Finally, treatment of methicillin-resistant S. aureus (MRSA) with 1 results in the small colony variant phenotype and thus 1 phenocopies knockout of the menB gene. Taken together the data indicate that the antibacterial activity of 1 results from a specific effect on MK biosynthesis. We also evaluated the in vivo efficacy of 1 using two mouse models of MRSA infection. Notably, compound 1 increased survival in a systemic infection model and resulted in a dose-dependent decrease in bacterial load in a thigh infection model, validating MenB as a target for the development of new anti-MRSA candidates.

Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues

1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase catalyzes an essential intramolecular Claisen condensation in menaquinone biosynthesis and is an important target for the development of new antibiotics. This enzyme in Mycobacterium tuberculosis is cofactor-free and is classified as a type II DHNA-CoA synthase, differing from type I enzymes, which rely on exogenous bicarbonate for catalysis. Its crystal structures in complex with product analogues have been determined at high resolution to reveal ligand-dependent structural changes, which include the ordering of a 27-residue active-site loop (amino acids 107-133) and the reorientation of the carboxy-terminal helix (amino acids 289-301) that forms part of the active site from the opposing subunit across the trimer-trimer interface. These structural changes result in closure of the active site to the bulk solution, which is likely to take place through an induced-fit mechanism, similar to that observed for type I DHNA-CoA synthases. These findings demonstrate that the ligand-dependent conformational changes are a conserved feature of all DHNA-CoA synthases, providing new insights into the catalytic mechanism of this essential tubercular enzyme.