Thymoquinone Inhibits Escherichia coli ATP Synthase and Cell Growth

Spectroscopic Characterization and Biological Effects of 1-Oxo-bisabolone-rich Pulicaria burchardii Hutch. subsp. burchardii Essential Oil Against Viruses, Bacteria, and Spore Germination

Pulicaria species are used as herbal medicine and in the preparation of decoctions in several Asian and African regions. Among them, the plant Pulicaria burchardii is known for its medicinal properties, but comprehensive studies on its biological activity are still limited. This study examined the properties of the essential oil (EO) extracted by P. burchiardii and collected in Morocco during the flowering period. The focus was on its antimicrobial, anti-germinative, antioxidant, and antiviral activities, with the aim of evaluating its potential use in food preservation and beyond. The EO was subjected to various analyses to determine its chemical composition and biological efficacy. Specifically, GCMS and NMR analyses revealed that the EO is rich in oxygenated sesquiterpenes (72.59%), with 1-oxo-bisabolone being the predominant component (65.09%). The antimicrobial activity was tested against various Gram-positive and Gram-negative bacteria, demonstrating a significant inhibition of bacterial growth, particularly against Bacillus subtilis (MIC value of 0.6 mg/mL). The anti-germinative property was evaluated on spores of B. subtilis and other bacilli, such as Bacillus cereus, revealing a notable ability to prevent germination. For antiviral activity, the EO was tested against several pathogenic viruses including SARS-CoV-2 and HSV-1, showing an effective broad-spectrum reduction in viral replication in vitro. This study demonstrated that P. burchardii essential oil had excellent antibacterial and antiviral capabilities. The future challenge will focus mainly on the principal compound, 1-oxo-bisabolone, to demonstrate its real effectiveness as an antibacterial and/or antiviral.

Antibacterial phenolic compounds from the flowering plants of Asia and the Pacific: coming to the light

CONTEXT

The emergence of pan-resistant bacteria requires the development of new antibiotics and antibiotic potentiators.

OBJECTIVE

This review identifies antibacterial phenolic compounds that have been identified in Asian and Pacific Angiosperms from 1945 to 2023 and analyzes their strengths and spectra of activity, distributions, molecular masses, solubilities, modes of action, structures-activities, as well as their synergistic effects with antibiotics, toxicities, and clinical potential.

METHODS

All data in this review was compiled from Google Scholar, PubMed, Science Direct, Web of Science, and library search; other sources were excluded. We used the following combination of keywords: 'Phenolic compound', 'Plants', and 'Antibacterial'. This produced 736 results. Each result was examined and articles that did not contain information relevant to the topic or coming from non-peer-reviewed journals were excluded. Each of the remaining 467 selected articles was read critically for the information that it contained.

RESULTS

Out of ∼350 antibacterial phenolic compounds identified, 44 were very strongly active, mainly targeting the cytoplasmic membrane of Gram-positive bacteria, and with a molecular mass between 200 and 400 g/mol. 2-Methoxy-7-methyljuglone, [6]-gingerol, anacardic acid, baicalin, vitexin, and malabaricone A and B have the potential to be developed as antibacterial leads.

CONCLUSIONS

Angiosperms from Asia and the Pacific provide a rich source of natural products with the potential to be developed as leads for treating bacterial infections.

In Silico and In Vitro Studies to Explore the Effect of Thymoquinone on Isocitrate Lyase, Biofilm Formation, and the Expression of Some Virulence Genes in Candida albicans

Thymoquinone (TQ), a bioactive compound from black cumin (Nigella sativa), has demonstrated a broad range of therapeutic effects. The aim of this study is to evaluate the antifungal efficacy of TQ by targeting key virulence factors in Candida albicans, specifically focusing on isocitrate lyase (ICL) activity, biofilm formation, and gene expression. This study explored TQ's impact on ICL, a decisive enzyme in the glyoxylate cycle, along with its effect on hyphal formation, biofilm development, and the virulent gene expression of C. albicans through in silico and in vitro studies. Molecular docking revealed a binding energy of -6.4 kcal/mol between TQ and ICL, indicating moderate affinity. The stability of the ICL-TQ complex was validated through 50 ns molecular dynamics simulations, showing the root mean square deviation (RMSD) values of 0.35 nm for ICL and 0.38 nm for the complex. In vitro studies further validated these findings, showing a dose-dependent inhibition of ICL activity. TQ at 2 µg/mL reduced enzyme activity by 57%, and at 4 µg/mL, by 91.4%. Additionally, TQ disrupted the yeast-to-hyphae switch, a key virulence factor, with 1 and 2 µg/mL doses significantly inhibiting hyphal formation. The biofilm formation was similarly affected, with a 58% reduction at 2 µg/mL and an 83% reduction at 4 µg/mL. TQ also downregulated the ALS1 and HWP1 genes that are associated with adhesion and biofilm development, demonstrating its broad-spectrum antifungal activity. These findings suggest that TQ is a promising candidate for antifungal therapies, targeting multiple virulence factors in C. albicans and potentially overcoming biofilm-associated drug resistance. Future research should focus on in vivo validation, optimization for clinical applications, and expanding its spectrum against other drug-resistant fungal species.

ATP synthase of E. coli: F1-ATPase activity is functionally decoupled from the proton-transporting complex (FO) by tributyltin

The F-type ATP synthase/ATPase (FOF1) is important for cellular bioenergetics in eukaryotes and bacteria. We recently showed that venturicidins, a class of macrolides that inhibit the proton transporting complex (FO), can also induce time-dependent functional decoupling of F1-ATPase from FO on membranes from Escherichia coli and Pseudomonas aeruginosa. This dysregulated ATPase activity could deplete bacterial ATP levels and contribute to venturicidin's capacity to enhance the bactericidal action of aminoglycosides antibiotics. We now show that a distinct type of FO inhibitor, tributyltin, also can decouple FOF1-ATPase activity of E. coli membranes. In contrast to the action of venturicidins, decoupling by tributyltin is not dependent on ATP, indicating mechanistic differences. Tributyltin disrupts the coupling role of the ε subunit of F1 but does not induce dissociation of the F1-ATPase complex from membrane-embedded FO. Understanding such decoupling mechanisms could support development of novel antibacterial compounds that target dysregulation of FOF1 functions.

Antibacterial and Antifungal Terpenes from the Medicinal Angiosperms of Asia and the Pacific: Haystacks and Gold Needles

This review identifies terpenes isolated from the medicinal Angiosperms of Asia and the Pacific with antibacterial and/or antifungal activities and analyses their distribution, molecular mass, solubility, and modes of action. All data in this review were compiled from Google Scholar, PubMed, Science Direct, Web of Science, ChemSpider, PubChem, and library searches from 1968 to 2022. About 300 antibacterial and/or antifungal terpenes were identified during this period. Terpenes with a MIC ≤ 2 µg/mL are mostly amphiphilic and active against Gram-positive bacteria, with a molecular mass ranging from about 150 to 550 g/mol, and a polar surface area around 20 Ų. Carvacrol, celastrol, cuminol, dysoxyhainic acid I, ent-1β,14β-diacetoxy-7α-hydroxykaur-16-en-15-one, ergosterol-5,8-endoperoxide, geranylgeraniol, gossypol, 16α-hydroxy-cleroda-3,13 (14)Z-diene-15,16-olide, 7-hydroxycadalene, 17-hydroxyjolkinolide B, (20R)-3β-hydroxy-24,25,26,27-tetranor-5α cycloartan-23,21-olide, mansonone F, (+)-6,6'-methoxygossypol, polygodial, pristimerin, terpinen-4-ol, and α-terpineol are chemical frameworks that could be candidates for the further development of lead antibacterial or antifungal drugs.

Antibacterial Activity of Thymoquinone Against Shigella flexneri and Its Effect on Biofilm Formation

Thymoquinone (TQ) has been demonstrated to have anti-cancer, anti-inflammatory, antioxidant, and anti-diabetic activities. Shigella flexneri is the main pathogen causing shigellosis in developing countries. In this study, the antibacterial activity of TQ against S. flexneri and its possible antibacterial mechanism were studied. In addition, the inhibitory effect of TQ on the formation of S. flexneri biofilm was also investigated. The results showed that both the minimum inhibitory concentration and the minimum bactericidal concentration of TQ against S. flexneri ATCC 12022 were 0.2 mg/mL. After treatment with TQ at 0.4 mg/mL in Luria-Bertani broth for 3 h, or treatment with 0.2 mg/mL TQ in phosphate-buffered saline for 60 min, the number of S. flexneri (initial number is 6.5 log colony-forming units/mL) dropped below the detection limit. TQ also displayed good antibacterial activity in contaminated lettuce juice. TQ caused an increase in intracellular reactive oxygen species level, a decrease in intracellular adenosine triphosphate (ATP) concentration, a change in the intracellular protein, damage to cell membrane integrity and changes in cell morphology. In addition, TQ showed the ability to inhibit the formation of S. flexneri biofilm; treatment resulted in a decrease in the amount of biofilm and extracellular polysaccharides, and the destruction of biofilm structure. These findings indicated that TQ had strong antimicrobial and antibiofilm activities and a potential to be applied in the fruit and vegetable processing industry or other food industries to control S. flexneri.

Proton Pumping ATPases: Rotational Catalysis, Physiological Roles in Oral Pathogenic Bacteria, and Inhibitors

Proton pumping ATPases, both F-type and V/A-type ATPases, generate ATP using electrochemical energy or pump protons/sodium ions by hydrolyzing ATP. The enzymatic reaction and proton transport are coupled through subunit rotation, and this unique rotational mechanism (rotational catalysis) has been intensively studied. Single-molecule and thermodynamic analyses have revealed the detailed rotational mechanism, including the catalytically inhibited state and the roles of subunit interactions. In mammals, F- and V-ATPases are involved in ATP synthesis and organelle acidification, respectively. Most bacteria, including anaerobes, have F- and/or A-ATPases in the inner membrane. However, these ATPases are not believed to be essential in anaerobic bacteria since anaerobes generate sufficient ATP without oxidative phosphorylation. Recent studies suggest that F- and A-ATPases perform indispensable functions beyond ATP synthesis in oral pathogenic anaerobes; F-ATPase is involved in acid tolerance in Streptococcus mutans, and A-ATPase mediates nutrient import in Porphyromonas gingivalis. Consistently, inhibitors of oral bacterial F- and A-ATPases, such as phytopolyphenols and bedaquiline, strongly diminish growth and survival. Herein, we discuss rotational catalysis of bacterial F- and A-ATPases, and discuss their physiological roles, focusing on oral bacteria. We also review the effects of ATPase inhibitors on the growth and survival of oral pathogenic bacteria. The features of the catalytic mechanism and unique physiological roles in oral bacteria highlight the potential for proton pumping ATPases to serve as targets for oral antimicrobial agents.

GSH Protects the Escherichia coli Cells from High Concentrations of Thymoquinone

The aim of the present study was to evaluate the potential protective effect of glutathione (GSH) on Escherichia coli cells grown in a high concentration of thymoquinone (TQ). This quinone, as the main active compound of Nigella sativa seed oil, exhibits a wide range of biological activities. At low concentrations, it acts as an antioxidant, and at high concentrations, an antimicrobial agent. Therefore, any interactions between thymoquinone and glutathione are crucial for cellular defense against oxidative stress. In this study, we found that GSH can conjugate with thymoquinone and its derivatives in vitro, and only fivefold excess of GSH was sufficient to completely deplete TQ and its derivatives. We also carried out studies on cultures of GSH-deficient Escherichia coli strains grown on a minimal medium in the presence of different concentrations of TQ. The strains harboring mutations in gene ΔgshA and ΔgshB were about two- and fourfold more sensitive (256 and 128 µg/mL, respectively) than the wild type. It was also revealed that TQ concentration has an influence on reactive oxygen species (ROS) production in E. coli strains—at the same thymoquinone concentration, the level of ROS was higher in GSH-deficient E. coli strains than in wild type.

Thymoquinone Induced Leishmanicidal Effect via Programmed Cell Death in Leishmania donovani

Visceral leishmaniasis (VL) or kala-azar is a vector-borne dreaded protozoal infection that is caused by the parasite Leishmania donovani. With increases in the dramatic infection rates, present drug toxicity, resistance, and the absence of an approved vaccine, the development of new antileishmanial compounds from plant sources remains the keystone for the control of visceral leishmaniasis. In this study, we evaluated the leishmanicidal effect of thymoquinone against L. donovani with an in vitro and ex vivo model. Thymoquinone exhibited potent antipromastigote activity with IC₅₀ and IC₉₀ concentrations achieved at 6.33 ± 1.21 and 20.71 ± 2.15 μM, respectively, whereas the IC₅₀ and IC₉₀ concentrations were found to be 7.83 ± 1.65 and 27.25 ± 2.20 μM against the intramacrophagic form of amastigotes, respectively. Morphological changes in promastigotes and growth reversibility study following treatment confirmed the leishmanicidal effect of thymoquinone. Further, thymoquinone exhibited leishmanicidal activities against L. donovani promastigote through cytoplasmic shrinkage, membrane blebbing, chromatin condensation, cellular and nuclear shrinkage, and DNA fragmentation, as observed under scanning and transmission electron microscopy analyses. The antileishmanial activity was exerted via programmed cell death as proved by exposure of phosphatidylserine, DNA nicking by TUNEL assay, and loss of mitochondrial membrane potential. Thymoquinone at a concentration of 200 μM was devoid of any cytotoxic effects against mammalian macrophage cells. Thymoquinone showed strong leishmanicidal activity against L. donovani, which is mediated via an apoptosis mode of parasitic cell death, and accordingly, thymoquinone may be the source of a new lead molecule for the cure of VL.

Effects of biochar, farm manure, and pressmud on mineral nutrients and cadmium availability to wheat (Triticum aestivum L.) in Cd-contaminated soil

The contamination of agricultural soils with cadmium (Cd) is one of the serious worldwide concerns for food security. Biochar and organic manures have been known for enhancing plant growth and minimizing toxic trace element stress in plants. However, less is known about the effect of different organic amendments on Cd and uptake of essential nutrients by wheat. Thus, the effects of rice straw biochar (RSB), maize stalk biochar (MSB), farmyard manure (FYM), and pressmud (PRM) at a rate of 1% w/w were tested for Cd immobilization in soil and mineral nutrient availability to wheat crop grown in Cd-spiked soil (6.0 mg kg^1 ). The amendments were added in Cd-spiked soil before 12 days of seed sowing and wheat plants were harvested after maturity (115 days after sowing). The findings revealed that the use of amendments improved the number of grains per spike, straw and grain yield of wheat relative to control treatment. The treatments minimized the Cd and enhanced the contents of zinc (Zn), nitrogen (N), phosphorus (P), and potassium (K) in the leaves and grain of the wheat plants. Cadmium concentrations decreased by 35, 38, 68, and 63% in wheat grain, and grain yield increased by 19, 31, 68, and 58% with the application of FYM, PRM, MSB, and RSB, respectively. Overall, the application of MSB was more efficient in decreasing Cd concentrations in leaf and grains of wheat as compared to other conventional organic amendments.

Therapeutic perspectives of the black cumin component thymoquinone: A review

The dietary phytochemical thymoquinone (TQ), belonging to the family of quinones, mainly obtained from the black and angular seeds of Nigella sativa, is one of the promising monoterpenoid hydrocarbons, which has been receiving massive attention for its therapeutic potential and pharmacological properties. It plays an important role as a chemopreventive and therapeutic agent in the treatment of various diseases and illnesses. The aim of this review is to present a summary of the most recent literature pertaining to the use of TQ for the prevention and treatment of various diseases along with possible mechanisms of action, and the potential use of this natural product as a complementary or alternative medicine. Research findings indicated that TQ exhibits numerous pharmacological activities including antioxidant, anti-inflammatory, cardioprotective, hepatoprotective, antidiabetic, neuroprotective, and anticancer, among others. Conclusions of this review on the therapeutic aspects of TQ highlight the medicinal and folk values of this compound against various diseases and ailments. In short, TQ could be a novel drug in clinical trials, as we hope.

Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis

The subgingival microbial communities of domestic cats remain incompletely characterized and it is unknown whether their functional profiles are associated with disease. In this study, we used a shotgun metagenomic approach to explore the functional potential of subgingival microbial communities in client-owned cats, comparing findings between periodontally healthy cats and cats with naturally occurring chronic periodontitis, aggressive periodontitis, and feline chronic gingivostomatitis. Subgingival samples were subjected to shotgun sequencing and the metagenomic datasets were analyzed using the MG-RAST metagenomic analysis server and STAMP v2.1.3 (Statistical Analysis of Metagenomic Profiles) software. The microbial composition was also described to better understand the predicted features of the communities. The Respiration category in the level 1 Subsystems database varied significantly among groups. In this category, the abundance of V-Type ATP-synthase and Biogenesis of cytochrome c oxidases were significantly enriched in the diseased and in the healthy groups, respectively. Both features have been previously described in periodontal studies in people and are in consonance with the microbial composition of feline subgingival sites. In addition, the narH (nitrate reductase) gene frequency, identified using the KEGG Orthology database, was significantly increased in the healthy group. The results of this study provide preliminary functional insights of the microbial communities associated with periodontitis in domestic cats and suggest that the ATP-synthase and nitrate-nitrite-NO pathways may represent appropriate targets for the treatment of this common disease.

The Interactions between Polyphenols and Microorganisms, Especially Gut Microbiota

This review presents the comprehensive knowledge about the bidirectional relationship between polyphenols and the gut microbiome. The first part is related to polyphenols' impacts on various microorganisms, especially bacteria, and their influence on intestinal pathogens. The research data on the mechanisms of polyphenol action were collected together and organized. The impact of various polyphenols groups on intestinal bacteria both on the whole "microbiota" and on particular species, including probiotics, are presented. Moreover, the impact of polyphenols present in food (bound to the matrix) was compared with the purified polyphenols (such as in dietary supplements) as well as polyphenols in the form of derivatives (such as glycosides) with those in the form of aglycones. The second part of the paper discusses in detail the mechanisms (pathways) and the role of bacterial biotransformation of the most important groups of polyphenols, including the production of bioactive metabolites with a significant impact on the human organism (both positive and negative).

Corona virus versus existence of human on the earth: A computational and biophysical approach

SARS-CoV-2 has a positive sense RNA genome of 29.9 kb in size, showing high sequence similarity to the BAT-CoV, SARS-CoV, MERS-CoV. SARS-CoV-2 is composed of 14 open reading frames (ORFs), which encodes for a total of 27 proteins divided into structural and non-structural proteins (NSPs). The fundamental structural protein-encoding genes are a spike protein (S) gene, envelope protein (E) gene, a membrane protein (M) gene, and a nucleocapsid protein (N) gene. They make about 33% of the entire genome and are vital for the viral life cycle. Rest 67% is distributed among different NSPs (such as M^pro, helicase, and RNA-dependent RNA polymerase) encoding genes across the ORFs, which are involved in virus-cell receptor interactions during viral entry. Researchers are trying to formulate vaccines, therapeutic antibodies or protein-targeted antiviral drugs to control the spread. This review proceeds stepwise through the COVID-19 outbreak, structural and genomic organization, entry mechanism, pathogenesis, and finally highlighting the essential proteins involved at each step that might be potential targets for drug discovery. Currently, approved treatment modalities consist of only supportive care and oxygen supplementation. This review is established on the current knowledge that has expanded on structural motifs and topology of proteins and their functions.

In Vitro Effect of the Common Culinary Herb Winter Savory (Satureja montana) against the Infamous Food Pathogen Campylobacter jejuni

The culinary herb Satureja montana, known as winter savory, is an ingredient of traditional dishes known in different parts of the world. As an ingredient of foods it has the potential to improve their safety. In this study, the herb's activity was investigated against Campylobacter jejuni, the leading cause of the most prevalent bacterial gastroenteritis worldwide. The ethanolic extract and essential oil of the herb were chemically characterized and six pure compounds-carvacrol, thymol, thymoquinone, p-cymene, γ-terpinene, and rosmarinic acid-were chosen for further analysis. The antimicrobial activity of the ethanolic extract (MIC 250 mg/L) was 4-fold higher compared to the essential oil. Carvacrol, thymol and thymoquinone had the strongest antimicrobial effect (MIC 31.25 mg/L) and a strong synergistic activity between carvacrol and thymol was determined (FICi 0.2). Strong inhibitory effect on C. jejuni efflux pumps (2-fold inhibition) and disruption of membrane integrity (> 80% disruption) of the herb were determined as modes of action. For resistance against the herb, C. jejuni need efflux pumps, although increased resistance against this herb does not co-occur with increased efflux pump activity, as for antibiotics. This study shows the potential of a common culinary herb for the reduction of the food pathogen C. jejuni without increasing resistance.

A bioanalytical UHPLC based method used for the quantification of Thymoquinone-loaded-PLGA-nanoparticles in the treatment of epilepsy

To formulate a nanoformulation (PLGA-NPs) and to improve brain bioavailability for thymoquinone (THQ) through intranasal (i.n.) drug delivery, using a newly UHPLC-PDA developed the method and validated. Five different THQ-PLGA-NPs (THQ-N1 to THQ-N5) were prepared by emulsion solvent evaporation method. A new UHPLC method developed and validated for biodistribution studies in the rat’s brain, lungs and plasma. Optimized-THQ-N1-NPs showed a particle size of 97.36 ± 2.01 nm with a low PDI value of 0.263 ± 0.004, ZP of − 17.98 ± 1.09, EE of 82.49 ± 2.38% and DL of 5.09 ± 0.13%. THQ-N1-NPs showed sustained release pattern via in vitro release profile. A bioanalytical method was developed by UHPLC-PDA and validated for the evaluation of pharmacokinetics parameters, biodistribution studies, brain drug-targeting potential (89.89 ± 9.38%), and brain-targeting efficiency (8075.00 ± 113.05%) studies through intranasal administration which showed an improved THQ-brain- bioavailability, compared to i.v. Moreover, THQ-PLGA-NPs improved the seizure threshold treatment i.e. epilepsy increasing current electroshock (ICES) rodent models induced seizures in rats. A significant role of THQ-PLGA-NPs with high brain targeting efficiency of the nanoformulations was established. The reported data supports the treatment of epilepsy.

Enhancement of pyruvic acid production in Candida glabrata by engineering hypoxia-inducible factor 1

Dissolved oxygen (DO) supply plays essential roles in microbial organic acid production. Candida glabrata, as a dominant strain for producing pyruvic acid, principally converts glucose to pyruvic acid through glycolysis. However, this process relies excessively on high extracellular DO content. In this study, in combination with specific motif analysis of gene promoters, hypoxia-inducible factor 1 (HIF1) was engineered to improve the transcription level of some enzymes related to pyruvic acid synthesis under low DO level and directly led to increased pyruvic acid production and glycolysis efficiency. Moreover, the intracellular stability of HIF1 was further optimized from different aspects to maximize pyruvic acid accumulation. Finally, the pyruvic acid titer in a 5-L batch bioreactor with 10% DO level reached 53.1 g/L. As pyruvic acid is involved in the biosynthesis of various products, these findings suggest that HIF1-enabled regulation method has significant potential for increasing the synthesis of other chemicals in microorganisms.

Possible curative role of curcumin and silymarin against nephrotoxicity induced by gamma-rays in rats

Curcumin (CUR) and silymarin (SLM) are powerful antioxidant and anti-inflammatory compounds with beneficial protective effects against renal diseases. The purpose of this study was to evaluate the efficacy of CUR and SLM alone or in combination on radiation (IR) induced kidney injury. The results showed that CUR and SLM alone or in combination attenuated the oxidative stress denoted by a reduction in the level of malondialdehyde (MDA), hydrogen peroxide (H₂O₂) and advanced oxidation protein products (AOPP) along with a marked increase of glutathione GSH content and total antioxidant capacity (TAC). Additionally, a significant decrease in the level of blood urea nitrogen (BUN), creatinine, Cystatin-C (CYT-C), neutrophil gelatinase-associated lipocalin (N-GAL) and Kidney Injury Molecule-1 (Kim-1) was recorded. Moreover, the treatment resulted in a remarkable decline in the serum levels of interleukin-18(IL-18), tumor necrosis factor- alpha (TNF-α), C reactive protein (CRP), BCL2 associated X protein (Bax), Factor-related Apoptosis (FAS) and the activity of Caspase-3 associated by an increase of B-cell CLL/lymphoma 2 (Bcl2) level. The results were confirmed with the histopathological examination. Kidney of irradiated showed glomerular atrophy, massive necrotic changes of expanded tubules with hyaline cast inside some tubules and apoptotic changes were recorded in some renal tubules. While irradiated rats treated with CUR and SLM exhibited marked preservation of the cellular structure of their kidney tissue. In conclusion, the combination of CUR and SLM could be more potent than a single agent on the biochemical and histological changes of the irradiated rat renal tissue.

Functional importance of αAsp-350 in the catalytic sites of Escherichia coli ATP synthase

Negatively charged residue αAsp-350 of the highly conserved VISIT-DG sequence is required for Pi binding and maintenance of the phosphate-binding subdomain in the catalytic sites of Escherichia coli F₁F_o ATP synthase. αAsp-350 is situated in close proximity, 2.88 Å and 3.5 Å, to the conserved known phosphate-binding residues αR376 and βR182. αD350 is also in close proximity, 1.3 Å, to another functionally important residue αG351. Mutation of αAsp-350 to Ala, Gln, or Arg resulted in substantial loss of oxidative phosphorylation and reduction in ATPase activity by 6- to 16-fold. The loss of the acidic side chain in the form of αD350A, αD350Q, and αD350R caused loss of Pi binding. While removal of Arg in the form of αR376D resulted in the loss of Pi binding, the addition of Arg in the form of αG351R did not affect Pi binding. Our data demonstrates that αD350R helps in the proper orientation of αR376 and βR182 for Pi binding. Fluoroaluminate, fluoroscandium, and sodium azide caused almost complete inhibition of wild type enzyme and caused variable inhibition of αD350 mutant enzymes. NBD-Cl (4-chloro-7-nitrobenzo-2-oxa-1, 3-diazole) caused complete inhibition of wild type enzyme while some residual activity was left in mutant enzymes. Inhibition characteristics supported the conclusion that NBD-Cl reacts in βE (empty) catalytic sites. Phosphate protected against NBD-Cl inhibition of wild type and αG351R mutant enzymes but not inhibition of αD350A, αD350Q, αD350R, or αR376D mutant enzymes. These results demonstrate that αAsp-350 is an essential residue required for phosphate binding, through its interaction with αR376 and βR182, for normal function of phosphate binding subdomain and for transition state stabilization in ATP synthase catalytic sites.

Enhanced Pyruvate Production in Candida glabrata by Engineering ATP Futile Cycle System

Energy metabolism plays an important role in the growth and central metabolic pathways of cells. Manipulating energy metabolism is an efficient strategy to improve the formation of target products and to understand the effects of altering intracellular energy levels on global metabolic networks. Candida glabrata, as a dominant yeast strain for producing pyruvate, principally converts glucose to pyruvate through the glycolytic pathway. However, this process can be severely inhibited by a high intracellular ATP content. Here, in combination with the physiological characteristics of C. glabrata, efforts have been made to construct an ATP futile cycle system (ATP-FCS) in C. glabrata to decrease the intracellular ATP level without destroying F₀F₁-ATPase function. ATP-FCS was capable of decreasing the intracellular ATP level by 51.0% in C. glabrata. The decrease in the ATP level directly led to an increased pyruvate production and glycolysis efficiency. Moreover, we further optimized different aspects of the ATP-FCS to maximize pyruvate accumulation. Combining ATP-FCS with further genetic optimization strategies, we achieved a final pyruvate titer of 40.2 g/L, with 4.35 g pyruvate/g dry cell weight and a 0.44 g/g substrate conversion rate in 500 mL flasks, which represented increases of 98.5%, 322.3%, and 160%, respectively, compared with the original strain. Thus, these strategies hold great potential for increasing the synthesis of other organic acids in microbes.

Screening of Some Essential Oil Constituents as Potential Inhibitors of the ATP Synthase of Escherichia coli

Many novel bacterial targets and natural inhibitors of enzymes are currently being considered to overcome antibiotic resistance of Escherichia coli. Hence, in this study, 20 essential oil constituents were screened for their potential inhibitory effect on E. coli ATP synthase. This enzyme is involved in the hydrolysis of ATP into ADP and inorganic phosphate (Pi). First, E. coli membrane ATP synthase was isolated via cell lysis. A spectrophotometric method was optimized to quantify the released phosphate from ATP hydrolysis in order to follow the enzymatic activity. The method was validated by determining the kinetic parameters of this reaction (K_m = 144.66 μM and V_max = 270.27 μM/min), and through the inhibition assays of ATP synthase using three reference inhibitors, thymoquinone (half maximal inhibitory concentration [IC₅₀ ] = 50.93 μM), resveratrol (maximum inhibition of 40%), and quercetin (IC₅₀ = 29.01 μM). Among the studied essential oil components, α-terpinene was the most potent inhibitor (IC₅₀ = 19.74 μM) followed by β-pinene, isoeugenol, eugenol, and estragole.

Nigella sativa L. as an alternative antibiotic feed supplement and effect on growth performance in weanling pigs

BACKGROUND

Nigella sativa L. (NS) is a plant containing bioactive constituents such as thymoquinone. Extracts of NS improve performance and reduce enteropathogen colonization in poultry and small ruminants, but studies with swine are lacking. In two different studies oral administration of NS extracts at doses equivalent to 0, 1.5 and 4.5 g kg^-1 diet was assessed on piglet performance and intestinal carriage of wildtype Escherichia coli and Campylobacter, and Salmonella Typhimurium.

RESULTS

Wildtype E. coli populations in the jejunal and rectal content collected 9 days after treatment began were decreased (P ≤ 0.05). Populations recovered from pigs treated with extract at 1.5 and 4.5 g kg^-1 diet were 0.72-1.31 log₁₀ units lower than the controls (ranging from 6.05 to 6.61 log₁₀ CFU g^-1 ). Wildtype Campylobacter and Salmonella Typhimurium were unaffected by NS treatment. Feed efficiency over the 9 days improved linearly (P < 0.05) from 3.88 with 0 NS-treated pigs to 1.47 and 1.41 with pigs treated with NS at 1.5 and 4.5 g kg^-1 diet, respectively, possibly due to high glutamine/glutamic acid content of the NS extract.

CONCLUSION

NS supplementation of weanling pigs improved feed efficiency and helped control intestinal E. coli during this vulnerable production phase. © 2017 Society of Chemical Industry.

Neuropharmacological Potential and Delivery Prospects of Thymoquinone for Neurological Disorders

Thymoquinone (TQ) is an active ingredient isolated from Nigella sativa and has various pharmacological activities, such as protection against oxidative stress, inflammation, and infections. In addition, it might be a potential neuropharmacological agent because it exhibits versatile potential for attenuating neurological impairments. It features greater beneficial effects in toxin-induced neuroinflammation and neurotoxicity. In various models of neurological disorders, it demonstrates emergent functions, including safeguarding various neurodegenerative diseases and other neurological diseases, such as stroke, schizophrenia, and epilepsy. TQ also has potential effects in trauma mediating and chemical-, radiation-, and drug-induced central nervous system injuries. Considering the pharmacokinetic limitations, research has concentrated on different TQ novel formulations and delivery systems. Here, we visualize the neuropharmacological potential, challenges, and delivery prospects of TQ, specifically focusing on neurological disorders along with its chemistry, pharmacokinetics, and toxicity.

A Therapeutic Connection between Dietary Phytochemicals and ATP Synthase

For centuries, phytochemicals have been used to prevent and cure multiple health ailments. Phytochemicals have been reported to have antioxidant, antidiabetic, antitussive, antiparasitic, anticancer, and antimicrobial properties. Generally, the therapeutic use of phy-tochemicals is based on tradition or word of mouth with few evidence-based studies. Moreo-ver, molecular level interactions or molecular targets for the majority of phytochemicals are unknown. In recent years, antibiotic resistance by microbes has become a major healthcare concern. As such, the use of phytochemicals with antimicrobial properties has become perti-nent. Natural compounds from plants, vegetables, herbs, and spices with strong antimicrobial properties present an excellent opportunity for preventing and combating antibiotic resistant microbial infections. ATP synthase is the fundamental means of cellular energy. Inhibition of ATP synthase may deprive cells of required energy leading to cell death, and a variety of die-tary phytochemicals are known to inhibit ATP synthase. Structural modifications of phyto-chemicals have been shown to increase the inhibitory potency and extent of inhibition. Site-directed mutagenic analysis has elucidated the binding site(s) for some phytochemicals on ATP synthase. Amino acid variations in and around the phytochemical binding sites can re-sult in selective binding and inhibition of microbial ATP synthase. In this review, the therapeu-tic connection between dietary phytochemicals and ATP synthase is summarized based on the inhibition of ATP synthase by dietary phytochemicals. Research suggests selective target-ing of ATP synthase is a valuable alternative molecular level approach to combat antibiotic resistant microbial infections.

Understanding the link between antimicrobial properties of dietary olive phenolics and bacterial ATP synthase

The naturally occurring olive phenolics tyrosol, hydroxytyrosol, dihydroxyphenylglycol (DHPG), and oleuropein are known to have antioxidant, antitumor, and antibacterial properties. In the current study, we examined whether the antimicrobial properties of tyrosol, hydroxytyrosol, DHPG, and oleuropein were linked to the inhibition of bacterial ATP synthase. Tyrosol, hydroxytyrosol, DHPG, and oleuropein inhibited Escherichia coli wild-type and mutant membrane-bound F1Fo ATP synthase to variable degrees. The growth properties of wild-type, null, and mutant strains in presence of above olive phenolics were also abrogated to variable degrees on limiting glucose and succinate. Tyrosol and oleuropein synergistically inhibited the wild-type enzyme. Comparative wild-type and mutant F1Fo ATP synthase inhibitory profiles suggested that αArg-283 is an important residue and olive phenolics bind at the polyphenol binding pocket of ATP synthase. Growth patterns of wild-type, null, and mutant strains in the presence of tyrosol, hydroxytyrosol, DHPG, and oleuropein also hint at the possibility of additional molecular targets. Our results demonstrated that ATP synthase can be used as a molecular target and the antimicrobial properties of olive phenolics in general and tyrosol in particular can be linked to the binding and inhibition of bacterial ATP synthase.

Mitochondria-targeted antioxidants as highly effective antibiotics

Mitochondria-targeted antioxidants are known to alleviate mitochondrial oxidative damage that is associated with a variety of diseases. Here, we showed that SkQ1, a decyltriphenyl phosphonium cation conjugated to a quinone moiety, exhibited strong antibacterial activity towards Gram-positive Bacillus subtilis, Mycobacterium sp. and Staphylococcus aureus and Gram-negative Photobacterium phosphoreum and Rhodobacter sphaeroides in submicromolar and micromolar concentrations. SkQ1 exhibited less antibiotic activity towards Escherichia coli due to the presence of the highly effective multidrug resistance pump AcrAB-TolC. E. coli mutants lacking AcrAB-TolC showed similar SkQ1 sensitivity, as B. subtilis. Lowering of the bacterial membrane potential by SkQ1 might be involved in the mechanism of its bactericidal action. No significant cytotoxic effect on mammalian cells was observed at bacteriotoxic concentrations of SkQ1. Therefore, SkQ1 may be effective in protection of the infected mammals by killing invading bacteria.

Safranal and its analogs inhibit Escherichia coli ATP synthase and cell growth

Safranal, a dominant component of saffron, is known to have antitumor, cytotoxic, and antibacterial properties. In this study, we examined safranal and its structural analogs-thymol, carvacrol, damascenone, cuminol, 2,6,6-trimethyl-2-cyclohexene-1,4-dione (TMCHD), 4-isopropylbenzyl bromide (IPBB), and 4-tert-butylphenol (TBP) induced inhibition of Escherichia coli membrane bound F1Fo ATP synthase. Safranal and its analogs inhibited wild-type enzyme to variable degrees. While safranal caused 100% inhibition of wild-type F1Fo ATP synthase, only about 50% inhibition occurred for αR283D mutant ATP synthase. Moreover, safranal, thymol, carvacrol, damascenone, cuminol, TMCHD, IPBB, and TBP all fully abrogated the growth of wild-type E. coli cells and had partial or no effect on the growth of null and mutant E. coli strains. Therefore, the antimicrobial properties of safranal, thymol, carvacrol, damascenone, cuminol, TMCHD, IPBB, and TBP can be linked to their binding and inhibition of ATP synthase. Total loss of growth in wild-type and partial or no growth loss in null or mutant E. coli strains demonstrates that ATP synthase is a molecular target for safranal and its structural analogs. Partial inhibition of the αArg-283 mutant enzyme establishes that αArg-283 residue is required in the polyphenol binding pocket of ATP synthase for the binding of safranal. Furthermore, partial growth loss for the null and mutant strains in the presence of inhibitors also suggests the role of other targets and residues in the process of inhibition.

A nanotechnology based new approach for chemotherapy of Cutaneous Leishmaniasis: TIO2@AG nanoparticles - Nigella sativa oil combinations

Since toxicity and resistance are the major drawbacks of current antileishmanial drugs, studies have been recently focused on combination therapy in fight against leishmaniasis. Combination therapy generally provides opportunity to decrease toxicity of applied agents and enhance their antimicrobial performance. Moreover, this method can be effective in preventing drug resistance. Highly antileishmanial effects of silver doped titanium dioxide nanoparticles (TiAgNps) and Nigella sativa oil were demonstrated in previous studies. However, toxicity is still an important factor preventing use of these molecules in clinic. By considering high antileishmanial potential of each agent and basic principles of combination therapy, we propose that use of combinations including non-toxic concentrations of TiAgNps and N. sativa oil may compose more effective and safer formulations against Leishmania parasites. Therefore, the main goal of the present study was to investigate antileishmanial effects of non-toxic concentrations of TiAgNps and Nigella sativa oil combinations on promastigote and amastigote-macrophage culture systems and also to develop nanotechnology based new antileishmanial strategies against Cutaneous Leishmaniasis. Numerous parameters such as proliferation, metabolic activity, apoptosis, amastigote-promastigote conversion, infection index analysis and nitric oxide production were used to detect antileishmanial efficacies of combinations. Investigated all parameters demonstrated that TiAgNps-N. sativa oil combinations had significant antileishmanial effect on each life forms of parasites. Tested combinations were found to decrease proliferation rates of Leishmania tropica promastigotes in a range between 1,5-25 folds and metabolic activity values between 2 and 4 folds indicating that combination applications lead to virtually inhibition of promastigotes and elimination of parasites were directly related to apoptosis manner. TiAgNps-N. sativa combinations also demonstrated killing effects on L. tropica amastigotes by decreasing infection index values of macrophages 5-20 folds, inhibiting their metabolic activities up to 5 fold, preventing amastigote-promastigote conversion and producing high amounts of nitric oxide. All these results emphasize high potential of TiAgNps-N. sativa oil combinations as new, safer and effective antileishmanial formulations against Cutaneous Leishmaniasis.

Venom peptides cathelicidin and lycotoxin cause strong inhibition of Escherichia coli ATP synthase

Venom peptides are known to have strong antimicrobial activity and anticancer properties. King cobra cathelicidin or OH-CATH (KF-34), banded krait cathelicidin (BF-30), wolf spider lycotoxin I (IL-25), and wolf spider lycotoxin II (KE-27) venom peptides were found to strongly inhibit Escherichia coli membrane bound F1Fo ATP synthase. The potent inhibition of wild-type E. coli in comparison to the partial inhibition of null E. coli by KF-34, BF-30, Il-25, or KE-27 clearly links the bactericidal properties of these venom peptides to the binding and inhibition of ATP synthase along with the possibility of other inhibitory targets. The four venom peptides KF-34, BF-30, IL-25, and KE-27, caused ≥85% inhibition of wild-type membrane bound E.coli ATP synthase. Venom peptide induced inhibition of ATP synthase and the strong abrogation of wild-type E. coli cell growth in the presence of venom peptides demonstrates that ATP synthase is a potent membrane bound molecular target for venom peptides. Furthermore, the process of inhibition was found to be fully reversible.

Functional importance of αIle-346 and αIle-348 in the catalytic sites of Escherichia coli ATP synthase

We studied the functional role of highly conserved VISIT-DG sequence residues αIle-346 and αIle-348 in the catalytic sites of Escherichia coli F1Fo ATP synthase. αIle-346 is in close proximity, 2.98 and 3.63 Å, to the two known phosphate binding residues αR376 and βR182; αIle-348 is situated within 3.66 Å from βR182. Single or double mutants of both αI346 and αI348 resulted in a variable loss of oxidative phosphorylation and ATPase activity. Azide, fluoroaluminate, and fluoroscandium caused insignificant to significant inhibition of mutants. Whereas the wild-type enzyme was completely inhibited by NBD-Cl (7-chloro-4-nitrobenzo-2-oxa-1, 3-diazole), a variable extent of inhibition was observed for αI346 and αI348 mutants. MgPi protection against NBD-Cl induced inhibition of wild-type, αI346, and αI348 demonstrated that, although strongly conserved, αI346 and αI348 have no direct role in phosphate binding. Insertion of Arginine in the form of αI346R/βR182A, αI346R/αR376A, or αI348R/βR182A was able to compensate for the absence of known phosphate-binding Arginine residues βR182 and αR376. Results also suggest that αIle-346 and αIle-348 seem to have functional importance in upholding the phosphate-binding subdomain and transition state stabilization in the catalytic sites of E. coli ATP synthase.