Structure-based discovery and experimental verification of novel AI-2 quorum sensing inhibitors against Vibrio harveyi

Quorum sensing has been implicated in the control of pathologically relevant bacterial behavior such as secretion of virulence factors, biofilm formation, sporulation, and swarming motility. The AI-2 quorum sensing pathway is found in both gram-positive and gram-negative bacteria. Therefore, antagonizing AI-2 quorum sensing is a possible approach to modifying bacterial behaviour. However, efforts in developing inhibitors of AI-2-mediated quorum sensing are especially lacking. High-throughput virtual screening using the V. harveyi LuxP crystal structure identified two compounds that were found to antagonize AI-2-mediated quorum sensing in V. harveyi without cytotoxicity. The sulfone functionality of these inhibitors was identified as critical to their ability to mimic the natural ligand in their interactions with Arg 215 and Arg 310 of the active site.     

The Quorum Sensing Auto-Inducer 2 (AI-2) Stimulates Nitrogen Fixation and Favors Ethanol Production over Biomass Accumulation in Zymomonas mobilis

Autoinducer 2 (or AI-2) is one of the molecules used by bacteria to trigger the Quorum Sensing (QS) response, which activates expression of genes involved in a series of alternative mechanisms, when cells reach high population densities (including bioluminescence, motility, biofilm formation, stress resistance, and production of public goods, or pathogenicity factors, among others). Contrary to most autoinducers, AI-2 can induce QS responses in both Gram-negative and Gram-positive bacteria, and has been suggested to constitute a trans-specific system of bacterial communication, capable of affecting even bacteria that cannot produce this autoinducer. In this work, we demonstrate that the ethanologenic Gram-negative bacterium Zymomonas mobilis (a non-AI-2 producer) responds to exogenous AI-2 by modulating expression of genes involved in mechanisms typically associated with QS in other bacteria, such as motility, DNA repair, and nitrogen fixation. Interestingly, the metabolism of AI-2-induced Z. mobilis cells seems to favor ethanol production over biomass accumulation, probably as an adaptation to the high-energy demand of N₂ fixation. This opens the possibility of employing AI-2 during the industrial production of second-generation ethanol, as a way to boost N₂ fixation by these bacteria, which could reduce costs associated with the use of nitrogen-based fertilizers, without compromising ethanol production in industrial plants.     

Interspecies and Interkingdom Signaling via Quorum Signals

Quorum sensing (QS) is an evolutionarily conserved mechanism of cell-to-cell communication utilized by hundreds of different species of microbes. QS is mediated by small molecules and their corresponding receptors, many of which are similar in structure and function. Consequently, microbes have developed ways to detect signals produced by their prokaryotic and eukaryotic neighbors and alter their behavior accordingly. These interactions have been termed interspecies and interkingdom signaling, respectively. In most described cases, bacteria use this sensory information to either up-regulate their own virulence or down-regulate the virulence of their neighbor. In this review, we describe many of the known interspecies and interkingdom signaling events that are mediated by quorum signals, and discuss the impact these may have on the ability of microbes to interact with each other and with their hosts.     

Quorum Sensing and Quorum Quenching in the Phycosphere of Phytoplankton: a Case of Chemical Interactions in Ecology

The interactions between bacteria and phytoplankton regulate many important biogeochemical reactions in the marine environment, including those in the global carbon, nitrogen, and sulfur cycles. At the microscopic level, it is now well established that important consortia of bacteria colonize the phycosphere, the immediate environment of phytoplankton cells. In this microscale environment, abundant bacterial cells are organized in a structured biofilm, and exchange information through the diffusion of small molecules called semiochemicals. Among these processes, quorum sensing plays a particular role as, when a sufficient abundance of cells is reached, it allows bacteria to coordinate their gene expression and physiology at the population level. In contrast, quorum quenching mechanisms are employed by many different types of microorganisms that limit the coordination of antagonistic bacteria. This review synthesizes quorum sensing and quorum quenching mechanisms evidenced to date in the phycosphere, emphasizing the implications that these signaling systems have for the regulation of bacterial communities and their activities. The diversity of chemical compounds involved in these processes is examined. We further review the bacterial functions regulated in the phycosphere by quorum sensing, which include biofilm formation, nutrient acquisition, and emission of algaecides. We also discuss quorum quenching compounds as antagonists of quorum sensing, their function in the phycosphere, and their potential biotechnological applications. Overall, the current state of the art demonstrates that quorum sensing and quorum quenching regulate a balance between a symbiotic and a parasitic way of life between bacteria and their phytoplankton host.     

Dental Chatter: Bacterial Cross-Talk in the Biofilm of the Oral Cavity

Dental biofilms are composed of hundreds of bacterial species. These biofilms are diverse biological structures due to the heterogeneity of the many different types of supports in the oral cavity. The bacteria immobilized in these biofilms are exposed to rapid environmental changes such as pH, temperature, nutrition and anti-plaque agents. One mode in which these bacteria adapt in the dental biofilm is by quorum sensing. This cell-cell communication regulates diverse sets of adhesion modes, physiological changes, virulence properties, allowing the bacteria to persist in the dental biofilm under rapid environmental changes. In this review, we will concentrate mostly on the cariogenic bacterium Streptococcus mutans as one of the pivotal microorganisms in the supra-gingival biofilm that plays a major role in dental caries.     

Development of Quorum-Based Anti-Virulence Therapeutics Targeting Gram-Negative Bacterial Pathogens

Quorum sensing is a cell density-dependent signaling phenomenon used by bacteria for coordination of population-wide phenotypes, such as expression of virulence genes, antibiotic resistance and biofilm formation. Lately, disruption of bacterial communication has emerged as an anti-virulence strategy with enormous therapeutic potential given the increasing incidences of drug resistance in pathogenic bacteria. The quorum quenching therapeutic approach promises a lower risk of resistance development, since interference with virulence generally does not affect the growth and fitness of the bacteria and, hence, does not exert an associated selection pressure for drug-resistant strains. With better understanding of bacterial communication networks and mechanisms, many quorum quenching methods have been developed against various clinically significant bacterial pathogens. In particular, Gram-negative bacteria are an important group of pathogens, because, collectively, they are responsible for the majority of hospital-acquired infections. Here, we discuss the current understanding of existing quorum sensing mechanisms and present important inhibitory strategies that have been developed against this group of pathogenic bacteria.     

A New Cell-Based AI-2-Mediated Quorum Sensing Interference Assay in Screening of LsrK-Targeted Inhibitors

Quorum sensing (QS), a bacterial communication strategy, has been recognized as one of the control mechanisms of virulence in bacteria. Thus, targeting QS offers an interesting opportunity to impair bacterial pathogenicity and develop antivirulence agents. Aiming to enhance the discovery of QS inhibitors, we developed a bioreporter Escherichia coli JW5505 pET-Plsrlux and set up a cell-based assay for identifying inhibitors of autoinducer-2 (AI-2)-mediated QS. A comparative study on the performance of target- versus cell-based assays was performed, and 91 compounds selected with the potential to target the ATP binding pocket of LsrK, a key enzyme in AI-2 processing, were tested in an LsrK inhibition assay, providing 36 hits. The same set of compounds was tested by the AI-2-mediated QS interference assay, resulting in 24 active compounds. Among those, six were also found to be active against LsrK, whereas 18 might target other components of the pathway. Thus, this AI-2-mediated QS interference cell-based assay is an effective tool for complementing target-based assays, yet also stands as an independent assay for primary screening.     

"Clicking" on the lights to reveal bacterial social networking

"No man is an island." With apologies to John Donne, the same could be said for a bacterium. The discovery of bacterial quorum sensing and its relevance to microbial ecology and pathogenesis have fueled the increasing scrutiny of the molecular mechanisms responsible for the apparent group behavior of microbes. A number of chemically diverse small molecules act as diffusible signaling molecules that regulate gene expression in a population-dependent manner. Some of these signals, such as the N-acyl-L-homoserine lactones, are produced and sensed by others in the same or closely related species, and other chemical classes of signals are used more broadly for interspecies and even interkingdom communication. As a field, the study of these microbial social networks has been termed "sociomicrobiology".     

Quorum Sensing of Bacteria and Trans-Kingdom Interactions of N-Acyl Homoserine Lactones with Eukaryotes

Many environmental and interactive important traits of bacteria, such as antibiotic, siderophore or exoenzyme (like cellulose, pectinase) production, virulence factors of pathogens, as well as symbiotic interactions, are regulated in a population density-dependent manner by using small signaling molecules. This phenomenon, called quorum sensing (QS), is widespread among bacteria. Many different bacterial species are communicating or "speaking" through diffusible small molecules. The production often is sophisticatedly regulated via an autoinducing mechanism. A good example is the production of N-acyl homoserine lactones (AHL), which occur in many variations of molecular structure in a wide variety of Gram-negative bacteria. In Gram-positive bacteria, other compounds, such as peptides, regulate cellular activity and behavior by sensing the cell density. The degradation of the signaling molecule--called quorum quenching--is probably another important integral part in the complex quorum sensing circuit. Most interestingly, bacterial quorum sensing molecules also are recognized by eukaryotes that are colonized by QS-active bacteria. In this case, the cross-kingdom interaction can lead to specific adjustment and physiological adaptations in the colonized eukaryote. The responses are manifold, such as modifications of the defense system, modulation of the immune response, or changes in the hormonal status and growth responses. Thus, the interaction with the quorum sensing signaling molecules of bacteria can profoundly change the physiology of higher organisms too. Higher organisms are obligatorily associated with microbial communities, and these truly multi-organismic consortia, which are also called holobionts, can actually be steered via multiple interlinked signaling substances that originate not only from the host but also from the associated bacteria.     

A Nitric Oxide-Responsive Quorum Sensing Circuit in Vibrio harveyi Regulates Flagella Production and Biofilm Formation

Cell signaling plays an important role in the survival of bacterial colonies. They use small molecules to coordinate gene expression in a cell density dependent manner. This process, known as quorum sensing, helps bacteria regulate diverse functions such as bioluminescence, biofilm formation and virulence. In Vibrio harveyi, a bioluminescent marine bacterium, four parallel quorum-sensing systems have been identified to regulate light production. We have previously reported that nitric oxide (NO), through the H-NOX/HqsK quorum sensing pathway contributes to light production in V. harveyi through the LuxU/LuxO/LuxR quorum sensing pathway. In this study, we show that nitric oxide (NO) also regulates flagellar production and enhances biofilm formation. Our data suggest that V. harveyi is capable of switching between lifestyles to be able to adapt to changes in the environment.     

Novel Strategies for the Prevention and Treatment of Biofilm Related Infections

Biofilm formation by human bacterial pathogens on implanted medical devices causes major morbidity and mortality among patients, and leads to billions of dollars in healthcare cost. Biofilm is a complex bacterial community that is highly resistant to antibiotics and human immunity. As a result, novel therapeutic solutions other than the conventional antibiotic therapies are in urgent need. In this review, we will discuss the recent research in discovery of alternative approaches to prevent or treat biofilms. Current anti-biofilm technologies could be divided into two groups. The first group focuses on targeting the biofilm forming process of bacteria based on our understanding of the molecular mechanism of biofilm formation. Small molecules and enzymes have been developed to inhibit or disrupt biofilm formation. Another group of anti-biofilm technologies focuses on modifying the biomaterials used in medical devices to make them resistant to biofilm formation. While these novel anti-biofilm approaches are still in nascent phases of development, efforts devoted to these technologies could eventually lead to anti-biofilm therapies that are superior to the current antibiotic treatment.     

Targeting the Central Pocket of the Pseudomonas aeruginosa Lectin LecA

Pseudomonas aeruginosa is an opportunistic ESKAPE pathogen that produces two lectins, LecA and LecB, as part of its large arsenal of virulence factors. Both carbohydrate-binding proteins are central to the initial and later persistent infection processes, i. e. bacterial adhesion and biofilm formation. The biofilm matrix is a major resistance determinant and protects the bacteria against external threats such as the host immune system or antibiotic treatment. Therefore, the development of drugs against the P. aeruginosa biofilm is of particular interest to restore efficacy of antimicrobials. Carbohydrate-based inhibitors for LecA and LecB were previously shown to efficiently reduce biofilm formations. Here, we report a new approach for inhibiting LecA with synthetic molecules bridging the established carbohydrate-binding site and a central cavity located between two LecA protomers of the lectin tetramer. Inspired by in silico design, we synthesized various galactosidic LecA inhibitors with aromatic moieties targeting this central pocket. These compounds reached low micromolar affinities, validated in different biophysical assays. Finally, X-ray diffraction analysis revealed the interactions of this compound class with LecA. This new mode of action paves the way to a novel route towards inhibition of P. aeruginosa biofilms.     

Solid‐Phase Synthesis and Biological Evaluation of N‐Dipeptido L‐Homoserine Lactones as Quorum Sensing Activators

Bacteria use small signaling molecules to communicate in a process termed “quorum sensing” (QS), which enables the coordination of survival strategies, such as production of virulence factors and biofilm formation. In Gram‐negative bacteria, these signaling molecules are a series of N‐acylated L ‐homoserine lactones. With the goal of identifying non‐native compounds capable of modulating bacterial QS, a virtual library of N‐dipeptido L ‐homoserine lactones was screened in silico with two different crystal structures of LasR. The 30 most promising hits were synthesized on HMBA‐functionalized PEGA resin and released through an efficient acid‐mediated cyclative release mechanism. Subsequent screening for modulation of QS in Pseudomonas aeruginosa and E. coli identified six moderately strong activators. A follow‐up library designed from the preliminary derived structure–activity relationships was synthesized and evaluated for their ability to activate the QS system in this bacterium. This resulted in the identification of another six QS activators (two with low micromolar activity) thus illuminating structural features required for QS modulation.     

Palmitoyl-DL-carnitine is a multitarget inhibitor of Pseudomonas aeruginosa biofilm development

Bacteria growing in biofilms are often in metabolic and physiological states that do not respond well to antibiotics, and thus, are major contributors to chronic diseases. Biofilm inhibitors, therefore, have the potential to be used alone or as adjuvants to conventional antibiotic therapies. Here, we screened a chemically diverse collection of protein kinase inhibitors for molecules that perturb biofilm development. Among the inhibitory molecules identified, palmitoyl-DL-carnitine (pDLC) impaired Pseudomonas aeruginosa and Escherichia coli biofilm formation in a dose-dependent manner. The pDLC affected multiple pathways implicated in P. aeruginosa biofilm development; it stimulated motility, inhibited activity of the Las quorum sensing system, and overrode the biofilm-promoting effects of subminimal inhibitory concentrations of aminoglycosides and high levels of the second messenger, cyclic-di-GMP. Palmitic acid, but not carnitine, inhibited biofilm formation but did not stimulate motility, suggesting that pDLC works through unique mechanisms. The ability to target multiple pathways involved in biofilm formation is desirable in an inhibitor, which makes pDLC an interesting lead for antibiofilm therapies.     

The Diffusible Signal Factor Family of Bacterial Cell?Cell Signals

Bacterial cell-to-cell signals of the diffusible signal factor (DSF) family are cis-2-unsaturated fatty acids that differ in their chain length and branching patterns. Signaling involving DSF family members occurs in diverse bacteria to include plant and human pathogens. In the majority of these organisms, the perception of DSF is linked to turnover of the second messenger cyclic di-GMP by one of two “core” pathways. Additional “accessory” signal transduction pathways can also be found, but are not widely conserved. DSF signaling acts to regulate diverse functions to include biofilm formation and architecture, antibiotic resistance, and the production of virulence factors in pathogens. DSF family signals can also participate in interspecies signaling with other bacteria and interkingdom signaling with the yeast Candida albicans. Such interactions may have importance in modifying microbial behavior during polymicrobial infections.     

In-Silico Identified New Natural Sortase A Inhibitors Disrupt S. aureus Biofilm Formation

Sortase A (SrtA) is a membrane-associated enzyme that anchors surface-exposed proteins to the cell wall envelope of Gram-positive bacteria such as Staphylococcus aureus. As SrtA is essential for Gram-positive bacterial pathogenesis but dispensable for microbial growth or viability, SrtA is considered a favorable target for the enhancement of novel anti-infective drugs that aim to interfere with key bacterial virulence mechanisms, such as biofilm formation, without developing drug resistance. Here, we used virtual screening to search an in-house natural compound library and identified two natural compounds, N1287 (Skyrin) and N2576 ((4,5-dichloro-1H-pyrrol-2-yl)-[2,4-dihydroxy-3-(4-methyl-pentyl)-phenyl]-methanone) that inhibited the enzymatic activity of SrtA. These compounds also significantly reduced the growth of S. aureus but possessed moderate mammalian toxicity. Furthermore, S. aureus strains treated with these compounds exhibited reduction in adherence to host fibrinogen, as well as biofilm formation. Hence, these compounds may represent an anti-infective therapy without the side effects of antibiotics.     

Natural Quorum Sensing Inhibitors – Small Molecules,Big Messages

Due to the increasing emergence of antibiotic resistant bacterial strains within the past few decades, bacterial infections in general – and hospital-borne infections, in particular – have become increasingly difficult to fight. It is therefore crucial to find new strategies to fight pathogenic bacteria. Targeted inhibition of quorum sensing (QS) presents a promising alternative. QS is a cell density-dependent signaling pathway used for intra- and interspecies coordination of gene expression. In many bacteria, pathogenic phenotypes, as well as the expression of virulence factors, are under the control of QS regulons. A closer look at natural quorum sensing inhibitors may be helpful to identify potent compounds that can be used as alternatives to antibiotics. Moreover, it will also provide insight into the interactions between species that compete for the same habitat and resources. This review aims to summarize our current knowledge concerning natural QS inhibitors, as a starting point for the design and synthesis of new therapeutics to treat or prevent bacterial infections.     

Active Efflux Influences the Potency of Quorum Sensing Inhibitors in Pseudomonas aeruginosa

Many bacteria regulate gene expression through a cell–cell signaling process called quorum sensing (QS). In proteobacteria, QS is largely mediated by signaling molecules known as N‐acylated L ‐homoserine lactones (AHLs) and their associated intracellular LuxR‐type receptors. The design of non‐native small molecules capable of inhibiting LuxR‐type receptors (and thereby QS) in proteobacteria is an active area of research, and numerous lead compounds are AHL derivatives that mimic native AHL molecules. Much of this previous work has focused on the pathogen Pseudomonas aeruginosa, which controls an arsenal of virulence factors and biofilm formation through QS. The MexAB‐OprM efflux pump has been shown to play a role in the secretion of the major AHL signal in P. aeruginosa, N‐(3‐oxododecanoyl) L ‐homoserine lactone. In the current study, we show that a variety of non‐native AHLs and related derivatives capable of inhibiting LuxR‐type receptors in P. aeruginosa display significantly higher potency in a P. aeruginosa Δ(mexAB‐oprM) mutant, suggesting that MexAB‐OprM also recognizes these compounds as substrates. We also demonstrate that the potency of 5,6‐dimethyl‐2‐aminobenzimidazole, recently shown to be a QS and biofilm inhibitor in P. aeruginosa, is not affected by the presence/absence of the MexAB‐OprM pump. These results have implications for the use of non‐native AHLs and related derivatives as QS modulators in P. aeruginosa and other bacteria, and provide a potential design strategy for the development of new QS modulators that are resistant to active efflux.     

Environmental Stimuli Shape Biofilm Formation and the Virulence of Periodontal Pathogens

Periodontitis is a common inflammatory disease affecting the tooth-supporting structures. It is initiated by bacteria growing as a biofilm at the gingival margin, and communication of the biofilms differs in health and disease. The bacterial composition of periodontitis-associated biofilms has been well documented and is under continual investigation. However, the roles of several host response and inflammation driven environmental stimuli on biofilm formation is not well understood. This review article addresses the effects of environmental factors such as pH, temperature, cytokines, hormones, and oxidative stress on periodontal biofilm formation and bacterial virulence.     

Influence of Rhamnolipids and Ionic Cross-Linking Conditions on the Mechanical Properties of Alginate Hydrogels as a Model Bacterial Biofilm

The literature indicates the existence of a relationship between rhamnolipids and bacterial biofilm, as well as the ability of selected bacteria to produce rhamnolipids and alginate. However, the influence of biosurfactant molecules on the mechanical properties of biofilms are still not fully understood. The aim of this research is to determine the effect of rhamnolipids concentration, CaCl₂ concentration, and ionic cross-linking time on the mechanical properties of alginate hydrogels using a Box–Behnken design. The mechanical properties of cross-linked alginate hydrogels were characterized using a universal testing machine. It was assumed that the addition of rhamnolipids mainly affects the compression load, and the value of this parameter is lower for hydrogels produced with biosurfactant concentration below CMC than for hydrogels obtained in pure water. In contrast, the addition of rhamnolipids in an amount exceeding CMC causes an increase in compression load. In bacterial biofilms, the presence of rhamnolipid molecules does not exceed the CMC value, which may confirm the influence of this biosurfactant on the formation of the biofilm structure. Moreover, rhamnolipids interact with the hydrophobic part of the alginate copolymer chains, and then the hydrophilic groups of adsorbed biosurfactant molecules create additional calcium ion trapping sites.