Identification of small molecules that strongly inhibit bacterial quorum sensing using a high-throughput lipid vesicle lysis assay

Molecular Mechanisms of Virulence Regulation in Staphylococcus aureus: A Journey into Reconstitutive Biochemistry

ConspectusMethodological development in the fields of genetics, chemical biology, and biochemistry over the last several decades has provided researchers with a diverse set of powerful tools to investigate biological processes. Leveraging these innovations in concert, scientists can now characterize biological pathways at a level of complexity ranging from systems biology down to molecular and atomic detail.Throughout this Account, we illustrate how discoveries made using these tools build on each other to develop a comprehensive understanding of biological pathways. Advancements in genetic sequencing facilitates association of genotypes and phenotypes, independent of biochemical mechanism. Through the biochemical reconstitution of the interactions between biological macromolecules─including the small molecules (ligands and metabolites) and proteins─that participate in these biological pathways, scientists can characterize the specific molecular features that link genotype and phenotype. This facilitates identification of targets within these pathways that can be manipulated to achieve a greater understanding of the biological process or to develop interventions to improve human health outcomes.Specifically, we describe how this toolbox was leveraged to discover and characterize the molecular biochemistry underlying control of pathogenicity in the Gram-positive bacterium Staphylococcus aureus. Concurrent with advancements in the investigative tools available to the scientific community, we and others reported on the genetic, molecular, and biochemical/biophysical components of this regulatory system. Virulence control in S. aureus is achieved through a chemical system of bacterial cell-to-cell communication indexed to local population density, referred to as quorum sensing (QS). We and our collaborators identified that this QS system is encoded in the accessory gene regulator (agr) operon and functions via the biosynthesis, secretion, and accumulation of a short peptide signaling molecule─the autoinducing peptide (AIP)─in the local environment correlated with the growth of S. aureus in the same biological niche. Above a threshold concentration, these AIPs bind and activate a cell-surface receptor to stimulate an intracellular response resulting in altered gene expression and bacterial group behaviors. We discovered that chemical modification of these AIPs often generates molecules that exhibit potent inhibition of agr QS, with demonstrated therapeutic potential to treat S. aureus infections. We went on to characterize the biochemical mechanism of signaling molecule biosynthesis and receptor activation in controlled systems through in vitro reconstitution of the constituent enzymes and substrates. Biochemical reconstitution enabled quantitative assessment of biophysical parameters. These efforts culminated in the comprehensive characterization and functional in vitro reconstitution of agr QS in a synthetic system in a minimal model at the interface of genotype, mechanism, and phenotype.

Disarming Staphylococcus aureus: Review of Strategies Combating This Resilient Pathogen by Targeting Its Virulence

Staphylococcus aureus is a formidable pathogen notorious for its antibiotic resistance and diverse virulence mechanisms, including toxin production, biofilm formation, and immune evasion. This article explores innovative anti-virulence strategies to disarm S. aureus by targeting critical virulence factors without exerting bactericidal pressure. Key approaches include inhibiting adhesion and biofilm formation, neutralizing toxins, disrupting quorum sensing (e.g., Agr system inhibitors), and blocking iron acquisition pathways. Additionally, interventions targeting two-component regulatory systems are highlighted. While promising, challenges such as strain variability, biofilm resilience, pharmacokinetic limitations, and resistance evolution underscore the need for combination therapies and advanced formulations. Integrating anti-virulence strategies with traditional antibiotics and host-directed therapies offers a sustainable solution to combat multidrug-resistant S. aureus, particularly methicillin-resistant strains (MRSA), and mitigate the global public health crisis.

Recent advances in high-throughput screening methods for small molecule modulators in bacteria

Bacterial infections, especially those that are resistant to antibiotics, constitute an increasing threat to public health. Deeper understanding about the systems that govern resistant infections, followed by the design of new therapies is crucial to minimizing morbidity and mortality due to antibacterial resistance. To this end, the discovery of small molecules capable of modulating bacterial processes is an important goal. Herein, we summarize recent developments in high-throughput screening, including the use of in vitro biochemical assays, reporter fusion read-out methods, and live cell phenotypic assays in bacteria. We also highlight key advantages and disadvantages of each assay type, as well as exciting new innovations.

Monitoring host-pathogen interactions using chemical proteomics

With the rapid emergence and the dissemination of microbial resistance to conventional chemotherapy, the shortage of novel antimicrobial drugs has raised a global health threat. As molecular interactions between microbial pathogens and their mammalian hosts are crucial to establish virulence, pathogenicity, and infectivity, a detailed understanding of these interactions has the potential to reveal novel therapeutic targets and treatment strategies. Bidirectional molecular communication between microbes and eukaryotes is essential for both pathogenic and commensal organisms to colonise their host. In particular, several devastating pathogens exploit host signalling to adjust the expression of energetically costly virulent behaviours. Chemical proteomics has emerged as a powerful tool to interrogate the protein interaction partners of small molecules and has been successfully applied to advance host-pathogen communication studies. Here, we present recent significant progress made by this approach and provide a perspective for future studies.

Analysing Megasynthetase Mutants at High Throughput Using Droplet Microfluidics

Nonribosomal peptide synthetases (NRPSs) are giant enzymatic assembly lines that deliver many pharmaceutically valuable natural products, including antibiotics. As the search for new antibiotics motivates attempts to redesign nonribosomal metabolic pathways, more robust and rapid sorting and screening platforms are needed. Here, we establish a microfluidic platform that reliably detects production of the model nonribosomal peptide gramicidin S. The detection is based on calcein-filled sensor liposomes yielding increased fluorescence upon permeabilization. From a library of NRPS mutants, the sorting platform enriches the gramicidin S producer 14.5-fold, decreases internal stop codons 250-fold, and generates enrichment factors correlating with enzyme activity. Screening for NRPS activity with a reliable non-binary sensor will enable more sophisticated structure-activity studies and new engineering applications in the future.

The biofilm proteome of Staphylococcus aureus and its implications for therapeutic interventions to biofilm-associated infections

Staphylococcus aureus is a major healthcare concern due to its ability to inflict life-threatening infections and evolve antibiotic resistance at an alarming pace. It is frequently associated with hospital-acquired infections, especially device-associated infections. Systemic infections due to S. aureus are difficult to treat and are associated with significant mortality and morbidity. The situation is worsened by the ability of S. aureus to form social associations called biofilms. Biofilms embed a community of cells with the ability to communicate with each other and share resources within a polysaccharide or protein matrix. S. aureus establish biofilms on tissues and conditioned abiotic surfaces. Biofilms are hyper-tolerant to antibiotics and help evade host immune responses. Biofilms exacerbate the severity and recalcitrance of device-associated infections. The development of a biofilm involves various biomolecules, such as polysaccharides, proteins and nucleic acids, contributing to different structural and functional roles. Interconnected signaling pathways and regulatory molecules modulate the expression of these molecules. A comprehensive understanding of the molecular biology of biofilm development would help to devise effective anti-biofilm therapeutics. Although bactericidal agents, antimicrobial peptides, bacteriophages and nano-conjugated anti-biofilm agents have been employed with varying levels of success, there is still a requirement for effective and clinically viable anti-biofilm therapeutics. Proteins that are expressed and utilized during biofilm formation, constituting the biofilm proteome, are a particularly attractive target for anti-biofilm strategies. The proteome can be explored to identify potential anti-biofilm drug targets and utilized for rational drug discovery. With the aim of uncovering the biofilm proteome, this chapter explores the mechanism of biofilm formation and its regulation. Furthermore, it explores the antibiofilm therapeutics targeted against the biofilm proteome.

Chemical and biomolecular insights into the Staphylococcus aureus agr quorum sensing system: Current progress and ongoing challenges

Staphylococcus aureus is a ubiquitous bacterium that has become a major threat to human health due to its extensive toxin production and tremendous capacity for antibiotic resistance (e.g., MRSA "superbug" infections). Amid a worsening antibiotic resistance crisis, new strategies to combat this deadly microbe that remove the selective pressure of traditional approaches are in high demand. S. aureus utilizes an accessory gene regulator (agr) quorum sensing network to monitor its local cellular population and trigger a devastating communal attack, like an invading horde, once a threshold cell density has been reached. The role of the agr system in a range of disease types is still being unraveled. Herein, we discuss the present-day biochemical understanding of agr along with unresolved details, describe its connection to the progression of infection, and review how chemical strategies have been implemented to study and intercept this signaling pathway. This research is illuminating the potential of agr as an anti-virulence target in S. aureus and should inform the study of similar, yet less studied, agr systems in related bacterial pathogens.

β-Lactams from the Ocean

The title of this essay is as much a question as it is a statement. The discovery of the β-lactam antibiotics-including penicillins, cephalosporins, and carbapenems-as largely (if not exclusively) secondary metabolites of terrestrial fungi and bacteria, transformed modern medicine. The antibiotic β-lactams inactivate essential enzymes of bacterial cell-wall biosynthesis. Moreover, the ability of the β-lactams to function as enzyme inhibitors is of such great medical value, that inhibitors of the enzymes which degrade hydrolytically the β-lactams, the β-lactamases, have equal value. Given this privileged status for the β-lactam ring, it is therefore a disappointment that the exemplification of this ring in marine secondary metabolites is sparse. It may be that biologically active marine β-lactams are there, and simply have yet to be encountered. In this report, we posit a second explanation: that the value of the β-lactam to secure an ecological advantage in the marine environment might be compromised by its close structural similarity to the β-lactones of quorum sensing. The steric and reactivity similarities between the β-lactams and the β-lactones represent an outside-of-the-box opportunity for correlating new structures and new enzyme targets for the discovery of compelling biological activities.

Lactiplantibacillus plantarum-Derived Biosurfactant Attenuates Quorum Sensing-Mediated Virulence and Biofilm Formation in Pseudomonas aeruginosa and Chromobacterium violaceum

Quorum sensing (QS) controls the expression of diverse biological traits in bacteria, including virulence factors. Any natural bioactive compound that disables the QS system is being considered as a potential strategy to prevent bacterial infection. Various biological activities of biosurfactants have been observed, including anti-QS effects. In the present study, we investigated the effectiveness of a biosurfactant derived from Lactiplantibacillus plantarum on QS-regulated virulence factors and biofilm formation in Pseudomonas aeruginosa and Chromobacterium violaceum. The structural analogues of the crude biosurfactant were identified using gas chromatography–mass spectrometry (GC–MS). Moreover, the inhibitory prospects of identified structural analogues were assessed with QS-associated CviR, LasA, and LasI ligands via in silico molecular docking analysis. An L. plantarum-derived biosurfactant showed a promising dose-dependent interference with the production of both violacein and acyl homoserine lactone (AHL) in C. violaceum. In P. aeruginosa, at a sub-MIC concentration (2.5 mg/mL), QS inhibitory activity was also demonstrated by reduction in pyocyanin (66.63%), total protease (60.95%), LasA (56.62%), and LasB elastase (51.33%) activity. The swarming motility and exopolysaccharide production were also significantly reduced in both C. violaceum (61.13%) and P. aeruginosa (53.11%). When compared with control, biofilm formation was also considerably reduced in C. violaceum (68.12%) and P. aeruginosa (59.80%). A GC–MS analysis confirmed that the crude biosurfactant derived from L. plantarum was a glycolipid type. Among all, n-hexadecanoic acid, oleic acid, and 1H-indene,1-hexadecyl-2,3-dihydro had a high affinity for CviR, LasI, and LasA, respectively. Thus, our findings suggest that the crude biosurfactant of L. plantarum can be used as a new anti-QS/antibiofilm agent against biofilm-associated pathogenesis, which warrants further investigation to uncover its therapeutic efficacy.