Different drugs for bad bugs: antivirulence strategies in the age of antibiotic resistance

Multifaceted quorum-sensing inhibiting activity of 3-(Benzo[d][1,3]dioxol-4-yl)oxazolidin-2-one mitigates Pseudomonas aeruginosa virulence

As antibiotic resistance escalates into a global health crisis, novel therapeutic approaches against infectious diseases are in urgent need. Pseudomonas aeruginosa, an adaptable opportunistic pathogen, poses substantial challenges in treating a range of infections. The quorum-sensing (QS) system plays a pivotal role in orchestrating the production of a large set of virulence factors in a cell density-dependent manner, and the anti-virulence strategy targeting QS may show huge potential. Here, we present a comprehensive investigation into the potential of the synthesized compound 3-(benzo[d][1,3]dioxol-4-yl)oxazolidin-2-one (OZDO, C10H9NO4) as a QS inhibitor to curb the virulence of P. aeruginosa. By employing an integrated approach encompassing in silico screening, in vitro and in vivo functional identification, we elucidated the multifaceted effects of OZDO. Molecular docking predicted that OZDO interfered with three core regulatory proteins of P. aeruginosa QS system. Notably, OZDO exhibited significant inhibition on the production of pyocyanin, rhamnolipid and extracellular proteases, biofilm formation, and cell motilities of P. aeruginosa. Transcriptomic analysis and quantitative real-time PCR displayed the down-regulation of QS-controlled genes in OZDO-treated PAO1, reaffirming the QS-inhibition activity of OZDO. In vivo assessments using a Caenorhabditis elegans-infection model demonstrated OZDO mitigated P. aeruginosa pathogenicity, particularly against the hypervirulent strain PA14. Moreover, OZDO in combination with polymyxin B and aztreonam presented a promising avenue for innovative anti-infective therapy. Our study sheds light on the multifaceted potential of OZDO as an anti-virulence agent and its significance in combating P. aeruginosa-associated infections.

Resistance to quorum sensing inhibition spreads more slowly during host infection than antibiotic resistance

Antibiotic resistance is a rising problem and new and sustainable strategies to combat bacterial (intestinal) infections are therefore urgently needed. One promising strategy under intense investigation is the inhibition of quorum sensing, bacterial cell-to-cell communication with small molecules. A key question with respect to the application of quorum sensing inhibition is whether it will impose selective pressure for the spread of resistance. It was recently shown that resistance to quorum sensing inhibition will spread more slowly during infection of a host than resistance to traditional antibiotics.

Staphylococcus aureus: Current perspectives on molecular pathogenesis and virulence

Staphylococcus aureus has evolved a sophisticated regulatory system to control its virulence. One of the main roles of this interconnected network is to sense and respond to diverse environmental signals by altering the synthesis of virulence components required for survival in the host, including cell surface adhesins, extracellular enzymes and toxins. The accessory gene regulator (agr), a quorum sensing system that detects the local concentration of a cyclic peptide signaling molecule, is one of the well-studied of these S. aureus regulatory mechanisms. By using this system, S. aureus is able to sense its own population density and translate this information into a specific pattern of gene expression. In addition to Agr, this pathogen senses specific stimuli through various two-component systems and synchronizes responses with alternative sigma factors and cytoplasmic regulators of the SarA protein family. These different regulatory mechanisms combine host and environmental information into a network that guarantees the best possible response of pathogens to changing circumstances. In this article, an overview of the most significant and thoroughly studied regulatory systems of S. aureus is provided, along with a summary of their roles in host interactions.

Bacterial clustering biomaterials as anti-infective therapies

In Nature, bacterial clustering by host-released peptides or nucleic acids is an evolutionarily conserved immune defense strategy employed to prevent adhesion of pathogenic microbes, which is prerequisite for most infections. Synthetic anti-adhesion strategies present as non-lethal means of targeting bacteria and may potentially be used to avoid resistance against antimicrobial therapies. From bacteria-agglutinating biomolecules discovered in nature to synthetic designs involving peptides, cationic polymers and nanoparticles, the modes of actions appear broad and unconsolidated. Herein, we present a critical review and update of the state-of-the-art in synthetic bacteria-clustering designs with proposition of a more streamlined nomenclature and classification. Overall, this review aims to consolidate the conceptual framework in the field of bacterial clustering and highlight its potentials as an avenue for discovering novel antibacterial biomaterials.

Emerging synergistic strategies for enhanced antibacterial sonodynamic therapy: Advances and prospects

Antibacterial therapy has been extensively applied in medical field to alleviate the severity and mortality of infection. However, it still exists some issues such as drug side effects, limited efficacy and bacterial resistance. Among the alternative therapies, antibacterial sonodynamic therapy (aSDT) has been explored as a promising approach to tackle those crises. It is meaningful to investigate superior strategy to augment the therapeutic efficacy of aSDT. This review summarizes the potential aSDT-based antibacterial mechanisms and comprehensively discusses the prevailing synergistic strategies, such as nanomaterials-based aSDT antibacterial strategy, aSDT + strategy with physical, chemical and biological methods. Moreover, we also reviewed the medical applications of aSDT strategies. Finally, the perspectives on the current challenges that need be resolved in aSDT are proposed. We expect that this review could provide robust support to expedite the clinical applications of aSDT.

Phenylacetic acid catabolism modulates virulence factors and drug resistance in Acinetobacter baumannii MCC 2076

Acinetobacter baumannii has emerged as a major global health threat due to its remarkable ability of resistance, persistence in hostile environments and tolerance to stress conditions. Phenylacetic acid (PAA) catabolism, traditionally known for bacterial metabolic advantage, is now being investigated for its role in the pathogenesis of A. baumannii. This study aims to explore how PAA and its metabolic processes influence the virulence factors and antibiotic resistance of A. baumannii MCC 2076. We examined growth kinetics and PAA utilization to assess the time-dependent breakdown of PAA. In vitro analyses were conducted to evaluate biofilm formation, bacterial surface hydrophobicity, and tolerance to desiccation stress in PAA-catabolizing cells. Our findings revealed a two-fold increase in biofilm formation and an 8% enhancement in bacterial surface adherence. Additionally, we observed an increase in efflux pump activity and a decrease in outer membrane permeability when PAA served as a carbon source. All these factors may be responsible for 2- to 3-fold increase in the minimum inhibitory concentration (MIC) of ciprofloxacin, levofloxacin, ampicillin, and piperacillin. A. baumannii cells with an active paa operon demonstrated a higher survival rate under desiccation stress compared to control cells. RT-qPCR analysis indicated the upregulation of genes such as gacA, csuE, ompA, and adeR, which are associated with virulence related genes like biofilm forming, adherence and antibiotic resistance related genes. The catabolism of PAA is crucial, as its utilization significantly alters the virulence characteristics of A. baumannii MCC 2076. This study provides valuable insights into the PAA catabolic pathway's role in modulating virulence gene expression, potentially offering new therapeutic targets for combating A. baumannii infections.

Inhibiting Staphylococcus aureus Virulence Factors: Advances in Traditional Chinese Medicines and Active Compounds

Staphylococcus aureus is one of the most prevalent antibiotic-resistant bacteria, characterized by high morbidity and mortality. The pathogenicity of S. aureus relies on the production of multiple virulence factors. In recent years, antivirulence strategies have shown promise in developing antiinfective drugs by targeting the inhibition of bacterial virulence factors rather than directly killing pathogens. In Asia, some traditional Chinese medicines have a long history of antiinfective application and have demonstrated therapeutic efficacy. However, their antiinfective mechanism has not been fully elucidated. Recent studies have revealed that numerous extracts of TCM, as well as pure compounds from TCM, significantly inhibited the expression of virulence factors of S. aureus, which might be one of their antiinfective mechanisms with potential for the development of novel antiinfective agents. In this review, we summarized the major virulence factors of S. aureus and recent advances in TCM-derived antivirulence agents, including TCM formulae, single herbs, and isolated bioactive compounds, which showed antivirulence capability against S. aureus. Investigating the antivirulence mechanism of TCM not only enhances our understanding of TCM's antiinfective mechanisms but also facilitates the isolation of active compounds with therapeutic potential against S. aureus infection.

Analysis of ESAC-Net/EARS-Net Data from 29 EEA Countries for Spatiotemporal Associations Between Antimicrobial Use and Resistance-Implications for Antimicrobial Stewardship?

BACKGROUND/OBJECTIVES

Antimicrobial resistance is one of the foremost global health concerns of today, and it could offset much of the progress accrued in healthcare over the last century. Excessive antibiotic use accelerates this problem, but it is recognised that specific agents differ in their capacity to promote resistance, a concept recently promoted by the World Health Organisation in the form of its Access, Watch, Reserve (AWaRe) schema. Which, if any, agents should be construed as having a high proclivity for selection of resistance has been contested. The European Antimicrobial Resistance Surveillance Network (EARS-NET) and European Surveillance of Antimicrobial Consumption Network (ESAC-NET) curate population level data over time and throughout the European Economic Area (EEA). EARS-NET monitors resistance to antimicrobials amongst invasive isolates of sentinel pathogens whereas ESAC-NET tracks usage of systemic antimicrobials. Together, data from these networks were interrogated to delineate correlations between antimicrobial consumption and resistance.

METHODS

Using univariate and multivariate regression analyses, spatiotemporal associations between the use of specific antimicrobial classes and 14 key resistance phenotypes in five sentinel pathogens were assessed methodically for 29 EEA countries.

RESULTS

Use of second and third generation cephalosporins, extended spectrum penicillin/β-lactamase inhibitor combinations, carbapenems, fluoroquinolones, nitroimidazoles and macrolides strongly correlated with key resistance phenotypes, as did overall antimicrobial consumption.

CONCLUSIONS

The data obtained mostly support the WHO AWaRe schema with critical caveats. They have the potential to inform antimicrobial stewardship initiatives in the EEA, highlighting obstacles and shortcomings which may be modified in future to minimise positive selection for problematic resistance.

Discovery of synthetic small molecules targeting the central regulator of Salmonella pathogenicity

The enteric pathogen Salmonella enterica serovar Typhimurium relies on the activity of effector proteins to invade, replicate, and disseminate into host epithelial cells and other tissues, thereby causing disease. Secretion and injection of effector proteins into host cells is mediated by dedicated secretion systems, which hence represent major virulence determinants. Here, we report the identification of a synthetic small molecule with drug-like properties, C26, which suppresses the secretion of effector proteins and consequently hinders bacterial invasion of eukaryotic cells. C26 binds to and inhibits HilD, the transcriptional regulator of the major secretion systems. Although sharing the same binding pocket as the previously described long-chain fatty acid ligands, C26 inhibits HilD with a unique binding mode and a distinct mechanism. We provide evidence of intramacrophage activity and present analogs with improved potency and suitability as scaffolds to develop antivirulence agents against Salmonella infections in humans and animals.

Highly potent quinoxalinediones inhibit α-hemolysin and ameliorate Staphylococcus aureus lung infections

Hospital-acquired pneumonia caused by Staphylococcus aureus is associated with patient morbidity and mortality, despite adequate antibiotic therapy. This illustrates the need for treatments beyond antibiotics. The pore-forming heptameric toxin α-hemolysin (Hla) is a major pathogenicity factor of S. aureus and a clinically validated target. We identify quinoxalinediones (QDS) as highly potent Hla inhibitors, conferring protection against the hallmarks of Hla-induced pathogenicity such as Ca2+ influx, cytotoxicity, hemolysis, and monolayer destruction. The effects were exerted across major Hla subtypes in all relevant cell types. QDS prevented the formation of functional pores by interacting with Hla near the phospholipid-binding site. The QDS analog, H052, was active in mouse models of S. aureus lung infections, when administered prophylactically or therapeutically, either as monotherapy or when given in combination with the antibiotic linezolid. The study provides evidence that complex bacterial toxins can be targeted in vivo by drug-like small molecules.

Dihydromyricetin alleviates ETEC K88-induced intestinal inflammatory injury by inhibiting quorum sensing-related virulence factors

BACKGROUND

Enterotoxigenic Escherichia coli (ETEC) is responsible for piglet diarrhea and causes substantial economic loss in the pig industry. Along with the restriction of antibiotics, natural compounds targeting bacterial virulence factors are supposed to be efficacious and attractive alternatives for controlling ETEC infection. This study aimed to investigate the influence of dihydromyricetin (DMY), a natural flavonoid compound, on the expression of virulence factors of ETEC and intestinal inflammatory injury.

RESULTS

DMY interfered with the quorum sensing (QS) of ETEC K88 since it decreased AI-2 secretion and downregulated the expression of LuxS and Pfs, which dominate AI-2 production, and decreased the expression mRNA level of genes (lsrA, lsrB, lsrC, lsrD, lsrK, and lsrR) that are involved in AI-2 internalization and signal transduction. Additionally, DMY markedly dampened the expression of QS-related virulence genes (elt-1, estB, fliC, faeG), biofilm formation, cell adhesion, and stress tolerance of ETEC K88. Furthermore, DMY treatment applied to the ETEC K88 infection in mice model resulted in decreased amount of heat-labile (LT) and heat-stable (ST) enterotoxins, reduced production of cAMP and cGMP, downregulated protein level of CFTR and upregulated expression of NHE3 in the ileum. In addition, the mRNA expression of proinflammatory cytokines (TNF-α, IL-1β, and IL-6) and histological damage in the ileum were significantly decreased by DMY treatment.

CONCLUSIONS

DMY can inhibit the AI-2 QS and virulence factor expression, thereby attenuating the virulence of ETEC and alleviating intestinal inflammatory damage in ETEC K88-challenged mice. This study indicated that DMY has the potential to be a promising antivirulence agent for combating ETEC infection.

Artificial Intuition and accelerating the process of antimicrobial drug discovery

New drug development is a very challenging, expensive, and usually time-consuming process. This issue is very important with regard to antimicrobials, which are affected by the global issue of the development and spread of resistance. This framework underscores the urgency of accelerating drug development processes while reducing their costs. In this context, new bioinformatics tools can provide important support for drug development by limiting and shortening in vitro evaluation of the best outcomes, thereby minimizing costs. Recently, new Artificial Intelligence (AI)-based tools have been developed for de novo design of new molecules, or for the identification of features of inhibitors among a large set of molecules that can guide rational design. With this work, we present an Artificial Intuition (AI4)-based pharmacological analysis of a series of antimicrobial compounds that are known to be active against Mycobacterium tuberculosis. The compounds have been subjected to Molecular Dynamic Simulation (MDS), and the respective outputs processed with a Quantitative Complexity Management (QCM) tool in order to determine the corresponding complexity profiles. The comparison of different analogues in each series revealed a relationship between the complexity of the various chemical moieties and their importance for the biological activity of each compound, suggesting that QCM may be a useful tool in guiding the optimization process. This first attempt to apply the tool in the field of drug development has yielded interesting results, indicating that QCM, which powers AI4, can be implemented for rational drug design in the near future.

Terramide A: a novel ironophore targeting Acinetobacter baumannii with mechanistic insights into bacterial iron deprivation

Acetobacter baumannii poses escalating clinical challenges due to its exceptional adaptability, demanding innovative antimicrobial strategies. This study pioneers an investigation into the antibacterial efficacy and molecular mechanism of Terramide A, a hydroxamate siderophore isolated from Aspergillus terreus, against notorious A. baumannii. Employing a multidisciplinary approach integrating phenotypic characterization with mechanistic interrogation, we demonstrate that Terramide A exerts significant inhibitory effects against A. baumannii and P. aeruginosa, pathogens critically dependent on siderophore-mediated iron acquisition for survival and virulence. Structural characterization underlines the hydroxamate moieties of Terramide A presumably supports its hypothesized role as a fungal siderophore, involving competitive iron sequestration and bacterial homeostasis. Subsequently, multi-omics investigation of susceptible strain AB19606 delineated a metabolic collapse cascade due to iron acquisition competition: (1) impairment of central metabolism and energy production through oxidative phosphorylation (OXPHO) inhibitions; (2) compromised stress adaptation and bacterial flexibility; (3) compensatory overactivation of siderophores biosynthesis and transportation, depleting metabolic intermediates and exacerbating stress; (4) coordinated suppression of virulence determinants, such as secretory systems and biofilm formation. These molecular derangements translated into phenotypic deficits, including quorum sensing, diminished autoinducer peptides production, and morphological/functional abnormalities. In vivo evaluation in a rat skin wound infection model further demonstrated that Terramide A promotes wound healing and mitigates inflammation, supporting its antibacterial efficacy. These findings establish Terramide A as a promising antibacterial agent and provide critical insights into iron-competitive antimicrobial strategies to exploit micro-nutrient deprivation and metabolic dysfunction. However, further research is needed to optimize the siderophore-based scaffold, clarify its mechanisms, and assess therapeutic potential.

A comprehensive update on the use of molecular topology applications for anti-infective drug discovery

INTRODUCTION

The rapid emergence of infectious diseases poses a significant threat to global economies and public health. To combat this, it is crucial to develop effective treatments. One essential tool in drug design is molecular topology, which uses topological indices to build QSAR models. This mathematical framework describes chemical compound structures, facilitating easy characterization.

AREAS COVERED

Classical ligand-based molecular topology has a series of limitations that can be overcome by shifting focus into structure-based approaches. Recent developments have emerged, focusing on target protein topology rather than drug molecules. Techniques like TDA, ESPH, LWPH, and molecular GDL are among the new methods being explored. This review is based on literature searches utilizing PubMed, Web of Science, and Google Scholar to identify articles published between the year 2000 and 2024.

EXPERT OPINION

The authors believe that it is time to move away from traditional molecular topology and toward innovative approaches and technologies. Shifting focus from ligand-based to structure-based molecular topology, combined with new databases and algorithms, can aid in fighting drug-resistant microorganisms. This shift opens a broader chemical space for developing new anti-infective drugs, ultimately improving public health outcomes.

Non-Membrane Active Peptide Resensitizes MRSA to β-Lactam Antibiotics and Inhibits S. aureus Virulence

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious global health threat due to its high morbidity and mortality rates, creating a dire need for novel therapeutic strategies. Antimicrobial peptides (AMPs), with broad-spectrum activity and low propensity for resistance development, show promise as effective antibiotic adjuvants to reverse multidrug-resistance in bacteria. Herein, it is uncovered that a potent and non-toxic AMP termed GN1 substantially resensitizes MRSA to multiple β-lactam antibiotics at low concentrations. Mechanistic studies indicate that GN1 functions by suppressing both the production and enzymatic activity of MRSA-associated resistance determinants, including penicillin-binding protein 2a (PBP2a) and β-lactamase. Additionally, GN1 exhibits a robust anti-virulence profile by inhibiting MRSA biofilm formation and staphyloxanthin production. Furthermore, GN1 induces bacterial metabolic perturbation, resulting in glutamate accumulation and oxidative damage. Importantly, the combination of GN1 with β-lactam antibiotics effectively mitigates MRSA-induced infections in the animal infection models. Collectively, these findings suggest that GN1 represents a potent β-lactam adjuvant and anti-virulence agent, offering a safe and versatile solution to combat MRSA infections.

Pyrimidine sufficiency is required for Sae two-component system signaling in Staphylococcus aureus

Nucleotide metabolism in pathogens is essential for their virulence, supporting growth, survival, and immune evasion during infection. Virulence in Staphylococcus aureus is driven by the production of virulence factors that facilitate nutrient acquisition and promote immune evasion and subversion. One key virulence regulatory system is the Sae two-component system (TCS), which upregulates the production of various virulence factors. The sensor histidine kinase SaeS, a member of the intramembrane family of histidine kinases (IM-HKs), lacks a signal-binding domain, leaving the mechanisms by which these HKs sense signals and regulate gene expression unclear. We report that de novo pyrimidine biosynthesis is essential for maintaining Sae activity. Disruption of genes involved in pyrimidine biosynthesis reduces Sae-dependent promoter activity under pyrimidine-limited conditions. Phos-tag electrophoresis confirmed that pyrimidine limitation impacts SaeS kinase activity. The effect of pyrimidine limitation on SaeS was abrogated in a strain producing only the catalytic domain, suggesting that pyrimidines regulate SaeS activity at the membrane. Additionally, defective pyrimidine biosynthesis caused membrane defects and increased incorporation of free fatty acids into the membrane. Further, providing an extracellular sink for free fatty acids restored Sae activity in these mutants. Our study highlights the interplay between nucleotide metabolism and membrane integrity in regulating virulence factor expression through signal transduction systems in pathogens.

Nanoenabling MbtI Inhibitors for Next-Generation Tuberculosis Therapy

The urgent need for safer and innovative antitubercular agents remains a priority for the scientific community. In pursuit of this goal, we designed and evaluated novel 5-phenylfuran-2-carboxylic acid derivatives targeting Mycobacterium tuberculosis (Mtb) salicylate synthase (MbtI), a key enzyme, absent in humans, that plays a crucial role in Mtb virulence. Several potent MbtI inhibitors demonstrating significant antitubercular activity and a favorable safety profile were identified. Structure-guided optimization yielded 5-(3-cyano-5-isobutoxyphenyl)furan-2-carboxylic acid (1e), which exhibited strong MbtI inhibition (IC50 = 11.2 μM) and a promising in vitro antitubercular activity (MIC99 = 32 μM against M. bovis BCG). Esters of 1e were effectively loaded into poly(2-methacryloyloxyethyl phosphorylcholine)-poly(2-(diisopropylamino)ethyl methacrylate) (PMPC-PDPA) polymersomes (POs) and delivered to intracellular mycobacteria, resulting in reduced Mtb viability. This study provides a foundation for the use of POs in the development of future MbtI-targeted therapies for tuberculosis.

Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research

In the fight against bacterial infections, particularly those caused by multi-resistant pathogens known as "superbugs", the need for new antibacterials is undoubted in scientific communities and is by now also widely perceived by the general population. However, the antibacterial research landscape has changed considerably over the past years. With few exceptions, the majority of big pharma companies has left the field and thus, the decline in R&D on antibacterials severely impacts the drug pipeline. In recent years, antibacterial research has increasingly relied on smaller companies or academic research institutions, which mostly have only limited financial resources, to carry a drug discovery and development process from the beginning and through to the beginning of clinical phases. This review formulates the requirements for an antibacterial in regard of targeted pathogens, resistance mechanisms and drug discovery. Strategies are shown for the discovery of new antibacterial structures originating from natural sources, by chemical synthesis and more recently from artificial intelligence approaches. This is complemented by principles for the computer-aided design of antibacterials and the refinement of a lead structure. The second part of the article comprises a compilation of antibacterial molecules classified according to bacterial target structures, e.g. cell wall synthesis, protein synthesis, as well as more recently emerging target classes, e.g. fatty acid synthesis, proteases and membrane proteins. Aspects of the origin, the antibacterial spectrum, resistance and the current development status of the presented drug molecules are highlighted.

Alisol A 24-Acetate combats Methicillin-Resistant Staphylococcus aureus infection by targeting the mevalonate biosynthesis

Infections caused by Methicillin-resistant Staphylococcus aureus (MRSA) have emerged as one of the most pressing global public health challenges. In concert with global rise of antimicrobial resistance at alarming rate, there is an urgent need for alternative strategies to combat MRSA. Here, the high throughput screening indicated that the Alisol A 24-acetate (AA) effectively inhibits the mevalonate (MVA) synthesis in MRSA. The mechanistic analysis revealed that AA competitively inhibits the 3-hydroxy-3-methyl glutaryl coenzyme A reductase (HMGR) protein to blockade the MVA pathway, thereby disrupting the bacterial membrane integrity and functions. Further investigations showed that this disruption consequently restores the β-lactam susceptibility in MRSA by retarding the expression of PBP2a protein and dampens the virulence of MRSA by reducing the exotoxins secretion. In addition to the effect on MRSA, AA has been found to exert host-acting activity to reduce the MRSA-induced inflammation. The promising anti-MRSA activity of AA was further confirmed in vivo. Collectively, the current study highlighted the potential of AA as a proposing drug for combating MRSA and emphasize the MVA pathway as an ideal therapeutic target for MRSA treatment.

Antibacterials with Novel Chemical Scaffolds in Clinical Development

The rise of antimicrobial resistance represents a significant global health threat, driven by the diminishing efficacy of existing antibiotics, a lack of novel antibacterials entering the market, and an over- or misuse of existing antibiotics, which accelerates the evolution of resistant bacterial strains. This review focuses on innovative therapies by highlighting 19 novel antibacterials in clinical development as of June 2024. These selected compounds are characterized by new chemical scaffolds, novel molecular targets, and/or unique mechanisms of action, which render their potential to break antimicrobial resistance particularly high. A detailed analysis of the scientific foundations behind each of these compounds is provided, including their pharmacodynamic profiles, current development state, and potential for overcoming existing limitations in antibiotic therapy. By presenting this subset of chemically novel antibacterials, the review highlights the ability to innovate in antibiotic drug development to counteract bacterial resistance and improve treatment outcomes.

Chemical dissection of bacterial virulence

The emergence of antibiotic-resistant bacteria has intensified the need for novel therapeutic strategies targeting bacterial virulence rather than growth or survival. Bacterial virulence involves complex processes that enable pathogens to invade and survive within host cells. Chemical biology has become a powerful tool for dissecting these virulence mechanisms at the molecular level. This review highlights key chemical biology approaches for studying bacterial virulence, focusing on four areas: 1) regulation of virulence, where chemoproteomics has identified small molecule-protein interactions that modulate virulence gene expression; 2) identification of virulence proteins, using techniques like unnatural amino acid incorporation and activity-based protein profiling (ABPP) to uncover proteins involved in infection; 3) post-translational modifications of host proteins, where chemical probes have revealed how bacterial effectors alter host cell processes; and 4) effector-host protein interactions, with methods such as bifunctional unnatural amino acid incorporation facilitating the discovery of key host targets manipulated by bacterial effectors. Collectively, these chemical tools are providing new insights into pathogen-host interactions, offering potential therapeutic avenues that aim to disarm pathogens and combat antibiotic resistance.

Progress of Photoantibiotics in Overcoming Antibiotic Resistance

Antibiotic resistance has emerged as a global public health crisis in the 21st century, leading to treatment failures. To address this issue, the medical and pharmaceutical sectors are confronted with two challenges: i) finding potent new antimicrobial agents that would work against resistant-pathogens, and ii) developing conceptually new or unconventional strategies by which a particular antibiotic would remain effective persistently. Photopharmacology with the aid of reversibly controllable light-active antibiotics that we call "photoantibiotics" shows great promise to meet the second challenge, which has inspired many research laboratories worldwide to align their research in inventing or developing such antibiotics. In this review, we have given an overview of the progress made over the last ten years or so towards developing such photoantibiotics. Although making such antibiotics that hold high antimicrobial potency like the native drugs and subsequently maintain a significant activity difference between light-irradiated and non-irradiated states is very challenging, the progress being reported here demonstrates the feasibility of various approaches to engineer photoantibiotics. This review provides a future perspective on the use of such antibiotics in clinical practice with the identification of potential problems and their solutions.

Frontiers in superbug management: innovating approaches to combat antimicrobial resistance

Anti-microbial resistance (AMR) is a global health issue causing significant mortality and economic burden. Pharmaceutical companies' discontinuation of research hinders new agents, while MDR pathogens or "superbugs" worsen the problem. Superbugs pose a threat to common infections and medical procedures, exacerbated by limited antibiotic development and rapid antibiotic resistance. The rising tide of antimicrobial resistance threatens to undermine progress in controlling infectious diseases. This review examines the global proliferation of AMR, its underlying mechanisms, and contributing factors. The study explores various methodologies, emphasizing the significance of precise and timely identification of resistant strains. We discuss recent advancements in CRISPR/Cas9, nanoparticle technology, light-based techniques, and AI-powered antibiogram analysis for combating AMR. Traditional methods often fail to effectively combat multidrug-resistant bacteria, as CRISPR-Cas9 technology offers a more effective approach by cutting specific DNA sequences, precision targeting and genome editing. AI-based smartphone applications for antibiogram analysis in resource-limited settings face challenges like internet connectivity, device compatibility, data quality, energy consumption, and algorithmic limitations. Additionally, light-based antimicrobial techniques are increasingly being used to effectively kill antibiotic-resistant microbial species and treat localized infections. This review provides an in-depth overview of AMR covering epidemiology, evolution, mechanisms, infection prevention, control measures, antibiotic access, stewardship, surveillance, challenges and emerging non-antibiotic therapeutic approaches.

An alternative approach to combat multidrug-resistant bacteria: new insights into traditional Chinese medicine monomers combined with antibiotics

Antibiotic treatment is crucial for controlling bacterial infections, but it is greatly hindered by the global prevalence of multidrug-resistant (MDR) bacteria. Although traditional Chinese medicine (TCM) monomers have shown high efficacy against MDR infections, the inactivation of bacteria induced by TCM is often incomplete and leads to infection relapse. The synergistic combination of TCM and antibiotics emerges as a promising strategy to mitigate the limitations inherent in both treatment modalities when independently administered. This review begins with a succinct exploration of the molecular mechanisms such as the antibiotic resistance, which informs the antibiotic discovery efforts. We subsequently provide an overview of the therapeutic effects of TCM/antibiotic combinations that have been developed. Finally, the factors that affect the therapeutic outcomes of these combinations and their underlying molecular mechanisms are systematically summarized. This overview offers insights into alternative strategies to treat clinical infections associated with MDR bacteria and the development of novel TCM/antibiotic combination therapies, with the goal of guiding their appropriate usage and further development.

Dual role of Baimao-Longdan-Congrong-Fang in inhibiting Staphylococcus aureus virulence factors and regulating TNF-α/TNFR1/NF-κB/MMP9 axis

BACKGROUND

Baimao-Longdan-Congrong-Fang (BLCF), a traditional Chinese herbal formula described in the Taiping Shenghui Fang (998 AD), consists of medicinal plants with heat-clearing and tonifying properties. BLCF has a promise as a treatment for Staphylococcus aureus (S. aureus) pneumonia, according to its historical use and current pharmacological research.

PURPOSE

In this study, the inhibitory effects of BLCF on S. aureus virulence factors were evaluated in vitro, and its mechanisms of action were investigated in a methicillin-resistant S. aureus (MRSA) pneumonia mouse model.

METHODS

The inhibitory effect of BLCF on S. aureus virulence factors, including sortase A (SrtA) and α-hemolysin (Hla), was investigated by fluorescence resonance energy transfer (FRET) and hemolysis assays. A C57BL/6J mouse model of MRSA pneumonia was employed to evaluate its therapeutic efficacy. Accordingly, an integrated strategy of medicinal chemistry, network pharmacology analysis, GEO database analysis, bioinformatics, molecular docking, molecular dynamics simulation, GeneMANIA-based functional association (GMFA), and GSEA was used to identify and illustrate potential therapeutic targets and mechanisms. Subsequently, the mechanistic results were confirmed by Western blot analysis and RT-qPCR.

RESULTS

While BLCF exhibited weak inhibitory activity against S. aureus USA300, Newman, and SA37 strains, it significantly suppressed SrtA-related virulence functions without affecting bacterial growth. FRET and hemolysis assays confirmed that BLCF inhibited SrtA activity (IC50 = 1.25 mg/mL) while decreasing hemolytic activity. Furthermore, BLCF protected mice from MRSA infection, increasing their survival rates. Bioinformatics analysis identified 26 active compounds and 2 hub genes (Tnf and Mmp9) that were associated with 5 types of immune cell, including activated CD4 T cells, myeloid-derived suppressor cells, activated dendritic cells, macrophages, and mast cells. Molecular docking revealed 3 active compounds (isoacteoside, verbascoside, and echinacoside) that exhibited strong binding affinities to TNF, MMP9, and SrtA. Molecular dynamics simulations validated the stable interactions between isoacteoside and the target proteins, yielding binding energies of -136.76 ± 8.83 kJ/mol, -174.98 ± 14.89 kJ/mol, and -186.34 ± 9.06 kJ/mol, respectively. The therapeutic effect of BLCF was closely linked to the NF-κB signaling pathway, as revealed by GMFA and GSEA analyses. In vivo, BLCF reduced lung bacterial load, improved the wet/dry ratio, and decreased inflammatory cytokines, thereby enhancing lung histopathology through modulation of the TNF-α/TNFR1/NF-κB/MMP9 axis.

CONCLUSIONS

BLCF can effectively treat MRSA pneumonia in mice by inhibiting SrtA activity, decreasing hemolytic activity, and regulating the TNF-α/TNFR1/NF-κB/MMP9 axis. These findings suggest BLCF, a traditional herbal formula, as a promising novel therapeutic approach to treat pneumonia.

A fucose-binding superlectin from Enterobacter cloacae with high Lewis and ABO blood group antigen specificity

Bacteria frequently employ carbohydrate-binding proteins, so-called lectins, to colonize and persist in a host. Thus, bacterial lectins are attractive targets for the development of new anti-infectives. To find new potential targets for anti-infectives against pathogenic bacteria, we searched for homologs of Pseudomonas aeruginosa lectins and identified homologs of LecA in Enterobacter species. Here, we recombinantly produced and biophysically characterized a homolog that comprises one LecA domain and one additional, novel protein domain. This protein was termed Enterobacter cloacae lectin A (EclA) and found to bind l-fucose. Glycan array analysis revealed a high specificity for the LewisA antigen and the type II H-antigen (blood group O) for EclA, while related antigens LewisX, Y, and B, as well as blood group A or B were not bound. We developed a competitive binding assay to quantify blood group antigen-binding specificity in solution. Finally, the crystal structure of EclA could be solved in complex with methyl α-l-selenofucoside. It revealed the unexpected binding of the carbohydrate ligand to the second domain, which comprises a novel fold that dimerizes via strand-swapping resulting in an intertwined beta sheet.

Multifaceted Antipathogenic Activity of Two Novel Natural Products, Chermesiterpenoid B and Chermesiterpenoid B Seco Acid Methyl Ester, Against Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen that causes both acute and chronic infections due to its virulence factors, biofilm formation and the ability to suppress the host immune system. Quorum sensing (QS) plays a key role in regulating these pathogenic traits and also downregulates the expression of peroxisome proliferator-activated receptor-γ (PPAR-γ) in host cells. In this study, we isolated two novel natural products from the jellyfish-derived fungus Penicillium chermesinum, chermesiterpenoid B (Che B) seco acid methyl ester (Che B ester) and Che B. Both compounds act as partial agonists of PPAR-γ and exhibit anti-QS activity. Che B ester and Che B were found to inhibit biofilm formation, reduce the production of proteases and decrease the infectivity of P. aeruginosa, all without affecting bacterial growth. In host cells, Che B ester and Che B reduced P. aeruginosa-induced inflammation by activating PPAR-γ. This multifaceted function makes these compounds promising candidates for developing new antipathogenic agents against bacterial infections with few side effects.

Novel inhibition of Staphylococcus aureus sortase A by plantamajoside: implications for controlling multidrug-resistant infections

In confronting the significant challenge posed by multidrug-resistant (MDR) pathogens, particularly methicillin-resistant Staphylococcus aureus (MRSA), the development of innovative anti-infective strategies is essential. Our research focuses on sortase A (SrtA), a vital enzyme for anchoring surface proteins in S. aureus. We discovered that plantamajoside (PMS), a phenylpropanoid glycoside extracted from Plantago asiatica L. (Plantaginaceae), acts as an effective and reversible inhibitor of SrtA, with a notable IC50 value of 22.93 µg/mL. This breakthrough provides a novel approach to combat both resistance and virulence in MRSA. PMS significantly inhibits S. aureus adhesion to fibrinogen, reducing biofilm formation and hindering the anchoring of staphylococcal protein A to the cell wall. Live-dead cell assays demonstrated increased survival rates in PMS-treated MRSA-infected A549 cells. Fluorescence quenching experiments revealed a robust interaction between PMS and SrtA, with mechanistic analyses pinpointing the critical R197 amino acid residue as the target site. In vivo, PMS was highly effective in a Galleria mellonella infection model, reducing mortality rates in MRSA-infected larvae. Additionally, PMS demonstrated therapeutic efficacy in a mouse pneumonia model, improved survival rates, reduced the bacterial load in pulmonary tissues, and mitigated lung damage. These results validate PMS as a promising compound to mitigate MRSA virulence and thwart resistance by targeting SrtA. This study highlights PMS as a leading candidate for controlling MRSA infections, showing the potential of targeting specific bacterial mechanisms in the fight against MDR infections.IMPORTANCEThe increasing issue of antibiotic resistance, particularly in methicillin-resistant Staphylococcus aureus (MRSA), demands innovative solutions. Our study presents plantamajoside (PMS) as a novel inhibitor of sortase A (SrtA), a key enzyme in S. aureus pathogenicity. By targeting SrtA, PMS shows promise in curbing the ability of MRSA to adhere, invade, and form biofilms, thereby reducing its virulence without exerting selective pressure for resistance. This research is significant because it introduces a potential new strategy in the antimicrobial arsenal, aligning with the global effort to combat drug-resistant infections. This study is crucial because it identifies a natural compound that can reduce the harmful effects of MRSA, a type of bacteria that is very hard to treat owing to resistance to many antibiotics. This discovery could lead to new treatments that are less likely to cause bacteria to become resistant, which is a major win in the fight against infections that are difficult to cure.

Multidrug-resistant Gram-negative bacterial infections

Multidrug-resistant Gram-negative bacterial infections cause significant morbidity and mortality globally. These pathogens easily acquire antimicrobial resistance (AMR), further highlighting their clinical significance. Third-generation cephalosporin-resistant and carbapenem-resistant Enterobacterales (eg, Escherichia coli and Klebsiella spp), multidrug-resistant Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii are the most problematic and have been identified as priority pathogens. In response, several new diagnostic technologies aimed at rapidly detecting AMR have been developed, including biochemical, molecular, genomic, and proteomic techniques. The last decade has also seen the licensing of multiple antibiotics that have changed the treatment landscape for these challenging infections.

Exploring nagZ as a virulence biomarker and treatment target in Enterobacter cloacae

BACKGROUND

Enterobacter cloacae is increasingly prevalent and resistant to multiple antibiotics, making it a significant pathogen in healthcare settings with high mortality rates. However, its pathogenic mechanisms are not fully understood.

RESULTS

In this study, we explored the role of nagZ in regulating the virulence of E. cloacae and its potential as a therapeutic target. Our research showed that pathogenic strains of E. cloacae express higher levels of nagZ than colonizing strains, particularly in simulated infection environments. Deleting nagZ significantly reduced E. cloacae virulence in various infection models, including Galleria mellonella larvae, mice, and RAW264.7 cells. Moreover, nagZ knockout decreased the bacterium's ability to induce inflammatory factor levels, while complementing nagZ in knockout strains partially rescued this ability. Importantly, the absence of nagZ also enhanced the antibacterial efficacy of ceftazidime against E. cloacae.

CONCLUSIONS

These findings underscore the crucial role of nagZ in E. cloacae pathogenesis and highlight its potential as a novel therapeutic target for treating infections caused by this pathogen.

VFDB 2025: an integrated resource for exploring anti-virulence compounds

With the escalating crisis of bacterial multidrug resistance, anti-virulence therapeutic strategies have emerged as a highly promising alternative to conventional antibiotic treatments. Anti-virulence compounds are specifically designed to target virulence factors (VFs), disarming pathogens without affecting bacterial growth and thus reduce the selective pressure for resistance development. However, due to the complexity of bacterial pathogenesis, no anti-virulence small molecules have been approved for clinical use thus far, despite the documentation of hundreds of potential candidates. To provide valuable reference resources for drug design, repurposing, and target selection, the virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has systematically collected public data on anti-virulence compounds through extensive literature mining, and further integrated this information with its existing knowledge of bacterial VFs. To date, the VFDB has curated a comprehensive dataset of 902 anti-virulence compounds across 17 superclasses reported by 262 studies worldwide. By cross-linking the current knowledge of bacterial VFs with information on relevant compounds (e.g. classification, chemical structure, molecular targets and mechanisms of action), the VFDB aims to bridge the gap between chemists and microbiologists, providing crucial insights for the development of innovative and effective antibacterial therapies to combat bacterial infections and address antibiotic resistance.

The association of dextran sodium sulfate to the bioactive agent I-modulia® attenuates Staphylococcus aureus virulence expression and δ-toxin production

As a part of the human skin commensal bacterial community, Staphylococcus aureus contributes to the host's immune system education. Nevertheless, it is also considered as an opportunistic pathogen involved in cutaneous infections or skin pathologies, in particular atopic dermatitis. To switch to a pathogenic behavior, S. aureus uses regulatory mechanisms to collectively produce virulence factors. Deprivation of these factors has emerged as a promising way to prevent or treat Staphylococcal diseases in facilitating the role of the immune system, while preserving the protective one of the commensal communities. This study focuses on the anti-virulent effect of dextran sodium sulfate (DSS) and I-modulia®, two natural products that have already proven their value in skincare. The anti-virulent capacity of DSS was first demonstrated by a dose-dependent inhibition of δ-toxin release, a virulence factor known to be a potent inducer of mast cell degranulation, on in vitro S. aureus cultures at high and low virulent states. A transcriptomic study was then implemented for a comprehensive overview of the anti-virulent impact. The results have shown the downregulation of many transcripts related to host immune evasion (scn, sbi), as well as exotoxins (α,γ-toxin) and adhesins production (map, emp), mostly under the control of SaeRS Two-Component System (TCS), one of the two major virulence regulators in S. aureus. Interestingly, genes related to secretion systems and the synthesis of exo-proteases were significantly downregulated when DSS was used in combination with I-modulia®. The repression of these genes was not previously observed and reflects a broader inhibitory action. We have also demonstrated that the inhibition of virulence factors didn't affect S. aureus viability. Our findings suggest that combining DSS and I-modulia® could be a promising therapeutic strategy to counteract microbial dysbiosis in the treatment of S. aureus skin pathologies in re-empowering the host's natural immune defenses.

A Phage-Based Approach to Identify Antivirulence Inhibitors of Bacterial Type IV Pili

The increasing threat of antibiotic resistance underscores the urgent need for innovative strategies to combat infectious diseases, including the development of antivirulants. Microbial pathogens rely on their virulence factors to initiate and sustain infections. Antivirulants are small molecules designed to target virulence factors, thereby attenuating the virulence of infectious microbes. The bacterial type IV pilus (T4P), an extracellular protein filament that depends on the T4P machinery (T4PM) for its biogenesis, dynamics and function, is a key virulence factor in many significant bacterial pathogens. While the T4PM presents a promising antivirulence target, the systematic identification of inhibitors for its multiple protein constituents remains a considerable challenge. Here we report a novel high-throughput screening (HTS) approach for discovering T4P inhibitors. It uses Pseudomonas aeruginosa, a high-priority pathogen, in combination with its T4P-targeting phage, φKMV. Screening of a library of 2168 compounds using an optimised protocol led to the identification of tuspetinib, based on its deterrence of the lysis of P. aeruginosa by φKMV. Our findings show that tuspetinib also inhibits two additional T4P-targeting phages, while having no effect on a phage that recognises lipopolysaccharides as its receptor. Additionally, tuspetinib impedes T4P-mediated motility in P. aeruginosa and Acinetobacter species without impacting growth or flagellar motility. This bacterium-phage pairing approach is applicable to a broad range of virulence factors that are required for phage infection, paving ways for the development of advanced chemotherapeutics against antibiotic-resistant infections.

Use of adjuvants to improve antibiotic efficacy and reduce the burden of antimicrobial resistance

INTRODUCTION

The increase in antibiotic resistance, together with the absence of novel antibiotics, makes mandatory the introduction of novel strategies to optimize the use of existing antibiotics. Among these strategies, the use of molecules that increase their activity looks promising.

AREAS COVERED

Different categories of adjuvants have been reviewed. Anti-resistance adjuvants increase the activity of antibiotics by inhibiting antibiotic resistance determinants. Anti-virulence approaches focus on the infection process itself; reducing virulence in combination with an antibiotic can improve therapeutic efficacy. Combination of phages with antibiotics can also be useful, since they present different mechanisms of action and targets. Finally, combining antibiotics with adjuvants in the same molecule may serve to improve antibiotics' efficacy and to overcome potential problems of differential pharmacokinetics/pharmacodynamics.

EXPERT OPINION

The successful combination of inhibitors of β-lactamases with β-lactams has shown that adjuvants can improve the efficacy of current antibiotics. In this sense, novel anti-resistance adjuvants able to inhibit efflux pumps are still needed, as well as anti-virulence compounds that improve the efficacy of antibiotics by interfering with the infection process. Although adjuvants may present different pharmacodynamics/pharmacokinetics than antibiotics, conjugates containing both compounds can solve this problem. Finally, already approved drugs can be a promising source of antibiotic adjuvants.

6-aryloxy-2-aminopyrimidine-benzonitrile hybrids as anti-infective agents: Synthesis, bioevaluation, and molecular docking

This report explores the potential of novel 6-aryloxy-2-aminopyrimidine-benzonitrile scaffolds as promising anti-infective agents in the face of the increasing threat of infectious diseases. Starting from 2-amino-4,6-dichloropyrimidine, a series of 24 compounds inspired from the antiviral drugs dapivirine, etravirine, and rilpivirine were designed and synthesized via a two-step reaction sequence in good yields. Biological testing of synthetic analogs revealed potent inhibition against both viral and tuberculosis targets. Notably, compounds 5p (2,4-dimethyl substitution; IC50 = 44 ± 4.9 µM; selectivity index [SI] = 20) and 5 s (3-thiophenphenyl; IC50 = 6 ± 1 µM; SI = 120) showed significant antiviral activity against pandemic influenza virus A/Puerto Rico/8/34 (H1N1) with positive toxicity profiles and also exhibited good IC50 values (5p, IC50 = 10 ± 2 µM; SI = 9 and 5 s, IC50 = 16 ± 2 µM; SI = 60) against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Wuhan strain) compared with favipiravir. In addition, analogs 5a, 5r, 5t, and 5u showed good antitubercular activity against Mycobacterium tuberculosis H37Rv strain and compounds 3, 5f, 5n, and 5q showed moderate antibacterial activity against gram+ve and gram-ve bacterial strains, suggesting that this scaffold has a broad spectrum of therapeutic effects.

Effect of leucine on mitochondria and oxidative stress to reduce virulence and pathogenicity of Acinetobacter baumannii

Elucidating the virulence mechanisms of A. baumannii is essential for developing strategies to mitigate pathogenicity. Although high-virulent strains are associated with increased mortality rate in severely infected patients, the underlying mechanisms remains not well understood. Our analysis revealed leucine as a pivotal biomarker, with the 11dP and paaK being significant contributors to virulence. The ATP-dependent activity and antioxidant activity were identified as the most important pathways in distinguishing the virulence of A. baumannii. Exogenous leucine was found to modulate mitochondria dysfunction and oxidative stress, thereby diminishing the pathogenicity of A. baumannii towards Beas 2B cells. Moreover, leucine reduced the virulence of A. baumannii to Galleria mellonella (G. mellonella) and alleviated pathological damage to lung tissues in mice. Our study offers a novel treatment strategy based on metabolomics, which may assist in the exploration and management of infections caused by highly virulent pathogens. It sets a new course for reducing the impact of highly virulent A. baumannii infections and has significant implications for the development of future therapeutic interventions.

Toward Mycobacterium tuberculosis Virulence Inhibition: Beyond Cell Wall

Mycobacterium tuberculosis (Mtb) is one of the most successful bacterial pathogens in human history. Even in the antibiotic era, Mtb is widespread and causes millions of new cases of tuberculosis each year. The ability to disrupt the host's innate and adaptive immunity, as well as natural persistence, complicates disease control. Tuberculosis traditional therapy involves the long-term use of several antibiotics. Treatment failures are often associated with the development of resistance to one or more drugs. The development of medicines that act on new targets will expand treatment options for tuberculosis caused by multidrug-resistant or extensively drug-resistant Mtb. Therefore, the development of drugs that target virulence factors is an attractive strategy. Such medicines do not have a direct bacteriostatic or bactericidal effect, but can disarm the pathogen so that the host immune system becomes able to eliminate it. Although cell wall-associated targets are being actively studied for anti-TB drug development, other virulence factors important for adaptation and host interaction are also worth comprehensive analysis. In this review, specific Mtb virulence factors (such as secreted phosphatases, regulatory systems, and the ESX-1 secretion system) are identified as promising targets for novel anti-virulence drug development. Additionally, models for the search of virulence inhibitors are discussed, such as virtual screening in silico, in vitro enzyme inhibition assay, the use of recombinant Mtb strains with reporter constructs, phenotypic analysis using in vitro cell infection models and specific environments.

Protocol for developing Pseudomonas aeruginosa type III secretion system-neutralizing monoclonal antibodies from human B cells

Monoclonal antibodies (mAbs) targeting bacterial virulence factors may represent promising therapeutics in the fight against severe bacterial infections. Here, we present an approach for developing human-derived antibodies targeting the type III secretion system (T3SS) of Pseudomonas aeruginosa (PA) by neutralizing the function of the T3SS-tip protein PcrV. The protocol involves identifying individuals with protective antibodies, isolating PcrV-specific B cells from these individuals, and producing and testing anti-PcrV mAbs derived from single B cells. For complete details on the use and execution of this protocol, please refer to Simonis et al.1.

Substrate-Based Ligand Design for Phenazine Biosynthesis Enzyme PhzF

The phenazine pyocyanin is an important virulence factor of the pathogen Pseudomonas aeruginosa, which is on the WHO list of antibiotic resistant "priority pathogens". In this study the isomerase PhzF, a key bacterial enzyme of the pyocyanin biosynthetic pathway, was investigated as a pathoblocker target. The aim of the pathoblocker strategy is to reduce the virulence of the pathogen without killing it, thus preventing the rapid development of resistance. Based on crystal structures of PhzF, derivatives of the inhibitor 3-hydroxyanthranilic acid were designed. Co-crystal structures of the synthesized derivatives with PhzF revealed spacial limitations of the binding pocket of PhzF in the closed conformation. In contrast, ligands aligned to the open conformation of PhzF provided more room for structural modifications. The intrinsic fluorescence of small 3-hydroxyanthranilic acid derivatives enabled direct affinity determinations using FRET assays. The analysis of structure-activity relationships showed that the carboxylic acid moiety is essential for binding to the target enzyme. The results of this study provide fundamental structural insights that will be useful for the design of PhzF-inhibitors.

Quercetin: a promising virulence inhibitor of Pseudomonas aeruginosa LasB in vitro

With the inappropriate use of antibiotics, antibiotic resistance has emerged as a major dilemma for patients infected with Pseudomonas aeruginosa. Elastase B (LasB), a crucial extracellular virulence factor secreted by P. aeruginosa, has been identified as a key target for antivirulence therapy. Quercetin, a natural flavonoid, exhibits promising potential as an antivirulence agent. We aim to evaluate the impact of quercetin on P. aeruginosa LasB and elucidate the underlying mechanism. Molecular docking and molecular dynamics simulation revealed a rather favorable intermolecular interaction between quercetin and LasB. At the sub-MICs of ≤256 μg/ml, quercetin was found to effectively inhibit the production and activity of LasB elastase, as well as downregulate the transcription level of the lasB gene in both PAO1 and clinical strains of P. aeruginosa. Through correlation analysis, significant positive correlations were shown between the virulence gene lasB and the QS system regulatory genes lasI, lasR, rhlI, and rhlR in clinical strains of P. aeruginosa. Then, we found the lasB gene expression and LasB activity were significantly deficient in PAO1 ΔlasI and ΔlasIΔrhlI mutants. In addition, quercetin significantly downregulated the expression levels of regulated genes lasI, lasR, rhlI, rhlR, pqsA, and pqsR as well as effectively attenuated the synthesis of signaling molecules 3-oxo-C12-HSL and C4-HSL in the QS system of PAO1. Quercetin was also able to compete with the natural ligands OdDHL, BHL, and PQS for binding to the receptor proteins LasR, RhlR, and PqsR, respectively, resulting in the formation of more stabilized complexes. Taken together, quercetin exhibits enormous potential in combating LasB production and activity by disrupting the QS system of P. aeruginosa in vitro, thereby offering an alternative approach for the antivirulence therapy of P. aeruginosa infections. KEY POINTS: • Quercetin diminished the content and activity of LasB elastase of P. aeruginosa. • Quercetin inhibited the QS system activity of P. aeruginosa. • Quercetin acted on LasB based on the QS system.

DA, Brinsmade SR. CodY controls the SaeR/S two-component system by modulating branched-chain fatty acid synthesis in Staphylococcus aureus

Staphylococcus aureus is a Gram-positive, opportunistic human pathogen that is a leading cause of skin and soft tissue infections and invasive disease worldwide. Virulence in this bacterium is tightly controlled by a network of regulatory factors. One such factor is the global regulatory protein CodY. CodY links branched-chain amino acid sufficiency to the production of surface-associated and secreted factors that facilitate immune evasion and subversion. Our previous work revealed that CodY regulates virulence factor gene expression indirectly in part by controlling the activity of the SaeRS two-component system (TCS). While this is correlated with an increase in membrane anteiso-15:0 and -17:0 branched-chain fatty acids (BCFAs) derived from isoleucine, the true mechanism of control has remained elusive. Herein, we report that CodY-dependent regulation of SaeS sensor kinase activity requires BCFA synthesis. During periods of nutrient sufficiency, BCFA synthesis and Sae TCS activity are kept relatively low by CodY-dependent repression of the ilv-leu operon and the isoleucine-specific permease gene brnQ2. In a codY null mutant, which simulates extreme nutrient limitation, de-repression of ilv-leu and brnQ2 directs the synthesis of enzymes in redundant de novo and import pathways to upregulate production of BCFA precursors. Overexpression of brnQ2, independent of CodY, is sufficient to increase membrane anteiso BCFAs, Sae-dependent promoter activity, and SaeR ~P levels. Our results further clarify the molecular mechanisms by which CodY controls virulence in S. aureus.IMPORTANCEExpression of bacterial virulence genes often correlates with the exhaustion of nutrients, but how the signaling of nutrient availability and the resulting physiological responses are coordinated is unclear. In S. aureus, CodY controls the activity of two major regulators of virulence-the Agr and Sae two-component systems (TCSs)-by unknown mechanisms. This work identifies a mechanism by which CodY controls the activity of the sensor kinase SaeS by modulating the levels of anteiso branched-chain amino acids that are incorporated into the membrane. Understanding the mechanism adds to our understanding of how bacterial physiology and metabolism are linked to virulence and underscores the role virulence in maintaining homeostasis. Understanding the mechanism also opens potential avenues for targeted therapeutic strategies against S. aureus infections.

Post-translational toxin modification by lactate controls Staphylococcus aureus virulence

Diverse post-translational modifications have been shown to play important roles in regulating protein function in eukaryotes. By contrast, the roles of post-translational modifications in bacteria are not so well understood, particularly as they relate to pathogenesis. Here, we demonstrate post-translational protein modification by covalent addition of lactate to lysine residues (lactylation) in the human pathogen Staphylococcus aureus. Lactylation is dependent on lactate concentration and specifically affects alpha-toxin, in which a single lactylated lysine is required for full activity and virulence in infection models. Given that lactate levels typically increase during infection, our results suggest that the pathogen can use protein lactylation as a mechanism to increase toxin-mediated virulence during infection.

Evaluation of LPRDA Pentapeptide for the Prevention and Treatment of Staphylococcus aureus Peritoneal Infection

Targeting virulence determinants is a promising approach to controlling S. aureus infections in the face of the global spread of antibiotic resistance. S. aureus-induced peritonitis often occurs in dialysis, implant and trauma patients. To develop novel prevention and treatment options for peritoneal infection, we investigated the oligopeptide sortase A inhibitor LPRDA as a non-conventional antibacterial that does not affect staphylococcal survival. Administration of LPRDA prior to S. aureus challenge reduced the bacterial load of internal organs and bacterial colonization of the abdominal cavity in animals. In addition, LPRDA inhibited α-hemolysin production in 80% of the 35 reference and clinical S. aureus strains tested. Consequent research of LPRDA interactions with cefazolin and vancomycin has demonstrated the potential for combined application of the antivirulent and antibiotic agents under study.

Compounds Derived from 5-Fluoropyridine and Benzo[b]thiophene: Killing Mycobacterium tuberculosis and Reducing its Virulence

The rise of drug-resistant Mycobacterium tuberculosis (Mtb) has extended the duration of tuberculosis (TB) treatment and reduced the likelihood of cure. One strategy to combat this issue is the development of inhibitors targeting the virulence factors of bacterial pathogens. Mtb' catalase (KatG) is crucial for its detoxification mechanisms and also serves as a significant virulence factor for the bacterium. In this study, twelve derivatives synthesized from 5-fluoropyridine and benzo[b]thiophene demonstrated antimycobacterial efficacy with minimum inhibitory concentrations (MICs) varying between 0.5 and 32 μg/mL. Compound 2, 1-(benzo[b]thiophen-2-ylmethylene) thiosemicarbazide, emerged as the most potent candidate. It effectively inhibited Mtb KatG, enhanced the production of reactive oxygen species (ROS) in Mtb, and achieved Mtb killing within 96 hours at a concentration of 2 μg/mL (4×MIC). Molecular docking simulations revealed that compound 2 binds tightly to the active site of Mtb-KatG with a docking score of 114, indicating that it may serve as a potent inhibitor of Mtb-KatG. The rabbit skin tuberculosis model was employed to assess the virulence of Mtb. Animal study results indicated that the granulomas induced by Mtb after treatment with compound 2 were reduced in size, exhibited a lower bacterial load, and the bacteria were no longer aggregated, in contrast to those caused by untreated Mtb. Hence, compound 2 can be regarded as a molecule capable of neutralizing the virulence factors of Mtb. This research offers insights into the design of anti-Mtb molecules with novel mechanisms of action.

Inhibition of Staphylococcus epidermidis and Pseudomonas aeruginosa biofilms by grape and rice agroindustrial residues

Agroindustrial wastes are generated daily and seem to be rich in bioactive molecules. Thus, they can potentially be used as source of compounds able to control bacterial biofilms. We investigated the potential of extracts from the residues of rice and grape to combat clinically important bacterial biofilms. Extracts of grape pomace and rice bran were obtained using different extractive methodologies and subjected to the evaluation of its antimicrobial and antibiofilm activities. After the in vivo toxicity, the chemical characterization of the most promising extract was assessed. The mass spectrometry analysis revealed the presence of dipeptides, alkaloids and phenolic compounds. Most grape extracts presented antibiofilm and antimicrobial activities against Staphylococcus epidermidis ATCC 35984 and Pseudomonas aeruginosa PA14. The hydromethanolic grape pomace extract obtained by ultrasound assisted extraction (MeOH 80 UAE) presented the most promising activity, being able to inhibit in 99 % and 80 % the biofilm formation of S. epidermidis and P. aeruginosa, respectively. Against the gram-negative model, this extract eradicated the biofilm by 80 %, induced the swarming motility and displayed a physical effect. It also did not present acute or chronic toxicity in Caenorhabditis elegans model. In this way, agroindustrial residues represent a promising source of molecules capable of controlling bacterial biofilms.

Ensemble Docking as a Tool for the Rational Design of Peptidomimetic Staphylococcus aureus Sortase A Inhibitors

Sortase A (SrtA) of Staphylococcus aureus has long been shown to be a relevant molecular target for antibacterial development. Moreover, the designed SrtA inhibitors act via the antivirulence mechanism, potentially causing less evolutional pressure and reduced antimicrobial resistance. However, no marketed drugs or even drug candidates have been reported until recently, despite numerous efforts in the field. SrtA has been shown to be a tough target for rational structure-based drug design (SBDD), which hampers the regular development of small-molecule inhibitors using the available arsenal of drug discovery tools. Recently, several oligopeptides resembling the sorting sequence LPxTG (Leu-Pro-Any-Thr-Gly) of the native substrates of SrtA were reported to be active in the micromolar range. Despite the good experimental design of those works, their molecular modeling parts are still not convincing enough to be used as a basis for a rational modification of peptidic inhibitors. In this work, we propose to use the ensemble docking approach, in which the relevant SrtA conformations are extracted from the molecular dynamics simulation of the LPRDA (Leu-Pro-Arg-Asp-Ala)-SrtA complex, to effectively represent the most significant and diverse target conformations. The developed protocol is shown to describe the known experimental data well and then is applied to a series of new peptidomimetic molecules resembling the active oligopeptide structures reported previously in order to prioritize structures from this work for further synthesis and activity testing. The proposed approach is compared to existing alternatives, and further directions for its development are outlined.

Identification of small molecule inhibitors of the Chloracidobacterium thermophilum type IV pilus protein PilB by ensemble virtual screening

Antivirulence strategy has been explored as an alternative to traditional antibiotic development. The bacterial type IV pilus is a virulence factor involved in host invasion and colonization in many antibiotic resistant pathogens. The PilB ATPase hydrolyzes ATP to drive the assembly of the pilus filament from pilin subunits. We evaluated Chloracidobacterium thermophilum PilB (CtPilB) as a model for structure-based virtual screening by molecular docking and molecular dynamics (MD) simulations. A hexameric structure of CtPilB was generated through homology modeling based on an existing crystal structure of a PilB from Geobacter metallireducens. Four representative structures were obtained from molecular dynamics simulations to examine the conformational plasticity of PilB and improve docking analyses by ensemble docking. Structural analyses after 1 μs of simulation revealed conformational changes in individual PilB subunits are dependent on ligand presence. Further, ensemble virtual screening of a library of 4234 compounds retrieved from the ZINC15 database identified five promising PilB inhibitors. Molecular docking and binding analyses using the four representative structures from MD simulations revealed that top-ranked compounds interact with multiple Walker A residues, one Asp-box residue, and one arginine finger, indicating these are key residues in inhibitor binding within the ATP binding pocket. The use of multiple conformations in molecular screening can provide greater insight into compound flexibility within receptor sites and better inform future drug development for therapeutics targeting the type IV pilus assembly ATPase.

Napthalimide-based nuclease inhibitor: A multifunctional therapeutic material to bolster MRSA uptake by macrophage-like cells and mitigate pathogen adhesion on orthopaedic implant

The healthcare burden rendered by methicillin-resistant Staphylococcus aureus (MRSA) warrants the development of therapeutics that offer a distinct benefit in the clinics as compared to conventional antibiotics. The present study describes the potential of napthalimide-based synthetic ligands (C1-C3) as inhibitors of the staphylococcal nuclease known as micrococcal nuclease (MNase), a key virulence factor of the pathogen. Amongst the ligands, the most potent MNase inhibitor C1 rendered non-competitive inhibition, reduced MNase turnover number (Kcat) and catalytic efficiency (Kcat/Km) with an IC50 value of ~950 nM. CD spectroscopy suggested distortion of MNase conformation in presence of C1. Flow cytometry and confocal microscopy indicated that C1 restored the ability of activated THP-1 cells to engulf DNA-entrapped MRSA cells. Interestingly, C1 could inhibit MRSA adhesion onto collagen. For potential application, C1-loaded pluronic F-127 micellar nanocarrier (C1-PMC) was generated, wherein the anti-adhesion activity of the pluronic carrier (PMC) and C1 was harnessed in tandem to deter MRSA cell adhesion onto collagen. MRSA biofilm formation was hindered on C1-PMC-coated titanium (Ti) wire, while eluates from C1-PMC-coated Ti wires were non-toxic to HEK 293, MG-63 and THP-1 cells. The multifunctional C1 provides a blueprint for designing therapeutic materials that hold translational potential for mitigation of MRSA infections.

Chemical-mediated virulence: the effects of host chemicals on microbial virulence and potential new antivirulence strategies

The rising antimicrobial resistance rates and declining antimicrobial discovery necessitate alternative strategies to combat multidrug-resistant pathogens. Targeting microbial virulence is an emerging area of interest. Traditionally, virulence factors were largely restricted to bacteria-derived toxins, adhesins, capsules, quorum sensing systems, secretion systems, factors required to sense, respond to, acquire, or synthesize, and utilize trace elements (such as iron and other metals) and micronutrients (such as vitamins), and other factors bacteria use to establish infection, form biofilms, or damage the host tissues and regulatory elements thereof. However, this traditional definition overlooks bacterial virulence that may be induced or influenced by host-produced metabolites or other chemicals that bacteria may encounter at the infection site. This review will discuss virulence from a non-traditional perspective, shedding light on chemical-mediated host-pathogen interactions and outlining currently available mechanistic insight into increased bacterial virulence in response to host factors. This review aims to define a possibly underestimated theme of chemically mediated host-pathogen interactions and encourage future validation and characterization of the contribution of host chemicals to microbial virulence in vivo. From this perspective, we discuss proposed antivirulence compounds and suggest new potential targets for antimicrobials that prevent chemical-mediated virulence. We also explore proposed host-targeting therapeutics reducing the level of host chemicals that induce microbial virulence, serving as virulence attenuators. Understanding the host chemical-mediated virulence may enable new antimicrobial solutions to fight multidrug-resistant pathogens.

Structure-Activity Relationship of Inositol Thiophosphate Analogs as Allosteric Activators of Clostridioides difficile Toxin B

Clostridioides difficile is a bacterium that causes life-threatening intestinal infections. Infection symptoms are mediated by a toxin secreted by the bacterium. Toxin pathogenesis is modulated by the intracellular molecule, inositol-hexakisphosphate (IP6). IP6 binds to a cysteine protease domain (CPD) on the toxin, inducing autoproteolysis, which liberates a virulence factor in the cell cytosol. We developed second-generation IP6 analogs designed to induce autoproteolysis in the gut lumen, prior to toxin uptake, circumventing pathogenesis. We synthesized a panel of thiophosphate-/sulfate-containing IP6 analogs and characterized their toxin binding affinity, autoproteolysis induction, and cation interactions. Our top candidate was soluble in extracellular cation concentrations, unlike IP6. The IP6 analogs were more negatively charged than IP6, which improved affinity and stabilization of the CPD, enhancing toxin autoproteolysis. Our data illustrate the optimization of IP6 with thiophosphate biomimetic which are more capable of inducing toxin autoproteolysis than the native ligand, warranting further studies in vivo.