A peptide based on homologous sequences of the β-barrel assembly machinery component BamD potentiates antibiotic susceptibility of Pseudomonas aeruginosa

Inhibitors targeting BamA in gram-negative bacteria

Antibiotic resistance has led to an increase in the number of patient hospitalizations and deaths. The situation for gram-negative bacteria is especially dire as the last new class of antibiotics active against these bacteria was introduced to the clinic over 60 years ago, thus there is an immediate unmet need for new antibiotic classes able to overcome resistance. The outer membrane, a unique and essential structure in gram-negative bacteria, contains multiple potential antibacterial targets including BamA, an outer membrane protein that folds and inserts transmembrane β-barrel proteins. BamA is essential and conserved, and its outer membrane location eliminates a barrier that molecules must overcome to access this target. Recently, antibacterial small molecules, natural products, peptides, and antibodies that inhibit BamA activity have been reported, validating the druggability of this target and generating potential leads for antibiotic development. This review will describe these BamA inhibitors, highlight their key attributes, and identify challenges with this potential target.

Drug Binding to BamA Targets Its Lateral Gate

BamA, the core component of the β-barrel assembly machinery (BAM) complex, is an outer-membrane protein (OMP) in Gram-negative bacteria. Its function is to insert and fold substrate OMPs into the outer membrane (OM). Evidence suggests that BamA follows the asymmetric hybrid-barrel model where the first and last strands of BamA separate, a process known as lateral gate opening, to allow nascent substrate OMP β-strands to sequentially insert and fold through β-augmentation. Recently, multiple lead compounds that interfere with BamA's function have been identified. We modeled and then docked one of these compounds into either the extracellular loops of BamA or the open lateral gate. With the compound docked in the loops, we found that the lateral gate remains closed during 5 μs molecular dynamics simulations. The same compound when docked in the open lateral gate stays bound to the β16 strand of BamA during the simulation, which would prevent substrate OMP folding. In addition, we simulated mutants of BamA that are resistant to one or more of the identified lead compounds. In these simulations, we observed a differing degree and/or frequency of opening of BamA's lateral gate compared to BamA-apo, suggesting that the mutations grant resistance by altering the dynamics at the gate. We conclude that the compounds act by inhibiting BamA lateral gate opening and/or binding of substrate, thus preventing subsequent OMP folding and insertion.

Siderophore conjugation with cleavable linkers boosts the potency of RNA polymerase inhibitors against multidrug-resistant E. coli

The growing antibiotic resistance, foremost in Gram-negative bacteria, requires novel therapeutic approaches. We aimed to enhance the potency of well-established antibiotics targeting the RNA polymerase (RNAP) by utilizing the microbial iron transport machinery to improve drug translocation across their cell membrane. As covalent modifications resulted in moderate-low antibiotic activity, cleavable linkers were designed that permit a release of the antibiotic payload inside the bacteria and unperturbed target binding. A panel of ten cleavable siderophore-ciprofloxacin conjugates with systematic variation at the chelator and the linker moiety was used to identify the quinone trimethyl lock in conjugates 8 and 12 as the superior linker system, displaying minimal inhibitory concentrations (MICs) of ≤1 μM. Then, rifamycins, sorangicin A and corallopyronin A, representatives of three structurally and mechanistically different natural product RNAP inhibitor classes, were conjugated via the quinone linker to hexadentate hydroxamate and catecholate siderophores in 15-19 synthetic steps. MIC assays revealed an up to 32-fold increase in antibiotic activity against multidrug-resistant E. coli for conjugates such as 24 or 29 compared to free rifamycin. Experiments with knockout mutants in the transport system showed that translocation and antibiotic effects were conferred by several outer membrane receptors, whose coupling to the TonB protein was essential for activity. A functional release mechanism was demonstrated analytically by enzyme assays in vitro, and a combination of subcellular fractionation and quantitative mass spectrometry proved cellular uptake of the conjugate, release of the antibiotic, and its increased accumulation in the cytosol of bacteria. The study demonstrates how the potency of existing antibiotics against resistant Gram-negative pathogens can be boosted by adding functions for active transport and intracellular release.

β-Barrel Assembly Machinery (BAM) Complex as Novel Antibacterial Drug Target

The outer membrane of Gram-negative bacteria is closely related to the pathogenicity and drug resistance of bacteria. Outer membrane proteins (OMPs) are a class of proteins with important biological functions on the outer membrane. The β-barrel assembly machinery (BAM) complex plays a key role in OMP biogenesis, which ensures that the OMP is inserted into the outer membrane in a correct folding manner and performs nutrient uptake, antibiotic resistance, cell adhesion, cell signaling, and maintenance of membrane stability and other functions. The BAM complex is highly conserved among Gram-negative bacteria. The abnormality of the BAM complex will lead to the obstruction of OMP folding, affect the function of the outer membrane, and eventually lead to bacterial death. In view of the important role of the BAM complex in OMP biogenesis, the BAM complex has become an attractive target for the development of new antibacterial drugs against Gram-negative bacteria. Here, we summarize the structure and function of the BAM complex and review the latest research progress of antibacterial drugs targeting BAM in order to provide a new perspective for the development of antibiotics.

Targeting BAM for Novel Therapeutics against Pathogenic Gram-Negative Bacteria

The growing emergence of multidrug resistance in bacterial pathogens is an immediate threat to human health worldwide. Unfortunately, there has not been a matching increase in the discovery of new antibiotics to combat this alarming trend. Novel contemporary approaches aimed at antibiotic discovery against Gram-negative bacterial pathogens have expanded focus to also include essential surface-exposed receptors and protein complexes, which have classically been targeted for vaccine development. One surface-exposed protein complex that has gained recent attention is the β-barrel assembly machinery (BAM), which is conserved and essential across all Gram-negative bacteria. BAM is responsible for the biogenesis of β-barrel outer membrane proteins (β-OMPs) into the outer membrane. These β-OMPs serve essential roles for the cell including nutrient uptake, signaling, and adhesion, but can also serve as virulence factors mediating pathogenesis. The mechanism for how BAM mediates β-OMP biogenesis is known to be dynamic and complex, offering multiple modes for inhibition by small molecules and targeting by larger biologics. In this review, we introduce BAM and establish why it is a promising and exciting new therapeutic target and present recent studies reporting novel compounds and vaccines targeting BAM across various bacteria. These reports have fueled ongoing and future research on BAM and have boosted interest in BAM for its therapeutic promise in combatting multidrug resistance in Gram-negative bacterial pathogens.

Uniform, Length-Tunable Antibacterial 1D Diblock Copolymer Nanofibers

The rapid increase in antibiotic resistant strains of bacteria has led to an urgent need to develop new methods of treating bacterial infections. Antibacterial polymeric nanoparticles are of interest for...

Combining Cell Envelope Stress Reporter Assays in a Screening Approach to Identify BAM Complex Inhibitors

The development of new antibiotics is particularly problematic in Gram-negative bacteria due to the presence of the outer membrane (OM), which serves as a permeability barrier. Recently, the β-barrel assembly machine (BAM), located in the OM and responsible for β-barrel type OM protein (OMP) assembly, has been validated as a novel target for antibiotics. Here, we identified potential BAM complex inhibitors using a screening approach that reports on cell envelope σE and Rcs stress in Escherichia coli. Screening a library consisting of 316 953 compounds yielded five compounds that induced σE and Rcs stress responses, while not inducing the intracellular heat-shock response. Two of the five compounds (compounds 2 and 14) showed the characteristics of known BAM complex inhibitors: synergy with OMP biogenesis mutants, decrease in the abundance of various OMPs, and loss of OM integrity. Importantly, compound 2 also inhibited BAM-dependent OMP folding in an in vitro refolding assay using purified BAM complex reconstituted in proteoliposomes.

Modulators of protein-protein interactions as antimicrobial agents

Protein-Protein interactions (PPIs) are involved in a myriad of cellular processes in all living organisms and the modulation of PPIs is already under investigation for the development of new drugs targeting cancers, autoimmune diseases and viruses. PPIs are also involved in the regulation of vital functions in bacteria and, therefore, targeting bacterial PPIs offers an attractive strategy for the development of antibiotics with novel modes of action. The latter are urgently needed to tackle multidrug-resistant and multidrug-tolerant bacteria. In this review, we describe recent developments in the modulation of PPIs in pathogenic bacteria for antibiotic development, including advanced small molecule and peptide inhibitors acting on bacterial PPIs involved in division, replication and transcription, outer membrane protein biogenesis, with an additional focus on toxin-antitoxin systems as upcoming drug targets.

Pseudomonas aeruginosa Presents Multiple Vital Changes in Its Proteome in the Presence of 3-Hydroxyphenylacetic Acid, a Promising Antimicrobial Agent

Pseudomonas aeruginosa, a widely distributed opportunistic pathogen, is an important threat to human health for causing serious infections worldwide. Due to its antibiotic resistance and virulence factors, it is so difficult to combat this bacterium; thus, new antimicrobial agents are in search. 3-Hydroxyphenylacetic acid (3-HPAA), which is a phenolic acid mostly found in olive oil wastewater, can be a promising candidate with its dose-dependent antimicrobial properties. Elucidating the molecular mechanism of action is crucial for future examinations and the presentation of 3-HPAA as a new agent. In this study, the antimicrobial activity of 3-HPAA on P. aeruginosa and its action mechanism was investigated via shot-gun proteomics. The data, which are available via ProteomeXchange with identifier PXD016243, were examined by STRING analysis to determine the interaction networks of proteins. KEGG Pathway enrichment analysis via the DAVID bioinformatics tool was also performed to investigate the metabolic pathways that undetected and newly detected groups of the proteins. The results displayed remarkable changes after 3-HPAA exposure in the protein profile of P. aeruginosa related to DNA replication and repair, RNA modifications, ribosomes and proteins, cell envelope, oxidative stress, as well as nutrient availability. 3-HPAA showed its antimicrobial action on P. aeruginosa by affecting multiple bacterial processes; hence, it could be categorized as a multitarget antimicrobial agent.

Inhibition of autotransporter biogenesis by small molecules

Disarming pathogens by targeting virulence factors is a promising alternative to classic antibiotics. Many virulence factors in Gram-negative bacteria are secreted via the autotransporter (AT) pathway, also known as Type 5 secretion. These factors are secreted with the assistance of two membrane-based protein complexes: Sec and Bam. To identify inhibitors of the AT pathway, we used transcriptomics analysis to develop a fluorescence-based high-throughput assay that reports on the stress induced by the model AT hemoglobin protease (Hbp) when its secretion across the outer membrane is inhibited. Screening a library of 1600 fragments yielded the compound VUF15259 that provokes cell envelope stress and secretion inhibition of the ATs Hbp and Antigen-43. VUF15259 also impairs β-barrel folding activity of various outer membrane proteins. Furthermore, we found that mutants that are compromised in outer membrane protein biogenesis are more susceptible to VUF15259. Finally, VUF15259 induces the release of vesicles that appear to assemble in short chains. Taken together, VUF15259 is the first reported compound that inhibits AT secretion and our data are mostly consistent with VUF15259 interfering with the Bam-complex as potential mode of action. The validation of the presented assay incites its use to screen larger compound libraries with drug-like compounds.

Biogenesis and function of the autotransporter adhesins YadA, intimin and invasin

Bacteria often express numerous virulence factors. These virulence factors make them successful pathogens, by e.g. mediating attachment to host cells and thereby facilitating persistence or invasion, or by contributing to the evasion of the host immune system to allow proliferation and spread within the host and in the environment. The site of first contact of Gram negative bacteria with the host is the bacterial outer membrane (OM). Consisting of an asymmetrical lipid bilayer with phospholipids forming the inner, and lipopolysaccharides forming the outer leaflet, the OM harbors numerous integral membrane proteins that are almost exclusively β-barrel proteins. One distinct family of OM β-barrel proteins strongly linked to bacterial virulence are the autotransporter (AT) proteins. During the last years huge progress has been made to better understand the mechanisms underlying the insertion of AT proteins into the OM and also AT function for interaction with the host. This review shortly summarizes our current knowledge about outer membrane protein (OMP) and more specifically AT biogenesis and function. We focused on the AT proteins that we haved studied in most detail: i.e. the Yersinia adhesin A (YadA) and invasin of Yersinia enterocolitica (Ye) as well as its homolog intimin (Int) expressed by enteropathogenic Escherichia coli. In addition, this review provides a short outlook about how we could possibly use this knowledge to fight infection.

Lectin-Like Bacteriocins

Bacteria produce a diverse array of antagonistic compounds to restrict growth of microbial rivals. Contributing to this warfare are bacteriocins: secreted antibacterial peptides, proteins and multi-protein complexes. These compounds typically eliminate competitors closely related to the producer. Lectin-like bacteriocins (LlpAs) constitute a distinct class of such proteins, produced by Pseudomonas as well as some other proteobacterial genera. LlpAs share a common architecture consisting of two B-lectin domains, followed by a short carboxy-terminal extension. Two surface-exposed moieties on susceptible Pseudomonas cells are targeted by the respective lectin modules. The carboxy-terminal domain binds D-rhamnose residues present in the lipopolysaccharide layer, whereas the amino-terminal domain interacts with a polymorphic external loop of the outer-membrane protein insertase BamA, hence determining selectivity. The absence of a toxin-immunity module as found in modular bacteriocins and other polymorphic toxin systems, hints toward a novel mode of killing initiated at the cellular surface, not requiring bacteriocin import. Despite significant progress in understanding the function of LlpAs, outstanding questions include the secretion machinery recruited by lectin-like bacteriocins for their release, as well as a better understanding of the environmental signals initiating their expression.

Hitting with a BAM: Selective Killing by Lectin-Like Bacteriocins

Lectin-like bacteriocins (LlpAs) are secreted by proteobacteria and selectively kill strains of their own or related species, and they are composed of two B-lectin domains with divergent sequences. In Pseudomonas spp., initial binding of these antibacterial proteins to cells is mediated by the carboxy-terminal domain through d-rhamnose residues present in the common polysaccharide antigen of their lipopolysaccharide, whereas the amino-terminal domain accounts for strain selectivity of killing. Here, we show that spontaneous LlpA-resistant mutants carry mutations in one of three surface-exposed moieties of the essential β-barrel outer membrane protein insertase BamA, the core component of the BAM complex. Polymorphism of this loop in different Pseudomonas groups is linked to LlpA susceptibility, and targeted cells all share the same signature motif in this loop. Since heterologous expression of such a bamA gene confers LlpA susceptibility upon a resistant strain, BamA represents the primary bacteriocin selectivity determinant in pseudomonads. Contrary to modular bacteriocins that require uptake via the Tol or Ton system, parasitism of BamA as an LlpA receptor advocates a novel bacteriocin killing mechanism initiated by impairment of the BAM machinery.

Bacteria secrete a variety of molecules to eliminate microbial rivals. Bacteriocins are a pivotal group of peptides and proteins that assist in this fight, specifically killing related bacteria. In Gram-negative bacteria, these antibacterial proteins often comprise distinct domains for initial binding to a target cell’s surface and subsequent killing via enzymatic or pore-forming activity. Here, we show that lectin-like bacteriocins, a family of bacteriocins that lack the prototypical modular toxin architecture, also stand out by parasitizing BamA, the core component of the outer membrane protein assembly machinery. A particular surface-exposed loop of BamA, critical for its function, serves as a key discriminant for cellular recognition, and polymorphisms in this loop determine whether a strain is susceptible or immune to a particular bacteriocin. These findings suggest a novel mechanism of contact-dependent killing that does not require cellular uptake. The evolutionary advantage of piracy of an essential cellular compound is highlighted by the observation that contact-dependent growth inhibition, a distinct antagonistic system, can equally take advantage of this receptor.

Proteomic Analysis of Alterations in Aeromonas hydrophila Outer Membrane Proteins in Response to Oxytetracycline Stress

In Gram-negative bacteria, the outer membrane proteins (OMPs) perform a crucial role in antibiotic resistance, but it is largely unknown how they behave in response to antibiotic stress. In this study, we treated Aeromonas hydrophila with two different doses of oxytetracycline (OXY) to induce antibiotic stress. Proteins were isolated from sarcosine-insoluble fractions and quantitatively examined by using tandem mass tag labeling-based mass spectrometry to identify differentially expressed proteins. As a result, we identified 125 differential proteins in the 5 μg/ml OXY treatment group, including 20 OMPs, and 150 proteins from the 10 μg/ml OXY group, including 22 OMPs. Gene ontology analysis showed that translation-related proteins, including 30S and 50S ribosome proteins, were significantly enriched in increasing abundance under OXY stress; whereas the downregulated proteins were associated with the transport process, such as maltodextrin, maltose, and oligosaccharide transport. We then validated a subset of the identified differential proteins by using Western blot and quantitative polymerase chain reaction analyses. Finally, the quantitative real-time PCR (qPCR) results showed that at the transcription level, the expression of five OMP genes, including AHA_1280 (protein name A0KHS0), AHA_1281 (A0KHS1), AHA_1447 (A0KI84, BamE), AHA_1861 (A0KJE1), and AHA_2766 (A0KLX3), and one lipoprotein gene AHA_1740 (A0KJ25) was consistent with proteomic results under 5 and 10 μg/ml OXY treatment, respectively. In addition, the Western blotting also demonstrated that two altered OMP proteins A0KHS1 and A0KHH2 were upregulated for both OXY treatment groups. This study indicates that bacteria regulate the expression levels of OMPs in response to antibiotic stress and further contribute to our understanding of the functions of OMPs in antibiotic resistance. Moreover, our results suggest that the upregulation of translation and downregulation of the transport process may affect bacterial fitness during OXY stress. These findings may provide new clues to the antibiotic resistance mechanism in A. hydrophila.

Discovery of Next-Generation Antimicrobials through Bacterial Self-Screening of Surface-Displayed Peptide Libraries

Peptides have great potential to combat antibiotic resistance. While many platforms can screen peptides for their ability to bind to target cells, there are virtually no platforms that directly assess the functionality of peptides. This limitation is exacerbated when identifying antimicrobial peptides because the phenotype, death, selects against itself and has caused a scientific bottleneck that confines research to a few naturally occurring classes of antimicrobial peptides. We have used this seeming dissonance to develop Surface Localized Antimicrobial Display (SLAY), a platform that allows screening of unlimited numbers of peptides of any length, composition, and structure in a single tube for antimicrobial activity. Using SLAY, we screened ∼800,000 random peptide sequences for antimicrobial function and identified thousands of active sequences, dramatically increasing the number of known antimicrobial sequences. SLAY hits present with different potential mechanisms of peptide action and access to areas of antimicrobial physicochemical space beyond what nature has evolved. VIDEO ABSTRACT.

A Genetic Screen Reveals Novel Targets to Render Pseudomonas aeruginosa Sensitive to Lysozyme and Cell Wall-Targeting Antibiotics

Pseudomonas aeruginosa is capable of establishing airway infections. Human airway mucus contains a large amount of lysozyme, which hydrolyzes bacterial cell walls. P. aeruginosa, however, is known to be resistant to lysozyme. Here, we performed a genetic screen using a mutant library of PAO1, a prototype P. aeruginosa strain, and identified two mutants (ΔbamB and ΔfabY) that exhibited decrease in survival after lysozyme treatment. The bamB and fabY genes encode an outer membrane assembly protein and a fatty acid synthesis enzyme, respectively. These two mutants displayed retarded growth in the airway mucus secretion (AMS). In addition, these mutants exhibited reduced virulence and compromised survival fitness in two different in vivo infection models. The mutants also showed susceptibility to several antibiotics. Especially, ΔbamB mutant was very sensitive to vancomycin, ampicillin, and ceftazidime that target cell wall synthesis. The ΔfabY displayed compromised membrane integrity. In conclusion, this study uncovered a common aspect of two different P. aeruginosa mutants with pleiotropic phenotypes, and suggests that BamB and FabY could be novel potential drug targets for the treatment of P. aeruginosa infection.

Drug discovery strategies to outer membrane targets in Gram-negative pathogens

This review will cover selected recent examples of drug discovery strategies which target the outer membrane (OM) of Gram-negative bacteria either by disruption of outer membrane function or by inhibition of essential gene products necessary for outer membrane assembly. Significant advances in pathway elucidation, structural biology and molecular inhibitor designs have created new opportunities for drug discovery within this target-class space.

The cell wall amidase AmiB is essential for Pseudomonas aeruginosa cell division, drug resistance and viability

The physiological function of cell wall amidases has been investigated in several proteobacterial species. In all cases, they have been implicated in the cleavage of cell wall material synthesized by the cytokinetic ring. Although typically non-essential, this activity is critical for daughter cell separation and outer membrane invagination during division. In Escherichia coli, proteins with LytM domains also participate in cell separation by stimulating amidase activity. Here, we investigated the function of amidases and LytM proteins in the opportunistic pathogen Pseudomonas aeruginosa. In agreement with studies in other organisms, (Pa) AmiB and three LytM proteins were found to play crucial roles in P. aeruginosa cell separation, envelope integrity and antibiotic resistance. Importantly, the phenotype of amidase-defective P. aeruginosa cells also differed in informative ways from the E. coli paradigm; (Pa) AmiB was found to be essential for viability and the successful completion of cell constriction. Our results thus reveal a key role for amidase activity in cytokinetic ring contraction. Furthermore, we show that the essential function of (Pa) AmiB can be bypassed in mutants activated for a Cpx-like envelope stress response, suggesting that this signaling system may elicit the repair of division machinery defects in addition to general envelope damage.