Small Molecule Anti-biofilm Agents Developed on the Basis of Mechanistic Understanding of Biofilm Formation

Antimicrobial Peptides Derived From Insects Offer a Novel Therapeutic Option to Combat Biofilm: A Review

Biofilms form a complex layer with defined structures, that attach on biotic or abiotic surfaces, are tough to eradicate and tend to cause some resistance against most antibiotics. Several studies confirmed that biofilm-producing bacteria exhibit higher resistance compared to the planktonic form of the same species. Antibiotic resistance factors are well understood in planktonic bacteria which is not so in case of biofilm producing forms. This may be due to the lack of available drugs with known resistance mechanisms for biofilms. Existing antibiotics cannot eradicate most biofilms, especially of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). Insects produce complex and diverse set of chemicals for survival and defense. Antimicrobial peptides (AMPs), produced by most insects, generally have a broad spectrum of activity and the potential to bypass the resistance mechanisms of classical antibiotics. Besides, AMPs may well act synergistically with classical antibiotics for a double-pronged attack on infections. Thus, AMPs could be promising alternatives to overcome medically important biofilms, decrease the possibility of acquired resistance and treatment of multidrug-resistant pathogens including ESKAPE. The present review focuses on insect-derived AMPs with special reference to anti-biofilm-based strategies. It covers the AMP composition, pathways and mechanisms of action, the formation of biofilms, impact of biofilms on human diseases, current strategies as well as therapeutic options to combat biofilm with antimicrobial peptides from insects. In addition, the review also illustrates the importance of bioinformatics tools and molecular docking studies to boost the importance of select bioactive peptides those can be developed as drugs, as well as suggestions for further basic and clinical research.

Discovery of novel β-turn mimetic-based peptides as novel quorum sensing inhibitors of gram-negative bacteria

To date, a very limited number of peptides reported as quorum sensing inhibitors. Herein, we report the synthesis and evaluation of a series of β-turn mimetic-based peptides as potent quorum sensing inhibitors and antibiofilm formation. In this series, peptides P1, P4, and P5 showed very promising anti-quorum sensing activity on lasB-gfp reporter strain of Pseudomonas aeruginosa without affecting bacterial growth. Under our condition, these compounds also showed good anti-violacein production of Chromobacterium violaceum. In terms of antibiofilm formation, except P5, two β-turn mimetic-based peptides P1 and P4 showed maximum inhibition of 80% total biomass of Pseudomonas aeruginosa. This report provides the first β-turn mimetic-based scaffold for future drug development.

Effect of hydrodynamic cavitation water treatment on Pseudomonas aeruginosa quorum-sensing molecules

Hydrodynamic cavitation treatment was used for the functional inactivation of quorum-sensing lactone molecules of Pseudomonas aeruginosa. Hydroxyl radicals formed as well as the shear effects during the cavitation process induced the inactivation of the signal molecules through hydrolysis reaction coupled with bacterial destruction. Concentration of two different types of homoserine lactones (HSL) molecules was tested after the treatment at various rotational speeds. It was found that the strongest effects can be achieved at speeds > 2000 rpm. This value is considered as an onset speed of dominant cavitation, and it is in agreement with literature data. The experimental trends were in agreement with the calculations based on the finite element modelling, which show a significant increase in average shear stress at higher rotational speeds. Overall, the work has demonstrated the possible effects of hydrodynamic cavitation on the quorum-sensing molecules of Pseudomonas aeruginosa for the first time.

An Improved 2-Aminoimidazole Based Anti-Biofilm Coating for Orthopedic Implants: Activity, Stability, and in vivo Biocompatibility

Orthopedic device-related infections remain a serious challenge to treat. Central to these infections are bacterial biofilms that form on the orthopedic implant itself. These biofilms shield the bacteria from the host immune system and most common antibiotic drugs, which renders them essentially antibiotic-tolerant. There is an urgent clinical need for novel strategies to prevent these serious infections that do not involve conventional antibiotics. Recently, a novel antibiofilm coating for titanium surfaces was developed based on 5-(4-bromophenyl)-N-cyclopentyl-1-octyl-1H-imidazol-2-amine as an active biofilm inhibitor. In the current study we present an optimized coating protocol that allowed for a 5-fold higher load of this active compound, whilst shortening the manufacturing process. When applied to titanium disks, the newly optimized coating was resilient to the most common sterilization procedures and it induced a 1 log reduction in biofilm cells of a clinical Staphylococcus aureus isolate (JAR060131) in vitro, without affecting the planktonic phase. Moreover, the antibiofilm effect of the coating in combination with the antibiotic cefuroxime was higher than cefuroxime treatment alone. Furthermore, the coating was successfully applied to a human-scale fracture fixation device resulting in a loading that was comparable to the titanium disk model. Finally, an in vivo biocompatibility and healing study in a rabbit osteotomy model indicated that these coated implants did not negatively affect fracture healing or osteointegration. These findings put our technology one step closer to clinical trials, confirming its potential in fighting orthopedic infections without compromising healing.

Matrix inhibition by Salmonella excludes uropathogenic E. coli from biofilm

Biofilm is a predominant lifestyle of bacteria that comprises of cells as collectives enmeshed in a polymeric matrix. Biofilm formation is vital for bacterial species as it provides access to nutrients and protects the cells from environmental stresses. Here we show that interference in biofilm matrix production is a strategy by the competing bacterial species to reduce the ability of the other species to colonize a surface. Escherichia coli colonies that differ in matrix production display different morphologies on Congo red agar media, which we exploited for screening bacterial isolates capable of inhibiting the matrix. The cell-free supernatants from growth culture of the screened isolates impaired uropathogenic E. coli (UPEC) UTI89 strain's biofilm. A physicochemical analysis suggested that the compound could be a glycopeptide or a polysaccharide. Isolates that inhibited matrix production belonged to species of the family Enterobacteriaceae such as Shigella, Escherichia, Enterobacter and Salmonella. Competition experiments between the isolates and the UPEC strain resulted in mutual inhibition, particularly during biofilm formation causing significant reduction in productivity and fitness. Furthermore, we show that Salmonella strains competitively excluded the UPEC strain in the biofilm by inhibiting its matrix production, highlighting the role of interference competition.

Natural and Enantiopure Alkylglycerols as Antibiofilms Against Clinical Bacterial Isolates and Quorum Sensing Inhibitors of Chromobacterium violaceum ATCC 12472

Resistance mechanisms occur in almost all clinical bacterial isolates and represent one of the most worrisome health problems worldwide. Bacteria can form biofilms and communicate through quorum sensing (QS), which allow them to develop resistance against conventional antibiotics. Thus, new therapeutic candidates are sought. We focus on alkylglycerols (AKGs) because of their recently discovered quorum sensing inhibition (QSI) ability and antibiofilm potential. Fifteen natural enantiopure AKGs were tested to determine their effect on the biofilm formation of other clinical bacterial isolates, two reference strains and their QSI was determined using Chromobacterium violaceum ATCC 12472. The highest biofilm inhibition rates (%) and minimum QS inhibitory concentration were determined by a microtiter plate assay and ciprofloxacin was used as the standard antibiotic. At subinhibitory concentrations, each AKG reduced biofilm formation in a concentration-dependent manner against seven bacterial isolates, with values up to 97.2%. Each AKG displayed QSI at different levels of ability without affecting the growth of C. violaceum. AKG (2S)-3-O-(cis-13’-docosenyl)-1,2-propanediol was the best QS inhibitor (20 μM), while (2S)-3-O-(cis-9’-hexadecenyl)-1,2-propanediol was the least effective (795 μM). The results showed for the first time the QSI activity of this natural AKG series and suggest that AKGs could be promising candidates for further studies on preventing antimicrobial resistance.

Regulatory Networks of the T4SS Control: From Host Cell Sensing to the Biogenesis and the Activity during the Infection

Delivery of effectors, DNA or proteins, that hijack host cell processes to the benefit of bacteria is a mechanism widely used by bacterial pathogens. It is achieved by complex effector injection devices, the secretion systems, among which Type 4 Secretion Systems (T4SSs) play a key role in bacterial virulence of numerous animal and plant pathogens. Considerable progress has recently been made in the structure-function analyses of T4SSs. Nevertheless, the signals and processes that trigger machine assembly and activity during infection, as well as those involved in substrate recognition and transfer, are complex and still poorly understood. In this review, we aim at summarizing the last updates of the knowledge on signaling pathways that regulate the biogenesis and the activity of T4SSs in important bacterial pathogens.

Mechanisms and Control Strategies of Antibiotic Resistance in Pathological Biofilms

Bacterial biofilm is a community of bacteria that are embedded and structured in a self-secreted extracellular matrix. An important clinical-related characteristic of bacterial biofilms is that they are much more resistant to antimicrobial agents than the planktonic cells (up to 1,000 times), which is one of the main causes of antibiotic resistance in clinics. Therefore, infections caused by biofilms are notoriously difficult to eradicate, such as lung infection caused by Pseudomonas aeruginosa in cystic fibrosis patients. Understanding the resistance mechanisms of biofilms will provide direct insights into how we overcome such resistance. In this review, we summarize the characteristics of biofilms and chronic infections associated with bacterial biofilms. We examine the current understanding and research progress on the major mechanisms of antibiotic resistance in biofilms, including quorum sensing. We also discuss the potential strategies that may overcome biofilm-related antibiotic resistance, focusing on targeting biofilm EPSs, blocking quorum sensing signaling, and using recombinant phages.

A solvent-free and efficient synthesis of bicyclic 2-pyridone derivatives for endoplasmic reticulum imaging

A solvent-free method was developed for the synthesis of bicyclic 2-pyridone (DHIP) derivatives, which demonstrated excellent endoplasmic reticulum (ER) targeting and antibacterial activity after a slight structure regulation.

2-Aminoimidazoles as potent inhibitors of contaminating brewery biofilms

Cleaning and disinfection protocols are not always able to remove biofilm microbes present in breweries, indicating that novel anti-biofilm strategies are needed. The preventive activities of three in-house synthesized members of the 2-aminoimidazole class of anti-biofilm molecules were studied against 17 natural brewery biofilms and benchmarked against 18 known inhibitors. Two 2-aminoimidazoles belonged to the top six inhibitors, which were retested against 12 defined brewery biofilm models. For the three best inhibitors, tannic acid (n° 1), 2-aminoimidazole imi-AAC-5 (n° 2), and baicalein (n° 3), the effect on the microbial metabolic activity was evaluated. Here, the top three inhibitors showed similar effectiveness, with baicalein possessing a slightly higher efficacy. Even though the 2-aminoimidazole was the second-best inhibitor, it showed a lower biocidal activity than tannic acid, making it less prone to resistance evolution. Overall, this study supports the potential of 2-aminoimidazoles as a preventive anti-biofilm strategy.

A Label-Free Cellular Proteomics Approach to Decipher the Antifungal Action of DiMIQ, a Potent Indolo[2,3-b]Quinoline Agent, against Candida albicans Biofilms

Candida albicans forms extremely drug-resistant biofilms, which present a serious threat to public health globally. Biofilm-based infections are difficult to treat due to the lack of efficient antifungal therapeutics, resulting in an urgent demand for the development of novel antibiofilm strategies. In this study, the antibiofilm activity of DiMIQ (5,11-dimethyl-5H-indolo[2,3-b]quinoline) was evaluated against C. albicans biofilms. DiMIQ is a synthetic derivative of indoquinoline alkaloid neocryptolepine isolated from a medicinal African plant, Cryptolepis sanguinolenta. Antifungal activity of DiMIQ was determined using the XTT assay, followed by cell wall and extracellular matrix profiling and cellular proteomes. Here, we demonstrated that DiMIQ inhibited C. albicans biofilm formation and altered fungal cell walls and the extracellular matrix. Cellular proteomics revealed inhibitory action against numerous translation-involved ribosomal proteins, enzymes involved in general energy producing processes and select amino acid metabolic pathways including alanine, aspartate, glutamate, valine, leucine and isoleucine. DiMIQ also stimulated pathways of cellular oxidation, metabolism of carbohydrates, amino acids (glycine, serine, threonine, arginine, phenylalanine, tyrosine, tryptophan) and nucleic acids (aminoacyl-tRNA biosynthesis, RNA transport, nucleotide metabolism). Our findings suggest that DiMIQ inhibits C. albicans biofilms by arresting translation and multidirectional pathway reshaping of cellular metabolism. Overall, this agent may provide a potent alternative to treating biofilm-associated Candida infections.

Natural Anti-biofilm Agents: Strategies to Control Biofilm-Forming Pathogens

Pathogenic microorganisms and their chronic pathogenicity are significant concerns in biomedical research. Biofilm-linked persistent infections are not easy to treat due to resident multidrug-resistant microbes. Low efficiency of various treatments and in vivo toxicity of available antibiotics drive the researchers toward the discovery of many effective natural anti-biofilm agents. Natural extracts and natural product-based anti-biofilm agents are more efficient than the chemically synthesized counterparts with lesser side effects. The present review primarily focuses on various natural anti-biofilm agents, i.e., phytochemicals, biosurfactants, antimicrobial peptides, and microbial enzymes along with their sources, mechanism of action via interfering in the quorum-sensing pathways, disruption of extracellular polymeric substance, adhesion mechanism, and their inhibitory concentrations existing in literature so far. This study provides a better understanding that a particular natural anti-biofilm molecule exhibits a different mode of actions and biofilm inhibitory activity against more than one pathogenic species. This information can be exploited further to improve the therapeutic strategy by a combination of more than one natural anti-biofilm compounds from diverse sources.

Genomic Features of a Food-Derived Pseudomonas aeruginosa Strain PAEM and Biofilm-Associated Gene Expression under a Marine Bacterial α-Galactosidase

The biofilm-producing strains of P. aeruginosa colonize various surfaces, including food products and industry equipment that can cause serious human and animal health problems. The biofilms enable microorganisms to evolve the resistance to antibiotics and disinfectants. Analysis of the P. aeruginosa strain (serotype O6, sequence type 2502), isolated from an environment of meat processing (PAEM) during a ready-to-cook product storage (−20 °C), showed both the mosaic similarity and differences between free-living and clinical strains by their coding DNA sequences. Therefore, a cold shock protein (CspA) has been suggested for consideration of the evolution probability of the cold-adapted P. aeruginosa strains. In addition, the study of the action of cold-active enzymes from marine bacteria against the food-derived pathogen could contribute to the methods for controlling P. aeruginosa biofilms. The genes responsible for bacterial biofilm regulation are predominantly controlled by quorum sensing, and they directly or indirectly participate in the synthesis of extracellular polysaccharides, which are the main element of the intercellular matrix. The levels of expression for 14 biofilm-associated genes of the food-derived P. aeruginosa strain PAEM in the presence of different concentrations of the glycoside hydrolase of family 36, α-galactosidase α-PsGal, from the marine bacterium Pseudoalteromonas sp. KMM 701 were determined. The real-time PCR data clustered these genes into five groups according to the pattern of positive or negative regulation of their expression in response to the action of α-galactosidase. The results revealed a dose-dependent mechanism of the enzymatic effect on the PAEM biofilm synthesis and dispersal genes.

Synthesis, ADMET Properties, and In Vitro Antimicrobial and Antibiofilm Activity of 5-Nitro-2-thiophenecarbaldehyde N-((E)-(5-Nitrothienyl)methylidene)hydrazone (KTU-286) against Staphylococcus aureus with Defined Resistance Mechanisms

The emergence of drug-resistant Staphylococcus aureus is responsible for high morbidity and mortality worldwide. New therapeutic options are needed to fight the increasing antimicrobial resistance among S. aureus in the clinical setting. We, therefore, characterized the in silico absorption, distribution, metabolism, elimination, and toxicity (ADMET) and in vitro antimicrobial activity of 5-nitro-2-thiophenecarbaldehyde N-((E)-(5-nitrothienyl)methylidene)hydrazone (KTU-286) against drug-resistant S. aureus strains with genetically defined resistance mechanisms. The antimicrobial activity of KTU-286 was determined by CLSI recommendations. The ADMET properties were estimated by using in silico modeling. The activity on biofilm integrity was examined by crystal violet assay. KTU-286 demonstrated low estimated toxicity and low skin permeability. The highest antimicrobial activity was observed among pan-susceptible (Pan-S) S. aureus (minimal inhibitory concentration (MIC) 0.5–2.0 µg/mL, IC₅₀ = 0.460 µg/mL), followed by vancomycin resistant S. aureus (VRSA) (MIC 4.0 µg/mL, IC₅₀ = 1.697 µg/mL) and methicillin-resistant S. aureus (MRSA) (MIC 1.0–16.0 µg/mL, IC₅₀ = 2.282 µg/mL). KTU-286 resulted in significant (p < 0.05) loss of S. aureus biofilm integrity in vitro. Further studies are needed for a better understanding of safety, synergistic relationship, and therapeutic potency of KTU-286.

Antibiofilm activity of lactoferrin-derived synthetic peptides against Pseudomonas aeruginosa PAO1

Many pathogenic bacteria can protect themselves from the effects of antibiotics and the host immune response system by forming biofilms. Biofilms are polymer-entrapped bacterial cells, which adhere to each other and are often attached to a surface. Eradication of bacterial biofilms typically requires much higher concentrations of antibiotics than are normally needed to kill cultured planktonic cells, raising serious clinical concerns. In an attempt to prevent the formation of biofilms or to break up existing biofilms of pathogenic bacteria, herein we have used the standard crystal violet assay as well as the Calgary biofilm device to test several lactoferrin- and lactoferricin-derived antimicrobial peptides for their antibiofilm activity against Pseudomonas aeruginosa PAO1. Our results revealed that the short bovine lactoferricin-derived RRWQWR-NH₂ (20-25) hexapeptide has no activity against P. aeruginosa PAO1. Moreover, the longer human lactoferricin-derived peptide GRRRRSVQWCA (1-11) and the bovine lactoferrampin (268-284) peptide were also almost devoid of activity. However, several different "mix-and-match" dimeric versions of the two lactoferricin-derived peptides proved quite effective in preventing the formation of biofilms at low concentrations, and in some cases, could even eradicate an existing biofilm. Moreover, the full-length bovine lactoferricinB (17-41) peptide also displayed considerable antimicrobial activity. Some of the longer lactoferricin-derived dimeric peptides acted through a bactericidal mechanism, whereas others seemed to interfere in cell-signalling processes. Taken together, our results indicate that synthetic dimeric peptides comprising short naturally occurring human and bovine lactoferricin constructs could be further developed as antibiofilm agents.

A Novel Small Molecule, 1,3-di-m-tolyl-urea, Inhibits and Disrupts Multispecies Oral Biofilms

An imbalance of homeostasis between the microbial communities and the host system leads to dysbiosis in oral micro flora. DMTU (1,3-di-m-tolyl-urea) is a biocompatible compound that was shown to inhibit Streptococcus mutans biofilm by inhibiting its communication system (quorum sensing). Here, we hypothesized that DMTU is able to inhibit multispecies biofilms. We developed a multispecies oral biofilm model, comprising an early colonizer Streptococcus gordonii, a bridge colonizer Fusobacterium nucleatum, and late colonizers Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. We performed comprehensive investigations to demonstrate the effect of DMTU on planktonic cells and biofilms. Our findings showed that DMTU inhibits and disrupts multispecies biofilms without bactericidal effects. Mechanistic studies revealed a significant down regulation of biofilm and virulence-related genes in P. gingivalis. Taken together, our study highlights the potential of DMTU to inhibit polymicrobial biofilm communities and their virulence.

Recent Advances in Surface Nanoengineering for Biofilm Prevention and Control. Part II: Active, Combined Active and Passive, and Smart Bacteria-Responsive Antibiofilm Nanocoatings

The second part of our review describing new achievements in the field of biofilm prevention and control, begins with a discussion of the active antibiofilm nanocoatings. We present the antibiofilm strategies based on antimicrobial agents that kill pathogens, inhibit their growth, or disrupt the molecular mechanisms of biofilm-associated increase in resistance and tolerance. These agents of various chemical structures act through a plethora of mechanisms targeting vital bacterial metabolic pathways or cellular structures like cell walls and cell membranes or interfering with the processes that underlie different stages of the biofilm life cycle. We illustrate the latter action mechanisms through inhibitors of the quorum sensing signaling pathway, inhibitors of cyclic-di-GMP signaling system, inhibitors of (p)ppGpp regulated stringent response, and disruptors of the biofilm extracellular polymeric substances matrix (EPS). Both main types of active antibiofilm surfaces, namely non-leaching or contact killing systems, which rely on the covalent immobilization of the antimicrobial agent on the surface of the coatings and drug-releasing systems in which the antimicrobial agent is physically entrapped in the bulk of the coatings, are presented, highlighting the advantages of each coating type in terms of antibacterial efficacy, biocompatibility, selective toxicity, as well as drawbacks and limitations. Developments regarding combined strategies that join in a unique platform, both passive and active elements are not omitted. In such platforms with dual functionality, passive and active strategies can be applied either simultaneously or sequentially. We especially emphasize those systems that can be reversely and repeatedly switched between the non-fouling status and the bacterial killing status, thereby allowing several bacteria-killing/surface regeneration cycles to be performed without significant loss of the initial bactericidal activity. Eventually, smart antibiofilm coatings that release their antimicrobial payload on demand, being activated by various triggers such as changes in local pH, temperature, or enzymatic triggers, are presented. Special emphasis is given to the most recent trend in the field of anti-infective surfaces, specifically smart self-defensive surfaces for which activation and switch to the bactericidal status are triggered by the pathogens themselves.

Targeting a bacterial DNABII protein with a chimeric peptide immunogen or humanised monoclonal antibody to prevent or treat recalcitrant biofilm-mediated infections

Background:

Chronic and recurrent bacterial diseases are recalcitrant to treatment due to the ability of the causative agents to establish biofilms, thus development of means to prevent or resolve these structures are greatly needed. Our approach targets the DNABII family of bacterial DNA-binding proteins, which serve as critical structural components within the extracellular DNA scaffold of biofilms formed by all bacterial species tested to date. DNABII-directed antibodies rapidly disrupt biofilms and release the resident bacteria which promote their subsequent clearance by either host immune effectors or antibiotics that are now effective at a notably reduced concentration.

Methods:

First, as a therapeutic approach, we used intact IgG or Fab fragments against a chimeric peptide immunogen designed to target protective epitopes within the DNA-binding tip domains of integration host factor to disrupt established biofilms in vitro and to mediate resolution of existing disease in vivo. Second, we performed preventative active immunisation with the chimeric peptide to induce the formation of antibody that blocks biofilm formation and disease development in a model of viral-bacterial superinfection. Further, toward the path for clinical use, we humanised a monoclonal antibody against the chimeric peptide immunogen, then characterised and validated that it maintained therapeutic efficacy.

Findings:

We demonstrated efficacy of each approach in two well-established pre-clinical models of otitis media induced by the prevalent respiratory tract pathogen nontypeable Haemophilus influenzae, a common biofilm disease.

Interpretation:

Collectively, our data revealed two approaches with substantive efficacy and potential for broad application to combat diseases with a biofilm component.

Funding

Supported by R01 DC011818 to LOB and SDG.

Protein interaction studies of curli fimbriae in Escherichia coli biofilms

Catheter-associated urinary tract infections (CAUTIs) caused by biofilms on indwelling medical devices are the most common type of nosocomial infections, a major health concern due to complications and frequent recurrence. The infections are most often caused by Escherichia coli. Curli are proteinaceous components of a complex extracellular matrix produced by various strains of Enterobacteriaceae. Curli fibers are involved with adhesion to surfaces, cell aggregation and biofilm formation. Therefore, it is of interest to study the protein interactions in curli biogenesis, identifying proteins involved in curli biogenesis, the interactions and development of a combinatorial library of novel lead molecules against biofilm formation by Escherichia coli. Targeting the CsgG protein of Escherichia coli could provide new treatment modalities to fight CAUTIs, better. This study may also help study infections caused by various strains of Enterobacteriaceae, in general.