Small-molecule Antibiotics Research Articles

A lack of synergy between membrane-permeabilizing cationic antimicrobial peptides and conventional antibiotics

The rapid rise in morbidity and mortality from drug-resistant pathogenic bacteria has generated elevated interest in combination therapy using antimicrobial agents. Antimicrobial peptides (AMPs) are a candidate drug class to advance the development of combination therapies. Although the literature is ambiguous, the generic membrane disrupting activity of AMPs could enable them to synergize with conventional small molecule antibiotics by increasing access to the cell and by triggering membrane damage mediators. We used a novel assay to measure interactions, expressed as fractional inhibitory concentration (FIC), between four conventional antibiotics in combination with four well-characterized, membrane permeabilizing AMPs, against three species of Gram negative and Gram positive bacteria, giving 40 total pair-wise measurements of FIC with statistical uncertainties. We chose a set of AMPs that are known to dramatically disrupt the membranes of both Gram negative and Gram positive bacteria. Yet none of the membrane permeabilizing antimicrobial peptides interacted synergistically with any of the conventional antibiotic drugs in any organism. Large-scale membrane disruption and permeabilization by AMPs is not sufficient to drive them to act synergistically with chemical antibiotics in either Gram negative or Gram positive microbes.

Covalent modification of a ten-residue cationic antimicrobial peptide with levofloxacin.

The rampant spread of antibiotic resistant bacteria has spurred interest in alternative strategies for developing next-generation antibacterial therapies. As such, there has been growing interest in cationic antimicrobial peptides (CAMPs) and their therapeutic applications. Modification of CAMPs via conjugation to auxiliary compounds, including small molecule drugs, is a new approach to developing effective, broad-spectrum antibacterial agents with novel physicochemical properties and versatile antibacterial mechanisms. Here, we've explored design parameters for engineering CAMPs conjugated to small molecules with favorable physicochemical and antibacterial properties by covalently affixing a fluoroquinolone antibiotic, levofloxacin, to the ten-residue CAMP Pep-4. Relative to the unmodified Pep-4, the conjugate was found to demonstrate substantially increased antibacterial potency under high salt concentrations. Historically, it has been observed that most CAMPs lose antibacterial effectiveness in such high ionic strength environments, a fact that has presented a challenge to their development as therapeutics. Physicochemical studies revealed that P4LC was more hydrophobic than Pep-4, while mechanistic findings indicated that the conjugate was more effective at disrupting bacterial membrane integrity. Although the inherent antibacterial effect of the incorporated levofloxacin molecules did not appear to be substantially realized in this conjugate, these findings nevertheless suggest that covalent attachment of small molecule antibiotics with favorable physicochemical properties to CAMPs could be a promising strategy for enhancing peptide performance and overall therapeutic potential. These results have broader applicability to the development of future CAMP-antibiotic conjugates for potential therapeutic applications.

Metagenomic approaches for the discovery of new bioactive natural products

One of the key insights to arise from the large-scale sequencing of bacterial genomic DNA is that traditional methods used to discover bacterial natural products have only provided access to a small fraction of the biosynthetic diversity encoded by prokaryotes. These studies indicate that 1) the majority of bacteria present in nature have not been cultured in the laboratory and 2) only a small subset of the biosynthetic gene clusters found in the genomes of cultured bacteria is expressed under laboratory fermentation conditions. We are using both functional and sequence-based strategies to access previously inaccessible bioactive small molecules from both environmental bacteria. New small molecule antibiotics and anticancer agents that we have uncovered in these studies, as well as the modes of action of these metabolites, their distribution in the environment and improved methods for accessing them will be described.

Nanoscale Structure–Activity Relationships, Mode of Action, and Biocompatibility of Gold Nanoparticle Antibiotics

The emergence of resistance to multiple antimicrobial agents by pathogenic bacteria has become a significant global public health threat. Multi-drug-resistant (MDR) Gram-negative bacteria have become particularly problematic, as no new classes of small-molecule antibiotics for Gram-negative bacteria have emerged in over two decades. We have developed a combinatorial screening process for identifying mixed ligand monolayer/gold nanoparticle conjugates (2.4 nm diameter) with antibiotic activity. The method previously led to the discovery of several conjugates with potent activity against the Gram-negative bacterium Escherichia coli. Here we show that these conjugates are also active against MDR E. coli and MDR Klebsiella pneumoniae. Moreover, we have shown that resistance to these nanoparticles develops significantly more slowly than to a commercial small-molecule drug. These results, combined with their relatively low toxicity to mammalian cells and biocompatibility in vivo, suggest that gold nanoparticles may be viable new candidates for the treatment of MDR Gram-negative bacterial infections.

Assessing Specific Oligonucleotides and Small Molecule Antibiotics for the Ability to Inhibit the CRD-BP-CD44 RNA Interaction

Studies on Coding Region Determinant-Binding Protein (CRD-BP) and its orthologs have confirmed their functional role in mRNA stability and localization. CRD-BP is present in extremely low levels in normal adult tissues, but it is over-expressed in many types of aggressive human cancers and in neonatal tissues. Although the exact role of CRD-BP in tumour progression is unclear, cumulative evidence suggests that its ability to physically associate with target mRNAs is an important criterion for its oncogenic role. CRD-BP has high affinity for the 3′UTR of the oncogenic CD44 mRNA and depletion of CRD-BP in cells led to destabilization of CD44 mRNA, decreased CD44 expression, reduced adhesion and disruption of invadopodia formation. Here, we further characterize the CRD-BP-CD44 RNA interaction and assess specific antisense oligonucleotides and small molecule antibiotics for their ability to inhibit the CRD-BP-CD44 RNA interaction. CRD-BP has a high affinity for binding to CD44 RNA nts 2862–3055 with a Kd of 645 nM. Out of ten antisense oligonucleotides spanning nts 2862–3055, only three antisense oligonucleotides (DD4, DD7 and DD10) were effective in competing with CRD-BP for binding to 32P-labeled CD44 RNA. The potency of DD4, DD7 and DD10 in inhibiting the CRD-BP-CD44 RNA interaction in vitro correlated with their ability to specifically reduce the steady-state level of CD44 mRNA in cells. The aminoglycoside antibiotics neomycin, paramomycin, kanamycin and streptomycin effectively inhibited the CRD-BP-CD44 RNA interaction in vitro. Assessing the potential inhibitory effect of aminoglycoside antibiotics including neomycin on the CRD-BP-CD44 mRNA interaction in cells proved difficult, likely due to their propensity to non-specifically bind nucleic acids. Our results have important implications for future studies in finding small molecules and nucleic acid-based inhibitors that interfere with protein-RNA interactions.

Roche Signals Return to Antibiotics Development with Polyphor Licensing Deal

After exiting antibiotics R&D in 2000 with the spin out of its anti-infectives discovery division into Basilea Pharmaceutica, Roche has highlighted its renewed commitment to the field by licensing global rights to develop and commercialise Polyphor’s macrocyclic antibiotic POL7080, which has potential in the treatment of multidrug-resistant Pseudomonas aeruginosa infections. Derived from Polyphor’s protein epitope mimetics (PEM) drug discovery platform, POL7080 has demonstrated clinical safety and tolerability in a Phase I study. The deal follows a February 2013 collaboration between Genentech and RQx Pharmaceuticals for the discovery and development of novel small molecule antibiotics active against an undisclosed target.

Small molecule design strategy to overcome antibiotic resistance

AbstractPurpose Although antimicrobial peptides have been shown to avert resistance, most small molecule antibiotics do not share that characteristic. Antimicrobial peptides though are often less stable environmentally and have difficult delivery problems. However, small molecules are much easier to develop from a pharmaceutical perspective. This study has combined the properties of antimicrobial peptides into a small molecule platform.Methods Using our design platform which consists of microbiology, biophysical (including NMR), and animal data we have used the molecular backbone of a xanthone, alpha‐mangostin which is extracted from the pericarp of the SE Asian fruit, mangosteen. The xanthone is a heterocyclic planar molecule with sites at carbons 3 and 6 modifiable with amino acids or other functional groups. Stable, water soluble compounds have been developed whose activities are tested in vitro in microbiological assays as well as in mouse models of corneal infection. These molecules have been tested in MIC, time kill studies and in simulations of resistance.Results The results show that the antimicrobial activities of the cationic xanthone derivatives can be generally predicted based on the pKa values of the corresponding amines. We have identified AM‐0016 (3b) as the most potent compound in the series with potent antimicrobial activity with MIC values of 0.095‐0.39 (µg/mL) against Gram‐positive bacteria including MRSA, improved selectivity up to 200, rapid time‐kill in 10‐30mins,Conclusion A series of novel antimicrobials have been designed and prepared by cationic modifications of α‐mangostin, a natural xanthones with a planar hydrophobic core, to yield an amphiphilic structure which improves selectivity for bacterial membranes through the hydrophobic‐water interface perturbation.

Allosteric control of the ribosome by small-molecule antibiotics.

Protein synthesis is targeted by numerous, chemically distinct antibiotics that bind and inhibit key functional centers of the ribosome. Using single-molecule imaging and X-ray crystallography, we show that the aminoglycoside neomycin blocks aminoacyl-transfer RNA (aa-tRNA) selection and translocation as well as ribosome recycling by binding to helix 69 (H69) of 23S ribosomal RNA within the large subunit of the Escherichia coli ribosome. There, neomycin prevents the remodeling of intersubunit bridges that normally accompanies the process of subunit rotation to stabilize a partially rotated ribosome configuration in which peptidyl (P)-site tRNA is constrained in a previously unidentified hybrid position. Direct measurements show that this neomycin-stabilized intermediate is incompatible with the translation factor binding that is required for distinct protein synthesis reactions. These findings reveal the functional importance of reversible intersubunit rotation to the translation mechanism and shed new light on the allosteric control of ribosome functions by small-molecule antibiotics.

Mechanistic insights into antibiotic action on the ribosome through single‐molecule fluorescence imaging

Single-molecule fluorescence imaging has provided unprecedented access to the dynamics of ribosome function, revealing transient intermediate states that are critical to ribosome activity. Imaging platforms have now been developed that are capable of probing many hundreds of molecules simultaneously at temporal and spatial resolutions approaching the sub-millisecond time and the sub-nanometer scales. These advances enable both steady- and pre-steady state measurements of individual steps in the translation process as well as processive reactions. The data generated using these methods have yielded new, quantitative structural and kinetic insights into ribosomal activity. They have also shed light on the mechanisms of antibiotic targeting the translation apparatus, revealing features of the structure-function relationship that would be difficult to obtain by other means. This review provides an overview of the types of information that can be obtained using such imaging platforms and a blueprint for using the technique to assess how small-molecule antibiotics alter macromolecular functions.

Ubiquitous Detection of Gram-Positive Bacteria with Bioorthogonal Magnetofluorescent Nanoparticles

The ability to rapidly diagnose gram-positive pathogenic bacteria would have far reaching biomedical and technological applications. Here we describe the bioorthogonal modification of small molecule antibiotics (vancomycin and daptomycin), which bind to the cell wall of gram-positive bacteria. The bound antibiotics conjugates can be reacted orthogonally with tetrazine-modified nanoparticles, via an almost instantaneous cycloaddition, which subsequently renders the bacteria detectable by optical or magnetic sensing. We show that this approach is specific, selective, fast and biocompatible. Furthermore, it can be adapted to the detection of intracellular pathogens. Importantly, this strategy enables detection of entire classes of bacteria, a feat that is difficult to achieve using current antibody approaches. Compared to covalent nanoparticle conjugates, our bioorthogonal method demonstrated 1-2 orders of magnitude greater sensitivity. This bioorthogonal labeling method could ultimately be applied to a variety of other small molecules with specificity for infectious pathogens, enabling their detection and diagnosis.

Phage Therapy: Delivering on the Promise

Bacteriophages are viruses that infect and, in many cases, destroy their bacterial targets. Within a few years of their initial discovery they were being investigated as therapeutic agents for infectious disease, an approach known as phage therapy. However, the nature of these exquisitely specific agents was not understood and much early use was both uninformed and unsuccessful. As a result they were replaced by chemical antibiotics once these became available. Although work on phage therapy continued (and continues) in Eastern Europe, this was not conducted to a standard allowing it to support clinical uses in areas regulated by the European Medicines Agency or the US FDA. To develop phage therapy for these areas requires work carried out in accordance with the requirements of these agencies, and, driven by the current crisis of antibiotic resistance, such clinical trials are now under way. The first Phase I clinical trial of safety was reported in 2005, and the results of the first Phase II clinical trial of efficacy of a bacteriophage therapeutic was published in 2009. While the delivery of these relatively large and complex agents to the site of disease can be more challenging than for conventional, small-molecule antibiotics, bacteriophages are then able to multiply locally even from an extremely low (picogram range) initial dose. This multiplication where and only where they are needed underlies the potential for bacteriophage therapeutics to become a much needed and powerful weapon against bacterial disease.

Road to Clinical Efficacy: Challenges and Novel Strategies for Antimicrobial Peptide Development

Since the discovery of magainins, cecropins and defensins 30 years ago, antimicrobial peptides (AMPs) have been hailed as a potential solution to the dearth of novel antibiotic development. AMPs have shown robust activity against a wide variety of pathogens, including drug-resistant bacteria. Unlike small-molecule antibiotics, however, AMPs have failed to translate this success to the clinic. Only the polymyxins, gramicidins, nisin and daptomycin are currently approved for medical use; the latter is the only example to have been developed in the last several decades. Nonetheless, researchers continue to isolate, modify and develop novel AMPs for therapeutic applications. Efforts have focused on increasing stability, reducing cytotoxicity, improving antimicrobial activity and incorporating AMPs in novel formulations, including nanoscale particles. As peptide synthesis and recombinant production methodologies improve, and more relevant bioassays become available, it becomes increasingly likely that AMPs will break the regulatory barrier and enter the marketplace as valuable antimicrobial weapons in the next 10 years.

Small Molecule-Capped Gold Nanoparticles as Potent Antibacterial Agents That Target Gram-Negative Bacteria

This report illustrates a new strategy in designing antibacterial agents--a series of commercially available compounds, amino-substituted pyrimidines (themselves completely inactive as antibiotics), when presented on gold nanoparticles (NPs), show antibacterial activities against multidrug-resistant clinical isolates, without external sources of energy such as IR. These pyrimidine-capped gold NPs exert their antibiotic actions via sequestration of magnesium or calcium ions to disrupt the bacterial cell membrane, resulting in leakage of cytoplasmic contents including nucleic acids from compromised cell membranes, and via interaction with DNA and inhibition of protein synthesis by internalized NPs. These amino-substituted pyrimidine-capped gold NPs induce bacterial resistance more slowly compared with conventional, small-molecule antibiotics and appear harmless to human cells; these NPs may hence be useful for clinical applications.

Synergy among antibacterial peptides and between peptides and small-molecule antibiotics

Antimicrobial peptides are key components of native immunity. Unlike most common small-molecule antibiotics, antimicrobial peptides have been refined by evolution to work synergistically within the host environment. The mechanisms of synergy are complex and specific, and it is only now that they are beginning to be understood. Thus, antimicrobial peptides are top candidates to broaden our limited therapeutic arsenal, and are very well suited to be used in synergic combinations with currently available antibiotics. In order for this promising strategy to become a reality, however, some key steps in basic and translational research need to be improved. These include the standardization and critical evaluation of testing and quantification methods, the characterization of the molecular mechanism of action, the study of indirect antibacterial activity such as immune-response modulation, and several other aspects that will be presented and discussed, with a focus primarily on antibacterial therapy. There will be a special focus on advances and innovations that might significantly improve the future perspectives of antimicrobial peptides from a therapeutic point-of-view.

A highly thermostable antimicrobial peptide from Aspergillus clavatus ES1: biochemical and molecular characterization

Antimicrobial peptides (AMPs) are extremely attractive candidates as therapeutic agents due to their wide spectrum of antimicrobial activity and mechanism of action, which differs from that of small-molecule antibiotics. In this study, a 6.0-kDa antimicrobial peptide from Aspergillus clavatus ES1, designated as AcAMP, was isolated by a one-step heat treatment. AcAMP was sensitive to proteolytic enzymes, stable between pH 5.0 and 10.0, and heat resistant (15 min at 100 degrees C). The acamp gene encoding AcAMP peptide was isolated by reverse-transcriptase polymerase chain reaction (RT-PCR) and cloned in pCRII-TOPO vector. Sequence analysis of the complementary DNA (cDNA) acamp gene revealed an open reading frame of 282 bp encoding a peptide of 94 amino acid residues consisting of a 21-aa signal peptide, a 22-aa pro-peptide, and a 51-aa mature peptide. The deduced amino acid sequence showed high identity with other ascomycete antifungal peptides. AcAMP belongs to the group of small, cysteine-rich, basic proteins with antimicrobial activity. In addition to its antifungal activity, AcAMP is the first fungal peptide exhibiting antibacterial activity against several Gram-positive and Gram-negative bacteria. Based on all these features, AcAMP can be considered as a promising new member of the restraint family of ascomycete antimicrobial peptides that might be used in biological control of plant diseases and also for potential applications in food preservation.

The Antibacterial Effect of a Proline-Rich Antibacterial Peptide A3-APO

Antimicrobial resistance is an emerging worldwide concern in light of the widespread antimicrobial drug use in humans, livestock and companion animals. The treatment of life-threatening infections is especially problematic because clinical strains rapidly acquire multiple-drug resistance. Antimicrobial peptides have long been considered to be viable alternatives to small molecule antibiotics. However, the peptides' parenteral use is frequently hampered by inadequate safety margins and rapid renal clearance leaving them suitable only for topical applications. The proline-rich peptide A3-APO represents a family of a new class of synthetic dimers that kill bacteria by a dual mode of action and carry domains for interaction with both the bacterial membrane and an intracellular target. From a series of designer antibacterial peptides, A3-APO emerged as a viable preclinical candidate by virtue of its superior ability to disintegrate the bacterial membrane, inhibit the 70-kDa heat shock protein DnaK alone or in synergy with small molecule antibiotics, lack of eukaryotic toxicity and withstand proteolytic degradation in body fluids. As many other proline-rich peptides, A3-APO binds to the C-terminal helical lid of bacterial DnaK and inhibits chaperone-assisted protein folding in bacteria but not in mammalian Hsp70. In this review, the structure, pharmacokinetic properties, antimicrobial spectrum of peptide A3-APO and its in vivo metabolite are summarized and the in vitro and in vivo antimicrobial effects (antimicrobial susceptibilities, postantibiotic effects, resistance induction) are discussed in detail.

Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: Time-dependent inhibition and specificity in ligand binding.

The UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosamine deacetylase LpxC is an essential enzyme of lipid A biosynthesis in Gram-negative bacteria and a promising antibiotic target. CHIR-090, the most potent LpxC inhibitor discovered to date, displays two-step time-dependent inhibition and kills a wide range of Gram-negative pathogens as effectively as ciprofloxacin or tobramycin. In this study, we report the solution structure of the LpxC-CHIR-090 complex. CHIR-090 exploits conserved features of LpxC that are critical for catalysis, including the hydrophobic passage and essential active-site residues. CHIR-090 is adjacent to, but does not occupy, the UDP-binding pocket of LpxC, suggesting that a fragment-based approach may facilitate further optimization of LpxC inhibitors. Additionally, we identified key residues in the Insert II hydrophobic passage that modulate time-dependent inhibition and CHIR-090 resistance. CHIR-090 shares a similar, although previously unrecognized, chemical scaffold with other small-molecule antibiotics such as L-161,240 targeting LpxC, and provides a template for understanding the binding mode of these inhibitors. Consistent with this model, we provide evidence that L-161,240 also occupies the hydrophobic passage.

Stability and Activity in Sputum of G10KHc, a Potent Anti‐Pseudomonas Antimicrobial Peptide

G10KHc, a specifically targeted antimicrobial peptide developed in our laboratory, has shown rapid and selective killing activity against Pseudomonas aeruginosa in culture medium. Because of the major role played by this pathogen in cystic fibrosis, we sought to evaluate the utility of G10KHc under more physiologic conditions in vitro. In the current study, we found that robust G10KHc activity could be maintained in expectorated sputum if serine protease-dependent digestion associated with this fluid was inhibited, either by chemical antagonists or by the construction of a D-amino acid enantiomer of G10KHc. Further investigations revealed that specifically targeted antimicrobial peptide activity in sputum could be further enhanced when samples were treated with a combination of peptide and recombinant human DNase. Our results illustrate the importance of investigating combination therapy to treat cystic fibrosis, especially if protease-sensitive peptide-based agents, such as G10KHc, are to be developed as alternatives to, or in conjunction with, conventional small-molecule antibiotics.

An antibiotic produced by an insect-pathogenic bacterium suppresses host defenses through phenoloxidase inhibition

Photorhabdus is a virulent pathogen that kills its insect host by overcoming immune responses. The bacterium also secretes a range of antibiotics to suppress the growth of other invading microorganisms. Here we show that Photorhabdus produces a small-molecule antibiotic (E)-1,3-dihydroxy-2-(isopropyl)-5-(2-phenylethenyl)benzene (ST) that also acts as an inhibitor of phenoloxidase (PO) in the insect host Manduca sexta. The Photorhabdus gene stlA encodes an enzyme that produces cinnamic acid, a key precursor for production of ST, and a mutation in stlA results in loss of ST production and PO inhibitory activity, which are both restored by genetic complementation of the mutant and also by supplying cinnamic acid. ST is produced both in vitro and in vivo in sufficient quantities to account for PO inhibition and is the only detectable solvent-extractable inhibitor. A Photorhabdus stlA- mutant is significantly less virulent, proliferates slower within the host, and provokes the formation of significantly more melanotic nodules than wild-type bacteria. Virulence of the stlA- mutant is also rescued by supplying cinnamic acid. The proximate cause of the virulence effect, however, is the inhibition of PO, because the effect of the stlA- mutation on virulence is abolished in insects in which PO has been knocked down by RNA interference (RNAi). Thus, ST has a dual function both as a PO inhibitor to counter host immune reactions and also as an antibiotic to exclude microbial competitors from the insect cadaver.