No abstract

Recently, we documented that the short, proline-rich antibacterial peptides pyrrhocoricin, drosocin, and apidaecin interact with the bacterial heat shock protein DnaK, and peptide binding to DnaK can be correlated with antimicrobial activity. In the current report we studied the mechanism of action of these peptides and their binding sites to Escherichia coli DnaK. Biologically active pyrrhocoricin made of L-amino acids diminished the ATPase activity of recombinant DnaK. The inactive D-pyrrhocoricin analogue and the membrane-active antibacterial peptide cecropin A or magainin 2 failed to inhibit the DnaK-mediated phosphate release from adenosine 5'-triphosphate (ATP). The effect of pyrrhocoricin on DnaK's other significant biological function, the refolding of misfolded proteins, was studied by assaying the alkaline phosphatase and beta-galactosidase activity of live bacteria. Remarkably, both enzyme activities were reduced upon incubation with L-pyrrhocoricin or drosocin. D-Pyrrhocoricin, magainin 2, or buforin II, an antimicrobial peptide involved in binding to bacterial nucleic acids, had only negligible effect. According to fluorescence polarization and dot blot analysis of synthetic DnaK fragments and labeled pyrrhocoricin analogues, pyrrhocoricin bound with a K(d) of 50.8 microM to the hinge region around the C-terminal helices D and E, at the vicinity of amino acids 583 and 615. Pyrrhocoricin binding was not observed to the homologous DnaK fragment of Staphylococcus aureus, a pyrrhocoricin nonresponsive strain. In line with the lack of ATPase inhibition, drosocin binding appears to be slightly shifted toward the D helix. Our data suggest that drosocin and pyrrhocoricin binding prevents the frequent opening and closing of the multihelical lid over the peptide-binding pocket of DnaK, permanently closes the cavity, and inhibits chaperone-assisted protein folding. The biochemical results were strongly supported by molecular modeling of DnaK-pyrrhocoricin interactions. Due to the prominent sequence variations of procaryotic and eucaryotic DnaK molecules in the multihelical lid region, our findings pave the road for the design of strain-specific antibacterial peptides and peptidomimetics. Far-fetched applications of the species-specific inhibition of chaperone-assisted protein folding include the control of not only bacteria but also fungi, parasites, insects, and perhaps rodents.

Members of the proline‐rich antibacterial peptide family, pyrrhocoricin, apidaecin and drosocin appear to kill responsive bacterial species by binding to the multihelical lid region of the bacterial DnaK protein. Pyrrhocoricin, the most potent among these peptides, is nontoxic to healthy mice, and can protect these animals from bacterial challenge. A structure–antibacterial activity study of pyrrhocoricin against Escherichia coli and Agrobacterium tumefaciens identified the N‐terminal half, residues 2–10, the region responsible for inhibition of the ATPase activity, as the fragment that contains the active segment. While fluorescein‐labeled versions of the native peptides entered E. coli cells, deletion of the C‐terminal half of pyrrhocoricin significantly reduced the peptide's ability to enter bacterial or mammalian cells. These findings highlighted pyrrhocoricin's suitability for combating intracellular pathogens and raised the possibility that the proline‐rich antibacterial peptides can deliver drug leads into mammalian cells. By observing strong relationships between the binding to a synthetic fragment of the target protein and antibacterial activities of pyrrhocoricin analogs modified at strategic positions, we further verified that DnaK was the bacterial target macromolecule. Inaddition, the antimicrobial activity spectrum of native pyrrhocoricin against 11 bacterial and fungal strains and the binding of labeled pyrrhocoricin to synthetic DnaK D‐E helix fragments of the appropriate species could be correlated. Mutational analysis on a synthetic E. coli DnaK fragment identified a possible binding surface for pyrrhocoricin.

The most potent known naturally occurring BowmanBirk inhibitor, sunflower trypsin inhibitor-1 (SFTI-1), is a bicyclic 14-amino acid peptide from sunflower seeds comprising one disulfide bond and a cyclic backbone. At present, little is known about the cyclization mechanism of SFTI-1. We show here that an acyclic permutant of SFTI-1 open at its scissile bond, SFTI-1[6,5], also functions as an inhibitor of trypsin and that it can be enzymatically backbone-cyclized by incubation with bovine ␤-trypsin. The resulting ratio of cyclic SFTI-1 to SFTI-1[6,5] is ϳ9:1 regardless of whether trypsin is incubated with SFTI-1[6,5] or SFTI-1. Enzymatic resynthesis of the scissile bond to form cyclic SFTI-1 is a novel mechanism of cyclization of SFTI-1[6,5]. Such a reaction could potentially occur on a trypsin affinity column as used in the original isolation procedure of SFTI-1. We therefore extracted SFTI-1 from sunflower seeds without a trypsin purification step and confirmed that the backbone of SFTI-1 is indeed naturally cyclic. Structural studies on SFTI-1[6,5] revealed high heterogeneity, and multiple species of SFTI-1[6,5] were identified. The main species closely resembles the structure of cyclic SFTI-1 with the broken binding loop able to rotate between a cis/trans geometry of the I7-P8 bond with the cis conformer being similar to the canonical binding loop conformation. The non-reactive loop adopts a ␤-hairpin structure as in cyclic wild-type SFTI-1. Another species exhibits an isoaspartate residue at position 14 and provides implications for possible in vivo cyclization mechanisms.Over recent years there has been much interest in the discovery of circular proteins in higher organisms (1) and in the development in synthetic approaches to cyclize proteins (2). In general, backbone cyclic peptides have several advantages over their non-cyclic counterparts. They are resistant to attack by exopeptidases, making them less vulnerable to degradation and can have an increased thermal stability (3). Also, unfavorable entropic losses upon binding to target proteins are significantly reduced, resulting in a thermodynamically more efficient binding interaction (1). These biological advantages of backbone cyclized peptides may lead to their use as scaffolds for the design of stable pharmaceuticals and pesticides (4).The new generation of circular peptides/proteins discovered in the last few years differs from previously known cyclic peptides such as cyclosporins in that the latter are generally not direct gene products but are synthesized in bacteria by multifunctional enzymes and often contain non-conventional amino acids (5). By contrast, recently discovered circular miniproteins such as the plant cyclotides (6) are gene products that are post-translationally processed to cyclize their conventional peptide backbone (7). Although in vitro cyclization procedures are now being developed for the synthetic production of circular proteins, little is known about the mechanisms and driving force behind in vivo cyclization of naturally o...

No abstract

A significant number of Escherichia coli and Klebsiella pneumoniae bacterial strains in urinary tract infections are resistant to fluoroquinolones. Peptide antibiotics are viable alternatives although these are usually either toxic or insufficiently active. By applying multiple alignment and sequence optimization steps, we designed multifunctional proline-rich antibacterial peptides that maintained their DnaK-binding ability in bacteria and low toxicity in eukaryotes, but entered bacterial cells much more avidly than earlier peptide derivatives. The resulting chimeric and statistical analogues exhibited 8-32 microg/mL minimal inhibitory concentration efficacies in Muller-Hinton broth against a series of clinical pathogens. Significantly, the best peptide, compound 5, A3-APO, retained full antibacterial activity in the presence of mouse serum. Across a set of eight fluoroquinolone-resistant clinical isolates, peptide 5 was 4 times more potent than ciprofloxacin. On the basis of the in vitro efficacy, toxicity, and pharmacokinetics data, we estimate that peptide 5 will be suitable for treating infections in the 3-5 mg/kg dose range.

Pyrrhocoricin and drosocin, representatives of the short, proline-rich antimicrobial peptide family kill bacteria by inactivating the bacterial heat shock protein DnaK and inhibiting chaperone-assisted protein folding. The molecular architecture of these peptides features an N-terminal DnaK-binding half and a C-terminal delivery unit, capable of crossing bacterial membranes. Cell penetration is enhanced if multiple copies of pyrrhocoricin are conjugated. To obtain drug leads with improved antimicrobial properties, and possible utility as therapeutic agents, we synthesized chimeric dimers, in which pyrrhocoricin's potent DnaK-binding domain was connected to drosocin's superior cell penetrating module. Indeed, the new constructs not only exhibited enhanced in vitro antibacterial properties against the originally sensitive strains Escherichia coli, Klebsiella pneumoniae and Salmonella typhimurium, but also showed activity against Staphylococcus aureus, a bacterial strain resistant to native pyrrhocoricin and drosocin. The improved antimicrobial profile could be demonstrated with assays designed to distinguish intracellular or membrane activities. While a novel mixed pyrrhocoricin-drosocin dimer and the purely pyrrhocoricinbased old dimer bound E. coli DnaK with an identical 4 lM K d , the mixed dimers penetrated a significantly larger number of E. coli and S. aureus cells than the previous analogs and destroyed a larger percentage of bacterial membrane structures. Toxicity to human red blood cells could not be observed up to the highest peptide concentration tested, 640 lM. In addition, repetitive reculturing of E. coli or S. aureus cells with sublethal concentrations of the mixed dimer did not result in resistance induction to the novel peptide antibiotic. The new concept of pyrrhocoricin-drosocin mixed dimers yields antibacterial peptide derivatives acting with a multiple mode of action, and can serve as a useful addition to the current antimicrobial therapy repertoire.

An effort was made to discover mast cell degranulating (MCD) peptide analogs that bind with high affinity to mast cell receptors without triggering secretion of histamine or other mediators of the allergic reaction initiated by immunoglobulin E (IgE) after mast cell activation. Such compounds could serve as inhibitors of IgE binding to mast cell receptors. An alanine scan of MCD peptide reported previously showed that the analog [Ala12]MCD was 120-fold less potent in histamine-releasing activity and fivefold more potent in binding affinity to mast cell receptors than the parent MCD peptide. Because this analog showed marginal intrinsic activity and good binding affinity it was subsequently tested in the present study as an IgE inhibitor. In contrast to MCD peptide, [Ala12]MCD showed a 50% inhibition of IgE binding to the Fc epsilon RI alpha mast cell receptor by using rat basophilic leukemia (RBL-2H3) mast cells and fluorescence polarization. Furthermore, in a beta-hexosaminidase secretory assay, the peptide also showed a 50% inhibition of the secretion of this enzyme caused by IgE. An attempt was made to relate structural changes and biologic differences between the [Ala12]MCD analog and the parent MCD peptide. The present results show that [Ala12]MCD may provide a base for designing agents to prevent IgE/Fc epsilon RI alpha interactions and, consequently, allergic conditions.