Dimeric versions of two short N-cadherin binding motifs (HAVDI and INPISG) function as N-cadherin agonists.

N-cadherin is a member of the classical cadherin family of homophilic binding molecules. Peptide competition studies have identified the HAVDI and INPISGQ sequences as functional binding motifs in extracellular domain 1 (ECD1) of N-cadherin. Whereas monomeric versions of these motifs function as specific N-cadherin antagonists, we now show that cyclic peptides containing a tandem repeat of the individual motifs function as N-cadherin agonists. In this context, when presented to neurons as soluble molecules, the dimeric versions of the motifs stimulate neurite outgrowth in a similar manner to native N-cadherin. The response to the dimeric agonist peptides was inhibited by monomeric versions of the same motif and also by recombinant N-cadherin ECD1 protein. The responses were also inhibited by antibodies to a fibroblast growth factor receptor (FGFR) binding motif in ECD4 of N-cadherin and by a specific FGFR antagonist (PD17304). These data suggest that the peptides function by binding to and clustering N-cadherin in neurons and thereby activating an N-cadherin/FGFR signaling cascade. The novel agonists will be invaluable for dissecting out those cadherin functions that rely on signaling as opposed to adhesion and clearly have the potential to be developed as therapeutic agents for the promotion of cell survival and axonal regeneration.     

A novel family of cyclic peptide antagonists suggests that N-cadherin specificity is determined by amino acids that flank the HAV motif

The classical cadherins (e.g. N-, E-, and P- cadherin) are well established homophilic adhesion molecules; however, the mechanism that governs cadherin specificity remains contentious. The classical cadherins contain an evolutionarily conserved His-Ala-Val (HAV) sequence, and linear peptides harboring this motif are capable of inhibiting a variety of cadherin-dependent processes. We now demonstrate that short cyclic HAV peptides can inhibit N-cadherin function. Interestingly, the nature of the amino acids that flank the HAV motif determine both the activity and specificity of the peptides. For example, when the HAV motif is flanked by a single aspartic acid, which mimics the natural HAVD sequence of N-cadherin, the peptide becomes a much more effective inhibitor of N-cadherin function. In contrast, when the HAV motif is flanked by a single serine, which mimics the natural HAVS sequence of E-cadherin, it loses its ability to inhibit the N-cadherin response. Our results demonstrate that subtle changes in the amino acids that flank the HAV motif can account for cadherin specificity and that small cyclic peptides can inhibit cadherin function. An emerging role for cadherins in a number of pathological processes suggests that the cyclic peptides reported in this study might be developed as therapeutic agents.     

An optimized solid phase synthesis strategy--including on-resin lactamization--of astressin, its retro-, inverso-, and retro-inverso isomers as corticotropin releasing factor antagonists.

This report describes an optimized solid phase synthesis strategy for astressin and new derivatives thereof. The synthesis is based on 9-fluorenylmethyloxycarbonyl/allyl/tert-butyl chemistry. The glutamic acid and lysine residue, which together form the cyclic constraint by coupling of their side chains, were protected by allyl functionalities during the synthesis of the linear peptide. Allyl removal by Pd(0) and the construction of the lactam bridge have been performed on-resin after completion of the chain assembly. This synthetic methodology resulted in high chemical yields (58-72%) and excellent purities of the crude peptides. The peptides were tested for their binding at the corticotropin releasing factor receptor, type 1, and their corticotropin releasing factor antagonistic activity. Furthermore, astressin and its analogs were studied by CD in order to determine the secondary structure in solution. Since the linear form of astressin and also the cyclic inverso isomer were found to be fully inactive, it can be concluded that a cyclic constraint and a right-handed alpha-helix, respectively, are of utmost importance for these peptides to act as corticotropin releasing factor antagonists.     

Identification of a novel N-cadherin antagonist

The cell adhesion molecule, N-cadherin plays a pivotal role in many biological and disease processes. Drugs that modulate N-cadherin function should therefore be useful therapeutic agents. We have used phage display technology to identify amino acid sequences capable of binding to N-cadherin. All of these sequences harbor a Trp residue in the second position from the N-terminus. A synthetic linear peptide containing one of these sequences, H-SWTLYTPSGQSK-NH(2) was found to bind a chimeric protein composed of the N-cadherin ectodomain fused to the immunoglobulin G1 Fc fragment with an affinity (K(D)) of 10.7microM, as determined by surface plasmon resonance. It also blocked the aggregation of beads coated with this chimeric protein. Furthermore, this peptide disrupted adhesion and tube formation by N-cadherin-expressing human umbilical vein endothelial cells in vitro. These observations suggest that N-cadherin antagonists have the potential of serving as anti-angiogenic agents. The peptide, H-SWTLYTPSGQSK-NH(2) should prove useful for studies designed to evaluate N-cadherin function in various biological processes.     

Synthetic peptides based on the calmodulin-binding domain of myosin light chain kinase inhibit activation of other calmodulin-dependent enzymes

Nanomolar concentrations of synthetic peptides corresponding to the calmodulin-binding domain of skeletal muscle myosin light chain kinase were found to inhibit calmodulin activation of seven well-characterized calmodulin-dependent enzymes: brain 61 kDa cyclic nucleotide phosphodiesterase, brain adenylate cyclase, Bordetella pertussis adenylate cyclase, red blood cell membrane Ca++-pump ATPase, brain calmodulin-dependent protein phosphatase (calcineurin), skeletal muscle phosphorylase b kinase, and brain multifunctional Ca++ (calmodulin)-dependent protein kinase. Inhibition could be entirely overcome by the addition of excess calmodulin. Thus, the myosin light chain kinase peptides used in this study may be useful antagonists for studying calmodulin-dependent enzymes and processes.     

Overlapping synthetic peptides as a tool to map protein-protein interactions ̶ FSH as a model system of nonadditive interactions

In earlier work, we used partially overlapped synthetic peptides as a tool to find regions of interaction between the human FSH hormone and its receptor, aiming to find possible antagonists or agonists. Years later, the FSH and FSH receptor 3D structures were reported by other laboratories. The 3D results were in close agreement with the interacting regions predicted by using synthetic peptides. These earlier studies are reviewed here, and the predicted regions of interaction compared to the FSH and FSH receptor 3D structures to illustrate the usefulness of the synthetic peptide strategy to find binding regions. Different contact regions contribute multiplicatively to the high affinity of the entire ligand; thus, peptides covering a fraction of the anchor sites and with low free energy density cannot reach the affinity of the entire molecule. The earlier use of multiple linear regression to find the relevant predictors for effective binding, and a new way to estimate ΔG° and nonadditive interactions for the synthetic peptides in solution, by using the buried surface area (BSA), will be discussed.     

Backbone cyclic pheromone biosynthesis activating neuropeptide (PBAN) antagonists: inhibition of melanization in the moth Spodoptera littoralis (Insecta, Lepidoptera)

Antagonistic and agonistic activities of backbone cyclic (BBC) pheromone biosynthesis activating neuropeptide (PBAN) analogues were evaluated in an attempt to identify potent melanotropic antagonists, to gain an insight into their structure-activity relationship (SAR), and to discover molecules with selective and non-selective melanotropic and pheromonotropic properties. Eight potent melanotropic BBC antagonists and seven agonists were disclosed. SAR studies revealed that the structural requirements of the melanotropic and pheromonotropic agonists and antagonists are different. The cyclic structure of the BBC peptides was unimportant for antagonistic activity, and linearization retained their melanotropic and pheromonotropic antagonistic properties. Comparison of the antagonistic activities of the BBC and precyclic peptides with respect to both functions revealed eight selective antagonists (six that were selective melanotropic antagonists and two selective pheromonotropic antagonists) and four non-selective (melanotropic and pheromonotropic) antagonists. The selective melanotropic antagonists exhibited both, pure or mixed agonistic/antagonistic activities. The selective pheromonotropic compounds were pure antagonists. All non-selective compounds were pure antagonists. Comparison of the agonistic activities of the BBC peptides with respect to both functions revealed six selective melanotropic agonists and one non-selective agonistic compound. All compounds (whether selective or non-selective) exhibited pure agonistic activity. Discovery of the selective compounds hints at the possibility that the receptors that mediate the respective activities may have different properties.     

N-cadherin antagonists as oncology therapeutics

The cell adhesion molecule (CAM), N-cadherin, has emerged as an important oncology therapeutic target. N-cadherin is a transmembrane glycoprotein mediating the formation and structural integrity of blood vessels. Its expression has also been documented in numerous types of poorly differentiated tumours. This CAM is involved in regulating the proliferation, survival, invasiveness and metastasis of cancer cells. Disruption of N-cadherin homophilic intercellular interactions using peptide or small molecule antagonists is a promising novel strategy for anti-cancer therapies. This review discusses: the discovery of N-cadherin, the mechanism by which N-cadherin promotes cell adhesion, the role of N-cadherin in blood vessel formation and maintenance, participation of N-cadherin in cancer progression, the different types of N-cadherin antagonists and the use of N-cadherin antagonists as anti-cancer drugs.     

Synthesis and cytotoxicity of the depsipeptides analogues of callipeltin B

Solid phase synthesis of the cyclic depsipeptides of callipeltin B analogues and evaluation of cytotoxicity of synthetic peptides are described. We attempted to synthesize cyclic depsipeptides via the esterification or the amide bond formation for cyclization steps. In the assay of synthetic peptides, the linear peptide (10) exhibited modest cytotoxicity against HeLa cells.     

Design, structure and biological activity of beta-turn peptides of CD2 protein for inhibition of T-cell adhesion.

The interaction between cell-adhesion molecules CD2 and CD58 is critical for an immune response. Modulation or inhibition of these interactions has been shown to be therapeutically useful. Synthetic 12-mer linear and cyclic peptides, and cyclic hexapeptides based on rat CD2 protein, were designed to modulate CD2-CD58 interaction. The synthetic peptides effectively blocked the interaction between CD2-CD58 proteins as demonstrated by antibody binding, E-rosetting and heterotypic adhesion assays. NMR and molecular modeling studies indicated that the synthetic cyclic peptides exhibit beta-turn structure in solution and closely mimic the beta-turn structure of the surface epitopes of the CD2 protein. Docking studies of CD2 peptides and CD58 protein revealed the possible binding sites of the cyclic peptides on CD58 protein. The designed cyclic peptides with beta-turn structure have the ability to modulate the CD2-CD58 interaction.     

Topical application of integrin antagonists inhibits proliferative retinopathy.

The expression of alphav-integrins is highly selective for angiogenic endothelial cells; ligation inhibition by cyclic RGD peptides prevents pathological neovascularization in tumor or retinopathy models to a large extent. We have previously demonstrated that proliferative retinopathy in a mouse model of retinopathy of prematurity (ROP model) can be reduced by more than 70%. To minimize systemic side effects and unwanted interference with responsive angiogenesis, we investigated topical application of cyclic RGD-peptides. In preliminary experiments, we could exclude any inhibiting effects of the carrier solution containing EDTA, Na2S, mannitol, hydroxyethyl starch, and benzalconium chloride on the inhibitory effect of cyclic RGD peptides. Retinal presence of small molecular-mass integrin antagonists after topical application was confirmed using fluorescein-labeled cyclic RGD peptide. Topical application of the peptide to the eye inhibited proliferative retinopathy in a dose-dependent fashion with a maximum of almost 50%. These results suggest that small molecular-mass peptide antagonists of alphav-type integrins are efficient in inhibiting proliferative retinopathy by topical application.     

CycLS: Accurate,whole-library sequencing of cyclic peptides using tandem mass spectrometry

Cyclic peptides are of great interest as therapeutic compounds due to their potential for specificity and intracellular activity, but specific compounds can be difficult to identify from large libraries without resorting to molecular encoding techniques. Large libraries of cyclic peptides are often DNA-encoded or linearized before sequencing, but both of those deconvolution strategies constrain the chemistry, assays, and quantification methods which can be used. We developed an automated sequencing program, CycLS, to identify cyclic peptides contained within large synthetic libraries. CycLS facilitates quick and easy identification of all library-members via tandem mass spectrometry data without requiring any specific chemical moieties or modifications within the library. Validation of CycLS against a library of 400 cyclic hexapeptide peptoid hybrids (peptomers) of unique mass yielded a result of 95% accuracy when compared against a simulated library size of 234,256 compounds. CycLS was also evaluated by resynthesizing pure compounds from a separate 1800-member library of cyclic hexapeptides and hexapeptomers with high mass redundancy. Of 22 peptides resynthesized, 17 recapitulated the retention times and fragmentation patterns assigned to them from the whole-library bulk assay results. Implementing a database-matching approach, CycLS is fast and provides a robust method for sequencing cyclic peptides that is particularly applicable to the deconvolution of synthetic libraries.     

Cyclic amino acid linkers stabilizing key loops of brain derived neurotrophic factor

Based on β-turn-like BDNF loops 2 and 4, involved in receptor interaction, cyclic peptide replicas were designed, synthesized and tested. In addition to the native turn residues, the cyclic peptides include a linker unit between the N- and C-termini, selected by molecular modeling among various non-proteinogenic cyclic amino acids. NMR conformational studies showed that most of the cyclic peptides were able to adopt turn-like structures. Several of the analogues displayed significant inhibition of the BDNF-induced TrkB receptor phosphorylation, and hence could be useful templates for developing improved antagonists for this receptor.     

Structural diversity of marine cyclic peptides and their molecular mechanisms for anticancer,antibacterial, antifungal,and other clinical applications

Many cyclic peptides and analogues derived from marine sources are known to possess biological properties, including anticancer, antitumor, antibacterial, antifungal, antiparasitic, anti-inflammation, anti-proliferative, anti-hypertensive, cytotoxic, and antibiotic properties. These compounds demonstrate different activities and modes of action according to their structure such as cyclic oligopeptide, cyclic lipopeptide, cyclic glycopeptide and cyclic depsipeptide. The recent advances in application of the above-mentioned cyclic peptides were reported in dolastatins, soblidotin, didemnin B, aplidine, salinosporamide A, kahalalide F and bryostatin 1 and they are currently in clinical trials. These cyclic peptides are possible novel drugs discovered and developed from marine origin. Literature data concerning the potential properties of marine cyclic peptides were reviewed here, and the structural diversity and biological activities of marine cyclic peptides are discussed in relation to the molecular mechanisms of these marine cyclic peptides.     

Novel, potent calmodulin antagonists derived from an all-D hexapeptide combinatorial library that inhibit in vivo cell proliferation: activity and structural characterization.

Calmodulin is known to bind to various amphipathic helical peptide sequences, and the calmodulin-peptide binding surface has been shown to be remarkably tolerant sterically. D-Amino acid peptides, therefore, represent potential nonhydrolysable intracellular antagonists of calmodulin. In the present study, synthetic combinatorial libraries have been used to develop novel D-amino acid hexapeptide antagonists to calmodulin-regulated phosphodiesterase activity. Five hexapeptides were identified from a library containing over 52 million sequences. These peptides inhibited cell proliferation both in cell culture using normal rat kidney cells and by injection via the femoral vein following partial hepatectomy of rat liver cells. These hexapeptides showed no toxic effect on the cells. Despite their short length, the identified hexapeptides appear to adopt a partial helical conformation similar to other known calmodulin-binding peptides, as shown by CD spectroscopy in the presence of calmodulin and NMR spectroscopy in DMSO. The present peptides are the shortest peptide calmodulin antagonists reported to date showing potential in vivo activity.     

Nucleo amino acids as arginine mimetics in cyclic peptides

Summary A general strategy for the synthesis of Fmoc protected nucleobase modifed amino acids is presented. Fmoc protected nucleo amino acids bearing a natural purine (guanine) as well as an artificial purine (isoadenine) in the side chain have been synthesized and incorporated into cyclic pentapeptides. The structure of the cyclic peptides is based on the well known RGD peptides, which act as selective integrin antagonists. The nucleo amino acids serve as conformationally constrained arginine mimetics with a reduced basicity of the guanidino moiety.     

Enantio- and diastereoselective syntheses of cyclic Calpha-tetrasubstituted alpha-amino acids and their use to induce stable conformations in short peptides

C(alpha)-tetrasubstituted alpha-amino acids are widely used to design and prepare peptides and peptide mimics with constrained conformations. Subcategories of these compounds are cyclic C(alpha)-tetrasubstituted alpha-amino acids, in which both alpha-substituents are covalently connected. This survey presents recent advances in the synthesis and application of cyclic C(alpha)-tetrasubstituted alpha-amino acids in a systematic order beginning with cyclopropane amino acids, continuing with four, five, six membered rings, and ring structures larger than six-membered. We discuss synthetic routes to the cyclic C(alpha)-tetrasubstituted alpha-amino acids and their use as conformation determining elements in peptides.     

Diketopiperazines in peptide and combinatorial chemistry.

Diketopiperazines (DKPs), the smallest cyclic peptides, represent an important class of biologically active natural products and their research has been fundamental to many aspects of peptide chemistry. The advent of combinatorial chemistry has revived interest in DKPs for two reasons: firstly, they are simple heterocyclic scaffolds in which diversity can be introduced and stereochemically controlled at up to four positions; secondly, they can be prepared from readily available alpha-amino acids using very robust chemistry. Here synthetic methods, conformation, as well as applications of DKPs are summarized and discussed critically.     

Identification of novel non-peptide CXCR4 antagonists by ligand-based design approach

The design and synthesis of novel non-peptide CXCR4 antagonists is described. The peptide backbone of highly potent cyclic peptide-based CXCR4 antagonists was entirely replaced by an indole framework, which was expected to reproduce the disposition of the key pharmacophores consistent with those of potential bioactive conformations of the original peptides. A structure–activity relationship study on a series of modified indoles identified novel small-molecule antagonists having three pharmacophore functional groups through the appropriate linkers.     

Phosphorylation of atrial natriuretic peptides by cyclic AMP-dependent protein kinase

Atrial natriuretic peptides refer to a family of related peptides secreted by atria that appear to have an important role in the control of blood pressure. The structure of these peptides shows the amino acid sequence Arg101-Arg102-Ser103-Ser104, which is a typical recognition sequence (Arg-Arg-X-Ser) for phosphorylation by cyclic AMP-dependent protein kinase. With this background, we tested two synthetic atrial natriuretic peptides (Arg101-Tyr126 and Gly96-Tyr126) as substrates for in vitro phosphorylation by the catalytic subunit of cyclic AMP-dependent protein kinase. The tested atrial natriuretic peptides were found to be substrates for the reaction. Sequence studies demonstrated that the site of phosphorylation was located, as expected, at Ser104. Kinetic studies demonstrate that both atrial natriuretic peptides are excellent substrates for cyclic AMP-dependent protein kinase. In particular, the longer peptide Gly96-Tyr126 exhibited an apparent Km value of about 0.5 microM, to our knowledge the lowest reported Km for a cyclic AMP-dependent protein kinase substrate. Preliminary studies to measure the biological activity of the in vitro phosphorylated atrial peptides indicate that these compounds are more effective than the corresponding dephospho forms in stimulating Na/K/Cl cotransport in cultured vascular smooth muscle cells.