Combinatorial Biomimetic Chemistry: Parallel Synthesis of a Small Library of β‐Hairpin Mimetics Based on Loop III from Human Platelet‐Derived Growth Factor B

Combinatorial diversity in hypervariable β‐hairpin loops is exploited by the immune system to select binding sites on antibodies for a wide variety of different protein antigens. In a first step towards mimicking this strategy in vitro, for the selection of novel protein ligands, an approach is described here for the parallel synthesis of small libraries of conformationally defined β‐hairpin protein epitope mimetics. Starting from a protruding hairpin loop in platelet‐derived growth factor B (PDGF‐B), 8 and 12 residues were first transplanted from the protein to a D ‐Pro‐L ‐Pro template, to afford the cyclic peptide‐loop mimetics 1 and 2 , respectively. NMR and MD studies in aqueous solution show that both mimetics populate conformations which closely mimic the β‐hairpin in the crystal structure of the native protein (Fig. 5). Based on 1 as a scaffold, a library of 24 mimetics was synthesized in which the four residues at the tip of the loop (VRKK) were held constant, and flanking residues at positions 1, 2, 7, and 8 in the hairpin were varied (Fig. 7). The library was prepared by parallel synthesis in a two‐stage solid‐phase assembly/solution‐phase cyclization process. The products were analyzed by MS, NMR, and CD. 2D‐NOESY revealed for most library members characteristic long‐range NOEs that show that the hairpin conformation is stably maintained. The results suggest that this approach may be useful for the synthesis of much larger libraries of peptide and protein mimetics based on a β‐hairpin scaffold.     

Cyclic Peptidomimetics Derived from the Apical Membrane Antigen I of Plasmodium falciparum and Their Use in Malaria Vaccine Design

A library of 35 cyclic peptidomimetics has been prepared, by a combination of solid‐ and solution‐phase methods, which, together, scan amino acid residues 444–489 in a protruding loop in the subdomain‐III of the apical membrane antigen‐I (AMA‐I), an integral membrane protein found on the surface of Plasmodium falciparum merozoites. The mimetics each contain twelve residues from AMA‐I linked through the N‐ and C‐termini to a β‐hairpin‐inducing template, comprising the dipeptide D ‐proline‐L ‐Apro (Apro=cis‐4‐amino‐L ‐proline). These peptidomimetics were each coupled via the 4‐amino group to a phospholipid, which allows their incorporation into reconstituted influenza virus‐like particles (virosomes) for immunization of mice, as well as their use in ELISA to characterize epitopes recognized by anti‐AMA‐I growth‐inhibitory monoclonal antibodies.     

Reliable folding of hybrid tetrapeptides into short β-hairpins

Five hybrid tetrapeptides, each consisting a central dipeptide segment of α-amino acid residues flanked by two aromatic γ-amino acid residues, are found to fold into well-defined β-hairpin conformations as shown by NMR, computational study, and X-ray structures. The turn loop of this β-hairpin motif accommodates different two-residue α-amino acid sequences from the highly flexible Gly-Gly, to the more restricted D-Pro-Gly. The presence of α-amino acid side chains enhances the stabilities of the ...     

Synthesis and Solution Conformation of β‐Hairpin Mimetics Utilizing a Template Derived from (2S,3R,4R)‐Diaminoproline

A novel template was synthesized for stabilizing β‐hairpin conformations in cyclic peptide mimetics. The template is a diketopiperazine derived formally from L ‐aspartic acid and (2S,3R,4R)‐diaminoproline, the latter being available by an efficient synthetic route from vitamin C. The template was incorporated by solid‐phase peptide synthesis into a cyclic loop mimetic containing the sequence (‐Ala‐Asn‐Pro‐Asn‐Ala‐Ala‐template‐). This mimetic was shown by NMR to adopt a stable β‐hairpin conformation in (D₆)DMSO solution. The template may prove to be generally useful for creating small‐molecule mimetics of hairpin loops on proteins of diverse function.     

A β-hairpin epitope as novel structural requirement for protein arginine rhamnosylation

For canonical asparagine glycosylation, the primary amino acid sequence that directs glycosylation at specific asparagine residues is well-established. Here we reveal that a recently discovered bacterial enzyme EarP, that transfers rhamnose to a specific arginine residue in its acceptor protein EF-P, specifically recognizes a β-hairpin loop. Notably, while the in vitro rhamnosyltransferase activity of EarP is abolished when presented with linear substrate peptide sequences derived from EF-P, the enzyme readily glycosylates the same sequence in a cyclized β-hairpin mimic. Additional studies with other substrate-mimicking cyclic peptides revealed that EarP activity is sensitive to the method used to induce cyclization and in some cases is tolerant to amino acid sequence variation. Using detailed NMR approaches, we established that the active peptide substrates all share some degree of β-hairpin formation, and therefore conclude that the β-hairpin epitope is the major determinant of arginine-rhamnosylation by EarP. Our findings add a novel recognition motif to the existing knowledge on substrate specificity of protein glycosylation, and are expected to guide future identifications of rhamnosylation sites in other protein substrates.

For bacterial arginine rhamnosylation, the rhamnosyltransferase EarP specifically recognizes a β-hairpin structure in the acceptor substrate.     

A Chirally Stable,Atropoisomeric, Cα‐Tetrasubstituted α‐Amino Acid: Incorporation into Model Peptides and Conformational Preference

A variety of model peptides, including four complete homologous series, to the pentamer level, characterized by the recently proposed binaphthyl‐based, axially chiral, C^α‐tetrasubstituted, cyclic α‐amino acid Bin, in combination with Ala, Gly, or Aib residues, was synthesized by solution methods and fully characterized. The solution conformational propensity of these peptides was determined by FT‐IR absorption and ¹H‐NMR techniques. Moreover, the molecular structures of the free amino acid (S)‐enantiomer and an N^α‐acylated dipeptide alkylamide with the heterochiral sequence ‐(R)‐Bin‐Phe‐ were assessed in the crystal state by X‐ray diffraction. Taken together, the results point to the conclusion that β‐bends and 3₁₀ helices are preferentially adopted by Bin‐containing peptides, although the fully extended conformation would also be adopted in solution by the short oligomers to some extent. We also confirmed the tendency of (R)‐Bin to fold a peptide chain into right‐handed bend and helical structures. The absolute configuration of the Bin residue(s) was correlated with the typically intense exciton‐split Cotton effect of the ¹B_b binaphthyl transition near 225 nm.     

Synthesis of a Novel Tricyclic Dipeptide Template and Its Incorporation into a Cyclic Peptide Mimetic Containing an NPNA Motif

A novel tricyclic dipeptide template, formally derived by coupling (2S,4S)-4-aminoproline (Pro(NH₂)) and (S)-2-(carboxymethyl)proline (Pro(CH₂COOH)) as a diketopiperazine, has been synthesized in a form suitable for solid-phase peptide synthesis using Fmoc chemistry. This template was incorporated into the cyclic molecule cyclo(-Ala¹-Asn²-Pro³-Asn⁴-Ala⁵-Ala⁶-Temp-) (Temp = template), whose conformation in H₂O was studied by NMR methods. Average solution structures derived by restrained simulated annealing point to a highly populated βI-turn within the Asn-Pro-Asn-Ala motif and also indicate which conformations are likely to be preferred by the template.     

Synthesis of a Type-VIβ-Turn Peptide Mimetic and Its Incorporation into a High-Affinity Somatostatin Receptor Ligand

The synthesis of a cis-Phe-Pro dipeptide mimetic is described, which adopts a type-VIβ-turn conformation. In this mimetic, the α-positions of Phe and Pro are joined by a CH₂CH₂ bridge, thereby forming a fused bicyclic system, and fixing a geometry similar to that seen in cis-Phe-Pro units in protein crystal structures. The dipeptide mimetic 20 was synthesized in optically pure form starting from (R)-α-allylproline ( 6 ; Schemes 1, 3, and 4), with a free carboxylic acid and an Fmoc-protected N-terminus, thereby allowing its incorporation into linear and cyclic peptides using standard solid-phase methods. The mimetic 20 was incorporated into the cyclic somatostatin analogue cyclo(-Phe = Pro-Phe-D -Trp-Lys-Thr-), where Phe = Pro represents the mimetic. This analogue shows a high affinity (pIC₅₀ 8.6) for somatostatin receptors on rat-brain cortex membranes. Based on NMR studies in aqueous solution, likely low-energy conformations for this analogue were deduced using restrained dynamic simulated annealing. The conformations found, which include a distorted type-II′ turn at D -Trp-Lys, are similar to low-energy conformations deduced elsewhere for cyclo(-Phe-Pro-Phe-D -Trp-Lys-Thr-), as well as to those seen in crystal structures of the somatostatin analogue octreotide.     

Design,synthesis and structural analysis of mixed α/β-peptides that adopt stable cyclic hairpin-like conformations

The strategic replacement of four α-amino acid residues of a cyclo-(ααααα)₂ peptide by β-, β²- or β³-amino acids residues provided a series of novel 2:1 α/β-mixed peptides that were designed to adopt cyclic hairpin-like structures. It was shown that conformationally stable cyclo-(αβαβα)₂ isomers can be obtained using both enantiomers of the central two basic α-amino acid residues, a known α-amino acid turn sequence and several combinations of facing β-amino acid residues with no side chain or a hydrophobic side chain having specific regio- and stereochemistry. The X-ray analysis of two derivatives provides molecular details of the intra-molecular hydrogen bonding interaction, dihedral angles of the backbone and side chain positioning of the novel cyclic hairpin-like structures. One of these isomers forms an unprecedented hexagon-shaped nano-channel assembly in the crystal structure. Well-defined cyclic hairpin-like structures as described here and derivatives that can be readily designed based on this research can be used as scaffolds onto which functional groups can be grafted in a spatially controlled manner and as β-hairpin mimics with specific biological properties.     

Synthesis and Conformational Studies of a Hybrid Cyclic Peptide Based on cis‐β‐Furanoid Sugar Amino Acid (FSAA) and Ornithine

The conformational control of a 14‐helix nucleating template, cis‐β‐furanoid sugar amino acid (FSAA), over a flexible δ‐amino acid, ornithine is studied in a FSAA‐ornithine cyclic tetrapeptide. Extensive NMR and MD studies reveal that the cyclic peptide adopts a three‐dimentional bowl‐shape cavity, which promotes six‐ and seven‐membered intra‐ and inter‐residue H‐bonding, in polar and non‐polar solvents, respectively.     

Linear,Peptidase‐Resistant β2/β3‐Di‐ and α/β3‐Tetrapeptide Derivatives with Nanomolar Affinities to a Human Somatostatin Receptor,Preliminary Communication

N‐Acyl‐β²/β³‐dipeptide‐amide somatostatin analogs, 5 – 8 , with β²‐HTrp‐β³‐HLys ('natural' sequence) and β²‐HLys‐β³‐HTrp (retro‐sequence) have been synthesized (in solution). Depending on their relative configurations and on the nature of the terminal N‐acyl and terminal C‐amino group, the linear β‐dipeptide derivatives have affinities for the human receptor hsst 4, ranging from 250 to >10000 nanomolar (Fig. 3). Also, N‐Ac‐tetrapeptide amides 9 and 10 , which contain one α‐ and three β‐amino acid residues (N‐β‐α‐β‐β‐C), have been prepared (solid‐phase synthesis), with the natural (Phe, Trp, Lys, Thr) and the retro‐sequence (Thr, Lys, Trp, Phe) of side chains and with two different configurations, each, of the two central amino acid residues. The novel ‘mixed', linear α/β‐peptides have affinities for the hsst 4 receptor ranging from 23 to >10000 nanomolar (Fig. 4), and, like ‘pure' β‐peptides, they are completely stable to a series of proteolytic enzymes. Thus, the peptidic turn of the cyclic tetradecapeptide somatostatin (Fig. 1) can be mimicked by simple linear di‐ and tetrapeptides. The tendency of β‐dipeptides for forming hydrogen‐bonded rings is confirmed by calculations at the B3LYP/6‐31G(d,p) level (Fig. 2). The reported results open new avenues for the design of low‐molecular‐weight peptidic drugs.     

A Tricyclic Template Derived from (2S,4R)-4-Hydroxyproline for the Synthesis of Protein Loop Mimetics

A tricyclic diketopiperazine, formally derived by coupling (2S,4S)-4-aminoproline (Pro(NH₂)) and (2S,4R)-4-(carboxymethyl)proline (Pro(CH₂COOH)), is synthesized starting from readily available (2S,4R)-4-hydroxyproline. The resulting tricyclic template has carboxy and amino groups to which a peptide chain may be attached. The Fmoc-protected template 5 is incorporated into the cyclic molecule cyclo(-Ala¹-Asn²-Pro³-Asn⁴-Ala⁵-) ( 6 ) where Pro(NH₂)⁷ = Pro(CH₂COOH)⁸ represents the template, using solid-phase peptide synthesis with cyclization in solution. The molecule is shown by NMR and dynamic simulated annealing methods to adopt a preferred conformation in aqueous solution, which includes an extended backbone at the residues Asn²-Pro³-Asn⁴, and a type-Iβ-turn at . These studies show that this novel template may be used in the synthesis of cyclic peptide and protein mimetics having defined secondary structure in aqueous environments.     

Automated Solid‐Phase Synthesis and Structural Investigation of β‐Peptidosulfonamides and β‐Peptidosulfonamide/β‐Peptide Hybrids: β‐Peptidosulfonamide and β‐Peptide Foldamers are Two of a Different Kind

Fmoc‐protected β‐aminoethane sulfonylchlorides can be employed for efficient automated solid phase synthesis of β‐peptidosulfonamides and β‐peptidosulfonamide/β‐peptide hybrids containing one or more β‐peptidosulfonamide residues. Thus, Fmoc‐protected β‐aminoethane sulfonylchlorides 5a – c led to the hexa‐β‐peptidosulfonamide 9 and the nona‐β‐peptidosulfonamide 10 . In addition, the β‐peptidosulfonamide/β‐peptide hybrids 13 and 16 , consisting of six and nine β‐residues, respectively, and containing a single β‐peptidosulfonamide unit in the middle, as well as the peptidosulfonamide/β‐peptide hybrid 15 with nine β‐residues, including an N‐terminal β‐peptidosulfonamide residue, were synthesized by automated solid‐phase synthesis. Both CD and NMR spectroscopic measurements did not indicate any helical secondary structure for 9 and 10 . As was shown by CD‐measurements, the β‐peptidosulfonamide residue in the hybrids 13, 15 , and 16 acts as a ‘helix breaker', especially when located in the middle of the hybrid chain ( 13 and 16 ), but, although to a lesser extent, also at the N‐terminus.     

Interfacial supramolecular biomimetic epoxidation catalysed by cyclic dipeptides

We synthesised a library of cis- and trans-cyclic dipeptides and evaluated their efficacy as catalysts in the asymmetric Weitz-Scheffer epoxidation of trans-chalcone. A thorough investigation relying on structure-activity studies and computational studies provided insights into the mechanism of the process. Our results revealed some structural features required for efficient conversion and for introduction of chirality into the product. The cyclic dipeptide acts as a catalyst by templating a supramolecular arrangement at the aqueous-organic interface required for efficient transformations to occur. Among all cyclic dipeptides investigated, cyclo(Leu-Leu) was the most efficient supramolecular catalyst.     

Der Einfluss von D-Aminosäureresten auf das konformative Verhalten von Kollagenmodellpeptiden

The influence of D -amino acid residues upon the conformative behaviour of collagen model peptides. (L -Pro-L -Pro-Gly)₁₀ and (L -Pro-D (L )-Pro-Gly)₁₀ with 10 percent D -Prolin residues have been synthesized by the Merrifield technique. Further Poly-(Gly-Pro-Pro) and Poly-(Ala-Gly-Pro) with various amounts of D -amino acid residues have been synthesized by polycondensation of the proper tripeptides. The conformational behaviour of all these polypeptides has been studied by measurements at varying temperatures of optical rotation, circular dichroism and molecular weight. The results show that limited amounts of D -amino acid residues do not impedecollagen-like triple helical conformations. The denaturation temperatures, however, are considerably lowered by D -amino acid residues. The implications of these findings for the understanding of the properties of partially racemized degraded gelatins with relatively low gel melting points are discussed.     

Intramolecular Transfer of Excitation Energy,Complexation with Metal Ions,and Interactions with Liposomes of Cyclo [tryptophyl-sarcosyl-sarcosyl-Nϵ-dansyllysyl-prolyl]

A cyclic pentapeptide containing an energy donor group and an energy acceptor group within the molecule, cyclo [Trp-Sar-Sar-Lys (DNS)-Pro], was synthesized. Its conformation, complexation with metal ions, intramolecular energy transfer, and interaction with liposomes were investigated. The precursor, cyclo [Trp-Sar-Sar Lys ( Z )-Pro], contained one cis-sarcosyl peptide bond and a β-turn in which the Pro-residue occupied the 3rd position. This cyclic pentapeptide formed a complex selectively with Ba²⁺ and its binding constant in 95% aqueous methanol solution was 2.0 × 10³ 1 · mol^?1. The intramolecular energy-transfer efficiency of cyclo [Trp-Sar-Sar-Lys (DNS)-Pro] was almost constant between ? 60° and 40° in ethanol, while it increased at temperatures lower than 34° in liposomes as a result of the pre-transition of the lipid assembly. On the other hand, the intramolecular energy transfer efficiency of cyclo [Trp-Sar-Sar-Lys (DNS)-Pro] decreased upon complexation with Ba²⁺.     

Mixed Oligoureas Based on Constrained Bicyclic and Acyclic β‐Amino Acids Derivatives: On the Significance of the Subunit Configuration for Folding

The combination of a non‐functionalized constrained bicyclo[2.2.2]octane motif along with urea linkages allowed the formation of a highly rigid 2.5_12/14 helical system both in solution and the solid state. In this work, we aimed at developing stable and functionalized systems as promising materials for biological applications in investigating the impact of this constrained motif and its configuration on homo and heterochiral mixed‐oligourea helix formation. Di‐, tetra‐, hexa‐, and octa‐oligoureas alternating the highly constrained bicyclic motif of (R) or (S) configuration with acyclic (S)‐β³‐amino acid derivatives were constructed. Circular dichroism (CD), NMR experiments, and the X‐ray crystal structure of the octamer unequivocally proved that the alternating heterochiral R/S sequences form a stable left‐handed 2.5‐helix in contrast to the mixed (S/S)‐oligoureas, which did not adopt any defined secondary structure. We observed that the (?)‐synclinal conformation around the C_α? C_β bond of the acyclic residues, although sterically less favorable than the (+)‐synclinal conformation, was imposed by the (R)‐bicyclic amino carbamoyl (BAC) residue. This highlighted the strong ability of the BAC residue to drive helical folding in heterochiral compounds. The role of the stereochemistry of the BAC unit was assessed and a model was proposed to explain the misfolding of the S/S sequences.     

Synthesis of Unnatural Lipohilic N-(9H-Fluoren-9-ylmethoxy)carbonyl-Substituted α-Amino Acids and Their Incorporation into Cyclic RGD-Peptides: A structure-activity study

The α_v/β₃ integrin is implicated in human tumor metastasis and angiogenesis. It has been shown that structures of the sequence cyclo(-Arg¹-Gly²-Asp³-D -Phe⁴-Xaa⁵-) ( I ) and cyclo(-Arg¹-Gly²-Asp³-Phe⁴-D -Xaa⁵-) ( II ) bind with high affinity and the latter with high selectivity to this receptor. The residues Xaa and D -Xaa accept a broad variety of amino acids. Here, we report on the synthesis, activities, and conformational analysis of cyclic Arg-Gly-Asp (RGD) peptides containing liophilic amino acids Xaa or D -Xaa in position 5. For I , these were (2S)-2-aminohexadecanoic acid (Ahd) and N′-hexadecylglycine (Hd-Gly) and in II , D -Ahd and Hd-Gly, and, for control purposes, Ahd were incorporated (Fig. 1). The enantiomerically pure a-amino acids were obtained by non-enantioselective synthesis and subsequent enzymatic separation of isomers using acylase I (Scheme). Hd-Gly was prepared in a modified procedure according to Stewart from ethyl bromoacetate and hexadecylamine (Scheme). The synthesis and physicochemical properties of the corresponding (9H-fluoren-9-ylmethoxy)carbonyl (Fmoc) derivatives, compatible with solid-phase peptide synthesis, are described. Structure elucidation by NMR reveals that the lipid modification has no significant impact on the template structures when incorporated into them. For peptides I with Xaa = Ahd or Hd-Gly ( 1 or 2 ), a βII′/γ-turn-like arrangement with D -Phe in i+1 position of the β-turn is found. Peptides II with D -Xaa = D -Ahd or Hd-Gly ( 3 or 4 ) exhibit a βII′/γ-turn conformation with Gly in i+1 position of the β-turn, whereas II with Ahd instead of D -Xaa, i.e., lacking a D -amino acid in position 4 or 5 ( 5 ). adopts no defined conformation. However, in assays of receptor specificity employing human α_vv/β₃ integrin, the compounds exhibit IC₅₀ values ranging from nanomolar to less than millimolar. These results indicate that although the arrangement of the pharmacophoric groups is preserved in the target compounds, the biological activity is highly dependent on spatial requirements of the lipid anchor in the receptor binding pocket. Obviously, only certain positions do not affect the binding.     

Design of Amphiphilic Peptide Geometry towards Biomimetic Self‐Assembly of Chiral Mesoporous Silica

In nature, diatoms and sponges are exquisite examples of well‐defined structures produced by silica biomineralisation, in which proteins play an important role. However, the artificial peptide templating route for the silica mesostructure remains a formidable and unsolved challenge. Herein, we report our effort on the design of amphiphilic peptides for synthesising a highly ordered two‐dimensional (2D)‐hexagonal and lamellar chiral silica mesostructure using trimethoxysilylpropyl‐N,N,N‐trimethylammonium chloride as the co‐structure directing agent (CSDA). The geometry of the peptide was designed by adding proline residues into the hydrophobic chain of the peptide to break the β‐sheet conformation by weakening the intermolecular hydrogen bonds; this led to the mesophase transformation from the most general lamellar structure to the 2D hexagonal P6mm mesostructure by increasing the amphiphilic molecules packing parameter g. Enantiomerically pure chiral mesostructures were formed thanks to the intrinsic chirality and relatively strong intermolecular hydrogen bonds of peptides.     

Der Einfluss der O-Acetylierung auf das konformative Verhalten des Kollagen-Modellpeptides (L-Pro-L-Hyp-Gly)10 und von Gelatine

The Influence of O-Acetylation upon the Conformational Behaviour of the Collagen Model Peptide (L -pro-L -Hyp-Gly)₁₀ and of Gelatin (L -Pro-L -Hyp-Gly)₁₀ which can be considered as a model peptide for collagen structure studies has been synthesized by the Merrifield technique. Subsequently, the hydroxyprolin residues have been acetylated by acetic acid anhydride in trifluoroacetic acid. In the same way, the hydroxyl groups of commercial bovine gelatin have been selectively acetylated. The influence of blocking the hydroxyl groups upon the thermal stability of the tripel helix formed by (L -Pro-L -Hyp-Gly)₁₀ and upon the transition temperature and the gel stability of the gelatin has been investigated by the measurement of optical rotation, circular dichroism, molecular weights and gel melting points. The results show that O-acetylation reduces the thermal stability of the collagen-like tripel helices formed in solution by the synthetic peptide and during the gelation process of gelatin. Our experiments support data previously published by various authors indicating that the hydroxyl group of hydroxyprolin plays an important role in stabilizing the collagen tripel helix. The possibility to use O-acetylated gelatin with its reduced gel forming capability for the preparation of plasma substitute solutions is discussed.