Polymer-supported synthesis of a close analog (i.e. A) of an early lead, a 14- membered ring peptidomimetic D3, was described. The monovalent molecule was attached to different length linkers, and they were then paired sequentially on a triazine scaffold via our previously published methodology to give a small library of bivalent compounds 1 representing all combinations of linkers of the different lengths in a fast and efficient combinatorial manner. Cellular assays identified 1-ss as a TrkA receptor antagonist towards NGF and it was shown to bind TrkA with ~200 nM affinity and retains high selectivity towards TrkA in binding assays. A set of monovalent diketopiperazine (DKP) mimics 4-7 was synthesized efficiently from corresponding dipeptides via intramolecular SN2 cyclization reactions in solution. These DKP compounds contain two amino acid side-chain functionalities to mimic the sequences that occur at “hot-spots” in loop regions. The monovalent mimics were assembled into a library of biotin-labeled bivalent molecules 9 via the combinatorial strategy described above with some modification. In primary screening, compound 9gg showed preferential binding to TrkC receptors in FACScan assay and blocked the trophic activity of NT-3 in TrkC cells at 10 uM in cell survival assay. The preparation of monovalent 1,3,4-oxadizole-based mimics 12 was achieved from corresponding amino acid building blocks on gram scale in a highly efficient solution phase parallel synthesis manner in good yields. These heterocyclic compounds feature various natural amino acid side-chain functionalities including those occuring most frequently at hot-spots such as those of Tyr, Lys, Glu and Ser. Attempts to assemble them into bivalent molecules were done by coupling the monovalent mimics to the triazine scaffold sequentially in solution and simply manipulating the solvent systems. For some reasons, some reactions did not proceed cleanly. Studies have been carried out and the problems were partially solved. The biological activities of these oxadiazoles are under investigation. So far, six compounds have shown activities in four different bioassays. Two different peptidomimetic types that resemble protein A and protein G binding regions were generated and tested as binding factors in affinity columns for purification of IgG. They are cyclic hexapeptides 19, which were prepared via Fmoc- SPPS and solution phase intramoleculer macrocyclization, and heterocycle-based small molecules 22 and 23 featuring a variety of aromatic functionalities generated via solution phase parallel synthesis. Four compounds showed some affinity towards a Fab fragment of IgG in SAR screening, and they were attached to a dendrimer core on a solid support to give four multivalent mimetics 25.

Copper-mediated alkyne-azide cycloadditions yield 1,4-disubstituted triazoles with high chemoselectivity that can be used in many ways. For instance, when alkyne or azido peptide units combine via this pathway the reaction is relatively insensitive to the amino acid side-chains. This serves as an excellent way to produce peptidomimetics, particularly because there is some stereoelectronic similarity between 1,2,3-triazoles and amide bonds. Linear peptidomimetic substrates 60 were used to form the cyclic derivatives 61 via copper catalyzed azide alkyne cycloadditions. This reaction is fast, simple to perform and compatible with many solvents and functional groups. A library of eight cyclic peptidomimetics was prepared in solution and the low yield was mostly due to formation of dimers. Computational, NMR, and CD analyses of compounds 61a-c indicate that their most favorable conformational states include type I and type II β-turn conformations. Monovalent triazole mimics were prepared via cycloaddition reactions in solution. These triazole compounds contain two amino acid chain functionalities at 1- and 4- positions. One is derived from a natural amino acid and the other is a functional group that resembles the side chains of an amino acid. The 1,3-dipolar cycloaddition reactions allow quick and efficient generation of the desired peptidomimetics in good yields. Two monovalent mimics were coupled to the linker scaffold sequentially in solution by simply manipulating the solvent systems. This method allows us to prepare large libraries of bivalent compounds quickly and efficiently. The two monomers were combined with each other cleanly, to achieve one-compound-per-well in sufficient purity for biological testing. Oxidative coupling to give 5,5’-bistriazoles is discussed. The bistriazole products predominate in the copper accelerated “click reaction” of alkynes and azides when carbonate bases are used as additives (ca 1 – 2 M). The reaction seems to be more efficient for propargylic ethers and less hindered substrates. Use of optically active azides could afford separable atropisomeric products, providing a convenient access into optically pure derivatives.

This thesis describes investigations into the synthesis and secondary structural properties of novel carbohydrate-derived peptidomimetics. The syntheses from diacetone-D-glucose of five diastereomeric 3-azido-tetrahydrofuran carboxylates are described. These highly functionalised β-amino acid equivalents are accessed via the diacetone-3-azido-3-deoxy sugars and 3-azido-3-deoxy-1,4-lactones. An acid-catalysed rearrangement results in the formation of the tetrahydrofuran ring with the protected amine functionality already in place in a position β- to the carboxylate group. Attempts to synthesise "carbopeptoids" via various oligomerisation strategies, including three novel approaches to oligomerisation, are delineated. The first approach attempted involves an iterative addition of a bicyclic lactone, which acts as the activated acid component, to the substrate containing an amine functionality. A new solid-phase oligomerisation strategy, whereby the coupling reagent is tethered to the polystyrene support and the substrates remain in solution, is described. The third attempted novel oligomerisation strategy involves activation by microwave irradiation, in the absence of coupling reagents. The conventional coupling using a carbodiimide coupling reagent proves to be a highly efficient means to access oligomers up to six residues in length, and is utilised for the synthesis of the homooligomers of four diastereomeric carbohydrate-derived β-amino acids. The prospect that the carbopeptoids may emulate the helical conformations reported for closely related 2-aminocyclopentanecarboxylic acid oligomers is investigated. Different methods of spectroscopic analysis of the tetrameric and hexameric oligomers are discussed. Circular dichroism spectroscopy provides a rapid diagnostic tool for the investigation of peptide bond orientations and forms the basis for a postulation on a possible stabilised hydrogen-bonding secondary structural conformation in two tetrameric species. Several nuclear magnetic resonance spectroscopic experiments are performed, enabling the assignment of each signal in the proton spectrum for a hexameric oligomer. However the resulting data does not provide sufficient evidence for a well-defined secondary structural motif, and so the potential conformational preference postulated on the basis of circular dichroism spectroscopy is not confirmed.

In an effort to partially mimic the complex interaction between nerve growth factor (NGF) and its membrane-bound tyrosine kinase A receptor (TrkA), several small organic molecules with functionalities similar to the side-chains of the amino acid residues of NGF critical to binding were devised. These molecules were studied computationally using the program Affinity. Each molecule was individually docked onto one of the binding sites on TrkA as determined by mutagenesis studies and the x-ray crystal structure obtained from the Protein Data Bank. One of the strategies to enhance binding of active peptidomimetics to their target proteins is to link them together to form either homodimers or heterodimers. However, these dimers have low solubility in water and mimic only residues that are close together on the protein. Triethylene oxide- and hexaethylene oxide-based linker molecules were designed to circumvent these limitations. The increased polarity will improve the watersolubility and the added lengths, which can be controlled and varied by simple chemical manipulations, will allow for mimicking critical residues that are farther apart on the protein.

The synthesis of 5-membered heterocyclic rings that bear both amine and carboxylic acid functional groups has been investigated using a 1,3-dipolar cycloaddition reaction strategy. These molecules, on incorporation into a chain of amino acids, have the potential to restrict the conformational freedom of the peptide. Cycloaddition of a nitrile oxide, derived from a Boc-protected naturally-occurring a-amino acid, with a pyrrolidine en amine led to a Boc-protected 3-aminoalkylisoxazole amino acid ester. The nitrogen and carbon termini of this isoxazole were coupled to other a-amino acids. Analysis of the dipeptide from coupling to (S)-alanine indicated that the integrity of the chiral centre of the isoxazole had been retained during the synthesis. Molecular modelling of a tripeptide unit incorporating the isoxazole showed that the presence of the ring had, as intended, restricted the conformational freedom of the molecule. Analogous cycloadditions using azomethine imines as the dipole yielded the corresponding tetrahydropyrazoles (pyrazolidines). These dipoles were generated by reaction of an aldehyde with a 1,2-disubstituted hydrazine, followed by elimination of the elements of water from the resulting aminol. Reaction with a dipolarophile bearing an electron withdrawing substituent gave predominantly the 4-substituted pyrazolidine. A study of the scope of the reaction found that, although the required carboxylic acid group could easily be incorporated by use of methyl acrylate as the dipolarophile, it proved impossible to attach an amine group to the ring using this methodology. However, by using one of the nitrogen atoms in the ring as the N-terminus, two pyrazolidines with protected amine and carboxylic acid groups were prepared, and these can be thought of as conformationally restricted B-amino acids.

No description available.

Peptides are short, sequence and length specific oligomers composed of small amino acid residues. Nature has refined these peptide sequences and their endogenous function through evolution. In addition, peptides have played an important role in medicine, which has lead to further research into developing peptides as lead pharmaceuticals (therapeutic peptides). Unfortunately, therapeutic peptides are inferior as drug candidates due to their low oral bioavailability; immunogenicity and potential to be attacked by peptidases. Fortunately, peptides can be modified by steric constraints, cyclization, and/or replacement of the peptide backbone itself creating a mimic (peptidomimetic) of the original peptide. Peptidomimetics are deliberately designed to have increased protease resistance, reduced immunogenicity and improved bioavailability when compared to the original endogenous peptide. One such peptide, Magainin is a O One such peptide, Magainin is a well-studied, a-helical peptide found in African clawed frogs. This peptide has antibiotic properties (against pathogenic bacteria), which partly arises from the hydrophilic portion of the peptide having basic amino acid side chains periodically disposed on one side of the a-helix. This property of magainin causes its attraction to negatively charged bacteria cell membranes. Unfortunately, as in the case of other antibiotics, pathogenic bacteria have developed effective countermeasures against magainin. We designed a peptidomimetic based on magainin and implemented a plan to determine what type of molecules could be assembled for a magainin mimic. We successfully utilized molecular modeling (Monte Carlo conformational search), as well as results from previous experiments to elucidate what type of molecules, as well as how many molecules would be necessary to create a novel helical-like magainin peptidomimetic. It was discovered that C2 symmetric diamines would be best at generating the helical-like motif and the amino acid lysine to generate the basic side chain. The next step was the successful connection of two C2 symmetric molecules via a urea linkage and then one more connection to a lysine (a-amino group) residue, creating a short sequence of oligoureas (trimers). Finally, attempts to connect the oligoureas trimers were attempted using a solid-phase synthesis approach to generate a functional magainin mimic.

Grâce à des propriétés physico-chimiques particulières, le fluor prend de plus en plus d’importance dans la chimie médicinale et plus particulièrement dans les peptidomimétiques. Dans ce mémoire, deux classes de peptidomimétiques fluorées ont été étudiées.Dans la première partie, de nouveaux groupements N-Rf ; les hydrazines difluoro ou trifluorométhylées et les 1,2,3 triazoles N-difluorométhylés ont été préparés et des études de leurs propriétés structurales ont montré l’intérêt de l’incorporation du fluor sur la conformation des pseudopeptides via des interactions NH-F.Dans la seconde partie, de nouveaux peptidomimétiques comportant des groupements cyclopropanes trifluorométhylés ont été conçus et synthétisés en tant qu’inhibiteurs potentiels du protéasome 26S (un macro-complexe protéique impliqué dans la dégradation de nombreuses protéines intracellulaires et qui a fait ses preuves en tant que cible pour le traitement de cancers). / Through special physico-chemical properties, fluorine is becoming increasingly important in medicinal chemistry and particularly in peptidomimetics. In this paper, two classes of fluorinated peptidomimetics were studied.In the first part, new N-Rf moieties; difluoro or trifluoromethylated hydrazines and N-difluoromethyl 1,2,3 triazoles were prepared and the study of their structural properties have shown the benefit of the incorporation of fluorine on the conformation of the peptidomimetics via NH-F interactions.In the second part, new trifluoromethylated cyclopropanes containing peptidomimetics were designed and synthesized as potential inhibitors of the 26S proteasome, a macro-complex protein involved in the degradation of many intracellular proteins and which has been recognized as a target for cancer treatment.

<p>The G protein-coupled receptors (GPCRs) are important targets in drug discovery. In several cases, the endogenous ligands that activate the GPCRs of pharmaceutical interest are peptides. Unfortunately, peptides are in general not suitable as drugs, since the peptide structure is associated with several disadvantages, such as low oral bioavailability, rapid degradation and low receptor subtype selectivity. Thus, there is a strong need for drug-like nonpeptide ligands to peptide-activated GPCRs. However, to discover nonpeptide ligands that mimic the effect of the endogenous peptide, i.e. peptidomimetics, is a tremendous challenge. In fact, morphine and the related opioids were the only known examples of peptidomimetics before 1995 and these ligands were known long before the native endogenous peptide ligands were discovered. </p><p>The main objective of the work described in this thesis was to design, synthesize and biologically evaluate selective nonpeptide agonists to the peptide-activated GPCR AT₂. The AT₂ receptor belongs to the renin–angiotensin system, where the octapeptide angiotensin II (Ang II) is the major effector peptide. Ang II mediates its effects through the two GPCRs AT₁ and AT₂. The AT₁ receptor is already an established target in the treatment of hypertension. The physiological role of the AT₂ receptor, which is up-regulated in certain pathological conditions, is not fully understood but it seems to include positive effects such as vasodilatation, tissue repair, tissue regeneration and neuronal differentiation. </p><p>In the current investigation we started from the nonpeptide and nonselective (AT₁/ AT₂) compound L-162,313. This ligand is a known AT₁ receptor agonist but its effect on the AT₂ receptor was unknown at the start of this project. We were able to show that it acts as an agonist also at the AT₂ receptor. Furthermore, stepwise synthetic modifications of L-162,313 led to the identification of the first selective nonpeptide AT₂ receptor agonist. Following the discovery of this compound several selective nonpeptide AT₂ receptor agonists were identified. It was also revealed that a minor structural alteration of one of these compounds interconverted the functional activity from agonism to antagonism. The structural requirement for agonism vs antagonism was therefore studied. The functionality switch was suggested, at least partly, to be due to the spatial relationship between the methyleneimidazole group and the isobutyl side chain of the compounds. To further investigate the bioactive conformation(s) of this series of compounds enantiomerically pure analogues with conformationally constrained isobutyl chains were prepared. This study revealed that the direction of the isobutyl side chain determine whether the compounds act as agonists or antagonists at the AT₂ receptor. Further investigations are required to fully elucidate the bioactive conformation(s) of these nonpeptide AT₂ receptor agonists.</p><p>We believe that the selective nonpeptide AT₂ receptor agonists and antagonists identified in this thesis will serve as important research tools in the continuing investigation of the physiological role of the AT₂ receptor. We also believe that these drug-like compounds might provide potential leads in drug discovery processes.</p>

Quenched Molecular Dynamics (QMD) used to explore molecular conformations was developed to operate in Insight II platform for two simulation engines: CHARMm and Discover. Two scripts and procedures were written for molecular minimization, dynamics, minimization of each of several hundred conformers, and cut off. Experience with Insight II/Discover versus Quanta/CHARMm, and between Insight II/CHARMm versus Quanta/CHARMm has taught that the forcefield is the key factor in QMD studies. Protein A has been used for the purification of commercial antibodies, but it is expensive. Seven peptidomimetics of protein A were designed based on the hot-spots located at the helix-loop-helix region of protein A, and synthesized via solid phase using the Fmoc approach. These peptidomimetics were characterized by MS and NMR. The conformations of four peptidomimetics were studied by NMR and CD in water/hexafluoroisopropanol (pH 4). The CD and NMR data show that addition of hexafluoroisopropanol stabilizes their a-helical conformations. The structures of these peptidomimetics in solution were generated with Quanta/CHARMm using NMR data as limits for the QMD technique. Protein G has also been used to purify antibodies, but it is expensive too. A number of protein G mimics were designed as trivalent molecules. An efficient preparation of trivalent molecules having a useful primary amine arm has been developed through solid phase synthesis. The cheap, commercially available poly(propylene imine) dendrimers were used as scaffolds which allow multimerization of functionalized compounds. A small library of trivalent compounds were synthesized using this approach. A portion of compounds in this library were tested by Amersham Biosciences. The seven amino acid modified DAB-Am-4 exhibits strong binding to the IgG/Fab, and is a potential ligand for IgG purification. The interactions between neurotrophins (ie NGF and NT-3) and their receptors are typical drug targets. Fourteen second-generation peptidomimetics showing NGF-like or NT3-like activities in a preliminary bioassay, were resynthesized and tested again. Preliminary and retested data were compared. To access a direct binding assay, five fluorescently labeled peptidomimetics 41a-e were synthesized for a fluorescence activated cell sorting (FACScan) assay. Six monomeric precursors 42 and 43 were prepared on large scales for the library of bivalent turn analogs