Solid-phase syntheses of two 14-membered ring peptidomimetics were done to determine whether or not a beta-turn structure can facilitate macrocyclization. NMR methods, together with CD and QMD calculations, do not fully support this assumption. However, cyclizations of more ordered structures like those of compounds 2 were more efficient than those for highly strained ring systems like 1. A small library of 18-membered ring peptidomimetics that accommodate an extra amino acid residue was synthesized on resin. Their syntheses were not complicated by head-to-tail dimer impurity, unlike those for previously synthesized 14-membered systems. These larger macrocycles exhibit beta-turn structures as verified by NMR, CD and QMD techniques. Moreover, two compounds in this series (3a and 3g) were shown to have agonistic properties for TrkC in cell survival assays. Dimerization of monovalent mimics was achieved first by modifying the organic template so that monovalent mimics with requisite functional groups can be synthesized. Second, the monovalent units were dimerized using sequential nucleophilic substitutions on fluorescently labeled dichlorotriazine. Our rationale to make bivalent compounds out of monovalent ones was justified when compound 4 was shown to bind TrkA with a 20 nM affinity. Reactions of amino acids with NH4SCN under acylating conditions produced 2-thiohydantoins in which the nitrogen of the amino acid (N1) was acylated. This was proven by 2-D NMR which showed no cross-peak between the NH signal observed and the Cα±-H of the amino acid. When the compound was deacylated, a new NH signal appeared and the corresponding cross-peak with the Cα±-H was observed. Solution-phase syntheses of non-peptidic mimics were achieved by doing a double substitution on a dihalogenated nitrobenzene scaffold. Sonogashira and SNAr reactions were done to install the required side-chains to give the desired compounds. These non-peptidic compounds can be easily adapted to our DTAF-Inp dimerization protocol since the nitro groups can be easily reduced. Attempts to make a spirotetracyclic peptidomimetic with three side chain mimics were done by synthesizing the spirocyclic diketopiperazine precursor. The synthesis of the DKP was achieved by making the cyclic quaternary amino acid that was coupled to another amino acid via the HOAt-EDC method. This protocol gave dipeptides in high yields. These dipeptides were deprotected and cyclized to the DKP under mildly acidic conditions in toluene.

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. 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. 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. 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.

The secondary structure of peptides is of pivotal importance for their biological function. The introduction of photoswitchable moieties into the backbones of peptides provides a unique way of regulating their conformation using an external stimulus, i.e., light. This thesis addresses the design, synthesis, and conformational analysis of photoswitchable peptidomimetics (PSPM). Examples of photomodulation of their functional properties are given. PSPM were prepared by incorporation of stilbene and thioaurone chromophores (switches) into dipeptides. Synthetic schemes for preparing these chromophores have been developed. Their suitability for incorporation into peptidomimetics has been demonstrated, and the resulting PSPM have been subjected to photoisomerization as well as computational and spectroscopic conformational analysis. The chromophore’s potential as a β-hairpin inducer was particularly interesting. To investigate the factors that govern the formation of β-hairpins, a series of decapeptides were prepared. Turn regions consisting of amino acids or chromophores were combined with antiparallel peptide strands with hydrophobic side chains. Linear tryptophan zipper peptidomimetics and cyclic peptidomimetics with a second, hairpin-inducing turn region were particularly promising. Comparison between switches revealed that the more flexible stilbene is a better choice for upholding the β-hairpin conformation than the thioaurone. The catalytic properties of an artificial hydrolase with a helix-loop-helix structure can be improved by introducing a stilbene photoswitch into the loop region. Photoisomerization regulates the catalytic activity of this peptidomimetic, and provides a means to control its aggregation state. The activity of the enzyme Mycobacterium tuberculosis ribonucleotide reductase was realized by incorporating a stilbene moiety into a linear peptide. Here, one photoisomer proved to be an inhibitor at nM concentrations. A significantly lower effect was observed for the other isomer. Finally, the decomposition of thioaurones, mainly to thioflavonols and thiaindenes, under conditions used for solid-phase peptide synthesis has been mapped. These findings are expected to have implications for future use of this chromophore.

Over the years, the Burgess group has been focusing on the preparation and testing of small molecules that mimic protein secondary structures for protein-protein interactions. The most successful compounds made are C10 peptide macrocycles that effectively mimic β-turns and have given promising results from biological testing. These peptide macrocycles have also been dimerized to give even more effective ligands for protein-protein interaction. The successes of the peptide macrocycles have enabled us to look into increasing the chemical diversity of our libraries. This we believe will not only improve our ability to obtain high affinity ligands for the receptors of interest, but will also allow us to investigate other receptors. To achieve this, peptoids were incorporated into the C10 system to replace the peptides in the i+1 and i+2 positions. With the help of Microwave irradiation, semi-peptoid macrocycles were synthesized with a total reaction time of less than 2 h. These compounds were characterized and found to mimic β-turn, and show promising biological activity towards the Insulin-like growth factor 1 receptor (IGF-IR).

Solid-phase syntheses of two 14-membered ring peptidomimetics were done to determine whether or not a beta-turn structure can facilitate macrocyclization. NMR methods, together with CD and QMD calculations, do not fully support this assumption. However, cyclizations of more ordered structures like those of compounds 2 were more efficient than those for highly strained ring systems like 1. A small library of 18-membered ring peptidomimetics that accommodate an extra amino acid residue was synthesized on resin. Their syntheses were not complicated by head-to-tail dimer impurity, unlike those for previously synthesized 14-membered systems. These larger macrocycles exhibit beta-turn structures as verified by NMR, CD and QMD techniques. Moreover, two compounds in this series (3a and 3g) were shown to have agonistic properties for TrkC in cell survival assays. Dimerization of monovalent mimics was achieved first by modifying the organic template so that monovalent mimics with requisite functional groups can be synthesized. Second, the monovalent units were dimerized using sequential nucleophilic substitutions on fluorescently labeled dichlorotriazine. Our rationale to make bivalent compounds out of monovalent ones was justified when compound 4 was shown to bind TrkA with a 20 nM affinity. Reactions of amino acids with NH4SCN under acylating conditions produced 2-thiohydantoins in which the nitrogen of the amino acid (N1) was acylated. This was proven by 2-D NMR which showed no cross-peak between the NH signal observed and the Cα±-H of the amino acid. When the compound was deacylated, a new NH signal appeared and the corresponding cross-peak with the Cα±-H was observed. Solution-phase syntheses of non-peptidic mimics were achieved by doing a double substitution on a dihalogenated nitrobenzene scaffold. Sonogashira and SNAr reactions were done to install the required side-chains to give the desired compounds. These non-peptidic compounds can be easily adapted to our DTAF-Inp dimerization protocol since the nitro groups can be easily reduced. Attempts to make a spirotetracyclic peptidomimetic with three side chain mimics were done by synthesizing the spirocyclic diketopiperazine precursor. The synthesis of the DKP was achieved by making the cyclic quaternary amino acid that was coupled to another amino acid via the HOAt-EDC method. This protocol gave dipeptides in high yields. These dipeptides were deprotected and cyclized to the DKP under mildly acidic conditions in toluene.

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

Seven novel, amphiphilic AApeptides were prepared. Two cationic, lipo-α-AApeptides, NA-75 and NA-77 were found to possess potent antimicrobial activity against Gram-positive bacteria, with almost no hemolytic activity. In addition to NA-75 and 77, four amphiphilic, γ-AApeptides, NA-133, 135, 137, and 139, and one anionic lipo-α-AApeptide, NA-81, were prepared for molecular self-assembly studies, with several interesting nanostructures observed by TEM. Mineralization of calcium carbonate from gaseous CO2 and Ca2+ in the presence of the 7 AApeptide amphiphiles was also observed by optical microscopy. Several AApeptides were found to be able to influence CaCO3 crystal morphology. Another α-AApeptide, NA-63, was synthesized by a novel, alternative method, which has several potential advantages over the previous synthesis methods.

abstract: The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino acids (2.1 - 2.5) into E. coli dihydrofolate reductase (DHFR). The second project (Chapter 3) focused on the study of the modified ribosomes facilitating the incorporation of the dipeptide glycylphenylalanine (3.25) and fluorescent dipeptidomimetic 3.26 into DHFR. These ribosomes also had modifications in the peptidyltransferase center in the 23S rRNA of the 50S ribosomal subunit. The modified DHFRs having beta-amino acids 2.3 and 2.5, dipeptide glycylphenylalanine (3.25) and dipeptidomimetic 3.26 were successfully characterized by the MALDI-MS analysis of the peptide fragments produced by "in-gel" trypsin digestion of the modified proteins. The fluorescent spectra of the dipeptidomimetic 3.26 and modified DHFR having fluorescent dipeptidomimetic 3.26 were also measured. The type I and II DNA topoisomerases have been firmly established as effective molecular targets for many antitumor drugs. A "classical" topoisomerase I or II poison acts by misaligning the free hydroxyl group of the sugar moiety of DNA and preventing the reverse transesterfication reaction to religate DNA. There have been only two classes of compounds, saintopin and topopyrones, reported as dual topoisomerase I and II poisons. Chapter 4 describes the synthesis and biological evaluation of topopyrones. Compound 4.10, employed at 20 µM, was as efficient as 0.5 uM camptothecin, a potent topoisomerase I poison, in stabilizing the covalent binary complex (~30%). When compared with a known topoisomerase II poison, etoposide (at 0.5 uM), topopyorone 4.10 produced similar levels of stabilized DNA-enzyme binary complex (~34%) at 5 uM concentration. / Dissertation/Thesis / Ph.D. Chemistry 2013

Alzheimer's diseases(AD) has been discovered and under research for more than 70 years, However there is no cure for these progressive and devastating diseases. Based on the following hypothsis: Aß metabolite problem/over production result in the accumulation, and lead to aggregation is the cause of Alzheimer’s disease. AApeptide and Melatonin derivatives can bind to Aß and block the aggregation of β amyloid monomers, decrease the toxicity of Aß to neurons and slow the progressive of Alzheimer’s diseases. In addition, AApeptide which mimic transmembrane peptide Tat will have similar transmembrane function. We have set up our goals as follows: 1) Using newly discovered peptidomimetics, AApeptides. We moved on to research to discover their potential of transmembrane activity and anti-Alzheimer's acitiviy. 2) In Addition, studies of small molecule melatonin derivatives were also progressed. Methods include in this research includes bioorganic synthesis, identification of spectroscopy and relative assays targeting on biological efficiency of Anti-Alzheimer’s diseases. The details of which will be described in Chapters. In conclusions, two sets of transmembrane peptidomimetics for drug transportation has been successfully evaluated and potential of AA peptide small molecules, melatonin derivativesare also evaluated. These works have gained good progress in research between AApeptide and Alzheimer’s Diseases. These works also established basis of research in developing peptidomimimetics as potential pharmacies against Alzheimer’s diseases.

Methyl reader proteins recognize and bind to post-translationally methylated residues and have functional roles in diverse cellular processes including gene regulation, development and oncogenesis. The CBX polycomb paralog family of methyllysine readers recognize trimethyllysine lysine residues on histone tail 3 and repress transcription by compacting chromatin. The polycomb paralogs form multi-protein complexes that silence the expression of tumour suppressor genes, and play important roles in regulating cell cycle and differentiation. Each paralog is structurally similar, yet has distinct functions, of which many are unknown. My work has focused on the design and synthesis of CBX inhibitors and on the development of new methodologies for the discovery of inhibitors targeting methyllysine readers. In this work, I report on a series of potent peptidic inhibitors that selectively target the CBX polycombs, as well as the first selective inhibitor for the family member CBX6, and dual-active inhibitors that target CBX6/CBX8. The results demonstrate the potential to achieve selectivity through interactions outside of the methyllysine binding domain. Structural determinants in the binding pocket of each protein that differ within the family and give rise to selectivity were discovered. I will also report on a series of peptidomimetic CBX inhibitors that are active in cells. Cellular active inhibitors are critical for understanding the biological role of each CBX protein and their potential as therapeutic targets. New high-throughput approaches are needed to efficiently target methyllysine readers by chemical inhibition. I describe in this work a strategy for creating massive libraries of phage-displayed peptidic inhibitors containing methyllysine mimics. Synthetic optimization on cysteine-containing peptide phage constructs allowed for the successful installation of Kme3 mimics. This is the first report of a post-translational methylated peptide phage library. The methodology I developed can be used in a synthetic chemistry-driven adaptation of traditional phage display for the screening of millions of peptide-based compounds. Strategies that allow for diversity and high throughput screening will aid in future efforts in targeting the highly similar CBX proteins. / Graduate / 2021-06-01