Thesis (M.Med.Sc.)--University of Hong Kong, 2002. / Includes bibliographical references (leaves 69-72). Also available in print.

Universiẗat, Diss., 2003--München.

Braunschweig, Techn. Universiẗat, Diss., 2000.

Köln, Universiẗat, Diss., 2001.

Thesis advisor: Jianmin Gao / Thesis advisor: Eranthie Weerapana / Cyclic peptides provide a privileged scaffold when optimizing interactions with various biological targets. Their rigidified structure decreases the entropic cost of binding by preorganizing residues in a fixed conformation, which may enhance binding affinity. These molecules occupy a larger chemical space than typical small molecule drugs and may provide good candidates for inhibiting protein-protein interactions or being able to interact with previously undruggable targets. Given the benefits of these structures we aim to develop a one-bead-one-compound peptide library for screening against relevant biological targets. Herein we describe several routes to achieving cyclic peptides through side chain interactions and head-to tail amide bond linkages. Additional considerations for the development of the on resin library such as linker strategies and sequencing methods will be discussed. / Thesis (MS) — Boston College, 2015. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Synthesis of peptides anchored to DNA by intercalating chromophores can incorporate the design principle of the naturally occurring peptide based antibiotics. This work is concerned with the synthesis of DNA anchored cysteinyl peptides designed to be potentially nucleotide sequence specific with possible affinity for the AP-l transcription site. Previous work has shown that anthraquinones and anthrapyrazoles (APZs) substituted with cationic side groups are excellent DNA intercalating agents. In this work a series of APZ analogues has been synthesised which are coupled onto the amino terminus of varying peptide sequences. Three derivatives of APZs were prepared namely 2-, 2,5- and 2,7-substituted. Eight short polypeptides (see below), all varying slightly in sequence but all containing the KCR motif (with one exception where a Cys was replaced with Ser) were combined with the APZ chromophore to give a series of intercalator-peptide molecules. Peptides were synthesised using the Fmoc strategy on a solid phase peptide synthesizer (SPPS). The peptides were then isolated by reversed-phase HPLC using a water: acetonitrile gradient. Characterisation of the peptides was carried out by matrix assisted laser desorption ionisation (MALDI) mass spectrometry and two dimensional nmr (i.e. COSY and NOESy). Anthraquinone linked peptide ligands were also synthesised using similar synthetic routes, and tested for their activity. Coupling of the two components was achieved via activation of the carboxylic acid group using PyBOP or via formation of a reactive aziridinium ion. All intercalator-peptides prepared were examined for their DNA binding properties. The methods included the effect of intercalator-peptides on the thermal denaturation of DNA and the competitive displacement of ethidium by fluorimetry. It was shown that the APZ binds to DNA by intercalation. Peptides prepared were: H2N-A-K-C-R-A-C02H; H2N-A-K-C-R-A-CONH2; H2N-A-K-S-R-A-CONH2; H2N-A-K-C-R-N-A-CONH2; H2N-A-K-C-R-K-A-CONH2; H2N-A-K-C-R-N-R-A-CONH2; H2N-A-K-C-R-K-R-ACONH2; H2N-A-A-K-C-R-A-A-CONH2. The biological activities of the intercalatorpeptides were then investigated using an electrophoretic mobility shift assay (EMSA), making use of cell nuclear extracts rich in AP-l and also c-Jun homodimer recombinant proteins. It was shown that most of the intercalatorpeptides were capable of inhibiting AP-l (fos/jun) heterodimer protein from binding to the AP-l DNA consensus sequence. Importantly, the intercalatorpeptides showed superior activity over the intercalator or peptide moieties alone. The order of binding affinity was intercalator-peptide> intercalator» peptide.

No description available.

Spinal cord injuries (SCI) are characterized by the inability of mature neurons to regenerate or repair by themselves. In an attempt to overcome the SCI, a novel photo-sensitive cyclic Arg-Gly-Asp-Ser (RGDS) peptide was synthesized using solid phase peptide synthesis (SPSS) to control 3T3 fibroblast cell attachment on hyaluronic acid (HA) hydrogel. The circular RGDS peptide was designed using RGDS sequence labeled with Anp group (3-Na-fmoc-amino-3-(2-nitrophenyl) propionic acid) at the N terminus. The peptide was photo-labile cyclic caged to shelter its bioactivity and UV light was used to make the peptide uncaged. Accuracy of the cyclic caged RGDS peptide was confirmed by high-performance liquid chromatography (HPLC) and mass spectrum (MS). The molecular weight of cyclic caged RGDS peptide was confirmed as 881 by matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrum. Stability of the cyclic caged RGDS peptide under various pH conditions was verified by circular dichroism spectroscopy. The bioactivity of cyclic caged and uncaged RGDS peptide was tested by photo-controllable directing cell growth based on cell attachment study, cell counting study, and cell morphology study. Three dimensional model structures of cyclic caged and uncaged RGDS peptides were computed by Hyperchem program. The first order reaction theory of Anp uncaging reaction was confirmed by kinetic study. Bioactivity caging and uncaging property of the peptide was also fully confirmed by cell attachment study. This cyclic caged RGDS peptide would be a promising tool in cell patterning for repairing of SCI.

Spinal cord injuries (SCI) are characterized by the inability of mature neurons to regenerate or repair by themselves. In an attempt to overcome the SCI, a novel photo-sensitive cyclic Arg-Gly-Asp-Ser (RGDS) peptide was synthesized using solid phase peptide synthesis (SPSS) to control 3T3 fibroblast cell attachment on hyaluronic acid (HA) hydrogel. The circular RGDS peptide was designed using RGDS sequence labeled with Anp group (3-Na-fmoc-amino-3-(2-nitrophenyl) propionic acid) at the N terminus. The peptide was photo-labile cyclic caged to shelter its bioactivity and UV light was used to make the peptide uncaged. Accuracy of the cyclic caged RGDS peptide was confirmed by high-performance liquid chromatography (HPLC) and mass spectrum (MS). The molecular weight of cyclic caged RGDS peptide was confirmed as 881 by matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrum. Stability of the cyclic caged RGDS peptide under various pH conditions was verified by circular dichroism spectroscopy. The bioactivity of cyclic caged and uncaged RGDS peptide was tested by photo-controllable directing cell growth based on cell attachment study, cell counting study, and cell morphology study. Three dimensional model structures of cyclic caged and uncaged RGDS peptides were computed by Hyperchem program. The first order reaction theory of Anp uncaging reaction was confirmed by kinetic study. Bioactivity caging and uncaging property of the peptide was also fully confirmed by cell attachment study. This cyclic caged RGDS peptide would be a promising tool in cell patterning for repairing of SCI.

Despite many medical advances, antibiotic resistant bacteria increasingly plague the modern world, necessitating discovery of new antibiotics. One area of nature that can provide inspiration for antibiotics is antimicrobial peptides. Many of these peptides exist in nature, with some classes that have not been studied or characterized well. One such class is the defensin-like peptides generated by the plant Medicago truncatula as part of their symbiotic relationship with Sinorhizobium meliloti. Nodule-specific Cysteine Rich (NCR) peptides are defined by the presence of multiple cysteines, and regulate the growth of S. meliloti within plant cells. While some of these NCR peptides have been shown to have antimicrobial properties, hundreds of peptides remain uncharacterized. We have developed an assay for further characterization of these peptides in E. coli. Of the seven peptides that have been tested using this assay, three have exhibited definitive antimicrobial properties against both E. coli and S. meliloti. Additionally, we have developed a system for discovering novel antimicrobial peptides. This platform, called PepSeq, uses the expression of random peptides in E. coli combined with deep sequencing to detect antimicrobial activity. This technology is capable of screening through millions of peptide molecules simultaneously. Using this platform, we have discovered and confirmed six novel antimicrobial peptides, with hundreds of additional predicted antimicrobial peptides. In addition to the peptides we have analyzed using PepSeq, additional peptide scaffolds could be used to discover more potent antimicrobial peptides.