The de novo design of peptides is a central area of research in chemical biology. Although it is now possible to design helical peptide structures from first principle, designing â-sheets remains a challenge. Significant advances in this area have been made by using molecular scaffolds, which stabilize â-sheets through intramolecular H-bonding involving the scaffold or which direct supramolecular assembly of the conjugate. In my thesis, I have made use of novel strategies, using ferrocene (Fc) as a central scaffold for controlling the secondary structure of peptides. This approach has been highly successful. Four major new strategies are introduced and described in this thesis: <p>a) Cyclization of Fc-peptide conjugates of the type Fc[CO-Xxx-CSA]2 (Xxx = Gly, Ala, Val, Leu) and Fc[CO-Gly-Xxx-CSA]2 (Xxx = Val, Ile; CSA = cysteamine) leads to the clean formation of novel cyclic bioorganometallic conjugates, which exhibit strong intramolecular hydrogen bonding interactions that restrict the mobility of the podand peptide chains. In the latter system, this intermolecular hydrogen bonding interaction was exploited for the design of a novel â-barrel-like structure. For Fc[CO-Gly-Val-CSA]2 and Fc[CO-Gly-Ile-CSA]2 discrete cyclic supramolecular assemblies were formed in which the individual molecules assemble along the rims of the molecules, resulting in the formation of tubular peptide superstructures that possess a central cavity and are filled with water molecules. <p>b) Prior to my work, work by Hirao and Metzler-Nolte clearly showed that the two podand peptide chains in Fc-peptide conjugates are pointing away from each other. This would indicate that extended â-sheets cannot be formed by simply extending the podand peptide chains. In my work, I clearly demonstrate that, in contrast to earlier results, it is possible to use the Fc scaffold to stabilize â-sheet-like interactions in longer peptide chains. Two systems are described in this thesis Fc[CO-Gly-Val-Cys(Bz)-OMe]2 and Fc[CO-Gly-Ile-Cys(Bz)-OMe]2. In both the cases, amino acids are employed that have a high propensity for â-sheet formation. Both Fc-peptide conjugates exhibit strong interstrand hydrogen bonding, resembling that found in â-sheets.<p>c) In this work, I have demonstrated the use of ferrocene amino acid (Fca) to control the structure in peptides. In contrast to previous work by Metzler-Nolte, my work is largely focusing on the design of a repetitive Fca-peptide motif. It is proposed that this repetition will enable strong interactions between the peptide portions of the conjugate, resulting in the formation of an extended structure. To this effect, a series of Fca-conjugates of the type Boc-[Fca-Ala]n-OMe (n = 1-4) was synthesized and fully characterized. All systems display the expected interaction between the Ala residues having a 12-membered hydrogen bonded ring. Such a structural motif resembles that found in naturally occurring â-helical structures of the spike-region of some viral proteins. <p>d) I have also demonstrated the use of a novel Fc-derivative, Fc[NH-Boc]2, to control the structure of podand amino acid chains. Fc-diamine was synthesized by the convenient carbazide route giving this useful scaffold in high yield. This material was converted into its peptide conjugate and the resulting conjugate displays the elusive 14-membered hydrogen bonding ring. <p>Thus, in my work, I have provided a new complementary tool for peptide design that will undoubtedly find applications for the design of de novo proteins in the near future.
| Identifer | oai:union.ndltd.org:USASK/oai:usask.ca:etd-06142007-063338 |
| Date | 14 June 2007 |
| Creators | Chowdhury, Somenath |
| Contributors | Scott, Robert, Paige, Matthew F., Mueller, Jens, Kraatz, Heinz-Bernhard, Evitts, Richard W. |
| Publisher | University of Saskatchewan |
| Source Sets | University of Saskatchewan Library |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://library.usask.ca/theses/available/etd-06142007-063338/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to University of Saskatchewan or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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