Structure elucidation of selectin antagonists in solution and synthesis of sialyl Lewis x mimics pre-organized in their bioactive conformation

Zierke, Mirko. Structure elucidation of selectin antagonists in solution and synthesis of sialyl Lewis x mimics pre-organized in their bioactive conformation. 2015, Doctoral Thesis, University of Basel, Faculty of Science.


Official URL: http://edoc.unibas.ch/diss/DissB_11267

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Selectins are an extensively studied class of carbohydrate binding proteins. They mediate the first contact and rolling of leukocytes on endothelia cells, initiating leukocyte infiltration from blood circulation to the diseased or infected tissue. Many inflammatory diseases are associated with an excessive extravasation of leukocytes to the inflamed tissue, and several kinds of metastatic cancer adopt the selectin mediated pathways. Thus, blocking selectins with synthetic antagonists is a promising therapeutic approach.
The common carbohydrate epitope present in all physiological selectin ligands is the tetrasaccharide sialyl Lewisx (sLex). To overcome the problem of structural complexity, nature rigidifies the 3 dimensional Lex core conformation by several stabilizing elements and thus, pre-organizes the pharmacophores in their bioactive conformation. For the development of potent sLex mimics it is crucial to understand the principles of stabilization and to adopt and optimize these structural motives.
Schematically sLex can be divided into a rigid Lex trisaccharide core and a rather flexible neuraminic acid part. The first part of the thesis is focused on the core trisaccharide Lex, which bears five of six pharmacophores. Since there are contradictory reports about the conformation of Lewis antigens in solution, i.e. do they adopt a single conformation or are they flexible, the conformations of Lex and related oligosaccharides in solution were investigated.
• An universal approach to analyze conformations of small molecules at room temperature in solution was developed. By converting the small Lex trisaccharide in a high-molecular-weight glycoconjugate the tumbling time was drastically increased, which is essential to obtain sufficient structural information by NMR spectroscopy. Thus, we achieved a well-defined solution conformation of Lex, which disclosed a nonconventional CH···O hydrogen bond as a major stabilizing element (Chapter 3.1.1/Publication).
• It could be shown that nonconventional CH···O hydrogen bonds are a common structural element stabilizing the conformation of various branched oligosaccharides. A widespread database search revealed numerous fucosylated carbohydrate structures that fulfill the requirements of nonconventional CH···O hydrogen bonds. Furthermore, the structures of six representative fucosylated carbohydrates were elucidated in solution. All of them are stabilized by nonconventional CH···O hydrogen bonds (Chapter 3.1.2/Manuscript).
In the second part of this thesis, the effects of neuraminic acid replacements in sLex mimics on conformational flexibility were evaluated, and antagonists with an acid pharmacophore pre-organized in the bioactive conformation were synthesized.
• By solving the solution conformation of a potent selectin antagonist, it was shown that the acid pharmacophore is pre-organized prior to binding by intramolecular interactions of hydrophobic residues. This antagonist showed stronger binding affinities over mimics with a flexible acid moiety. Based on these results, a series of selectin antagonists was designed and synthesized, where the acid pharmacophore is incorporated in a ring system and therefore, locked in the bioactive conformation (Chapter 3.2.1/Manuscript). The synthesis of two additional cyclic selectin antagonist series was not successful. Possible reasons are discussed in chapter
• In chapter 3.2.2, the potential for a bioisosteric replacement of the acid pharmacophore in cyclic selectin antagonists was evaluated by synthesis, biological assays and ab initio calculations (Manuscript).
Advisors:Ernst, Beat
Committee Members:Wittmann, Valentin
Faculties and Departments:05 Faculty of Science > Departement Pharmazeutische Wissenschaften > Ehemalige Einheiten Pharmazie > Molekulare Pharmazie (Ernst)
UniBasel Contributors:Zierke, Mirko and Ernst, Beat
Item Type:Thesis
Thesis Subtype:Doctoral Thesis
Thesis no:11267
Thesis status:Complete
Number of Pages:230 p.
Identification Number:
edoc DOI:
Last Modified:22 Jan 2018 15:52
Deposited On:29 Jun 2015 09:20

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