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Molecular Tweezers with Additional Binding Sites against Protein Aggregation

Dutt, Som

My doctoral thesis aims at the development of molecular tweezers with increased affinity and specificity for amyloidogenic proteins. A particular focus lies on the amyloid-β protein, a major pathological hallmark of Alzheimer’s disease. In Klärner group, a molecular tweezer called the phosphate tweezer was developed which selectively binds to the amino acid lysine and arginine both in peptides and proteins, and thereby inhibits the aggregation and toxicity of amyloid proteins. However, the symmetrical prototype which carries two phosphate anions at its periphery, does not distinguish between well-accessible lysines on a protein surface. In my thesis I try to develop symmetrical and unsymmetrical molecular tweezers with new recognition sites, which become selective for a given protein/epitope.

In the first part of the work, I explored the chemical and biological effects of replacing the phosphate anions by other anionic groups of biological relevance. For this purpose, I synthesized the sulfate tweezer and carried out comparative binding studies among the phosphate, phosphonate, sulfate and methyl carboxylate tweezers with basic amino acids and relevant peptide guests. Using NMR, fluorescence, ITC, and molecular simulation, I observed substantial differences in the binding characteristics of all the four tweezer types toward their peptide guests.

In collaboration, we studied the inhibition potential of the phosphate tweezer against the pathologic aggregation of the islet amyloid polypeptide (IAPP), a protein involved in the type II diabetes. For more structural insight, I carried out an investigation about complexes between the tweezer and IAPP fragments by NMR, fluorescence and ITC experiments. Biological experiments and QM/MM calculations were performed in collaborations.

In the second part of my work, I synthesized several unsymmetrical molecular tweezers that carry a phosphate group on one side and several different linkers on the other side of tweezer’s central benzene ring. These tweezers with attached linker units display varying affinities for lysine and arginine derivatives from milimolar to micromolar. Biological experiments of these unsymmetrical tweezers are currently underway in Prof. Bitan’s lab (neurology, UCLA). Lastly, I developed an even more general and potent synthetic route for the synthesis of unsymmetrical molecular tweezers which keep both the phosphate groups on the tweezer. One of the two phosphate groups is substituted with an alkyne or an ester linker unit. The alkyne linker tweezer can be coupled with an azide containing recognition site via alkyne-azide click reaction, whereas, the ester linker tweezer can be coupled with an amine containing recognition site to synthesize more powerful unsymmetrical molecular tweezer.


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Dutt, Som: Molecular Tweezers with Additional Binding Sites against Protein Aggregation. 2012.


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