SFI UREKA Site in Molecular Recognition
Translating Design into Application

Molecular Design

Project 3:      Synthesis of Peptidomimetics that Recognize a-helical Binding Protein Receptors  

Supervisor:     Prof. Paul V. Murphy, School of Chemistry

Project Summary:   The recruited student will contribute to the Murphy group effort funded by SFI to synthesise peptidomimetics based on macrocyclic compounds, in particular peptidomimetics that target receptors that recognize a-helical binding proteins.  In this project mimetics of the surface of the Bak peptide (an a-helical peptide) based on macrocycles (glycomacrocycles) will be synthesised.  Ultimately the binding interaction of the newly synthesised helical mimetics with Bcl proteins will be evaluated.  The project requires the synthesis of appropriately protected building blocks that can be converted into a wide range of a-helical peptidomimetics for biological evaluation. 

The student will work on the synthesis of a building blocks required for achieving success in the project on alpha helical peptide mimetic design and synthesis.  This is closely related to work ongoing in the lab that has been funded by SFI.  Within the laboratory our research group has now fully completed the synthesis of one novel a-helical mimetic and the group now wish to expand the building blocks available to generate a wide range of mimetics.  A UREKA funded project will help in this regard.

The student will work beside a postdoctoral researcher, Dr. Dilip Jarikote on the optimization of the synthesis of building blocks for the construction of the desired macrocycles.  The building blocks, a C-glucuronide and a C-glucosyl amine derivative are required within the research group and these will be accessed from readily available methyl a-D-glucopyranoside.  The role of the student will be to work on the preparation of the building blocks  and to use these to generate the novel peptidomimetic structures.

The student will carry out organic synthesis and learn the required techniques.  This will include exposure to use of MS, NMR, IR and interpretation of the data obtained from these techniques in structure determination.  In addition the student will develop their ability to separate their target compounds from mixtures using HPLC and column chromatography.  They will receive some training in molecular modelling. It will help the student to improve their practical and research skills with a view to obtaining a place ultimately as a graduate student, particularly if they are interested in developing their skills in organic synthesis and carbohydrate chemistry.

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