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January 2010 - March 2011

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University of Minnesota Twin Cities
College of Pharmacy
Department of Medicinal Chemistry

PI: Barry C. Finzel

Crystallographic Investigation of Ligand-Protein Interactions and Structure-Aided Ligand Design

These researchers study the interactions in small molecule-macromolecular complexes of therapeutically important protein targets for use in structure-based drug/ligand design. Their primary experimental technique is x-ray crystallography, which requires significant computational resources. They are using MSI laboratories to assist in processing and analyzing multi-gigabyte data sets from diffraction data; they then use the processed data to determine the protein/complex structure. The structure is then finalized by iterative cycles of model fitting using graphic workstations and refinement. Experimental analyses are followed with the application of a variety of computational and visualization techniques to provide insights into the structural basis for ligand binding that can be applied to compound optimization and proposals for chemical synthesis. Completed structures will be prepared for deposition in the Research Collaboratory for Structural Bioinformatics database and for publication. An effort is also underway to develop web-based services for protein structure and substructure overlay based on conserved structural markers in drug receptor molecules. Such a tool is expected to support the teaching and data management in structure-based drug design.

Group Members

Ramprasad Reddy Akavaram, Graduate Student
Ran Dai, Graduate Student
Teresa de la Mora-Rey, Graduate Student
Todd W. Geders, Research Associate
Ryan Holton, Undergraduate Student
Li-Kai Liu, Graduate Student
Aravind Ragapindi, Graduate Student
Aravind Srivatsa Ravindran, Graduate Student