Research Projects 2006

Our summer research program is designed to match each student with a faculty member to optimize the research experience for all participants. The application form asks you to rank your top three preferences of projects. If you want more information about a specific project (for example what background you need and which techniques you will learn) please contact the faculty directly via e-mail. General inquiries may be directed to Prof. Michael Carrasco at mcarrasco@scu.edu.

Porphyrin-DNA Interactions

Amy Shachter, Ph.D.; Bioinorganic Chemistry (ashachter@scu.edu)

Cationic porphyrins are a class of compounds with great potential as anticancer and antiviral (HIV-1) agents. Characterizing porphyrin-DNA interactions is essential to understanding cytotoxic activity and designing optimal therapeutic agents. Porphyrins typically interact with DNA by intercalating between base pairs or through outside binding in the minor groove. To systematically determine the influence of N-alkyl chain length, N-alkyl chain functionality, and peripheral charge distribution (3-pyridyl vs. 4-pyridyl) on cationic porphyrin-DNA interactions, we synthesized a series of twenty cationic porphyrins. Characterization of the DNA binding of the porphyrins and metal derivatives using visible and circular dichroism spectroscopy will be the focus of the project.

Investigations of Drug-Lipid Binding Interactions in Model Membrane Bilayers

Linda Brunauer, Ph.D.; Biochemistry (lbrunauer@scu.edu)

Tricyclic drugs long have been used in the treatment of various neurological imbalances. While much of the research in this area has been focused at the drug-receptor interface, it is important also to investigate drug interactions at the plasma membrane level, as it is necessary for these drugs to establish membrane interactions that favor their passage across membrane barriers, in order to accumulate in the nervous system in large enough quantities to elicit biological effects. Drug-membrane interactions can be divided into two categories: interactions promoting drug permeability, and interactions promoting drug retention (binding). Both types of interactions involve electrostatic interactions, though not much comprehensive data on either are available. In the proposed project the importance of membrane phospholipid composition in supporting the binding of a variety of tricyclic drugs will be examined.

Peptide and Protein Bioconjugate Chemistry

Michael Carrasco, Ph.D.; Bioorganic Chemistry (mcarrasco@scu.edu)

This research is focused on (1) the site-specific attachment of small organic molecules to peptides and proteins and (2) how the structure and function of the peptides and proteins are altered by the attached molecules. Standard synthetic organic and biochemical techniques are combined with novel methods developed for the total chemical synthesis of peptides and proteins to accomplish these goals. Student projects will range from the synthesis of novel amino acid derivatives to the combinatorial synthesis of peptide arrays and studying how glycosylation affects the thermostability of a protein.

Photoreversible Reactions of Metal Complexes
Patrick Hoggard, Ph.D., Inorganic Chemistry (phoggard@scu.edu)

Many metal complexes in solution undergo a reaction when exposed to light. We are investigating systems in which this reaction can be reversed and regenerate the starting complex by a different pathway, for example by exposing the product to a different wavelength of light. Photoreversible reactions offer numerous possibilities for applications (for example, as optical switches) , but we are most interested in their potential to degrade halocarbon pollutants by light, as in the example shown, with the ultimate goal of using sunlight. In this example, iron(III) chloride in chloroform (which becomes HFeCl₄ after exposure to light) is converted to iron(II) chloride, which then regenerates iron(III), requiring oxygen, but no additional light. In the process, the CHCl₃ solvent is degraded, eventually to HCl and CO₂. Although this works very well in chloroform, it doesn’t work in water with dissolved chloroform, which is one of our goals. Other metal complexes we are currently studying are more promising.

Investigations of structural alterations in tissue proteins due to AGE formation

Ram Subramaniam, Ph.D.; Biochemistry (rsubramaniam@scu.edu)

In diabetes, as well as in aging, excess sugars react with proteins in the body to form irreversible complex structures. The reaction occurs between the carbonyl groups on the sugars and the side chain amino groups on proteins via a reaction known as Maillard reaction to form the so-called Advanced Glycation Endproducts (AGEs). The AGE structures alter the proteins in the body both structurally and functionally.

In this REU project we will study the changes in the structural features of tissue proteins such as albumin upon modification to form AGE structures. We will study such aspects as the secondary structure of the protein, modification of total thiol content and metal binding properties of the protein.

Reengineering the Central Binding Core of HIV Protease Inhibitors

Brian J. McNelis, Ph.D.; Organic Chemistry (bmcnelis@scu.edu)

HIV protease inhibition is an important pharmacological approach to combating the onset of AIDS in HIV infected patients. There are problems with this approach such as the development of resistant mutant virons and the cost of producing the present commercial medications. We are presently designing and building number of novel HIV protease inhibitors in my laboratory. These compounds differ dramatically from the previous inhibitors that have been described in the literature by utilizing a unique scaffold to present the important functionality in the correct 3-dimensional orientation in the HIV protease active-site. These protease inhibitors are straightforward to prepare and customize and should have comparable activity to known inhibitors. The ease of synthesis and the biological relevance of this research make it ideal for engagement of undergraduates. In designing a novel HIV protease inhibitor that is cost effective to prepare, we are hoping to address both the efficacy and distribution of these medicines. Presently, the high cost of these drugs practically prohibits treatment of HIV infected patients in the Third World. By redesigning these inhibitors to address this need, we hope to produce compounds that could lead to wider distribution of these pharmaceuticals.

 

Development of Aptamer-Based Affinity Assays for Biologically Significant Small Molecules and Proteins
Steven W. Suljak, Ph.D., Analytical Chemistry (ssuljak@scu.edu)

Aptamers are a recently developed class of molecules that have received increasing attention for high-affinity, specific molecular recognition. Aptamers consist of single-stranded DNA or RNA and are selected for their binding to targets through a combinatorial process termed SELEX. As alternatives to antibodies, aptamers have several inherent advantages, including cheap and facile synthesis, ease of sit-specific labeling with fluorophores, and a virtually limitless spectrum of potential targets ranging from large proteins to small organic molecules such as amino acids. Our research incorporates these advantages of aptamers to develop improved and novel bioanalytical methodologies for the analysis of biologically important small molecules in proteins.
REU students will have the opportunity to develop the application of aptamers to two primary modes of biochemical analysis. First, modified versions of traditional immunoassays will be developed that incorporate a monoclonal capture antibody but substitute target-specific aptamers for the detection antibodies. These hybrid aptamer-antibody assays will be used to investigate the structural binding interactions of proteins with their ligands. Second, aptamers will be incorporated into capillary electrophoresis methods as affinity probes for biological targets. Students will develop separation strategies to resolve unbound, labeled aptamers from their target bound complexes, using previously identified aptamers for dopamine and AMP. Other studies can focus on evaluating the degree of selectivity and sensitivity in monitoring protein modification achievable by capillary electrophoresis. In particular, DNA and RNA aptamers for the putative cancer marker vascular endothelial growth factor (VEGF) will be used to differentiate between unmodified VEGF peptide fragments and synthetic variants (phosphorylated or N-glycosylated) produced as a model for detecting post-translational modifications. Development of these separation strategies will provide a framework for more comprehensive functional proteomic studies for drug discovery or evaluation.