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Department ofChemistry and Biochemistry

Faculty Research Projects

Faculty  analytical biological  environ-
inorganic materials medicinal physical organic
Abbyad x x       x x  
Brunauer   x       x    
Carrasco   x           x
Carter-O'Connell   x       x x  
Fuller           x x x
McNelis     x   x     x
Shachter   x   x        
B Stokes               x
G Stokes   x       x x  
Suljak x x       x    
Tillman         x     x
Wheeler   x x x x x    


Microfluidic Nanoliter Droplets for Applications in Biological and Chemical Assays

Paul Abbyad, Ph.D. Physical Chemistry | Abbyad Research Lab

Microfluidics, the flow of liquids in micrometer sized channels, allows a reduction in reagent volumes and cost for biological and chemical assays.  An emerging technology, microfluidic droplets, adds new functionality by confining reagents and cells in small droplets. The content of each droplet does not mix and therefore droplets can be considered test tubes of nanoliter volume.  Droplets can then be used as microreactors for chemical reactions or can be analyzed sequentially or in parallel for large scale biological assays.  Our lab develops novel microfluidic technology for the analysis and sorting of single cells that provide functionality and sensitivity not achieved by conventional methods.

Investigations of Drug-Lipid Binding Interactions in Model Membrane Bilayers

Linda Brunauer, Ph.D. Biochemistry

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.

Exploring the Targets of PARPs in Physiology and Disease

Ian Carter-O'Connell, Ph.D. Biochemistry

​Post-translational modification of protein substrates serves as a dynamic biochemical mechanism to alter and regulate protein function. The transmission of cellular signals through the chemical modification of proteins is a tightly regulated process that cells rely on in order to function properly. Not surprisingly, misregulation of these processes is a hallmark of pathophysiology and disease. In the Carter-O'Connell lab we are focused on using biochemistry to uncover the role of one such modification, ADP-ribosylation, in both normal human physiology (cell development, signal transduction, gene regulation) and disease (such as cancer). We aim to couple a deeper understanding of the fundamental principles that govern ADP-ribose transfer in the cell to the biological outcomes of normal and malignant ADP-ribose signaling.

Synthesis and Study of Combinatorial Neoglycopeptide Arrays

Michael R. Carrasco, Ph.D. Organic Chemistry

As part of a research program aimed at studying how attached molecules affect the structure and function of peptides, we have recently synthesized several novel aminooxy amino acids.1,2 After their incorporation into peptides, these amino acids reveal side chains that can be reacted chemoselectively with reducing sugars to generate neoglycopeptides (Fig. 1). Importantly, our neoglycopeptides maintain biological relevance to natural glycopeptides because the sugars remain in their cyclic conformations and are close to the peptide backbone. Moreover, our strategy allows the facile combining of many different sugars with any given peptide. As a result, with a small amount of synthesis, we can create large numbers of neoglycopeptides.

Student projects will involve the synthesis of neoglycopeptide arrays and the subsequent use of these arrays to address biological issues of structure and function. The synthesis of the arrays exposes students to (1) the organic synthesis of novel amino acids, (2) solid phase peptide synthesis, and (3) sugar/peptide conjugation reactions along with extensive use of the analytical techniques of nuclear magnetic resonance (NMR), high performance liquid chromatography (HPLC), and electrospray ionization mass spectrometry (ESI-MS). The arrays will be used to address how attached sugars protect peptides from proteolysis, how they affect secondary structure, and how they affect the thermostability of peptides and small proteins.

Fig. 1.  A chemoselective reaction for synthesis of a neoglycopeptide.  The aminooxy group reacts selectively with the sugar in the presence of many other functional groups.

Synthetic Counterparts for Important Biomolecules

Amelia Fuller, Ph.D. Organic Chemistry | Fuller Research Lab

Biomolecules, including proteins and natural products, have an incredibly diverse repertoire of function in Nature, and it would be advantageous to replicate these functions with synthetic molecules that could serve as sensors, materials, or therapeutics. Research in my lab aims to prepare and study molecules that emulate the structures and, ultimately, the functions of important biomolecules. To this end, we have two major projects:

1. Evaluating the structures of water-soluble peptoids
Peptoids are -substituted glycine oligomers, and they are synthetic mimics of peptides. We are interested in understanding how to make and study peptoids that have structures similar to those found in proteins, including helices and helix bundles.

2. Synthesis and biological evaluation of new oligoamides
We are developing efficient synthetic methods to prepare new peptidomimetic molecules that have structures that emulate those found in bioactive natural products. With the help of collaborators, we evaluate our synthetic molecules as potential antimicrobial compounds.

Students in my lab learn a variety of experimental techniques including modern synthesis methods and various spectroscopic methods (e.g., NMR, fluorescence, circular dichroism).

Reengineering the Central Binding Core of HIV Protease Inhibitors

Brian J. McNelis, Ph.D. Organic Chemistry

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.

Interactions of Endocrine-Disrupting Pollutants with Membranes and Surfaces

Grace Stokes, Ph.D. Physical Chemistry | Grace Stokes Research Lab

Our biophysical chemistry lab uses surface-specific laser spectroscopy methods to characterize model systems that mimic the conditions, concentrations, and heterogeneous structures found in the human body and in natural environments. Our goal is to predict how chemical structure impacts adsorption thermodynamics and surface orientation. Currently, we are studying interactions of supported lipid bilayers with 1) small molecule drugs, and 2) protein-mimicking peptoids. We are also extending these studies to better understand how the presence of integral membrane proteins impact these interactions.

Development of Aptamer-Based Affinity Assays for Biologically Significant Small Molecules and Proteins

Steven W. Suljak, Ph.D. Analytical Chemistry

Research in the Suljak laboratory is focused on developing strategies for chemical analysis utilizing aptamers, single-stranded DNA or RNA molecules that tightly bind specific target molecules.  Our current efforts are aimed at identifying novel aptamers that can distinguish between proteins with particular post-translational modifications implicated in diseases such as cancer.

Synthesis of Topologically Interesting Polymers

Eric Tillman, Ph.D. Organic Chemistry

Our research is in the area of organic/polymer synthesis.  We primarily use atom transfer radical reactions to both build polymer chains and employ these polymers in further reactions.  We aim to develop synthetic pathways leading to architecturally interesting macromolecules, such as monocyclic and bicyclic polymers, star polymers, and other topologies.  To accomplish this, we rely on understanding and then using coupling reactions that join polymer chains together.  Much of our focus is the mechanistic study and optimization of these reactions, which might be done by radical-radical coupling, capturing chain ends with radical traps, or “click”-type chemistry.  Research students learn how to synthesize polymers using air-sensitive techniques, and characterize their polymeric products using spectroscopy and chromatography.

Biological and Environmental Impacts of Metal Nanoparticles

Korin Wheeler, Ph.D. Bioinorganic Chemistry | Wheeler Research Lab

We aim to use various biochemical techniques to understand the biological and environmental impacts of metal nanoparticles. The properties of nanomaterials differ substantially from bulk materials of the same composition; the reactivity of nanoproducts is complicated by small alterations in parameters such as shape and size. With the current data on nanoparticles, the bioavailability or toxicity for a given nanoproduct is essentially unpredictable. A mechanistic understanding of the bio-physicochemical interface of nanoparticles is essential for a sustainable increase of nanotechnologies in the marketplace.