Participant: PROMISE AGEP Research Symposium
Department: Chemistry and Biochemistry
Institution: University of Maryland Baltimore County (UMBC)
Screening Small Molecule Inhibitors Against the Core Encapsidation Signal of HIV-1 RNA
Julie Nyman1, Sapna Basappa1, Ugonna Mbaekwe1, Jessica Zaki1, and Michael Summers1
1Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, 21250
The core encapsidation signal (CES) of the human immunodefiency virus type I (HIV-1) is required for the efficient packaging of the RNA genome into new virions. Because the CES is highly conserved, it offers potential as a drug target. Nuclear magnetic resonance (NMR) spectroscopy will be used to characterize the binding between this drug target and small molecule inhibitors. Preliminary NMR data was collected in a 20 mM Tris, pH 7.5, buffer, and the resulting spectra indicated that thirty of the seventy-nine tested inhibitors were binding. Using isothermal titration calorimetry (ITC), the interactions between the CES and small molecule ligands were further probed to elucidate thermodynamic parameters. To see whether these findings were also observed in physiologically relevant conditions, buffers were prepared that contained Tris and combinations of magnesium chloride, potassium chloride and sodium chloride salts. The binding interactions were again tested using NMR and ITC. The previously observed binding interactions were no longer seen, suggesting that salts present in the buffers prevent the binding of certain small molecule inhibitors to the CES RNA. Using additional ITC and NMR, screening of the interactions between the CES RNA and small molecules in physiologically relevant conditions will commence.
Acknowledgement: Dr. Amanda Hargrove and Dr. Hashim Al-Hashimi at Duke University provided the chemical libraries. Dr. Sarah Keane at the University of Michigan, Dr. Jan Marchant, Christy Gaines, and Dr. Pengei Ding at UMBC offered NMR, ITC, and molecular modeling advice.
Julie Nyman is a third-year graduate student in the Graduate Program in Life Sciences Intercampus Graduate Program in Biochemistry and Molecular Biology at the University of Maryland Baltimore (UMB) and University of Maryland Baltimore County (UMBC). She works in the lab of Dr. Michael Summers at UMBC.
The road to graduate school has been long and difficult but highlights her perseverance and determination. When she was thirteen years old, she had two emergency surgeries to remove a benign brain tumor. After much therapy, the support of her family and friends and her perseverance, she returned to school to complete her high school education with her original class. She graduated with honors and pursued a biochemistry degree at Hood College, Frederick, Maryland. After successfully graduating, she began the search for science research jobs while gaining invaluable interpersonal skills from a part time job at Target. Eventually, she applied and was accepted into the graduate program at UMB and UMBC. At UMBC, she has the opportunity to interact with many undergraduate students and to develop her interpersonal as well as teaching skills. In addition, the weekly group meetings hone her presentation skills. While performing Ph.D. research, she has had the opportunity to present at the Structural Biology Related to HIV/AIDS Conference at the NIH as well as at the Graduate Research Conference at UMBC.
GENERAL SUMMARY OF GRADUATE RESEARCH
The human immunodeficiency virus type 1 (HIV-1) infects more than 1.2 million people in the US and approximately 37 million worldwide (CDC; WHO). Current treatments target the proteins involved in viral processes; however, proteins mutate. Recently, a new drug target- the Core encapsidation signal (CES) of HIV-1 RNA, has been identified that is highly conserved. The CES is required for the efficient packaging of the unspliced, dimeric RNA genome into new viruses.
I use nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC) to screen small molecule inhibitors against the CES of HIV-1. NMR allows for the identification of the specific nucleotides that are affected by the binding of an inhibitor. ITC produces the thermodynamic parameters of the binding. After characterization by NMR and ITC, I hope to determine the structure of the CES RNA in complex with the small molecule inhibitor that binds the tightest.
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