DNA remains an underrepresented target for small molecule therapeutic agents. There is mounting evidence to indicate that non-B DNA structures play prominent roles in gene expression and in the function of telomeres. Targeting these structural elements is an attractive and innovative strategy for the development of new therapeutic agents. The use of small molecules in such an antigene strategy is promising for many reasons. Targeting the gene before its amplification to produce multiple mRNA and protein molecules is advantageous because there are fewer targets to hit. In addition, is easier to manipulate small molecules (rather than therapeutic DNA or RNA molecules) chemically to optimize binding and pharmacological properties. We seek renewal for our innovative and highly productive program to develop an integrated virtual and actual screening platform for the discovery of new lead compounds that bind selectively to unique DNA structures of biological significance. Progress during the initial funding period was outstanding, and we achieved most of the specific aims proposed in our initial proposal. We have discovered several compounds that bind selectively to particular quadruplex structures, a target of intense current interest. We propose studies that will continue to develop and optimize the integrated screening platform. During the next funding period, we will focus on the discovery of lead compounds that bind selectively to biologically important quadruplex and DNA-RNA hybrid structures. In order to do this, we will develop structural models for complex quadruplex structures using a novel approach that integrates molecular dynamics simulations with rigorous experimental validation. We will characterize the biophysical and functional properties of the novel quadruplex binders we have discovered during the initial funding period.
Specific aims i nclude: 1. Development and refinement of the virtual screening platform. 2. Development of higher-throughput assays for ligand binding. 3. Discovery of lead compounds that bind to functionally important nucleic acid structures. 4. Biophysical and biological characterization of novel G-quadruplex binding agents discovered during the initial funding period. The proposed studies will deliver an improved integrated platform for the discovery of novel lead compounds and a thorough characterization of several newly-discovered quadruplex binders with unique chemical scaffolds.

Public Health Relevance

This project will develop an integrated computational and experimental screening platform for the discovery of new drugs that target specific structures of functional importance within the genome. The initial funding period for this project was successful and productive, and we will continue our efforts. Several novel lead compounds were discovered that bind to functionally important quadruplex structures. We will characterize the biophysical and biological properties of these novel agents.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
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University of Louisville
Internal Medicine/Medicine
Schools of Medicine
United States
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Del Villar-Guerra, Rafael; Gray, Robert D; Trent, John O et al. (2018) A rapid fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand-nucleic acid structural selectivity. Nucleic Acids Res 46:e41
Del Villar-Guerra, Rafael; Trent, John O; Chaires, Jonathan B (2018) G-Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy. Angew Chem Int Ed Engl 57:7171-7175
Monsen, Robert C; Trent, John O (2018) G-quadruplex virtual drug screening: A review. Biochimie 152:134-148
Del Villar-Guerra, Rafael; Gray, Robert D; Chaires, Jonathan B (2017) Characterization of Quadruplex DNA Structure by Circular Dichroism. Curr Protoc Nucleic Acid Chem 68:17.8.1-17.8.16
Rigo, Riccardo; Dean, William L; Gray, Robert D et al. (2017) Conformational profiling of a G-rich sequence within the c-KIT promoter. Nucleic Acids Res 45:13056-13067
Bon?ina, MatjaĆŸ; Vesnaver, Gorazd; Chaires, Jonathan Brad et al. (2016) Unraveling the Thermodynamics of the Folding and Interconversion of Human Telomere G-Quadruplexes. Angew Chem Int Ed Engl 55:10340-4
Miller, M Clarke; Ohrenberg, Carl J; Kuttan, Ashani et al. (2015) Separation of Quadruplex Polymorphism in DNA Sequences by Reversed-Phase Chromatography. Curr Protoc Nucleic Acid Chem 61:17.7.1-18
Chaires, Jonathan B; Dean, William L; Le, Huy T et al. (2015) Hydrodynamic Models of G-Quadruplex Structures. Methods Enzymol 562:287-304
Chaires, Jonathan B (2015) A small molecule--DNA binding landscape. Biopolymers 103:473-9
Gray, Robert D; Trent, John O; Chaires, Jonathan B (2014) Folding and unfolding pathways of the human telomeric G-quadruplex. J Mol Biol 426:1629-50

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