Antiviral compounds for high-risk, cancer-causing human papillomavirus (HPV) are extremely important even though anti-HPV vaccines are on the market. The proposed work determines the biophysics of interactions between antiviral polyamides (PAs) and their viral DNA targets, in order to determine the mechanism of action. The scope has been expanded from anti-HPV16 compounds to new anti-HPV compounds active against three cancer-causing viral subtypes. Active compounds eliminate viral episomes from human cell and tissue culture;they are potential drugs for the prevention of cervical cancer after HPV has been contracted. PAs having the same apparent DNA-binding preferences show dramatically different antiviral activities. It is proposed that a fundamental biophysical explanation of this behavior exists, one that goes beyond the known rules for PA-DNA interactions. Therefore, collaboration has begun around biophysical spectroscopy, DNA binding/footprinting assays, synthetic chemistry, virology and cellular-molecular biology.
The aims are:
Aim 1 Determine the binding position and affinity on the HPV16 genome of active PAs by footprinting the viral DNA as a function of PA concentration. The genome will be analyzed as overlapping 500 bp sequences using capillary electrophoresis and hydroxy radical footprinting. Binding constants determined for long DNA fragments will be compared with those from simpler models (minimal double-stranded or hairpin DNA). Independent physical methods such as fluorescence anisotropy (in competition binding studies), isothermal calorimetry and surface plasmon resonance will allow benchmarking against the literature and avoid artifacts.
Aim 2 Footprint the HPV18 genome in vitro with antiviral PAs. Identify related binding sites for both HPV16 and 18. Carry out NMR structural work on DNA sequences of importance to both HPV16 and 18 as bound to active PAs;use NMR structural results as the basis for molecular modeling of additional interactions.
Aim 3 Footprint active PAs on the HPV16 and 18 genomes in vivo in human cell culture. Examine the genomes using approximately 500 bp fragments generated by PCR that overlap to cover all sequence space. Determine experimental conditions and provide absolute binding constants with the aid of PA concentrations in cells measured by confocal and flow cytometry methods. Measure viral DNA concentrations vs. time using QPCR to make sure in vivo footprinting conditions are suitable. Identify structure-dependent uptake of PAs, potentially explaining why some isomeric PAs range from highly active to inactive antiviral agents. As an additional test of conclusions from footprinting, the site-directed mutagenesis of HPV18 sites identified during footprinting of antiviral PAs will help determine the importance of specific PA binding sites to the mechanism of antiviral action and viral episome maintenance. Provide new rules for interruption by polyamides of the high-risk HPV viral life cycle.

Public Health Relevance

The studies proposed here are of relevance to society because they relate directly to fighting several medically-important viral diseases. The work is specifically relevant to the prevention of cervical cancer. The medical value of the project is important because effective antiviral medication to fight HPV has not been developed. The antiviral agents we have discovered, and which we study here, have the potential to save lives when used in conjunction with regular check-ups and vaccination, and have the potential to contribute significantly to the control and elimination of cervical cancer.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
1R01AI083803-01A1
Application #
7987715
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Dempsey, Walla L
Project Start
2010-05-01
Project End
2015-04-30
Budget Start
2010-05-01
Budget End
2011-04-30
Support Year
1
Fiscal Year
2010
Total Cost
$371,097
Indirect Cost
Name
University of Missouri-St. Louis
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
804883825
City
Saint Louis
State
MO
Country
United States
Zip Code
63121
Castaneda, C H; Scuderi, M J; Edwards, T G et al. (2016) Improved Antiviral Activity of a Polyamide Against High-Risk Human Papillomavirus Via N-Terminal Guanidinium Substitution. Medchemcomm 7:2076-2082
Vasilieva, Elena; Niederschulte, Jacquelyn; Song, Yang et al. (2016) Interactions of two large antiviral polyamides with the long control region of HPV16. Biochimie 127:103-14
He, Gaofei; Bashkin, James K (2015) What is the antiviral potential of pyrrole-imidazole polyamides? Future Med Chem 7:1953-5
Vasilieva, Elena; Song, Yang; Koeller, Kevin J et al. (2015) 134 Large antiviral polyamide-DNA interactions. J Biomol Struct Dyn 33 Suppl 1:86-7
He, Gaofei; Tolic, Ana; Bashkin, James K et al. (2015) Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors. Nucleic Acids Res 43:4322-31
He, Gaofei; Vasilieva, Elena; Harris Jr, George Davis et al. (2014) Binding studies of a large antiviral polyamide to a natural HPV sequence. Biochimie 102:83-91
Koeller, Kevin J; Harris, G Davis; Aston, Karl et al. (2014) DNA Binding Polyamides and the Importance of DNA Recognition in their use as Gene-Specific and Antiviral Agents. Med Chem (Los Angeles) 4:338-344
Wang, Shuo; Aston, Karl; Koeller, Kevin J et al. (2014) Modulation of DNA-polyamide interaction by ?-alanine substitutions: a study of positional effects on binding affinity, kinetics and thermodynamics. Org Biomol Chem 12:7523-36
Bashkin, James K; Aston, Karl; Ramos, Joseph P et al. (2013) Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with ýý-alanine. Biochimie 95:271-9
He, Gaofei; Vasilieva, Elena; Bashkin, James K et al. (2013) Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis. Anal Biochem 439:99-101

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