Pharmaceutical Chemistry

Biography

Biography: James K. Bashkin

Abstract

The current study investigates the application of pyrrole-imidazole polyamides to fighting viral diseases in cell and tissue culture. We first reported the use of polyamides against high-risk human papillomavirus (HPV) types 16, 18 and 31 in 2011. A previous report on repressing latency of HIV with polyamides had appeared from the Dervan group in 2004, while inhibition of Maloney murine leukemia virus integration with the same class of molecules was reported the previous year, and so-called "paradoxical effects," meaning the authors did not understand their observations, were reported in for effects of polyamides on HLTV-1 transcription by the same group in 2004. Through extensive molecular biology and biophysical studies (with Professor Cynthia M. Dupureur and group), we have explained the "paradoxical effects" and find these rule-breaking effects to be the basis of our observed antiviral activity. We have shown the the "rules" for DNA recognition by polyamides reported so widely by Dervan et al. do not apply to longer molecules, where enthalpy plays no role in the free energy of binding, and entropy likely associated with deaggregation of polyamides is the determining factor in providing favorable, negative Gibbs free energies  of binding.This deaggregation appears to be aided by increasing the positive charge on both the C- and N-termini of polyamides, resulting in improved antiviral parameters (IC₅₀ and IC₉₀) and improved thermodynamic binding parameters such as the dissociation constants.We now have IC₅₀ values as low as 8-13 nM. Of interest to medicinal and pharmaceutical chemists, our polyamides were predicted by many to be incapable of entry into cells. However, the opposite is usually the case, and active uptake is often the reason, though we have not identified the specific uptake mechanism yet. Uptake into some cells is extremely effective, including essentially primary keratinocytyes infected with episomal HPV. Another example is a range of blood cells: iv pharmacokinetics are hampered by the immediate uptake of compounds into blood cells, leaving none in the plasma to be measured and making bioavailability, by definition, zero, even though the blood cells transport the compounds to internal organs such as bone marrow, liver, and spleen.

Conclusion: It can be extremely important to ignore "rules" of science and medicinal chemistry and simply carry out experiments to see the results. Even highly flawed prior literature can inspire effective strategies for drug discovery. However, novel molecular structures may require additional creativity in the formulation and drug delivery aspects of drug development. We even found activity against Vesicular Stomatitis Virus (VSV) shortly after the two most prominent groups reported poor polyamide-RNA interactions. Their data were not wrong, but they failed to account for the range of RNA structures found in RNA genomes, which go far beyond the A-form helix of double-stranded RNA.