Antitumor activity of Py-Im polyamides

Molecules that inhibit DNA dependent processes are the most commonly used agents for the treatment of cancer. The genotoxicity associated with their mechanisms of action, unfortunately, make them extremely toxic to the patient and cancer cells alike. The work presented in this thesis outlines the development of Py-Im polyamides as non-genotoxic DNA-targeted antitumor molecules that interfere with RNA polymerase II elongation. We initially characterized the pharmacokinetic profiles of two hairpin polyamides to establish their bioavailability in the serum and tissues after a single administration. We next determined the molecular mechanism that contributes to toxicity of a hairpin polyamide in human prostate cancer cells in cell culture and we demonstrated antitumor effects of the compound against LNCaP xenografts in mice. Finally, we conducted animal toxicity experiments on 4 polyamides that vary on the gamma-turn with respect to the substitution of amino and acetamide groups at the alpha and beta positions. From this study we identified a second generation compound that retains antitumor activity with significantly reduce animal toxicity. This work sets the foundation for the development of Py-Im polyamides as DNA targeted therapeutics for the treatment of advanced prostate cancer.

Targeting DNA repeat sequences with Py-Im polyamides

Hairpin pyrrole-imdazole polyamides are cell-permeable, sequence-programmable oligomers that bind in the minor groove of DNA. This thesis describes studies of Py-Im polyamides targeted to biologically important DNA repeat sequences for the purpose of modulating disease states. Design of a hairpin polyamide that binds the CG dyad, a site of DNA methylation that can become dysregulated in cancer, is described. We report the synthesis of a DNA methylation antagonist, its sequence specificity and affinity informed by Bind-n-Seq and iteratively designed, which improves inhibitory activity in a cell-free assay by 1000-fold to low nanomolar IC50. Additionally, a hairpin polyamide targeted to the telomeric sequence is found to trigger a slow necrotic-type cell death with the release of inflammatory molecules in a model of B cell lymphoma. The effects of the polyamide are unique in this class of oligomers; its effects are characterized and a functional assay of phagocytosis by macrophages is described. Additionally, hairpin polyamides targeted to pathologically expanded CTG•CAG triplet repeat DNA sequences, the molecular cause of myotonic dystrophy type 1, are synthesized and assessed for toxicity. Lastly, ChIP-seq of Hypoxia-Inducible Factor is performed under hypoxia-induced conditions. The study results show that ChIP-seq can be employed to understand the genome-wide perturbation of Hypoxia-Inducible Factor occupancy by a Py-Im polyamide.

Investigations of Pyrrole-Imidazole Polyamide Effects on DNA Replication

Pyrrole–Imidazole polyamides are programmable, cell-permeable small molecules that bind in the minor groove of double-stranded DNA sequence-specifically. Polyamide binding has been shown to alter the local helical structure of DNA, disrupt protein-DNA interactions, and modulate endogenous gene expression. Py–Im polyamides targeted to the androgen receptor-DNA interface have been observed to decrease expression of androgen-regulated genes, upregulate p53, and induce apoptosis in a hormone-sensitive prostate cancer cell line. Here we report that androgen response element (ARE)-targeted polyamides induced DNA replication stress in a hormone-insensitive prostate cancer cell line. The ATR checkpoint kinase was activated in response to this stress, causing phosphorylation of MCM2, and FANCD2 was monoubiquitinated. Surprisingly, little single-stranded DNA was exhibited, and the ATR targets RPA2 and Chk1 were not phosphorylated. We conclude that polyamide induces relatively low level replication stress, and suggest inhibition of the replicative helicase as a putative mechanism based on in vitro assays. We also demonstrate polyamide-induced inhibition of DNA replication in cell free extracts from X. laevis oocytes. In this system, inhibition of chromatin decondensation is observed, preventing DNA replication initiation. Finally, we show that Py-Im polyamides targeted to the ARE and ETS binding sequence downregulate AR- and ERG-driven signaling in a prostate cancer cell line harboring the TMPRSS2-ERG fusion. In a mouse xenograft model, ARE-targeted polyamide treatment reduced growth of the tumor.

A multiple scattering problem

The present work deals with the problem of the interaction of the electromagnetic radiation with a statistical distribution of nonmagnetic dielectric particles immersed in an infinite homogeneous isotropic, non-magnetic medium. The wavelength of the incident radiation can be less, equal or greater than the linear dimension of a particle. The distance between any two particles is several wavelengths. A single particle in the absence of the others is assumed to scatter like a Rayleigh-Gans particle, i.e. interaction between the volume elements (self-interaction) is neglected. The interaction of the particles is taken into account (multiple scattering) and conditions are set up for the case of a lossless medium which guarantee that the multiple scattering contribution is more important than the self-interaction one. These conditions relate the wavelength λ and the linear dimensions of a particle a and of the region occupied by the particles D. It is found that for constant λ/a, D is proportional to λ and that |Δχ|, where Δχ is the difference in the dielectric susceptibilities between particle and medium, has to lie within a certain range.

The total scattering field is obtained as a series the several terms of which represent the corresponding multiple scattering orders. The first term is a single scattering term. The ensemble average of the total scattering intensity is then obtained as a series which does not involve terms due to products between terms of different orders. Thus the waves corresponding to different orders are independent and their Stokes parameters add.

The second and third order intensity terms are explicitly computed. The method used suggests a general approach for computing any order. It is found that in general the first order scattering intensity pattern (or phase function) peaks in the forward direction Θ = 0. The second order tends to smooth out the pattern giving a maximum in the Θ = π/2 direction and minima in the Θ = 0 , Θ = π directions. This ceases to be true if ka (where k = 2π/λ) becomes large (> 20). For large ka the forward direction is further enhanced. Similar features are expected from the higher orders even though the critical value of ka may increase with the order.

The first order polarization of the scattered wave is determined. The ensemble average of the Stokes parameters of the scattered wave is explicitly computed for the second order. A similar method can be applied for any order. It is found that the polarization of the scattered wave depends on the polarization of the incident wave. If the latter is elliptically polarized then the first order scattered wave is elliptically polarized, but in the Θ = π/2 direction is linearly polarized. If the incident wave is circularly polarized the first order scattered wave is elliptically polarized except for the directions Θ = π/2 (linearly polarized) and Θ = 0, π (circularly polarized). The handedness of the Θ = 0 wave is the same as that of the incident whereas the handedness of the Θ = π wave is opposite. If the incident wave is linearly polarized the first order scattered wave is also linearly polarized. The second order makes the total scattered wave to be elliptically polarized for any Θ no matter what the incident wave is. However, the handedness of the total scattered wave is not altered by the second order. Higher orders have similar effects as the second order.

If the medium is lossy the general approach employed for the lossless case is still valid. Only the algebra increases in complexity. It is found that the results of the lossless case are insensitive in the first order of k_imD where k_im = imaginary part of the wave vector k and D a linear characteristic dimension of the region occupied by the particles. Thus moderately extended regions and small losses make (k_imD)² ≪ 1 and the lossy character of the medium does not alter the results of the lossless case. In general the presence of the losses tends to reduce the forward scattering.