Biological activity of Pyrrole-Imidazole polyamides in vivo

This thesis focuses on biological activity of pyrrole-imidazole polyamides in vivo. The work presented includes experiments underlining sequence selectivity of these compounds in living cells and potential methods to improve it. A large fraction of this thesis is devoted to activity of Py-Im in murine models of cancer. We investigated the pharmacokinetics and biodistribution of two compounds – targeted to 5'-WGGWCW-3' and 5'-WTWCGW-3' sequences – and characterized their activity by measuring their effects on tumor growth, gene expression in vivo and in tissue culture, and their effects on physiology of tumors. The initial theoretical studies suggested that a large fraction of genomic sites are bound by Py-Im polyamides non-specifically and experimental data shows that the programmed binding sequence is not a sole determinant of the patterns of gene regulation. Despite the likely presence of non-specific effects of Py-Im polyamides in living cells, in vivo administration of Py-Im polyamides resulted in tolerable host toxicity and anti-tumor activity. Py-Im polyamide targeted to Estrogen Receptor Response Element showed downregulation of ER-driven gene expression in tumor cells, while the compound targeted to hypoxia response element reduced vascularization of tumors and their growth rate, induced apoptosis of cells in hypoxic areas and reduced expression of proangiogenic and prometastatic factors. Further studies, showed that polyamides distributed to many of the tested tissues and their FITC-conjugates showed nuclear uptake. The gene expression effects were also present in murine tissues, such as liver and kidneys, indicating a potential for use for Py-Im polyamides in non-cancerous diseases.

Preparation of Industrially Important Hydroxy Acids and Diacids from 2,2-Disubstituted Propane-1,3-Diols and Linear Primary Diols by Green Chemistry Methods

Environmentally benign and economical methods for the preparation of industrially important hydroxy acids and diacids were developed. The carboxylic acids, used in polyesters, alkyd resins, and polyamides, were obtained by the oxidation of the corresponding alcohols with hydrogen peroxide or air catalyzed by sodium tungstate or supported noble metals. These oxidations were carried out using water as a solvent. The alcohols are also a useful alternative to the conventional reactants, hydroxyaldehydes and cycloalkanes. The oxidation of 2,2-disubstituted propane-1,3-diols with hydrogen peroxide catalyzed by sodium tungstate afforded 2,2-disubstituted 3-hydroxypropanoic acids and 1,1-disubstituted ethane-1,2-diols as products. A computational study of the Baeyer-Villiger rearrangement of the intermediate 2,2-disubstituted 3-hydroxypropanals gave in-depth data of the mechanism of the reaction. Linear primary diols having chain length of at least six carbons were easily oxidized with hydrogen peroxide to linear dicarboxylic acids catalyzed by sodium tungstate. The Pt/C catalyzed air oxidation of 2,2-disubstituted propane-1,3-diols and linear primary diols afforded the highest yield of the corresponding hydroxy acids, while the Pt, Bi/C catalyzed oxidation of the diols afforded the highest yield of the corresponding diacids. The mechanism of the promoted oxidation was best described by the ensemble effect, and by the formation of a complex of the hydroxy and the carboxy groups of the hydroxy acids with bismuth atoms. The Pt, Bi/C catalyzed air oxidation of 2-substituted 2-hydroxymethylpropane-1,3-diols gave 2-substituted malonic acids by the decarboxylation of the corresponding triacids. Activated carbon was the best support and bismuth the most efficient promoter in the air oxidation of 2,2-dialkylpropane-1,3-diols to diacids. In oxidations carried out in organic solvents barium sulfate could be a valuable alternative to activated carbon as a non-flammable support. In the Pt/C catalyzed air oxidation of 2,2-disubstituted propane-1,3-diols to 2,2-disubstituted 3-hydroxypropanoic acids the small size of the 2-substituents enhanced the rate of the oxidation. When the potential of platinum of the catalyst was not controlled, the highest yield of the diacids in the Pt, Bi/C catalyzed air oxidation of 2,2-dialkylpropane-1,3-diols was obtained in the regime of mass transfer. The most favorable pH of the reaction mixture of the promoted oxidation was 10. The reaction temperature of 40°C prevented the decarboxylation of the diacids.

DNA binding properties of novel dansylated distamycin analogues in which the fluorophore is directly conjugated to the N-methyl-pyrrole carboxamide backbone

Polyamides that are structural analogues of the naturally occurring DNA minor groove binding antibiotic distamycin (Dst) are promising candidates as gene modulators. Developing strategies for the large scale screening and monitoring of the cellular distribution of such ligands would aid the faster discovery of molecules, which would have eventual utility in molecular biology and medicine. Attachment of fluorescent tags would be a useful step towards this end. A fundamental question in this connection is whether the tag modifies the DNA binding affinity of the parent compounds. Towards answering this question, we have developed two oligopeptides that bear the dansyl (N, N-dimethylaminonaphthalene sulfonamido fluorophore) coupled directly to the N-terminus of the conjugated N-methylpyrrole carboxamide network, and possess three or four N-methyl pyrrole carboxamide units (abbreviated as Dn3 and Dn4 respectively). DNA binding abilities of these molecules were assessed from fluorescence titration experiments, duplex-DNA T-m analysis (employing both UV and fluorescence spectroscopy), induced circular dichroism measurements (ICD), salt dependence of ICD and apparent binding constant measurements (K-app) employing ethidium bromide (EtBr) displacement assay. Both these molecules 'reported' DNA binding in the form of an enhanced fluorescence emission. As judged from the ICD measurements, salt dependence of ICD, T-m analysis and K-app measurements, the binding affinities of the molecules that possessed dansyl group at their N-termini were lower than the ones with equivalent number of amide units, but possessed N-methylpyrrole carboxamide unit at their N-termini. These results would have implications in the future design of fluorescent polyamides.

Cleavage of DNA by polyamide-seco-CBI conjugates

Small molecules that bind to any predetermined DNA sequence in the human genome are potentially useful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) N-methylpyrrole (Py) are cell permeable small molecules that bind DNA according to a set of "pairing rules" with affinities and specificities similar to many naturally occurring DNA binding proteins. Py-Im polyamides offer a general approach to the chemical regulation of gene expression. We demonstrate here that polyamide containing a DNA alkylating moiety seco-CBI can specifically direct sequence specific DNA alkylation. We can also control the strand of DNA that is alkylated, depending on the enantiomer of seco-CBI used and the orientation of the polyamide relative to the alkylation site (Chapter 2). This class of molecules has been applied to a gene repair system in collaboration with the Baltimore group at Caltech (Chapter 3). Also reported are additional seco-CBI polyamide conjugates synthesized to study other systems (HIV-1 and COX-2) (Appendix 1).

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.

Synthesis of isomeric bis(amine anhydride)s for novel poly(amine imide)s by Pd-catalyzed amination of 4-chlorophthalic anhydride

Two novel bis(amine anhydride) monomers, N,N'-bis(3,4-dicarboxyphenyl)-1,4-phenylenediamine dianhydride I and N,/N'-bis(3,4-dicarboxyphenyl)-1,3-phenylenediamine dianhydride 11, were prepared via palladium-catalyzed amination reaction of 4-chloro-N-methylphthaliniide with 1,4-phenylenediamine or 1,3-phenylenediamine, followed by alkaline hydrolysis of the intermediate bis(amine imide)s and subsequent dehydration of the resulting tetraacids. A series of new poly(amine imide)s were prepared from the synthesized dianhydride monomers with various diamines in NMP via conventional two-step method.

Amphiphilic Core-Shell Nanocarriers Based On Hyperbranched Poly(ester amide)-star-PCL: Synthesis, Characterization, and Potential as Efficient Phase Transfer Agent

Amphiphilic biodegradable star-shaped polymer was conveniently prepared by the Sn(Oct)(2)-catalyzed ring opening polymerization of c-caprolactone (CL) with hyperbranched poly(ester amide) (PEA) as a macroinitiator. Various monomer/initiator ratios were employed to vary the length of the PCL arms. H-1 NMR and FTIR characterizations showed the successful synthesis of star polymer with high initiation efficiency. SEC analysis using triple detectors, RI, light scattering, and viscosity confirmed the controlled manner of polymerization and the star architecture.

Effect of main-chain rigidity on the phase transitional behavior of comblike polymers

The influence of the rigidity of polymer backbones on the side-chain crystallization and phase transition behavior was systematically investigated by a combination of differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD), Fourier transform infrared spectroscopy (FTIR), and high-resolution solid-state nuclear magnetic resonance spectroscopy (NMR). DSC investigation indicated that the crystallization number of alkyl carbon atoms of the side chains grafted onto the rigid polymer backbone, poly(p-benzamide) (PBA), is much lower than that of the alkyl carbon atoms of the side chains grafted onto the flexible polymer backbone, poly(ethyleneimine) (PEI), implying that the conformational state of the polymer backbones has a strong effect on the side-chain crystallization behavior in comblike polymers. WAXD and FTIR results proved that these two comblike polymers pack into hexagonal (PBA18C) and orthorhombic (PEI18C) crystals, respectively, depending on the adjusting ability of the polymer backbones for particular conformational states. It was also found that the presence of the crystalline-amorphous interphase (delta = 31.6 ppm) in PBA18C detected by solid-state C-13 NMR spectroscopy can be attributed to the rigid PBA backbone, which restricts the mobility of the alkyl side chains.

Synthesis of bis(amine anhydride)s for novel high T(g)s and organosoluble poly(amine imide)s by palladium-catalyzed amination of 4-chlorophthalide anhydride

Two novel bis(amine anhydride)s, NN-bis(3,4-dicarboxyphenyl)aniline dianhydride (I) and N,N-bis(3,4-dicarboxyphenyl)-p-tert-butylaniline (II), were synthesized from the palladium-catalyzed amination reaction of N-methyl-protected 4-chlorophthalic anhydride with arylamines, followed by alkaline hydrolysis of the intermediate bis(amine-phthalimide)s and subsequent dehydration of the resulting tetraacids. The X-ray structures of anhydride I and II were determined. The obtained dianhydride monomers were reacted with various aromatic diamines to produce a series of novel polyimides. Because of the incorporation of bulky, propeller-shaped triphenylamine units along the polymer backbone, all polyimides exhibited good solubility in many aprotic solvents while maintaining their high thermal properties. These polymers had glass transition temperatures in the range of 298-408 degrees C. Thermogravimetric analysis showed that all polymers were stable, with 10% weight loss recorded above 525 degrees C in nitrogen.The tough polymer films, obtained by casting from solution, had tensile strength, elongation at break, and tensile modulus values in the range of 95-164 MPa, 8.8-15.7%, and 1.3-2.2 GPa, respectively.

Synthesis and properties of novel soluble polyimides having a spirobisindane-linked dianhydride unit

A new synthetic procedure was elaborated allowing the preparation of semiaromatic dianhydride. N-Methyl protected 4-chlorophthalic anhydride was nitrated with HNO3 to produce N-methyl-4-chloro-5-nitrophthalimide (1). The aromatic nucleophilic substitution reaction between 5,5',6,6'-tetrahydroxy-3,3,3',3'-tetramethyl-1,1-spirobisindane and 1 afforded spirobisindane-linked bis(N-methylphthalimide) (2), which was hydrolyzed and subsequently dehydrated to give the corresponding dianhydride (3). The latter was polymerized with five different aromatic diamines to afford a series of aromatic polyimides. The properties of polyimides such as inherent viscosity, solubility, UV transparency and thermal stability were investigated to illustrate the contribution of the introduction of spirobisindane groups into the polyimide backbone. The resulting polyimides were readily soluble in polar solvents such as chloroform, THF and N-methyl-2-pyrrolidone. The glass-transition temperatures of these polyimides were in the range of 254-292 degrees C. The tensile strength, elongation at break, and Young's modulus of the polyimide film were 68.8-106.6 MPa, 5.9-9.8%, 1.7-2.0 GPa, respectively. The polymer films were colorless and transparent with the absorption cutoff wavelength at 286-308 nm.

Synthesis and properties of novel organosoluble polyimides derived from 1,4-bis[4-(3,4-dicarboxylphenoxy)]triptycene dianhydride and various aromatic diamines

A novel triptycene-based dianhydride, 1,4-bis[4-(3,4-dicarboxylphenoxy)]triptycene dianhydride, was prepared from 4-nitro-N-methylphthalimide and potassium phenolate of 1,4-dihydroxytriptycene (1). The aromatic nucleophilic substitution reaction between 4-nitro-N-methylphthalimide and I afforded triptycene-based bis(N-methylphthalimide) (2), which hydrolyzed and subsequently dehydrated to give the corresponding dianhydride (3). A series of new polyimides containing triptycene moieties were prepared from the dianhydride monomer (3) and various diamines in in-cresol via conventional one-step polycondensation method. Most of the resulting polyimides were soluble in common organic solvents, such as chloroform, THF, DMAc and DMSO. The polyimides exhibited excellent thermal and thermo-oxidative stabilities with the onset decomposition temperature and 10% weight loss temperature ranging from 448 to 486 degrees C and 526 to 565 degrees C in nitrogen atmosphere, respectively. The glass transition temperatures of the polyimides were in the range of 221-296 degrees C. The polyimide films were found to be transparent, flexible, and tough. The films had tensile strengths, elongations at break, and tensile moduli in the ranges 95-118 MPa, 5.3-16.2%, and 1.03-1.38 GPa, respectively. Wide-angle X-ray diffraction measurements revealed that these polyimides were amorphous.

Synthesis and gas transport property of polyimide from 2,2 '-disubstituted biphenyltetracarboxylic dianhydrides (BPDA)

A series of dianhydride monomers, 2,2'-disubstituted-4,4',5,5'-biphenyltetracarboxylic dianhydride (substituents = phenoxy, p-methylphenoxy, p-tert-butylphenoxy, nitro, and methoxy) were synthesized by the nitration of an N-methyl protected 3,3',4,4'-biphenyttetracarboxylic dianhydride (BPDA) and subsequent aromatic nucleophilic substitutions with aroxides (NaOAr) or methoxide. These dianhydrides were polymerized with various aromatic diamines in refluxing m-cresol containing isoquinoline to afford a series of aromatic polyintides. The effects of varying 2,2'-substituents of the dianhydride (BPDA) moiety on the properties of polyimides were investigated. It was found that polyimides from the dianhydrides containing phenoxy, p-methylphenoxy, and p-tert-butylphenoxy side groups possessed excellent solubility and film forming capability whereas polyimides from 2,2'-dinitro-BPDA and 2,2'-dimethoxy-BPDA were less soluble in organic solvent. The soluble polymers formed flexible, tough and transparent films. The films had a tensile strength, elongation at break, and Young's modulus in the ranges 102-168 MPa, 8-21%, 2.02-2.38 GPa, respectively. The polymer gas permeability coefficients (P) and ideal selectivities for N-2, O-2, CO2 and CH4 were determined for the -OAr substituted polyimides. The oxygen permeability coefficient (P-O2) and permselectivity of oxygen to nitrogen (PO2/N-2) of the films were in the ranges 3.4-11.3 barrer and 3.8-4.6, respectively.

Synthesis and characterization of soluble poly(amideimide)s bearing triethylamine sulfonate groups as gas dehumidification membrane material

A series of soluble poly(amide-imide)s (PAIs) bearing triethylammonium sulfonate groups were synthesized directly using trimellitic anhydride chloride (TMAC) polycondensation with sulfonated diamine such as 2,2'-benzidinedisulfonic acid (BDSA), 4,4'-diaminodiphenyl ether-2,2'-disulfonic acid (ODADS), and nonsulfonated diamine 4,4-diaminodiphenyl methane in the presence of triethylamine. The resulting copolymers exhibited high molecular weights (high inherent viscosity), and a combination of desirable properties such as good solubility in dipolar aprotic solvents, film-forming capability, and good mechanical properties. Wide-angle X-ray diffraction revealed that the polymers were amorphous. These copolymers showed high permeability coefficients of water vapor because of the presence of the hydrophilic triethylammonium sulfonate groups. The water vapor permeability coefficients (P-w) and permselectivity coefficients of water vapor to nitrogen and methane [alpha(H2O/N-2) and (alpha(H2O/CH4)] Of the films increased with increasing the amount of the triethylammonium sulfonated groups.

Facile synthesis and characterization of hyperbranched poly(ether amide)s generated from Michael addition polymerization of in situ created AB(2) monomers

A new straightforward strategy for synthesis of novel hyperbranched poly (ether amide)s from readily available monomers has been developed. By optimizing the reaction conditions, the AB(2)-type monomers were formed dominantly during the initial reaction stage. Without any purification, the AB(2) intermediate was subjected to further polymerization in the presence (or absence) of an initiator, to prepare the hyperbranched polymer-bearing multihydroxyl end-groups. The influence of monomer, initiator, and solvent on polymerization and the molecular weight (MW) of the resultant polymers was studied thoroughly. The MALDI-TOF MS of the polymers indicated that the polymerization proceeded in the proposed way. Analyses of H-1 NMR and C-13 NMR spectra revealed the branched structures of the polymers obtained. These polymers exhibit high-moderate MWs and broad MW distributions determined by gel permeation chromatography (GPC) in combination with triple detectors, including refractive index, light scattering, and viscosity detectors. In addition, the examination of the solution behavior of these polymers showed that the values of intrinsic viscosity [eta] and the Mark-Houwink exponent a were remarkably lower compared with their linear analogs, because of their branched nature.

Crystallization kinetics and morphology of nylon 1212

The isothermal and non-isothermal crystallization processes of nylon 1212 were investigated by polarized optical microscopy. The crystal growth rates of nylon 1212 measured in isothermal conditions at temperatures ranged from 182 to 132 degreesC are well comparable with those measured by non-isothermal procedures (cooling rates ranged from 0.5 to 11 degreesC/min). The kinetic data were examined with the Hoffman-Lauritzen nucleation theory on the basis of the obtained values of the thermodynamic parameters of nylon 1212. The classical regime I --> II and regime II --> III transitions occur at the temperatures of 179 and 159 degreesC, respectively. The crystal growth parameters were calculated with (100) plane assumed to be the growth plane. The regime I --> II --> III transition is accompanied by a morphological transition from elliptical-shaped structure to banded spherulite and then non-banded spherulite. The development of morphology during isothermal and non-isothermal processes shows a good agreement.