Binding site size limitations of imidazole-pyrrole polyamides for recognition in the minor groove of DNA

The discovery that the three ring polyamide Im-Py-Py-Dp containing imidazole (Im) and pyrrole (Py) carboxamides binds the DNA sequence 5'-(A,T)G(A,T)C(A,T)-3' as an antiparallel dimer offers a new model for the design of ligands for specific recognition of sequences in the minor groove containing both G,C and A,T base pairs. In Chapter 2, experiments are described in which the sequential addition of five N- methylpyrrolecarboxamides to the imidazole-pyrrole polyamide Im-Py-Py-Dp affords a series of six homologous polyamides, Im-(Py)_2-7-Dp, that differ in the size of their binding site, apparent first order binding affinity, and sequence specificity. These results demonstrate that DNA sequences up to nine base pairs in length can be specifically recognized by imidazole-pyrrole polyamides containing three to seven rings by 2:1 polyamide-DNA complex formation in the minor groove. Recognition of a nine base pair site defines the new lower limit of the binding site size that can be recognized by polyamides containing exclusively imidazole and pyrrolecarboxamides. The results of this study should provide useful guidelines for the design of new polyamides that bind longer DNA sites with enhanced affinity and specificity.

In Chapter 3 the design and synthesis of the hairpin polyamide Im-Py-Im-Py-γ-Im- Py-Im-Py-Dp is described. Quantitative DNase I footprint titration experiments reveal that Im-Py-Im-Py-γ-Im-Py-Im-Py-Dp binds six base pair 5'-(A,T)GCGC(A,T)-3' sequences with 30-fold higher affinity than the unlinked polyamide Im-Py-Im-Py-Dp. The hairpin polyamide does not discriminate between A•T and T•A at the first and sixth positions of the binding site as three sites 5'-TGCGCT-3', 5'-TGCGCA-3', and 5 'AGCGCT- 3' are bound with similar affinity. However, Im-Py-Im-Py-γ-Im-Py-Im-PyDp is specific for and discriminates between G•C and C•G base pairs in the 5'-GCGC-3' core as evidenced by lower affinities for the mismatched sites 5'-AACGCA-3', 5'- TGCGTT-3', 5'-TGCGGT-3', and 5'-ACCGCT-3'.

In Chapter 4, experiments are described in which a kinetically stable hexa-aza Schiff base La³⁺ complex is covalently attached to a Tat(49-72) peptide which has been shown to bind the HIV-1 TAR RNA sequence. Although these metallo-peptides cleave TAR site-specifically in the hexanucleotide loop to afford products consistent with hydrolysis, a series of control experiments suggests that the observed cleavage is not caused by a sequence-specifically bound Tat(49-72)-La(L)³⁺ peptide.

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.

High-dimensional assembly depending on polyoxoanion templates, metal ion coordination geometries, and a flexible bis(imidazole) ligand

By introducing the flexible 1,1'-(1,4-butanediyl)bis(imidazole) (bbi) ligand into the polyoxovanadate system, five novel polyoxoanion-templated architectures based on [As8V14O42](4-) and [V16O38Cl](6-) building blocks were obtained: [M(bbi)(2)](2)[As8V14O42(H2O)] [M = Co (1), Ni (2), and Zn (3)], [Cu(bbi)](4)[As8V14O42(H2O)] (4), and [Cu(bbi)](6)[V16O38Cl] (5). Compounds 1-3 are isostructural, and they exhibit a binodal (4,6)-connected 2D structure with Schlafli symbol (3(4)center dot 4(2))(3(4)center dot 4(4)center dot 5(4)center dot 6(3))(2), in which the polyoxoanion induces a closed four-membered circuit of M-4(bbi)(4). Compound 4 exhibits an interesting 3D framework constructed from tetradentate [As8V14O42](4-) cluster anions and cationic ladderlike double chains. There exists a bigger M-8(bbi)(6)O-2 circuit in 4. The 3D extended structure of 5 is composed of heptadentate [V16O38Cl](6-) anions and flexural cationic chains; the latter consists of six Cu(bbi) segments arranged alternately. It presents the largest 24-membered circuit of M-24(bbi)(24) so far observed made of bbi molecules and transition-metal cations. Investigation of their structural relations shows the important template role of the polyoxoanions and the synergetic interactions among the polyoxoanions, transition-metal ions, and flexible ligand in the assembly process.

Syntheses, crystal structures and properties of two Cu(II) coordination polymers: Cu(C3N2H4)(2)(HL)(2) andCU(C3N2H4)(2)L with C3N2H4 = imidazole, H2L = adipic acid

The reactions of freshly prepared Cu(OH)(2).xH(2)O and Cu(OH)(2-2y)(CO3)(y).zH(2)O precipitates with imidazole and adipic acid in CH3OH/H2O at pH = 5.4 yielded CU(C3N2H4)(2)(HL)(2) 1 and CU(C3N2H4)(2)L 2, respectively. Complex 1 consists of ribbon-like polymeric chains (1)(infinity)[CU(C3N2H4)(2)(HL)(4/2)], in which the octahedrally coordinated Cu atoms are doubly bridged by bis-monodentate hydrogen adipato ligands. The interchain N-H...O hydrogen bonding interactions are responsible for supramolecular assembly of the polymeric chains into open 3D frameworks and two-fold interpenetration of the resulting open frameworks completes the crystal structure of 1. Within complex 2, the Cu atoms are penta-coordinated to form CuN2O3 square pyramids and condensed into CU2N4O4 dimers, which are doubly bridged by twisted bis-monodentate adipato ligands into polymeric chains (1)(infinity)([CU(C3N2H4)(2)](2)L-4/2) with 4- and 18-membered rings progressing alternatively. The polymeric chains are assembled due to interchain N-H...O hydrogen bonding interactions. The thermal and magnetic behaviors of 1 and 2 is discussed.

Novel < 110 >-oriented organic-inorganic perovskite compound stabilized by N-(3-aminopropyl) imidazole with improved optical properties

In the organic-inorganic perovskites family, the < 100 >-oriented type has been extensively investigated as a result of its unique magnetic, optical, and electrical properties, and only one type of < 110 >-oriented hybrid perovskite stabilized by methylammonium and iodoformamidinium cations or the latter themselves has been known so far. In this paper, another novel < 110 >-oriented organic-inorganic perovskite (C6H13N3)-PbBr4 (compound 1) has been prepared by reacting N-(3-aminopropyl)imidazole (API) with PbBr2 in hydrobromic acid. The crystal structure is determined, which indicates that the perovskite is stabilized by API. The introduction of the optically active organic ligand API into the hybrid perovskite results in a red shift and a great enhancement of photoluminescence in the perovskite with respect to organic ligand API itself. These results have been explained according to calculation based on density-functional theory. Moreover, the excellent film processing ability for the perovskite (C6H13N3)PbBr4 together with the improved optical properties makes it have potential application in optoelectronic devices.

Tuning of emission: Synthesis, structure and photophysical properties of imidazole, oxazole and thiazole-based iridium (III) complexes

Three new iridium (III) complexes with two cyclometalated (CN)-N-boolean AND ligands (imidazole, oxazole and thiazole-based, respectively) and one acetylacetone (acac) ancillary ligand have been synthesized and fully characterized. The structure of the thiazole-based complex has been determined by single crystal X-ray diffraction analysis. The Ir center was located in a distorted octahedral environment by three chelating ligands with the N-N in the trans and C-C in the cis configuration. By changing the hetero-atom of (CN)-N-boolean AND ligands the order S, O and N, a marked and systematic hypsochromic shift of the maximum emission peak of the complexes was realized. The imidazole-based complex emits at a wavelength of 500 nm, which is in the blue to green region. The tuning of emission wavelengths is consistent with the variation of the energy gap estimated front electrochemistry results. An electroluminescent device using the thiazole-based complex as a dopant in the emitting layer has been fabricated. A highly efficient yellow emission with a maximum luminous efficiency of 9.8 cd/A at a current density of 24.2 mA/cm(2) and a maximum brightness of 7985 cd/m(2) at 19.6 V has been achieved.

Synthesis and structural characterization of a new molecule-based complex constructed from dodecamolybdophosphoric acid and imidazole

A new compound, (CH5N2)(3)(PMo12O40CH4N23H2O)-C-.-H-. (1), was synthesized and structurally characterized by elemental analyses, IR spectra, UV spectra, NMR spectra and ESR spectra. This is, to our knowledge, the first example of an imidazole-polyoxometalate species. The compound was recrystallized from N,N-dimethylformamide (DMF), and then black block-like crystals of (C3H5N2)(4)((PMoMo11O40)-Mo-V-O-VI)(.)4C(3)H(7)NO(.) 2H(2)O (2), were obtained. It crystallizes in a triclinic space group P (1) over bar with n=12.423(3) Angstrom, b=12.666(3) Angstrom, c=13.341(3) Angstrom, alpha=70.56(3)degrees, beta=71.16(3)degrees, gamma=64.18(3)degrees, V= 1742.3(6) Angstrom(3), Z=1, R1 = 0.0585, wR2 = 0.1885. An X-ray crystallographic study showed that the crystal structure is constructed by electrostatic attractions and hydrogen bonds between a dodecamolybdophosphoric anion and an imidazole. The imidazole and DMF molecules occupy cavities in a polyoxometalate lattice ordered along a c-axis. The structure of (2) is similar to that of (1) from a comparison of both IR spectra and TGA Curves.

Networks with hexagonal circuits in co-ordination polymers of metal ions (Zn-II, Cd-II) with 1,1 '-(1,4-butanediyl)bis(imidazole)

Three new compounds, [ZnL1.5(H2O)(SO4)]. 6H(2)O 1, [ZnL1.5(H2O)(2)][NO3](2). 2H(2)O 2 and [CdL1.5(H2O)(2)(SO4)]. 4H(2)O 3 were obtained from self-assembly of the corresponding metal salts with 1,1'-(1,4-butanediyl)bis(imidazole) (L). In both 1 and 2 zinc ion is five-co-ordinated, showing a less-common trigonal bipyramidal co-ordination polyhedron, while cadmium ion of 3 is six-co-ordinated with a common octahedral arrangement. The sulfate ions of 1 and 3 are co-ordinated, however the nitrate ions of 2 are not. Each of the three compounds is composed of a (6, 3) network with the hexagonal smallest circuit containing six metal ions and six L; each L is co-ordinated to two metal ions, acting as a bridging ligand. In 1 the 2-D sheet of (6, 3) networks is interpenetrated in an inclined mode by symmetry related, identical sheets to give an interlocked 3-D structure, while the (6, 3) networks of both 2 and 3 stack in a parallel fashion to construct frameworks having channels.

Investigation of metalloporphyrins and their imidazole complexes using electrospray ionization mass spectrometry

Three compounds of metalloporphyrins were studied using electrospray ionization mass spectrometry. The bonding power between substitutional phenyl and porphyrin cycle and the coordinate conditions of metalloporphyrins with imidazole were discussed. The experimental result indicated that the bonding power between substitutional phenyl and porphyrin cycle in metalloporphyrins became weak from Mn, Fe to Co. The complexes abundances formed by metallophorphyrin with imidazole were stronger with the increase of the ligand concentration. At the same ligand concentration, the abundance of the complexes was intensified gradually and the stability of the ligands was become stronger from Mn, Fe to Co.

Synthesis and characterization of a new layered zinc phosphate: (C3H4N2)(3)Zn-4(HPO4)(PO4)(2) with imidazole coordinating to Zn atoms

A new two-dimensional hybrid zinc phosphate with electro-neutral open-framework has been hydrothermally synthesized by using imidazole as a structure-directing agent, whose structure is characterized with 3-, 4-, 5, and 12-ring layers and coordination bonds between imidazole groups and zinc atoms, resulting in primary building units of ZnO2N2 and ZnO3N.

Diisothiocyanatobis(1-vinyl-1H-imidazole-kappa N-3)-copper(II)

In the title compound, [Cu(NCS)(2)(C5H6N2)(2)], each Cu atom is coordinated by two N atoms from two Eim (Eim = 1-vinyl-1H-imidazole) ligands and two N atoms from two isothiocyanate groups. The Cu atom adopts a square-planar geometry. The mean Cu-N(Eim) and Cu-N(NCS) distances are 1.960 (6) and 1.993 (6) angstrom, respectively.

2-(2-Phenyl-1H-phenanthro-[9,10-d]imidazole-1-yl)-acetic acid (PPIA) and its application for determination of amines by high performance liquid chromatography with fluorescence detection and identification with mass spectroscopy/atmospheric pressure chemical ionization

A simple, sensitive, and mild method for the determination of amino compounds based on a condensation reaction with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC-HCI) as the dehydrant with fluorescence detection has been developed. Amines were derivatized to their acidamides with labeling reagent 2-(2-phenyl-1H-phenanthro-[9,10-d]imidazole-1-yl)-acetic acid (PPIA). Studies on derivatization conditions indicated that the coupling reaction proceeded rapidly and smoothly in the presence of a base catalyst in acetonitrile to give the corresponding sensitively fluorescent derivatives with an excitation maximum at lambda(ex) 260nm and an emission maximum at lambda(em) 380nm. The labeled derivatives exhibited high stability and were enough to be efficiently analyzed by high-performance liquid chromatography. Identification of derivatives was carried out by online post-column mass spectrometry (LC/APCI-MS/MS) and showed an intense protonated molecular ion corresponding m/z [MH](+) under APCI in positive-ion mode. At the same time, the fluorescence properties of derivatives in various solvents or at different temperature were investigated. The method, in conjunction with a gradient elution, offered a baseline resolution of the common amine derivatives on a reversed-phase Eclipse XDB-C-8 column. LC separation for the derivatized amines showed good reproducibility with acetonitrile-water as mobile phase. Detection limits calculated from 0.78 pmol injection, at a signal-to-noise ratio of 3, were 3.1-18.2 fmol. The mean intra- and inter-assay precision for all amine levels were < 3.85% and 2.11%, respectively. Excellent linear responses were observed with coefficients of > 0.9996. The established method for the determination of aliphatic amines from real wastewater and biological samples was satisfactory. (c) 2006 Elsevier B.V. All rights reserved.

Interactions of 1-Methylimidazole with UO2(CH3CO2)2 and UO2(NO3)2: Structural, Spectroscopic and Theoretical Evidence for Imidazole Binding to the Uranyl Ion

The first definitive high-resolution single-crystal X-ray structure for the coordination of the 1-methylimidazole (Meimid) ligand to UO2(Ac)2 (Ac = CH3CO2) is reported. The crystal structure evidence is confirmed by IR, Raman, and UV-vis spectroscopic data. Direct participation of the nitrogen atom of the Meimid ligand in binding to the uranium center is confirmed. Structural analysis at the DFT (B3LYP) level of theory showed a conformational difference of the Meimid ligand in the free gas-phase complex versus the solid state due to small energetic differences and crystal packing effects. Energetic analysis at the MP2 level in the gas phase supported stronger Meimid binding over H2O binding to both UO2(Ac)2 and UO2(NO3)2. In addition, self-consistent reaction field COSMO calculations were used to assess the aqueous phase energetics of combination and displacement reactions involving H2O and Meimid ligands to UO2R2 (R = Ac, NO3). For both UO2(NO3)2 and UO2(Ac)2, the displacement of H2O by Meimid was predicted to be energetically favorable, consistent with experimental results that suggest Meimid may bind uranyl at physiological pH. Also, log(Knitrate/KAc) calculations supported experimental evidence that the binding stoichiometry of the Meimid ligand is dependent upon the nature of the reactant uranyl complex. These results clearly demonstrate that imidazole binds to uranyl and suggest that binding of histidine residues to uranyl could occur under normal biological conditions.

Reaction of elemental chalcogens with imidazolium acetates to yield imidazole-2-chalcogenones: direct evidence for ionic liquids as proto-carbenes

Mechanistic analysis of the reaction between elemental sulfur or selenium and 1,3-dialkylimidazolium acetate ionic liquids, in the absence of an external base or solvent, affords evidence for the equilibrium presence of carbene species in these ionic liquids. It demonstrates the potential to control, through anion selection, the concentration of carbene in stable ionic liquids.