Ethynyl and Propynylpyrene Inhibitors of Cytochrome P450

Abstract  

The single-crystal X-ray structures and in vivo activities of three aryl acetylenic inhibitors of cytochromes P450 1A1, 1A2, 2A6, and 2B1 have been determined and are reported herein. These are 1-ethynylpyrene, 1-propynylpyrene, and 4-propynylpyrene. To investigate electronic influences on the mechanism of enzyme inhibition, the experimental electron density distribution of 1-ethynylpyrene has been determined using low-temperature X-ray diffraction measurements, and the resulting net atomic charges compared with various theoretical calculations. A total of 82,390 reflections were measured with Mo Kα radiation to a (sinθ/λ)_max = 0.985 Å⁻¹. Averaging symmetry equivalent reflections yielded 8,889 unique reflections. A least squares refinement procedure was used in which multipole parameters were added to describe the distortions of the atomic electron distributions from spherical symmetry. A map of the model electron density distribution of 1-ethynylpyrene was obtained. Net atomic charges calculated from refined monopole population parameters yielded charges that showed that the terminal acetylenic carbon atom (C18) is more negative than the internal carbon (C17). Net atomic charges calculated by ab initio, density functional theory, and semi-empirical methods are consistent with this trend suggesting that the terminal acetylenic carbon atom is more likely to be the site of oxidation. This is consistent with the inhibition mechanism pathway that results in the formation of a reactive ketene intermediate. This is also consistent with assay results that determined that 1-ethynylpyrene acts as a mechanism-based inhibitor of P450s 1A1 and 1A2 and as a reversible inhibitor of P450 2B1. Crystallographic data: 1-ethynylpyrene, C₁₈H₁₀, P2₁/c, a = 14.571(2) Å, b = 3.9094(5) Å, c = 20.242(3) Å, β = 105.042(2)°, V = 1,113.5(2) Å³; 1-propynylpyrene, C₁₉H₁₂, P2₁/n, a = 8.970(2) Å, b = 10.136(1) Å, c = 14.080(3) Å, β = 99.77(2)°, V = 1,261.5(4) Å³; 4-propynylpyrene, C₁₉H₁₂, Pbca, a = 9.904(1) Å, b = 13.174(2) Å, c = 19.401(1) Å, V = 2,531.4(5) Å³.     

Monitoring hydrate formation and dissociation in sandstone and bulk with magnetic resonance imaging

Magnetic resonance imaging (MRI) has been shown to be a very effective tool for monitoring the formation and dissociation of hydrates because of the large intensity contrast between the images of the liquid components and the solid hydrate. Tetrahydrofuran/water hydrate was used because the two liquid components are miscible and form hydrate at ambient pressure. These properties made this feasibility study proceed much faster than using methane/water, which requires high pressure to form the hydrate. The formation and dissociation was monitored first in a THF/water-saturated Berea sandstone plug and second in the bulk. In both cases it appeared that nucleation was needed to begin the formation process, i.e., the presence of surfaces in the sandstone and shaking of the bulk solution. Dissociation appeared to be dominated by the rate of thermal energy transfer. The dissociation temperature of hydrate formed in the sandstone plug was not significantly different from the dissociation temperature in bulk.     

Magnetic nanoparticles as an orthogonal support of polymer resins: applications to solid-phase suzuki cross-coupling reactions

[reaction: see text] Most of the reactants immobilized on conventional solid-phase resins are buried inside the interiors of lightly cross-linked polystyrene beads. An orthogonal support of solid-phase resins needs to be small enough to penetrate the interpolymeric chain spaces of a swollen resin to reach reaction sites. In this paper, we report the use of magnetic nanoparticles ( approximately 4 nm) as an orthogonal matrix to assist solid-phase reactions. A magnetic nanoparticle-supported homogeneous Pd catalyst was employed for promoting the Suzuki cross-coupling of an aryl halide on resins and an excessive arylboronic acid in solution. The workup separating three components (the catalyst, product, and remaining arylborate) is a chromatography-free process. The Pd catalyst was magnetically isolated and recycled from the reaction mixture by applying an external magnetic field. Then, a filtration process was followed to recover the excess borate reagent from the resins/product. Our work here presents the first example of an orthogonal matrix of solid-phase resins and shows the promise of employing nanomaterials in organic synthesis.     

Constructing orthogonal pandiagonal Latin squares and panmagic squares from modular n‐queens solutions

In this article, we show how to construct pairs of orthogonal pandiagonal Latin squares and panmagic squares from certain types of modular n‐queens solutions. We prove that when these modular n‐queens solutions are symmetric, the panmagic squares thus constructed will be associative, where for an n × n associative magic square A = (a_ij), for all i and j it holds that a_ij + an?i?1,n?j?1 = c for a fixed c. We further show how to construct orthogonal Latin squares whose modular difference diagonals are Latin from any modular n‐queens solution. As well, we analyze constructing orthogonal pandiagonal Latin squares from particular classes of non‐linear modular n‐queens solutions. These pandiagonal Latin squares are not row cyclic, giving a partial solution to a problem of Hedayat. © 2007 Wiley Periodicals, Inc. J Combin Designs 15: 221–234, 2007     

Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks--on the benefit of restoring the cyclic sugar backbone

Oligodeoxynucleotides incorporating a reactive functionality can cause irreversible cross-linking to the target sequence and have been widely studied for their potential in inhibition of gene expression or development of diagnostic probes for gene analysis. Reactive oligonucleotides further show potential in a supramolecular context for the construction of nanometer-sized DNA-based objects. Inspired by the cytochrome P450 catalyzed transformation of furan into a reactive enal species, we recently introduced a furan-oxidation-based methodology for cross-linking of nucleic acids. Previous experiments using a simple acyclic building block equipped with a furan moiety for incorporation into oligodeoxynucleotides have shown that cross-linking occurs in a very fast and efficient way and that substantial amounts of stable, site-selectively cross-linked species can be isolated. Given the destabilization of duplexes observed upon introduction of the initially designed furan-modified building block into DNA duplexes, we explore here the potential benefits of two new building blocks featuring an extended aromatic system and a restored cyclic backbone. Thorough experimental analysis of cross-linking reactions in a series of contexts, combined with theoretical calculations, permit structural characterization of the formed species and allow assessment of the origin of the enhanced cross-link selectivity. Our experiments clearly show that the modular nature of the furan-modified building blocks used in the current cross-linking strategy allow for fine tuning of both yield and selectivity of the interstrand cross-linking reaction.     

New class of potent catalysts of O2.-dismutation. Mn(III) ortho-methoxyethylpyridyl- and di-ortho-methoxyethylimidazolylporphyrins

Three new Mn(III) porphyrin catalysts of O2.-dismutation (superoxide dismutase mimics), bearing ether oxygen atoms within their side chains, were synthesized and characterized: Mn(III) 5,10,15,20-tetrakis[N-(2-methoxyethyl)pyridinium-2-yl]porphyrin (MnTMOE-2-PyP(5+)), Mn(III)5,10,15,20-tetrakis[N-methyl-N'-(2-methoxyethyl)imidazolium-2-yl]porphyrin (MnTM,MOE-2-ImP(5+)) and Mn(III) 5,10,15,20-tetrakis[N,N'-di(2-methoxyethyl)imidazolium-2-yl]porphyrin (MnTDMOE-2-ImP(5+)). Their catalytic rate constants for O2.-dismutation (disproportionation) and the related metal-centered redox potentials vs. NHE are: log k(cat)= 8.04 (E(1/2)=+251 mV) for MnTMOE-2-PyP(5+), log k(cat)= 7.98 (E(1/2)=+356 mV) for MnTM,MOE-2-ImP(5+) and log k(cat)= 7.59 (E(1/2)=+365 mV) for MnTDMOE-2-ImP(5+). The new porphyrins were compared to the previously described SOD mimics Mn(III) 5,10,15,20-tetrakis(N-ethylpyridinium-2-yl)porphyrin (MnTE-2-PyP(5+)), Mn(III) 5,10,15,20-tetrakis(N-n-butylpyridinium-2-yl)porphyrin (MnTnBu-2-PyP(5+)) and Mn(III) 5,10,15,20-tetrakis(N,N'-diethylimidazolium-2-yl)porphyrin (MnTDE-2-ImP(5+)). MnTMOE-2-PyP(5+) has side chains of the same length and the same E(1/2), as MnTnBu-2-PyP(5+)(k(cat)= 7.25, E(1/2)=+ 254 mV), yet it is 6-fold more potent a catalyst of O2.-dismutation , presumably due to the presence of the ether oxygen. The log k(cat)vs. E(1/2) relationship for all Mn porphyrin-based SOD mimics thus far studied is discussed. None of the new compounds were toxic to Escherichia coli in the concentration range studied (up to 30 microM), and protected SOD-deficient E. coli in a concentration-dependent manner. At 3 microM levels, the MnTDMOE-2-ImP(5+), bearing an oxygen atom within each of the eight side chains, was the most effective and offered much higher protection than MnTE-2-PyP(5+), while MnTDE-2-ImP(5+) was of very low efficacy.     

Heats of formation of C(6)H(5)(•), C(6)H(5)(+), and C(6)H(5)NO by threshold photoelectron photoion coincidence and active thermochemical tables analysis

Threshold photoelectron photoion coincidence has been used to prepare selected internal energy distributions of nitrosobenzene ions [C(6)H(5)NO(+)]. Dissociation to C(6)H(5)(+) + NO products was measured over a range of internal energies and rate constants from 10(3) to 10(7) s(-1) and fitted with the statistical theory of unimolecular decay. A 0 K dissociative photoionization onset energy of 10.607 ± 0.020 eV was derived by using the simplified statistical adiabatic channel model. The thermochemical network of Active Thermochemical Tables (ATcT) was expanded to include phenyl and phenylium, as well as nitrosobenzene. The current ATcT heats of formation of these three species at 0 K (298.15 K) are 350.6 (337.3) ± 0.6, 1148.7 (1136.8) ± 1.0, and 215.6 (198.6) ± 1.5 kJ mol(-1), respectively. The resulting adiabatic ionization energy of phenyl is 8.272 ± 0.010 eV. The new ATcT thermochemistry for phenyl entails a 0 K (298.15 K) C-H bond dissociation enthalpy of benzene of 465.9 (472.1) ± 0.6 kJ mol(-1). Several related thermochemical quantities from ATcT, including the current enthalpies of formation of benzene, monohalobenzenes, and their ions, as well as interim ATcT values for the constituent atoms, are also given.     

Synthesis,characterization, and star polymer assembly of boronic acid end‐functionalized polycaprolactone

Boronic acid end‐functionalized polycaprolactone (PCL) polymers were synthesized by ring‐opening polymerization using a pinacol boronate ester‐containing (Bpin) initiator. The polymerization provides access to boron‐terminated polymers (i.e. Bpin‐PCL‐OH) with narrow molecular weight distributions (PDI = 1.09). Postsynthetic manipulation of the polymer's terminal hydroxyl group by copper‐catalyzed azide‐alkyne cycloaddition chemistry provides a series of bis end‐functionalized polymers with significant structural diversity at the termini. Deprotection of the boronate ester end group was accomplished with an acidic solid phase DOWEX resin. The boronate ester deprotection methodology does not result in hydrolysis of the polymeric backbone. The boronic acid‐tipped polymers were converted into star polymer assemblies using thermal dehydration and ligand‐facilitated trimerization. Thermal dehydration of (HO)₂B‐PCL‐OAc to the corresponding boroxine‐based star polymer assembly was inefficient and lead to degradation products. Ligand‐facilitated trimerization using either pyridine or 7‐azaindole as the Lewis base was efficient and mild. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Structure of the asparagine-linked sugar chains of porcine kidney and human urine cerebroside sulfate activator protein

The specific sugar residues and their linkages in the oligosaccharides from pig kidney and human urine cerebroside sulfate activator proteins (saposin B), although previously hypothesized, have been unambiguously characterized. Exhaustive sequential exoglycosidase digestion of the trimethyl-p-aminophenyl derivatives, followed by either matrix-assisted laser desorption/ionization and/or mass spectrometry, was used to define the residues and their linkages. The oligosaccharides were enzymatically released from the proteins by treatment with peptidyl-N-glycosidase F and separated from the proteins by reversed-phase high-performance liquid chromatography (HPLC). Reducing termini were converted to the trimethyl-p-aminophenyl derivative and the samples were further purified by normal-phase HPLC. The derivatized carbohydrates were then treated sequentially with a series of exoglycosidases of defined specificity, and the products of each digestion were examined by mass spectrometry. The pentasaccharides from pig kidney and human urine protein were shown to be of the asparagine-linked complex type composed of mannose-alpha 1-6-mannose-beta 1-4-N-acetylglucosamine-N-acetylglucosamine(alpha 1-6-fucose). This highly degraded structure probably represents the final product of intra-lysosomal exoglycosidase digestion. Oligosaccharide sequencing by specific exoglycosidase degradation coupled with mass spectrometry is more rapid than conventional oligosaccharide sequencing. The procedures developed will be useful for sequencing other oligosaccharides including those from other members of the lipid-binding protein class to which cerebroside sulfate activator belongs. (c) 2000 John Wiley & Sons, Ltd.     

Investigation of cytolysin variants by peptide mapping: enhanced protein characterization using complementary ionization and mass spectrometric techniques

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) have been used in conjunction with time-of-flight (TOF) and quadrupole ion trap (IT) mass spectrometry, respectively, to analyze various cytolysin proteins isolated from the sea anemone Stichodactyla helianthus and digested by the protease trypsin. By employing different ionization methods, the subsequent changes in ionization selectivity for the peptides in the digested protein samples resulted in ion abundance variation reflected in the mass spectra. Upon investigation of this variation generated by the two ionization processes, it has been shown in this study that enhanced protein coverage (e.g., >95% for cytolysin III) can be achieved. Additionally, capillary and microbore reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with ESI mass spectrometry (MS) as well as flow injection analysis by nanoflow ESI-MS afforded the necessary limit of detection (LOD) for detailed structural information of the cytolysin proteins by tandem mass spectrometry (MS/MS) methods. It can be concluded that cytolysins II and III correspond to sticholysins I and II, that "cytolysin I" is a mixture of modified forms of cytolysins II and III, and that "cytolysin IV" is an incompletely processed precursor of cytolysin III.