Chemical basis of DNA sugar-phosphate cleavage by low-energy electrons

DNA damage by low-energy electrons (LEE) was examined using a novel system in which thin solid films of oligonucleotide tetramers (CGTA and GCAT) were irradiated with monoenergetic electrons (10 eV) under ultrahigh vacuum. The products of irradiation were examined by HPLC. These analyses permitted the quantitation of 16 nonmodified nucleobase, nucleoside, and nucleotide fragments of each tetramer resulting from the cleavage of phosphodiester and N-glycosidic bonds. The distribution of nonmodified products suggests a mechanism of damage involving initial electron attachment to nucleobase moieties, followed by electron transfer to the sugar-phosphate backbone, and subsequent dissociation of the phosphodiester bond. Moreover, virtually all the nonmodified fragments contained a terminal phosphate group at the site of cleavage. These results demonstrate that the phosphodiester bond breaks by a distinct pathway in which the negative charge localizes on the phosphodiester bond giving rise to nonmodified fragments with an intact phosphate group. Conversely, the radical must localize on the sugar moiety to give as yet unidentified modifications. In summary, the reaction of LEE with simple tetramers involved dissociative electron attachment leading to phosphodiester bond cleavage and the formation of nonmodified fragments.     

Organosulfur compounds: electrophilic reagents in transition-metal-catalyzed carbon-carbon bond-forming reactions

Transition-metal-catalyzed carbon-carbon bond-forming reactions are among the most powerful methods in organic synthesis and play a crucial role in modern materials science and medicinal chemistry. Recent developments in the area of ligands and additives permit the cross-coupling of a large variety of reactants, including inexpensive and readily available sulfonyl chlorides. Their desulfitative carbon-carbon cross-coupling reactions (Negishi, Stille, carbonylative Stille, Suzuki-Miyaura, and Sonogashira-Hagihara-type cross-couplings and Mizoroki-Heck-type arylations) are reviewed together with carbon-carbon cross-coupling reactions with other organosulfur compounds as electrophilic reagents.     

Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures

Fingerprint-based similarity searching is widely used for virtual screening when only a single bioactive reference structure is available. This paper reviews three distinct ways of carrying out such searches when multiple bioactive reference structures are available: merging the individual fingerprints into a single combined fingerprint; applying data fusion to the similarity rankings resulting from individual similarity searches; and approximations to substructural analysis. Extended searches on the MDL Drug Data Report database suggest that fusing similarity scores is the most effective general approach, with the best individual results coming from the binary kernel discrimination technique.     

Revision of the stereochemistry of the reductive Heck cyclisation of 1-(2-iodobenzoyl)-4-substituted-1.4-dihydro-pyridine-3-carbaldehyde aminals

The stereochemistry of reductive and non reductive Heck cyclisations of 4-substituted-1.4-dihydropyridines is reexamined. The both reactions occur mainly via an anti (from the C₄ substituent) 5-exo process without any epimerisation of the C₄-H.     

A general approach toward the synthesis of C-nucleoside pyrazolo[1,5-a]-1,3,5-triazines and their 3',5'-bisphosphate C-nucleotide analogues as the first reported in vivo stable P2Y(1)-receptor antagonists

In our effort to identify potent purinergic P2Y(1) receptor antagonists as potent platelet aggregation inhibitors with enhanced metabolic stability, we developed an efficient route for the large-scale preparation of 2'-deoxy-C-nucleosides of pyrazolo[1,5-a]-1,3,5-triazine. The key strategic elements of this novel synthetic approach involved the following: (i) the use of a novel activating group, the N-methyl-N-phenylamino group, which was easily generated in high yield by treatment of the pyrazolo[1,5-a]-1,3,5-triazin-4-one (5) with phosphorus oxychloride and dimethylaniline under high pressure, (ii) a regio- and stereospecific palladium-mediated coupling reaction of the readily available unprotected glycal 1,4-anhydro-2-deoxy-D-erythro-pent-1-enitol (4b) and the 8-iodo derivative (16), and (iii) the stereoselective reduction of the ketone group of the furanosyl ring followed by the subsequent displacement of the N-methyl-N-phenylamino group upon treatment with methylamine. The beta configuration at the anomeric C-1' position of the glycal moieties was perfectly retained throughout this conversion. This procedure afforded 8-(2'-deoxy-beta-D-ribofuranosyl)-2-methyl-4-(N-methylamino)pyrazolo[1,5-a]-1,3,5-triazine (21) and 8-(2'-deoxy-beta-D-xylofuranosyl)-2-methyl-4-(N-methylamino)pyrazolo[1,5-a]-1,3,5-triazine (24) with an overall yield of 50% and 39%, respectively. Finally, the conversion of nucleosides 21 and 24 to the pyrazolotriazine C-nucleotides 3',5'-bisphosphate 2 and 3',5'-cyclophosphate 26 is also described herein and represents the first reported nucleotide derivatives within the pyrazolo[1,5-a]-1,3,5-triazine series. Preliminary biological testing has shown that compound 2 strongly inhibits ADP-induced human platelet aggregation and shape change and possesses significant efficacies 30 min after injection in rat, highlighting a strong P2Y(1)-receptor antagonist activity in vitro combined with a prolonged duration of action in vivo.     

Oxidation of heme to beta- and delta-biliverdin by Pseudomonas aeruginosa heme oxygenase as a consequence of an unusual seating of the heme

The origin of the unusual regioselectivity of heme oxygenation, i.e. the oxidation of heme to delta-biliverdin (70%) and beta-biliverdin (30%), that is exhibited by heme oxygenase from Pseudomonas aeruginosa (pa-HO) has been studied by (1)H NMR, (13)C NMR, and resonance Raman spectroscopies. Whereas resonance Raman indicates that the heme-iron ligation in pa-HO is homologous to that observed in previously studied alpha-hydroxylating heme oxygenases, the NMR spectroscopic studies suggest that the heme in this enzyme is seated in a manner that is distinct from that observed for all other alpha-hydroxylating heme oxygenase enzymes for which a structure is known. In pa-HO, the heme is rotated in-plane approximately 110 degrees, so the delta-meso-carbon of the major orientational isomer is located within the HO-fold in the place where the alpha-hydroxylating enzymes typically place the alpha-meso-carbon. The unusual heme seating displayed by pa-HO places the heme propionates so that these groups point in the direction of the solvent-exposed heme edge and appears to originate in large part from the absence of stabilizing interactions between the polypeptide and the heme propionates, which are typically found in alpha-hydroxylating heme oxygenase enzymes. These interactions typically involve Lys-16 and Tyr-112, in Neisseriae meningitidis HO, and Lys-16 and Tyr-134, in human and rat HO-1. The corresponding residues in pa-HO are Asn-19 and Phe-117, respectively. In agreement with this hypothesis, we found that the Asn-19 Lys/Phe-117 Tyr double mutant of pa-HO exists as a mixture of molecules exhibiting two distinct heme seatings; one seating is identical to that exhibited by wild-type pa-HO, whereas the alternative seating is very similar to that typical of alpha-hydroxylating heme oxygenase enzymes and is related to the wild-type seating by approximately 110 degrees in-plane rotation of the heme. Furthermore, each of these heme seatings in the pa-HO double mutant gives rise to a subset of two heme isomeric orientations that are related to each other by 180 degrees rotation about the alpha-gamma-meso-axis. The coexistence of these molecules in solution, in the proportions suggested by the corresponding area under the peaks in the (1)H NMR spectrum, explains the unusual regioselectivity of heme oxygenation observed with the double mutant, which we found produces alpha- (55%), delta- (35%), and beta-biliverdin (10%). Alpha-biliverdin is obtained by oxidation of the heme seated similar to that of alpha-hydroxylating enzymes, whereas beta- and delta-biliverdin are formed from the oxidation of heme seated as in wild-type pa-HO.     

Thermal and electrochemical C-X activation (X = Cl,Br, I) by the strong Lewis acid Pd3(dppm)3(CO)2+ cluster and its catalytic applications

The stoichiometric and catalytic activations of alkyl halides and acid chlorides by the unsatured Pd(3)(dppm)(3)(CO)(2+) cluster (Pd(3)(2+)) are investigated in detail. A series of alkyl halides (R-X; R = t-Bu, Et, Pr, Bu, allyl; X = Cl, Br, I) react slowly with Pd(3)(2+) to form the corresponding Pd(3)(X)(+) adduct and "R(+)". This activation can proceed much faster if it is electrochemically induced via the formation of the paramagnetic species Pd(3)(+). The latter is the first confidently identified paramagnetic Pd cluster. The kinetic constants extracted from the evolution of the UV-vis spectra for the thermal activation, as well as the amount of electricity to bring the activation to completion for the electrochemically induced reactions, correlate the relative C-X bond strength and the steric factors. The highly reactive "R(+)" species has been trapped using phenol to afford the corresponding ether. On the other hand, the acid chlorides react rapidly with Pd(3)(2+) where no induction is necessary. The analysis of the cyclic voltammograms (CV) establishes that a dissociative mechanism operates (RCOCl --> RCO(+) + Cl(-); R = t-Bu, Ph) prior to Cl(-) scavenging by the Pd(3)(2+) species. For the other acid chlorides (R = n-C(6)H(13), Me(2)CH, Et, Me, Pr), a second associative process (Pd(3)(2+) + RCOCl --> Pd(3)(2+.....)Cl(CO)(R)) is seen. Addition of Cu(NCMe)(4)(+) or Ag(+) leads to the abstraction of Cl(-) from Pd(3)(Cl)(+) to form Pd(3)(2+) and the insoluble MCl materials (M = Cu, Ag) allowing to regenerate the starting unsaturated cluster, where the precipitation of MX drives the reaction. By using a copper anode, the quasi-quantitative catalytic generation of the acylium ion ("RCO(+)") operates cleanly and rapidly. The trapping of "RCO(+)" with PF(6)(-) or BF(4)(-) leads to the corresponding acid fluorides and, with an alcohol (R'OH), to the corresponding ester catalytically, under mild conditions. Attempts were made to trap the key intermediates "Pd(3)(Cl)(+)...M(+)" (M(+) = Cu(+), Ag(+)), which was successfully performed for Pd(3)(ClAg)(2+), as characterized by (31)P NMR, IR, and FAB mass spectrometry. During the course of this investigation, the rare case of PF(6)(-) hydrolysis has been observed, where the product PF(2)O(2)(-) anion is observed in the complex Pd(3)(PF(2)O(2))(+), where the substrate is well-located inside the cavity formed by the dppm-Ph groups above the unsatured face of the Pd(3)(2+) center. This work shows that Pd(3)(2+) is a stronger Lewis acid in CH(2)Cl(2) and THF than AlCl(3), Ag(+), Cu(+), and Tl(+).     

A New Total Synthesis of D-threo-L-talo-Octose

A new approach to the total, asymmetric synthesis of D -threo-L -talo-octose ((?)- 1 ) and its derivatives is presented. It is based on the chemoselective Wittig-Horner monoolefination of a 5-deoxy-D -ribo-hexodialdose derivative 4 obtained by selective reduction of (?)-5-deoxy-2.3-O-isopropylidene-/β-D -ribo-hexofuranurono-6,1-lactone ((?)- 3 ). Allylic bromination of the resulting methyl (E)-oct-6-enofuranuronate (+)- 5 followed by intramolecular nucleophilic displacement of the so-obtained bromides gave a 13.3:1 mixture of (?)-methyl (E)-l,4-anhydro-6,7-dideoxy-2,3-O-isopropylidene-β-L -talo-oct-6-enopyranuronate ((?)- 8 ) and methyl (E)-l,4-anhydro-6,7-dideoxy-2,3-O-isopropylidene-α-D -allo-oct-6-enopyranuronate ( 9 ). The double hydroxylation of the enoate (?)- 8 followed Kishi's rule and gave the corresponding D -threo-β-L -talo-octopyranuronate derivative (?)- 11 with a good diastereoselectivity. Reduction of ester (?)- 11 and deprotection led to pure (?)- 1 .     

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

Stable and soluble oligo(3,4-ethylenedioxythiophene)s end-capped with alkyl chains

The synthesis of a new series of stable and soluble EDOT oligomers end-capped with n-hexyl groups is described. Optical and electrochemical results indicate that the synergy between the direct electron-releasing effects of the ethylenedioxy groups and the self-rigidification resulting from intramolecular interactions controls to a large extent the HOMO-LUMO gap.