A novel nucleophilic approach to 1-alkyladenosines. A two-step synthesis of [1-N-15] adenosine from inosine

A novel ANRORC mechanism in the reaction of 1-(2,4-dinitrobenzenesulfonyl)inosines with amines has allowed the preparation of 1-alkyladenosines and [1-15N]adenosines in a straightforward way from inosines

The Performance of Several Docking Programs at Reproducing Protein-Macrolide-Like Crystal Structures

The accuracy of five docking programs at reproducing crystallographic structures of complexes of 8 macrolides and 12 related macrocyclic structures, all with their corresponding receptors, was evaluated. Self-docking calculations indicated excellent performance in all cases (mean RMSD values ≤ 1.0) and confirmed the speed of AutoDock Vina. Afterwards, the lowest-energy conformer of each molecule and all the conformers lying 0-10 kcal/mol above it (as given by Macrocycle, from MacroModel 10.0) were subjected to standard docking calculations. While each docking method has its own merits, the observed speed of the programs was as follows: Glide 6.6 > AutoDock Vina 1.1.2 > DOCK 6.5 >> AutoDock 4.2.6 > AutoDock 3.0.5. For most of the complexes, the five methods predicted quite correct poses of ligands at the binding sites, but the lower RMSD values for the poses of highest affinity were in the order: Glide 6.6 ≈ AutoDock Vina ≈ DOCK 6.5 > AutoDock 4.2.6 >> AutoDock 3.0.5. By choosing the poses closest to the crystal structure the order was: AutoDock Vina > Glide 6.6 ≈ DOCK 6.5 ≥ AutoDock 4.2.6 >> AutoDock 3.0.5. Re-scoring (AutoDock 4.2.6//AutoDock Vina, Amber Score and MM-GBSA) improved the agreement between the calculated and experimental data. For all intents and purposes, these three methods are equally reliable

Synthesis of benzo-, pyrido-, thieno- and imidazo-fused N-hydroxy-4-oxopyrimidine-2-carboxylic acid derivatives

N-Hydroxy-4-oxoquinazoline-2-carboxamide derivatives (cyclic hydroxamic acids) and related pyrido- and thieno-substituted analogues, as well as a N-hydroxyhypoxanthine-2-carboxamide were synthesised for the first time, by means of a four-step sequence that involves a smooth reaction of aminohydroxamates with methyl trimethoxyacetate. Other strategies were unsuccessful

(Z)-Oxopropene-1,3-diyl, a linker for the conjugation of the thiol group of cysteine with amino-derivatized drugs

We have developed a conjugation reaction based on the thia-Michael addition to activated triple bonds, which can be an alternative to maleimides, the most commonly used reagents to link thiol groups (of Cys) to drugs and labels. An amino group is converted into its propynamide and, in aqueous media at 37 °C and pH 7.4, Cys derivatives are added. The oxopropene-1,3-diyl linker is formed with excellent Z selectivity without secondary reactions. No exchange with other thiols is observed

Computer-aided insight into the relative stability of enamines

Venerable aldol, Michael, and Mannich reactions have undergone a renaissance in the past fifteen years, as a consequence of the development of direct organocatalytic versions, mediated by chiral amines. Chiral enamines are key intermediates in these reactions. This review focuses on the formation of enamines from secondary amines and their relative thermodynamic stability, as well as on the reverse reactions (hydrolysis). Experimental results and predictions based on MO calculations are reviewed to show which enamine forms may predominate in the reaction medium and to compare several secondary amines as organocatalysts.1 Introduction2 Relative Stability of Enamines as Determined Experimentally3 Pyrrolidine Enamines4 Enamines of the Jorgensen-Hayashi Catalyst5 Proline Enamines6 Free Enthalpies and Polar Solvent Effects7 Comparison of Organocatalysts8 Summary and Outlook9 Appendi

Tosvinyl and besvinyl as protecting groups of imides, azinones, nucleosides, sultams, and lactams. Catalytic conjugate additions to tosylacetylene.

The use of the 2-(4-methylphenylsulfonyl)ethenyl (tosvinyl, Tsv) group for the protection of the NH group of a series of imides, azinones (including AZT), inosines, and cyclic sulfonamides has been examined. The Tsv-protected derivatives are obtained in excellent yields by conjugate addition to tosylacetylene (ethynyl p-tolyl sulfone). The stereochemistry of the double bond can be controlled at will: with only 1 mol % of Et3N or with catalytic amounts of NaH, the Z stereoisomers are generated almost exclusively, while the E isomers are obtained using a stoichiometric amount of DMAP. Analogous phenylsulfonylvinyl-protected groups (with the besvinyl or Bsv group instead of Tsv) are obtained stereospecifically by reaction with (Z)- or (E)-bis(phenylsulfonyl)ethene. For lactams and oxazolidinones, this last method is much better. The Tsv and Bsv groups are stable in the presence of non-nucleophilic bases and to acids. They can be removed highly effectively via a conjugate addition-elimination mechanism using pyrrolidine or sodium dodecanethiolate as nucleophiles

Formal total synthesis of amphidinolide E

A formal total synthesis of the cytotoxic macrolide amphidinolide E is reported. The strategic steps are three Julia-Kocienski reactions (J-K), for the formation of the C5-C6, C9-C10, and C17-C18 double bonds, a Suzuki-Molander C21-C22 bond formation reaction, and a Kita-Trost macrolactonization. The 'instability' of the two dienic systems and of the stereocenter at C2 (allylic methine, alpha to the carboxy group) and the protecting groups at C17-OH and C18-OH have posed difficult challenges. Each Julia-Kocienski olefination has been systematically optimized to provide the highest possible E/Z ratios

NMR and computational studies on the reactions of enamines with nitroalkenes that may pass through cyclobutanes

The addition of aldehyde enamines to nitroalkenes affords cyclobutanes in all solvents, with all of the pyrrolidine and proline derivatives tested by us and with all of the substrates we have examined. Depending on the temperature, concentration of water, solvent polarity, and other factors, the opening and hydrolysis of such a four-membered ring may take place rapidly or last for several days, producing the final Michael-like adducts (4-nitrobutanals). Thirteen new cyclobutanes have now been characterized by NMR spectroscopy. As could be expected, s-trans-enamine conformers give rise to all-trans-(4S)-4-nitrocyclobutylpyrrolidines, while s-cis-enamine conformers afford all-trans-(4R)-4-nitrocyclobutylpyrrolidines. These four-membered rings can isomerize to adduct enamines, which should be hydrolyzed via their iminium ions. MP2 and M06-2X calculations predict that one iminium ion is more stable than the other iminium species, so that protonation of the adduct enamines can be quite stereoselective; in the presence of water, the so-called syn adducts (e.g., OCH-*CHR-*CHPh-CH2NO2, with R and Ph syn) eventually become the major products. Why one syn adduct is obtained with aldehydes, whereas cyclic ketones (the predicted ring-fused cyclobutanes of which isomerize to their enamines more easily) produce the other syn adduct, is also explained by means of molecular orbital calculations. Nitro-Michael reactions of aldehyde enamines that "stop" at the nitrocyclobutane stage and final enamine stage do not work catalytically, as known, but those of cyclic ketone enamines that do not work stop at the final enamine stage (if their hydrolysis to the corresponding nitroethylketones is less favorable than expected). These and other facts are accounted for, and the proposals of the groups led by Seebach and Hayashi, Blackmond, and Pihko and Papai are reconciled

A synthetic approach to palmerolides via Negishi cross coupling. The challenge of the C15-C16 bond formation

The esterification of fragment C1-C8 (2) with fragment C16-C23 (3) to give iodo derivative 4, followed by a Pd-catalysed coupling with a C9-C15 fragment (7 or 8), may provide a common precursor of most palmerolides. Ligands and reaction conditions were exhaustively examined to perform the C15-C16 bond formation via Negishi reaction. With simple models, pre-activated Pd-Xantphos and Pd-DPEphos complexes were the most efficient catalysts at RT. Zincation of the C9-C15 fragment (8) and cross coupling with 4 required 3 equiv of t-BuLi, 10 mol % of Pd-Xantphos and 60 °C

Discovery of non-nucleoside inhibitors of HIV-1 reverse transcriptase competing with the nucleotide substrate

How odd! A new class of non-nucleoside reverse transcriptase inhibitors with a 6-vinylpyrimidine scaffold (1) has been found to inhibit HIV-1 reverse transcriptase (RT) by competition with the nucleotide substrate after binding to the non-nucleoside inhibitor binding pocket of the enzyme. Molecular modeling studies have been performed to elucidate their peculiar behavior