Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations

Six docking programs (FlexX, GOLD, ICM, LigandFit, the Northwestern University version of DOCK, and QXP) were evaluated in terms of their ability to reproduce experimentally observed binding modes (poses) of small-molecule ligands to macromolecular targets. The accuracy of a pose was assessed in two ways: First, the RMS deviation of the predicted pose from the crystal structure was calculated. Second, the predicted pose was compared to the experimentally observed one regarding the presence of key interactions with the protein. The latter assessment is referred to as interactions-based accuracy classification (IBAC). In a number of cases significant discrepancies were found between IBAC and RMSD-based classifications. Despite being more subjective, the IBAC proved to be a more meaningful measure of docking accuracy in all these cases.     

Selective coupling of methylene groups at a Rh/Os core, yielding C2, C3, or C4 fragments: roles of the adjacent metals in carbon-carbon bond formation

The mixed-metal complex, [RhOs(CO)(4)(dppm)(2)][BF(4)] (1; dppm = micro-Ph(2)PCH(2)PPh(2)) reacts with diazomethane to yield a number of products resulting from methylene incorporation into the bimetallic core. At -80 degrees C the reaction between 1 and CH(2)N(2) yields the methylene-bridged [RhOs(CO)(3)(micro-CH(2))(micro-CO)(dppm)(2)][BF(4)] (2), which reacts further at ambient temperature to give the allyl methyl species, [RhOs(eta(1)-C(3)H(5))(CH(3))(CO)(3)(dppm)(2)][BF(4)] (4). At intermediate temperatures compounds 1 and 2 react with diazomethane to yield the butanediyl complex [RhOs(C(4)H(8))(CO)(3)(dppm)(2)][BF(4)] (3) by the incorporation and coupling of four methylene units. Compound 2 is proposed to be an intermediate in the formation of 3 and 4 from 1 and on the basis of labeling studies a mechanism has been proposed in which sequential insertions of diazomethane-generated methylene fragments into the Rh-C bond of bridging hydrocarbyl fragments occur. Reaction of the tricarbonyl species, [RhOs(CO)(3)(micro-CH(2))(dppm)(2)][BF(4)] with diazomethane over a range of temperatures generates the ethylene complex [RhOs(eta(2)-C(2)H(4))(CO)(3)(dppm)(2)][BF(4)] (7a), but no further incorporation of methylene groups is observed. This observation suggests that carbonyl loss in the formation of the above allyl and butanediyl species only occurs after incorporation of the third methylene fragment. Attempts to generate C(2)-bridged species by the reaction of 1 with ethylene gave no reaction, however, in the presence of trimethylamine oxide the ethylene adducts [RhOs(eta(2)-C(2)H(4))(CO)(3)(dppm)(2)][BF(4)] (7b; an isomer of 7a) and [RhOs(eta(2)-C(2)H(4))(2)(CO)(2)(dppm)(2)][BF(4)] (8) were obtained. The relationship of the above products to the selective coupling of methylene groups, and the roles of the different metals are discussed.     

X=Y-ZH systems as potential 1,3-dipoles. Part 61: Metal exchanged zeolites, silver(I) oxide, Ni(II) and Cu(I) complexes as catalysts for 1,3-dipolar cycloaddition reactions of imines generating proline derivatives

A range of regio- and stereo-selective 1,3-dipolar reactions of imines of α-amino esters, generating polysubstituted prolines, catalysed by silver(I) exchanged zeolites or silver(I) supported on titania, both in combination with DBU, are described. The use of a catalytic amount of silver(I) oxide, Ni(II) complexes and cuprous iodide as catalysts for the cycloaddition reactions are also disclosed.     

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

Background  

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases.