Activation of the glmS Ribozyme Nucleophile via Overdetermined Hydrogen Bonding.

RNA enzymes, or ribozymes, catalyze internal phosphodiester bond cleavage using diverse catalytic strategies. These include the four classic strategies: in-line nucleophilic attack, deprotonation of the 2'-OH nucleophile, protonation of the 5'-O leaving group, and stabilization of developing charge on the nonbridging oxygen atoms of the scissile phosphate. In addition, we recently identified two additional ribozyme strategies: acidification of the 2'-OH and release of the 2'-OH from inhibitory interactions. Herein, we report inverse thio effects in the presence of glmS ribozyme variants and a 1-deoxyglucosamine 6-phosphate cofactor analogue and demonstrate that activation of the 2'-OH nucleophile is promoted by competitive hydrogen bonding among diverse ribozyme moieties for the pro-RP nonbridging oxygen. We conclude that the glmS ribozyme uses an overdetermined set of competing hydrogen bond donors in its active site to ensure potent activation and regulation by the cofactor. Nucleophile activation through competitive, overdetermined hydrogen bonding could be a general strategy for ribozyme activation and may be applicable for controlling the function of ribozymes and riboswitches in the laboratory.

Indolidenes and Indolidenium Intermediates in the Synthesis of Cyclopent[b]indoles: Mechanistic Studies on Intramolecular Cyclizations.

Tetracyclic products featuring predominantly a trans-hexahydroindane unit annelated onto the C(2)/C(3) positions of indole can be accessed by intramolecular cyclocondensation of tethered alkenyl sulfides with either indolidene or indolidenium cation intermediates. Studies with geometrically pure E- and Z-alkenyl sulfide isomers reveal a likely dichotomy of reaction paths that provide mixtures of both regioisomers and stereoisomers of the hexahydroindane adducts.

Intramolecular [3 + 2] cyclocondensations of alkenes with indolidenes and indolidenium cations.

C(2)-C(3) cyclopentannelated indole constructs are prepared by either (a) a cyclization cascade of an alkenyl sulfide tethered to a 2-azido-1-allenylbenzene core or (b) cationic cyclization of a tethered alkenyl sulfide with a putative 2-indolidenium cation. In both cases, issues of C-C versus C-N bond formation emerge, and the results indicate that the former is favored.