1-(4-Chlorophenyl)-2-phenyl-2-(3-phenyl-1-isoquinolylsulfanyl)ethanone

The title compound, C29H20ClNOS, is a 1-substituted-3-phenylisoquinoline that crystallizes with four independent molecules in the asymmtric unit. The four molecules have similar C-S-C angles. The most noteworthy differences between the molecules relate to the inclination of the 3-phenyl subsituent with respect to the isoquinoline fused-ring [dihedral angles of 21.2 (1), 25.6 (2), 34.3 (1) and 36.5 (2)degrees].

1,1`-[4-(2-Methoxyphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-diyl]diethanone

In the title compound, C18H21NO3, the 1,4-dihydropyridine ring exhibits a flattened boat conformation. The methoxyphenyl ring is nearly planar [r.m.s. deviation = 0.0723 (1) angstrom] and is perpendicular to the base of the boat [dihedral angle = 88.98 (4)degrees]. Intermolecular N-H center dot center dot center dot O and C-H center dot center dot center dot O hydrogen bonds exist in the crystal structure.

Interaction of substrate uridyl 3',5'-adenosine with ribonuclease A:a molecular dynamics study

A wealth of information available from x-ray crystallographic structures of enzyme-ligand complexes makes it possible to study interactions at the molecular level. However, further investigation is needed when i) the binding of the natural substrate must be characterized, because ligands in the stable enzyme-ligand complexes are generally inhibitors or the analogs of substrate and transition state, and when ii) ligand binding is in part poorly characterized. We have investigated these aspects i? the binding of substrate uridyl 3',5'-adenosine (UpA) to ribonuclease A (RNase A). Based on the systematically docked RNase A-UpA complex resulting from our previous study, we have undertaken a molecular dynamics simulation of the complex with solvent molecules. The molecular dynamics trajectories of this complex are analyzed to provide structural explanations for varied experimental observations on the ligand binding at the B2 subsite of ribonuclease A. The present study suggests that B2 subsite stabilization can be effected by different active site groups, depending on the substrate conformation. Thus when adenosine ribose pucker is O4'-endo, Gln69 and Glu111 form hydrogen-bonding contacts with adenine base, and when it is C2'-endo, Asn71 is the only amino acid residue in direct contact with this base. The latter observation is in support of previous mutagenesis and kinetics studies. Possible roles for the solvent molecules in the binding subsites are described. Furthermore, the substrate conformation is also examined along the simulation pathway to see if any conformer has the properties of a transition state. This study has also helped us to recognize that small but concerted changes in the conformation of the substrate can result in substrate geometry favorable for 2',3' cyclization. The identified geometry is suitable for intraligand proton transfer between 2'-hydroxyl and phosphate oxygen atom. The possibility of intraligand proton transfer as suggested previously and the mode of transfer before the formation of cyclic intermediate during transphosphorylation are discussed.