Computational Study of Phosphatase Activity in Soluble Epoxide Hydrolase: High Efficiency through a Water Bridge Mediated Proton Shuttle

Recently, a new branch of fatty acid metabolism has been opened by the novel phosphatase activity found in the N-terminal domain of the, hence bifunctional, soluble epoxide hydrolase (sEH). Importantly, this finding has also provided a new site for drug targeting in sEH's activity regulation. Classical MD and hybrid Car-Parrinello QM/MM calculations have been performed to investigate the reaction mechanism of the phosphoenzyme intermediate formation in the first step of the catalysis. The results support a concerted multi-event reaction mechanism: (1) a dissociative in-line nucleophilic substitution for the phosphoryl transfer reaction; (2) a double proton transfer involved in the formation of a good leaving group in the transition state. The presence of a water bridge in the substrate/enzyme complex allowed an efficient proton shuttle, showing its key role in speeding up the catalysis. The calculated free energy of the favored catalytic pathway is approximately 19 kcal/mol, in excellent agreement with experimental data.

A Computational Study of the Binding of Propidium to the Peripheral Anionic Site of Human Acetylcholinesterase

Combined docking and molecular dynamics (MD) simulations were carried out in order to investigate the binding mode of propidium at the human acetylcholinesterase (HuAChE) peripheral site. Two different docking protocols followed by cluster analyses were performed, allowing the identification of five high-populated and low-energy configuration families. To dynamically explore the behavior of the ligand at the peripheral HuAChE binding site, six complexes (five low-energy and one high-energy) were submitted to 2.5 ns of MD simulations. The representative propidium/HuAChE binding modes were chosen on the basis of both the docking energy score and the dynamic stability of the complexes throughout the MD simulations. The most stable poses of propidium at HuAChE PAS were similar to those experimentally determined with the murine enzyme. We therefore suggest that the present modeling protocol might be used in the dynamic investigation of the interactions of a small-molecule inhibitor with a surface-like binding site of a protein. Finally, because of the biological relevance of the target studied here, the present results can be of interest for the rational design of molecules potentially useful in the treatment of the Alzheimer's disease.

Synthesis, Biological Activity, and Three-Dimensional Quantitative Structure−Activity Relationship Model for a Series of Benzo[c]quinolizin-3-ones, Nonsteroidal Inhibitors of Human Steroid 5α-Reductase 1

New 5alpha-reductase 1 (5alphaR-1) inhibitors were designed to complete a consistent set of analogues suitable for a 3D QSAR study. These compounds were synthesized by a modification of the aza-Robinson annulation, further functionalized by Pd-catalyzed cross-coupling processes, and were tested with human 5alphaR-1 expressed in Chinese hamster ovary 1827 cells. It turned out that the potency of the resulting inhibitors was strongly dependent on the type of substitution at the 8 position, with the IC(50) values ranging from 8.1 to 1050 nM. The construction of this homogeneous set of molecules allowed a 3D QSAR study. In particular, comparative molecular field analysis (CoMFA) was used to correlate the potency of the inhibitors with their physicochemical features. Highly accurate evaluations of the atomic point charges were carried out by means of quantum chemical calculations at the DFT/B3LYP level of theory followed by the RESP fitting procedure. It turned out that increasing the reliability of electrostatic parameters greatly affected the statistical results of the QSAR analysis. The 3D QSAR model proposed could be very useful in the further development of 5alphaR-1 inhibitors, which are suitable candidates to be evaluated as drugs in the treatment of 5alphaR-1 related diseases such as acne and alopecia in men and hirsutism in women.

Density functional study of the enzymatic reaction catalyzed by a cyclin-dependent kinase

Density functional theory (DFT) calculations were carried out to study the molecular mechanism of the phosphoryl transfer reaction catalyzed by cyclin-dependent kinases (CDKs). The DFT study presented here shows that CDKs catalyze the phosphoryl transfer reaction from ATP to the serine substrate through a single step mechanism with a SN2-like transition state.

Bombesin and thrombin affect discrete pools of intracellular calcium through different G-proteins

In mouse NIH 3T3 cells, the mitogens bombesin and thrombin induced Ca2+ release from intracellular stores. Ca2+ release induced by bombesin was inhibited by the Ca(2+)-ATPase inhibitor thapsigargin, while Ca2+ release induced by thrombin was unaffected by this agent. The Ca(2+)-release response to bombesin was not affected by pertussis toxin, but the response to thrombin was abolished by the toxin. Stable transfectants overexpressing the G-protein subunit type alpha 9 showed an accentuated response to bombesin, indicating that the bombesin receptor was coupled to a Gq-like G-protein. Together, these results show that the two mitogenic receptors are coupled to distinct G-proteins that affect functionally different pools of Ca2+. Organization of signalling pathways in this manner may allow cells to differentially encode information from different signals.