EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

The completion of the Human Genome Project, the growing effort on proteomics, and the Structural Genomics Initiative have recently intensified the attention being paid to reliable computer docking programs able to identify molecules that can affect the function of a macromolecule through molecular complexation. We report herein an automated computer docking program, EUDOC, for prediction of ligand-receptor complexes from 3D receptor structures, including metalloproteins, and for identification of a subset enriched in drug leads from chemical databases. This program was evaluated from the standpoints of force field and sampling issues using 154 experimentally determined ligand-receptor complexes and four "real-life" applications of the EUDOC program. The results provide evidence for the reliability and accuracy of the EUDOC program. In addition, key principles underlying molecular recognition, and the effects of structural water molecules in the active site and different atomic charge models on docking results are discussed. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1750-1771, 2001     

Hydrogel supported chiral imidazolidinone for organocatalytic enantioselective reduction of olefins in water

Chiral products play an important role particularly in the field of medicinal chemistry, where it is known that enantiomers often have very different biological properties and effects. One of the most powerful tool to obtain a product as a single enantiomer is asymmetric catalysis. Recently, organocatalysis, i.e. the use of small organic molecules to catalyze enantioselective transformations, has emerged as a prominent field in asymmetric synthesis. In this work, the use of hydrogels as a support for a chiral imidazolidinone organocatalyst (MacMillan catalyst) and its application in the reduction of activated olefins mediated by the Hantzsch ester is reported for the first time. Results showed a good activity of hydrogels in respect to both yield and enantioselection.     

Mass spectrometry strategies applied to the characterization of proline-rich peptides from secretory parotid granules of pig (Sus scrofa)

Basic proline-rich proteins (bPRPs) are a class of proteins widely present in saliva of humans and other mammals. They are synthesized as preproproteins and enzymatically cleaved into small peptides before secretion from the salivary glands. Recently, we characterized two proline-rich peptides (SP-A and SP-B) in parotid secretory granules of pig (Sus Scrofa) that are derived from three isoforms of a PRP proprotein (Swiss-Prot data bank: Q95JC9-1, Q95JC9-2 and Q95JC9-3). Together the coding regions for SP-A and SP-B, which are repeated many times, account for 52-70% of the coding regions of the PRP proproteins. This study was undertaken to identify peptides encoded by unassigned regions of the PRP proproteins. RP-HPLC-ESI-IT-MS analysis of enriched granule preparations from pig parotid glands by two different analytical strategies identified ten new proline-rich peptides derived from the three proproteins. Together with the coding regions for SP-A and SP-B already identified it was possible to assign 68-75% of the proproteins coding regions. The peptide sequences indicated a number of unusual proteolytic cleavage sites suggesting the presence of unknown proprotein convertases.     

Multivariate optimization approach for the analysis of butyltin compounds in mussel tissues by gas chromatography-mass spectrometry

The derivatization with NaBEt(4) for the determination of butyltin compounds in mussel tissues (Mytilus galloprovincialis) by GC-MS was optimized using a central composite design. The effects of NaBEt(4) concentration, pH and acetate buffer concentration on the derivatization efficiency were considered. Solid-phase extraction with Florisil cartridges was performed, demonstrating that the clean-up drastically reduces the background and improves the sensitivity. The good accuracy of the method was verified on a certified reference material (ERM 477); the figures of merit for all the three analytes, evaluated under optimum conditions, were satisfactory. The optimized derivatization procedure was applied to the determination of the analytes in mussels exposed to tributyltin (TBT). All considered tissues showed considerable accumulation of TBT, especially gills.     

An efficient approach to chiral C8/C9-piperazino-substituted 1,4-benzodiazepin-2-ones as peptidomimetic scaffolds

A promising way to interfere with biological processes is through the modulation of protein-protein interactions by means of small molecules acting as peptidomimetics. The 1,4-benzodiazepine scaffold has been widely reported as a peptide-mimicking, pharmacogenic system. While several synthetic pathways to C6-8 substituted benzodiazepines have been disclosed, few 1,4-benzodiazepines substituted at C9 have been reported. Herein, we describe a versatile approach to introduce cyclic, protonatable functionality at C8/C9. Introduction of the piperazine system at C8 and C9 gave access to a unique functionalization of the versatile benzodiazepine skeleton, broadening tailoring options on the benzofused side of the molecule, and the possibility of discovering novel peptidomimetics potentially able to modulate protein-protein interactions. Coupling of activated amino acids with poorly reactive anilines under mild conditions, while avoiding racemization, gave easy access to these compounds. Efficient amino acid activation was obtained by exploiting the rapid formation of acid chlorides under low temperature and acid/base free conditions, using triphenylphosphine and hexachloroacetone. This procedure successfully resulted in high reaction yields, did not produce racemization (ee > 98%, as demonstrated by using chiral solvating agents), and was compatible with the acid sensitive protecting groups present in the substrates.     

Pore-Scale Modeling of Viscous Flow and Induced Forces in Dense Sphere Packings

We propose a method for effectively upscaling incompressible viscous flow in large random polydispersed sphere packings: the emphasis of this method is on the determination of the forces applied on the solid particles by the fluid. Pore bodies and their connections are defined locally through a regular Delaunay triangulation of the packings. Viscous flow equations are upscaled at the pore level, and approximated with a finite volume numerical scheme. We compare numerical simulations of the proposed method to detailed finite element simulations of the Stokes equations for assemblies of 8–200 spheres. A good agreement is found both in terms of forces exerted on the solid particles and effective permeability coefficients.     

A note on Lorentz transformations and simultaneity in classical physics and special relativity

Since early models of wave propagation in both stationary and moving media during the nineteenth century, the Lorentz transformation (LT) has played a key role in describing characteristic wave phenomena, e.g., the Doppler shift effect. In these models LT connects two different events generated by wave propagations, as observed in two reference systems and the synchronism is absolute. In relativistic physics LT implements the relativity principle. As a consequence, it connects two space-time event coordinates that both correspond to the same physical event and “absolute synchronization” is not allowed. The relativistic interpretation started from Einstein’s early criticism of the notion of “simultaneity” and Minkowski’s invariance of the space-time interval. In this paper, the two different roles of LT, i.e., in classical wave propagation theories and in relativistic physics, are discussed. Einstein’s early criticism is also re-examined with respect to LT in view of its significance for the notion of simultaneity. Indeed, that early criticism is found to be defective. Our analysis is also useful for general readers in view of its impact on modern speculations about the existence of a preferred system of reference Σ, where light propagation is isotropic, and related implications.

     

Mechanism of boron diffusion in amorphous silicon

We have elucidated the mechanism for B migration in the amorphous (a-) Si network. B diffusivity in a-Si is much higher than in crystalline Si; it is transient and increases with B concentration up to 2 x 10(20) B/cm(3). At higher density, B atoms in a-Si quickly precipitate. B diffusion is indirect, mediated by dangling bonds (DB) present in a-Si. The density of DB is enhanced by B accommodation in the a-Si network and decreases because of a-Si relaxation. Accurate data simulations allow one to extract the DB diffusivity, whose activation energy is 2.6 eV. Implications of these results are discussed.     

Enhancements of the G-Scheme Framework

The G-Scheme is a well established framework for multi-scale adaptive model reduction, whose effectiveness was demonstrated with reference to a number of test models, together with an identification of the critical areas that were in need of further theoretical and computational refinement. In this communication, we report on how we enhanced the solver performance. Two new features involving (i) the criteria to identify the fast and slow subspace dimensions, and (ii) a criterion to decide if and when the reuse of the CSP Basis is feasible without deteriorating the overall performance of the solver, have been proved able to increase significantly the computational efficiency of the solver without sacrificing its accuracy.