Mapping protein pockets through their potential small-molecule binding volumes: QSCD applied to biological protein structures

Previously we demonstrated a method, Quantized Surface Complementarity Diversity (QSCD), of defining molecular diversity by measuring shape and functional complementarity of molecules to a basis set of theoretical target surfaces [Wintner E.A. and Moallemi C.C., J. Med. Chem., 43 (2000) 1993]. In this paper we demonstrate a method of mapping actual protein pockets to the same basis set of theoretical target surfaces, thereby allowing categorization of protein pockets by their properties of shape and functionality. The key step in the mapping is a `dissection' algorithm that breaks any protein pocket into a set of potential small molecule binding volumes. It is these binding volumes that are mapped to the basis set of theoretical target surfaces, thus measuring a protein pocket not as a single surface but as a collection of molecular recognition environments.     

The interaction of highly helical structural mutants with the NOP receptor discloses the role of the address domain of nociceptin/orphanin FQ

Nociceptin is a heptadecapeptide whose sequence is similar to that of Dynorphin A, sharing a message domain characterized by two glycines and two aromatic residues, and a highly basic C-terminal address domain but, in spite of these similarities, displays no opioid activity. Establishing the relative importance of the message and address domains of nociceptin has so far been hampered by its extreme conformational flexibility. Here we show that mutants of this peptide, designed to increase the helical content in the address domain, can be employed to explain the mode of interaction with the NOP receptor. Nociceptin analogues in which Ala residues are substituted with aminoisobutyric acid (Aib) show a substantial increment of activity in their interaction with the NOP receptor. The increment of biological activity was attributed to the well-documented ability of Aib to induce helicity. Here we have verified this working hypothesis by a conformational investigation extended to new analogues in which the role of Aib is taken up by Leu. The NMR conformational analysis confirms that all Ala/Aib peptides as well as [Leu(7,11)]-N/OFQ-amide and [Leu(11,15)]-N/OFQ-amide mutants (N/OFQ=nociceptin/orphanin FQ) have comparable helix content in helix-promoting media. We show that the helical address domain of nociceptin can place key basic residues at an optimal distance from complementary acidic groups of the EL(2) loop of the receptor. Our structural data are used to rationalize pharmacological data which show that although [Leu(11,15)]-N/OFQ-amide has an activity comparable to those of Ala/Aib peptides, [Leu(7,11)]-N/OFQ-amide is less active than N/OFQ-amide. We hypothesize that bulky residues cannot be hosted in or near the hinge region (Thr(5)-Gly(6)-Ala(7)) without severe steric clash with the receptor. This hypothesis is also consistent with previous data on this hinge region obtained by systematic substitution of Thr, Gly, and Ala with Pro.     

Synthesis, Characterization, and Catalytic Activity of Rh(I) Complexes with (S)-BINAPO, an Axially Chiral Inducer Capable of Hemilabile P,O-Heterobidentate Coordination

Summary.  The reaction of dinuclear rhodium(I) derivatives of the formula [Rh(DIOL)X]₂ with the axially chiral phosphinyl phosphane 2-(diphenylphosphinyl)-2′-(diphenylphosphanyl)-1,1′-binaphthalene ((S)-BINAPO, 1) leads to the formation of cationic complexes [(BINAPO)Rh(DIOL)]⁺ where the ligand (S)-BINAPO consistently displays a P,O-chelate coordination which is mantained even in solvents of fair polarity. The mononuclear rhodium(I) complexes (S)-2-diphenylphosphanyl-2′-diphenylphosphinyl-1,1′-binaphthalene-(1,5-cyclooctadiene) rhodium tetrafluoroborate (3b) and (S)-2-diphenylphosphanyl-2′-diphenylphosphinyl-1,1′-binaphthalene-(1,4-norbornadiene) rhodium tetrafluoroborate (3c) with 1,5-cyclooctadiene (COD) and 2,5-norbornadiene (NBD) as the diolefin were isolated and characterized. Both show a fluxional behaviour in solution which is due to the mobility of the diolefin rather than to a displacement-recombination of the oxygenated arm of the ligand. The mobility of the 1,4-norbornadiene ligand in 3c is extremely pronounced and the coordinated diolefin flexibility could be frozen only at about 200 K. These complexes are active but poorly stereoselective catalysts for the hydrogenation, hydroboration, and hydroformylation of alkenes. Received June 16, 2000. Accepted (revised) July 24, 2000     

Palladium-Nanoparticle-Catalysed Ullmann Reactions in Ionic Liquids with Aldehydes as the Reductants: Scope and Mechanism

An efficient Ullmann-type reductive homocoupling of aryl, vinyl and heteroaryl halides can be promoted by an aldehyde in tetraalkylammonium ionic liquids under very mild reaction conditions. This simple procedure generates symmetrical biaryls under relatively mild conditions. The ionic liquid is crucial for this process because it behaves simultaneously as a base, ligand and reaction medium. The role of the aldehyde is also discussed and a general mechanism for this unusual reaction is proposed. These results open the way to a new efficient method of Pd-catalysed dehydrogenation of carbonyl compounds.     

NA48 results on neutral kaon and hyperon rare decays

The NA48 Collaboration has performed an extensive program of kaon and hyperon rare decays using the data collected during the period 1997–2001. This program includes new tests of chiral perturbation theory, new measurements of theη mass andK _s lifetime and the possibility to measure the Cabibbo angle using Ξ beta decays.     

Synthesis and characterization of CdS nanoparticles embedded in a polymethylmethacrylate matrix

CdS nanopowder capped with sodium bis(2-ethylhexyl)sulfosuccinate was synthesized by using water-in-oil microemulsions. The CdS nanoparticles of about 5 nm obtained were embedded in polymethylmethacrylate matrix by a photocuring process. The transparent yellow solid compound was characterized by optical absorption and emission spectroscopy, high-resolution transmission electron microscopy, and energy-dispersive X-ray spectroscopy. The properties of this compound were compared with those of the nanopowder dispersed in heptane and in methylmethacrylate. The results obtained indicate that the nanoparticles are homogeneously dispersed in the matrix and do not change in size during the embedding process. Even if the surface slightly changes its luminescence properties, as a consequence of the different new chemical environment, the final product seems to be suitable for practical applications.     

Enantioselective hydrogenation of polar substrates in inverted supercritical CO2/aqueous biphasic media

An inverted supercritical CO2/aqueous biphasic catalytic system allows highly enantioselective hydrogenation of polar water-soluble substrates and efficient recycling of the CO2-philic catalysts.     

Temperature dependence of damping and frequency shifts of the scissors mode of a trapped Bose-Einstein condensate

We have studied the properties of the scissors mode of a trapped Bose-Einstein condensate of 87Rb atoms at finite temperature. We measured a significant shift in the frequency of the mode below the hydrodynamic limit and a strong dependence of the damping rate as the temperature increased. We compared our damping rate results to recent theoretical calculations for other observed collective modes, finding a fair agreement. From the frequency measurements we deduce the moment of inertia of the gas and show that it is quenched below the transition point, because of the superfluid nature of the condensed gas.