Classification of water molecules in protein binding sites

Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecular receptor. An understanding of the nature and role of each water molecule in the active site of a protein could greatly increase the efficiency of rational drug design approaches: if the propensity of a water molecule for displacement can be determined, then synthetic effort may be most profitably applied to the design of specific ligands with the displacement of this water molecule in mind. In this paper, a thermodynamic analysis of water molecules in the binding sites of six proteins, each complexed with a number of inhibitors, is presented. Two classes of water molecules were identified: those conserved and not displaced by any of the ligands, and those that are displaced by some ligands. The absolute binding free energies of 54 water molecules were calculated using the double decoupling method, with replica exchange thermodynamic integration in Monte Carlo simulations. It was found that conserved water molecules are on average more tightly bound than displaced water molecules. In addition, Bayesian statistics is used to calculate the probability that a particular water molecule may be displaced by an appropriately designed ligand, given the calculated binding free energy of the water molecule. This approach therefore allows the numerical assessment of whether or not a given water molecule should be targeted for displacement as part of a rational drug design strategy.     

Enantiomerically enriched atropisomeric N,N′-diaryl ureas by oxidative kinetic resolution of their 2-sulfanyl derivatives

Atropisomeric N-methyl-N,N′-diaryl ureas may be obtained in enantiomerically enriched form by oxidative kinetic resolution of their sulfide derivatives. The atropisomeric sulfides may be obtained in up to 97:3 er and display high stability to racemisation (half-lives at 25 °C of up to 500 years). Unlike related fully alkylated ureas, the product sulfoxides exhibit relatively weak thermodynamic conformational selectivity.     

Polyglycerol-derived amphiphiles for the solubilization of single-walled carbon nanotubes in water: a structure-property study

A series of nonionic amphiphiles derived from polyglycerol dendrons were studied for their ability to solubilize and isolate single-walled carbon nanotubes. The amphiphiles possessed differently sized polar head groups, hydrophobic tail units, and various aromatic and non-aromatic groups between the head and tail groups. Absorbance analysis revealed that amphiphiles with anchor groups derived from pyrene were far inferior to those that possessed simple linear aliphatic tail groups. Absorbance and near-infrared fluorescence analyses revealed a weak dependence on the dendron size of the head group, but a strong positive trend in suspended nanotube density and fluorescence intensity for amphiphiles with longer tail units. Variations in the moieties linking the head and tail groups led to a range of effects on the suspensions, with linkers imparting flexibility and a bent shape that gave improved performance overall. This was illustrated most dramatically by a pair of benzamide-containing amphiphiles, the para isomer of which showed evidence in the fluorescence data of increased nanotube aggregate formation when compared with the meta isomer. In addition, statistical AFM was used to illustrate more directly the microscopic differences between amphiphiles that were effective at nanotube bundle disruption and those that were not.     

Oligoether-strapped calix[4]pyrrole: an ion-pair receptor displaying cation-dependent chloride anion transport

A ditopic ion-pair receptor (1), which has tunable cation- and anion-binding sites, has been synthesized and characterized. Spectroscopic analyses provide support for the conclusion that receptor 1 binds fluoride and chloride anions strongly and forms stable 1:1 complexes ([1·F](-) and [1·Cl](-)) with appropriately chosen salts of these anions in acetonitrile. When the anion complexes of 1 were treated with alkali metal ions (Li(+), Na(+), K(+), Cs(+), as their perchlorate salts), ion-dependent interactions were observed that were found to depend on both the choice of added cation and the initially complexed anion. In the case of [1·F](-), no appreciable interaction with the K(+) ion was seen. On the other hand, when this complex was treated with Li(+) or Na(+) ions, decomplexation of the bound fluoride anion was observed. In contrast to what was seen with Li(+), Na(+), K(+), treating [1·F](-) with Cs(+) ions gave rise to a stable, host-separated ion-pair complex, [F·1·Cs], which contains the Cs(+) ion bound in the cup-like portion of the calix[4]pyrrole. Different complexation behavior was seen in the case of the chloride complex, [1·Cl](-). Here, no appreciable interaction was observed with Na(+) or K(+). In contrast, treating with Li(+) produces a tight ion-pair complex, [1·Li·Cl], in which the cation is bound to the crown moiety. In analogy to what was seen for [1·F](-), treatment of [1·Cl](-) with Cs(+) ions gives rise to a host-separated ion-pair complex, [Cl·1·Cs], in which the cation is bound to the cup of the calix[4]pyrrole. As inferred from liposomal model membrane transport studies, system 1 can act as an effective carrier for several chloride anion salts of Group 1 cations, operating through both symport (chloride+cation co-transport) and antiport (nitrate-for-chloride exchange) mechanisms. This transport behavior stands in contrast to what is seen for simple octamethylcalix[4]pyrrole, which acts as an effective carrier for cesium chloride but does not operates through a nitrate-for-chloride anion exchange mechanism.     

Catalytic enantioselective protonation of nitronates utilizing an organocatalyst chiral only at sulfur

The highly enantioselective protonation of nitronates formed upon the addition of α-substituted Meldrum's acids to terminally unsubstituted nitroalkenes is described. This work represents the first enantioselective catalytic addition of any type of nucleophile to this class of nitroalkenes. Moreover, for the successful implementation of this method, a new type of N-sulfinyl urea catalyst with chirality residing only at the sulfinyl group was developed, thereby enabling the incorporation of a diverse range of achiral diamine motifs. Finally, the Meldrum's acid addition products were readily converted to pharmaceutically relevant 3,5-disubstituted pyrrolidinones in high yield.     

Fullerene-derivatized amino acids: synthesis, characterization, antioxidant properties, and solid-phase peptide synthesis

A series of [60]fullerene-substituted phenylalanine (Baa) and lysine derivatives have been prepared by the condensation of 1,2-(4'-oxocyclohexano)fullerene with the appropriately protected (4-amino)phenylalanine and lysine, respectively. Conversion of the imine to the corresponding amine is achieved by di-acid catalyzed hydroboration. The reduction of the imine is not accompanied by hydroboration of the fullerene cage. The [70]fullerene phenylalanine derivative has also been prepared as have the di-amino acid derivatives. The compounds were characterized by MALDI-TOF mass spectrometry, UV/Vis spectroscopy, and cyclic voltammetry. 1H and 13C NMR spectroscopy allowed the observation of diastereomers. Fullerene-substituted peptides may be synthesized on relatively large scale by solid-phase peptide synthesis. The presence of the C60-substituted amino acid in a peptide has a significant effect on the secondary structures and self-assembly properties of peptides as compared to the native peptide. The antioxidant assay of Baa and a Baa-derived anionic peptide was determined to be significantly more potent than Trolox.     

Interplay of Interactions Governing the Dynamic Conversions of Acyclic and Macrocyclic Helicates

Systemic change : A system of transformations between helical structures was observed to be governed by interactions mediated by the electronic effects of substituents, entropic effects, the conformational preferences of organic building blocks, and the coordinative preferences of the metal ion. All of these effects were important, but all must be considered together to allow the prediction of the product observed (see scheme).

     

Formation of self-assembled chains of tetrathiafulvalene on a Cu(100) surface

Formation of self-assembled chains of tetrathiafulvalene (TTF) on the Cu(100) surface has been investigated by scanning tunneling microscopy and density functional theory calculations that include semiempirical van der Waals (vdW) interaction corrections. The calculations show that the chain structures observed in the experiments can only be explained by including the vdW interactions. The molecules are tilted along the chain in order to achieve maximal intermolecular interaction. The chains are metastable on the surface, which is consistent with the experimental observation that they disappear after annealing. The fact that all TTF chains observed in the experiment are short might be possibly explained by the interplay between the stabilizing vdW molecule-molecule interaction and the destabilizing rearrangement of surface atoms due to the strong molecule-substrate interaction.     

Direct synthesis of chiral tertiary diphosphines via Pd(II)-catalyzed asymmetric hydrophosphination of dienones

A highly diastereo- and enantioselective Pd(II)-catalyzed hydrophosphination of dienones with Ph(2)PH involving formation of double C*-P bonds has been developed, providing a series of chiral tertiary diphosphines (chiral PCP pincer ligands) in high yields. A catalytic cycle for the reaction was proposed.