Protein binding of coherin and other small molecules by thin-layer gel chromatography

The protein binding stoichiometry of small molecules is here determined on a nanomole scale by a simplified procedure utilizing chromatography on thin layers of cross-linked dextran gels. New data are presented on the thin layer chromatographic properties of representative ligands, including a-amino acids, peptides, dyes and fluorigenic reagents, in relation to their molecular weights, polar characteristics, gel water regain values and denaturants, providing criteria for the general application of this method to studies of ligand binding with large as well as small molecules. By this procedure coherin peptides, A1 and B1--4, respectively, bind to coherin C in the molar ratio, 2:1, with a binding constant of about 10(5) M-1. Coherin C is believed to act as a carrier peptide.     

The consequences of translational and rotational entropy lost by small molecules on binding to proteins

When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15–20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes.     

Selective dimerization of α-methylstyrene catalyzed by a solid acid

A novel solid acid prepared from concentrated sulfuric, boric and phosphoric acid is a highly selective catalyst for the dimerization of α-methylstyrene at room temperature to generate 4-methyl-2,4-diphenyl-1-pentene.     

Ab initio calculation of core-electron binding energies in small molecules

Vertical ionization potentials for core orbitals of HF, H₂O, CO, HCN, and H₂CO are calculated with an ab initio transition operator method, followed by Rayleigh-Schrödinger perturbation theory. The results are improved by using a transition atomic basis set. Relativistic corrections are estimated. The average absolute deviation of our final results from experiment is 0.4 eV for the eight cases studied.     

Targeting apoptosis via chemical design: inhibition of bid-induced cell death by small organic molecules

Bid is a key member of the Bcl-2 family proteins involved in the control of the apoptotic cascade in cells, leading to cell death. Uncontrolled cell death is associated with several human pathologies, such as neurodegenerative diseases and ischemic injuries. Therefore, Bid represents a potential yet unexplored and challenging target for strategies aimed at the development of therapeutic agents. Here we show that a multidisciplinary NMR-based approach that we named SAR by ILOEs (structure activity relationships by interligand nuclear Overhauser effect) allowed us to rationally design a series of 4-phenylsulfanyl-phenylamine derivatives that are capable of occupying a deep hydrophobic crevice on the surface of Bid. These compounds represent the first antiapoptotic small molecules targeting a Bcl-2 protein as shown by their ability to inhibit tBid-induced SMAC release, caspase-3 activation, and cell death.     

Anticalins versus antibodies: made-to-order binding proteins for small molecules

Engineering proteins to bind small molecules presents a challenge as daunting as drug discovery, for both hinge upon our understanding of receptor-ligand molecular recognition. However, powerful techniques from combinatorial molecular biology can be used to rapidly select artificial receptors. While traditionally researchers have relied upon antibody technologies as a source of new binding proteins, the lipocalin scaffold has recently emerged as an adaptable receptor for small molecule binding. 'Anticalins', engineered lipocalin variants, offer some advantages over traditional antibody technology and illuminate features of molecular recognition between receptors and small molecule ligands.     

Selective reductive dimerization of homocubane series oximes

The mixture of di- and monoethylene ketals obtained by the reaction of 1,9-dibromopentacyc lo[5.4.0.0^2,6.0^3,10.0^5,9]-undeca-8,11-dione followed by hydrolysis and ring contraction by Faworsky method was converted into a mixture of ethylene ketals of 7-bromopentacyclo[5.3.0.0^2,5.0^3,9.0^4,8]decan-6-one-4- and 5-bromopentacyclo[5.3.0.0^2,5.0^3,9.0^4,8]decan-6-one-8-carboxylic acid where the carboxy group was replaced by bromine along the procedure of Hunsdiecker-Borodine-Cristol. 6-Ethylene ketal of the pentacyclo[5.3.0.0^2,5.0^3,9.0^4,8] decan-6-one obtained by the debromination of ethylene ketals of 4,7- and 5,8-dibromopentacyclo[5.3.0.0^2,5.0^3,9.0^4,8] decan-6-one was hydrolyzed to ketone whose oxime was selectively reduced on a platinum catalyst into the di-6-pentacyclo[5.3.0.0^2,5.0^3,9.0^4,8]decylamine. The reaction of reductive dimerization was also characteristic of pentacyclo[4.3.0.0^2,5.0^3,8.0^4,7]-nonan-9-one and pentacyclo[6.3.0.0^2,6.0^3,10.0^5,9]undecan-4-one oximes, whereas the composition of the reduction products of pentacyclo[5.4.0.0^2,6.0^3,10.0^5,9]undecan-8-one oxime depended on the amount of the catalyst.     

Concurrent binding and delivery of proteins and lipophilic small molecules using polymeric nanogels

Supramolecular nanoassemblies, which are capable of binding and delivering either lipophilic small molecules or hydrophilic molecules, are of great interest. Concurrently binding and delivering this combination of molecules is cumbersome, because of the opposing supramolecular host requirements. We describe the development of a versatile nanoassembly system that is capable of binding and delivering both, a protein and a lipophilic small molecule, simultaneously inside the cells.     

Multivalent binding of small guest molecules and proteins to molecular printboards inside microchannels

Beta-Cyclodextrin (beta-CD) monolayers have been immobilized in microchannels. The host-guest interactions on the beta-CD monolayers inside the channels were comparable to the interactions on beta-CD monolayers on planar surfaces, and a divalent fluorescent guest attached with a comparable binding strength. Proteins were attached to these monolayers inside microchannels in a selective manner by employing a strategy that uses streptavidin and orthogonal linker molecules. The design of the chip, which involved a large channel that splits into four smaller channels, allowed the channels to be addressed separately and led to the selective immobilization of antibodies. Experiments with labeled antibodies showed the selective immobilization of these antibodies in the separate channels.     

Per(6-guanidino-6-deoxy)cyclodextrins: synthesis, characterisation and binding behaviour toward selected small molecules and DNA

Per(6-guanidino-6-deoxy)-cyclodextrins , and are novel derivatives, resulting from homogeneous introduction of the guanidino group at the primary side of alpha-, beta- and gamma-cyclodextrins. The products were obtained from the corresponding amino derivatives, as direct guanidinylation of the known bromo-cyclodextrins provided mixtures. The new compounds were fully characterized by NMR spectroscopy and other analytical methods, and their interaction with guest molecules was studied. Strong complexation with 4-nitrophenyl phosphate () disodium salt was observed (K(binding) approximately 5 x 10(4) M(-1)), whereas the non-phosphorylated substrate nitrobenzene () formed a very weak complex. 2D ROESY spectra revealed cavity inclusion in both cases, however the orientation of was opposite to that of , such that the phosphate group is oriented toward the primary side facing the guanidine groups. The strong affinity of towards the phosphorylated guest suggested that interaction with DNA was possible. The new compounds were found to completely inhibit the migration of ultra pure calf thymus DNA during agarose gel electrophoresis, whereas no effects were observed with guanidine alone or with the plain cyclodextrins. Further, the condensation of DNA into nanoparticles in the presence of was demonstrated by atomic force microscopy, confirming strong electrostatic interaction between the biopolymer and the multicationic products . The strong guanidine-phosphate interactions between and DNA were therefore attributed to the clustering of the guanidine groups in the primary area of the cyclodextrin. Cavity effects could not be assessed.     

Selective activation of organic molecules by elemental fluorine

Reactions on tertiary hydrogen atoms, attached to unactivated saturated carbons, are very rare and usually inefficient. The electron density however, of a carbon-tertiary hydrogen bond is relatively high and therefore there is a chance it will react with a strong electrophile. One of the strongest electrophiles existing is, of course, the electrophilic fluorine. Two main sources for such an unusual species exist. One source is the various fluoroxy compounds like CF₃OF or CF₃COOF ant the other is the elemental fluorine itself.Indeed, when fluorine is allowed to react, at low temperatures, with various alkylcyclohexanol esters, a highly regio- and an absolutely stereospecific electrophilic substitution on the tertiary unactivated hydrogen takes place as for example:

The radical pathway possibility of these reactions is excluded and it is believed that they are of ionic nature. By dehydrofluorination, a double bond is introduced in sites that no other reagent is known to do, thus activating the molecule towards further chemical transformations. The influence of the electron-withdrawing group on the reaction center will also be discussed.The described reaction is not restricted only to cyclic compounds as aliphatic chains also react as expected, i.e.

The scope of these unusual reactions in both alicyclic and aliphatic fields will be evaluated.     

Selective dimerization of styrene to 1,3-diphenyl-1-butene by acetyl perchlorate

The linear unsaturated dimer of styrene, 1,3-diphenyl-1-butene, was obtained exclusively in the oligomerization of styrene by acetyl perchlorate in various solvents. In benzene, the linear dimer was produced in more than 90% yield at 50°C. In n-hexane and cyclohexane, the yield of the linear dimer was lower. The yield of the linear dimer was strongly dependent on the nature of solvent. When an increasing amount of 1,2-dichloroethane was added to benzene, the yield of the linear dimer gradually decreased. On the other hand, when a small amount of 1,2-dichloroethane was added to n-hexane or cyclohexane, the yield of the linear dimer increased. The yield of the linear dimer was almost independent of the reaction temperature and the initiator concentration. For comparison, the dimerization of α-methylstyrene was carried out, and the effects of the initiator and the solvent on the structure of dimers were investigated. On the basis of these results, the mechanism of the dimerization of styrene initiated by acetyl perchlorate is discussed.