Hetero-calix[4]pyrroles: incorporation of furans, thiophenes, thiazoles or fluorenes as a part of the macrocycle

Furans, thiazoles, fluorene or thiophene incorporated calix[4]pyrrole analogues were synthesized and characterized. The synthesis was achieved by utilization of various building blocks such as 7, 13, 14, 18 and 21. Acid catalyzed condensation of those building blocks with acetone or meso-disubstituted dipyrromethanes afforded desired macrocycles.     

An optical surface plasmon resonance biosensor for determination of tetanus toxin

Surface plasmon resonance (SPR) has been successfully applied for the simple, rapid, and label-free assay of various biomolecules. This assay evaluates a novel wavelength modulation SPR biosensor for the detection of tetanus toxin. The wavelength modulation SPR biosensor is designed based on fixing the incident angle of light and measuring the reflected intensities in the resonance wavelength range spanning 400-800 nm simultaneously. Tetanus toxin (TeNT), one of the most potent toxins known, is synthesized as a 150 kDa single polypeptide chain. The SPR biosensor has been shown to be capable of directly detecting concentration of tetanus toxin as low as 0.028 Lf ml⁻¹. Under selected experimental conditions, the SPR biosensor has a good reproducibility, sensitivity and reversibility. The results illustrate how wavelength modulation SPR biosensor can be used to detect biomolecular interactions.     

New methods for data analysis of isothermal titration calorimetry

Heat divided by ligand concentration vs. heat, similar to the Scatchard plot, was introduced to obtain the equilibrium constant (K) and the enthalpy of binding (DH) using isothermal titration calorimetry data. Values of K and DH obtained by this linear pseudo-Scatchard plot for a system with a set of independent binding sites (such as binding fluoride ions on urease and monosaccharide methyl a-D-mannopyranoside on concavalin A) were remarkably like that obtained from a normal fitting Wiseman method and other our technical methods. On applying this graphical method to study the binding of copper ion on myelin basic protein (MBP), a concave downward curve obtained was consistent with the positive cooperativity in the binding. A graphical fitting by simple method for determination of thermodynamic parameters was also introduced. This method is general, without any assumption and restriction made in previous method. This general method was applied to the product inhibition study of adenosine deaminase. This revised version was published online in July 2006 with corrections to the Cover Date.     

Volumes,heat capacities and solubilities of amyl compounds in decyltrimethylammonium bromide aqueous solutions

Apparent molar heat capacities and volumes of amylamine (PentNH₂) 0.02m, capronitrile (PentCN) 0.02m and nitropentane (PentNO₂) 0.009m in decyltrimethylammonium bromide (DeTAB) micellar solutions, in water and in octane were measured at 25°C. By assuming that their concentration approaches the standard infinite dilution state, heat capacities and volumes were rationalized by means of previously reported equations following which the distribution constant between the aqueous and the micellar phase and heat capacity and volume of the additives in both phases are simultaneously derived. The present results are compared to those we have previously obtained for pentanol (PentOH). The thermodynamic properties of PentNH₂ in water and in micellar phase are substantially identical to those of PentOH but different from those of PentCN and PentNO₂ whereas the opposite behavior was observed in their pure liquid state and in octane. The nature of the solvent medium seems to affect the thermodynamic behavior of PentNH₂. Also, the study of the apparent molar heat capacities of the amyl compounds investigated here in micellar solutions as a function of surfactant concentration shows evidence of a maximum at about 0.4m DeTAB, which can be attributed to a micellar structural transition. Accordingly, the solubilities of PentCN and PentNO₂ as a function of the DeTAB concentration drop in the neighborhood of the concentration where heat capacities display the maximum.     

Nucleotide/Protein Interaction: Energetic and Structural Features of Na,K-ATPase

Microcalorimetric titrations allow to recognize and investigate high-affinity ligand binding to Na,K-ATPase. Titrations with the cardiac glycoside Ouabain, which acts as a specific inhibitor of the enzyme, have provided not only the thermodynamic parameters of high-affinity binding with a stoichiometric coefficient of about 0.6 but also evidence for low-affinity binding to the lipid. The marked enthalpic contribution of -95 kJ mol^-1 at 298.2 K is partially compensated by a large negative entropy change, attributed to an increased interaction between water and the protein. The calorimetric ADP and ATP titrations at 298.2 K are indicative of high-affinity nucleotide binding either in 3 mM NaCl, 3 mM MgCl₂ or at high ionic strength such as 120 mM choline chloride. However, no binding is detected in the buffer solution alone at low ionic strength. The affinities for ADP and ATP are similar, around 10⁶ M^-1 and the stoichiometric coefficients are close to that of Ouabain binding. The exothermic binding of ADP is characterized by a ΔH and ΔS value of -65 kJ mol^-1 and -100 J mol^-1 K^-1, respectively. TheΔH value for ATP binding is larger than for ADP and is compensated by a larger, unfavorable ΔS value. This leads to an enthalpy/entropy compensation, which could express that H-bond formation represents the major type of interaction. As for Ouabain, the negative ΔS values that are also characteristic of nucleotide binding can indicate an increase of solvate interaction with the protein due to a conformational transition occurring subsequent to the binding process. The resulting binding constants are discussed with regard to the results of other studies employing different techniques. A molecular interaction model for nucleotide binding is suggested. This revised version was published online in July 2006 with corrections to the Cover Date.     

Influence of response factors on determining equilibrium association constants of non-covalent complexes by electrospray ionization mass spectrometry

A method for determining the equilibrium association constant of a complexation reaction A + B left harpoon over right harpoon AB by electrospray ionization mass spectrometry is described. The method consists in measuring the relative intensities of the peaks corresponding to A and to AB in equimolar A-B solutions at different concentrations C(0). The results are fitted by a non-linear least-squares procedure, with the two variable parameters being the equilibrium association constant K(a) and a factor R, defined by I(AB)/I(A) = R x [AB]/[A]. The factor R is the ratio between the response factors of AB and A, and corrects for the relative electrospray responses of the complex and the free substrate A, mass discrimination of instrumental origin and/or moderate in-source dissociation. The method is illustrated with the following two systems: complexes between a double-stranded 12-base pair oligonucleotide and minor groove binders, and cyclodextrin complexes with alpha,omega-dicarboxylic acids. For the oligonucleotide complexes, it is found that the response of the complex is not dramatically different to the response of the free oligonucleotide duplex, as the double helix conformation is disturbed by the drug only to a minor extent. In the case of cyclodextrin complexes, these complexes were found to have a much higher response than free cyclodextrin. This may be due to the fact that cyclodextrin is neutral in solution, whereas the complex is charged, but it can also stem from the fact that a significant proportion of the complex is in a non-inclusion geometry. The present method requires the exact determination of the concentrations of the reactants and is applicable to 1 : 1 complexes.     

2-(8-羟基喹啉-5-磺酸-7-偶氮)-1,8-二羟基-3,6-萘二磺酸与牛血清白蛋白的相互作用

用平衡透析法和分光光度法研究了 2 (8 羟基喹啉 5 磺酸 7 偶氮 ) 1,8 二羟基 3,6 萘二磺酸与牛血清白蛋白 (BSA)在酸性溶液中的结合反应 ,认为 8Q5SAC与BSA之间的结合力是以静电引力为主的非共键作用力 ,并探讨了其结合模型。在 2 98K下 ,测得这一反应的最大结合数为 35～ 40 ,结合常数为 6 .1× 10 5L mol。还研究了溶液基本条件如酸度和离子强度等对 8Q5SAC与牛血清白蛋白分子复合物形成的影响 ,在pH =3.34条件下 ,标准工作曲线的线性范围为 0 .2 0～ 46 .90mg L。     

Scoring functions: A view from the bench

Computational approaches to drug design are presently hindered by the complexity of the physical chemistry which underlies weak, non- covalent interactions between protein targets and small molecule ligands. Although a number of programs are now available for the design of novel potential ligands, it remains a key problem to rank these rapidly and reliably by estimated binding affinity. Such a step is necessary to select only the most promising candidates for synthesis and experimental characterisation. To calculate ligand affinity quickly and reliably is an extremely difficult problem, but it may well prove possible to estimate sufficiently accurately given an appropriate set of parameters to score individual protein–ligand interactions. Improvements in the situation will require a wider set of thermodynamically characterised systems than is currently available.     

Preparation and properties of sclerotium rolfsii invertase immobilized on indion 48-R

Crude extracellular invertase fromSclerotium rolfsii, when coupled to glutaraldehyde activated Indion 48-R, retained 70–80% activity of the soluble enzyme. Immobilization resulted in a decrease in the pH and temperature optima but it increased the temperature stability. K_m and V_max also increased as a result of immobilization. Both soluble and immobilized invertase showed inhibition at high substrate concentrations. The bound enzyme showed excellent stability to repeated use and retained approx 90% of its initial activity after 8 cycles of use.     

The matching of electrostatic extrema: A useful method in drug design? A study of phosphodiesterase III inhibitors

Summary Ligands which bind to a specific protein binding site are often expected to have a similar electrostatic environment which complements that of the binding site. One method of assessing molecular electrostatic similarity is to examine the possible overlay of the maxima and minima in the electrostatic potential outside the molecules and thereby match the regions where strong electrostatic interactions, including hydrogen bonds, with the residues of the binding site may be possible. This approach is validated with accurate calculations of the electrostatic potential, derived from a distributed multipole analysis of an ab initio charge density of the molecule, so that the effects of lone pair and -electron density are correctly included. We have applied this method to the phosphodiesterase (PDE) III substrate adenosine-3,5-cyclic monophosphate (cAMP) and a range of nonspecific and specific PDE III inhibitors. Despite the structural variation between cAMP and the inhibitors, it is possible to match three or four extrema to produce relative orientations in which the inhibitors are sufficiently sterically and electrostatically similar to the natural substrate to account for their affinity for PDE III. This matching of extrema is more apparent using the accurate electrostatic models than it was when this approach was first applied, using semiempirical point charge models. These results reinforce the hypothesis of electrostatic similarity and give weight to the technique of extrema matching as a useful tool in drug design.