Biomedical subjects

Annick Dejaegere

Publications and source records attributed to Annick Dejaegere.

8 recordsLinked to original sources

PubMed2006

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems.

A density functional study of the hydrolysis reaction of phosphodiesters with a series of attacking nucleophiles in the gas phase and in solution is presented. The nucleophiles HOH, HO-, CH3OH, and CH3O- were studied in reactions with ethylene phosphate, 2'3'-ribose cyclic phosphate and in their neutral (protonated) and monoanionic forms. Stationary-point geometries for the reactions were determined at the density functional B3LYP/6-31++G(d,p) level followed by energy refinement at the B3LYP/6-311++G(3df,2p) level. Solvation effects were estimated by using a dielectric approximation with the polarizable continuum model (PCM) at the gas-phase optimized geometries. This series of reactions characterizes factors that influence the intrinsic reactivity of the model phosphate compounds, including the effect of nucleophile, protonation state, cyclic structure, and solvent. The present study of the in-line mechanism for phosphodiester hydrolysis, a reaction of considerable biological importance, has implications for enzymatic mechanisms. The analysis generally supports the associative mechanism for phosphate ester hydrolysis. The results highlight the importance for the reaction barrier of charge neutralization resulting from the protonation of the nonbridging phosphoryl oxygens and the role of internal hydrogen transfer in the gas-phase mechanism. It also shows that solvent stabilization has a profound influence on the relative barrier heights for the dianionic, monoanionic, and neutral reactions. The calculations provide a comprehensive data set for the in-line hydrolysis mechanisms that can be used for the development of improved semiempirical quantum models for phosphate hydrolysis reactions.

Anions↗

PubMed2006

On the affinity regulation of the metal-ion-dependent adhesion sites in integrins.

Density functional theory and a polarizable continuum model are used to (i) understand the affinity modulating mechanisms of the interaction between the metal-ion-dependent adhesion site (MIDAS) of a selected integrin, lymphocyte function-associated antigen-1 (LFA-1) and a ligand mimetic acetate molecule and to (ii) propose a new, promising family of inhibitors to block the interaction of the integrin with intercellular adhesion molecule-1 (ICAM-1). We quantify the effect of isolated factors, such as the metal coordination, the nature of the ligand or the cation present on the MIDAS, and the effect of the permittivity of the media. We show that the affinity for ligand decreases when metal coordination changes from the open conformation to the closed conformation. In addition, Mn2+ and Zn2+ showed to be good competitors for the octahedrically coordinated Mg2+ and yielded excellent affinity values, whereas Ca2+ in an octahedric environment would decrease the affinity for the ligand. Our affinity studies of the open MIDAS showed that nitronate-derived or carboxylic acid-containing ligands may represent new promising scaffolds of future inhibitors. Finally, we show that affinities are always highly favored by low-dielectric environments, which explains the propensity of MIDAS motifs to be surrounded by hydrophobic residues in integrins and highlights the importance of including hydrophobic groups in the inhibitors.

Binding Sites↗

PubMed2006

Dual specificity of the interfacial inhibitor brefeldin a for arf proteins and sec7 domains.

Guanine nucleotide exchange factors (GEFs), which activate small GTP-binding proteins (SMG) by stimulating their GDP/GTP exchange, are emerging as candidate targets for the inhibition of cellular pathways involved in diseases. However, their specific inhibition by competitive inhibitors is challenging, because GEF and SMG families comprise highly similar members. Nature shows us an alternative strategy called interfacial inhibition, exemplified by Brefeldin A (BFA). BFA inhibits the activation of Arf1 by its GEFs in vivo by stabilizing an abortive complex between Arf-GDP and the catalytic Sec7 domain of some of its GEFs. Here we characterize the specificity of BFA toward wild-type (ARNO and BIG1) and mutant Sec7 domains and toward class I, II, and III Arfs. We find that BFA sensitivity of the exchange reaction depends on the nature of both the Sec7 domain and the Arf protein. A single Phe/Tyr substitution is sufficient to achieve BFA sensitivity of the Sec7 domain, which is supported by our characterization of brefeldin C (BFC), a BFA analog that cannot interact with the Tyr residue, and by free energy computations. We further show that Arf1 and Arf5, but not Arf6, are BFA-sensitive, despite their having every BFA-interacting residue in common. Analysis of Arf6 mutants points to the dynamics of the interswitch, which is involved in membrane-to-nucleotide signal propagation, as contributing to, although not sufficient for, BFA sensitivity. Altogether, our results reveal the Tyr/Phe substitution as a novel tool for monitoring BFA sensitivity of cellular ArfGEFs and document the exquisite and dual specificity that can be achieved by an interfacial inhibitor.

ADP-Ribosylation Factors↗

PubMed2005

Variations in antigen-antibody association kinetics as a function of pH and salt concentration: a QSAR and molecular modeling study.

The relationship between three environmental factors (ionic strength, pH, and temperature) and antigen-antibody binding kinetics was investigated using QSAR (quantitative structure-activity relationship) and molecular modeling approaches. The interaction used for this analysis is that between the camel antibody fragment cAbLys3 and lysozyme. Binding kinetics were measured using a Biacore 2000 instrument, at NaCl concentrations between 50 and 500 mM, at pH's between 5 and 10, and at temperatures between 15 and 30 degrees C, according to multivariate experimental designs. Variations in kinetic on- and off-rate parameters were up to 400- and 16-fold, respectively. Mathematical models that relate log k(on) to experimental conditions were developed. They indicated an influence of all three factors, with a clear dependency between pH and NaCl concentration for their effect on k(on). These models were able to predict on-rate parameters under new experimental conditions. Titration calculations using continuum electrostatics were performed on the crystallographic structures of the isolated and bound proteins to gain structural insight for the on-rate enhancement observed at pH <6.5 and low salt concentrations. These calculations rule out electrostatic steering linked to global and/or local charge variations in the molecules as the factor responsible for the on-rate enhancement at low pH. His 111 of cAbLys3, located at the binding interface, can adopt two side chain orientations with different intramolecular contacts. The results of the calculations suggest an alternative mechanism whereby the conformation of the interfacial His 111 depends on the charge, and these differences in conformation may influence the solvation energy and the subsequent binding kinetics. Our results stress the complex relationship between environmental conditions and molecular binding properties.

Animals↗

PubMed2005

Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics.

The calculation of binding affinities for flexible ligands has hitherto required the availability of reliable molecular mechanics parameters for the ligands, a restriction that can in principle be lifted by using a mixed quantum mechanics/molecular mechanics (QM/MM) representation in which the ligand is treated quantum mechanically. The feasibility of this approach is evaluated here, combining QM/MM with the Poisson-Boltzmann/surface area model of continuum solvation and testing the method on a set of 47 benzamidine derivatives binding to trypsin. The experimental range of the absolute binding energy (DeltaG = -3.9 to -7.6 kcal/mol) is reproduced well, with a root-mean-square (RMS) error of 1.2 kcal/mol. When QM/MM is applied without reoptimization to the very different ligands of FK506 binding protein the RMS error is only 0.7 kcal/mol. The results show that QM/MM is a promising new avenue for automated docking and scoring of flexible ligands. Suggestions are made for further improvements in accuracy.

Ligands↗

PubMed2005

Magnetic effects of disulfide bridges: a density functional and semiempirical study.

Density functional chemical shielding calculations are reported for methane and hydrogen disulfide dimers. The calculations show that the contributions of disulfide bridges to the chemical shielding of neighboring protons is sizable at distances that are frequently sampled in protein structures. A semiempirical model of the quantum chemical data is developed. It is shown that magnetic anisotropy effects of disulfide are poorly described by the McConnell equation, both qualitatively and quantitatively. In particular, the ratio of magnetic anisotropy contributions to shielding along and perpendicular to the magnetic anisotropy principal axis do not conform to the predictions of the McConnell equation, and magnetic anisotropy effects are not null along the magic angle axis. A sulfur-based model of the magnetic anisotropy of the disulfide is developed and shown to give much better agreement with the quantum chemical data.

Anisotropy↗

PubMed2002

Structure activity relationship by NMR and by computer: a comparative study.

There has recently been considerable interest in using NMR spectroscopy to identify ligand binding sites of macromolecules. In particular, a modular approach has been put forward by Fesik et al. (Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Science 1996, 274, 1531-1534) in which small ligands that bind to a particular target are identified in a first round of screening and subsequently linked together to form ligands of higher affinity. Similar strategies have also been proposed for in silico drug design, where the binding sites of small chemical groups are identified, and complete ligands are subsequently assembled from different groups that have favorable interactions with the macromolecular target. In this paper, we compare experimental and computational results on a selected target (FKBP12). The binding sites of three small ligands ((2S)1-acetylprolinemethylester, 1-formylpiperidine, 1-piperidinecarboxamide) in FKBP12 were identified independently by NMR and by computational methods. The subsequent comparison of the experimental and computational data showed that the computational method identified and ranked favorably ligand positions that satisfy the experimental NOE constraints.

Binding Sites↗

PubMed2002

Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis.

Knowledge of the pK(a) of phosphoranes is important for the interpretation of phosphate ester hydrolysis. Calculated pK(a)'s of the model phosphorane, ethylene phosphorane, are reported. The method of calculation is based on the use of dimethyl phosphate as a reference state for evaluating relative pK(a) values, and on the optimization of the oxygen and acidic hydrogen van der Waals radii to give reasonable pK(1)(a), pK(2)(a), and pK(3)(a) for phosphoric acid in solution. Density functional theory is employed to calculate the gas-phase protonation energies, and continuum dielectric methods are used to determine the solvation corrections. The calculated pK(1)(a) and p(2)(a) for the model phosphorane are 7.9 and 14.3, respectively. These values are within the range of proposed experimental values, 6.5-11.0 for pK(1)(a), and 11.3-15.0 for pK(2)(a). The mechanistic implications of the calculated pK(a)'s are discussed.

Hydrolysis↗