CO diffusion as a re-orientation mechanism in the NaY zeolite.

Our work is devoted to DFT calculations of the relative rotational and diffusional barriers for CO motions in zeolite NaY. The diffusion jump of CO adsorbed in NaY from NaII to Na'II has been confirmed as the favored way for CO re-coordination via either the C or the O atom to the Na cations instead of the CO rotation, hence explaining the mechanism which is responsible for the CO exchange between different positions and the changes in the intensities of the vibrational IR spectra. The fine structure of the vibrational C-O bands is explained by the different CO locations of adsorbed mono- and dicarbonyl species. The calculated activation energy of intra-cage CO diffusion from NaII-CO to Na'II-OC matches the respective experimental barrier observed in the NaX zeolite.

siRNA and pharmacological inhibition of endocytic pathways to characterize the differential role of macropinocytosis and the actin cytoskeleton on cellular uptake of dextran and cationic cell penetrating peptides octaarginine (R8) and HIV-Tat.

Cell penetrating peptides (CPPs) have been extensively studied as vectors for cellular delivery of therapeutic macromolecules. It is widely accepted that they can enter cells directly across the plasma membrane but also gain access through endocytic pathways that are yet to be fully defined. Here we developed siRNA methods in epithelial cell lines, HeLa and A431, to inhibit endocytic pathways regulated by clathrin heavy chain, flotillin-1, caveolin-1, dynamin-2 and Pak-1. In each case, functional uptake assays were developed to characterize the requirement for these proteins, and the pathways they regulate, in the internalisation of defined endocytic probes and also the CPPs octaarginine and HIV-Tat. Peptide uptake was only inhibited in A431 cells depleted of the macropinocytosis regulator Pak-1, but experimental variables including choice of cell line, pharmacological inhibitor, macropinocytic probe and serum starvation significantly influence our ability to assess and assign this pathway as an important route for CPP uptake. Actin disruption with Cytochalasin D inhibited peptide entry in both cell lines but the effects of this agent on dextran uptake was cell line dependent, reducing uptake in HeLa cells and increasing uptake in A431 cells. This was further supported in experiments inducing actin stabilisation by Jasplakinolide, emphasising that the actin cytoskeleton can both promote and hinder endocytosis. Overall the data identify important aspects regarding the comparative mechanisms of CPP uptake and macropinocytosis, and accentuate the significant methodological challenges of studying this pathway as an endocytic portal and an entry route for drug delivery vectors.

Ion-exchanged binuclear Ca2OX clusters, X = 1-4, as active sites of selective oxidation over MOR and FAU zeolites.

A new series of calcium oxide clusters Ca(2)O(X) (X = 1-4) at cationic positions of mordenite (MOR) and faujasite (FAU) is studied via the isolated cluster approach. Active oxide framework fragments are represented via 8-membered window (8R) in MOR, and two 6R and 4R windows (6R+4R) possessing one common Si-O-Si moiety in FAU. Structural similarities between the Ca(2)O(X)(8R) and Ca(2)O(X)(6R+4R) moieties are considered up to X = 4. High oxidation possibilities of the Ca(2)O(2)(nR) and Ca(2)O(3)(nR) systems are demonstrated relative to CO, whose oxidation over the Ca-exchanged zeolite forms is well studied experimentally. Relevance of the oxide cluster models with respect to trapping and desorption of singlet dioxygen is discussed.

Fragment-based prediction of cytochromes P450 2D6 and 1A2 inhibition by recursive partitioning.

The evaluation of the ADME (absorption, distribution, metabolism, and excretion) properties of drug candidates is an important stage in drug discovery. To speed up the numerous tests carried out on large databases of compounds, the help of robust and accurate in silico filters is increasingly required. We propose here a method to build predictive and interpretable models for the prediction of cytochrome P450 (CYP) 1A2 and 2D6 inhibition using recursive partitioning (RP), a well-known technique for the construction of decision trees. The originality of the work is the use of several descriptions of the molecules in terms of fragments, i.e. the MACCS keys and five in-house fingerprints based on the electron density properties of fragments, employed to draw easily understandable structure-activity models. The classifiers reached performances of 87.5% and 76.5% of prediction on a validation set for CYP1A2 and CYP2D6, respectively. The analysis of the first nodes of the RP trees permits us to highlight some relations between the structural fragments and the inhibition of CYPs.

Electric field convergence versus atomic basis sets in all-siliceous zeolites.

The electrostatic potential (EP) and electric field (EF) are calculated in the TON and CHA zeolites using periodic hybrid B3LYP, PBE, and PW91 functionals considering eight basis sets. Relative root mean square differences between the EP or EF values estimated between the different basis sets are evaluated in several domains available for adsorbate molecules in both zeolites. The EP is interpreted in terms of ionicity of the framework.

Quick scheme for evaluation of atomic charges in arbitrary aluminophosphate sieves on the basis of electron densities calculated with DFT methods.

It is demonstrated that unique and simple analytical functions are justified for the atomic charge dependences q of the T (T = Al, P) and O atoms of aluminophosphates (AlPOs) using DFT calculations with several basis sets, starting from STO-3G to 3-21G and 6-21G**. Three internal (bonds, angles, ...) coordinates for the charge dependences of the T atoms and four coordinates for the O are sufficient to reach a precision of 1.8% for the fitted q(Al), 1.0% for q(P), and 2.5% for q(O) relatively to the values calculated at any basis set level. The proposed strategy consists in an iterative scheme starting from charge dependences based on the neighbor's positions only. Electrostatic potential values are computed to illustrate the differences between the calculated and fitted charges in the considered AlPO models.

Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density.

The aim of our study is the development of a method for calculating the interface of dimerization of protein-protein complexes based on simplified medium-resolution structures. In particular, we wished to evaluate if the existing concepts for the computation of the Solvent-Accessible Surface Area (SASA) of macromolecules could be applied to medium-resolution models. Therefore, we selected a set of 140 protein chains and computed their reduced representations by topological analysis of their electron density maps at 2.85 A crystallographic resolution. This procedure leads to a limited number of critical points (CPs) that can be identified and associated to backbone and side-chain parts. To evaluate the SASA and interfaces of dimerization of the reduced representations, we chose and modified two existing programs that calculate the SASA of atomic representations, and tested (1) several radii tables of amino acids, (2) the influence of the backbone and side-chain points, and (3) the radius of the solvent molecule, which rolls over the surface. The results are shown in terms of relative error compared to the values calculated on the corresponding atomic representations of the proteins.

Application of a Kohonen neural network to the analysis of data regarding the alkylation of toluene with methanol catalyzed by ZSM-5 type zeolites.

para-Xylene is widely used in chemical industry. It can be synthesized by alkylation of toluene with methanol using zeolite ZSM-5 as catalyst. The proportion of para-xylene, among its other isomers and other reaction byproducts, depends on the reaction conditions. As this process still remains largely empirical, we attempted to build a theoretical model able to predict the para-xylene yield under specific reaction conditions. We have consequently collected data regarding this reaction from the literature and exploited the potency of a particular artificial neural network (ANN), the counter-propagation ANN based on the Kohonen technique. The results show that such an approach is suitable to establish a predictive model of the yield in para-xylene on the basis of reaction parameters. The quality of the model could be further improved by considering a larger valuable data set, e.g. including experiments characterized by a low yield in para-xylene.

A new graph descriptor for molecules containing cycles. Application as screening criterion for searching molecular structures within large databases of organic compounds.

The search of molecular structures inside a large database of chemical compounds is a critical step for many computer programs used in several domains of chemistry. During the last years, the size of many chemical databases has dramatically increased, hence in the meantime, search engines needed to be more and more powerful. The speed and the efficiency of screening processes of the chemical compounds are thus essential. Looking forward for algorithms dedicated to structure and substructure search, we have developed a new graph descriptor for structures containing cycles in order to find efficient indexation and classification criteria of molecular structures. This graph descriptor can be used as a screening criteria for structure and substructure search in large databases of organic compounds.

Critical point representations of electron density maps for the comparison of benzodiazepine-type ligands.

A procedure for the comparison of three-dimensional electron density distributions is proposed for similarity searches between pharmacological ligands at various levels of crystallographic resolution. First, a graph representation of molecular electron density distributions is generated using a critical point analysis approach. Pairwise as well as multiple comparisons between the obtained graphs of critical points are then carried out using a Monte Carlo/simulated annealing technique, and results are compared with genetic algorithm solutions.

Comparison of benzodiazepine-like compounds using topological analysis and genetic algorithms.

Four compounds within a set of ligands for the benzodiazepine receptors are characterized by their electron density maps at different resolution levels and reconstructed from calculated structure factors. The resulting complex three-dimensional density maps are first simplified into connected graphs using topological analysis. Then, an original genetic algorithm method, GAGS (Genetic Algorithm for Graph Similarity search), is developed and implemented in order to compare the connected graphs. Finally, the analysis of the best solutions of the algorithm are expressed in terms of functional group superimpositions. The GAGS analysis is applied to different resolution levels of the electron density maps and the resulting models are compared in order to assess the influence of the resolution on the resulting pharmacophore models.

Similarity and complementarity of molecular shapes: applicability of a topological analysis approach.

Developments based on a topological analysis approach of electron density maps are presented and applied to two different fields: the interpretation of electron density maps of proteins and the description of shape complementarity between a cyclodextrin host and a guest molecule. A global representation of the electron density distribution, through the location, identification and linkage of its critical points (points where the gradient of the density vanishes, i.e., peaks and passes), is generated using the program ORCRIT. On one hand, the interpretation of protein electron density maps is based on similarity evaluations between graphs of critical points and known structures. So far, the method has been applied to 3 A resolution maps for the recognition of secondary structure motifs using a procedure relevant to expert systems in artificial intelligence. Satisfying matches between critical point graphs and their corresponding protein structure depict the ability of the topological analysis to catch the essential secondary structural features in electron density maps. On the other hand, mapping the accessible volume of a host molecule is achieved by representing the peaks as ellipsoids with axes related to local curvature of the electron density function. Related energies of the interacting species can also be estimated. A qualitative comparison is made between the results generated by the topological analysis and energy values obtained by conventional molecular mechanics calculations. A positive comparison and a close complementarity between cyclodextrin and ligands shows that the topological analysis method gives a good representation of the electron density function.

Experimental and theoretical study of reversible monoamine oxidase inhibitors: structural approach of the active site of the enzyme.

Experimental and theoretical physico-chemical methods were used to investigate the interaction between aryl-oxazolidinones and monoamine oxidase (MAO). Several arguments suggest that these compounds interact with the flavin adenine dinucleotide (FAD) cofactor of MAO. The calculation using ab initio molecular orbital methods of the electronic properties of flavin and befloxatone, a reversible inhibitor of MAO A, led to a description of the interaction between aryl-oxazolidinones and the cofactor of the enzyme. Structure activity relationship results revealed additional sites of interaction with the protein core of MAO A. As a result of this work, a model is proposed for the reversible inhibition of MAO by oxazolidinones via long distance, reversible interactions with the FAD cofactor of the enzyme.

Structure and molecular modeling of GABAA receptor antagonists.

The recently described potent and selective GABAA antagonist SR 95531 (gabazine) is compared to six other GABAA antagonists: (+)-bicuculline, (-)-securinine, (+)-tubocurarine, iso-THAZ, R-5135, and pitrazepine. Starting from ab initio molecular orbital calculations performed on crystal atomic coordinates, attempts were made to identify in each structure the functional groups that are involved in receptor recognition and binding. A molecular modeling study revealed that (a) all compounds possess accessible cationic and anionic sites separated by an 4.6-5.2 A intercharge distance, (b) the antagonistic nature of the compounds can be explained by the presence of additional binding sites, (c) the correct spatial orientation of the additional binding sites is crucial for GABAA selectivity, and (d) the criteria determining the potency of the antagonist effect are an accurate intercharge distance (greater than 5 A) and the existence of hydrogen-bonding functionalities on one of the additional ring system. The presented pharmacophore accounts also for the inactivity of closely related compounds such as (-)-bicuculline, adlumidine, virosecurinine, allosecurinine, and the 4,6-diphenyl analogue of gabazine.

Structural requirements of Na+-dependent antidopaminergic agents: Tropapride, Piquindone, Zetidoline, and Metoclopramide. Comparison with Na+-independent ligands.

Molecular graphic design coupled with PCILO and crystallographic results have been used to investigate the three-dimensional structure of Tropapride, Piquindone, Zetidoline, and Metoclopramide, four dopamine D-2 receptor antagonists showing Na+-dependent binding. Three putative pharmacophoric elements, a nitrogen lone pair, a phenyl ring and a carbonyl moiety, are similarly oriented in all the Na+-dependent drugs. Conversely, for Na+-independent analogs, the two latter pharmacophoric elements play a subordinate role, but two pi-electron regions are systematically localized on the other side of the molecule: the first is a phenyl group while the second is a carbonyl function as in butyrophenones, a cyano group as in R48455, or a phenyl ring as in diphenylbutylpiperidines or tricyclics. The presence of a benzyl ring on this side in Tropapride might explain its weak extrapyramidal effects.

Stereoelectronic study of zetidoline, a dopamine D2 receptor antagonist.

A combination of experimental and theoretical methods were used to investigate the stereoelectronic structure of zetidoline, a dopamine D2 receptor antagonist showing Na+-dependent binding. The solid-state conformation of zetidoline is characterized by synplanarity (coplanarity of the two rings with the chloro substituent and the carbonyl group on the same side). The side chain in the crystal adopts a folded conformation which places the azetidine nitrogen atom at about 8 A from the center of the aromatic ring. Quantum mechanical calculations indicate the synperiplanar and antiperiplanar conformations of the ring system to be of approximately equal energies. The molecular electrostatic potential of zetidoline in a nearly extended conformation shows a remarkable similarity with that of orthopramides (e.g. metoclopramide) and indolones (e.g. piquindone), i.e. two groups of drugs displaying the same D2 selectivity and Na+-dependent binding. We postulate that the close stereoelectronic similarity between zetidoline, orthopramides, and indolones accounts for their identical mechanism of action in the molecular level.

3- and 5-isoxazolol zwitterions: an ab initio molecular orbital study relating to GABA agonism and antagonism.

The Hartree-Fock ab initio molecular orbital method has been applied to eight compounds: GABA (gamma-amino butyric acid) (1), its partially rigidified analog, TACA (trans-4-aminocrotonic acid) (2), six isoxazolol analogs; muscimol (5-aminomethylisoxazol-3-ol (3), THIP (4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridin-3-ol) (4), THAZ (5,6,7,8-tetrahydro-4H-isoxazolo[4,5-d]azepin-3-ol) (5), isomuscimol (3-aminomethylisoxazol-5-ol) (6), iso-THIP (4,5,6,7-tetrahydroisoxazolo[3,4-c] pyridin-5-ol) (7), and iso-THAZ (5,6,7,8-tetrahydro-4H-isoxazolo[3,4-d]azepin-5-ol) (8). GABA is an endogenous inhibitory transmitter. The four following molecules (2), (3), (4) and (5) are agonist: they bind themselves to the GABA receptors and induce approximately the same effect as GABA. (6) is lightly agonist, presenting a lower affinity. Compounds (7) and (8) are antagonists, giving rise to convulsion. Optimized molecular conformations of GABA (1), muscimol (3) and isomuscimol (6) are discussed. Geometric and electronic parameters showing the presence of intramolecular hydrogen bonds are presented. The permutation of the heteroatoms in the isoxazole ring has no effect on the side-chain orientation explaining maybe the agonist character of isomuscimol, being able to adopt easily and exactly the active conformation. Atomic charge distributions and electronic overlap populations for all compounds have been computed in order to try to understand why their GABAergic activities can be so different. The computed values show that the 3-isoxazolol ring mimics in a good way the carboxylic function of GABA. They also illustrate the larger electronic delocalization within the 5-isoxazolol ring and therefore the resulting antagonist character, except for isomuscimol.

Interaction of K+ ion with the solvated gramicidin A transmembrane channel.

Using Urry's gramicidin A (GA) atomic coordinates and ab into calculations, the interaction energies of a K+ ion with GA are examined. From these energies the values of the fitting parameters are obtained for 6-12-1 atom-atom pair potentials. The potential of the GA channel as experienced by the ion is analyzed in detail. An energy profile of the K+ ion in the GA channel is obtained by analyzing iso-energy maps. Using Monte Carlo simulations, the energy profiles of the K+ ion with the solvated GA channel are analyzed and the hydration structures in the presence of the K+ ion are studied.

Water structure in the Gramicidin A transmembrane channel.

The interaction energy and the structure of water molecules either inside the Gramicidin A transmembrane channel or at its two extremities is examined with the use of iso-energy maps and Monte Carlo simulations. The shape of the channel as experienced by water is analyzed in detail. Variations in the hydration structure due to the presence of a sodium ion placed at several positions along the channel are simulated, analyzed and discussed. Preliminary data on Li+ and K+ interacting with Gramicidin A and the system of water molecules are reported. The Gramicidin A atomic coordinates have been taken from Urry's recent papers (Urry, D.W. (1971) Proc. Natl. Acad. Sci. U.S.A. 68, 672-676 and Urry, D.W., Trapane, T.L. and Prasad, K.U. (1982) Int. J. Quant. Chem. Quant. Biol. Symp. 9, 31-40).