Binding mode of Pyridoclax to myeloid cell leukemia-1 (Mcl-1) revealed by nuclear magnetic resonance spectroscopy, docking and molecular dynamics approaches.

Myeloid cell leukemia-1 (Mcl-1) is an anti-apoptotic member of the Bcl-2 family proteins. Its amplification is one of the most frequent genetic aberrations found in human cancers. Pyridoclax, a promising BH3 mimetic inhibitor, interacts directly with Mcl-1 and induces massive apoptosis at a concentration of 15 µM in combination with anti-Bcl-xL strategies in chemo-resistant ovarian cancer cell lines. In this study, a combined experimental and theoretical approach was used to investigate the binding mode of Pyridoclax to Mcl-1. The representative poses generated from dynamics simulations compared with NMR data revealed: (i) Pyridoclax bound to P1 and P2 pockets of Mcl-1 BH3 binding groove through its styryl and methyl groups establishing mainly hydrophobic contacts, (ii) one of the ending pyridines interacts through electrostatic interaction with K234 side chain, a negatively charged residue present only in this position in Mcl-1. Communicated by Ramaswamy H. Sarma.

Molecular basis of agonist docking in a human GPR103 homology model by site-directed mutagenesis and structure-activity relationship studies.

BACKGROUND AND PURPOSE: The neuropeptide 26RFa and its cognate receptor GPR103 are involved in the control of food intake and bone mineralization. Here, we have tested, experimentally, the predicted ligand-receptor interactions by site-directed mutagenesis of GPR103 and designed point-substituted 26RFa analogues. EXPERIMENTAL APPROACH: Using the X-ray structure of the ß2 -adrenoceptor, a 3-D molecular model of GPR103 has been built. The bioactive C-terminal octapeptide 26RFa(19-26) , KGGFSFRF-NH2 , was docked in this GPR103 model and the ligand-receptor complex was submitted to energy minimization. KEY RESULTS: In the most stable complex, the Phe-Arg-Phe-NH2 part was oriented inside the receptor cavity, whereas the N-terminal Lys residue remained outside. A strong intermolecular interaction was predicted between the Arg(25) residue of 26RFa and the Gln(125) residue located in the third transmembrane helix of GPR103. To confirm this interaction experimentally, we tested the ability of 26RFa and Arg-modified 26RFa analogues to activate the wild-type and the Q125A mutant receptors transiently expressed in CHO cells. 26RFa (10(-6) M) enhanced [Ca(2+) ]i in wild-type GPR103-transfected cells, but failed to increase [Ca(2+) ]i in Q125A mutant receptor-expressing cells. Moreover, asymmetric dimethylation of the side chain of arginine led to a 26RFa analogue, [ADMA(25) ]26RFa(20-26) , that was unable to activate the wild-type GPR103, but antagonized 26RFa-evoked [Ca(2+) ]i increase. CONCLUSION AND IMPLICATIONS: Altogether, these data provide strong evidence for a functional interaction between the Arg(25) residue of 26RFa and the Gln(125) residue of GPR103 upon ligand-receptor activation, which can be exploited for the rational design of potent GPR103 agonists and antagonists.

The maximum common substructure as a molecular depiction in a supervised classification context: experiments in quantitative structure/biodegradability relationships.

The maximum common structure between two molecules (MCS) induces a similarity that enables one to group compounds sharing the same pattern. This text relates a study based on such a structural depiction in a context of quantitative structure/biodegradability relationships (QSBR). The similarity indices are based exclusively on the MCS. First, the results of statistical tests prove that these indices significantly group compounds of similar activity together. These first conclusions enable the elaboration of classification models using those structural similarities. In a second part, a population of classifiers relying on the maximum common structure and the k-nearest-neighbor algorithm is explored. Finally, a thorough examination of the best models is conducted.

Study of substrate specificity of human aromatase by site directed mutagenesis.

Human aromatase is responsible for estrogen biosynthesis and is implicated, in particular, in reproduction and estrogen-dependent tumor proliferation. The molecular structure model is largely derived from the X-ray structure of bacterial cytochromes sharing only 15-20% identities with hP-450arom. In the present study, site directed mutagenesis experiments were performed to examine the role of K119, C124, I125, K130, E302, F320, D309, H475, D476, S470, I471 and I474 of aromatase in catalysis and for substrate binding. The catalytic properties of mutants, transfected in 293 cells, were evaluated using androstenedione, testosterone or nor-testosterone as substrates. In addition, inhibition profiles for these mutants with indane or indolizinone derivatives were obtained. Our results, together with computer modeling, show that catalytic properties of mutants vary in accordance with the substrate used, suggesting possible differences in substrates positioning within the active site. In this respect, importance of residues H475, D476 and K130 was discussed. These results allow us to hypothesize that E302 could be involved in the aromatization mechanism with nor-androgens, whereas D309 remains involved in androgen aromatization. This study highlights the flexibility of the substrate-enzyme complex conformation, and thus sheds new light on residues that may be responsible for substrate specificity between species or aromatase isoforms.

Prediction of the Daphnia acute toxicity from heterogeneous data.

Two descriptors (log(P(ow)), 'hardness') were selected to predict the Daphnia acute toxicity of a training set of heterogeneous chemical compounds. The data were extracted from 523 notification files about new chemicals stored at the French Department of Environment. The selection of the descriptors was carried out using a statistical method coupling ordinary least square (OLS) regression and genetic algorithm (GA). The validity limits for the final equation are discussed by comparing the actual and predicted activities of several compounds. The study points out the interest of the 'hardness' parameter for quantitative structure-activity relationships (QSAR) with a heterogeneous data set.

Association of two 3D QSAR analyses. application to the study of partial agonist serotonin-3 ligands.

CATALYST and COMFA, two software packages for 3D QSAR studies, were associated to correlate the three-dimensional structures of 75 serotonin 5-HT3 ligands to their biological affinities. The conformational analysis and the influence of chemical function-based alignments (the basis of this association) on final results are discussed in this publication. These two analyses allow for precisely quantitating the weights of significant chemical groups or functions on the biological affinities.

First tricyclic oximino derivatives as 5-HT3 ligands.

The design and synthesis of a new type of 5-HT3 ligand with subnanomolar affinity are described. The O-dialkylaminoethyloximinothienopyrrolizine structure was deduced from molecular modeling studies by replacement of an amidine moiety by an oximino one.

New aromatase inhibitors. Synthesis and biological activity of aryl-substituted pyrrolizine and indolizine derivatives.

We report herein the design and the synthesis of some aryl-substituted pyrrolizine and indolizine derivatives, on the basis of a hypothetical pharmacophore structure designed to fit the catalytic site of the human cytochrome P450 aromatase. The in vitro biological evaluation of these compounds allowed us to point out two new potent non-steroidal aromatase inhibitors, MR 20494 and MR 20492, with IC50 values in the range of 0.1 microM.

MR 20492 and MR 20494: two indolizinone derivatives that strongly inhibit human aromatase.

In this study, we describe the synthesis of a new family of indolizinone derivatives designed to fit an extrahydrophobic pocket within the active site of aromatase and to strongly inhibit human aromatase. This could help improve the specificity of the inhibitors. Equine aromatase, very well characterized biochemically, is used as a comparative model. Indeed, in a previous comparison between both human and equine aromatases, we described the importance of the interaction between the inhibitor and this pocket for the indane derivative MR 20814. MR 20492 and MR 20494 are more potent inhibitors of human aromatase (Ki/Km: 1.0+/-0.3 and 0.5+/-0.3, respectively). The Ki/Km for MR 20494 is slightly higher than that obtained for fadrozole (0.1+/-0.0) and Ki/Km for both indolizinone derivatives are lower than those obtained for 4-hydroxyandrostenedione (1.9+/-0.8) and MR 20814 (8.1+/-.7). These new compounds are not enzyme inactivators. Moreover, as indicated by the higher Ki/Km values obtained with equine enzyme (9.0+/-0.6 and 6.1+/-1.6 for MR 20492 and MR 20494, respectively), both human and equine aromatase active sites appear to be structurally different. Difference absorption spectra study (350-500 nm) revealed that MR20492 and MR20494 were characterized by a combination of type-I and -II spectra with both enzymes. This result could be due to the isomerization of the molecule in polar solvent (Z and E forms). The evaluation of these new molecules, as well as 4-hydroxyandrostenedione and fadrozole, on aromatase activity in transfected 293 cell cultures evidenced a strong inhibition (IC50: 0.20+/-0.03 microM, 0.20+/-0.02 microM and 0.50+/-0.40 microM for MR 20494, fadrozole and 4-OHA, respectively) except for MR 20492 (3.9+/-0.9 microM) and MR 20814 (10.5+/-0.6 microM). These results proved that these molecules formed part of a promising family of potent inhibitors and that they penetrate 293 cells, without evidencing any cytotoxicity in Hela cells with MTT assay. This is thus encouraging for the development of new drugs for the treatment of estrogen-dependent cancers, these molecules also constitute new tools for understanding the aromatase active site.

Prediction of the fish acute toxicity from heterogeneous data coming from notification files.

Four descriptors (Molecular weight, log(Pow), hardness and free energy of solvation) were selected to predict, on a training set of heterogeneous chemical compounds, the fish acute toxicity. The data were extracted from 523 notification files of new chemicals stored at the French Department of the Environment. The selection of the descriptors was carried out by using a statistical technique coupling OLS regression and genetic algorithm. The limits of validity for the final equation are discussed by comparing the actual and predicted activities on several compounds.

Applicability of CATALYST in ecotoxicology, a new promising tool for 3D-QSAR: study of chlorophenols.

With the aim of applying recent quantitative structure-activity relationship (QSAR) descriptors coming from the pharmaceutical sciences to the modelization of ecotoxicity data, this work deals with the establishment of 3D-QSAR on chlorophenols by using for the first time in this field the recent CATALYST software. The training set has been intentionally chosen simply because of its homogeneous character and the abundance of reliable experimental values. Among 69 data sets collected in the literature on these chemicals, 9 were selected to have fulfilled CATALYST simulation conditions. The principle of CATALYST is briefly described. The different investigations have led to nine 3D-QSAR called "hypotheses," meeting the criteria of high statistical significance attested by costs and correlation coefficient values. The ecotoxicity values calculated from the 9 models established in this study. Analysis of the graphical representations of hypotheses led to hypotheses about the toxicity mechanisms. A comparison is finally made between the CATALYST models and those previously derived by other modeling methods.

Definition of a pharmacophore for partial agonists of serotonin 5-HT3 receptors.

A definition of a partial agonists serotonin 5-HT3 pharmacophore was carried out by considering a three-dimensional model which correlates the chemical structures of series of piperazinopyrrolothienopyrazines, piperazinopyridopyrrolopyrazines, piperazinopyrroloquinolaxines, piperazinopyridopyrroloquinoxalines, aminoalkyloximinopyrroloindoles, aminoalkyloximinothienopyrrolizines, and aminoalkyloximinopyrrolizines with the biological affinities. The model is formed by five features corresponding to two hydrogen bond acceptors, one aromatic ring, one hydrophobic group, and one positive ionizable site (quaternary ammonium ions). The nature of the features and the distances between them explain the partial agonist activities of these compounds.

Design and synthesis of a new type of non steroidal human aromatase inhibitors.

The structure-activity relationship study of one of recently described aromatase inhibitors, compound 1 (MR20814), allowed us to design some related derivatives as potential new inhibitors. Among those we synthesized, chlorophenylpyridylmethylenetetrahydroindolizinone 5 (MR20492) exhibited in vitro a ten-fold higher inhibition of the enzyme (IC50 = 0.2 +/- 0.0 microM and Ki = 10.3 +/- 3.3 nM).

Applicability of the free energies of solvation for the prediction of ecotoxicity: study of chlorophenols.

Free energies of solvation of chlorophenols were calculated in two solvents: water and n-hexadecane from the AMSOL program. These free energies of solvation are the sum of two terms: polarization free energies (delta GENP) and cavity, dispersion, solvent structure free energies (G degree CDS). This study shows, in the case of chlorophenols, that a direct relation exists between one of the two components for the calculation of free energy (G degree CDS) in water and n-hexadecane, and the ecotoxicity values for five biological systems. We point out the interest of using these new descriptors in QSAR study.

Applicability of CoMFA in ecotoxicology: a critical study on chlorophenols.

Comparative molecular field analysis (CoMFA) is used to relate ecotoxicological data with steric and electrostatic fields of chemicals forming an intentionally selected homogeneous set, the chlorophenols, for which reliable data are abundant in literature. Among these data, those concerning 16 different biological systems were selected, leading to predictive CoMFA QSAR in 14 of the cases. This is attested by cross-validation and bootstrapping, which also authorize the prediction of the chlorophenols toxicity values, when they are missing. The quality of obtained CoMFA models and the applicability of the method are discussed. The results are very promising, and they encourage further investigation into CoMFA in ecotoxicology.

Comparative molecular field analysis of CCK-A antagonists using field-fit as an alignment technique. A convenient guide to design new CCK-A ligands.

Comparative molecular field analysis (CoMFA) has been used as a three-dimensional quantitative structure-activity relationship (QSAR) method to correlate the affinities of several antagonists towards CCK-A receptors with their steric and electrostatic fields. In this publication, we describe, for the first time, a field-fit operation as an alignment technique. These results could serve as a guide for the design of new non-peptide antagonists.