M. Cristina Menziani

Theoretical investigation of substrate specificity for cytochromes P450 IA2, P450 IID6 and P450 IIIA4.

Three-dimensional models of the cytochromes P450 IA2, P450 IID6 and P450 IIIA4 were built by means of comparative modeling using the X-ray crystallographic structures of P450 CAM, P450 BM-3, P450 TERP and P450 ERYF as templates. The three cytochromes were analyzed both in their intrinsic structural features and in their interaction properties with fifty specific and non-specific substrates. Substrate/enzyme complexes were obtained by means of both automated rigid and flexible body docking. The comparative analysis of the three cytochromes and the selected substrates, in their free and bound forms, allowed for the building of semi-quantitative models of substrate specificity based on both molecular and intermolecular interaction descriptors. The results of this study provide new insights into the molecular determinants of substrate specificity for the three different eukaryotic P450 isozymes and constitute a useful tool for predicting the specificity of new compounds.

Novel Potent 5-HT3 Receptor Ligands Based on the Pyrrolidone Structure: Synthesis, Biological Evaluation, and Computational Rationalization of the Ligand–Receptor Interaction Modalities

Novel conformationally constrained derivatives of classical 5-HT(3) receptor antagonists were designed and synthesized with the aim of probing the central 5-HT(3) receptor recognition site in a systematic way. The newly-synthesized compounds were tested for their potential ability to inhibit [(3)H]granisetron specific binding to 5-HT(3) receptor in rat cortical membranes. These studies revealed subnanomolar affinity in some of the compounds under study. The most potent ligand in this series was found to be quinuclidine derivative (S)-7i, which showed an affinity comparable with that of the reference ligand granisetron. The potential 5-HT(3) agonist/antagonist activity of some selected compounds was assessed in vitro on the 5-HT(3) receptor-dependent [(14)C]guanidinium uptake in NG 108-15 cells. Both of the tropane derivatives tested in this functional assay (7a and 9a) showed antagonist properties, while the quinuclidine derivatives studied [the enantiomers of compounds 7i, 8g, and 9g, and compound (R)-8h] showed a full range of intrinsic efficacies. Therefore, the functional behavior of these 5-HT(3) receptor ligands appears to be affected by the structural features of both the azabicyclo moiety and the heteroaromatic portion. In agreement with the data obtained on NG 108-15 cells, investigations on the 5-HT(3) receptor-dependent Bezold-Jarisch reflex in urethane-anaesthetized rats confirmed the 5-HT(3) receptor antagonist properties of compounds 7a and (S)-7i showing for these compounds ID(50) values of 2.8 and 181 microg/kg, respectively. Finally, compounds 7a, (S)-7i and 9a (at the doses of 0.01, 1.0, and 0.01 mg/kg ip, respectively) prevented scopolamine-induced amnesia in the mouse passive avoidance test suggestive of a potential usefulness in cognitive disorders for these compounds. Qualitative and quantitative structure-affinity relationship studies were carried out by means of theoretical descriptors derived on a single structure and ad-hoc defined size and shape descriptors (indirect approach). The results showed to be useful in capturing information relevant to ligand-receptor interaction. Additional information derived by the analysis of the energy minimized 3-D structures of the ligand-receptor complexes (direct approach) suggested interesting mechanistic and methodological considerations on the binding mode multiplicity at the 5-HT(3) receptors and on the degree of tolerance allowed in the alignment of molecules for the indirect approach, respectively.

Insights into MAPK p38α DFG flip mechanism by accelerated molecular dynamics

The DFG motif at the beginning of the activation loop of the MAPK p38alpha undergoes a local structural reorganization upon binding of allosteric type-II and type-III inhibitors, which causes the residue F169 to move from a buried conformation (defined as DFG-in) to a solvent exposed conformation (defined as DFG-out). Although both experimental and computer simulation studies had been performed with the aim of unveiling the details of the DFG-in to DFG-out transition, the molecular mechanism is still far from being unequivocally depicted. Here, the accelerated molecular dynamics (AMD) technique has been applied to model the active loop flexibility of p38alpha and sample special protein conformations which can be accessible only in some conditions or time periods. Starting from the assumption of an experimentally known initial and final state of the protein, the study allowed the description of the interaction network and the structural intermediates which lead the protein to change its loop conformation and active site accessibility. Besides a few important hydrogen bond interactions, a primary role seems to be played by cation-pi interactions, involving the DFG-loop residue F(169), which participate in the stabilization of an intermediate conformation and in its consequent transition to the DFG-out conformation. From this study, insights which may prove useful for inhibitor design and/or site directed mutagenesis studies are derived.

The Interactions of the 5-HT3 Receptor with Arylpiperazine, Tropane, and Quinuclidine Ligands

The serotonin 5-HT(3) receptor subtype is unique among the receptors for this neurotransmitter because it has been demonstrated to be a ligand-gated ion channel capable of mediating rapid intercellular communication. This review covers the authors work performed during more than a decade in the development of 5-HT(3) receptor ligands belonging to the classes of arylpiperazines, tropanes, and quinuclidine derivatives. The discussion is focused mainly on what the authors have learned about the interaction of these structurally different ligands with their receptor and shows the way their ideas evolved along with the progress of the project. Furthermore, a summary of the most significant structure-affinity relationships, derived from the original work, is reported to support the discussion.

An ab initio parameterized interatomic force field for hydroxyapatite

A classical interatomic force field for hydroxyapatite has been parameterized from periodic ab initio calculations carried out on the hexagonal structure (space group P63). The GULP program has been used for fitting geometry and phonon frequencies computed with the CRYSTAL06 program using the B3LYP hybrid functional and Gaussian-type basis set of polarized double zeta quality. Polarization effects and covalent bonding have been included through the shell-ion model potential. Excellent agreement has been found in reproducing structural features, lattice dynamics, the OH stretching vibrations and relative phase stabilities between the monoclinic structure (space group P21/b) and the hexagonal one. Transferability from hydroxyapatite to other calcium phosphates has also been demonstrated.

Theoretical quantitative structure-activity relationship analysis of congeneric and non-congeneric α1-adrenoceptor antagonists: a chemometric study

Abstract Molecular orbital calculations (AM1) and molecular modelling procedures ( quanta/charm m) have been performed both on a congeneric (prazosin analogs) and on a non-congeneric series of α1-adrenergic antagonists. A large variety of theoretical molecular descriptors has been obtained and compared by principal component analysis (PCA). The generating optimal least squares estimations (GOLPE) procedure has been used to derive quantitative structure-activity relationships (QSARs). Good predictive QSAR models with a restricted pool of informative theoretical descriptors have been obtained. These results support the generality of the theoretical QSAR approach proposed; in fact both congeneric and non-congeneric molecular series were satisfactorily modeled. Moreover, the high and well-defined physical information content encoded in the theoretical descriptors considered allows the rationalization of the structural heterogeneity of the molecules examined as differences in the complementary intermolecular interactions of the studied ligands towards their common receptor.

Theoretical quantitative structure-activity relationship analysis on three dimensional models of ligand-m1 muscarinic receptor complexes.

The heuristic-direct QSAR (quantitative structure-activity relationships) approach has been applied to a series of 34 muscarinic receptor ligands, including antagonists, weak partial agonists, partial agonists and full agonists, interacting with the human ml-muscarinic receptor subtype. The first step of this procedure consists of the computer-aided 3D-model building of the receptor. The second step involves docking simulations with selected ligands, maximizing the complementarity between ligand and receptor. In the third step, a detailed and extensive correlation analysis between the computed interaction energies, their components and the experimental pharmacological affinity and action is accomplished in order to evaluate the consistency of the QSAR model proposed and to provide a quantitative tool for comparisons among the different complexes considered. In this context, good linear correlations have been obtained between ad hoc theoretical intermolecular interaction descriptors and the pharmacological action, which allow one to classify quantitatively and predict the pharmacological action of new ligands. Finally, according to the ml-receptor model proposed, it has been possible to speculate on the amino acid residues which are mainly involved in the interaction with the ligands, and on the nature of the prevailing intermolecular interactions which are responsible for the different behaviour of antagonists, weak partial agonists, partial agonists and full agonists.

Molecular modelling and quantitative structure- activity relationship analysis using theoretical descriptors of 1,4-benzodioxan (WB-4101) related compounds α1-adrenergic antagonists

Abstract Quantitative structure-activity relationship analysis using theoretical molecular descriptors was done on a set of 30 1,4-benzodioxan (WB-4101) related compounds which are α 1 -adrenoceptor antagonists. The results obtained confirm quantitatively and in terms of reactivity and molecular shape descriptors, the results of previous qualitative structure-activity relationship studies. It was found that the protonated amine function plays a crucial role in the potency of the α 1 -adrenoceptor antagonism due to a charge reinforced hydrogen bond with a primary nucleophilic site of the receptor. Furthermore, the more electrophilic (high SN1 lumo values) the NH 2 + group, the stronger the charge reinforced hydrogen bond with the receptor and the higher the blocking activity. It was also found that the three-dimen-sional shape of the antagonists is more similar to the shape of the most active reference molecule (WB-4101) the more potent antagonists are. Finally, the reactivity ( E lumo and the ad hoc shape ( V D (norm)) descriptors were used to obtain a bilinear equation which accounts for about 77% of the total variance in the pharmacological data.

Conformational analysis, molecular modeling and quantitative structure-activity relationship studies of 2,4-diamino-6,7-dimethoxy-2-substituted quinazoline α1-adrenergic antagonists

Abstract Conformational analysis (AM1), modeling of the molecular shape (spquanta)3.0) and quantitative structure-activity relationship analysis were done on a set of 16 2,4-diamino-6,7-dimethoxy-2-substituted quinazoline α1-adrenoceptor antagonists (prazosin analogs). The results obtained show that the 2-substituents of the analogs considered are quite flexible. Furthermore, they suggest that, once the electronic requirements of the common quinazoline moiety are satisfied, the binding affinities are modulated by the molecular shape of the quinazoline 2-substituent, through the optimization of both dispersive and steric interactions and the hydrophobic contribution.

Theoretical versus empirical molecular descriptors in monosubstituted benzenes: A chemometric study

Abstract Cocchi, M., Menziani, M.C., De Benedetti, P.G. and Cruciani, G., 1992. Theoretical versus empirical molecular descriptors in monosubstituted benzenes. A chemometric study. Chemometrics and Intelligent Laboratory Systems, 14: 209–224. Quantum chemical methods and molecular modeling techniques allow the definition of a large number of molecular and local quantities characterizing the reactivity, the shape and the binding properties of a molecule as well as of molecular fragments and substituents. This study is focused on a systematic comparison of the theoretical molecular descriptors with both empirical (Hammetts and Tafts substituent constants, hydrophobic parameter, Verloops steric parameters etc.) and experimental (substituent induced chemical shifts, molecular weight and molecular refractivity) descriptors. Fifty selected monosubstituted benzenes, including some charged substituents have been computed in the AM1 framework. Several theoretical descriptors have been extracted from the AM1 electronic wavefunction as well as molecular modeling techniques and they have been analyzed by principal component analysis and the partial least squares method. The results obtained are consistent with previous principal component studies concerning empirical descriptors, and highlight the interdependencies among theoretical and empirical molecular descriptors.