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

Quantitative prediction of antitarget interaction profiles for chemical compounds

The evaluation of possible interactions between chemical compounds and antitarget proteins is an important task of the research and development process. Here, we describe the development and validation of QSAR models for the prediction of antitarget end-points, created on the basis of multilevel and quantitative neighborhoods of atom descriptors and self-consistent regression. Data on 4000 chemical compounds interacting with 18 antitarget proteins (13 receptors, 2 enzymes, and 3 transporters) were used to model 32 sets of end-points (IC(50), K(i), and K(act)). Each set was randomly divided into training and test sets in a ratio of 80% to 20%, respectively. The test sets were used for external validation of QSAR models created on the basis of the training sets. The coverage of prediction for all test sets exceeded 95%, and for half of the test sets, it was 100%. The accuracy of prediction for 29 of the end-points, based on the external test sets, was typically in the range of R(2)(test) = 0.6-0.9; three tests sets had lower R(2)(test) values, specifically 0.55-0.6. The proposed approach showed a reasonable accuracy of prediction for 91% of the antitarget end-points and high coverage for all external test sets. On the basis of the created models, we have developed a freely available online service for in silico prediction of 32 antitarget end-points: http://www.pharmaexpert.ru/GUSAR/antitargets.html.

Design, synthesis, and biological characterization of bivalent 1-methyl-1,2,5,6-tetrahydropyridyl-1,2,5-thiadiazole derivatives as selective muscarinic agonists

Selective muscarinic agonists could be useful in the treatment of neurological disorders such as Alzheimer's disease, schizophrenia, and chronic pain. Many muscarinic agonists have been developed, yet most exhibit at best limited functional selectivity for a given receptor subtype perhaps because of the high degree of sequence homology within the putative binding site, which appears to be buried within the transmembrane domains. Bivalent compounds containing essentially two agonist pharmacophores within the same molecule were synthesized and tested for receptor binding affinity and muscarinic agonist activity. A series of bis-1,2,5-thiadiazole derivatives of 1,2,5,6-tetrahydropyridine linked by an alkyloxy moiety exhibited very high affinity (K(i) < 1 nM) and strong agonist activity. The degree of activity depended on the length of the linking alkyl group, which could be replaced by a poly(ethylene glycol) moiety, resulting in improved water solubility, binding affinity, and agonist potency.

The solid-state structures of (-)-scopolamine free base, (-)-scopolamine methobromide, (-)-scopolamine hydrobromide trihydrate, and of the pseudopolymorphic forms of (-)-scopolamine hydrochloride anhydrate and 1.66hydrate

(-)-Scopolamine hydrochloride anhydrate gives crystals belonging to the orthorhombic space group P212121 and at 293(2) K: a = 7.097(2), b = 10.686(2), c = 22.623(2) Å, V = 1715.7(6) Å3, Z = 4, R(F) = 0.039, and Rw(F) = 0.053. (-)-Scopolamine hydrochloride 1.66hydrate yields crystals belonging to the tetragonal space group P43212 and at 293(2) K: a = b = 11.843(6), c = 26.211(4) Å, V = 3676(3) Å3, Z = 8, R(F) = 0.047, and Rw(F2) = 0.135. (-)-Scopolamine methobromide affords crystals belonging to the orthorhombic space group P212121 and at 293(2) K: a = 7.0403(8), b = 10.926(2), c = 23.364(5) Å, V = 1797.2(6) Å3, Z = 4, R(F) = 0.039, and Rw(F) = 0.052. The two hydrochloride pseudopolymorphs were isostructural to the corresponding two hydrobromide analogues. Both hydrohalide hydrated crystals have a water molecule occupying a general position of symmetry, and another water molecule occupying a special position of C2-rotation symmetry. The hydrated hydrochloride salt also had an additional 0.322(17) partial occupancy water molecule (absent in the hydrobromide sesquihydrate) occupying another special position of C2-rotation symmetry, i.e., the extra water molecule occupied the special position in statistically ca. one-third of the unit-cells to give a total hydrate stoichiometry of 1.66 molecules of water. While the two hydrohalide anhydrates exhibited extended tropate ester conformations (phenyl-ring antiperiplanar to oxirane moiety) vs. compact conformations (phenyl-ring near the scopine underside) for the two hydrated hydrohalides, all four displayed other common structural features: axial N-methyl stereochemistry, antiperiplanar methylol oxygen/aromatic C(ipso) relationships, and phenyl-ring eclipsing of the C(alpha)-H bond. The CPMAS 13C NMR spectrum of (-)-scopolamine hydrobromide "trihydrate" shows it to be a conglomerate of (-)-scopolamine hydrobromide sesquihydrate plus two or more hydrated species (three ca. equal intensity carbonyl signals at 5.0 kHz spin-rate). High-speed rotor spinning (e.g., ca. 10 kHz and higher) causes a temperature-induced phase-transition to yield only the sesquihydrate form. The same transformation was noted with a 18 K rotor-temperature increase and an invariant 5.0 kHz spin-rate. The sesquihydrate spectrum remained after spin-rate decrease to 5.0 kHz, but the three component mixture 5.0 kHz spectrum was regenerated after three weeks sample storage within the capped rotor. The (-)-scopolamine free base crystalline melt CPMAS spectrum also shows a mixture of at least three hydrated species.Key words: stereochemistry, X-ray crystallography, solid-state NMR, CPMAS, anticholinergic.

Synthesis and binding mode of heterocyclic analogues of suramin inhibiting the human basic fibroblast growth factor

The design, synthesis, and biological evaluation of a series of pyrrole and pyrazole congeners 2 of suramin, directed toward the development and identification of new ligands that complex the human fibroblast growth factor (bFGF), thereby inhibiting tumor-promoted angiogenesis, is reported. Compounds 2 were evaluated for their ability to inhibit binding of bFGF to its receptor, in vivo bFGF-induced angiogenesis, and neovascularization of the chorioallantoic membrane in comparison with suramin. These assays showed that ligands 2 exhibit moderate to good activity, comparable to that of suramin, and are less toxic than suramin itself. In this study, affinity data of ligands in combination with the crystal structure of bFGF were used to explain structure-affinity relationships and to gain an insight into the possible mode of ligand-protein interaction. Due to the lack of experimental structural data on the ligand-bFGF complexes, molecular mechanics techniques were used to obtain putative bioactive conformations and to generate docked complexes with the three-dimensional structure of bFGF. These experiments led to suggest that compounds 2 give rise to 1:1 complexes with bFGF through an unprecedented, bidentate attachment of their naphthylsulfonate groups to two main domains, commonly referred to as the heparin binding site and the receptor binding site, on bFGF, thus preventing the interaction of the growth factor with its receptor.

Pentatomic cyclic antagonists and muscarinic receptors: a 30-year review

This work is a sequel to and completes the review, that recently appeared in this journal, of pentatomic cyclic muscarinic agonists. It reports the results of structure-activity relationship (SAR) studies of pentatomic cyclic antagonists on muscarinic receptors and compares these results with some recent advances in molecular biology and quantitative structure-activity relationship (QSAR) studies.

Modelling of the binding site of the human m1 muscarinic receptor: experimental validation and refinement

Our model of the human m1 muscarinic receptor has been refined on the basis of the recently published projection map of bovine rhodopsin. The refined model has a slightly different helix arrangement, which reveals the presence of an extra hydrophobic pocket located between helices 3, 4 and 5. The interaction of series of agonists and antagonists with the m1 muscarinic receptor has been studied experimentally by site-directed mutagenesis. In order to account for the observed results, three-dimensional models of m1 ligands docked in the target receptor are proposed. Qualitatively, the obtained models are in good agreement with the experimental observations. Agonists and partial agonists have a relatively small size. They can bind to the same region of the receptor using, however, different anchoring receptor residues. Antagonists are usually larger molecules, filling almost completely the same pocket as agonists. They can usually produce much stronger interactions with aromatic residues. Experimental data combined with molecular modelling studies highlight how subtle and diverse receptor-ligand interactions could be.

Alpha 1-adrenoceptor subtype selectivity: molecular modelling and theoretical quantitative structure-affinity relationships

This study constitutes a preliminary rationalization, at the molecular level, of antagonist selectivity towards the three cloned alpha 1-adrenergic receptor (alpha 1-AR) subtypes. Molecular dynamics simulations allowed a structural/dynamics analysis of the seven alpha-helix-bundle models of the bovine alpha 1a-, hamster alpha 1b-, and rat alpha 1d-AR subtypes. The results showed that the transmembrane domains of these subtypes have different dynamic behaviours and different topographies of the binding sites, which are mainly constituted by conserved residues. In particular, the alpha 1a-AR binding site is more flexible and topographically different with respect to the other two subtypes. The results of the theoretical structural/dynamics analysis of the isolated receptors are consistent with the binding affinities of the 16 antagonists tested towards the three cloned alpha 1-AR subtypes. Moreover, the theoretical quantitative structure-affinity relationships obtained from the antagonist-receptor interaction models further corroborates the hypothesis that selectivity towards one preferential subtype is mainly modulated by receptor and/or ligand distortion energies. In other words, subtype selectivity seems to be mainly guided by the dynamic complementarity (induced fit) between ligand and receptor. On the basis of the quantitative models presented it is possible to predict both affinities and selectivities of putative alpha 1-AR ligands as well as to estimate the theoretical alpha 1-AR subtype affinities and selectivities of existing antagonists.

Molecular dynamics simulations of m3-muscarinic receptor activation and QSAR analysis

Molecular dynamics simulations of the rat m3-muscarinic seven-helix-bundle receptor models were performed on the free, agonist-bound and antagonist-bound forms. A comparative structural/dynamics analysis was performed in order to explain the perturbations induced by the functionally different ligands when binding to their target receptor. Theoretical quantitative structure-activity relationship models were developed; a good correlation was obtained between the interaction energies of the minimized average ligand-receptor complexes and the pharmacological affinities of the considered ligands. The consistency obtained between the structural rearrangement of the transmembrane seven-helix-bundle models considered and the experimental pharmacological efficacies and affinities of the ligands constitutes an important validation of the 3-D models proposed and allows the inference of the mechanism of ligand-induced or mutation-induced receptor activation at the molecular level.