André Michel

A Three Binding Site Hypothesis for the Interaction of Ligands with Monoamine G Protein-coupled Receptors: Implications for Combinatorial Ligand Design

Three-dimensional models of ligand-receptor complexes based on site-directed mutagenesis experiments of the monoamine G protein-coupled receptors reveal the existence of three distinct drug binding sites inside the receptors. Here, we develop this “three-site” hypothesis and outline its implications for the modular design of ligands for monoamine GPCRs. Molecular models of receptor-ligand complexes are built for the 5-HT1A receptor where mutagenesis studies map three spatially distinct binding regions which correspond to the binding sites of the “small, one site-filling” ligands 5-HT, propranolol and 8-OH-DPAT, respectively. The models of the 5-HT1A ligand-receptor complexes provide a frame for the discussion of other ligand-receptor interactions, including α1 and β2 adrenoceptors, D1 and D2 dopamine, and 5-HT1D and 5-HT2A receptors, where mutagenesis and modelling studies also showed occupation of the corresponding three binding locations. All three binding sites are located within the highly conserved seven helix transmembrane domain of the receptor and overlap partially at the prominent Asp residue in TM3 which constitutes the benchmark anchor site for monoamine ligands. The analysis of the sequence similarity, for each binding site, among the monoamine GPCR superfamily shows that the three loci display different degrees of evolutionary conservation. This result suggests different roles for each of the binding sites in intrinsic receptor functions and provides additional insights for the design of ligand functionality and selectivity. The existence of three distinct binding sites is also reflected by the architecture of known high affinity ligands which crosslink two or three “one site-filling” fragments around a basic amino group. Typical ligands reported in the Cipsline/MDDR portfolio illustrate this point despite the occasional difficulty of attributing the individual ligand fragments to a specific receptor site. The database exploration illustrates the binding site promiscuity of some fragments which is particularly evident for symmetrical ligands and which has implications for 3D QSAR methods dependent on alignments. We propose to generate by deconvolution of known ligands three distinct databases of site-specific bioisosters which should provide keystones for the design of novel recomposed monoamine GPCR ligands. The systematic exploration of the “three site” hypothesis should open novel perspectives for the understanding of ligand recognition for this class of therapeutically important receptors.

Multiconformational investigations of polypeptidic structures, using clustering methods and principal components analysis

Abstract Recently, we have applied random-search and energy minimization procedures in the framework of molecular mechanics in order to investigate the structural properties of polypeptides. Consequently, populations of conformers were generated and analyzed. The problem of the identification of conformation domains was addressed using factorial analysis such as clustering methods and principal components analysis. A strategy to apply such techniques to conformational populations is presented here. The results obtained for proline-containing peptides demonstrate the existence of five families of conformations, describing completely the generated population. The homogeneity and variability within families are discussed in terms of their characteristic molecular structures.

Facile synthesis of thioglucose analogs of the anticancer agent etoposide

Abstract Thioglucose-derived analogs of the clinical anticancer agent etoposide have been synthesized via a novel strategy of coupling the sugar and aglycone moieties.

Solid-state stereochemistry of anhydrous (–)-scopolamine hydrobromide

The solid-state structure of anhydrous (Nr,Cα-S)-(–)-scopolamine hydrobromide [(–)-hyoscine], an acetylcholine antagonist, has been determined by single crystal X-ray diffraction analysis. (–)-Scopolamine hydrobromide [anhydrous form] gives crystals belonging to the orthorhombic P212121 space group, and at 298 K: a= 7.348(1), b= 10.482(1), c= 22.867(1)A, V= 1 761.26(1)A3, Z= 4, R(F)= 0.053, and RW(F)= 0.049. The (S)-absolute configuration was determined from the effects of anomalous dispersion of the bromide atom. The N-methyl group exists in an axial, configuration similar to that previously described for the hemihydrate. However, in the anhydrous form the tropate residue exhibits a different conformation from that noted for the hemihydrate. The tropate ester moiety in (Nr,Cα-S)-(–)-scopolamine hydrobromide [anhydrous form] and (Ns,Cα-S)N-butylhyoscinium bromide both exhibit very similar crystalline-state conformations, while that in the hemihydrate form is reasonably similar to (Ns,Cα-S)-(–)-hyoscyamine hydrobromide [(–)-atropine].

A Structural Rationale for the Design of Water Soluble Peptide-Derived Neurokinin-1 Antagonists

Molecular models of a pharmacophore for NK1 neurokinin antagonists and of ligand-receptor complexes for the human NK1 G protein-coupled receptor are presented. The models develop a structural rationale for the discovery of the recently described highly potent peptidomimetic NK1 antagonists S18523 and S19752 which were designed to be water soluble. Water solubility was conferred on these compounds by introduction of an anionic butyl-tetrazole substituent on the scaffold of dipeptide-derived NK1 antagonist analogues. The models provide convincing evidence that the anionic butyl-tetrazole moieties of S18523 and S19752 protrude outside the membrane-spanning domain of the receptor and do not interfere significantly with the core of the antagonist binding site. It is emphasized that this result could only be obtained through the combination of the two modelling approaches. The result suggest a general way to modify the transport properties of the peptidomimetic antagonists without altering the receptor-binding interaction, and it outlines the potential of including the combination of pharmacophore models and crude models of receptor-ligand complexes early in the drug design process.

A proposal for the molecular basis of μ and δ opiate receptor differentiation based on modeling of two types of cyclic enkephalins and a narcotic alkaloid

SummaryThe molecular basis underlying the divergent receptor selectivity of two cyclic opioid peptides Tyr-c[Nδ-d-Orn2-Gly-Phe-Leu-] (c-ORN) and [d-Pen2, l-Cys5]-enkephalinamide (c-PEN) was investigated using a molecular modeling approach. Ring closure and conformational searching procedures were used to determine low-energy cyclic backbone conformers. Following reinsertion of amino acid side chains, the narcotic alkaloid 7α-[(1R)-1-methyl-1-hydroxy-3-phenylpropyl]-6,14-endoethenotetrahydro oripavine (PEO) was used as a flexible template for bimolecular superpositions with each of the determined peptide ring conformers using the coplanarity and cocentricity of the phenolic rings as the minimum constraint. A vector space of PEO, accounting for all possible orientations for the C21-aromatic ring of PEO served as a geometrical locus for the aromatic ring of the Phe4 residue in the opioid peptides. Although a vast number of polypeptide conformations satisfied the criteria of the opiate pharmacophore, they could be grouped into three classes differing in magnitude and sign of the torsional angle values of the tyrosyl side chain. Only class III conformers for both c-ORN and c-PEN, having tyramine dihedral angles χ1 =−150° ± 30° and χ2=−155° ± 20°, had significant structural and conformational properties that were mutually compatible while respecting the PEO vector space. Comparison of these properties in the context of the divergent receptor selectivity of the studied opioid peptides suggests that the increased distortion of the peptide backbone in the closure region of c-PEN together with the pendant β,β-dimethyl group, combine to generate a steric volume which is absent in c-ORN and that may be incompatible with a restrictive topography of the μ receptor. The nature and stereo-chemistry of substituents adjacent to the closure region of the peptides could also modulate receptor selection by interacting with a charged (δ) or neutral (μ) subsite.

Solution- and solid-state stereochemistry of (–)-α-lobeline hydrochloride and hydrobromide, a respiratory-stimulant drug

The solid-state structure of (–)-α-lobeline hydrobromide has been determined by single crystal X-ray diffraction analysis. (–)-α-Lobeline hydrobromide gives crystals belonging to the orthorhombic P212121 space group, and at 298 K: a= 6.0100(3), b= 11.7177(4), c= 28.977(2)A, V= 2040.7(2), Z= 4, R(F)= 0.030, and Rw(F)= 0.022. The (2R,6S,CβS)-absolute configuration was determined from the effects of anomalous dispersion of the bromine atom. The N-methyl group exists in an axial configuration similar to that previously described for the hydrochloride salt. However, in the hydrobromide salt the β-hydroxyphenethyl residue exhibits a different conformation from that noted for the hydrochloride salt. 1H and 13C NMR spectroscopy for the hydrochloride salt dissolved in CD2Cl2 shows axial- and equatorial-N-methyl solution-state diastereoisomers in the ratio ca. 5 : 1, respectively. The major contributors to the time-averaged structures of the salt in D2O and the free base in CDCl3 also show axial N-methyl orientations. Conformational differences for the acetophenonyl and β-hydroxyphenethyl moieties were found in the two N-methyl epimers, as well as in the time-averaged salt (D2O) and free base (CDCl3) structures. The putative bioactive conformation of the nicotine agonist was found to have a different acetophenonyl arm conformation than that found in both crystals.

Development of an ADME and drug–drug interactions knowledge database for the acceleration of drug discovery and development

It is widely recognised that predicting or determining the absorption, distribution, metabolism and excretion (ADME) properties of a compound as early as possible in the drug discovery process helps to prevent costly late-stage failures. Although in recent years high-throughput in vitro absorption distribution metabolism excretion toxicity (ADMET) screens have been implemented, more efficient in silico filters are still highly needed to predict and model the most relevant metabolic and pharmacokinetic end points, and thereby accelerate drug discovery and development. The usefulness of the data generated and published for the chemist, biologist or project manager who ultimately wants to understand and optimise the ADME properties of lead compounds cannot be argued with. Collecting and comparing data is an overwhelming task for the time-pressed scientist. Aureus Pharma provides a uniquely specialised solution for knowledge generation in drug discovery. AurSCOPE® ADME/DDI (drug–drug interaction) is a fully annotated, structured knowledge database containing all the pertinent biological and chemical information on the metabolic properties of drugs. This Aureus knowledge database has proven to be highly useful in designing predictive models and identifying potential drug–drug interactions.

Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin

SummaryThe conformation in dimethylsulfoxide of the somatostatin derivative angiopeptin and of three disulfide-free analogs was estimated by two-dimensional nuclear magnetic resonance spectroscopy at room temperature. The resulting 3D molecular graphics were compared and shown to reflect the observed differences in the inhibition of restenosis after rat aorta balloon injury by these octapeptide inhibitors. Angiopeptin and its active analog 2 displayed a relatively rigid conformation of the cyclic hexapeptide backbone due to the presence of two well-defined hydrogen bonds, further stabilized by a third hydrogen bond outside the ring. No such constraints were detected for the two biologically inactive analogs, which, compared to 2, had a two-atom longer or shorter hexapeptide ring. The well-defined structure of compound 2 may serve as an improved pharmacophore for this new class of drugs.

Solid-state structure of (+)-phendimetrazine bitartarate, an anorexic drug

The anorexic drug (+)-(2S, 3S, 4S)-phendimetrazine-2′R, 3′R)-bitartarate crystallized in the orthorhombic space groupP212121 and at 293 K∶a=7.7710(4),b=13.1379(7),c=15.9913(9) Å,V=1632.6(2) Å3,Z=4,R(F)=0.062, andRw(F)=0.026. A chair conformation 2,3-trans-1,4-oxazine ring with equatorially oriented 2-phenyl,3-methyl, andN-methyl substituents was found as predicted by an earlier reported solid-state CP-MAS13C-NMR investigation of crystalline (±)-phendimetrazine bitartarate. The O-CH2-CH2-N torsion angle of −58.4(6)° in the solid-state agrees nicely with the 56.0(7)° dihedral angle value estimated by1H NMR spectroscopy for the major (equatorialN-methyl) phendimetrazine mesylate species in CD2Cl2 solution. A common solid-state conformational arrangement was found for (+)-phendimetrazine and a series of six other anorexic drugs structurally analogous to (+)-(2S, 3S)-pseudoephedrine. In this arrangement, NCH(Me)CPh has (S)-configuration, there is a (−)-gaucheMe-CH-C-Ph torsion angle, an antiperiplanarN-CH-C-Ph torsion angle, and the phenyl ring approximately eclipses the C-H bond of the attached carbon (e.g., H-C-Cipso-Cortho ca. 4° for 2,3-transphendimetrazine). Nonbonded interactions involving the 3-methyl and the 2-phenyl groups open up the H-C-Cipso-Cortho angle in a series of solid-state structures containing the epimeric (−)-(2R, 3S)-ephedrine moiety (e.g., ca. 45° for molecular mechanics calculated 2,3-cis-phendimetrazine model).