Validation of experimental charge densities: refinement of the macrolide antibiotic roxithromycin.

Multipole refinements of larger organic molecules have so far been limited to a few exceptional cases. We report an investigation of the detailed experimental electron-density distribution (EDD) of roxithromycin, a macrolide antibiotic consisting of 134 atoms. Although the experimental multipole refinement on high-resolution synchrotron data converged smoothly, validation of the electron density by calculation of an `experiment minus invariom' difference density revealed conformational disorder of the H atoms. Hydrogen disorder is shown to affect the EDD, the electrostatic potential and atomic properties as defined by Bader's quantum theory of atoms in molecules. A procedure to obtain the electron density distribution in the presence of disorder is proposed.

The invariom model and its application: refinement of D,L-serine at different temperatures and resolution.

Three X-ray data sets of the same D,L-serine crystal were measured at temperatures of 298, 100 and 20 K. These data were then evaluated using invarioms and the Hansen & Coppens aspherical-atom model. Multipole populations for invarioms, which are pseudoatoms that remain approximately invariant in an intermolecular transfer, were theoretically predicted using different density functional theorem (DFT) basis sets. The invariom parameters were kept fixed and positional and thermal parameters were refined to compare the fitting against the multi-temperature data at different resolutions. The deconvolution of thermal motion and electron density with respect to data resolution was studied by application of the Hirshfeld test. Above a resolution of sin theta/lambda approximately 0.55 A-1, or d approximately 0.9 A, this test was fulfilled. When the Hirshfeld test is fulfilled, a successful modeling of the aspherical electron density with invarioms is achieved, which was proven by Fourier methods. Molecular geometry improves, especially for H atoms, when using the invariom method compared to the independent-atom model, as a comparison with neutron data shows. Based on this example, the general applicability of the invariom concept to organic molecules is proven and the aspherical density modeling of a larger biomacromolecule is within reach.

Synthesis, absolute configuration, stereoselectivity, and receptor selectivity of (alpha R, beta S)-alpha,beta-dimethylhistamine, a novel high potent histamine H3 receptor agonist.

Depending on the selected synthetic pathway, structural variations of the neurotransmitter histamine led to mixtures of alpha,beta-dimethylhistamines as well as to the corresponding pure optical isomers. One of these isomers, namely (alpha R,beta S)-alpha,beta-dimethylhistamine, proved to be a highly potent H3 receptor agonist with exceptional receptor selectivity. The absolute configuration of the compound was determined by X-ray structure analysis of its dihydrobromide using the anomalous dispersion of bromine. The optical purity of both enantiomers of erythro-alpha,beta-dimethylhistamine was checked by 1HNMR investigations after acylation of the amines with (R)-2-methoxy-2-phenylacetyl chloride. As expected H3 receptors distinguish in a very strong way between the title compound and its alpha S,beta R-configured enantiomer. The agonistic potency of the latter is 2 orders of magnitude lower than the potency of (alpha R,beta S)-alpha,beta-dimethylhistamine.

Guanidine derivatives as combined thromboxane A2 receptor antagonists and synthase inhibitors.

A new series of omega-disubstituted alkenoic acid derivatives derived from samixogrel 5 were designed and synthesized as combined thromboxane A2 receptor antagonists/thromboxane A2 synthase inhibitors with improved solubility and reduced protein binding compared to 5. Hexenoic acid derivatives with a 3-pyridyl group and 3-(2-cyano-3-alkyl-guanidino)phenyl substituent were found to be optimal with regard to this dual mode of action. The most potent compound, E-6-(3-(2-cyano-3-tert-butyl-guanidino)phenyl)-6-(3-pyridyl)hex-5-eno ic acid, "terbogrel" 32 inhibits the thromboxane A2 synthase in human gel-filtered platelets with an IC50 value of 4.0 +/- 0.5 nM (n = 4). Radioligand binding studies with 3H-SQ 29,548 revealed that 32 blocks the thromboxane A2/endoperoxide receptor on washed human platelets with an IC50 of 11 +/- 6 nM (n = 2) and with an IC50 of 38 +/- 1 nM (n = 15) in platelet-rich plasma. Terbogrel inhibits the collagen-induced platelet aggregation in human platelet-rich plasma and whole blood with an IC50 of 310 +/- 18 nM (n = 8) and 52 +/- 20 nM (n = 6), respectively. This was shown to translate into a potent antithrombotic effect in vivo as demonstrated in studies using a model of arterial thrombosis in rabbits (ED50 = 0.19 +/- 0.07 mg/kg; n = 20). Thus, terbogrel is the first compound with a guanidino moiety demonstrating both a potent TXA2 synthase inhibition and a potent TXA2 receptor antagonism and has been selected for further clinical development.

Repaglinide and related hypoglycemic benzoic acid derivatives.

The structure-activity relationships in two series of hypoglycemic benzoic acid derivatives (5, 6) were investigated. Series 5 resulted from meglitinide (3) when the 2-methoxy was replaced by an alkyleneimino residue. Maximum activity was observed with the cis-3, 5-dimethyl-piperidino (5h) and the octamethyleneimino (5l) residues. Series 6 resulted from the meglitinide analogon 4 bearing an inversed amido function when the 2-methoxy, the 5-fluoro, and the alpha-methyl residue were replaced by a 2-piperidino, a 5-hydrogen, and a larger alpha-alkyl residue, respectively. An alkoxy residue ortho to the carboxy group further increased activity and duration of action in the rat. The most active racemic compound, 6al (R4 = isobutyl; R = ethoxy), turned out to be 12 times more active than the sulfonylurea (SU) glibenclamide (1). Activity was found to reside predominantly in the (S)-enantiomers. Compared with the SUs 1 and 2 (glimepiride), the most active enantiomer, (S)-6al (AG-EE 623 ZW; repaglinide; ED50 = 10 micro/kg po), is 25 and 18 times more active. Repaglinide turned out to be a useful therapeutic for type 2 diabetic patients; approval was granted recently by the FDA and the EMEA. From investigations on the pharmacophoric groups in compounds of type 5 and 6, it was concluded that in addition to the two already known-the acidic group (COOH; SO2NH) and the amidic spacer (CONH; NHCO)-the ortho residue R1 (alkyleneimino; alkoxy; oxo) must be regarded as a third one. A general pharmacophore model suitable for hypoglycemic benzoic acid derivatives, SUs, and sulfonamides is proposed (Figure 6). Furthermore, from superpositions of low-energy conformations (LECs) of 1, 2, and (S)-6al, it was concluded that a common binding conformation (LEC II; Figure 10B) may exist and that differences in binding to the SU receptor and in the mechanism of insulin release between repaglinide and the two SUs may be due to specific hydrophobic differences.

Specific bradycardic agents. 1. Chemistry, pharmacology, and structure-activity relationships of substituted benzazepinones, a-new class of compounds exerting antiischemic properties.

Structural modification of the calcium-antagonist verapamil (1) by replacement of the lipophilic alpha-isopropylacetonitrile moiety by various heterocyclic ring systems has led to a new class of cardiovascular compounds which are characterized by a specific bradycardic activity. These agents reduce heart rate without binding to classical calcium channels or beta-adrenoceptors, interacting instead specifically with structures at the sino atrial node. Therefore they have also been termed sinus node inhibitors. The prototype falipamil (2) has been submitted to further optimization mainly by manipulation of the phthalmidine moiety. This has resulted in a second generation of specific bradycardic agents with increased potency and selectively and prolonged duration of action represented by the benzazepinone-derivative UL-FS 49 (4). Structure-activity relationships within this novel class of compounds have revealed a marked dependence of activity on the substitution pattern of the aromatic rings, the nature of the central nitrogen atom, and the length of the connecting alkyl chains. The crucial role of the benzazepinone ring for bradycardic activity can be best explained by its special impact on the overall molecular conformation.

Synthesis, X-ray crystallography, and pharmacokinetics of novel azomethine prodrugs of (R)-alpha-methylhistamine: highly potent and selective histamine H3 receptor agonists.

Since various neuroregulatory functions of the histamine H3 receptor have been proved during the last few years, the H3 receptor is of current interest. Azomethine derivatives of the highly potent histamine H3 receptor agonist (R)-alpha-methylhistamine (1) were prepared as lipophilic prodrugs to improve the bioavailability of the hydrophilic drug, particularly its entry into the brain. Additionally, azomethine derivatization provides protection against histamine methyltransferase, the major metabolizing enzyme in man, and thus efficiently enhances the bioavailability of 1. The molecular conformations of (R)-2(-)[[N(-)[1-(1H-imidazol-4-yl)-2-propyl]- imino]phenylmethyl]phenol (9a) and (R)-4-fluoro-2(-)[[N(-)[1-(1H-imidazol-4-yl)-2-propyl[imino]- (4-chlorophenyl)methyl]phenol (9p) were determined by X-ray structure analysis. An intramolecular hydrogen bond which is essential for the stability of these azomethines was thereby confirmed. Moreover, the pharmacokinetic parameters of the prodrugs were investigated in vitro as well as in vivo. The halogenated azomethines have an effect following peroral administration in mice, and some of them seem to be highly potent for the central nervous system (CNS) delivery of 1. At present the most potent prodrug of 1 is (R)-4-chloro-2(-)[[N(-)[1-(1H-imidazol-4-yl)-2-propyl]imino](4- chlorophenyl)methyl]phenol (9q), reaching by far the highest CNS level of 1 (Cmax = 71 ng/g). Prodrugs of this type are not only valuable pharmacological tools but may also become H3 histaminergic drugs for therapeutic use.

New histamine H(3)-receptor ligands of the proxifan series: imoproxifan and other selective antagonists with high oral in vivo potency.

Histamine H(3)-receptor antagonists of the proxifan series are described. The novel compounds possess a 4-(3-(phenoxy)propyl)-1H-imidazole structure and various functional groups, e.g., an oxime moiety, on the phenyl ring. Synthesis of the novel compounds and X-ray crystallography of one highly potent oxime derivative, named imoproxifan (4-(3-(1H-imidazol-4-yl)propyloxy)phenylethanone oxime), are described. Most of the title compounds possess high antagonist potency in histamine H(3)-receptor assays in vitro as well as in vivo in mouse CNS following po administration. Structure-activity relationships are discussed. Imoproxifan displays subnanomolar potency on a functional assay on synaptosomes of rat cerebral cortex (K(i) = 0.26 nM). In vivo, imoproxifan increases the central N(tau)-methylhistamine level with an ED(50) of 0.034 mg/kg po. A receptor profile on several functional in vitro assays was determined for imoproxifan, demonstrating high selectivity toward the histamine H(3) receptor for this promising candidate for further development.

Chiral acetals as stereoinductors: diastereoface selective alkylation of dihydrobenzoxazine-derived amide enolates

Novel dihydrobenzoxazine-derived acetals of type 3 have been developed for asymmetric C-alkylations of propionyl amide enolates. High stereoselectivities are obtained for amides 15 and 22 which are rationalized in terms of intramolecular metal chelate formation.

Synthesis and Structure of a New Macrocyclic Polyhydroxylated Gadolinium Chelate Used as a Contrast Agent for Magnetic Resonance Imaging.

Three approaches to the synthesis of a new ligand 1,4,7-tris(carboxymethyl)-10-(1-(hydroxymethyl)-2,3-dihydroxypropyl)-1,4,7,10-tetraazacyclododecane (6) are described. This ligand forms the both thermodynamically and kinetically very stable gadolinium chelate Gadobutrol (1), which is a neutral and highly hydrophilic compound that is used for magnetic resonance imaging in the clinic. According to the crystal structure the Gd(III) ion in 1 is nine coordinated. The ligand provides eight coordination sites whereas the ninth coordination partner surprisingly is a carboxylate oxygen of a neighboring centrosymmetrically-related complex molecule. Ligand 6 was also utilized to prepare the calcium complex 12 which is used as an additive in the pharmaceutical formulation of 1. For the calcium complex 12, two complex molecules adopting almost identical conformations are present in the crystal.

X-ray analysis of 3-O-(6-O-acetyl-2,4-diazido-3-O-benzyl-2,4-dideoxy-alpha-D-gl glucopyranosyl)-1,6-anhydro-2,4-diazido-2,4-dideoxy-beta-D- glucopyranose, a disaccharide having an unusual alpha-D-(1----3) linkage.

The crystal structure of 3-O-(6-O-acetyl-2,4-diazido-3-O-benzyl-2,4-dideoxy-alpha-D- glucopyranosyl)-1,6-anhydro- 2,4-diazido-2,4-dideoxy-beta-D-glucopyranose, C21H24N12O7, mol. wt. 556.5, was investigated by X-ray analysis. The disaccharide crystallizes in the triclinic space group P1, with a = 889.3(5), b = 869.6(5), and c = 999.5(6) pm, and alpha = 105.83(4) degrees, beta = 116.22(4) degrees, gamma = 88.42(4) degrees, Z = 1, and rho = 1.394 g.cm-3. Phase determination failed with direct methods, but, as the 1,6-anhydride component of the molecule was already known from a previous structure analysis, the vector-search method could be applied in solving the structure. Diffractometer data were refined to an R value of 0.063 (Rw = 0.080) for 2102 observed reflections. The anhydro-bridged system has a distorted 1C4(D) conformation, in agreement with that of other anhydropyranoses so far investigated. A comparison shows that, for the specific kind of distortion, mainly the anti-reflex effect is responsible, whereas 1,3-diaxial interactions have a minor influence. The nonbridged ring adopts an almost perfect 4C1(D) conformation. The anomeric effect is observed in both of the sugar-ring systems in terms of bond-length shortening. The disaccharide has an alpha-D-Glc-4C1-(1a----3e)-D-Glc-1C4 glycosidic linkage. No previous X-ray investigation of a compound of this type is known. The pyranoid rings are almost perpendicular to each other. The phi, psi angles of the glycosidic linkage are +78.1(5) and -86.0(4) degrees.(ABSTRACT TRUNCATED AT 250 WORDS)

Crystal and molecular structures of 6-O-acetyl-2,3,4-trideoxy-alpha-DL-glycero-hex-2-enopyranose and 3-O-(6-O-acetyl-2,3,4-trideoxy-alpha-L-glycero-hex-2-enopyranosyl++ +)-1,2 ;5,6-di-O-isopropylidene-alpha-D-glucofuranose.

6-O-acetyl-2,3,4-trideoxy-alpha-DL-glycero-hex-2-enopyranose (1) and 3-O-(6-O-acetyl-2,3,4-trideoxy-alpha-L-glycero-hex-2-enopyranosyl) -1,2;5,6-di-O-isopropylidene-alpha-D-glucofuranose (2) have been investigated by X-ray diffraction methods. Compound 1 crystallises in the monoclinic system, space group P21/a, with cell constants a = 21.123(5), b = 4.439(2), c = 10.085(2) A, and beta = 110.22(2) degrees. Compound 2 crystallises in the orthorhombic system, space group P212121, with cell constants a = 22.110(6), b = 11.651(4), and c = 8.658(3) A. The intensity data were collected in a four-circle automatic diffractometer, with 1488 reflections for 1, and 2151 for 2. The structures were solved by direct methods. The atomic parameters were refined in an anisotropic mode by the full-matrix, least-squares procedure against 1065 and 1884 observed reflections for 1 and 2, respectively, giving R = 0.046 for each compound. The 2-enopyranose rings in 1 and 2 adopt half-chair conformations (H), and that in 2 is markedly deformed. The 1,2-dioxolane ring in 2 has an envelope (E) conformation, whereas the 5,6-dioxolane ring is dynamically disordered and can be represented by a conformational hybrid (E + P). The alpha-D-glucofuranose ring in 2 has a twist conformation (T). The glycoside bond in 2 is characterized by phi and psi torsion angles of 47(2) degrees and 32(2) degrees, respectively.

Epimerization of erythromycin derivatives.

Dirithromycin (3) isomerizes upon dissolution in different solvents. From X-ray analysis of V-T 108, an analogue of dirithromycin, and comparative 1H and 13C NMR, and MS data, the isomer of dirithromycin was confirmed to be the C-16-(S)-epimer. The ratio of the two epimers at equilibrium conditions was approximately 8:2 (R/S) in methanol at room temperature.

Low-temperature crystallization and structure determination of N-(trifluoromethyl)formamide, N-(2,2,2-trifluoroethyl)formamide and 2,2,2-trifluoroethyl isocyanide.

Crystals of N-(trifluoromethyl)formamide, C(2)H(2)F(3)NO, (I), N-(2,2,2-trifluoroethyl)formamide, C(3)H(4)F(3)NO, (II), and 2,2,2-trifluoroethyl isocyanide, C(3)H(2)F(3)N, (III), were grown in situ on an X-ray diffractometer and analysed by single-crystal X-ray diffraction methods at low temperatures. Crystal data: (I) orthorhombic, P2(1)2(1)2(1), a = 4.547 (2) Å, b = 5.947 (3) Å, c = 14.731 (9) Å, V = 398.3 (4) Å(3), Z = 4, M(r) = 113.05, T = 143 K, D(x) = 1.885 Mg m(-3); (II) monoclinic, P2(1)/n, a = 4.807 (1) Å, b = 16.707 (3) Å, c = 6.708 (1) Å, beta = 109.90 (1) degrees, V = 506.6 (2) Å(3), Z = 4, M(r) = 127.07, T = 141 K, D(x) = 1.666 Mg m(-3); (III) orthorhombic, P2(1)2(1)2(1), a = 5.668 (2) Å, b = 9.266 (3) Å, c = 8.626 (2) Å, V = 453.0 (2) Å(3), Z = 4, M(r) = 109.06, T = 163 K, D(x) = 1.599 Mg m(-3). The results showed that in the crystal both formamides (I) and (II) are exclusively present in the form of the Z isomer, although measurements of solutions of (I) have shown that the E isomer prevails [Lentz et al. (1987). Angew. Chem. 99, 951-953]. In addition ab initio calculations for (I) predicted the E isomer to be the more stable one. In compound (III) the isocyanide group is staggered with respect to the trifluoroethyl group. In the crystal packing of (I) and (II) intermolecular N-H.O hydrogen bonds generate infinite chains. In (I), these chains are linked to form sheets by C-H.O contacts. In the crystal structure of (III) each isocyanide dipole is surrounded by four electronegative F atoms with intermolecular C.F contacts between 3.4 and 3.5 Å.

3-(tert-Butyloxycarbonylamino)bicyclo

In the room-temperature X-ray structure of the N-Boc-protected derivative of the novel 3-aminobicyclo[1.1.1]pentanecarboxylic acid, C(11)H(17)NO(4), the interbridgehead distance in the bicyclo[1.1. 1]pentane cage is 1.852 (2) A. The carboxyl and parts of the blocked amino group are almost in plane with one of the cage triangles. N-H. O and O-H.O hydrogen bonds generate infinite corrugated molecular chains in the crystal lattice.

Introduction and validation of an invariom database for amino-acid, peptide and protein molecules.

A database of invarioms for structural refinement of amino-acid, oligopeptide and protein molecules is presented. The spherical scattering factors of the independent atom or promolecule model are replaced by ;individual' aspherical scattering factors that take into account the chemical environment of a bonded atom. All amino acids were analysed in terms of their invariom fragments. In order to generate 73 database entries that cover this class of compounds, 37 model compounds were geometry-optimized and theoretical structure factors were calculated. Multipole refinements were then performed on these theoretical structure factors to yield the invariom database. Validation of this database on an extensive number of experimental small-molecule crystal structures of varying quality and resolution shows that invariom modelling improves various figures of merit. Differences in figures of merit between invariom and promolecule models give insight into the importance of disorder for future protein-invariom refinements. The suitability of structural data for application of invarioms can be predicted by Cruickshank's diffraction-component precision index [Cruickshank (1999), Acta Cryst. D55, 583-601].

Atomic and bond topological properties of the tripeptide L-alanyl-L-alanyl-L-alanine based on its experimental charge density obtained at 20 K.

A 20 K high resolution X-ray data set of L-Ala-L-Ala-L-Ala*1/2 H2O was measured using an ultra-low temperature laboratory setup, that combines area detection and a closed cycle helium cryostat. The charge density determination includes integration of atomic basins and topological analysis according to Bader's quantum theory of atoms in molecules. Two tripeptide units are found in the asymmetric unit, allowing the assessment of transferability of bond topological and atomic properties taking also into consideration previous data of oligopeptides. With respect to invariom modeling the limits of such transferability are investigated and the results of this study show the validity of the nearest/next-nearest neighbour approximation and support the use of database approaches for electron density modeling of macromolecules.

Submolecular partitioning of morphine hydrate based on its experimental charge density at 25 K.

The electron density distribution of morphine hydrate has been determined from high-resolution single-crystal X-ray diffraction measurements at 25 K. A topological analysis was applied and, in order to analyze the submolecular transferability based on an experimental electron density, a partitioning of the molecule into atomic regions was carried out, making use of Bader's zero-flux surfaces to yield atomic volumes and charges. The properties obtained were compared with the theoretical calculations of smaller fragment molecules, from which the complete morphine molecule can be reconstructed, and with theoretical studies of another opiate, Oripavine PEO, reported in the literature.

Conformational analysis of the antiulcer drug pirenzepine. X-ray investigations, molecular mechanics and quantum mechanical calculations and comparisons with structurally or pharmacologically related compounds.

The crystal structures of the antiulcer drug 5,11-dihydro-11-[(4-methyl-1-piperazinyl) acetyl]-6H-pyrido[2,3-b] [1,4]benzodiazepin-6-one dihydrochloride (pirenzepine dihydrochloride, L-S 519 CL 2, Gastrozepin) and its monoprotonated form (pirenzepine monohydrochloride, L-S 519 CL) were determined by X-ray analysis. Molecular mechanics (MMPI) and semiempirical quantum chemical (MNDO) calculations showed that the calculated minimum energy conformations of the tricycle and of the exocyclic amide group are in agreement with the crystal structures. The conformational energies of pirenzepine as a function of four important torsional angles were calculated using different semiempirical quantum chemical methods with the CNDO/2 (complete neglect of differential overlap)-, MNDO (modified neglect of diatomic overlap)- and PCILO (perturbative configuration interaction using localized orbitals)-approximations. The conformation of one local energy minimum corresponds closely to the crystal structure of pirenzepine monohydrochloride. This conformation has a spatial arrangement which is analogous to a single consistent conformation known from the literature of 24 anticholinergic agents determined from their crystal structures by a computer graphics analysis. On the other hand there are no structural relationships of any low energy conformation of pirenzepine to conformations of other classes of tricyclic compounds which could rationalize their antidepressant, neuroleptic or antihistaminic activity. This finding explains the absence of any central effect of pirenzepine following intracerebral application. The computational elucidation of the conformational requirements for the interaction with the muscarinic receptors may be helpful for the interpretation of the selectivity of pirenzepine within the muscarinic system.