Crystal structure and molecular modeling of 17-DMAG in complex with human Hsp90

Hsp90 is an attractive chemotherapeutic target because it chaperones the folding of proteins found in multiple signal transduction pathways. We describe the 1.75 A resolution crystal structure of human Hsp90 alpha (residues 9-236) complexed with 17-desmethoxy-17-N,N-dimethylaminoethylamino-geldanamycin (17-DMAG). The structure revealed an altered set of interactions between the 17-substituent and the protein compared to geldanamycin and the 17-dimethylaminoethyl moiety pointing into solvent, but otherwise was similar to that reported for the complex with geldanamycin. Targeted molecular dynamics simulations and energetic analysis indicate that geldanamycin undergoes two major conformational changes when it binds Hsp90, with the key step of the conversion being the trans to cis conformational change of the macrocycle amide bond. We speculate that 17-DMAG analogs constrained to a cis-amide in the ground state could provide a significant increase in affinity for Hsp90.     

3D-QSAR and molecular modeling of HIV-1 integrase inhibitors

Three-dimensional quantitative structure-activity relationship (3D QSAR) methods were applied on a series of inhibitors of HIV-1 integrase with respect to their inhibition of 3-processing and 3-end joining steps in vitro.The training set consisted of 27 compounds belonging to the class of thiazolothiazepines. The predictive ability of each model was evaluated using test set I consisting of four thiazolothiazepines and test set II comprised of seven compounds belonging to an entirely different structural class of coumarins. Maximum Common Substructure (MCS) based method was used to align the molecules and this was compared with other known methods of alignment. Two methods of 3D QSAR: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were analyzed in terms of their predictive abilities. CoMSIA produced significantly better results for all correlations. The results indicate a strong correlation between the inhibitory activity of these compounds and the steric and electrostatic fields around them. CoMSIA models with considerable internal as well as external predictive ability were obtained. A poor correlation obtained with hydrophobic field indicates that the binding of thiazolothiazepines to HIV-1 integrase is mainly enthalpic in nature. Further the most active compound of the series was docked into the active site using the crystal structure of integrase. The binding site was formed by the amino acid residues 64-67, 116, 148, 151-152, 155-156, and 159. The comparison of coefficient contour maps with the steric and electrostatic properties of the receptor shows high level of compatibility.     

Crystal and molecular structure of the complex salt of peganine with zinc chloride

The crystal structure of peganine in its complex with ZnCl₂·2H₂O has been established by the x-ray structural method (diffractometer, CuK radiation, 1796 reflections, direct method, R = 0.079). A similarity has been found in the solvation of the crystalline complexes with ZnCl₂·HCl of the alkaloids peganine and deoxypeganine. A tendency to the averaging of the N 1=C2 and N3-C2 bonds in quinazolines protonated at N1 is observed.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Republic of Uzbekistan, Tashkent, fax (3712) 89 14 75. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp.426–430, May–June, 1995. Original article submitted June 20, 1994. submitted June 20, 1994.     

Three-dimensional structure of HIV-1 VIF constructed by comparative modeling and the function characterization analyzed by molecular dynamics simulation

VIF is one of the six accessory proteins of HIV-1. It has been shown to be necessary for the survival of HIV-1 in the human body and for the retention of viral infectivity. It is strongly expected that a new therapeutic strategy against HIV-1 infection could be realized by blocking the biological pathway to VIF. In this paper, a three-dimensional model of VIF was constructed by comparative modeling based on two templates, VHL and NarL, which were used to construct the C-terminal domain and N-terminal domain of VIF, respectively. A model of the VIF-ElonginB-ElonginC complex was constructed, and molecular dynamics simulations were used to investigate the interactions between VIF and ElonginB-ElonginC. Mutagenesis was used to identify the function of some conserved residues in the putative SOCS-box. The results showed that the mutations of the critical residues led to the disruption of the interactions between VIF and ElonginB-ElonginC, consistent with experimental observations. These novel models of VIF and its complex has therefore provided structural information for investigating the function of VIF at the molecular level.     

Crystal and molecular structure of 1-phenyl-2-nitroguanidine

The molecular structure of 1-phenyl-2-nitroguanidine is nonplanar, but contains two almost planar fragments: nitroguanyl and phenyl groups. Unlike previously studied nitroguanidines, in 1-phenyl-2-nitroguanidine, the nitro group is turned to the secondary amino group. However, the structural parameters of the nitroguanyl group are little different from those of nitroguanidine and its alkyl derivatives. In the benzene ring, the symmetry in the geometric parameters is not observed, which is explained by the intermolecular interaction with the neighboring molecule.     

Crystal and molecular structure of 1-methyl-1,2-dinitroguanidine

In 1-methyl-1,2-dinitroguanidine, the nitroguanyl group has planar geometry with an intramolecular hydrogen bond, although the conformation of the whole molecule is slightly nonplanar. Because of - electron density delocalization, the C-N, N-N, and N-O bond lengths are intermediate between the corresponding values for the single and double bonds. The distinction of the crystal structure is the absence of intermolecular hydrogen bonds.Original Russian Text Copyright © 2004 by A. D. Vasiliev, A. M. Astakhov, M. S. Molokeev, L. A. Kruglyakova, and R. S. StepanovTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 558–561, May–June 2004.     

Crystal structure of the molecular complex (1∶1) of (o-hydroxyphenylaminomethyl)chloromethylphosphinic acid with dioxane

The crystal structure of the molecular complex (11) of (o-hydroxyphenylaminomethyl)chloromethylphosphinic acid with dioxane has been studied by x-ray structural analysis and it has been established that the acid exists in the zwitterion form.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 572–574, March, 1990.     

Crystal and molecular structure and luminescence properties of the europium trifluoroacetate complex with dipyridyl

The crystal structure of [Eu(Dipy)(TFA)₃(H₂O)₃] · Dipy (where TFA^? is the trifluoroacetate anion and Dipy is, 2,2′-dipyridyl) has been studied by X-ray diffraction. The coordination polyhedron of the europium atom is a distorted square antiprism [EuO₆N₂] with the nonplanar quadrilateral faces. The coordinated and non-coordinated dipyridyl molecules are linked pairwise through π stacking interactions into an infinite pile with an overlap of up to 50% of the molecular surface areas. An increase in the luminescence intensity of the compound upon its UV irradiation is explained.     

Crystal and molecular structure of β-cyclodextrin inclusion complex with succinic acid

The crystal complex of β-cyclodextrin with succinic acid, intermediate product of hydrolysis reaction of succinic anhydride in the presence of β-cyclodextrin, was isolated and studied by X-ray analysis (monoclinic, space group P2₁, a = 15.1977(7) Å, b = 10.1763(5) Å, c = 20.6943(6) Å, β = 109.239(4)°, V = 3021.8(2) Å³, Z = 2, R ₁ = 0.0359, wR ₂ = 0.0947). It was proved that β-cyclodextrin and succinic acid form an inclusion complex, which exists in crystal state as a heptahydrate. The molecule of succinic acid is fully included in the β-cyclodextrin cavity with its carboxyl groups accessible for water molecules. Water molecules located at borders of cavity rims and in interstices between molecules of β-cyclodextrin participate in formation of intermolecular hydrogen bonds. The overall structure does not contain disordered fragments. The crystal conformation of succinic acid corresponds to one of possible conformers of the molecule in vacuo and is almost not disturbed by intermolecular interactions in crystal. Based on the analysis of structural features of the crystal conformation of succinic acid and character of its location in the β-cyclodextrin cavity, it was suggested that hydrolysis of succinic anhydride via ring opening and formation of succinic acid is mediated by cyclodextrin microenvironment and it likely occurs near the narrow rim of the macrocycle cavity.     

Crystal and molecular structures of the copper dichloride complex with 1-isopropenylimidazole

Crystal and molecular structures of the [CuL₂Cl₂] complex (L is 1-isopropenylimidazole) (I) are determined (R = 0.038, (wR ₂ = 0.092 for 2026 reflections with F _o ≥ 4σ(F _o); R ₁ = 0.123, wR ₂ = 0.117 for all reflections)) and compared with the structure of the known cobalt complex of analogous composition [CoL₂Cl₂] (II). Unlike complex II with the usual tetrahedral environment of the cobalt atom, the structure of the coordination polyhedron of the copper atom in compound I is intermediate between tetrahedron and square (the average dihedral angle between the ClCuN planes is 35.9°, and the ClCuCl (147.5°) and NCuN (163.1°) angles are much larger than the ClCuN angle of 90.1°–93.1°). The Cu-N (1.975(3), 1.959(3) Å) and Cu-Cl bonds (2.291(1), 2.278(1) Å) in complex I are typical of the copper(II) compounds. Different spatial structures of the 1-alkenylimidazole cycles in complexes I and II are found. Different short intermolecular contacts in crystals of compounds I (Cu…Cl, Cu…H) and II (Cl…C) result in the formation of chains with different mutual arrangements of molecules of the complexes.