The Crystal and Molecular Structure of 3′-Fluoro-3′-Deoxythymidine, a Potent Anti-HIV-1 Nucleoside

The crystal structure of 3′-fluoro-3′-deoxythymidine (FDT), a nucleoside analogue with high potency against human immunodeficiency virus type 1 (HIV-1) in cell culture, has been determined as part of studies aimed at determining correlations between the molecular conformations of anti-HIV nucleosides and their potency. FDT crystallizes with four molecules in the asymmetric unit. The largest differences between the four molecules are in the conformations about the glycosidic bond, but they are otherwise surprisingly similar in conformation. All four molecules have C3′- exo/C2′- endo dideoxyribose ring conformations, very similar to that of one of the two molecules of 3′-azido-3′-deoxythymidine (AZT) in its crystal structure. Revised

A Stereochemical Rationale for the Activity of Anti-HIV Nucleosides

Crystallographic studies have shown that, in the solid state, nucleosides active against the human immunodeficiency virus (HIV) generally exhibit moderate to extreme S-type furanose conformations (pseudorotational phase angle up to 215°). Following this lead, it is shown that using principles of conformational analysis, one can rationalize the activity or inactivity of other nucleoside analogues (including many not yet studied by X-ray methods) in terms of the effects of substituents on the furanose ring conformation. An analysis of the various 1,4 interactions of the O4′ lone pairs, O4′ itself, and the substituents on C2′ and C3′ shows that S-type conformations are stabilized (relative to N-type) in all the active ribose analogues, whereas this effect is absent in most inactive compounds. The gauche effect is a major determinant of activity, and the O4′ lone pairs, which have been neglected in many previous force field studies, may also be involved in stabilizing extreme S-type conformations. In such conformations (particularly for P > 180°) the + sc orientation of O5′ is destabilized, increasing access to the ap orientation, which may be more favourable for activity.

Structural biology of human follitropin and its receptor

In this review, the current understanding of structure-activity relationships of human follitropin and of the extracellular domain of its receptor is described. Comprehensive mutagenesis of human follitropin combined with the three-dimensional structure of human follitropin has ushered in a new era of understanding of how this complex hormone binds to and activates its receptor. Comparison of human choriogonadotropin and follitropin structures has proved invaluable in understanding how these human glycoprotein hormones have conserved primary sequence that enables high affinity binding while diverging in amino acids that provide specificity. Moreover, by comparison of the structures of deglycosylated and glycosylated human choriogonadotropin and glycosylated human follitropin, there appears to be no influence of oligosaccharides upon backbone conformation of human glycoprotein hormones. Extensive structure-activity relationships of human follitropin receptor have been studied, and new insights gained here as well. These studies indicate that follitropin binds to the central module of the extracellular domain of the follitropin receptor. Biophysical analyses of purified follitropin receptor extracellular domain further revealed conformational changes affected by hormone binding and by the solvent environment. Further, secondary structure analysis of the purified extracellular domain of follitropin receptor favors the leucine-rich repeat motif model of the glycoprotein hormone receptors. Together, the studies indicate that there are only a few residues that contribute to the overall energy of binding. Formation of a weak collisional complex between follitropin and its receptor likely involves complementation of compatible surfaces and steric hindrance by oligosaccharides, followed by conformational change and formation of active site residue salt bridges. In this regard and in light of these new data, current models of the glycoprotein hormone receptors may need to be re-evaluated.

Crystal structure of a deletion mutant of human thymidylate synthase Delta (7-29) and its ternary complex with Tomudex and dUMP

The crystal structures of a deletion mutant of human thymidylate synthase (TS) and its ternary complex with dUMP and Tomudex have been determined at 2.0 A and 2.5 A resolution, respectively. The mutant TS, which lacks 23 residues near the amino terminus, is as active as the wild-type enzyme. The ternary complex is observed in the open conformation, similar to that of the free enzyme and to that of the ternary complex of rat TS with the same ligands. This is in contrast to Escherichia coli TS, where the ternary complex with Tomudex and dUMP is observed in the closed conformation. While the ligands interact with each other in identical fashion regardless of the enzyme conformation, they are displaced by about 1.0 A away from the catalytic cysteine in the open conformation. As a result, the covalent bond between the catalytic cysteine sulfhydryl and the base of dUMP, which is the first step in the reaction mechanism of TS and is observed in all ternary complexes of the E. coli enzyme, is not formed. This displacement results from differences in the interactions between Tomudex and the protein that are caused by differences in the environment of the glutamyl tail of the Tomudex molecule. Despite the absence of the closed conformation, Tomudex inhibits human TS ten-fold more strongly than E. coli TS. These results suggest that formation of a covalent bond between the catalytic cysteine and the substrate dUMP is not required for effective inhibition of human TS by cofactor analogs and could have implications for drug design by eliminating this as a condition for lead compounds.

Three-dimensional structure of human follicle-stimulating hormone

The crystal structure of a betaThr26Ala mutant of human follicle-stimulating hormone (hFSH) has been determined to 3.0 A resolution. The hFSH mutant was expressed in baculovirus-infected Hi5 insect cells and purified by affinity chromatography, using a betahFSH-specific monoclonal antibody. The betaThr26Ala mutation results in elimination of the betaAsn24 glycosylation site, yielding protein more suitable for crystallization without affecting the receptor binding and signal transduction activity of the glycohormone. The crystal structure has two independent hFSH molecules in the asymmetric unit and a solvent content of about 80%. The alpha- and betasubunits of hFSH have similar folds, consisting of central cystine-knot motifs from which three beta-hairpins extend. The two subunits associate very tightly in a head-to-tail arrangement, forming an elongated, slightly curved structure, similar to that of human chorionic gonadotropin (hCG). The hFSH heterodimers differ only in the conformations of the amino and carboxy termini and the second loop of the beta-subunit (L2beta). Detailed comparison of the structures of hFSH and hCG reveals several differences in the beta-subunits that may be important with respect to receptor binding specificity or signal transduction. These differences include conformational changes and/or differential distributions of polar or charged residues in loops L3beta (hFSH residues 62-73), the cystine noose, or determinant loop (residues 87-94), and the carboxy-terminal loop (residues 94-104). An additional interesting feature of the hFSH structure is an extensive hydrophobic patch in the area formed by loops alphaL1, alphaL3, and betaL2. Glycosylation at alphaAsn52 is well known to be required for full signal transduction activity and heterodimer stability. The structure reveals an intersubunit hydrogen bonding interaction between this carbohydrate and betaTyr58, an indication of a mechanism by which the carbohydrate may stabilize the heterodimer.

Structural basis for the substrate specificity of endo-beta-N-acetylglucosaminidase F(3)

Endo-beta-N-acetylglucosaminidase F(3) cleaves the beta(1-4) link between the core GlcNAc's of asparagine-linked oligosaccharides, with specificity for biantennary and triantennary complex glycans. The crystal structures of Endo F(3) and the complex with its reaction product, the biantennary octasaccharide, Gal-beta(1-4)-GlcNAc-beta(1-2)-Man-alpha(1-3)[Gal-beta(1-4)-GlcNAc-be ta(1-2)-Man-alpha(1-6)]-Man-beta(1-4)-GlcNAc, have been determined to 1.8 and 2.1 A resolution, respectively. Comparison of the structure of Endo F(3) with that of Endo F(1), which is specific for high-mannose oligosaccharides, reveals highly distinct folds and amino acid compositions at the oligosaccharide recognition sites. Binding of the oligosaccharide to the protein does not affect the protein conformation. The conformation of the oligosaccharide is similar to that seen for other biantennary oligosaccharides, with the exception of two links: the Gal-beta(1-4)-GlcNAc link of the alpha(1-3) branch and the GlcNAc-beta(1-2)-Man link of the alpha(1-6) branch. Especially the latter link is highly distorted and energetically unfavorable. Only the reducing-end GlcNAc and two Man's of the trimannose core are in direct contact with the protein. This is in contrast with biochemical data for Endo F(1) that shows that activity depends on the presence and identity of sugar residues beyond the trimannose core. The substrate specificity of Endo F(3) is based on steric exclusion of incompatible oligosaccharides rather than on protein-carbohydrate interactions that are unique to complexes with biantennary or triantennary complex glycans.

Mutations of endo-beta-N-acetylglucosaminidase H active site residueAs sp130 anG glu132: activities and conformations

Endo-beta-N-acetylglucosaminidase H hydrolyzes the beta-(1-4)-glycosidic link of the N,N'-diacetylchitobiose core of high-mannose and hybrid asparagine-linked oligosaccharides. Seven mutants of the active site residues, Asp130 and Glu132, have been prepared, assayed, and crystallized. They include single site mutants of each residue to the corresponding amide, to Ala and to the alternate acidic residue, and to the double amide mutant. The mutants of Asp130 are more active than the corresponding Glu132 mutants, consistent with the assignment of the latter residue as the primary catalytic residue. The amide mutants are more active than the alternate acidic residue mutants, which in turn are more active than the Ala mutants. The structures of the Asn mutant of Asp130 and the double mutant are very similar to that of the wild-type enzyme. Several residues surrounding the mutated residues, including some that form part of the core of the beta-barrel and especially Tyr168 and Tyr244, adopt a very different conformation in the structures of the other two mutants of Asp130 and in the Asp mutant of Glu132. The results show that the residues in the upper layers of the beta-barrel can organize into two very distinct packing arrangements that depend on subtle electrostatic and steric differences and that greatly affect the geometry of the substrate-binding cleft. Consequently, the relative activities of several of the mutants are defined by structural changes, leading to impaired substrate binding, in addition to changes in functionality.

Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI

I-DmoI is a 22 kDa endonuclease encoded by an intron in the 23 S rRNA gene of the hyperthermophilic archaeon Desulfurococcus mobilis. The structure of I-DmoI has been determined to 2.2 A resolution using multi-wavelength anomalous diffraction techniques. I-DmoI, a protein of the LAGLIDADG motif family, represents the first structure of a freestanding endonuclease with two LAGLIDADG motifs, and the first of a thermostable homing endonuclease. I-DmoI consists of two similar alpha/beta domains (alphabetabetaalphabetabetaalpha) related by pseudo 2-fold symmetry. The LAGLIDADG motifs are located at the carboxy-terminal end of the first alpha-helix of each domain. These helices form a two-helix bundle at the interface between the domains and are perpendicular to a saddle-shaped DNA binding surface, formed by two four-stranded antiparallel beta-sheets. Despite substantially different sequences, the overall fold of I-DmoI is similar to that of two other LAGLIDADG proteins for which the structures are known, I-CreI and the endonuclease domain of PI-SceI. The three structures differ most in the loops connecting the beta-strands, relating to the respective DNA target site sizes and geometries. In addition, the absence of conserved residues surrounding the active site, other than those within the LAGLIDADG motif, is of mechanistic importance. Finally, the carboxy-terminal domain of I-DmoI is smaller and has a more irregular fold than the amino-terminal domain, which is more similar to I-CreI, a symmetric homodimeric endonuclease. This is reversed compared to PI-SceI, where the amino-terminal domain is more similar to carboxy-terminal domain of I-DmoI and to I-CreI, with interesting evolutionary implications.

Crystal structure of thymidylate synthase A from Bacillus subtilis

Thymidylate synthase (TS) converts dUMP to dTMP by reductive methylation, where 5,10-methylenetetrahydrofolate is the source of both the methylene group and reducing equivalents. The mechanism of this reaction has been extensively studied, mainly using the enzyme from Escherichia coli. Bacillus subtilis contains two genes for TSs, ThyA and ThyB. The ThyB enzyme is very similar to other bacterial TSs, but the ThyA enzyme is quite different, both in sequence and activity. In ThyA TS, the active site histidine is replaced by valine. In addition, the B. subtilis enzyme has a 2.4-fold greater k(cat) than the E. coli enzyme. The structure of B. subtilis thymidylate synthase in a ternary complex with 5-fluoro-dUMP and 5,10-methylenetetrahydrofolate has been determined to 2.5 A resolution. Overall, the structure of B. subtilis TS (ThyA) is similar to that of the E. coli enzyme. However, there are significant differences in the structures of two loops, the dimer interface and the details of the active site. The effects of the replacement of histidine by valine and a serine to glutamine substitution in the active site area, and the addition of a loop over the carboxy terminus may account for the differences in k(cat) found between the two enzymes.

Crystallization and preliminary crystallographic analysis of the archaeal intron-encoded endonuclease I-DmoI

Two forms of the archaeal intron-encoded site-specific endonuclease I-DmoI, namely I-DmoIc and I-DmoIl, have been purified and crystallized. Crystals of I-DmoIc are rod-shaped and diffract to 3.0 A resolution, but further analysis was hampered by twinning. Crystals of I-DmoIl, which is a six-amino-acid C-terminal truncation of I-DmoIc, are plate shaped and belong to space group C2 with cell parameters a = 93.72, b = 37.03, c = 55.56 A, beta = 113.4 degrees, with one molecule per asymmetric unit (Vm = 2.01 A3 Da-1). The crystals diffract to at least 2.3 A resolution. A complete native data set has been measured and structure determination is on-going.

Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum

The crystal structure of recombinant glycosylasparaginase from Flavobacterium meningosepticum has been determined at 2.32 angstroms resolution. This enzyme is a glycoamidase that cleaves the link between the asparagine and the N-acetylglucosamine of N-linked oligosaccharides and plays a major role in the degradation of glycoproteins. The three-dimensional structure of the bacterial enzyme is very similar to that of the human enzyme, although it lacks the four disulfide bridges found in the human enzyme. The main difference is the absence of a small random coil domain at the end of the alpha-chain that forms part of the substrate binding cleft and that has a role in the stabilization of the tetramer of the human enzyme. The bacterial glycosylasparaginase is observed as an (alphabeta)2-tetramer in the crystal, despite being a dimer in solution. The study of the structure of the bacterial enzyme allows further evaluation of the effects of disease-causing mutations in the human enzyme and confirms the suitability of the bacterial enzyme as a model for functional analysis.

Active site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F

Crystallographic analysis and site-directed mutagenesis have been used to identify the catalytic and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F (PNGase F), an amidohydrolase that removes intact asparagine-linked oligosaccharide chains from glycoproteins and glycopeptides. Mutagenesis has shown that three acidic residues, Asp-60, Glu-206, and Glu-118, that are located in a cleft at the interface between the two domains of the protein are essential for activity. The D60N mutant has no detectable activity, while E206Q and E118Q have less than 0.01 and 0.1% of the wild-type activity, respectively. Crystallographic analysis, at 2.0-A resolution, of the complex of the wild-type enzyme with the product, N,N'-diacetylchitobiose, shows that Asp-60 is in direct contact with the substrate at the cleavage site, while Glu-206 makes contact through a bridging water molecule. This indicates that Asp-60 is the primary catalytic residue, while Glu-206 probably is important for stabilization of reaction intermediates. Glu-118 forms a hydrogen bond with O6 of the second N-acetylglucosamine residue of the substrate and the low activity of the E118Q mutant results from its reduced ability to bind the oligosaccharide. This analysis also suggests that the mechanism of action of PNGase F differs from those of L-asparaginase and glycosylasparaginase, which involve a threonine residue as the nucleophile.

Crystal structure of endo-beta-N-acetylglucosaminidase H at 1.9 A resolution: active-site geometry and substrate recognition

BACKGROUND

Endo-beta-N-acetylglucosaminidase H (Endo H), an endoglycosidase secreted by Streptomyces plicatus, hydrolyzes the glycosidic bond between the core N-acetyglucosamine residues of asparagine-linked high-mannose oligosaccharides. Endo H is a commonly used reagent in glycobiology research, including the characterization of oligosaccharides in glycoproteins. On-going crystallographic studies of Endo H and related endoglycosidases are aimed at identifying the molecular features that determine the different substrate specificities of these enzymes.

RESULTS

The three-dimensional structure of Endo H has been determined to 1.9 A resolution. The overall fold of the enzyme is that of an irregular (alpha/beta)8-barrel comprising eight beta-strand/loop/alpha-helix units. Units 5 and 6 have very short loop sections at the top of the molecule and their alpha-helices are replaced by sections of extended geometry. The loop of unit 2 includes a small two-stranded antiparallel beta-sheet. A shallow curved cleft runs across the surface of the molecule from the area of units 5 and 6, over the core of the beta-barrel to the area of the beta-sheet of loop 2. This cleft contains the putative catalytic residues Asp130 and Glu132 above the core of the beta-barrel. These residues are surrounded by several aromatic residues. The loop 2 area of the cleft is formed by neutral polar residues, mostly asparagines.

CONCLUSIONS

The structure of Endo H is very similar to that of Endo F1, a closely related endoglycosidase secreted by Flavobacterium meningosepticum. Detailed comparison of the structures of Endo H and Endo F1 supports the model previously proposed for substate binding and recognition, in which the area of loop 2 determines the substrate specificity and the alpha-helices of units 5 and 6 are missing to accommodate the protein moiety of the substrate.

Crystal structure of endo-beta-N-acetylglucosaminidase F1, an alpha/beta-barrel enzyme adapted for a complex substrate

Endo-beta-N-acetylglucosaminidase F1 (Endo F1) is an endoglycosidase, secreted by Flavobacterium meningosepticum, that cleaves asparagine-linked oligosaccharides after the first N-acetylglucosamine residue. The enzyme is selective for high-mannose oligosaccharide chains. The crystal structure of Endo F1 has been determined at 2.0-A resolution. The molecular fold consists of a highly irregular alpha/beta-barrel, a commonly observed motif consisting of a cyclic 8-fold repeat of beta-strand/loop/alpha-helix units with an eight-stranded parallel beta-barrel at the center. Endo F1 lacks two of the alpha-helices, those of units 5 and 6. Instead, the links after beta-strands 5 and 6 consist of a short turn followed by a section in an extended conformation that replaces the helix and a long loop at the bottom of the molecule. The absence of any excursion on top of the molecule following beta-strands 5 and 6 results in a pronounced depression in the rim of the barrel. This depression forms one end of a shallow cleft that runs across the surface of the molecule, over the core of the beta-barrel to the area between the loops of units 1 and 2. The active site residues, Asp130 and Glu132, are located at the carboxyl end of beta-strand 4 and extend into this cleft. These residues are surrounded by several tyrosine residues. The cleft area formed by loops 1 and 2 is lined with polar residues, mainly asparagines. The latter area is thought to be responsible for oligosaccharide binding and recognition while the protein moiety of the substrate would be located outside the molecule but adjacent to the area of loops 5 and 6.(ABSTRACT TRUNCATED AT 250 WORDS)

Crystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution

Peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F (PNGase F) is an amidase that cleaves the beta-aspartylglucosylamine bond of asparagine-linked glycans. The 34.8-kDa (314 amino acids) enzyme has a very broad substrate specificity and is extensively used for studies of the structure and function of glycoproteins. Enzymatic activity of PNGase F requires recognition of both the peptide and the carbohydrate components of the substrate. Only limited information regarding the mechanism of action of the enzyme is available. The three-dimensional structure of PNGase F has been determined by X-ray crystallography at 2.2-A resolution. The protein folds into two domains comprising residues 1-137 and 143-314, respectively. Both domains have eight-stranded antiparallel beta-sandwich motifs that are very similar in geometry. Both sandwiches have parallel principal axes and lie side by side. The covalent link between the domains is located at the top end of the molecule. Extensive hydrogen-bonding contacts occur along the full length of the interface between the two domains. Three different areas, all at the interface between the two domains, have been identified as possible locations for the active site of the enzyme. These include a hydrophobic bowl of about 20 A in diameter on one surface of the molecule, a long polar cleft on the opposite side, and a cleft at the bottom, which is lined with large aromatic residues including eight tryptophans.

Crystallization and preliminary crystallographic analysis of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase PNGase F

PNGase F is an amidase that hydrolyzes the beta-aspartylglucosylamine bond of asparagine-linked glycopeptides and glycoproteins. Enzymatic activity of PNGase F requires the recognition of both the peptide and the carbohydrate moiety. Crystals of PNGase F were grown by sitting drop vapor diffusion methods at 10 degrees C. The precipitating buffer contains both polyethylene glycol 3350 and (NH4)2SO4 in sodium acetate buffer at pH 4.3. The crystals belong to the orthorhombic space group C222(1) with cell dimensions: a = 87.16 A, b = 125.10 A, c = 79.33 A and diffract to 1.8 A resolution.

Crystallization and preliminary crystallographic analysis of two endo-beta-N-acetylglucosaminidases, endo H and endo F1

Endo H and F1 are endoglycosidases that cleave the oligosaccharide moiety of asparagine-linked glycoproteins by hydrolysis of the glycosidic bond in the N,N'-diacetylchitobiose core. The two enzymes are specific for high-mannose oligosaccharides. Here, we report the crystallization and preliminary crystallographic analysis of Endo H and Endo F1. Crystals were grown by hanging drop vapor diffusion methods. Both proteins crystallize from crystallization buffers containing polyethyleneglycol 8000 and zinc acetate as precipitating agents in cacodylate buffer. The crystals of Endo H belong to the tetragonal space group P4(1)2(1)2 (or P4(3)2(1)2) with cell dimensions: a = 85.22 A, c = 89.41 A. The crystals of Endo F1 belong to the hexagonal space group P6(1) (or P6(5)) with cell dimensions: a = 70.61 A, c = 100.32 A. Crystals of both proteins diffract to at least 1.8 A resolution.

Asymmetric synthesis of 1,3-dioxolane-pyrimidine nucleosides and their anti-HIV activity

In order to study the structure-activity relationships of dioxolane nucleosides as potential anti-HIV agents, various enantiomerically pure dioxolane-pyrimidine nucleosides have been synthesized and evaluated against HIV-1 in human peripheral blood mononuclear cells. The enantiomerically pure key intermediate 8 has been synthesized in nine steps from 1,6-anhydro-D-mannose (1), which was condensed with 5-substituted pyrimidines to obtain various dioxolane-pyrimidine nucleosides. Upon evaluation of these compounds, cytosine derivative 19 was found to exhibit the most potent anti-HIV agent although it is the most toxic. The order of anti-HIV potency was as follows: cytosine (beta-isomer) greater than thymine greater than cytosine (alpha-isomer) greater than 5-chlorouracil greater than 5-bromouracil greater than 5-fluorouracil derivatives. Uracil, 5-methylcytosine, and 5-iodouracil derivatives were found to be inactive. Interestingly, alpha-isomer 20 showed good anti-HIV activity without cytotoxicity. As expected, other alpha-isomers did not exhibit any significant antiviral activity. (-)-Dioxolane-T was 5-fold less effective against AZT-resistant virus than AZT-sensitive virus.

Structure of cis-1-([4-(1-imidazolylmethyl)cyclohexyl]methyl)imidazole- succinic acid complex

CGS 14796C, C14H20N4.C4H6O4, Mr = 362.43, monoclinic, C2/c, a = 28.148 (4), b = 9.722 (1), c = 19.200 (2) A, beta = 133.06 (1) degree, V = 3838.88 A3, Z = 8, Dx = 1.26 Mg m-3, lambda (Cu K alpha) = 1.5418 A, mu 0.702 mm-1, F(000) = 1552, T = 294 K, R = 0.075 for all 3285 reflections. The structure is composed of linear chains of alternating CGS 14796C and succinic acid molecules. The CGS 14796C molecule is in an extended conformation.

Structure of (+/-)-aminoglutethimide

(+/-)-3-(4-Aminophenyl)-3-ethyl-2,6-piperidinedione, C13H16N2O2, Mr = 232.3, monoclinic, P2(1)/n, a = 16.895 (2), b = 8.519 (1), c = 8.762 (1) A, beta = 95.71 (1) degree, V = 1254.9 (2) A3, Z = 4, Dx = 1.23 g cm-3, lambda(Mo K alpha) = 0.71069 A, mu = 0.785 cm-1, F(000) = 496, T = 294 K, R = 0.064 for all 3676 reflections. The molecule is L shaped with the p-aminophenyl and the piperidinedione groups forming the vertical arm and the base, respectively. The polar imide half of the piperidinedione group is in front of the L for the active + enantiomer and at the back for the less-active - enantiomer. The structure is very similar to that of phenobarbital. Intermolecular interactions include one strong and one weak hydrogen bond and an apparent interaction between one of the amino H atoms with the pi cloud of the phenyl ring.

Structure-activity studies of non-steroidal aromatase inhibitors: the crystal and molecular structures of CGS 16949A and CGS 18320B

The crystal and molecular structures of 4-(5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl)benzonitrile hydrochloride (CGS 16949A) and bis(p-cyanophenyl)imidazo-1-yl methane hemisuccinate (CGS 18320B) have been determined as part of structure-activity relationship studies of non-steroidal aromatase inhibitors. CGS 18320B crystallizes with two inhibitor molecules in the asymmetric unit that are similar in conformation. The cyanophenyl groups and the imidazole moieties in the CGS 18320B molecules display a propellor-like arrangement. The orientation of the imidazole ring in CGS 16949A, which is constrained by the piperidine ring, differs by about 80 degrees from the orientations in both CGS 18320B molecules. The conformations of both compounds are consistent with the proposed model (Banting et al. (1988) J. Enz. Inhibit., 2, 216) for inhibitor binding by positioning of the cyanophenyl group in the steroid A-ring binding site and interaction of the imidazole nitrogen with the iron of the haem.

Crystal structure analysis of auromomycin apoprotein (macromomycin) shows importance of protein side chains to chromophore binding selectivity

The crystal structure of macromomycin, the apoprotein of the antitumor antibiotic auromomycin, has been determined and refined at 1.6-A resolution. The overall structure is composed of a flattened seven-stranded antiparallel beta-barrel and two antiparallel beta-sheet ribbons. The barrel and the ribbons define a deep cleft that is the chromophore binding site. The cleft is very accessible and in this structure is occupied by two 2-methyl-2,4-pentanediol and two water molecules. The overall shape of the binding site is similar to that of the analogue actinoxanthin. Highly specific side chains that are not conserved between different analogues extend into the binding site and may be important to the chromophore binding specificity.

Correlation between preferred sugar ring conformation and activity of nucleoside analogues against human immunodeficiency virus

Analysis of the solid-state conformations of six active and two inactive anti-human immunodeficiency virus nucleoside analogues is used to correlate conformational features with the relative activities of the compounds. Ten of the 11 observations of the active compounds (3'-azido-3'-deoxythymidine, 3'-azido-2',3'-dideoxyuridine, 3'-azido-2',3'-dideoxy-5-ethyluridine, 2',3'-dideoxyadenosine, 2',3'-dideoxycytidine, and 3'-deoxythymidine) have C3'-exo sugar ring conformations. The only exception is one of the two molecules of 3'-deoxythymidine. Four have unusual low anti glycosyl link conformations coupled with unusual C3'-exo/C4'-endo sugar ring conformations. The inactive compounds, 2',3'-dideoxyuridine and 3'-(propyl-2-ene)-2',3'-dideoxyuridine, have C3'-endo conformations. The C3'-exo and C3'-endo conformations place C5' in axial and equatorial positions, respectively. This affects the location of the 5'-hydroxyl group in relation to the location of the base. The 5'-hydroxyl group is the site of phosphorylation of the nucleoside and the observation of this conformational preference of the active compounds may be of importance for the development of new nucleosides with activity against human immunodeficiency virus.

Crystallization of prostatic binding protein

Prostatic binding protein is a dimeric glycoprotein capable of binding a variety of steroids. This protein is a major component of rat prostate cytosol making it possible to purify milligram quantities. Hexagonal crystals of X-ray diffraction quality have been grown from phosphate buffered ammonium sulfate solution by vapor diffusion methods. These crystals which are reasonably stable to X-rays, show diffraction to 6.3 A and belong to space group P6(1) or P6(1)22 or the enantiomorphs. The unit cell has dimensions a = 88.7(5) A, c = 405(2) A, contains 24 molecules and has a specific volume of 2.8 A3/Dalton.

Structure of 4-methylumbelliferyl-beta-D-glucopyranoside

C16H17O8.1.5H2O, Mr = 364.33, monoclinic, C2, a = 14.314 (3), b = 6.851 (1), c = 18.178 (5) A, beta = 100.90 (2) degrees, V = 1750.46 A3, Z = 4, D chi = 1.382 Mg m-3, lambda(Mo K alpha) = 0.71069 A, mu = 0.933 mm(-1), F(000) = 768, T = 294 K, R = 0.078 for all 2160 reflections. The structure is characterized by the close stacking along the b axis of the planar 4-methylumbelliferyl ring system which is nearly perpendicular to b and the extensive hydrogen bonding scheme in which all hydroxyl groups are within 2.95 A of at least two other O atoms.

Crystal and molecular structure of tert.-butyloxycarbonyl-L-prolyl-alpha-aminoisobutyryl-L-alanyl-alpha- aminoisobutyrate methyl ester

Boc-Pro-Aib-Ala-Aib-OMe crystallizes in the orthorhombic space group P2(1)2(1)2 with cell dimensions a = 17.701 (3) A, b = 17.476 (4) A, c = 9.686 (2) A, V = 2996.3 A3. The first three residues form a single turn of a 3(10)-helix stabilized by two intramolecular hydrogen bonds. Comparison of the conformation of the methyl ester of the tetrapeptide with that of its benzyl ester shows differences in the individual torsion angles of up to 29 degrees, although the overall conformation is conserved.

Crystal and molecular structure of tert.-butyloxycarbonyl-L-hydroxy-prolyl-alpha-aminoisobutyryl-alpha-aminoisobutyryl-L-phenylalaninol

The crystal structure of the synthetic tetrapeptide, Boc-Hyp-Aib-Aib-Phol, an analogue of the C-terminal tetrapeptide in the antibiotic antiamoebin I, was determined as part of a study of the conformation of peptaibophol antibiotics. The crystals are orthorhombic, space group P212121, with cell parameters a = 16.576 (1) A, b = 17.657 (1) A, c = 10.435 (1) A, V = 3053.9 (2) A3, Z = 4, Dc = 1.163 g.cm-3. The three amino acids from a single turn of a 3 10-helix, stabilized by two intramolecular hydrogen bonds. The Aib residues adopt the usual conformation in the region between the 3 10- and alpha-helices. The terminal hydroxy methyl group of the phenylalaninol residue is disordered. The position of the benzyl side chain of the amino alcohol relative to the backbone corresponds to a conformation also observed in phenylalanine residues.