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S Neidle

Publications and source records attributed to S Neidle.

At least 109 records · Page 6Linked to original sources
PubMed1991

Studies on 1,3-diaryltriazene analogues of berenil: molecules with potential GC base-pair selectivity.

1,3-Bis(4-acetylphenyl)triazene (II): C16H15N3O2, Mr = 281.32, monoclinic, P2(1)/c, a = 14.002 (5), b = 12.359 (3), c = 8.457 (3) A, beta = 96.35 (2) degrees, V = 1454.5 A3, Z = 4, Dx = 1.287 Mg m-3, Cu K alpha, lambda = 1.54178 A, mu = 0.672 mm-1, F(000) = 592, T = 294 K, final R = 0.089 for 1890 unique observed reflections. 1,3-Bis(4-[2-dimethylamino)ethoxycarbonyl]phenyl)triazene monohydrate (III): C22H29N5O4.H2O, Mr = 445.52, triclinic, P1, a = 9.500 (2), b = 11.753 (3), c = 13.328 (2) A, alpha = 62.84 (1), beta = 66.60 (2), gamma = 77.58 (2) degrees, V = 1214.1 A3, Z = 2, Dx = 1.172 Mg m-3, Cu K alpha, lambda = 1.54178 A, mu = 0.640 mm-1, F(000) = 476, T = 294 K, final R = 0.063 for 1100 unique observed reflections. Both crystal structures have extended conformations for the 1,3-diaryltriazene groups, with a cisoid arrangement of phenyl rings. The terminal N--N bonds of each triazene are non-equivalent, and a hydrogen atom has been located in the N==N--NH moiety. Extensive molecular-orbital (MNDO) calculations on the model core 1,3-diphenyltriazene system have confirmed that this geometry is energetically favoured, and have revealed the shape of the energy surface for rotation about the N--NH bond in the triazene linkage.

Base Composition↗
PubMed1991

Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR.

The conformation of the EcoRI dodecamer d(CGCGAATTCGCG)2 has been examined in solution by 1H and 31P NMR. Spin-spin coupling constants and nuclear Overhauser (NOE) enhancement spectroscopy show that all deoxyriboses lie in the south domain, with a small admixture of the north conformation (0-20%). The time dependence of the nuclear Overhauser enhancements also reveals a relatively uniform conformation at the glycosidic bonds (average angle, chi = -114 degrees). The average helical twist is 36.5 degrees (9.8 base pairs per turn). Tilt angles are small (in the range 0 to -10 degrees), and roll angles are poorly determined. Unlike single-crystal X-ray studies of the same sequence, there is no evidence for asymmetry in the structure. Both the NOE intensities and 31P relaxation data imply conformational anomalies at the C3-G4/C9-G10 and the A5-A6/T7-T8 steps. Berenil binds in 1:1 stoichiometry to the dodecamer with high affinity (Kd = 1 microM at 298 K) and causes substantial changes in chemical shifts of the sugar protons of nucleotides Ado 5-Cyt 9 and of the H2 resonances of the two Ado residues. No significant asymmetry appears to be induced in the DNA conformation on binding, and there is no evidence for intercalation, although the binding site is not centrosymmetric. NOEs are observed between the aromatic protons of berenil and the H1' of both Thy 7 and Thy 8, as well as to Ado 5 and Ado 6 H2. These results firmly establish that berenil binds via the minor groove and closely approaches the nucleotides Ado 6, Thy 7, and Thy 8. On the basis of quantitative NOE spectroscopy and measurements of spin-spin coupling constants, changes in the conformations of the nucleotides are found to be small. Using the observed NOEs between the ligand and the DNA together with the derived glycosidic torsion angles, we have built models that satisfy all of the available solution data. The berenil molecule binds at the 5'-AAT (identical to 5'-ATT on the complementary strand) site such that (i) favorable hydrogen bonds are formed between the charged amidinium groups and the N3 atoms of Ado 6 and Ado 18 and (ii) the ligand is closely isohelical with the floor of the minor groove.

Base Sequence↗
PubMed1991

Molecular dynamics simulations of dinucleoside and dinucleoside-drug crystal hydrates.

Molecular dynamics simulations have been performed on the dinucleoside monophosphates rGpC and dCpG, the latter in its intercalation complex with the acridine drug proflavine. The simulations were performed on the crystal structures, with crystallographically-located solvent molecules. It was found that satisfactory results were best obtained with restraints placed on the movements of the water molecules. Motions of individual atoms have been examined in terms of rms fluctuations and anisotropy and correlation functions. Relative motions of groups (phosphates, sugars, bases and proflavine molecules) have been analysed.

Computer Simulation↗
PubMed1990

A molecular model for the enzyme cytochrome P450(17 alpha), a major target for the chemotherapy of prostatic cancer.

The enzyme cytochrome P450(17 alpha) catalyses two key steps in the biosynthesis of the androgens from pregnanes: the 17 alpha hydroxylation step and the subsequent 17-20 lyase reaction. Using a variety of techniques, including sequence alignment, secondary structure prediction, molecular mechanics and molecular dynamics, we have constructed a model for the three-dimensional structure of P450(17 alpha) based on that of P450cam, the only cytochrome P450 enzyme for which the crystal structure is known. The model suggests the possibility of two modes of binding of steroid substrates at the active site, perhaps reflecting the dual functionality of the enzyme.

Amino Acid Sequence↗
PubMed1990

Crystal and solution structures of the oligonucleotide d(ATGCGCAT)2: a combined X-ray and NMR study.

A combined crystal-structure determination and NMR analysis of the octanucleotide d(ATGCGCAT)2 is reported. The X-ray analysis shows that the structure is A-form duplex in crystal state. The NMR study shows that in solution this sequence is B-type. The conformational results from each technique are presented in detail. The implications of these findings in terms of conformational flexibility and ligand binding are discussed.

Base Sequence↗
PubMed1990

Interaction of berenil with the tyrT DNA sequence studied by footprinting and molecular modelling. Implications for the design of sequence-specific DNA recognition agents.

We have developed a technique of partially-restrained molecular mechanics enthalpy minimisation which enables the sequence-dependence of the DNA binding of a non-intercalating ligand to be studied for arbitrary sequences of considerable length (greater than = 60 base-pairs). The technique has been applied to analyse the binding of berenil to the minor groove of a 60 base-pair sequence derived from the tyrT promoter; the results are compared with those obtained by DNAse I and hydroxyl radical footprinting on the same sequence. The calculated and experimentally observed patterns of binding are in good agreement. Analysis of the modelling data highlights the importance of DNA flexibility in ligand binding. Further, the electrostatic component of the interaction tends to favour binding to AT-rich regions, whilst the van der Waals interaction energy term favours GC-rich ones. The results also suggest that an important contribution to the observed preference for binding in AT-rich regions arises from lower DNA perturbation energies and is not accompanied by reduced DNA structural perturbations in such sequences. It is therefore concluded that those modes of DNA distortion favourable to binding are probably more flexible in AT-rich regions. The structure of the modelled DNA sequence has also been analysed in terms of helical parameters. For the DNA energy-minimised in the absence of berenil, certain helical parameters show marked sequence-dependence. For example, purine-pyrimidine (R-Y) base pairs show a consistent positive buckle whereas this feature is consistently negative for Y-R pairs. Further, CG steps show lower than average values of slide while GC steps show lower than average values of rise. Similar analysis of the modelling data from the calculations including berenil highlights the importance of DNA flexibility in ligand binding. We observe that the binding of berenil induces characteristic responses in different helical parameters for the base-pairs around the binding site. For example, buckle and tilt tend to become more negative to the 5'-side of the binding site and more positive to the 3'-side, while the base steps at either side of the centre of the site show increased twist and decreased roll.

Amidines↗
PubMed1990

Conformational effects of nucleotide exchange in ras p21 proteins as studied by fluorescence spectroscopy.

The intrinsic fluorescence properties of the oncogene protein p21N-ras,p21H-ras and one of its transforming mutants, p21N-ras (Val12), have been investigated. A mutant containing a single tryptophan at position 28 in p21H-ras (Trp28) has been specifically engineered to provide a probe of protein conformation on nucleotide binding. The proteins produced essentially similar circular dichroism spectra typical of alpha/beta proteins. A decrease in the intensity of the fluorescence emission spectrum due to tyrosine occurred on GDP/GTP nucleotide exchange in the native and mutant proteins. Selective excitation of the single tryptophan in p21 produced a decrease in fluorescence intensity which was accompanied by a blue shift in the wavelength of maximum emission on nucleotide exchange. A reduction in the residual Mg2+ ion concentration enhanced this effect.

Circular Dichroism↗
PubMed1990

Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding.

The three-dimensional structure of a complex between the dodecanucleotide d(CGCGAATTCGCG) and the anti-trypanocidal drug berenil, has been determined to a resolution of 2.5 A. The structure has been solved by molecular replacement and refined to an R factor of 0.177. A total of 49 water molecules have been located. The drug is bound at the 5'-AAT-3' region of the oligonucleotide. At one end of the drug the amidinium group is in hydrogen-bonded contact with N3 of the adenine base complementary to the thymine of the AAT. The other amidinium group does not make direct interactions with the DNA. Instead, a water molecule mediates between them. This is in hydrogen-bonded contact with an amidinium nitrogen atom, N3 of the 5' end adenine base and the ring oxygen atom of an adjacent deoxyribose. Molecular mechanics calculations have been performed on this complex, with the drug at various positions along the sequence. These show that the observed position is only 0.8 kcal/mol higher in energy than the best position. It is suggested that there is a broad energy well in the AATT region for this drug, and that water molecules as well as the neighbouring sequence, will determine precise positioning. More general aspects of minor groove binding are discussed.

Amidines↗
PubMed1990

Crystallographic and molecular modeling studies on 3-ethyl-3-(4-pyridyl)piperidine-2,6-dione and its butyl analogue, inhibitors of mammalian aromatase. Comparison with natural substrates: prediction of enantioselectivity for N-alkyl derivatives.

Inhibitors of the cytochrome P450 enzyme aromatase, which is involved in the biosynthesis of estrogens from androgens, are of proven utility in the treatment of hormone-dependent breast cancer. The determination of the crystal structure of one such inhibitor, 3-ethyl-3-(4-pyridyl)piperidine-2,6-dione (2) and its 3-butyl analogue (3) is described. In the absence of three-dimensional structural information for the enzyme, conformational analysis and comparison with natural substrates has been performed in order to define possible "active" conformations. The enhanced inhibitory activity of 3 may be linked to hydrophobic interactions between the side chain and that portion of the enzyme that normally interacts with the B and C rings of a steroid substrate. Information gained from this study and previous studies by other workers has been combined in order to produce a hypothesis to explain the pattern of activity of N(1)-alkyl derivatives of 2. The successful application of this hypothesis to the prediction of the relative aromatase inhibitory activities of the two enantiomers of the N-octyl derivative (4) is described.

Aminoglutethimide↗
PubMed1990

Inhibitors of the P450 enzymes aromatase and lyase. Crystallographic and molecular modeling studies suggest structural features of pyridylacetic acid derivatives responsible for differences in enzyme inhibitory activity.

Derivatives of 4-pyridylacetic acid are known to be inhibitors of the cytochrome P450 enzymes aromatase and lyase (17 alpha-hydroxylase/C17-20lyase), and are therefore of interest in the treatment of hormone dependent breast and prostate cancers. We report the determination of the crystal structure of one such derivative, the 4-tert-butyl cyclohexyl ester, and molecular modeling studies on two related inhibitors, the cyclohexyl ester and its alpha-methyl derivative. These latter two compounds show a marked difference in their relative activities against aromatase and lyase. Two models are proposed for the interaction of these molecules with the target enzymes on the basis of their ability to adopt conformations that partially mimic steroid substrates. From these models an explanation can be advanced for the fact that, compared with the unmethylated analogue, the (racemic) alpha-methylated compound is seven times poorer as an inhibitor of aromatase but seven times better as an inhibitor of lyase. The model proposed for binding to aromatase places the alpha-carbon of the ester group in the position occupied by C(2) of steroid substrates. In contrast, that proposed for binding to lyase places this atom in the position occupied by C(17) of steroid substrates. The introduction of steric bulk at C(2) is known to be unfavorable for aromatase inhibition, while its introduction at C(17) may lead to a better mimicry of the steroid D-ring and so improve lyase inhibition.

Acetates↗
PubMed1990

Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG).

The crystal structure of the dodecanucleotide d(CGCAAGCTGGCG) has been determined to a resolution of 2.5 A and refined to an R factor of 19.3% for 1710 reflections. The sequence crystallizes as a B-type double helix, with two G(anti).A(syn) base pairs. These are stabilized by three-center hydrogen bonds to pyrimidines that induce perturbations in base-pair geometry. The central AGCT region of the helix has a wide (greater than 6 A) minor groove.

Adenine↗
PubMed1990

Molecular-mechanics modelling of drug-DNA structures; the effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model.

This study analyses the influence that the nature of the dielectric constant has on the final structures obtained from in vacuo molecular mechanics calculations on a drug-DNA complex and compares these structures with the energy minimised complex including explicit solvent molecules. Minimisations have been performed on a proflavine-decanucleotide structure, where the drug was intercalated at the d(CpG) site of the d(GpApTpApCpGpApTpApC) decamer duplex, using two expressions for the dielectric constant: a distance-independent, epsilon ij = EPS, and a distance-dependent, epsilon ij = EPS*Rij, form and for values of EPS from 1 to 8. Significantly different structures are obtained for the distance-independent and the distance-dependent expressions of the dielectric constant. The use of a distance-independent dielectric constant leads to distorted structures, which are very sensitive to slight changes in the value of EPS. The use of a distance-dependent dielectric constant leads to less distorted and more stable structures. The effects on helical parameters are analysed in detail. The structures obtained for different values of EPS (within the distance-dependent formalism) seem to converge for values of EPS equal to 4 or greater. Based on these results a distance-dependent form of the dielectric with an EPS value of 4 is recommended in order to produce reliable refined nucleic acid structures by molecular mechanics. These conclusions have been supported by molecular-mechanics minimisation of the same structure with the inclusion of explicit water molecules and counter-ions.

Base Composition↗
PubMed1990

Structural studies on bio-active compounds. Part XIV. Molecular modelling of the interactions between pentamidine and DNA.

Molecular mechanics modelling was carried out on the antimicrobial aromatic diamidine, pentamidine, bound to the minor groove of several AT-rich DNA octamers. The pentamidine molecule was found to span four base pairs, with its highly charged amidinium groups forming hydrogen bonds to the O2 of thymine or the N3 of adenine, but not to the backbone phosphate groups. The mean binding energy of the pentamidine-DNA complexes was -52 kcal/mol, of the same order as that of berenil-DNA complexes. There was no significant energy difference between those models which contained GC base pairs and those which did not. The presence of bound pentamidine resulted in some distortion of helix geometry involving helix opening towards the minor groove in most cases and a decrease in the number of residues per turn.

Base Sequence↗
PubMed1990

The non-covalent interaction of pyrrolo[2, 1-c] [1, 4]benzodiazepine-5, 11-diones with DNA.

A series of 15 pyrrolo[2, 1-c] [1, 4]benzodiazepine-5, 11-diones has been synthesized and evaluated for in vitro DNA binding by thermal denaturation and fluorescence quenching studies with calf thymus (CT) DNA. The results indicate that two compounds of the series, 7 and 8, elevate the melting point of DNA by 2.9 +/- 0.6 and 3.3 +/- 0.8 K, respectively. Similarly, a significant quenching of the fluorescence of the dihydroxy analogue 8 was observed upon interaction with CT-DNA. As controls, the dihydroxy isomer 9 with the reverse stereochemistry at C2 and the non-substituted parent dilactam 12, failed to increase the DNA melting point or exhibit significant quenching upon interaction with DNA. In addition, preliminary experiments with GC- and AT-rich polymers suggest some sequence-dependent properties for dilactams 7 and 8. Overall, these results indicate a highly specific structural requirement for DNA binding. Molecular modelling with d(GTAGATC), d(GCAGATC) and d(GCGTAGC) duplex sequences has provided a model based on hydrogen bonding between the dihydroxy dilactam 8 and DNA, that rationalizes some of the results obtained. It is possible that the observed interactions represent the non-covalent (binding) component of the interaction of covalently-bonding anthramycin-type anti-tumour antibiotics with DNA.

Anthramycin↗
PubMed1989

The anti-conformation of 2',3'-dideoxy nucleosides may be essential for anti-HIV activity: evidence from the crystal structure of 2',3'-dideoxy formycin A.

The crystal structure of the nucleoside 2',3'-dideoxyformycin A has been determined. The structure shows a syn conformation about the glycosidic bond, stabilised by an intramolecular hydrogen bond between the 05' and N3 atoms. HIV activity was examined in a syncytium inhibition assay. In contrast to the marked decrease in viral titre observed with 2',3'-dideoxycytidine, the formycin analogue produced no effect. It may be concluded that the syn conformation for a dideoxy nucleoside is probably deleterious to HIV inhibition of HIV replication.

Antiviral Agents↗
PubMed1989

Structures of three DNA cross-linking agents, ethane-1,2-di(methylsulfonate), propane-1,3-di(methylsulfonate) and n-butane-1,4-di(methylsulfonate).

(I): C4H10O6S2, Mr = 218.25, P2(1)/c, a = 7.2611 (9), b = 5.8726 (4), c = 10.6628 (19) A, beta = 103.95 (1) degree, V = 441.3 (2) A3, Z = 2, Dm = 1.65, Dx = 1.642 Mg m-3, lambda(Cu K alpha) = 1.54184 A, mu = 5.43 mm-1, F(000) = 228, R = 0.0336 and wR = 0.0346 for 745 unique reflections with F greater than or equal to 3 sigma (F), T = 298 K. (II): C5H12O6S2, Mr = 232.28, P2(1)/c, a = 11.030 (1), b = 8.452 (1), c = 11.162 (1) A, beta = 104.65 (1) degree, V = 1006.8 (3) A3, Z = 4, Dm 1.54, Dx = 1.532 Mg m-3, lambda(Cu K alpha) = 1.54184 A, mu = 4.79 mm-1, F(000) = 488, R = 0.0418 and wR = 0.0430 for 1666 unique reflections with F greater than or equal to 3 sigma(F), T = 298 K. (III): C6H14O6S2, Mr = 246.30, P1, a = 5.6147 (9), b = 6.8343 (6), c = 7.5434 (6) A, alpha = 110.61 (1), beta = 92.08 (1), gamma = 76.15 (1) degree, V = 262.7 (3) A3, Z = 1, Dm = 1.56, Dx = 1.557 Mg m-3, lambda(Cu K alpha) = 1.54184 A, mu = 4.79 mm-1, F(000) = 130, R = 0.0397 and wR = 0.0425 for 907 unique reflections with F greater than or equal to 3 sigma(F), T = 298 K. All three compounds have a common conformation in the C.O.SO2.CH3 part of the molecules due to weak O...H interactions. Compounds (I) and (III) have a trans conformation about the central C--C bond, whereas (II) is cis.

Busulfan↗
PubMed1989

Preliminary crystallographic data for NAD(P)H quinone reductase isolated from the Walker 256 rat carcinoma cell line.

An NAD(P)H quinone reductase isolated from Walker rat 256 carcinoma cells has been crystallized in a form suitable for high-resolution structural analysis. The crystals belong to orthorhombic space group P2(1)2(1)2(1) with cell parameters a = 168.15 A, b = 105.09 A and c = 67.38 A and contain four monomeric or two dimeric enzyme molecules per asymmetric unit. Diffraction extends beyond 2.3 A resolution.

Animals↗