Biomedical subjects

S Neidle

Publications and source records attributed to S Neidle.

At least 91 records · Page 5Linked to original sources

PubMed1993

Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine.

The crystal structure of the complex between propamidine and the self-complementary DNA dodecamer d(CGCGAATTCGCG) duplex has been determined to a resolution of 2.1 A and a R-factor of 17.4%. The propamidine binds to the DNA within the minor groove, with specific hydrogen-bonding interactions from the amidinium groups to the bases and sugar groups of the DNA, via a 4-base-pair binding site. A network of water molecules lies over the mouth of the minor groove. The structure provides a rationale for the superior DNA-binding properties of propamidine as compared to pentamidine [cf. Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. This is seen to result from (i) decreased minor groove width at the binding site and (ii) reduced mobility of the bound propamidine molecule.

Base Sequence↗

PubMed1993

NMR and molecular modeling studies of the interaction of berenil and pentamidine with d(CGCAAATTTGCG)2.

The interaction of two anti-trypanosomal agents, berenil and pentamidine, with the A+T-rich dodecamer d(CGCAAATTTGCG)2 has been examined by high-resolution 1H-NMR, optical spectroscopy, and molecular modeling. Proton assignments for the free DNA and each DNA-ligand complex were obtained using nuclear Overhauser enhancement spectroscopy and total correlation spectroscopy. Complexation induces large changes in chemical shift for protons in the DNA minor groove for the A5-T9 segment, and intermolecular NOEs reveal contacts between the DNA bases and each ligand. The asymmetric binding site for berenil indicated by the NMR data suggests that at least two overlapping sites are involved. Rapid exchange between symmetrically-equivalent binding sites, via dissociative rearrangement, is consistent with retention of twofold degeneracy for both the ligand and the DNA host. Calculations of binding energy confirm that this DNA duplex contains overlapping sites of similar binding affinity. In contrast, the larger pentamidine molecule occupies a site that spans four or five bp, with asymmetric binding to the minor-groove 5'-ATTT sequence. The B-type conformation of the DNA is not altered substantially by either ligand.

Base Sequence↗

PubMed1993

Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation.

The structure of the G.G mispaired dodecanucleotide d(CGCGAATTGGCG)2 has been solved by x-ray crystallography and refined to an R factor of 18.8% at 2.2 A resolution for 3513 reflections. The dodecamer crystallizes as a B-type DNA double helix. It contains two G(anti).G(syn) base pairs--i.e., G-4/G-16(anti).G-21/G-9(syn). The Hoogsteen base pairing involves atoms O-6 and N-7 of the guanine in the syn conformation with atoms N-1 and N-2 of the anti-paired purine. One G.G base pair has a bifurcated hydrogen bond between G-4(N-1)...G-21(N-7) and G-4(N-1)...G-21(O-6). There is little overall structural distortion of the double helix induced as a consequence of the mispairing. The helical width is significantly increased by comparison with the structure of the native duplex, and the minor groove width in the 5'-AATT region is decreased. The G.G base pairing induces high-BII phosphate conformations at residues G-9 and T-20 in addition to more normal BII conformations at G-10 and G-22. It is suggested that these backbone aberrations provide signals for the facile repairability of G.G mispairs in DNA.

Base Composition↗

PubMed1993

A detailed molecular model for human aromatase.

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 P-450arom (human aromatase) based on that of P-450cam, the only cytochrome P-450 enzyme for which the crystal structure is known. The predicted structure is found to be in good agreement with current experimental data; both direct, from site-directed mutagenesis studies, and indirect, from the consideration of the structures and activities of known substrates and inhibitors.

Amino Acid Sequence↗

PubMed1993

DNA minor groove recognition properties of pentamidine and its analogs: a molecular modeling study.

A molecular mechanics and molecular dynamics approach has been used to examine the structure of the complex formed between pentamidine and the d(CGCGAATTCGCG)2 duplex. Similar energy calculations have also been performed on complexes with closely related pentamidine analogs, using the complex with the parent drug as the starting point. The resulting structures of the drug-DNA complexes and their energetics have been examined and are compared with the reported DNA binding affinities. These studies provide rationalizations for the differences in binding behavior of pentamidine analogs with differing linker chain lengths and aromatic ring substitutions.

Base Sequence↗

PubMed1992

Prediction of the structure of the Y+.R-.R(+)-type DNA triple helix by molecular modelling.

Molecular mechanics has been used to predict the structure of the Y+.R-.R(+)-type DNA triple helix, in which a second polypurine strand binds antiparallel to the homopurine strand of a homopurine/homopyrimidine stretch of duplex DNA. From calculations on the sequence d(C)10.d(G)10.d(G)10, two likely structures emerge. One has the glycosidic torsions of the third strand bases in the anti-conformation and Hoogsteen hydrogen-bonds to the purine strand of the duplex, the other has the third strand purines in the syn orientation and uses a reverse-Hoogsteen hydrogen-bonding pattern. Despite the large structural differences between these two types of triplex, calculations performed in vacuo with a distance-dependent dielectric constant to mimic the shielding effect of solvent show them to be energetically very similar, with the latter (syn) slightly preferred. However, if explicit solvent molecules are included in the calculation, the anti conformation is found to be much preferred. This difference in the results seems to stem from an underestimation of short-range electrostatic interactions in the in vacuo simulations. When TAA or TAT base triples are substituted for the sixth CGG triple in the sequence, it is found that, for the solvated model, the third strand base of the TAA triple prefers the syn orientation while that in the TAT triple retains a preference, though reduced, for the anti conformation.

Base Sequence↗

PubMed1992

Substituent position dictates the intercalative DNA-binding mode for anthracene-9,10-dione antitumor drugs.

Molecular modeling studies [Islam, S.A., Neidle, S., Gandecha, B.M., Partridge, M., Patterson, L.H., & Brown, J.R. (1985) J. Med. Chem. 28, 857-864] have suggested that anthracene-9,10-dione (anthraquinone) derivatives substituted at the 1,4 and 1,8 positions with-NH(CH2)2NH(CH2CH3)2+ side chains intercalate with DNA with both substituents in the same groove (classical intercalation) while a similarly substituted 1,5 derivative intercalates in a threading mode with one side chain in each groove. Modeling studies also suggested that anthracene-9,10-dione (anthraquinone) derivatives substituted at the 2,6 positions with -NHCO(CH2)R (where R is a cationic group) should bind to DNA by the threading mode, and several such derivatives have been synthesized [Agbandjie, M., Jenkins, T.C., McKenna, R., Reszka, A., & Neidle, S. (1992) J. Med. Chem. 35, 1418-1429]. We have conducted stopped-flow kinetics association and dissociation experiments on the interaction of these anthraquinones with calf thymus DNA and with DNA polymers with alternating AT and GC base pairs to experimentally determine the binding mode and how the threading mode affects intercalation rates relative to similarly substituted classical intercalators. The binding modes, determined by analysis of relative rates, energies of activation, and effects of salt concentration on association and dissociation rate constants, agree completely with the modes predicted by molecular modeling methods. Association and dissociation rate constants for the threading mode are approximately a factor of 10 lower than constants for the classical intercalation mode, and the two modes, thus, have similar binding constants. Variations in rate constants for changes in cationic substituents at the 2 and 6 positions of the anthraquinone ring were surprisingly small.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1992

Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution.

The crystal structure of the dodecanucleotide duplex d(CGCAAATTTGCG)2 has been solved to 2.2 A resolution and refined to an R-factor of 18.1% with the inclusion of 71 water molecules. The structure shows propeller twists of up to -20 degrees for the A.T base-pairs, although there is probably only one (weak) three-centre hydrogen bond in the six base-pair AT narrow minor-groove region. An extensive ribbon of hydration has been located in this groove that has features distinctive from the classic "spine of hydration". Solvation around phosphate groups is described, with several instances of water molecules bridging between phosphates.

Base Composition↗

PubMed1992

Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.

The crystal structure of the complex formed between the dodecanucleotide d(CGCGAATTCGCG)2 and the drug pentamidine, which is active against the Pneumocystis carinii pathogen in AIDS patients, has been determined to a resolution of 2.1 A and an R-factor of 19.4%. Analysis of the structure has shown the drug to be bound in the 5'-AATT minor groove region of the duplex, with the amidinium groups H-bonded to adenine N3 atoms in an interstrand manner. The drug molecule adopts an extended conformation, and the immediate binding site spans four base pairs. Structural details of the drug-DNA interactions are discussed, and comparison is made with the dodecamer complex of the structurally similar berenil ligand.

Base Sequence↗

PubMed1992

A note on the conformational flexibility of the antiestrogenic drug tamoxifen: preferred conformations in the free state and bound to the protein calmodulin.

The conformational properties of the antiestrogenic drug tamoxifen, a triphenylbut-1-ene derivative, have been studied using molecular mechanics. Four distinct conformers have been identified, and the energy barriers between them have been established. The orientation of the ethyl group substituent has been examined in particular, since the lowest-energy conformers have this group orientated 180 degrees away from its position in the crystal structures of tamoxifen and its derivatives. These differences have implications for the interactions of tamoxifen with the calcium-binding protein calmodulin; relevant results from a molecular-modelling study of this protein-drug complex are presented.

Calmodulin↗

PubMed1992

A molecular modeling study of the interactions between the antiestrogen drug tamoxifen and several derivatives, and the calcium-binding protein calmodulin.

The interactions of the antiestrogenic drug tamoxifen with the calcium-binding protein calmodulin have been studied by computerized molecular modeling methods. Sites in both the N and C domains of the protein have been established, with one in the C domain having the highest calculated enthalpy of binding. The residues involved in the sites have been detailed. Modeling studies are reported for six tamoxifen derivatives, and their calculated enthalpies of binding are compared with the ability of the analogues to inhibit calmodulin-dependent cyclic AMP phosphodiesterase (PDE) (Rowlands et al. Biochem, Pharmacol. 1990, 40, 283-289). The poor binding properties of the piperazino and C-methyl derivatives are correctly predicted, whereas the superior affinity of 4-iodotamoxifen is not fully explained by the model.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed1992

Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features.

The AT-selective drug berenil has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The crystal structure has been solved to a resolution of 2.0 A and an R factor of 18.3%, with the location of 65 water molecules. The drug is symmetrically bound in the 5'-AATT region of the minor groove, with its amidinium groups hydrogen-bonding to O-2 atoms of the thymine base at each end of the binding site. This arrangement is distinct from that previously found for berenil with the sequence d(CGCGAATTCGCG)2, which has the drug bound to the sequencing 5'-ATT via hydrogen bonds to adenine N-3 atoms with the involvement of a bridging water molecule at one end of the binding site. The reasons for these differences are discussed in terms of changes in helical parameters; in particular propeller twist and base-pair roll are considered to be important. The conformational and base-pair geometry of the dodecanucleotide in the structure reported here, is closely similar to that for the native structure, suggesting that the 5'-AAATTT sequence does not significantly alter during drug binding, either because of its inflexibility or because its geometry is nearly ideal for berenil binding.

Base Sequence↗

PubMed1992

Anthracene-9,10-diones as potential anticancer agents. Synthesis, DNA-binding, and biological studies on a series of 2,6-disubstituted derivatives.

A series of 2,6-bis(omega-aminoalkanamido)anthracene-9,10-diones (9,10-anthraquinones), of general formula Ar(NHCO(CH2)nNR2)2, where Ar = anthracene-9,10-dione and n = 1 or 2, have been synthesized by treatment of the corresponding bis(omega-haloalkanamido) derivatives with appropriate secondary amines. The DNA-binding properties of these compounds were evaluated by thermal denaturation studies, unwinding of closed-circular DNA, determination of association constants in solution, and examined by molecular modeling. A representative compound in the series has been examined by X-ray crystallography. In vitro cytotoxicity data is reported for the compounds and some indications of structure-activity relationships have been discerned. In particular, those compounds with two methylene links (n = 2) in each side chain separating the amide and terminal amine moieties have superior activity and, in general, enhanced DNA binding characteristics. It is postulated that the mode of reversible binding of these compounds to DNA involves the side chains occupying both major and minor grooves and, further, that this may confer cytotoxic properties which are distinct from those of previously reported anthracene-9,10-dione cytotoxins.

Animals↗

PubMed1992

X-ray studies on anti-tumour triazenes. Structures of 1-(4-carbamoylphenyl)-3,3-dimethyltriazene 1-oxide and 3,3-dimethyl-1-(4-nitrophenyl)triazene.

The molecular structures of the title compounds have been determined by X-ray crystallographic methods. The analyses revealed differences in the geometry, and by inference the bond delocalization in these two triazenes owing to the presence in the 1-oxide structure of an N-O bond. The geometries are compared to the crystal structures of the isomeric 3-oxides [Kuroda & Wilman (1985). Acta Cryst. C41, 1543-1545; Neidle, Webster, Kuroda & Wilman (1987). Acta Cryst. C43, 674-676] which shows the dominance of an alternative tautomeric equilibrium for the triazene groups.

Computer Graphics↗

PubMed1992

Minor-groove width and accessibility in B-DNA drug and protein complexes.

A new definition is presented for minor-groove width in double-helical B-DNA structures. This uses interstrand H4' ... H5' rather than P ... P distances. It is shown by examination of various oligonucleotide crystal structures that these H4' ... H5' distances are a sensitive measure of minor-groove drug and protein binding, since these hydrogen atoms are in direct non-bonded contact with such bound ligands.

Base Composition↗

PubMed1992

Molecular dynamics simulation of the DNA triplex d(TC)5.d(GA)5.d(C+T)5.

A molecular dynamics simulation of the DNA triple helix d(TC)5.d(GA)5.d(C+T)5 is described (C+ represents a protonated cytosine residue). The simulation has been performed using the program AMBER 3.1 and includes counterions and explicit solvent under periodic boundary conditions. Both the dynamic and time-averaged behaviour of the system has been analysed. Considerable deviations from the fibre-diffraction model for DNA triple helix structure are observed, including the repuckering of the purine strand sugars that has been identified in some nuclear magnetic resonance (n.m.r.) studies. The simulation suggests that this conformational change may be driven by the possibility of improved interactions between the phosphate groups of this strand and both the solvent and counterions. Several examples of a particular conformational transition are observed, involving correlated changes in the backbone angles alpha and gamma. These transitions provide a possible explanation for some unusual n.m.r. data that have been reported. The structure of the triple helix major groove also suggests an explanation for the observed stabilization of DNA triplexes by polyvalent cations, and their ability to interact with drugs that bind in the minor groove of DNA duplexes.

Base Sequence↗

PubMed1992

Conformation and dynamics of drug-DNA intercalation.

Molecular dynamics simulations have been undertaken for a B-form dodecanucleotide duplex in solution with and without an intercalated proflavine molecule between the central C.G base pairs. The introduction of this simple intercalator affects both the conformational features and dynamic properties of the oligonucleotide double helix. Changes are seen in the rms atomic fluctuations and anisotropy of phosphate, sugar and base atoms. The backbone conformation is slightly changed on average and more sugars adopt the C3' endo conformation in the simulation of the complex compared with the simulation of the oligonucleotide alone. Both major and minor grooves becomes wider on average with the addition of the intercalating drug. Flanking A.T base pairs on both sides of the intercalation site have undergone an increase in flexibility, with the base pairs, especially at the 5' side, having the N1...N3 hydrogen bonds being broken.

Base Composition↗

PubMed1991

Structures of 1-(3,3-dimethylamino)propyl naphtho[2,1-b]thiophene-4- carboxylate and N-(3,3-dimethylamino)propyl-8-methoxynaphtho[2,1- b]thiophene-4-carboxamide, intercalators into double-helical DNA.

(1) C18H19NO2S, Mr = 313.42, monoclinic, P2(1)/c, a = 11.503 (3), b = 15.932 (2), c = 9.133 (2) A, beta = 102.17 (2) degrees, V = 1636.1 A3, lambda(Cu K alpha) = 1.54178 A, mu = 1.762 mm-1, F(000) = 664, T = 293 (1) K, R = 0.047 for 2044 significant reflections. (2) C19H21NO3S, Mr = 343.45, triclinic, Pl, a = 9.873 (2), b = 13.163 (3), c = 14.065 (3) A, alpha = 101.33, beta = 94.30 (3), gamma = 91.35 (3) degrees, V = 1785.8 A3, Z = 4, Dx = 1.28 Mg m-3, lambda(Cu K alpha) = 1.54178 A, mu = 1.699 mm-1, F(000) = 728, T = 293 (1) K, R = 0.052 for 1787 significant reflections. The torsion angle between the naphthothiophene ring and the carbonyl O atom of the side chain is 5.5 (4) degrees in structure (1) and 25 (2) and -32 (2) degrees in the two independent molecules of (2). This difference is due to out-of-plane distortions in (2) that arise from steric hindrance between H atoms on the amide and the ring system, at position 2.

Intercalating Agents↗