Stephen Neidle

Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors

The telomerase enzyme is a potential therapeutic target in many human cancers. A series of potent inhibitors has been designed by computer modeling, which exploit the unique structural features of quadruplex DNA. These 3,6,9-trisubstituted acridine inhibitors are predicted to interact selectively with the human DNA quadruplex structure, as a means of specifically inhibiting the action of human telomerase in extending the length of single-stranded telomeric DNA. The anilino substituent at the 9-position of the acridine chromophore is predicted to lie in a third groove of the quadruplex. Calculated relative binding energies predict enhanced selectivity compared with earlier 3,6-disubstituted compounds, as a result of this substituent. The ranking order of energies is in accord with equilibrium binding constants for quadruplex measured by surface plasmon resonance techniques, which also show reduced duplex binding compared with the disubstituted compounds. The 3,6,9-trisubstututed acridines have potent in vitro inhibitory activity against human telomerase, with EC50 values of up to 60 nM.

Structural and sequence-dependent aspects of drug intercalation into nucleic acids.

Information gained from X-ray crystallographic studies on drug-nucleic acid complexes is described, with emphasis on the intercalation process. Relevant data from NMR experiments are examined in order to highlight similarities and differences between solution and solid-state structures. Theoretical analyses of intercalation complexes are also discussed and evaluated, with respect to the structural methods, with special reference being made to nucleic acid conformation and positions of drug molecules in the binding sites.

The structure of the antitumor complex cis-(diammino) (1,1-cyclobutanedicarboxylato)-Pt(II): X ray and nmr studies

X-ray crystallography shows that Pt(NH 3 ) 2 (CBDCA) is a square-planar complex with the dicarboxylate chelate ring in the boat conformation and a planar cyclobutane ring. 1 H and 13 C nmr studies suggest that rapid chelate ring flipping occurs in solution. The value of 195 Pt nmr combined with 15 N labeling as an informative new method of studying carboxylate coordination is illustrated. nmr results are also reported for the analogous ethylmalonate complex.

Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction.

The crystal structure of a 3 : 2 complex of the frameshift mutagen proflavine with the dinucleoside phosphate cytidylyl-3′5′-guanosine has been determined. The complex has one drug molecule intercalated between Watson–Crick base pairs of the nucleotide duplex. The other two proflavine molecules are bound to the exterior of the miniature double helix. The orientation of the base pairs in this miniature double helix has aspects similar to that found in RNA 11.

The antitumor complex ethylenediamine platinum (II) malonate: X-ray structure analysis, and studies of its stability in solution

The anti-tumour compound ethylenediamine platinum (II) malonate has been examined by x-ray crystallography. The molecular structure has a square-planar arrangement around the platinum atom, with the malonate group in a boat conformation and cis to the ethylenediamine group. Solution studies have shown that the malonate ion may be readily displaced from the complex, especially by chloride ion, and at low pH. The implications of this finding for in vivo drug administration are discussed.

Monte Carlo Studies on Water in the dCpG/Proflavin Crystal Hydrate

The extensive water network identified in the crystallographic studies of the dCpG/Proflavin hydrate by Neidle, Berman and Shieh (Nature 288, 129, 1980) forms an ideal test case for a) assessing the accuracy of theoretical calculations on nucleic acid--water systems based on statistical thermodynamic computer simulation, and b) the possible use of computer simulation in predicting the water positions in crystal hydrates for use in the further refinement and interpretation of diffraction data. Monte Carlo studies have been carried out on water molecules in the unit cell of dCpG/proflavin, with the nucleic acid complex fixed and the condensed phase environment of the system treated by means of periodic boundary conditions. Intermolecular interactions are described by potential functions representative of quantum mechanical calculations developed by Clementi and coworkers, and widely used in recent studies of the aqueous hydration of various forms of DNA fragments. The results are analyzed in terms of hydrogen bond topology, hydrogen bond distances and energies, mean water positions, and water crystal probability density maps. Detailed comparison of calculated and experimentally observed results are given, and the sensitivity of results to choice of potential is determined by comparison with simulation results based on a set of empirical potentials.

Computer Modelling Studies of the Covalent Interactions between DNA and the Enantiomers of anti-7,8-Diol,9,10-Epoxy-Benzo[a]pyrene

The molecular structures of adducts between the + and - enantiomers of 7,8-diol 9,10-epoxy benzo[a]pyrene and a double-stranded model for DNA, have been examined by empirical energy calculations. Low-energy structures were only obtained for A form, and not B form DNA. Both + and - adducts are of approximately equal energy. Some structural differences in the orientation of the BP chromophore in the two adducts were found.

Synthesis of 9-[cis-3-(hydroxymethyl)cyclobutyl]-adenine and -guanine

2,2-Dichloro-3-(benzyloxymethyl)cyclobutanone 15, which was prepared in 50% yield by the cycloaddition of dichloroketene to allyl benzyl ether 14, was converted in four steps and in ∼ 40% overall yield into trans-3-(benzyloxymethyl)cyclobutanol 11b. The latter alcohol 11b was coupled under Mitsunobu conditions with 6-(4-chlorophenylsulfanyl)-9H-purine 21b and 6-(4-chlorophenylsulfanyl)-2-(phenylacetamido)-9H-purine 21c to give the 9-cyclobutylpurine derivatives 22 and 24, respectively, in 88 and 60% yield. The former product 22 was converted in three steps and in 39% overall yield into 9-[cis-3-(hydroxymethyl)cyclobutyl]adenine 6, and the latter product was converted in four steps and in 42% overall yield into 9-[cis-3-(hydroxymethyl)cyclobutyl]guanine 7. X-Ray crystallographic data relating to compounds 22 and 24 are also reported.

2′,3′-Anhydrouridine. A useful synthetic intermediate

2,2′-Anhydro-1-(β-D-arabinofuranosyl)uracil 1 reacts with sodium hydride in dry DMSO to give 2′,3′-anhydrouridine 2. When the latter compound 2 is heated below its melting point or treated with triethylamine in methanol, it isomerises back to the 2,2′-anhydronucleoside 1. Treatment of compound 1 with sodium ethanethiolate or the sodium salt of benzyl mercaptan in the presence of an excess of the corresponding thiol in DMA gives 2′-S-ethyl- or 2′-S-benzyl-2′-thiouridine (4 or 11) in high yield; however, treatment of the 2,2′-anhydronucleoside 1 first with sodium hydride in DMA and then with a deficiency (with respect to sodium hydride) of ethanethiol or benzyl mercaptan gives the corresponding 3′-S-ethyl or 3′-S-benzyl derivative (3 or 12) in high yield. When the 2,2′-anhydronucleoside 1 is allowed to react with an excess of potassium tert-butoxide in DMSO, the 3′,5′-anhydronucleoside 13 is obtained in good yield. The latter compound 13 undergoes hydrolysis in aqueous trifluoroacetic acid to give 1-(β-D-xylofuranosyl)uracil 14 in high yield. The 3′-S-benzyl derivative 12 is converted by Raney nickel desulfurisation into 3′-deoxyuridine 15 which, in turn, is converted into 3′-deoxycytidine 17 in good yield. X-Ray crystallographic data relating to compounds 11 and 12 are also reported.

X-Ray crystallographic determination of the molecular structures of cis- and trans-isomers of (±)-5-fluorocyclophosphamide {2-[bis-(2-chloroethyl)amino]-5-fluorotetrahydro-2H-1,3,2-oxazaphosphorine 2-oxide]}

The crystal and molecular structures of the cis- and trans-isomers of (±)-5-fluorocyclophosphamide have been determined by X-ray methods. The two independent molecules of the trans-isomer have almost identical conformations, with a distorted half-chair ring pucker. The cis-isomer has a boat ring conformation.