Synthesis and biological evaluation of hybrid acridine-HSP90 ligand conjugates as telomerase inhibitors.

The synthesis and biological evaluation of a series of bifunctional acridine-HSP90 inhibitor ligands as telomerase inhibitors is herein described. Four hybrid acridine-HSP90 inhibitor conjugates were prepared using a click-chemistry approach, and subsequently shown to display comparable results to the established telomerase inhibitor BRACO-19 in the TRAP-LIG telomerase assay. The conjugates also demonstrated significant cyctotoxity against a number of cancer cell lines, in the sub-µM range.

Developing and paying for medicines for orphan indications in oncology: utilitarian regulation vs equitable care?

Despite 'orphan drug' legislation, bringing new medicines for rare diseases to market and securing funding for their provision is sometimes both costly and problematic, even in the case of medicines for very rare 'ultra orphan' oncological indications. In this paper difficulties surrounding the introduction of a new treatment for osteosarcoma exemplify the challenges that innovators can face. The implications of current policy debate on 'value-based' medicines pricing in Europe, North America and elsewhere are also explored in the context of sustaining research into and facilitating cancer patient access to medicines for low-prevalence indications. Tensions exist between utilitarian strategies aimed at optimising the welfare of the majority in the society and minority-interest-focused approaches to equitable care provision. Current regulatory and pricing strategies should be revisited with the objective of facilitating fair and timely drug supply to patients without sacrificing safety or overall affordability. Failures effectively to tackle the problems considered here could undermine public interests in developing better therapies for cancer patients.

Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide.

We describe a novel self-assembling supramolecular nanotube system formed by a heterocyclic cationic molecule which was originally designed for its potential as an antiparasitic and DNA sequence recognition agent. Our structural characterisation work indicates that the nanotubes form via a hierarchical assembly mechanism that can be triggered and tuned by well-defined concentrations of simple alkali halide salts in water. The nanotubes assembled in NaCl have inner and outer diameters of ca. 22 nm and 26 nm respectively, with lengths that reach into several microns. Our results suggest the tubes consist of DB921 molecules stacked along the direction of the nanotube long axis. The tubes are stabilised by face-to-face π-π stacking and ionic interactions between the charged amidinium groups of the ligand and the negative halide ions. The assembly process of the nanotubes was followed using small-angle X-ray and neutron scattering, transmission electron microscopy and ultraviolet/visible spectroscopy. Our data demonstrate that assembly occurs through the formation of intermediate ribbon-like structures that in turn form helices that tighten and compact to form the final stable filament. This assembly process was tested using different alkali-metal salts, showing a strong preference for chloride or bromide anions and with little dependency on the type of cation. Our data further demonstrates the existence of a critical anion concentration above which the rate of self-assembly is greatly enhanced.

Stabilisation of TG- and AG-containing antiparallel DNA triplexes by triplex-binding ligands.

We have used DNase I footprinting to examine the interaction of several triplex-binding ligands with antiparallel TG- and AG-containing triplexes. We find that although a 17mer TG-containing oligonucleotide on its own fails to produce a footprint at concentrations as high as 30 microM, this interaction can be stabilised by several ligands. Within a series of disubstituted amidoanthraquinones we find that the 2,7- regioisomer affords the best stabilisation of this TG triplex, though the 1,8- isomer also stabilises this interaction to some extent. By contrast the 1,5- and 2,6- regioisomers show no interaction with TG triplexes. Similar studies with a 13mer AG-containing oligonucleotide show the opposite pattern of stabilisation: the 2,6- and 1,5- isomers stabilise this triplex, but the 2,7- and 1,8-compounds do not. The polycyclic compound BePI strongly stabilises TG- but not AG-containing triplexes, while a substituted naphthylquinoline interacts with both antiparallel triplex motifs.

Molecular structure of (+/-)-7,8,9,10-tetrahydroxy-7,8,9,10-tetrahydrobenzo(a)pyrene determined by x-ray crystallography.

The molecular structure of a tetrahydrotetrol that is formed by hydrolysis of (+/-)-7 alpha, 8 beta-dihydroxy-9 beta, 10 beta-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene, has been determined by X-ray crystallographic methods. The relative orientations of the four hydroxyl groups of the racemic tetrahydrotetrol (7 alpha, 8 beta, 9 beta, 10 alpha) indicate that the tetrahydrotetrol was formed by the trans opening of the epoxide ring of the diol-oxide. The hydroxyl groups at positions 7 and 8 adopt a diequatorial conformation, while those at positions 9 and 10 adopt a diaxial conformation. Several other geometric features are discussed.

The structure of Miracil D, a DNA-binding drug.

The crystal structure of the drug Miracil D has been determined. Although the accuracy of the analysis is limited by disorder, it is apparent that the thioxanthone ring system is planar. The proximal nitrogen atom of the side-chain probably forms an intramolecular hydrogen bond with the carbonyl oxygen. The rest of the side-chain has a large degree of conformational mobility.

Nucleic acid binding drugs. Part IV. The crystal structure of the anti-cancer agent daunomycin.

The crystal structure has been determined of the anti-cancer drug daunomycin, as the hydrochloride monohydrate pyridine salt. The overall structure, previously determined by X-ray analysis of an N-bromoacetyl derivative (Anguili, R., Foresti, E., Riva Di Sanserverino, L., Isaacs, N.W., Kennard, O., Motherwell, W.D.S., Wampler, D.L. and Arcamone, F. (1971) Nat. New Biol. 234, 78-80) has been confirmed, although substantial conformational differences are observed. The conformation described here is very similar to that found for the related drug carminomycin I (Wani, M.C., Taylor, H.L., Wall, M.E., McPhaill, A.T. and Onan, K.D. (1975) J. Am. Chem. Soc. 97, 5955-5956; Pettit, G.R., Einck, J.J., Herald, C.L., Ode, R.H. Von Dreele, R.B., Brown, P., Brazhnikova, M.G. and Gause, G.F. (1975) J. Am. Chem. Soc. 97, 7387-7388); it is suggested that this represents a significantly stable molecular conformation; an intramolecular C(7)...O(9) hydrogen bond is invoked to account for this. This conformation is likely to be at least close to that of daunomycin when bound to DNA.

The crystal and molecular structure of an osmium bispyridine adduct of thymine.

The bispyridine osmium adduct of thymine has been crystallised and subjected to an X-ray diffraction analysis. It crystallises in the triclinic space group P1, with cell dimensions a equals 7.975(3), b equals 10.381(3), c equals 11.036(3) A, alpha equals 82.73(2)degrees, beta equals 77.22(3) degrees, gamma equals 101.75(3), and with two molecules in the unit cell. The analysis has shown that the osmium reagent has added cis across the 5,6 thymine bond.

Netropsin, a DNA-binding oligopeptide structural and binding studies.

The crystal structure of netropsin, an oligopeptide which binds to DNA, has been determined. The molecule is bowed with the amide groups on the concave side, and the carbonyl and methyl groups on the convex side. The amide groups participate in extensive hydrogen bonding with water molecules; the charged amino end groups interact with the sulfate anions. Binding of netropsin to poly(dA) . poly(dT) under conditions of different ionic strength was also studied. Utilizing the crystallographic as well as the binding data, it is possible to build a model which explains the specificity of this antibiotic.

9-beta-D-Arabinofuranosyl-8-n-butylaminoadenine, a C-8 substituted nucleoside in the anti conformation. Crystallographic and NMR studies.

The protein NMR spectrum of 9-beta-D-arabinofuranosyl-8-n-butylaminoadenine shows an unusually low-field 5'-hydroxyl proton resonance, which has been interpreted in terms of an anti glycosidic conformation together with an 05' ... N8 intramolecular hydrogen bond. Confirmatory evidence for this was obtained by an X-ray crystallographic study; in the crystal, the glycosidic angle chi is 52.7 degrees and the sugar pucker is C3' endo-C4' exo.

Structure-activity relationships among guanine-quadruplex telomerase inhibitors.

The ribonucleoprotein telomerase is responsible for maintaining the length of telomeric ends of chromosomes in tumour cells. It is activated in over 85% of the tumour cells, and is emerging as a major target for cancer chemotherapy. A range of molecules containing tricyclic and tetracyclic aromatic chromophores has been shown to inhibit the telomerase enzyme system at the micromolar level. There is evidence that they do so via stabilisation of a guanine-quadruplex structure, which provides a stop signal for further telomere elongation. The known structure-activity relationships for these compounds are summarised, and pointers for the development of future molecules with enhanced selectivity are described.

A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure.

The dodecanucleotide d(CGCGAATTCGCG) has been crystallised in the space group P3(2)12, representing a new crystal form for this sequence. The structure has been solved by molecular replacement and refined at 1.8 A resolution. The present structure contrasts with previous ones for this sequence since it is situated on a crystallographic 2-fold axis, and the crystal symmetry reflects the palindromic nature of this sequence. Some features accord with previous observations, notably that the minor groove is hydrated with a continuous spine of solvent. There is no evidence of alkali metal ions within this spine. The minor groove retains its narrow width, although it is now symmetric and extends over the A/T tract. Various base and base-pair morphological parameters have been examined. Their values do not show significant correlations with earlier reports, suggesting that crystal packing effects on them are more dominant than has been hitherto realised.

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.

The high resolution crystal structure of the DNA decamer d(AGGCATGCCT).

The crystal structure of the DNA decamer d(AGGCATGCCT) has been determined to a resolution of 1.3 A and R factor of 13.9%. The structure has a unique conformation with each of the decamer single strands forming base-pairing interactions with two symmetry-related strands. The central eight bases of the decamer form an A-DNA octamer duplex with one symmetry-related strand whilst the terminal 5'-A and T-3' bases are flipped out and away from the octamer helix axis to form base-pairing interactions with a second symmetry-related strand. These A.T base-pairs lie perpendicular to the crystallographic c axis and pack within the unit cell in conjunction with a symmetry-related A.T base-pair displaced by 3.4 A degrees along the c axis. A novel base triplet interaction of the type A*(G.C) is present in the structure with interaction from the major groove side of the terminal 5'-A base to the minor groove of the central A-DNA octamer. This structure reports the first example of cobalt hexammine binding to a right-handed DNA duplex. The crystallographic asymmetric unit contains two cobalt hexammine ligands with one site in the major groove coordinating via hydrogen bonds to the 5'-AGG bases, and the second site located between DNA molecules and interacting with the oxygen atoms of phosphate groups.

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.

Sequence-dependent crossed helix packing in the crystal structure of a B-DNA decamer yields a detailed model for the Holliday junction.

The structure of the B-DNA decamer d(CGCAATTGCG)2 has been determined by X-ray diffraction analysis to a resolution of 2.3 A and an R-factor of 17.7%. The decamer crystallises in the monoclinic space group C2 and packs with a crossed arrangement of helices and a unique crossing contact distinct from all other decamer structures. This is believed to be a direct result of the sequence-dependent minor groove width of the duplex. Crossed helix structures of DNA are valuable starting points for modelling studies of the Holliday junction. Two unique sites are observed at the cross-over junction where strand exchange may occur. A Holliday junction model has been constructed for each case and modelled using molecular mechanics and dynamics techniques. One of these models was found to be fully consistent with the available physical data.

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.

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.

A thermodynamic and structural analysis of DNA minor-groove complex formation.

As part of an effort to develop a better understanding of the structural and thermodynamic principles of DNA minor groove recognition, we have investigated complexes of three diphenylfuran dications with the d(CGCGAATTCGCG)(2) duplex. The parent compound, furamidine (DB75), has two amidine substituents while DB244 has cyclopentyl amidine substituents and DB226 has 3-pentyl amidines. The structure for the DB244-DNA complex is reported here and is compared to the structure of the DB75 complex. Crystals were not obtained with DB226 but information from the DB75 and DB244 structures as well as previous NMR results on DB226 indicate that all three compounds bind in the minor groove at the AATT site of the duplex. DB244 and DB75 penetrate to the floor of the groove and form hydrogen bonds with T8 on one strand and T20 on the opposite strand while DB226 forms a complex with fewer interactions. Binding studies by surface plasmon resonance (SPR) yield -delta G degrees values in the order DB244>DB75>DB226 that are relatively constant with temperature. The equilibrium binding constants for DB244 are 10-20 times greater than that for DB226. Isothermal titration calorimetric (ITC) experiments indicate that, in contrast to delta G degrees, delta H degrees varies considerably with temperature to yield large negative delta Cp degrees values. The thermodynamic results, analyzed in terms of structures of the DNA complexes, provide an explanation of why DB244 binds more strongly to DNA than DB75, while DB266 binds more weakly. All three compounds have a major contribution to binding from hydrophobic interactions but the hydrophobic term is most favorable for DB244. DB244 also has strong contributions from molecular interactions in its DNA complex and all of these factors combine to give it the largest-delta G degrees for binding. Although the factors that influence the energetics of minor groove interactions are varied and complex, results from the literature coupled with those on the furan derivatives indicate that there are some common characteristics for minor groove recognition by unfused heterocyclic cations that can be used in molecular design.

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.