Phase Ib dose-escalation study of the hypoxia-modifier myo-inositol trispyrophosphate in patients with hepatopancreatobiliary tumors

Objective

Hypoxia is present in most solid tumors and acts as a driver of malignancy. Myo-inositol trispyrophosphate (ITPP) is a novel re-oxygenating compound without apparent toxicity. In preclinical models, it potentiates the efficacy of subsequent chemotherapy through vascular normalization. We sought to assess the safety, tolerability, and preliminary efficacy of ITPP.

Methods

In this monocentric, open-label, dose-escalation study following a 3+3 design, eligible patients with advanced primary and secondary hepatopancreatobiliary tumors received nine 8-h infusions of ITPP during 3 weeks across eight dose levels (1866–14,500 mg/m2/dose), followed by standard chemotherapy. Primary endpoints were safety and tolerability. Secondary endpoints were pharmacokinetics and estimation of efficacy based on radiological responses and angiogenic serum markers. Registration number: NCT02528526.

Results

From April 2015 to July 2018, a total of 28 enrolled patients were assessed for the primary endpoints. ITPP was safe up to single doses of 12,390 mg/m2, and 32 ITPP-related adverse events occurred: 19 (67.8%) hypercalcemia, 5 (17.8%) hyponatremia, and 4 (14.2%) hypomagnesemia. Following ITPP monotherapy, 52% of patients displayed morphological disease stabilization. Following subsequent chemotherapy, 10% showed a partial response, and 60% had stable disease. Angiogenic markers were decreased in 60% after ITPP and tended to correlate with responses and survival after chemotherapy.

Conclusion

Administration of ITPP is safe up to 12,390 mg/m2 with favorable pharmacokinetics. Preliminary translational efficacy data show decreased angiogenic markers, which might indicate an anti-hypoxic effect and enhancement of chemotherapy through ITPP.

Competition-driven selection in covalent dynamic networks and implementation in organic reactional selectivity

Competition among reagents in dynamic combinatorial libraries of increased complexity leads to reactional self-sorting. This fundamental principle allowed development of selective dynamic protecting groups for controlled sequential derivatization of polyamines.

Competition among reagents in dynamic combinatorial libraries of increased complexity leads to reactional self-sorting (improved regioselectivity) in mixtures of aldehydes and oligoamines. High selectivity of a given library component is transferred to a different reacting component of low selectivity through a network of underlying equilibrating reactions which provide component exchange between all species. The selectivity of various carbonyl compounds in reactions with amines was also assessed towards the formation of defined sequences of residues along oligoamine chains. The approach was further exploited for defining selective dynamic protecting groups (DPGs), based on the reversible linkage between the substrate and the protecting group. They represent an intermediate approach between the conventional protecting groups and the protecting-group-free approach in organic synthesis. Removal of the protecting group is effected via dynamic exchange trapping by formation of a more stable product. The establishment of equilibrium eliminates the need for isolation and purification of the dynamically protected intermediate(s) and enables as well the selective sequential derivatisation of oligoamines. The DPG concept can be generalised to other reversible reactions and can thus represent a valuable alternative in the design of total synthesis of complex molecules.

Selective adhesion, lipid exchange and membrane-fusion processes between vesicles of various sizes bearing complementary molecular recognition groups

Equimolar mixtures of large unilamellar vesicles (LUVs) obtained from mixtures of egg lecithin and lipids containing complementary hydrogen bonding head groups (barbituric acid (BAR) and 2,4,6-triaminopyrimidine (TAP)) were shown to aggregate and fuse. These events have been studied in detail using electron microscopy and dynamic light scattering, and by fluorimetry using membrane or water-soluble fluorescence probes. It was shown that aggregation was followed by two competitive processes: a) lipid mixing leading to redispersion of the vesicles; b) fusion events generating much larger vesicles. In order to better understand the nature of the interaction, the effects of ionic strength and surface concentration of recognition lipids on the aggregation process were investigated by dynamic light scattering. Additionally, it was possible to inhibit the aggregation kinetics through addition of a soluble barbituric acid competitor. The study was extended to giant unilamellar vesicles (GUVs) to investigate the size effect and visualise the phenomena in situ. The interactions between complementary LUVs and GUVs or GUVs and GUVs were studied by optical microscopy using dual fluorescent labelling of both vesicle populations. A selective adhesion of LUVs onto GUVs was observed by electron and optical microscopies, whereas no aggregation took place in case of a GUV/GUV mixture. Furthermore, a fusion assay of GUV and LUV using the difference of size between GUV and LUV and calceine self-quenching showed that no mixing between the aqueous pools occured.

Increasing the oxygen load by treatment with myo-inositol trispyrophosphate reduces growth of colon cancer and modulates the intestine homeobox gene Cdx2

Preventing tumor neovascularisation is one of the strategies recently developed to limit the dissemination of cancer cells and apparition of metastases. Although these approaches could improve the existing treatments, a number of unexpected negative effects have been reported, mainly linked to the hypoxic condition and the subsequent induction of the pro-oncogenic hypoxia inducible factor(s) resulting from cancer cells' oxygen starvation. Here, we checked in vivo on colon cancer cells an alternative approach. It is based on treatment with myo-inositol trispyrophosphate (ITPP), a molecule that leads to increased oxygenation of tumors. We provide evidence that ITPP increases the survival of mice in a model of carcinomatosis of human colon cancer cells implanted into the peritoneal cavity. ITPP also reduced the growth of subcutaneous colon cancer cells xenografted in nu/nu mice. In the subcutaneous tumors, ITPP stimulated the expression of the homeobox gene Cdx2 that is crucial for intestinal differentiation and that also has an anti-tumoral function. On this basis, human colon cancer cells were cultured in vitro in hypoxic conditions. Hypoxia was shown to decrease the level of Cdx2 protein, mRNA and the activity of the Cdx2 promoter. This decline was unrelated to the activation of HIF1α and HIF2α by hypoxia. However, it resulted from the activation of a phosphatidylinositol 3-kinases-like mitogen-activated protein kinase pathway, as assessed by the fact that LY294002 and U0126 restored high Cdx2 expression in hypoxia. Corroborating these results, U0126 recapitulated the increase of Cdx2 triggered by ITPP in subcutaneous colon tumor xenografts. The present study provides evidence that a chemical compound that increases oxygen pressure can antagonize the hypoxic setting and reduce the growth of human colon tumors implanted in nu/nu mice.

Supramolecular chemistry: receptors, catalysts, and carriers

Supramolecular chemistry is the study of the structures and functions of the supermolecules that result from binding substrates to molecular receptors. Macropolycyclic receptors and coreceptors have been designed that form cryptate inclusion complexes and display molecular recognition towards spherical, tetrahedral, and linear substrates of various kinds (metal cations, inorganic anions, and organic or biological cations or anions). Anion binding has led to the development of anion coordination chemistry. Metalloreceptors simultaneously bind organic molecules and metal ions; speleands combine polar and nonpolar binding subunits. Receptors bearing reactive functional groups may act as molecular reagents or catalysts, performing a chemical transformation on the bound substrates (by such reactions as hydrogen transfer, ester cleavage, and protoadenosinetriphosphatase and protokinase activities). Receptors fitted with lipophilic groups can operate as molecular carriers, translocating bound species through a membrane; this transport can be coupled to chemical potentials (proton and redox gradients).

Molecular devices: Caroviologens as an approach to molecular wires-synthesis and incorporation into vesicle membranes

Molecular wires, which would allow electron flow to take place between different components, are important elements in the design of molecular devices. An approach to such species would be molecules possessing an electron-conducting conjugated chain, terminal electroactive polar groups, and a length sufficient to span a lipid membrane. To this end, bispyridinium polyenes of different lengths have been synthesized and their incorporation into the bilayer membrane of sodium dihexadecyl phosphate vesicles has been studied. Since they combine the features of carotenoids and of viologens, they may be termed caroviologens. Vesicles containing the caroviologen whose length approximately corresponds to the thickness of the sodium dihexadecyl phosphate bilayer display temperature-dependent changes of its absorption spectrum reflecting the gel --> liquid-crystal phase transition of the membrane. The data agree with a structural model in which the caroviologens of sufficient length span the bilayer membrane, the pyridinium sites being close to the negatively charged outer and inner surfaces of the sodium dihexadecyl phosphate vesicles and the polyene chain crossing the lipidic interior of the membrane. These membranes may now be tested in processes in which the caroviologen would function as a continuous, transmembrane electron channel-i.e., as a molecular wire. Various further developments may be envisaged along these lines.

Photochemical generation of carbon monoxide and hydrogen by reduction of carbon dioxide and water under visible light irradiation

Visible light irradiation of solutions of Ru(2,2'-bipyridine)(3) (2+), cobalt(II) chloride, and carbon dioxide in acetonitrile/water/triethylamine generates simultaneously carbon monoxide and hydrogen. The reaction involves photoinduced reduction of CO(2) and H(2)O, triethylamine serving as electron donor in the Ru(2,2'-bipyridine)(3) (2+)/Co(2+) system. The amount of gas (CO + H(2)) produced and the selectivity ratio CO/H(2) depend markedly on the composition of the system. Addition of free bipyridine strongly decreases CO generation but increases H(2) production. With different tertiary amines, NR(3), both the quantity (CO + H(2)) and the ratio CO/H(2) increase markedly along the sequence R = methyl, ethyl, propyl. Higher selectivity for CO(2) reduction to CO in preference to water reduction occurs when triethanolamine is used instead of triethylamine. CoCl(2) is the most efficient mediator for both CO and H(2) generation and specifically promotes CO formation, whereas salts of other cations studied only yield H(2). The mechanism of the reaction may involve intermediate formation of Co(I) species. These processes represent an abiotic photosynthetic system allowing simultaneous generation of CO and H(2) and regulation of the CO/H(2) ratio. Mechanistic studies and explorations of other components that may increase efficiency and product selectivity should be carried out. The results obtained are also of significance for solar energy conversion with consumption of a pollutant, CO(2).

Room temperature dynamic polymers based on Diels-Alder chemistry

Dynamers based on reversible Diels-Alder chemistry have been obtained and shown to undergo dynamic exchange at room temperature. Their study in solution by small-angle neutron scattering indicated the formation of long and highly flexible chains. Polydispersed molecules gave T(g) values below room temperature, permitting the generation of a dynamic elastomer upon introduction of a dynamic cross-linking agent. The use of a system with a low equilibrium constant gives access to materials with interesting self-healing properties.

Single-molecule transport in three-terminal devices

Transport through single molecules has been studied using different test beds. In this paper we focus on three-terminal devices in which a molecule bridges the gap between two gold electrodes and a third electrode-the gate-is able to modulate the conduction properties of the junction. Depending on the electronic coupling, Γ, between the molecule and the gold electrodes, different transport regimes can be distinguished. We show measurements on junctions incorporating different single-molecule systems which demonstrate the distinction between these regimes, as well as the experimental limitations in controlling the exact value of Γ.

The Design of Cationic Lipids for Gene Delivery

Synthetic gene delivery vectors are gaining increasing importance in gene therapy as an alternative to recombinant viruses. Among the various types of non-viral vectors, cationic lipids are especially attractive as they can be prepared with relative ease and extensively characterised. Further, each of their constituent parts can be modified, thereby facilitating the elucidation of structure-activity relationships. In this forward-looking review, cationic lipid-mediated gene delivery will mainly be discussed in terms of the structure of the three basic constituent parts of any cationic lipid: the polar headgroup, hydrophobic moiety and linker. Particular emphasis will be placed on recent advances in the field as well as on our own original contributions. In addition to reviewing critical physicochemical features (such as headgroup hydration) of monovalent lipids, the use of headgroups with known nucleic-acid binding modes, such as linear and branched polyamines, aminoglycosides and guanidinium functions, will be comprehensively assessed. A particularly exciting innovation in linker design is the incorporation of environment-sensitive groups, the intracellular hydrolysis of which may lead to more controlled DNA delivery. Examples of pH-, redox- and enzyme-sensitive functional groups integrated into the linker are highlighted and the benefits of such degradable vectors can be evaluated in terms of transfection efficiency and cationic lipid-associated cytotoxicity. Finally, possible correlations between the length and type of hydrophobic moiety and transfection efficiency will be discussed. In conclusion it may be foreseen that in order to be successful, the future of cationic lipid-based gene delivery will probably require the development of sophisticated virus-like systems, which can be viewed as "programmed supramolecular systems" incorporating the various functions required to perform in a chronological order the different steps involved in gene transfection.

Molecular recognition of quadruplex DNA by quinacridine derivatives

The interaction of monomeric and dimeric quinacridines with quadruplex DNA has been investigated using a variety of biophysical methods. Both series of compounds were shown to exhibit a high affinity for the G4 conformation with two equivalent binding sites. As shown from the SPR and dialysis experiments the macrocyclic dimer appears more selective than its monomeric counterpart.

Electron transfer through bridging molecular structures

Pairs of reducible pentakis(thiophenyl)benzene subunits are linked by different molecular structures as model compounds for reducible molecular-wire-type synthons showing varying electron-transfer ability as a function of the bridging structures, consisting of either para-divinylbenzene, bis-hydrazone, or diacetylene. Their electron-transfer ability from one reducible subunit to the other was investigated by electrochemical and spectroelectrochemical methods. In the case of the bis-hydrazone bridge and the diacetylene bridge, the solid-state structures support the experimental findings. While the para-divinylbenzene bridge completely isolates the reducible subunits (class I system) the diacetylene bridge electronically connects the two reducible structures (class III system), demonstrating its potential application as a "molecular wire." The bis-hydrazone linked dimer displays electronic communication only to a small extend, which was only observed in the spectroelectrochemical investigation. The diacetylene connection as active electron-transfer linker together with poly(thiophenyl)benzene as reducible subunits was used to design more complex molecular architectures. Linear rodlike structures did allow adjustment of the length of these type of molecular wires and investigation of the extent of electron mobility. Cyclic structures addressed the possibility of moving electrons on a bent molecular wire.

Interaction of an acridine dimer with DNA quadruplex structures

The reactivation of telomerase activity in most cancer cells supports the concept that telomerase is a relevant target in oncology, and telomerase inhibitors have been proposed as new potential anticancer agents. The telomeric G-rich single-stranded DNA can adopt an intramolecular G-quadruplex structure in vitro, which has been shown to inhibit telomerase activity. The C-rich sequence can also adopt a quadruplex (intercalated) structure (i-DNA). Two acridine derivatives were shown to increase the melting temperature of the G- quadruplex and the C-quadruplex at 1 microM dye concentration. The increase in Tm value of the G-quadruplex was associated with telomerase inhibition in vitro. The most active compound, "BisA", showed an IC(50) value of 0.75 microM in a standard TRAP assay.

Direct photocleavage of HIV-DNA by quinacridine derivatives triggered by triplex formation

Amino-p-quinacridine compounds (PQs) have been shown to stabilize strongly and specifically triple-helical DNA. Moreover, these derivatives display photoactive properties that make them efficient DNA cleavage agents. We exploited these two properties (triplex-specific binding and photoactivity) to selectively cleave a double-stranded (ds)DNA sequence present in the HIV-1 genome. Cleavage was first carried out on a linearized plasmid (3300 bp) containing the HIV polypurine tract (PPT) that allowed targeting by a triplex-forming oligonucleotide (TFO). PQ(3)(), the most active compound of the series, efficiently cleaved double-stranded DNA in the vicinity of the PPT when this sequence had formed a triplex with a 16-mer TFO. Investigation of the cleavage at the molecular level was addressed on a short DNA fragment (56 bp); the photoinduced cleavage by PQ(3)() occurred only in the presence of the triple helix. Nevertheless, unusual cleavage patterns were observed: damage was observed at guanines located 6-9 bp away from the end of the triple helical site. This cleavage is very efficient (up to 60%), does not require alkaline treatment, and is observed on both strands. A quinacridine-TFO conjugate produced the same cleavage pattern. This observation, along with others, excludes the hypothesis of a triplex-induced allosteric binding site of PQ(3 )()adjacent to the damaged sequence and indicates that PQ(3 )()preferentially binds in the vicinity of the 5'-triplex junction. Irradiation in the presence of TFO-conjugates with acridine (an intercalative agent) and with the tripeptide lys-tryp-lys led to a complete inhibition of the photocleavage reaction. These results are interpreted in terms of competitive binding and of electron-transfer quenching. Together with the findings of simple mechanistic investigations, they led to the conclusion that the photoinduced damage proceeds through a direct electron transfer between the quinacridine and the guanines. This study addresses the chemical mechanism leading to strand breakage and characterizes the particular photosensitivity of the HIV-DNA target sequence which could be an oxidative hot spot for addressed photoinduced strand scission by photosensitizers.

Dominant/recessive behavior in the expression of molecular information: self-assembly of inorganic macrocyclic architectures containing coordinatively unsaturated ligands

The polytopic ligand 1 contains three different metal ion binding subunits forming two substructures that code for the self-assembly of two different coordination structures (helicate and grid type) under metal ion complexation. Reaction with Cu(II) and Zn(II) ions generates the coordinatively unsaturated architectures 8 and 9 resulting from the formation of two double helicate arrangements. Their crystal structure has been determined by x-ray diffraction. These results show that the double helical motif is expressed at the expense of the grid type one, indicating the dominant/recessive behavior of the system. Together with earlier studies on the linear combination and crossover processing schemes, the dominant/recessive generation of 8 and 9 completes the demonstration of principle of the modes of multiple expression of molecular information in a multicode programmed chemical system.

Sterically stabilized BGTC-based lipoplexes: structural features and gene transfection into the mouse airways in vivo

BACKGROUND

Colloidal stability of lipid/DNA aggregates is a major requirement for cationic lipid-mediated transfection which is particularly difficult to fulfil at the high DNA concentrations used for in vivo gene delivery. Thus, we have investigated the potential of poly(ethyleneglycol) (PEG) conjugates for steric stabilization of lipoplexes formed by bis(guanidinium)-tren-cholesterol/dioleoyl phosphatidylethanolamine (BGTC/DOPE) liposomes, a class of cationic liposomes we have developed over the past few years.

METHODS AND RESULTS

We demonstrate that adequate lipophilic PEG derivatives can stabilize BGTC/DOPE lipoplexes formed at high DNA concentration. We also report the results of cryotransmission electron microscopy studies indicating that PEG-stabilized lipoplexes form DNA-coated structures which assemble into clusters exhibiting various complex morphologies. Finally, we report data from in vivo transfection experiments suggesting that PEG-mediated colloidal stabilization of concentrated lipoplex solutions may allow enhanced transfection of the mouse airways via intranasal administration.

CONCLUSION

Our results represent an important step towards the design of multimodular BGTC-based systems for improved in vivo gene transfection.

Helical molecular programming: supramolecular double helices by dimerization of helical oligopyridine-dicarboxamide strands

Helically preorganized oligopyridine-dicarboxamide strands are found to undergo dimerization into double helical supramolecular architectures. Dimerization of single helical strands with five or seven pyridine rings has been characterized by NMR and mass spectrometry in various solvent/ temperature conditions. Solution studies and stochastic dynamic simulations consistently show an increasing duplex stability with increasing strand length. The double helical structures of three different dimers was characterized in the solid phase by X-ray diffraction analysis. Both aromatic stacking and hydrogen bonding contribute the double helical arrangement of the oligopyridinedicarboxamide strand. Inter-strand interactions involve extensive face-to-face overlap between aromatic rings, which is not possible in the single helical monomers. Most hydrogen bonds occur within each strand of the duplex and stabilize its helical shape. Some inter-strand hydrogen bonds are found in the crystal structures. Dynamic studies by NMR as well as by molecular modeling computations yield structural and kinetic information on the double helices and on monomer-dimer interconversion. In addition, they reveal the presence of a spring-like extension/compression as well as rotational displacement motions.

Helical molecular programming: folding of oligopyridine-dicarboxamides into molecular single helices

Molecular strands composed of alternating 2,6-diaminopyridine and 2,6-pyridinedicarbonyl units have been designed to self-organize into single stranded helical structures upon forming intramolecular hydrogen bonds. Pentameric strands 11, 12, and 14, heptameric strands 1 and 20, and undecameric strand 15 have been synthesized using stepwise convergent strategies. Single helical conformations have been characterized in the solid state by single crystal X-ray diffraction analysis for four of these compounds. Helices from pentameric strands 12 and 14 extend over one turn, and helices from heptameric 20 and undecameric 15 species extend to one and a half and two and a half turns, respectively. Intramolecular hydrogen bonds are responsible for the strong bending of the strands. 1H NMR shifts both in polar and nonpolar organic solvents indicate intramolecular overlap between the peripheral aromatic groups. Thus, helical conformations also predominate in solution. Molecular stochastic dynamic simulations of strand folding starting from a high energy extended linear conformer show a rapid (600 ps at 300 K) conversion into a stable helical conformation.

Dynamic deconvolution of a pre-equilibrated dynamic combinatorial library of acetylcholinesterase inhibitors

A dynamic combinatorial library composed of interconverting acylhydrazones has been generated and screened towards inhibition of acetylcholinesterase from the electric ray Torpedo marmorata. Starting from a small set (13) of initial hydrazide and aldehyde building blocks, a library containing possibly 66 different species was obtained in a single operation. Of all possible acylhydrazones formed, active compounds containing two terminal cationic recognition groups separated by an appropriate distance, permitting two-site binding, could be rapidly identified by using a dynamic deconvolution--screening procedure, based on the sequential removal of starting building blocks. A very potent bis-pyridinium inhibitor (K(i)=1.09 nM, alphaK(i)=2.80 nM) was selected from the process and the contribution of various structural features to inhibitory potency was evaluated.

Human DNA topoisomerase I inhibitory activities of synthetic polyamines relation to DNA aggregation

DNA aggregation by polyamines has acquired importance as a prerequisite for the cellular uptake of DNA for gene therapy. Intracellular polyamines are constitutive components of mammalian cells and their availability is critical for cell proliferation. Interference of polyamine biosynthesis by synthetic polyamines leads to cytotoxicity. Optimization of the polyamine structural parameters is necessary to control their DNA aggregation, cytotoxic or enzyme inhibitory activities. We designed two series of tetra- and hexamines and compared their human DNA topoisomerase I (top1) inhibitory effects with the DNA aggregation properties. We show that hexamines are more efficient inhibitors of DNA relaxation by top1 than tetramines and that they suppress the top1-mediated DNA cleavage while tetramines do not. The DNA aggregation abilities within two series of polyamines correlate with the length of their central methylene chain. By contrast, the top1 inhibition within two series does not show the same correlation but demonstrates a threshold inhibitory effect on going from the (CH(2))(12) to the (CH(2))(14) central chain. We show further that the structures of DNA aggregates formed by polyamines with the (CH(2))(10-12) or with the (CH(2))(14-16) chains are very different. The first are a fluid cholesteric-type phases, whereas the second are well-structured aggregates similar to columnar liquid crystals with high packing density of DNA duplexes. The structures of polyamines-induced DNA aggregates are proposed to be crucial for top1 catalysis. The structure-function correlation described here may serve as a guide for rational design of polyamines with desired DNA-aggregation or anti-top1 activities.

Electron transfer through molecular bridges between reducible pentakis(thiophenyl)benzene subunits

"Dimers" 3, 4 and 7, which consist of two reducible pentakis(thiophenyl)benzene subunits linked by different molecular structures, have been synthesised as model compounds for reducible molecular-wire-type synthons to represent differences in the electron-transfer ability as a function of the bridging structure. The bridging units consist of para-divinylbenzene in 3, bis-hydrazone in 4 and diacetylene in 7. Their ability to transfer electrons from one reducible subunit to the other was investigated by electrochemical and spectroelectrochemical methods and, in the case of 4 and 7, the solid-state structures support the experimental findings. The para-divinylbenzene bridge in 3 was found to completely isolate the reducible structures (Class I system). In contrast, the diacetylene bridge in 7 electronically connects the two reducible structures (Class III system) and, thus, demonstrates its potential application as a "molecular wire". The bis-hydrazone-linked compound 4 displayed only a low level of electronic connection between the subunits and was only observed in the spectroelectrochemical investigation.

Telomerase inhibitors based on quadruplex ligands selected by a fluorescence assay

The reactivation of telomerase activity in most cancer cells supports the concept that telomerase is a relevant target in oncology, and telomerase inhibitors have been proposed as new potential anticancer agents. The telomeric G-rich single-stranded DNA can adopt in vitro an intramolecular quadruplex structure, which has been shown to inhibit telomerase activity. We used a fluorescence assay to identify molecules that stabilize G-quadruplexes. Intramolecular folding of an oligonucleotide with four repeats of the human telomeric sequence into a G-quadruplex structure led to fluorescence excitation energy transfer between a donor (fluorescein) and an acceptor (tetramethylrhodamine) covalently attached to the 5' and 3' ends of the oligonucleotide, respectively. The melting of the G-quadruplex was monitored in the presence of putative G-quadruplex-binding molecules by measuring the fluorescence emission of the donor. A series of compounds (pentacyclic crescent-shaped dibenzophenanthroline derivatives) was shown to increase the melting temperature of the G-quadruplex by 2-20 degrees C at 1 microM dye concentration. This increase in T(m) value was well correlated with an increase in the efficiency of telomerase inhibition in vitro. The best telomerase inhibitor showed an IC(50) value of 28 nM in a standard telomerase repeat amplification protocol assay. Fluorescence energy transfer can thus be used to reveal the formation of four-stranded DNA structures, and its stabilization by quadruplex-binding agents, in an effort to discover new potent telomerase inhibitors.

Efficient gene transfection by bisguanylated diacetylene lipid formulations

We have previously shown that cationic cholesterol derivatives bearing guanidinium groups were efficient vectors for gene transfer. To further evaluate the potentiality of this novel class of cationic lipids, we undertook to study the transfection efficiency of guanidinium-based lipids with other hydrophobic moieties. Specifically, we synthesized a reagent where two guanidinium groups are linked to a diacetylene lipid which may provide the lipoplexes with favorable structural features. We report here that the cationic lipid bisguanidinium-diacetylene (BGDA) is highly efficient for in vitro gene transfection when formulated with dioleoylphosphatidyl ethanolamine (DOPE). We also show that liposomes composed of BGDA, DOPE, and a neutral diacetylene colipid, hydroxyethylenediacetylene (HEDA), are efficient for transfection. Thus, diacetylene-based lipids provide a novel scaffold for gene transfection and will be particularly useful for gaining new insights into the structure-activity relationships of the lipid/DNA complexes as they offer a means to study the effects of polymerizable domains.

Double-level "orthogonal" dynamic combinatorial libraries on transition metal template

Dynamic combinatorial libraries are mixtures of compounds that exist in a dynamic equilibrium and can be driven to compositional self adaptation via selective binding of a specific assembly of certain components to a molecular target. We present here an extension of this initial concept to dynamic libraries that consists of two levels, the first formed by the coordination of terpyridine-based ligands to the transition metal template, and the second, by the imine formation with the aldehyde substituents on the terpyridine moieties. Dialdehyde 7 has been synthesized, converted into a variety of ligands, oxime ethers L(11)-L(33) and acyl hydrazones L(44)-L(77), and subsequently into corresponding cobalt complexes. A typical complex, Co(L(22))(2)(2+) is shown to engage in rapid exchange with a competing ligand L(11) and with another complex, Co(L(22))(2)(2+) in 30% acetonitrile/water at pH 7.0 and 25 degrees C. The exchange in the corresponding Co(III) complexes is shown to be much slower. Imine exchange in the acyl hydrazone complexes (L(44)-L(77)) is strongly controlled by pH and temperature. The two types of exchange, ligand and imine, can thus be used as independent equilibrium processes controlled by different types of external intervention, i.e., via oxidation/reduction of the metal template and/or change in the pH/temperature of the medium. The resulting double-level dynamic libraries are therefore named orthogonal, in similarity with the orthogonal protecting groups in organic synthesis. Sample libraries of this type have been synthesized and showed the complete expected set of components in electrospray ionization MS.

Self-assembly and structure of interconverting multinuclear inorganic arrays: a

Coordination of the pentatopic ligand 3 with AgI leads to the simultaneous self-assembly of two polynuclear architectures: a [4 x 5] grid-type species 10 and a quadruple-helicate 11, which contain twenty and ten silver ions. respectively. Their structures have been established by X-ray diffraction analysis of the crystals obtained as a mixture on crystallisation. Complex 10 contains two [2 x 5]-AgI10 rectangular subgrids located on opposite sides of an array of parallel ligands of 3 that are twisted into a transoid N=C-C=N arrangement around the central C-C bond; it may thus be formulated as a grid of grids: [2 x (2 x 5)]. Complex 11 is an inorganic quadruple helicate that consists of two sets of two parallel ligands of 3 connected by an array of ten silver ions. Both compounds 10 and 11 are novel types of polynuclear complexes that are composed of two subunits. Their formation points to the possibility of generating specific arrays of metal ions by self-assembly, involving, in particular, a combination of subunits within the overall entity. They represent organised patterns of ion dots of special significance in view of their formal relationship to quantum dots.

Recognition-directed supramolecular assemblies of metal complexes of terpyridine derived ligands with self-complementary hydrogen bonding sites

The synthesis and X-ray structures of three metal complexes with terpyridine-derived ligands that contain amino-pyrimidine and amino-pyrazine moieties are presented. They have been designed in view of directing their self-assembly into specific supramolecular arrays through molecular recognition interactions. The solid-state structures indeed reveal extensive hydrogen-bonded networks. The Co complex 4a with PF6- counterions builds a two-dimensional infinite interwoven grid through strong double hydrogen bonds (d(N-H-N) =2.918-3.018 A) between the amino groups and the N atoms of the rings, with all H-bonding sites saturated. Changing the anions to BF4- in 4b leads to a similar infinite but partially broken grid with a quarter of the H-bonding sites unsaturated (d(N-H-N)=2.984-3.206 A). In the case of the Zn complex 12 with triflate anions, half of the hydrogen bonds are formed. Only one of the two orthogonal ligands has hydrogen bonds (d(N-H-N) = 3.082, 3.096 A) to the neighbouring complexes and thus builds linear, supramolecular, polymeric chains. These structural differences are mainly attributed to crystal-packing effects caused by the different anions. The data presented here may also be regarded as a prototype for the generation of organised arrays through sequential self-assembly processes.

Adaptive self-assembly: environment-induced formation and reversible switching of polynuclear metallocyclophanes

Ligand 3 has been shown to self-assemble under coordination of copper(II) cations in a 1:1 ratio in acetonitrile to give equilibrating mixtures of a [2 x 2] grid-type tetranuclear structure 1 and a hexanuclear achitecture of hexagonal shape 2. The latter was confirmed by determination of the crystal structure which further indicated that 2 contained acetonitrile molecules and hydroxo groups bound to the copper(II) centers, which are therefore five-coordinate. The structures assigned to 1 and 2 were further supported by the spectral (mass, UV/Vis) data. The self-assembly process is strongly dependent on the conditions of the medium. An increase in concentration in acetronitrile increases the relative amount of hexamer 2, which appears to be the favored entity at the highest concentrations that can be reached before precipitation occurs. On the other hand, in nitromethane only the tetranuclear complex 1 was detected by mass spectrometry. Replacement of nitromethane by acetonitrile and vice versa indicated the reversible switching between a solution containing either 1 alone or an equilibrium mixture of 1 and 2, respectively. In conclusion, the system described presents several remarkable features: 1) self-assembly with substrate binding, 2) dynamic combinatorial structure generation, and 3) environment-induced structural switching amounting in effect to a process of adaptive self-assembly.

Enforced helicity: efficient access to self-organized helical molecular strands by the imine route

The condensation of the two oligoheterocyclic aldehydes 8 and 16 with the bis-hydrazine 17 gives the bis-hydrazones 1 and 2. These molecular strands are shown to adopt helical conformations of 1.5 and 2.5 turns, respectively. The helical shape of 1 has been confirmed and structurally characterized by X-ray crystallography. The results indicate that the pyrimidine-hydrazone unit is a satisfatory helicity codon, so that the facile hydrazone formation provides an efficient procedure for generating helical structures. This greatly widens the scope of the methodology based on designed heterocyclic sequences for enforcing helicity in molecular strands, and opens interesting routes towards a variety of derived structures.

Interconversion of single and double helices formed from synthetic molecular strands

Synthetic single-helical conformations are quite common, but the formation of double helices based on recognition between the two constituent strands is relatively rare. Known examples include duplex formation through base-pair-specific hydrogen bonding and stacking, as found in nucleic acids and their analogues, and polypeptides composed of amino acids with alternating L and D configurations. Some synthetic polymers and self-assembled fibres have double-helical winding induced by van der Waals interactions. A third mode of non-covalent interaction, coordination of organic ligands to metal ions, can give rise to double, triple and quadruple helices, although in this case the assembly is driven by the coordination geometry of the metal and the structure of the ligands, rather than by direct inter-strand complementarity. Here we describe a family of oligomeric molecules with bent conformations, which exhibit dynamic exchange between single and double molecular helices in solution, through spiral sliding of the synthetic oligomer strands. The bent conformations leading to the helical shape of the molecules result from intramolecular hydrogen bonding within 2'-pyridyl-2-pyridinecarboxamide units, with extensive intermolecular aromatic stacking stabilizing the double-stranded helices that form through dimerization.

In situ generation and screening of a dynamic combinatorial carbohydrate library against concanavalin A

Dynamic combinatorial chemistry (DCC) is a recently introduced approach that is based on the generation of combinatorial libraries by reversible interconversion of the library constituents. In this study, the implementation of such libraries on carbohydrate-lectin interactions was examined. The dynamic carbohydrate libraries were generated from a small set (four or six compounds) of initial carbohydrate dimers through mild disulfide interchange, and selection was performed under two conditions defining either adaptive or pre-equilibrated libraries. Upon initiation, libraries were formed that contained comparable amounts of 10 or 21 individual dimeric species, dynamically interchanging during the scrambling process. They were probed with respect to binding to the plant lectin concanavalin A, either present during library generation or added after equilibration. The libraries could be generated easily both in the presence and absence of the receptor, and a bis-mannose structure was preferentially bound and selected from the mixture. Scrambling of the library in the presence of the receptor resulted in slightly higher yields than when the receptor was added after scrambling, indicating that the receptor to some extent acts as a thermodynamic trap during library generation. The present results illustrate the extention of the DCC approach to carbohydrate recognition groups, the generation of isoenergetic dynamic libraries, and the implementation of either adaptive or pre-equilibrated procedures.

Programmed chemical systems: multiple subprograms and multiple processing/expression of molecular information

Programmed chemical systems rest on the structural information stored in a molecular framework and on its reading and processing through non-covalent interactional algorithms to yield specific supramolecular entities. Beyond single-code self-assembly, which generates exclusively a single, specific superstructure, several codes may be implemented in the same overall program, thus opening the possibility to perform multiprogramming. Furthermore, the reading and processing of the same structural information through different interactional algorithms may lead to several different output entities, amounting to multiple expression of molecular information. Such features are revealed in the formation of double helicates, the assembly of metallosupramolecular architectures, and the differential reading of hydrogen bonding patterns in a molecular strand. They open novel perspectives within the framework of programmed chemical systems, concerning multiple processing capacity, and have intriguing implications from the biological point of view.

Multiple expression of molecular information: enforced generation of different supramolecular inorganic architectures by processing of the same ligand information through specific coordination algorithms

The multisubunit ligand 2 combines two complexation substructures known to undergo, with specific metal ions, distinct self-assembly processes to form a double-helical and a grid-type structure, respectively. The binding information contained in this molecular strand may be expected to generate, in a strictly predetermined and univocal fashion, two different, well-defined output inorganic architectures depending on the set of metal ions, that is, on the coordination algorithm used. Indeed, as predicted, the self-assembly of 2 with eight CuII and four CuI yields the intertwined structure D1. It results from a crossover of the two assembly subprograms and has been fully characterized by crystal structure determination. On the other hand, when the instructions of strand 2 are read out with a set of eight CuI and four MII (M = Fe, Co, Ni, Cu) ions, the architectures C1-C4, resulting from a linear combination of the two subprograms, are obtained, as indicated by the available physico-chemical and spectral data. Redox interconversion of D1 and C4 has been achieved. These results indicate that the same molecular information may yield different output structures depending on how it is processed, that is, depending on the interactional (coordination) algorithm used to read it. They have wide implications for the design and implementation of programmed chemical systems, pointing towards multiprocessing capacity, in a one code/ several outputs scheme, of potential significance for molecular computation processes and possibly even with respect to information processing in biology.

Template-induced and molecular recognition directed hierarchical generation of supramolecular assemblies from molecular strands

The linear oligo-isophthalamide strand 1 undergoes a conformational reorganization upon binding of a cyanuric acid template as effector to afford a helical disklike object possessing radially disposed alkyl residues. Solvophobic and stacking interactions, in turn, drive a "second level" self-assembly of the templated structure, the stacking of the helical disks, to yield fibers as revealed by electron microscopy. These data provide insight into the interplay of the different structural and interactional features of the molecular components towards the formation of supramolecular fibers through sequential hierarchical self-assembly events and suggest design strategies for the effector-controlled generation of related supramolecular assemblies.

Oriented crystalline monolayers and bilayers of 2 x 2 silver(I) grid architectures at the air-solution interface: their assembly and crystal structure elucidation

Oriented crystalline monolayers, approximately 14 A thick, of a 2 x 2 Ag+ grid complex, self-assembled at the air-solution interface starting from an water-insoluble ligand 3,6-bis[2-(6-phenylpyridine)]pyridazine spread on silver-ion-containing solutions, were examined by grazing-incidence X-ray diffraction and specular X-ray reflectivity using synchrotron radiation. The monolayer structure was refined, including a determination of the positions of the counter-ions, with the SHELX-97 computer program. The monolayers were transferred from the interface onto various solid supports and visualized by scanning force microscopy, and characterized by X-ray photoelectron spectroscopy in terms of molecular structure. On surface compression, the initial self-assembled monolayer undergoes a transition to a crystalline bilayer in which the two layers, almost retaining the original arrangement, are in registry. Such a phase transition is of relevance to the understanding of crystal nucleation.

Encoded Helical Self-Organization and Self-Assembly into Helical Fibers of an Oligoheterocyclic Pyridine - Pyridazine Molecular Strand

The conformational information of an oligoheterocyclic strand containing a repeating pyridine - pyridazine codon self-organizes into a helical molecular unit, which subsequently self-assembles into helical fibers and macrofibers in dichloromethane and pyridine. The spontaneous formation of helical structures is based on a general self-organization process enforced by the conformational information encoded within the molecular strand itself.

DNA double helix destabilizing properties of cyclobisintercaland compounds and competition with a single strand binding protein

The DNA helix destabilizing activity of a series of cyclobisintercaland compounds (CBIs) has been evaluated by measuring their ability to displace a 32P-labelled oligonucleotide primer (17-mer) hybridized to the single stranded DNA of M13. This destabilizing activity appears to be strongly dependent on the cyclic structure (the linear acyclic references are inactive) and the size of the macrocycle; both features being known to determine the preferential binding of the compound to ssDNA. Interestingly, CBIs induced the dissociation of the duplex template in a concentration range (0.5-1 microM) close to that required for the destabilizing activity of single stranded DNA binding proteins (SSBs). Therefore competition experiments between CBIs and an SSB protein (Eco SSB) for binding to a single stranded oligonucleotide target (36-mer) have been performed through gel electrophoresis and nitrocellulose binding assays and strong inhibitory effects on the formation of the SSB:36-mer complex have been observed.

Threading bis-intercalation of a macrocyclic bisacridine at abasic sites in DNA: nuclear magnetic resonance and molecular modeling study

The macrocyclic bisacridine (CBA) has been reported previously to specifically recognize single-stranded nucleic acid structures, especially DNA hairpins. The binding of the drug with an abasic site-containing oligonucleotide, was investigated by (1)H NMR and molecular modeling. We have used a DNA undecamer, the d(C(1)G(2)C(3)A(4)C(5)X(6)C(7)A(8)C(9)G(10)C(11)) x d(G(12)C(13)G(14)T(15)G(16)T(17)G(18)T(19)G(2)(0)C(21)G(22)) duplex in which the X residue is a stable analogue of the abasic site [3-hydroxy-2-(hydroxymethyl) tetrahydrofuran]. Analysis of the NMR data reveals that the bisacridine molecule forms two different intercalation complexes in a 80/20 (+/- 10) ratio. For the major complex, a molecular modeling study was performed guided by nineteen intermolecular drug-DNA restraints, determined from NOESY spectra. In this model, the ligand interacts in the threading binding mode with an acridine ring intercalated between the C(7)-A(8) and T(15)-G(16) base pairs, while the other acridine ring resides in the abasic pocket. The two linker chains are positioned in the minor and in the major groove, respectively. A comparable study was performed to evaluate the interaction of CBA with the parent unmodified duplex in which X(6) was replaced by an adenine residue. No complex formation was observed when operating in identical conditions. This shows the selective binding of CBA to the abasic site and its potential interest to target the abasic site lesion.

Controlled Arrangement of Supramolecular Metal Coordination Arrays on Surfaces

Metallo-supramolecular systems have been adsorbed in a controlled way onto graphite surfaces and visualized with molecular resolution for the first time. A parallel or orthogonal arrangement of the metal coordination arrays is evident depending on the specific ligands (see picture). Furthermore, simple nanomanipulations were performed by extracting single grids from the layer.

Structural characteristics of supramolecular assemblies formed by guanidinium-cholesterol reagents for gene transfection

We have recently discovered that cationic cholesterol derivatives characterized by guanidinium polar headgroups are very efficient for gene transfection in vitro and in vivo. In spite of being based on some rationale at the molecular level, the development of these new synthetic vectors was nevertheless empirical. Indeed, the factors and processes underlying cationic lipid-mediated gene transfer are still poorly understood. Thus, to get a better insight into the mechanisms involved, we have examined the supramolecular structure of lipid/DNA aggregates obtained when using reagent bis(guanidinium)-tren-cholesterol (BGTC), either alone or as a liposomal formulation with the neutral phospholipid dioleoyl phosphatidylethanolamine (DOPE). We here report the results of cryotransmission electron microscopy studies and small-angle x-ray scattering experiments, indicating the presence of multilamellar domains with a regular spacing of 70 A and 68 A in BGTC/DOPE-DNA and BGTC-DNA aggregates, respectively. In addition, DNA lipoplexes with similar lamellar patterns were detected inside transfected HeLa cells by conventional transmission electron microscopy. These results suggest that DNA condensation by multivalent guanidinium-cholesterol cationic lipids involves the formation of highly ordered multilamellar domains, the DNA molecules being intercalated between the lipid bilayers. These results also invite further investigation of the intracellular fate of the internalized lipid/DNA structures during their trafficking toward the cell nucleus. The identification of the basic features of active complexes should indeed help in the design of improved guanidinium-based vectors.

Selective photocleavage of single-stranded nucleic acids by cyclobisintercaland molecules

Irradiation of mixtures of a single-stranded circular plasmid and of a double-stranded supercoiled DNA in presence of the cyclobisintercaland compounds 2 or 3 shows that these reagents effect the selective photocleavage of the single-stranded entity. Furthermore, 2 also cleaves tRNAasp preferentially at single-stranded domains.

A macrocyclic bis-acridine shifts the equilibrium from duplexes towards DNA hairpins

Nucleic acids can undergo dynamic conformational changes associated with the regulation of biological processes. A molecule presenting larger affinities for alternative structures relative to a duplex is expected to modify such conformational equilibria. We have previously reported that macrocyclic bis-acridine binds preferentially to single-stranded regions, especially DNA hairpins, due to steric effects. Here, we show, using gel electrophoresis, fluorescence and melting temperature experiments, that the macrocycle bis-acridine shifts an equilibrium from a duplex towards the corresponding hairpins. Competition experiments enlighten the higher affinity of the macrocycle for hairpins compared with double-stranded DNA. The macrocycle bis-acridine destabilizes a synthetic polynucleotide, by the formation of premelted areas. By extrapolation, the macrocycle bis-acridine should be able to disrupt, at least locally, genomic DNA duplexes and to stabilize unpaired areas, especially palindromic ones forming hairpins. Such macrocyclic compounds may have potential applications in the therapy of diseases involving hairpins.

Virtual combinatorial libraries: dynamic generation of molecular and supramolecular diversity by self-assembly

Molecular and supramolecular diversity may be generated, respectively, by reversible, covalent or noncovalent self-assembly of basic components whose various potential combinations in number and nature represent a virtual combinatorial library. This concept is applied to the induction of inhibitors of carbonic anhydrase (CA) by reversible recombination of aldehyde and amine components. It is found that the presence of CA favors the formation of those condensation compounds that may be expected to present the strongest binding to the CA active site. The virtual combinatorial library approach may represent a powerful methodology for the discovery of substrates, inhibitors, receptors, catalysts, and carriers for a variety of processes.

Gene transfer by guanidinium-cholesterol cationic lipids into airway epithelial cells in vitro and in vivo

Synthetic vectors represent an attractive alternative approach to viral vectors for gene transfer, in particular into airway epithelial cells for lung-directed gene therapy for cystic fibrosis. Having recently found that guanidinium-cholesterol cationic lipids are efficient reagents for gene transfer into mammalian cell lines in vitro, we have investigated their use for gene delivery into primary airway epithelial cells in vitro and in vivo. The results obtained indicate that the lipid bis(guanidinium)-tren-cholesterol (BGTC) can be used to transfer a reporter gene into primary human airway epithelial cells in culture. Furthermore, liposomes composed of BGTC and dioleoyl phosphatidylethanolamine (DOPE) are efficient for gene delivery to the mouse airway epithelium in vivo. Transfected cells were detected both in the surface epithelium and in submucosal glands. In addition, the transfection efficiency of BGTC/DOPE liposomes in vivo was quantitatively assessed by using the luciferase reporter gene system.

Guanidinium-cholesterol cationic lipids: efficient vectors for the transfection of eukaryotic cells

Two cationic lipids, bis-guanidinium-spermidine-cholesterol (BGSC) and bis-guanidinium-trencholesterol (BGTC)-cholesterol derivatives bearing two guanidinium groups-have been synthesized and tested as artificial vectors for gene transfer. They combine the membrane compatible features of the cholesterol subunit and the favorable structural and high pKa features of the guanidinium functions for binding DNA via its phosphate groups. Reagent BGTC is very efficient for transfection into a variety of mammalian cell lines when used as a micellar solution. In addition, both BGTC and BGSC present also a high transfection activity when formulated as liposomes with the neutral phospholipid dioleoylphosphatidyl ethanolamine. These results reveal the usefulness of cholesterol derivatives bearing guanidinium groups for gene transfer.

Self-assembly of a heteroduplex helicate from two different ligand strands and Cu(II) cations

Cu(II) ions have been reacted with a 1/1 mixture of two linear ligands, one containing three 2,2'- bipyridine groups and the other three 2,2':6',2"-terpyridine groups. Absorption spectroscopy and fast atom bombardment mass spectrometry indicate the formation of a trinuclear complex containing one ligand of each kind. Determination of the crystal structure of this compound has confirmed that it is indeed a linear trinuclear complex in which two different ligands are wrapped in a helical fashion around the pentacoordinated metal ions. The central coordination geometry is trigonal bipyramidal; the two lateral Cu(II) ions are in a square pyramidal environment. Thus, a heteroduplex helicate is formed by the self-assembly of two different ligand strands and three specific metal ions induced by the coordination number and geometry of the latter. The self-assembly process may be considered to result from the reading of the steric and binding information present in the two ligands by Cu(II) ions through a pentacoordination algorithm. The same ligands have been shown earlier to yield homoduplex helicates from ions of tetrahedral and octahedral coordination geometry and strands of bidentate bipyridines and tridentate terpyridines, respectively. These two types of artificial double helical species may be related on one hand to the natural homoduplex nucleic acids and on the other hand to the DNA:RNA heteroduplex.

Synthesis of Oligobipyridine Strands Bearing Nucleoside and Amino Acid Side Chains

The synthesis is reported of derivatives of 6,6'-dimethyl-2,2'-bipyridine in which adenosine, thymidine aid tryptophan substituents are introduced at the 4,4'-positions as amide derivatives. Artificial oligonucleoside strands derived from the corresponding trisbipyridyl ligand , in which three bipyridyl ligands are separated by methyleneoxy bridges, have been prepared. The solubility of the nucleoside-substituted ligands in organic solvents is poor, but acylation of the ribose or deoxyribose units present in the ligands provides a mechanism whereby organic solubility can be improved. These ligands may be used for the preparation of metallo-exoreceptors , with the potential for recognition of biological targets such as nucleic acids. Preliminary metal ion complexation studies have been carried out.

Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase

The influence of nine synthetic polyamines on in vitro transcription with T7 RNA polymerase has been studied. The compounds used were linear or macrocyclic tetra- and hexaamine, varying in their size, shape and number of protonated groups. Their effect was tested on different types of templates, all presenting the T7 RNA promoter in a double-stranded form followed by sequences encoding short transcripts (25 to 35-mers) either on single- or double-stranded synthetic oligodeoxyribonucleotides. All polyamines used stimulate transcription of both types of templates at levels dependent on their size, shape, protonation degree, and concentration. For each compound, an optimal concentration could be defined; above this concentration, transcription inhibition occurred. Highest stimulation (up to 12-fold) was obtained by the largest cyclic compound called [38]N6C10.