C-lysine conjugates: pH-controlled light-activated reagents for efficient double-stranded DNA cleavage with implications for cancer therapy.

Double-stranded DNA cleavage of light-activated lysine conjugates is strongly enhanced at the slightly acidic pH (<7) suitable for selective targeting of cancer cells. This enhancement stems from the presence of two amino groups of different basicities. The first amino group plays an auxiliary role by enhancing solubility and affinity to DNA, whereas the second amino group, which is positioned next to the light-activated DNA cleaver, undergoes protonation at the desired pH threshold. This protonation results in two synergetic effects which account for the increased DNA-cleaving ability at the lower pH. First, lysine conjugates show tighter binding to DNA at the lower pH, which is consistent with the anticipated higher degree of interaction between two positively charged ammonium groups with the negatively charged phosphate backbone of DNA. Second, the unproductive pathway which quenches the excited state of the photocleaver through intramolecular electron transfer is eliminated once the donor amino group next to the chromophore is protonated. Experiments in the presence of traps for diffusing radicals show that reactive oxygen species do not contribute significantly to the mechanism of DNA cleavage at the lower pH, which is indicative of tighter binding to DNA under these conditions. This feature is valuable not only because many solid tumors are hypoxic but also because cleavage which does not depend on diffusing species is more localized and efficient. Sequence-selectivity experiments suggest combination of PET and base alkylation as the chemical basis for the observed DNA damage. The utility of these molecules for phototherapy of cancer is confirmed by the drastic increase in toxicity of five conjugates against cancer cell lines upon photoactivation.

Radical cascade transformations of tris(o-aryleneethynylenes) into substituted benzo[a]indeno[2,1-c]fluorenes.

Oligomeric o-aryleneethynylenes with three triple bonds undergo cascade radical transformations in reaction with a Bu 3SnH/AIBN system. These cascades involve three consecutive cycle closures with the formation of substituted benzo[ a]indeno[2,1- c]fluorene or benzo[1,2]fluoreno[4,3- b]silole derivatives. The success of this sequence depends on regioselectivity of the initial attack of the Bu 3Sn radical at the central triple bond of the o-aryleneethynylene moiety. The cascade is propagated through the sequence of 5-exo-dig and 6-exo-dig cyclizations which is followed by either a radical attack at the terminal Ar substituent or radical transposition which involves H-abstraction from the terminal TMS group and 5-endo-trig cyclization. Overall, the transformation has potential to be developed into an approach to a new type of graphite ribbons.

DNA damage-site recognition by lysine conjugates.

Simple lysine conjugates are capable of selective DNA damage at sites approximating a variety of naturally occurring DNA-damage patterns. This process transforms single-strand DNA cleavage into double-strand cleavage with a potential impact on gene and cancer therapy or on the design of DNA constructs that require disassembly at a specific location. This study constitutes an example of DNA damage site recognition by molecules that are two orders of magnitude smaller than DNA-processing enzymes and presents a strategy for site-selective cleavage of single-strand nucleotides, which is based on their annealing with two shorter counterstrands designed to recreate the above duplex damage site.

Two-photon excitation of substituted enediynes.

Electronic spectroscopy of nine benzannelated enediynes and a related fulvene was studied under one-photon and two-photon excitation conditions. We utilize measured absorbance and emission spectra and time-resolved fluorescence decays of these molecules to calculate their radiative lifetimes and fluorescence quantum yields. The fluorescence quantum yields for the other compounds were referenced to the fluorescence quantum yield of compound 3 and used to determine relative two-photon absorption cross-sections. Further insight into experimental studies has been achieved using time-dependent density functional (TD-DFT) computations. The probability of two-photon absorption (TPA) increases noticeably for excitation to the higher excited states. The photophysical properties of benzannelated enediynes are sensitive to substitutions at both the core and the periphery of the enediyne chromophore. Considerably enhanced two-photon absorption is observed in an enediyne with donor substitution in the middle and acceptor substitution at the termini. Excited states with B symmetry are not active in TPA spectra. From a practical point of view, this study extends the range of wavelengths applicable for activation of the enediyne moiety from 350 to 600 nm and provides a rational basis for future studies in this field. Our theoretical computations confirmed that lowest energy TPA in benzannelated enediynes involves different orbitals than lowest energy one-photon absorbance and provided further support to the notion that introduction of donor and acceptor substituents at different ends of a molecule increases TPA.

Ortho effect in the Bergman cyclization: comparison of experimental approaches and dissection of cycloaromatization kinetics.

Four different experimental sources of kinetic information were combined to study the effect of ortho substituents on the rate of Bergman cycloaromatization. All methods confirm that the cyclization barrier is highly sensitive to the nature of the ortho substituents. However, the measured activation energies strongly depend on the choice of experimental technique: even the relative trends provided by the different methods agree with each other only in the case of acceptor substituents. Both the onset peaks and the activation energies determined by differential scanning calorimetry (DSC; either in neat enediynes or in their solutions in 10.6 M 1,4-cyclohexadiene (1,4-CHD)) strongly overestimate the reactivity of 1,2-diethynylbenzene, suggesting that DSC cannot be taken as a reliable indicator of enediyne reactivity. This discrepancy is likely to stem from the presence of side reactions with low activation barriers, especially important when the reaction is conducted in neat enediyne. On the other hand, kinetic measurements based on monitoring the concentrations of enediyne reactants and naphthalene products provide reliable general trends that include the parent benzannelated enediyne. These measurements confirm that both ortho-NO2 and ortho-CHO substituents substantially decrease activation energies for the Bergman cyclization, supporting earlier computational predictions. A comparison of theory and experiment suggests that computations at the Moeller-Plesset second-order perturbation theory (MP2)/6-31G level provide an excellent alternative to DFT when an accurate description of the contribution of noncovalent interactions to the activation energy is needed. Activation energies derived from k(eff), the effective rate constant under the pseudo-first-order approximation, depend on the 1,4-CHD concentrations. The true rate constant, k(1), for the cyclization step and the ratio of constants for the retro-Bergman ring opening, k(-1), and the intermolecular H-atom abstraction, k2, were determined from the dependence of cycloaromatization kinetics of ortho- and para-NO2 substituted enediynes on the concentration of 1,4-CHD.

Triplet acetylenes as synthetic equivalents of 1,2-bicarbenes, part II: new supramolecular scaffolds from photochemical cycloaddition of diarylacetylenes to 1,4-cyclohexadienes.

1,5-Diaryl substituted homoquadricyclanes which are readily available through cascade photocycloaddition of diarylacetylenes to 1,4-cyclohexadienes are useful supramolecular scaffolds with an angle of about 60 degrees formed by the two aromatic rings defining a hydrophobic cavity. These structural features of pyridinyl homoquadricyclanes were applied to the design of composite organic/inorganic materials with topologies depending on the ratio of ligand to metal. The crystal structure of complex 1 (L1/AgNO(3) in a 1:1 ratio) shows an alternating ligand-metal polymer in which each of the silver ions in its linear coordination geometry is shared between two L1 molecules. A small change in the crystallization method yields a supramolecular rhomboid (complex 2, L1/AgNO(3) 3:2 ratio) which has two ligands that occupy opposite corners of the rhomboid and two silver atoms occupy the other two corners. Connection of the rhomboids units through a third molecule forms unique "beads on a string" polymeric chains. In complex 2, the silver ions adopt a distorted tetrahedral geometry with the nitrate anion occupying one of the vertices of the tetrahedron. The crystal packing of the chain of rhomboids generates cavities which are filled with disordered solvent molecules. Non-symmetrical homoquadricyclane L3 coordinates with silver only through the nitrogen of the pyridine ring but not through the nitrogen of the tetrafluoropyridine ring in which the electron density of the nitrogen lone-pair is very low. The substituents on the polycyclic moiety of the homoquadricyclane cause restricted rotation of the pyridine rings which suggests that the flexibility of such systems can be fine-tuned to create a family of supramolecular scaffolds of controlled rigidity.

Triplet acetylenes as synthetic equivalents of 1,2-bicarbenes: phantom n,pi state controls reactivity in triplet photocycloaddition.

Diaryl acetylenes, in which one of the aryl groups is either a pyridine or a pyrazine, undergo efficient triplet state photocycloaddition to 1,4-cyclohexadiene with formation of 1,5-diaryl substituted tetracyclo[3.3.0.0(2,8).0(4,6)]octanes (homoquadricyclanes). In the case of pyrazinyl acetylenes, the primary homoquadricyclane products undergo a secondary photochemical rearangement leading to diaryl substituted tricyclo[3.2.1.0(4,6)]oct-2-enes. Mechanistic and photophysical studies suggest that photocycloaddition proceeds through an electrophilic triplet excited state whereas the subsequent rearrangement to the tricyclooctenes proceeds through a singlet excited state. Chemical and quantum yields for the cycloaddition, in general, correlate with the electron acceptor character of aryl substituents but are attenuated by photophysical factors, such as the competition between the conversion of acetylene singlet excited state into the reactive triplet excited states (intersystem crossing: ISC) and/or to the radical-anion (photoelectron transfer from the diene to the excited acetylene: PET). Dramatically enhanced ISC between pi-pi S(1) state and "phantom" n,pi triplet excited state is likely to be important in directing reactivity to the triplet pathway. The role of PET can be minimized by the judicious choice of reaction conditions (solvent, concentration, etc.). From a practical perspective, such reactions are interesting because "capping" of the triple bond with the polycyclic framework orients the terminal aryl (4-pyridyl, 4-tetrafluoropyridyl, phenyl, etc.) groups in an almost perfect 60 degrees angle and renders such molecules promising supramolecular building blocks, especially in the design of metal coordination polymers.

Lysine-enediyne conjugates as photochemically triggered DNA double-strand cleavage agents.

Statistical analysis of DNA-photocleavage by two types of lysine-enediyne conjugates confirms that more double-strand breaks are produced than can be accounted for by coincident single-strand breaks.

Synthesis of selectively deuterated fulvenes and indenes from enediynes.

A facile enediyne--> fulvene--> indene transformation provides a route to all possible isotopomers of substituted fulvenes and indenes.

5-Exo-dig radical cyclization of enediynes: the first synthesis of tin-substituted benzofulvenes.

[reaction: see text] Bu(3)Sn-mediated 5-exo-dig radical cyclization of diaryl enediynes provides a mild and efficient approach to tin-substituted fulvenes. Further synthetic opportunities opened by this process and general factors responsible for the observed regio- and stereoselectivity are outlined.

C1-c5 photochemical cyclization of enediynes.

This study reports a new photochemical cyclization of tetrafluoropyridinyl (TFP)-substituted enediynes that is accompanied with four formal hydrogen-atom abstractions from organic substrates and is mechanistically different from the Bergman cyclization.

Tuning rate of the bergman cyclization of benzannelated enediynes with ortho substituents.

[reaction: see text] The Bergman cyclization of benzannelated enediynes is highly sensitive to ortho substitution. This finding opens possibilities for the rational design of conformer-specific and pH-dependent DNA-cleaving agents.