Protected 32P-labels in deoxyribonucleotides: investigation of sequence selectivity of DNA photocleavage by enediyne-, fulvene-, and acetylene-lysine conjugates

Enediynes bearing polyfluoroaryl sulfoxide as new antiproliferative agents with dual targeting of microtubules and DNA

A novel series of enediynes possessing pentafluorophenylsulfoxide have been developed. The innovative compounds possess antiproliferative activity against a broad panel of human cancer cells originating from breast, blood, lung, kidney, colon, prostate, pancreas or skin with IC₅₀ ranging from 0.6 to 3.4 μM. The antiproliferative activity of enediynes in darkness is associated to their ability to compromise microtubule network. In addition, exposure to UV leads to double-stranded DNA cleavage caused by the newly synthesized molecules reducing further their IC₅₀ in nanomolar range against human tumor cells, including chemo-resistant pancreatic cancer cells. Taken together, the examined data demonstrate that enediynes possessing pentafluorosulfoxide are promising molecules in the cancer therapy.

Selective tumor cell death induced by irradiated riboflavin through recognizing DNA G-T mismatch

Riboflavin (vitamin B2) has been thought to be a promising antitumoral agent in photodynamic therapy, though the further application of the method was limited by the unclear molecular mechanism. Our work reveals that riboflavin was able to recognize G–T mismatch specifically and induce single-strand breaks in duplex DNA targets efficiently under irradiation. In the presence of riboflavin, the photo-irradiation could induce the death of tumor cells that are defective in mismatch repair system selectively, highlighting the G–T mismatch as potential drug target for tumor cells. Moreover, riboflavin is a promising leading compound for further drug design due to its inherent specific recognition of the G–T mismatch.

The excited state antiaromatic benzene ring: a molecular Mr Hyde?

The antiaromatic character of benzene in its first ππ* excited triplet state (T1) was deduced more than four decades ago by Baird using perturbation molecular orbital (PMO) theory [J. Am. Chem. Soc. 1972, 94, 4941], and since then it has been confirmed through a range of high-level quantum chemical calculations. With focus on benzene we now first review theoretical and computational studies that examine and confirm Baird's rule on reversal in the electron count for aromaticity and antiaromaticity of annulenes in their lowest triplet states as compared to Hückel's rule for the ground state (S0). We also note that the rule according to quantum chemical calculations can be extended to the lowest singlet excited state (S1) of benzene. Importantly, Baird, as well as Aihara [Bull. Chem. Soc. Jpn. 1978, 51, 1788], early put forth that the destabilization and excited state antiaromaticity of the benzene ring should be reflected in its photochemical reactivity, yet, today these conclusions are often overlooked. Thus, in the second part of the article we review photochemical reactions of a series of benzene derivatives that to various extents should stem from the excited state antiaromatic character of the benzene ring. We argue that benzene can be viewed as a molecular "Dr Jekyll and Mr Hyde" with its largely unknown excited state antiaromaticity representing its "Mr Hyde" character. The recognition of the "Jekyll and Hyde" split personality feature of the benzene ring can likely be useful in a range of different areas.

Opening Enediyne Scissors Wider: pH-Dependent DNA Photocleavage by meta-Diyne Lysine Conjugates

Photochemical activation of meta-diynes incapable of Bergman and C1-C5 cyclizations still leads to efficient double-strand DNA cleavage. Spatial proximity of the two arylethynyl groups is not required for efficient DNA photocleavage by the enediyne-lysine conjugates. Efficiency of the cleavage is a function of the external pH and DNA damage is strongly enhanced at pH < 7. The pH-dependence of the DNA photocleavage activity stems from the protonation states of lysine amino groups, the internal electron donors responsible for intramolecular PET quenching and deactivation of the photoreactive excited states. DNA-binding analysis suggests intercalative DNA binding for phenyl substituted conjugate and groove binding for TFP-substituted conjugate. Additional insights in the possible mechanism for DNA damage from the ROS (Reactive Oxygen Species) scavenger experiments found that generation of singlet oxygen is partially involved in the DNA damage.

Photophysics of diphenylacetylene: light from the "dark state"

A weak band at the tail of the known tolane (diphenylacetylene, DPA) fluorescence spectrum in several solvents is assigned to the forbidden 1(1)A(u) → 1(1)A(g) transition on the basis of its lifetime (∼200 ps) and its fluorescence excitation spectra. The 1(1)A(u) state, generally called the dark state, is not truly dark. We report the temperature (T) dependence of DPA fluorescence quantum yields (ϕ(f)) in methylcyclohexane (MCH) solution and the fluorescence and phosphorescence quantum yields of DPA in glassy MCH at 77 K. Significant differences between fluorescence and phosphorescence excitation spectra reveal that, in addition to the 1(1)B(1u) ← 1(1)A(g) transition, the first DPA absorption band includes a transition to another excited state, most probably the 1(1)B(2u) state, from which intersystem crossing is more efficient. The T dependence of ϕ(f) values in MCH solution is shown to be consistent with the previously reported T dependence of the lifetimes of transient DPA singlet excited state absorptions in the picosecond time scale. Transient absorption decay rate constants in hexane, methylcyclohexane and decalin as a function of T are retreated. Application of the medium enhanced barrier model shows that the medium is fully engaged with the molecular motion that is involved in the activated nonradiative decay path of the 1(1)B(1u) state. In accord with theoretical calculations and experimental observations, that process is assigned to the diabatic internal conversion of the short-lived linear fluorescent π,π* (1(1)B(1u)) state, over a low intrinsic energy barrier, to the longer lived weakly fluorescent trans-bent π,σ* (1(1)A(u)), which is the precursor of the DPA triplet state. Absorption and fluorescence measurements in several solvents show that the 1(1)B(1u)-1(1)A(g) energy gap decreases linearly with increasing medium polarizability. Our results allow a more definitive state order assignment for DPA.

Selective transition state stabilization via hyperconjugative and conjugative assistance: stereoelectronic concept for copper-free click chemistry

Dissection of stereoelectronic effects in the transition states (TSs) for noncatalyzed azide-alkyne cycloadditions suggests two approaches to selective transition state stabilization in this reaction. First, the formation of both 1,4- and 1,5-isomers is facilitated via hyperconjugative assistance to alkyne bending and C···N bond formation provided by antiperiplanar σ-acceptors at the propargylic carbons. In addition, the 1,5-TS can be stabilized via attractive C-H···F interactions. Although the two effects cannot stabilize the same transition state for the cycloaddition to α,α-difluorocyclooctyne (DIFO), they can act in a complementary, rather than competing, fashion in acyclic alkynes where B3LYP calculations predict up to ∼1 million-fold rate increase relative to 2-butyne. This analysis of stereoelectronic effects is complemented by the distortion analysis, which provides another clear evidence of selective TS stabilization. Changes in electrostatic potential along the reaction path revealed that azide polarization may create unfavorable electrostatic interactions (i.e., for the 1,5-regioisomer formation from 1-fluoro-2-butyne and methyl azide). This observation suggests that more reactive azides can be designed via manipulation of charge distribution in the azide moiety. Combination of these effects with the other activation strategies should lead to the rational design of robust acyclic and cyclic alkyne reagents for fast and tunable "click chemistry". Further computational and experimental studies confirmed the generality of the above accelerating effects and compared them with the conjugative TS stabilization by π-acceptors.

A microfluidic device that generates hydroxyl radicals to probe the solvent accessible surface of nucleic acids

We describe a microfluidic device containing a mineral matrix capable of rapidly generating hydroxyl radicals that enables high-resolution structural studies of nucleic acids. Hydroxyl radicals cleave the solvent accessible backbone of DNA and RNA; the cleavage products can be detected with as fine as single nucleotide resolution. Protection from hydroxyl radical cleavage (footprinting) can identify sites of protein binding or the presence of tertiary structure. Here we report preparation of micron sized particles of iron sulfide (pyrite) and fabrication of a microfluidic prototype that together generate enough hydroxyl radicals within 20 ms to cleave DNA sufficiently for a footprinting analysis to be conducted. This prototype enables the development of high-throughput and/or rapid reaction devices with which to probe nucleic acid folding dynamics and ligand binding.

Fine-tuning alkyne cycloadditions: Insights into photochemistry responsible for the double-strand DNA cleavage via structural perturbations in diaryl alkyne conjugates

Hybrid molecules combining photoactivated aryl acetylenes and a dicationic lysine moiety cause the most efficient double-strand (ds) DNA cleavage known to date for a small molecule. In order to test the connection between the alkylating ability and the DNA-damaging properties of these compounds, we investigated the photoreactivity of three isomeric aryl-tetrafluoropyridinyl (TFP) alkynes with amide substituents in different positions (o-, m-, and p-) toward a model π-system. Reactions with 1,4-cyclohexadiene (1,4-CHD) were used to probe the alkylating properties of the triplet excited states in these three isomers whilst Stern-Volmer quenching experiments were used to investigate the kinetics of photoinduced electron transfer (PET). The three analogous isomeric lysine conjugates cleaved DNA with different efficiencies (34, 15, and 0% of ds DNA cleavage for p-, m-, and o-substituted lysine conjugates, respectively) consistent with the alkylating ability of the respective acetamides. The significant protecting effect of the hydroxyl radical and singlet oxygen scavengers to DNA cleavage was shown only with m-lysine conjugate. All three isomeric lysine conjugates inhibited human melanoma cell growth under photoactivation: The p-conjugate had the lowest CC(50) (50% cell cytotoxicity) value of 1.49 × 10(-7) M.

Fast oxy-cope rearrangements of bis-alkynes: competition with central C-C bond fragmentation and incorporation in tunable cascades diverging from a common bis-allenic intermediate

Fast anionic oxy-Cope rearrangements of 1,5-hexadiyn-3,4-olates can be incorporated into cascade transformations which rapidly assemble densely functionalized cyclobutenes or cyclopentenones via a common bis-allenic intermediate. The competition between fragmentation, 4π-electrocyclic closure, and aldol condensation can be efficiently controlled by the nature of the acetylenic substituents. The rearrangement of bis-alkynes with two hydroxyl substituents opens a conceptually interesting entry in the chemistry of ε-dicarbonyl compounds and suggests a new approach to analogues of rocaglamide/aglafolin.

Intracellular DNA damage by lysine-acetylene conjugates

Previously, we reported the design and properties of alkyne C-lysine conjugates, a powerful and tunable family of DNA cleaving reagents. We also reported that, upon photoactivation, these molecules are capable of inducing cancer cells death. To prove that the cell death stems from DNA cleavage by the conjugates, we investigated intracellular DNA damage induced by these molecules in LNCap cancer cells using single cell gel electrophoresis (SCGE) assays. The observation of highly efficient DNA damage confirmed that lysine acetylene conjugate is capable of cleaving the densely compacted intracellular DNA. This result provides a key mechanistic link between efficient DNA cleavage and cytotoxicity towards cancer cells for this family of light-activated anticancer agents.

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.

Efficient synthesis of the first betulonic acid-acetylene hybrids and their hepatoprotective and anti-inflammatory activity

The Sonogashira reaction can be applied for the preparation of acetylenic derivatives of betulonic acid where the triterpenoid moiety can serve as either the halo- or the acetylenic component. This reaction opened access to the first derivatives of betulonic acid containing either the arylethynyl (C[triple bond]C-Ar(Het) or the ethynyl (C[triple bond]CH) moieties. From the fundamental perspective, this work illustrates the possibility of selective Pd-catalyzed cross-coupling at terminal acetylenes in the presence of a terminal alkene. Hepatoprotective and anti-inflammatory properties of selected acetylenic derivatives of betulonic acid were investigated using the CCl4-induced hepatitis and carrageenan-induced edema models, respectively.

Design and synthesis of enediyne-peptide conjugates and their inhibiting activity against chymotrypsin

Novel enediyne-amino acid conjugates 1-4 have been synthesized. All of these effectively target the enzyme chymotrypsin inhibiting its proteolytic activity. The conjugate with a directly linked phenyl alanine is the most effective inhibitor with a K(i) of 3 microM. The mode of inhibition is mostly competitive or of a mixed type depending on the nature of the inhibitor.

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.