DNA major versus minor groove occupancy of monomeric and dimeric crystal violet derivatives. Toward structural correlations.

Six monomeric (1a-1f) and five dimeric (2a-2e) derivatives of the triphenylmethane dye crystal violet (CV) have been prepared. Evaluation of the binding of these compounds to CT DNA by competitive fluorescent intercalator displacement (FID) assays, viscosity experiments, and UV and CD spectroscopy suggest that monomeric derivative 1a and dimeric derivative 2d likely associate with the major groove of DNA, while dimeric derivatives 2a and 2e likely associate with the minor groove of DNA. Additional evidence for the groove occupancy assignments of these derivatives was obtained from ITC experiments and from differential inhibition of DNA cleavage by the major groove binding restriction enzyme BamHI, as revealed by agarose gel electrophoresis. The data indicate that major groove ligands may be optimally constructed from dye units containing a sterically bulky 3,5-dimethyl-N,N-dimethylaniline group; furthermore, the groove-selectivity of olefin-tethered dimer 2d suggests that stereoelectronic interactions (n â†’ π*) between the ligand and DNA are also an important design consideration in the crafting of major-groove binding ligands.

[3,3]-Sigmatropic rearrangements of propargyl alkynyl ethers. Synthesis of complex dienoates and unsaturated lactones.

In an extension of our studies on low-temperature rearrangements of 1-alkynyl ethers, we describe herein the [3,3]-sigmatropic rearrangement of in situ formed propargyl alkynyl ethers to allenyl ketenes, which furnish complex tert-butyl-(2E,4Z)-dienoates 2 in good yields upon tert-butanol addition. Similarly, sigmatropic rearrangements of in situ formed propargyl lithioalkynyl ethers yield methyl-(2Z,4Z)-dienoates 4 upon methanol addition or unsaturated lactones 6 upon aldehyde or ketone addition to the allenyl ynolate intermediate.

n-Butyllithium-Induced Tandem [3,3]-Sigmatropic Rearrangement and Carbonyl Olefination of Allyl-1,1-dichlorovinyl Ethers.

Exposure of dichlorovinyl ethers 1 to n-butyllithium and addition of saturated or unsaturated aldehydes, ketones, or esters at ambient temperature furnishes rearranged α,ß-unsaturated carboxylic acids, isolated as their corresponding methyl esters 2 in 48-91% overall yields. Exposure of dichlorovinyl ethers 1 to n-butyllithium, addition of aldehydes, ketones, dialdehydes, or diketones at -78 °C, and warming to 80 °C in the presence of SiO2 provide 1,4-dienes 3 or cycloalken-1-ols (or their dehydration products) 4 in 45-72% overall yields.

Total Syntheses and Absolute Configuration Assignment of (+)-Sootepdienone, (-)-Jambolanin C, (-)-Jambolanin I, and (-)-Gibberodione.

Total syntheses of the sesquiterpenes (+)-sootepdienone, (-)-jambolanin C, (-)-jambolanin I, and (-)-gibberodione have been accomplished in 10 steps each from R-(+)-pulegone, allowing assignment of the absolute configuration of the natural products. A key step in the synthetic pathways involves the one-carbon ring expansion of a cyclic allylic phosphonate to a substituted cycloheptenone by a tandem oxidative cleavage/intramolecular Horner-Wadsworth-Emmons reaction.

Synthesis and Stereochemical Assignment of Conioidine A: DNA- and HSA-Binding Studies of the Four Diastereomers.

Conioidine A (1), isolated in 1993 with unknown relative and absolute configuration, was suggested to be a DNA-binding compound by an indirect technique. Four stereoisomers of conioidine A have been synthesized from d- and l-proline, and the natural product has been identified as possessing (4R,6R) absolute configuration. Binding of the conioidine diastereomers to calf thymus DNA (CT DNA) and human serum albumin (HSA) has been investigated by fluorescence spectroscopy and isothermal titration calorimetry (ITC). All stereoisomers display at least an order of magnitude weaker binding to DNA than the control compound netropsin; however, a strong association with HSA was observed for the (4R,6S) stereoisomer.

Total Synthesis of Alvaradoins E and F, Uveoside, and 10-epi-Uveoside.

Concise total syntheses of the anthracenone C-glycosides alvaradoins E and F, uveoside, and 10-epi-uveoside (1-4) have been accomplished from chrysophanic acid 8 and bromosugar 9. Key steps in the syntheses include the DBU-induced coupling of 8 and 9 to produce ß-C-glycoside 11, and a Pb(OAc)4-mediated Kochi reaction to introduce the C-1' oxygen atom of the natural products. Isothermal titration calorimetry and fluorescence binding studies reveal that compounds 1 and 2 have good affinity for the plasma protein HSA.

Synthesis and DNA binding profile of monomeric, dimeric, and trimeric derivatives of crystal violet.

Monomeric, dimeric, and trimeric derivatives of the triphenylmethane dye crystal violet (1a-1f) have been synthesized for the purpose of evaluating their affinity and sequence selectivity for duplex DNA. Competitive ethidum displacement assays indicate that 1a-1f have apparent association constants for CT DNA in the range of 1.80-16.2 × 107 M-1 and binding site sizes of 10-14 bp. Viscosity experiments performed on ligand 1f confirmed that these dyes associate with duplex DNA by a non-intercalative mode of binding. Circular dichroism and competition binding studies of the tightest binding ligand 1e with known major and minor groove binding molecules suggest that these dye derivatives likely occupy the major groove of DNA. Data from the binding of 1e to polynucleotides indicate close to an order of magnitude preference for associating with AT rich homopolymers over GC rich homopolymers, suggesting a shape-selective match of the sterically bulky ligand with DNA containing a wider major groove.

Ring Expansion, Ring Contraction, and Annulation Reactions of Allylic Phosphonates under Oxidative Cleavage Conditions.

Oxidative cleavage of cycloalkenylalkylphosphonates 1 followed by treatment with base gives rise to homologated cycloalkenones 2 in good to excellent yields. Subjecting cycloalk-2-enylphosphonates 3 to identical conditions provides the one-carbon ring-contracted compounds 4 in excellent yields. Oxidative cleavage of γ,δ-unsaturated ketophosphonates 6 followed by treatment with base affords 2-cyclopenten-1-ones 7 in good overall yields. This method may offer a practical alternative to existing methods for effecting one-carbon ring expansion, ring contraction, and annulation reactions.

Dimeric and trimeric derivatives of the azinomycin B chromophore show enhanced DNA binding.

To explore the utility of the azinomycin B chromophore as a platform for the development of major-groove binding small molecules, we have prepared a series of 3-methoxy-5-methylnaphthalene derivatives containing diamine, triamine, and carbohydrate linker moieties. All bis- and tris-azinomycin derivatives are intercalators that display submicromolar binding affinities for calf-thymus DNA, as revealed by viscometry measurements and fluorescent intercalator displacement (FID) assays, respectively. Although the tightest binding ligand 1d (Ka = 2.42 × 107 M-1) has similar affinities for sequence diverse polynucleotides, competition binding studies with methylated phage DNA and known major and minor groove binding small molecules suggest that the tether moiety linking the naphthalene chromophores may occupy the major groove of DNA.

A protecting group-free synthesis of (-)-hortonones A-C from the Inhoffen-Lythgoe diol.

A synthesis of hortonones A-C has been accomplished from vitamin D2via the Inhoffen-Lythgoe diol without the use of protective groups. Key steps in the syntheses include a TMS-diazomethane mediated regioselective homologation of the cyclohexanone ring to a cycloheptanone moiety and a sodium naphthalenide-mediated allylic alcohol transposition. It has been found that the absolute configuration of the natural hortonones is opposite that of the synthetic material prepared from vitamin D2.

A Single-Flask Synthesis of Morita-Baylis-Hillman Adducts from Ethoxyacetylene and Carbonyl Compounds: Synthesis of Subamolides D and E.

Sequential treatment of (ethoxyethynyl)lithium with aldehydes and/or ketones (2 and 4) and BF3·OEt2 gives rise to ß-hydroxyenoates 5 in good to excellent overall yields. Similarly, the combination of 1 (M = Li) and dicarbonyl compounds 6 (X = O) or keto/aldehyde acetals (X = OMe) followed by the addition of a Lewis acid leads to five-, six-, and seven-membered hydroxycycloalkene carboxyates. The utility of this method is demonstrated in the synthesis of the α-alkylidene lactone natural products subamolide D and E.

Tandem Bond-Forming Reactions of 1-Alkynyl Ethers.

Electron-rich alkynes, such as ynamines, ynamides, and ynol ethers, are functional groups that possess significant potential in organic chemistry for the formation of carbon-carbon bonds. While the synthetic utility of ynamides has recently been expanded considerably, 1-alkynyl ethers, which possess many of the reactivity features of ynamides, have traditionally been far less investigated because of concerns about their stability. Like ynamides, ynol ethers are relatively unhindered to approach by functional groups present in the same or different molecules because of their linear geometry, and they can potentially form up to four new bonds in a single transformation. Ynol ethers also possess unique reactivity features that make them complementary to ynamides. Research over the past decade has shown that ynol ethers formed in situ from stable precursors engage in a variety of useful carbon-carbon bond-forming processes. Upon formation at -78 °C, allyl alkynyl ethers undergo a rapid [3,3]-sigmatropic rearrangement to form allyl ketene intermediates, which may be trapped with alcohol or amine nucleophiles to form γ,δ-unsaturated carboxylic acid derivatives. The process is stereospecific, takes place in minutes at cryogenic temperatures, and affords products containing (quaternary) stereogenic carbon atoms. Trapping of the intermediate allyl ketene with carbonyl compounds, epoxides, or oxetanes instead leads to complex α-functionalized ß-, γ-, or δ-lactones, respectively. [3,3]-Sigmatropic rearrangement of benzyl alkynyl ethers also takes place at temperatures ranging from -78 to 60 °C to afford substituted 2-indanones via intramolecular carbocyclization of the ketene intermediate. tert-Butyl alkynyl ethers containing pendant di- and trisubstituted alkenes and enol ethers are stable to chromatographic isolation and undergo a retro-ene/[2 + 2] cycloaddition reaction upon mild thermolysis (90 °C) to afford cis-fused cyclobutanones and donor-acceptor cyclobutanones in good to excellent yields and diastereoselectivities. This process, which takes place under neutral conditions and proceeds through an aldoketene intermediate, obviates the need to employ moisture-sensitive and/or unstable acid chlorides under basic conditions for intramolecular [2 + 2] cycloaddition reactions. Furthermore, Lewis acid-catalyzed intramolecular condensations of both ethyl and tert-butyl ynol ethers with tethered acetals efficiently provide protected five-, six-, and seven-membered cyclic Baylis-Hilman adducts. Metalated ethoxyacetylene can also participate in multiple bond-forming reactions that avoid isolation of the alkynyl ether intermediate. Lewis acid-promoted tandem additions employing epoxides/oxetanes and carbonyl compounds give rise to (Z)-α-alkylidene and α-benzylidene lactones stereoselectively in high overall yields. Three new carbon-carbon bonds and a ring are formed in this atom-economical single-flask transformation, resulting in a significant increase in molecular complexity. This Account provides a detailed overview of these useful transformations with the intention of stimulating further interest in and research on ynol ethers and their application in organic synthesis.

A Single-Flask Synthesis of α-Alkylidene and α-Benzylidene Lactones from Ethoxyacetylene, Epoxides/Oxetanes, and Carbonyl Compounds.

Low temperature treatment of (ethoxyethynyl)lithium with epoxides or oxetanes in the presence of BF3•OEt2, followed by addition of aldehydes or ketones and warming to room temperature, affords structurally diverse five- and six-membered α-alkylidene and α-benzylidene lactones (5) in good to excellent yields. This one-pot process, in which three new carbon-carbon bonds and a ring are formed, affords substituted α,ß-unsaturated lactones of predominantly Z-configuration. The reaction likely occurs via alkyne-carbonyl metathesis of a hydroxy-ynol ether intermediate, acid-promoted alkene E- to Z-isomerization, and lactonization.

Synthesis and DNA binding profile of N-mono- and N,N'-disubstituted indolo[3,2-b]carbazoles.

A series of N-monosubstituted and N,N'-disubstituted derivatives of the indolo[3,2-b]carbazole chromophore have been prepared, and their binding affinity for duplex DNA has been evaluated by ultraviolet and fluorescence spectroscopies. It has been found that indolo[3,2-b]carbazoles bearing basic N-alkyl substituents are intercalators that bind DNA with affinities in the micromolar and submicromolar range and a preference for associating with sequences of mixed composition and purine-pyrimidine steps.

Total synthesis of the antitumor natural product polycarcin V and evaluation of its DNA binding profile.

The convergent total synthesis of polycarcin V, a gilvocarcin-type natural product that shows significant cytotoxicity with selectivity for nonsmall-cell lung cancer, breast cancer, and melanoma cells, has been achieved in 13 steps from 7, 8, and 22; the sequence features a stereoselective α-C-glycosylation reaction for the union of protected carbohydrate 7 and naphthol 8. The association constant for the binding of polycarcin V to duplex DNA is similar to that previously reported for gilvocarcin V.

Synthesis of 3,3'-di-O-methyl ardimerin and exploration of its DNA binding properties.

The 3,3'-di-O-methyl derivative (15) of the bis-C-aryl glycoside natural product ardimerin (1) has been synthesized in 11 steps from 2,3,4,6-tetrabenzylglucose (2) and 1,2,3-trimethoxybenzene (3). Key steps in the synthesis involve a Lewis acid mediated Friedel-Crafts type glycosylation and a Yamaguchi lactonization under Yonemitsu conditions. 3,3'-Di-O-methyl ardimerin aggregates in aqueous solutions at concentrations greater than 1 µM, and both UV and fluorescence binding studies indicate that 15 has a low affinity for duplex DNA.

Low temperature n-butyllithium-induced [3,3]-sigmatropic rearrangement/electrophile trapping reactions of allyl-1,1-dichlorovinyl ethers. Synthesis of ß-, γ- and δ-lactones.

Treatment of allyl-1,1-dichlorovinyl ethers with n-BuLi at -78 °C, followed by quenching with ketones, epoxides, and oxetanes, leads to highly substituted ß-, γ-, and δ-lactones in good to excellent yields.

Anti-peroxyl radical quality and antibacterial properties of rooibos infusions and their pure glycosylated polyphenolic constituents.

The anti-peroxyl radical quality of two aqueous rooibos infusions and solutions of their most abundant glycosylated polyphenols was evaluated using pyrogallol red and fluorescein-based oxygen radical absorbance ratios. It was observed that the artificial infusions, prepared using only the most abundant polyphenols present in rooibos and at concentrations similar to those found in the natural infusions, showed greater antioxidant quality than the latter infusions, reaching values close to those reported for tea infusions. Additionally, the antimicrobial activity of the natural and artificial infusions was assessed against three species of bacteria: Gram (+) Staphylococus epidermidis and Staphylococcus aureus and Gram (-) Escherichia coli. When compared to the natural infusions the artificial beverages did not demonstrate any bacterostatic/cidal activity, suggesting that the antibacterial activity of rooibos is related to compounds other than the glycosylated polyphenols employed in our study.

Lewis acid catalyzed intramolecular condensation of ynol ether-acetals. Synthesis of alkoxycycloalkene carboxylates.

Treatment of ynol ether-tethered dialkyl acetals with catalytic quantities of scandium triflate in CH(3)CN gives rise to five-, six-, and seven-membered alkoxycycloalkene carboxylates in good to excellent yields. Tri- and tetrasubstituted carbocyclic and heterocyclic alkenes may be formed by this method, and the products obtained may serve as useful intermediates for natural product synthesis.

Total synthesis of indole-3-acetonitrile-4-methoxy-2-C-ß-D-glucopyranoside. Proposal for structural revision of the natural product.

Indole-3-acetonitrile-4-methoxy-2-C-ß-D-glucopyranoside (1), a novel C-glycoside from Isatis indigotica with important cytotoxic activity, has been prepared in ten steps from ethynyl-ß-C-glycoside 3 and 2-iodo-3-nitrophenyl acetate 6. Key steps in the synthesis include a Sonogashira coupling and a CuI-mediated indole formation. NMR spectroscopic data for synthetic 1 differs from that reported for the natural product. A revised structure for the natural product, containing an alternate carbohydrate substituent, is proposed.