Exploration of some indole-based hydroxamic acids as histone deacetylase inhibitors and antitumor agents

In our search for novel small molecules targeting histone deacetylases, we have designed and synthesized a series of novel hydroxamic acids incorporating indole moiety as a cap group (3a–l). Biological evaluation showed that these hydroxamic acids potently inhibited HDAC2 with IC₅₀ values in submicromolar range and up to tenfold (compound 3j) better than that of SAHA (also known as suberoylanilide hydroxamic acid). In four human cancer cell lines [SW620 (colon), PC-3 (prostate), AsPC-1 (pancreatic), NCI-H23 (lung)], the synthesized compounds that exhibited potent cytotoxicity with several compounds (3k, 3l) were found to be 12- to 77-fold more cytotoxic than SAHA. Docking experiments indicated that the compounds tightly bound to HDAC2 at the active binding site with binding affinities much higher than that of SAHA. Our present results demonstrate that these novel hydroxamic acids are potential for further development as anticancer agents.     

Nucleoside and oligonucleotide pyrene conjugates with 1,2,3-triazolyl or ethynyl linkers: synthesis,duplex stability,and fluorescence changes generated by the DNA-dye connector

Fluorescent nucleosides and oligonucleotides functionalized with pyrene were synthesized using ‘click’ chemistry or the Sonogashira cross-coupling reaction. The dye was connected to position-7 of 7-deaza-2′-deoxyguanosine or to the 2′-deoxyribofuranose moiety. Four different DNA-dye connectors with 1,2,3-triazolyl residues or triple bonds were constructed. Phosphoramidites of the pyrene conjugates (9, 14, 25) were prepared and used in solid-phase synthesis. Short linkers (2, 4) destabilize DNA, while long linkers (1) increased duplex stability. Nucleosides and oligonucleotides with single dye incorporations show linker dependent fluorescence. Linker dependent excimer emission with pyrenes in proximal positions was also observed. A ‘superchromophore’ formed by the 7-deaza-2′-deoxyguanosine ethynylpyrene conjugate shows strong red shifted fluorescence emission at 495 nm.     

Cobaltacarborane-phthalocyanine conjugates: Syntheses and photophysical properties

Syntheses of two new cobaltacarborane-phthalocyanine conjugates, one anionic (Pc 6) and one zwitterionic (Pc 7), were accomplished via cyclotetramerization of the corresponding cobaltacarborane-substituted phthalonitriles (4 or 5) with excess phthalonitrile in quinoline. X-ray structures of two phthalonitrile precursors (2 and 3) were obtained and are discussed, and the absorption and emission properties of the two cobaltacarborane-phthalocyanine conjugates in several solvents were investigated. The anionic conjugate 6 exists mainly as a monomer in polar organic solvents and has fluorescence quantum yields in the region 0.2-0.3. The zwitterionic conjugate 7 aggregates in solution and displays lower quantum yields ∼0.1 in organic solvents.     

Hydrogelation and spontaneous fiber formation of 8-aza-7-deazaadenine nucleoside ‘click’ conjugates

Nucleoside hydrogels based on benzyl azide ‘click’ conjugates of 8-aza-7-deaza-2′-deoxyadenosine bearing 7-ethynyl, 7-octa-(1,7-diynyl), and 7-tri-prop-2-ynyl-amine side chains were synthesized (1, 3, 4). The cycloaddition adduct with the shortest linker (1) yields the most powerful hydrogelator forming stable gels at a concentration of 0.3 wt % of 1 in water. One molecule of 1 catches 7500 water molecules. Cycloaddition of the 8-aza-7-deaza-7-azido-2′-deoxyadenosine (9) and 3-phenyl-1-propyne (10) leads to the isomeric conjugate 2, with a C-N connectivity between the nucleobase and triazole moiety. This gel is less stable than that of the adduct 1. Both gels show a similar stability over a wide pH range (4.0-10.0). Xerogels of 1 and 2 studied by scanning electron microscopy (SEM) reveal that both click adducts (1 and 2) form long fibers spontaneously.     

Intramolecular charge transfer dual fluorescent sensors from 4-(dialkylamino)benzanilides with metal binding site within electron acceptor

Three fluoroionophores (2a-c) were designed as the intramolecular charge transfer (CT) dual fluorescent sensors for metal cations with metal binding site within the electron acceptor. These sensors were derived from 4-dialkylaminobenzanilides (alkyl=methyl, ethyl, and n-butyl) with the amido phenyl ring being an arm of 15-crown-5 thus bearing binding site for alkaline and alkaline earth metal cations. Compounds 2a-c were expected to have two possible CT channels of opposite direction. The absorption and fluorescence spectra of 2a-c and their crown-ether free model molecules 3a-c in a variety of solvents were recorded. Dual fluorescence was observed with 2a-c and was assigned to the LE and the CT states, respectively. In nonpolar or less polar solvents the CT occurring with 2a-c was identified as that occurred with benzanilides (BA) with the amido anilines being the electron donor (the BA-like CT), while in polar solvents such as acetonitrile (ACN), the CT was still mainly the BA-like. In the presence of alkali and alkaline earth metal cations in ACN, the CT dual fluorescence underwent substantial changes so as increased total quantum yield, red-shifted LE band and enhanced CT to LE intensity ratio. Binding of the metal cations at the 15-crown-5 moiety of 2a-c was shown to turn the CT direction that the dialkylamino group in the binding complexes being the electron donor while the benzo-15-crown-5 moiety now being within the electron acceptor. The occurrence of this CT enhances metal cation binding to 15-crown-5 ether in 2a-c, which was confirmed by the observed higher metal binding constants. Compounds 2a-c as the CT dual fluorescent sensors were shown to operate under the mechanism of the metal cation binding induced switching of the CT character from the BA-like to that occurred with 4-(dimethylamino)benzamides (the DMABA-like). Compounds 2a-c therefore represent successful examples for the CT dual fluorescent sensors for cations with the metal binding site within the electron acceptor and can be employed as sensitive ratiometric fluorescent sensors for metal cations of improved sensing performance.     

Ferrocenoyl-amino acids: redox response towards di- and trivalent metal ions

The interaction of six ferrocene-amino acid conjugates (Fc-CO-Gly-OH (2a), Fc-CO-Asp-OH (3a), Fc-CO-Glu-OH (4a), 1,1′-Fc(CO-Gly-OH) (2b), 1,1′-Fc(CO-Asp-OH) (3b), and 1,1′-Fc(CO-Glu-OH) (4b)) with Mg²⁺, Ca²⁺, Zn²⁺, La³⁺, and Tb³⁺ was investigated in aqueous solutions using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Addition of metal ions to solutions caused, in some cases, large changes in the half-wave potential, E_1/2. Our electrochemical results show that the Gly systems, 2a and 2b, show a preference for binding Mg²⁺, whereas the Asp and Glu conjugates prefer binding Ln³⁺.     

Michael addition of chiral formaldehyde N,N-dialkylhydrazones to activated cyclic alkenes

The nucleophilic conjugate addition of chiral formaldehyde N,N-dialkylhydrazones 1 to doubly activated cyclic alkenes 2-8 proceeds smoothly to afford the corresponding Michael adducts 14, 16, 18, 20, 22, 24, and 25 in variable yields and selectivities. The reactions take place either spontaneously or in the presence of MgI₂ as a mild Lewis acid depending on the type of substrate. Release of the chiral auxiliary was achieved by transformation of the hydrazone moiety into acetals, dithioacetals or nitriles.     

Synthesis and DNA binding behavior of a naphthalene diimide derivative carrying two dicobalt hexacarbonyl complexes as an infrared DNA probe

Naphthalene diimide having two dicobalt hexacarbonyl complexes at its substituent termini 1 was designed and synthesized as an infrared probe for double stranded DNA. Spectrophotometric and viscometric DNA binding studies of 1 and naphthalene diimide having two acetylene moieties 2 as its precursor were carried out to prove their threading intercalation binding modes. Fourier Transform Infrared Reflection-Absorption Spectroscopy (FT-IR RAS) measurements were achieved for DNA-immobilized on a gold surface before and after hybridization with complementary DNA strand. Distinguished absorption peaks assigned to the dicobalt hexacarbonyl complexes were obtained in the case of the formation of double stranded DNA after treatment with 1. This result revealed that 1 can be used as an infrared probe for monitoring double stranded DNA.     

Syntheses of nucleosides with a 1′,2′-β-lactam moiety as potential inhibitors of hepatitis C virus NS5B polymerase

To discover novel nucleosides as potential anti-HCV agents, nucleosides with a 1′,2′-β-lactam moiety were designed as a hybrid scaffold of MK-608 and GS-6620. Synthetic strategies were successfully developed to prepare two series of C-nucleosides with a 1′,2′-β-lactam moiety: a 7-deaza-purine C-nucleoside analog 11 was prepared in 10 steps with an overall yield of 3.7%; a purine C-nucleoside analog 22 was prepared in 9 steps with an overall yield of 9.7%.     

Regulation of metal ion recognition by allosteric effects in thiacalix[4]crown based receptors

Three new ditopic receptors 3a-c based on thiacalix[4]arene of 1,3 alternate conformation possessing two different complexation sites have been designed and synthesized for both soft and hard metal ions. The imino nitrogens bind soft metal ion (Ag⁺/Pb²⁺/Cu²⁺) and the crown moiety binds K⁺ ion. The preliminary investigations show that 3a-c behave as ditopic receptors for Ag⁺/K⁺, Pb²⁺/K⁺, and Cu²⁺/K⁺ ions, respectively. In all the three receptors it was observed that the formation of 3a·Ag⁺/3b·Pb²⁺/3c·Cu²⁺ complex triggers the decomplexation of K⁺ ion from crown moiety and acts as a gateway, which regulates the binding of alkali metal to crown moiety. Thus, allosteric binding between metal ions ‘switch off’ the recognition ability of crown ether ring.     

Triphenylamine-based novel PET sensors in selective recognition of dicarboxylic acids

The triphenylamine-based chemosensors 1 and 2 have been designed and synthesized, for the first time, for the selective recognition of dicarboxylic acids. Carboxylic acid binding takes place through charge neutral pyridyl amide receptor sites with concomitant quenching of fluorescence of the triphenylamine moiety. The bindings were examined using ¹H NMR, fluorescence and UV-vis spectroscopic methods. The receptor 1 was found to be selective for glutaric and adipic acids and the macrocycle 2 was specific for 2,2-dimethylmalonic acid.     

Hydrogen-bonding interactions in ferrocene-peptide conjugates containing valine

The synthesis and characterization of a series of ferrocene (Fc) peptide conjugates containing the amino acid valine is reported, where the peptide substituents are part of the hydrophobic sequence of the amyloid β-peptide. The hydrogen-bonding (H-bonding) interaction in these compounds is studied by variable temperature ¹H NMR spectroscopy. The solid-state structures, determined by single crystal X-ray crystallography, of two of the conjugates (Fc[CO-Leu-Val-OMe]₂1 and Fc[CO-Gly-Val-OH]₂6) are reported. Both structures are stabilized by intramolecular H-bonds exhibiting the familiar “Herrick motif” involving the proximal amide NH and the amide CO of the adjacent amino acid. This motif is sufficiently rigid and is maintained in solution as suggested by CD studies. However, the intermolecular H-bonding patterns observed on conjugates 1 and 6 are significantly different resulting in very different supramolecular architectures. For conjugate 1, a more conventional set of head-to-tail stacking interactions which is stabilized by β-sheet-like H-bonding interactions between the individual molecules is observed. However, for conjugate 6, the presence of the C-terminal acid group and presumably the flexibility of the Gly linker enables the formation of a more open structure that contains hydrophobic channels occupied by solvent molecules.     

The use of 3,3-bis(2-imidazolyl) propionic acid (bip-OH) as a new chelating ligand for Re(CO)3 and Ru complexes: Formation of organometallic PNA oligomers with (bip)Re(CO)3 and their interaction with complementary DNA

We report the use of 3,3-bis(2-imidazolyl) propionic acid (bip-OH, 1) as a new chelating bis(imidazole) ligand. The synthesis and full characterization of complexes Re(bip-O)(CO)₃2 and [Ru(bpy)₂(bip-OH)]²⁺3 is reported. Both complexes show interesting spectroscopic properties, namely IR for compound 2 and ¹H NMR for 3, respectively. The free carboxylic acid functionality of 1 may be used for the coupling to biomolecules. We have prepared two peptide nucleic acid (PNA) decamers to which the rhenium complex 2 is coupled. All reactions were carried out by solid phase synthesis methods. The Re-PNA oligomer conjugates Re(CO)₃(bip- tgt cta gca a -NH₂) 4 and Re(CO)₃(bip- agg agc aac t-Lys-NH₂) 5 were obtained in good yield and high purity after HPLC purification and identified by their mass spectra. The interaction of 5 with complementary DNA yields a melting temperature of (53.9 ± 1) °C. This is the first DNA melting temperature reported for an organometallic metal-PNA conjugate.     

Novel bifunctional sulfonamides catalyze an enantioselective conjugate addition

A new bifunctional organocatalyst with a novel structural and functional motif has been developed. This bifunctional sulfonamide organocatalyst was used in the conjugate addition of 1,3-dicarbonyl compounds (13) to β-nitrostyrenes (12). Yields up to 91% and enantiomeric excesses up to 79% were obtained in this reaction. This catalyst activates both 13 via its basic moiety and 12 through hydrogen bonding.     

Electrochemical gene detection based on supramolecular complex formation by ferrocenyl-β-cyclodextrin and adamantylnaphthalene diimide bound to double stranded DNA

Adamantylnaphthalene diimide 1 was synthesized as a highly selective double stranded DNA (dsDNA) binding reagent. The binding studies with sonicated calf thymus DNA as a model of dsDNA revealed that 1 can bind to dsDNA by the threading mode, where the two adamantyl moieties are located in the major and minor grooves of dsDNA separately and the complex of 1 with DNA duplex was stabilized by capping of the adamantyl moieties of 1 bound to dsDNA by β-cyclodextrin. The adamantyl moieties of 1 could be incorporated also into the cavity of ferrocenyl-β-cyclodextrin (Fc-β-CD), resulting in the formation of a supramolecular complex. When this complex is formed on the DNA probe-immobilized electrode, electrochemical DNA detection was feasible: the electrode hybridized with target DNA gave rise to a current peak corresponding to the ferrocene oxidation upon treatment with 1 and Fc-β-CD.     

New tetracyclic heteroaromatic compounds based on dehydroamino acids: photophysical and electrochemical studies of interaction with DNA

A benzothienoindole (BTIN) and a benzofuroindole (BFIN) were synthesized in high yields, as potential new DNA target compounds, using a metal-assisted intramolecular C-N cyclization of the methyl esters of N-(tert-butoxycarbonyl)-β,β-bis(dibenzothien-4-yl or dibenzofur-4-yl)dehydroalanines. The latter were obtained by a bis-Suzuki coupling of a β,β-dibromodehydroalanine with the corresponding heteroarylboronic acids. The absorption and fluorescence properties of the new tetracyclic compounds were studied in different solvents and in the presence of salmon sperm DNA. The results in several solvents show that either BTIN or BFIN can be used as fluorescence solvent sensitive probes. Spectroscopic studies of their interaction with dsDNA allowed to determine binding constant (K_i) values and binding site sizes (n). Fluorescence quenching experiments using iodide ion showed that intercalation is the preferred mode of binding to DNA. From the results obtained, BTIN is the more intercalative compound and has a higher affinity to DNA. The interaction of BTIN with DNA was also studied electrochemically, by using differential pulse voltammetry (DPV) in connection with disposable pencil graphite electrode (PGE). After the interaction of BTIN with DNA, the oxidation signals of BTIN and adenine strongly decreased. The latter result was attributed to the binding of BTIN to DNA and the former points to a possible damage of the oxidizable groups of BTIN after intercalation into DNA. The results of spectroscopic and electrochemical studies of BTIN interaction with DNA are in good agreement.     

The synthesis of luminescent lanthanide-based chemosensors for the detection of zinc ions

Herein, we report the synthesis of two lanthanide-based chemosensors, Tb-5 and Eu-6, designed to sense free zinc ions (Zn²⁺) in aqueous solutions. The Tb-5 complex features a bis(2-pyridinylmethyl)amine moiety as a zinc(II)-responsive lanthanide-sensitising ‘antenna’, while Eu-6 incorporates a quinoline-based moiety for this purpose. Luminescence enhancements of 210% and 340% are observed upon addition of Zn²⁺ ions to Tb-5 and Eu-6, respectively. Both sensors are selective for Zn²⁺ ions over several other cations of environmental significance.     

Novel DNA bis-intercalators of isoquinolino[4,5-bc]acridines: design, synthesis and evaluation of cytotoxic activity

Mono- and dinuclear isoquinolino[4,5-bc]acridine derivatives were designed and facilely synthesized, their DNA-binding affinities and cytotoxic activities were evaluated. A4 induced unwinding of supercoiled plasmid pBR 322 DNA by (36±2)° while A6 induced that by (41±1)°, both of which were higher than the mono-analogue A1 ((19±2)°). A6 exhibited the highest in vitro antitumor activity against human lung cancer cell (A549) and A4 was the most active one against murine leukemia cell (P388). DNA binding constant and molecular model indicated that both the length of linker chain and the distance of interchromophore were key impact factors for DNA binding affinity and biological activity.     

A new fluorescent sensor for the detection of pyrophosphate based on a tetraphenylethylene moiety

We have developed a new fluorescent sensor 1-2Zn based on a tetraphenylethylene (TPE) moiety for the detection of PPi. This TPE-based chemosensor showed ‘turn-on’ fluorescence emission according to the concentration of PPi. The fluorescence enhancement upon binding of PPi to 1-2Zn resulted from the restriction of intramolecular rotation of phenyl rings in 1-2Zn.     

Adenine-based receptor for dicarboxylic acids

The adenine-based fluorescent receptor 1 was designed and synthesized for the selective recognition of dicarboxylic acids in CH₃CN. The recognition takes place through the Hoogsteen binding site of adenine with concomitant PET quenching of the anthracene moiety. The carboxylic acid binding to 1 was investigated by ¹H NMR, X-ray, UV-vis, and fluorescence spectroscopic methods. The Hoogsteen (HG) cleft of receptor 1 is found to be selective for glutaric acid.