Synthesis and Structure-Activity Relationship Analysis of 5-HT₇ Receptor Antagonists: Piperazin-1-yl Substituted Unfused Heterobiaryls.

A series of piperazin-1-yl substituted unfused heterobiaryls was synthesized as ligands of the 5-HT₇ receptors. The goal of this project was to elucidate the structural features that affect the 5-HT₇ binding affinity of this class of compounds represented by the model ligand 4-(3-furyl)-2-(4-methylpiperazin-1-yl)pyrimidine (2). The SAR studies included systematical structural changes of the pyrimidine core moiety in 2 to quinazoline, pyridine and benzene, changes of the 3-furyl group to other heteroaryl substituents, the presence of various analogs of the 4-methylpiperazin-1-yl group, as well as additional substitutions at positions 5 and 6 of the pyrimidine.

Near IR heptamethine cyanine dye-mediated cancer imaging.

Purpose: Near-IR fluorescence imaging has great potential for noninvasive in vivo imaging of tumors. In this study, we show the preferential uptake and retention of two hepatamethine cyanine dyes, IR-783 and MHI-148, in tumor cells and tissues.

Experimental Design: IR-783 and MHI-148 were investigated for their ability to accumulate in human cancer cells, tumor xenografts, and spontaneous mouse tumors in transgenic animals.

Conjugate addition of nucleophiles to the vinyl function of 2-chloro-4-vinylpyrimidine derivatives.

Conjugate addition reaction of various nucleophiles across the vinyl group of 2-chloro-4-vinylpyrimidine, 2-chloro-4-(1-phenylvinyl)pyrimidine and 2-chloro-4-vinylquinazoline provides the corresponding 2-chloro-4-(2-substituted ethyl)pyrimidines and 2-chloro-4-(2-substituted ethyl)quinazolines. Treatment of these products, without isolation, with N-methylpiperazine results in nucleophilic displacement of chloride and yields the corresponding 2,4-disubstituted pyrimidines and quinazolines.

Fluorescence lifetime properties of near-infrared cyanine dyes in relation to their structures.

Structurally diverse near-infrared (NIR) absorbing polymethine dyes were prepared and their fluorescence lifetimes (FLT) were evaluated in relation to their structural features. Comparative FLT analysis based on the modification of methine chain length and heterocyclic system showed that indolium or benz[e]indolium heptamethine dyes exhibited longer FLT than the benz[c,d]indolium trimethine dye. Modification of heterocyclic system alone with an intact chain length showed that indolium-based heptamethine dyes showed approximately 30% longer FLT than the benz[e]indolium-based dyes.

Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform.

Virtual Screening is an increasingly attractive way to discover new small molecules with potential medicinal value. We introduce a novel strategy that integrates use of the molecular docking software Surflex with experimental validation by the method of competition dialysis. This integrated approach was used to identify ligands that selectively bind to the triplex DNA poly(dA)-[poly(dT)](2).

A study of intramolecular H-complexes of novel bis(heptamethine cyanine) dyes.

Near-infrared (NIR) bis(heptamethine cyanine) (BHmC) dyes containing a flexible polymethylene linker between the two cyanine subunits are a novel class of compounds with versatile spectroscopic properties. The first bis-cyanine of this type is BHmC-10 (with a decamethylene bridge) that has been reported by us recently [G. Patonay, J.

Design, synthesis, and characterization of a calcium-sensitive near infrared dye.

Intracellular calcium concentration in biological cells varies from 0.1 to 10 muM depending upon cell signaling and disease states. A direct estimate of calcium concentration in cell tissues within this range is possible with a novel calcium-selective reagent 15C5-774.

Noncovalent labeling of biomolecules with red and near- infrared dyes.

Biopolymers such as proteins and nucleic acids can be labeled with a fluorescent marker to allow for their detection. Covalent labeling is achieved by the reaction of an appropriately functionalized dye marker with a reactive group on a biomolecule. The recent trend, however, is the use of noncovalent labeling that results from strong hydrophobic and/or ionic interactions between the marker and biomolecule of interest.

Noncovalent interactions with DNA: an overview.

Over the last four decades, intense research has focused on the effects of small organic compounds that noncovalently bind to nucleic acids. These interactions have been shown to disrupt replication and/or transcription culminating in cellular death. Accordingly, DNA binding compounds have potential applications as anti-cancer and anti-viral agents.

Fujita-Ban QSAR analysis and CoMFA study of quinoline antagonists of immunostimulatory CpG-oligodeoxynucleotides.

One hundred seven 2-arylquinolin-4-amines were assayed in vitro for inhibition of the immunostimulatory effect of oligodeoxynucleotides containing a CpG-motif. The compounds are functionalized with various basic and non-basic groups at the aryl moiety and at the amino substituent of the quinolin-4-amine, and some of them contain an additional substituent at position 6 or 7 of the quinoline. Activities of these antagonists, expressed as EC(50) values, range from 0.

Solvent and linker influences on AQ(*-)/dA(*+) charge-transfer state energetics and dynamics in anthraquinonyl-linker-deoxyadenosine conjugates.

The goal of this work is to produce high yields of long-lived AQ(*-)/dA(*+) charge transfer (CT) excited states (or photoproducts). This goal fits within a larger context of trying generally to produce high yields of long-lived CT excited states within DNA nucleoside conjugates that can be incorporated into DNA duplexes. Depending upon the energetics of the anthraquinonyl (AQ) (3)(pi,pi) state as well as the reduction potentials of the subunits in particular anthraquinonyl-adenine conjugates, CT quenching of the AQ (3)(pi,pi*) state may or may not occur in polar organic solvents.

EcoScale, a semi-quantitative tool to select an organic preparation based on economical and ecological parameters.

A novel post-synthesis analysis tool is presented which evaluates quality of the organic preparation based on yield, cost, safety, conditions and ease of workup/purification. The proposed approach is based on assigning a range of penalty points to these parameters. This semi-quantitative analysis can easily be modified by other synthetic chemists who may feel that some parameters should be assigned different relative penalty points.

Investigation of iminosulfuranes as novel transdermal penetration enhancers: enhancement activity and cytotoxicity.

Purpose: Very few chemical enhancers for transdermal drug delivery have been approved for clinical use due to irritancy and toxicity concerns. Novel chemical enhancers (iminosulfuranes) were synthesized and studied for their activity and toxicity.

Methods: Skin was treated with 0.

Spectroscopic study of a novel bis(heptamethine cyanine) dye and its interaction with human serum albumin.

A newly synthesized near-infrared (NIR) bis(heptamethine cyanine) dye 7 was evaluated for its utility as a non-covalent label for proteins. This dye forms inter- and intramolecular H-aggregates in polar solvents, even at very low concentrations. The intramolecular dimeric form of the dye can be described as a clam-shell complex with two interacting hydrophobic carbocyanine moieties.

Chiral discrimination in binding of enantiomers of 2-(aminoalkoxy)-substituted 4-(2-thienyl)pyrimidines and 4,6-bis(2-thienyl)pyrimidines with duplex DNA.

Thienylpyrimidines substituted at position 2 of the pyrimidine with a chiral aminoalkoxy group were synthesized. Upon interaction with duplex DNA, the unfused heteroaromatic system of these compounds intercalates with DNA base pairs and the protonated side chain is located in the major groove. The S-enantiomers bind more strongly than their R-counterparts with enantiomeric discrimination, as measured by a ratio of binding constants K(S)/K(R), ranging from 1.

New triple-helix DNA stabilizing agents.

Several substituted quinolin-4-amines and heteroaromatic analogs were synthesized and evaluated for interaction with triplex polydA.2polydT and duplex polydA.polydT by using UV-thermal melting experiments.

Covalent and noncovalent labeling schemes for near-infrared dyes in capillary electrophoresis protein applications.

Capillary electrophoresis (CE) is experiencing increased use in the field of separation science. Part of its growing popularity of capillary electrophoresis can be attributed to the high efficiency of the separations achievable with the technique, making it an attractive tool for bioanalytical applications. Laser-induced fluorescence (LIF) is a common detection method for CE.

Triplex selective 2-(2-naphthyl)quinoline compounds: origins of affinity and new design principles.

A novel competition dialysis assay was used to investigate the structural selectivity of a series of substituted 2-(2-naphthyl)quinoline compounds designed to target triplex DNA. The interaction of 14 compounds with 13 different nucleic acid sequences and structures was studied. A striking selectivity for the triplex structure poly dA:[poly dT](2) was found for the majority of compounds studied.

Synthesis and activity of substituted 2-phenylquinolin-4-amines, antagonists of immunostimulatory CpG-oligodeoxynucleotides.

Fifty-seven 2-phenylquinolines substituted at the phenyl group and C4 of the quinoline were synthesized and analyzed for inhibition of the immunostimulatory effect of oligodeoxynucleotides with a CpG-motif. The Fujita-Ban variant of the classical Free-Wilson analysis gave a highly significant correlation for a series of 48 relatively small molecules demonstrating that (i) the partial contributions of substituents to biological activity (EC(50)) are additive and (ii) assuming similar bioavailability for all quinolines studied, the larger molecules cannot be accommodated within a still unknown biological receptor. The results suggest interaction of a basic antagonist molecule with weakly acidic groups in the antagonist-receptor complex.

Bis-4-aminoquinolines: novel triple-helix DNA intercalators and antagonists of immunostimulatory CpG-oligodeoxynucleotides.

Six dimeric 2-(2-naphthyl)quinolin-4-amines with a linker between the amino groups and eight dimeric 2-(4-anilino)quinolin-4-amines linked between the anilino groups were synthesized and evaluated for their interaction with duplex/triplex DNA's and as antagonists of immunostimulatory oligodeoxynucleotides with a CpG-motif (CpG-ODN). The most powerful triple-helix DNA intercalator known to date, with high affinity toward T.A.

Handling and detection of 0.8 amol of a near-infrared cyanine dye by capillary electrophoresis with laser-induced fluorescence detection.

We are interested in the detection of DNA adducts and other trace analytes by labeling them with a fluorescent tag followed by use of capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) for high resolution and sensitivity. Towards this goal, here we report the following: (1) synthesis and handling properties of a near-IR, carboxyl-substituted heptamethine cyanine dye; (2) modification of an existing ball lens LIF detector to provide near-LIF detection with excitation at 785 nm for CE; and (3) corresponding handling and detection of as little as 0.8 amol of the dye by enrich-injection of 4.

DNA and protein applications of near-infrared dyes.

The near-infrared region of the spectrum (650-1100 nm) offers distinct advantages over the traditional UV/vis region for spectroscopic measurements. In the past, the lack of commercially available equipment capable of working in the near infrared limited the utility of near-infrared techniques. However, since the advent of photodiodes and semiconductor lasers, much progress has been made in the development of near-infrared techniques.

Glucopyranosides derived from 6-aryl-5-cyano-2-(methylthio)pyrimidin-4(3H)ones.

The reaction of 2,3.4,6-tetra-O-acetyl-alpha-D-glucopyranosyl bromide with a 6-aryl-5-cyano-2-(methylthio)pyrimidin-4(3H)one in aqueous acetone in the presence of KOH furnishes a 4-(beta-D-glucopyranosyloxy)pyrimidine and a 3-(beta-D-glucopyranosyl)pyrimidine as the major and minor product. respectively.