Comparison of volatiles emitted by male caribbean and mexican fruit flies

Volatiles emitted byAnastrepha suspensa andAnastrepha ludens males were trapped and compared by GC-MS. Both species emitted previously reported nine-carbon alcohols, (Z)-3-nonenol and (Z,Z)-3,6-nonadienol, and epimeric lactones, anastrephin and epianastrephin. A third isomeric lactone, the macrolide suspensolide, which was previously known only fromA. suspensa is reported here for the first time in the volatiles ofA. ludens. We also report that both species released different proportions of the same three sesquiterpene hydrocarbons:α-farnesene,β-bisabolene, andα-trans-bergamotene. Theβ-bisabolene was isolated in sufficient quantity fromA. suspensa volatiles to establish its absolute configuration as the (R)-(+)-enantiomer. Some plausible biosynthetic relationships of farnesol to the isoprenoid lactones and sesquiterpenes identified in this study are discussed. Finally, we report thatA. suspensa produces the monoterpene (Z)-β-ocimene whileA. ludens volatiles contained limonene.

Spectral characterization of a novel near-infrared cyanine dye: a study of its complexation with metal ions

The spectral features of the near-infrared (NIR) dye TG-170 in different solutions and its complexation with several metal ions were investigated. The absorbance maxima of the dye are at lambda=819, 805, and 791 nm in dimethyl sulfoxide (DMSO), methanol, and a buffer of pH 5.9, respectively. These values match the output of a commercially available laser diode (780 nm), thus making use of such a source practical for excitation. The emission wavelengths of the dye are at lambda(em) =822, 812, and 803 nm in DMSO, methanol, and the buffer, respectively. The molar absorptivity and fluorescence quantum yield increase accordingly. The addition of either an Al(III) ion or Be(II) ion resulted in fluorescence quenching of the dye. The Stern-Volmer quenching constant, K(SV), was calculated from the Stern-Volmer plot to be K(SV)=3.11x10(5) M(-1) for the Al(III) ion and K(SV)=1.17x10(6) M(-1) for the Be(II) ion. The molar ratio of the metal to the dye was established to be 1:1 for both metal ions. The stability constant, K(S), of the metal-dye complex was calculated to be 4.37x10(4) M(-1) for the Al-dye complex and 1.94x10(6) M(-1) for the Be-dye complex.

Mechanistic studies on percutaneous penetration enhancement by N-(4-halobenzoyl)-S,S-dimethyliminosulfuranes

Halogen-substituted iminosulfuranes are transdermal penetration enhancers (TPEs) in permeation studies using hairless mouse or human cadaver skin. The interaction of N--(4--R-benzoyl)-S,S-dimethyliminosulfuranes 1--4, where R=H, Cl, Br, and I, with l-alpha-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) has been studied using differential scanning calorimetry, isothermal titration calorimetry, nuclear Overhauser effect spectroscopy (NOESY), and NMR spectroscopy, and by calculation of the iminosulfurane polarizabilities in order to elucidate the molecular basis of the TPE activity. The active compounds reduce the melting temperature of the gel-to-liquid-crystal phase transition and induce multiple components in the transition excess heat capacity profile. The partitioning of the bromo derivative 3, the most active compound, into DMPC is unique in that 3 may be trapped in the bilayer, affording an enhanced residence time and a reason for its high TPE activity. The entropy decrease associated with the transfer of 3 to the bilayer is much lower than that for the other compounds, indicating that 3 occupies or induces sites that afford it considerable local motional freedom. Correlations between the iminosulfurane TPE activities, the partition coefficients, and NOESY crosspeak volume were observed. Molecular polarizabilities are not consistent with a TPE mode of action involving interaction of these agents with protein side chains.

Binding constant determination of drugs toward subdomain IIIA of human serum albumin by near-infrared dye-displacement capillary electrophoresis

Drug binding to serum albumin influences several important pharmacological properties such as toxicity, solubility, activity, distribution, and excretion. It is therefore of interest to have methodologies that allow for the determination of drug-albumin affinity constants while simultaneously providing information on the location of the drug binding site. In the present work we describe a method for the determination of binding constants of drugs known to bind to subdomain IIIA of serum albumin. Drugs used in the study were ketoprofen, ibuprofen, quinidine, naproxen, imipramine, and clofibrate. Binding constants of the drugs were determined by near-infrared dye-displacement capillary electrophoresis. The dye-displacement technique uses a competitive-type interaction between the drug of interest and a dye probe to arrive at a binding constant. A heptamethine cyanine dye was used as a probe for drug binding at subdomain IIIA of serum albumin. The utility of the dye as a noncovalent label for serum albumin was investigated. Additionally, the ability of the method to illustrate enantioselective binding is shown. The dye displacement technique has advantages over current electrophoresis-based techniques in that it is faster and uses less reagent.

Use of non-covalent labeling in illustrating ligand binding to human serum albumin via affinity capillary electrophoresis with near-infrared laser induced fluorescence detection

This paper demonstrates the use of a near-infrared (NIR) dye as a non-covalent label for human serum albumin (HSA). The dye is a water soluble, heptamethine cyanine dye. The utility of the dye as a tracer illustrating the binding of various drugs to HSA is demonstrated via affinity capillary electrophoresis with near-infrared laser-induced fluorescence detection (ACE-NIR-LIF). Additionally, the factors affecting the separation of relevant species were investigated. The change in quantum yield of the dye upon complexation with HSA was calculated. Spectrophotometric measurements were conducted to study the stoichiometry of the dye albumin complex.

Amplification of pepleomycin-mediated DNA cleavage and apoptosis by unfused aromatic cations

An important approach to improve chemotherapy of members of the bleomycin (BLM) family of antibiotics is to find compounds (amplifiers) that enhance the activity of BLM-mediated DNA cleavage and apoptosis. Using a DNA-sequencing technique and pulsed field gel electrophoresis, we have investigated whether BLM-mediated cleavage of isolated and cellular DNA is amplifed by three compounds (RW-12, LS-20, 1S-5Me) which have a conformationally flexible, unfused polyaromatic system and cationic side chain in the molecules. RW-12 enhanced most effectively both pepleomycin (PEM)-induced cytotoxicity and apoptosis. The order of the maximum enhancing effect of amplifiers on PEM-mediated DNA damage is RW-12 > LS-20 > 1S-5Me. RW-12 amplified PEM-mediated DNA cleavage most effectively not only in vitro but also in cultured cells. We have reported that the order of the DNA binding constants of these compounds is RW-12 > LS-20 > 1S-5Me. In this study, we found a good correlation between PEM-mediated cleavage of isolated DNA and cellular DNA. These results suggest that BLM amplifiers bind to DNA and by doing so enhance drug-mediated DNA degradation, ultimately leading to apoptosis. The present study on amplifiers of anticancer agents shows a novel approach to the potentially effective anticancer therapy.

Application of similarity matrices and genetic neural networks in quantitative structure-activity relationships of 2- or 4-(4-Methylpiperazino)pyrimidines: 5-HT(2A) receptor antagonists

Antagonists of the 5-HT(2A) receptor are being used to treat many psychiatric disorders. The present work focuses on a group of 27 antagonists possessing varying affinities toward the receptor. These are 26 title compounds and clozapine as a reference antagonist. The active conformers of the conformationally flexible ligands were proposed by using the active rigid analogue approach and performing similarity calculations. The calculations involved genetic neural network (GNN) computations deriving QSARs from similarity matrices (SM) with cross-validated correlation coefficients exceeding 0.92. The performance of neural networks with variety of architectures was studied. As the computations were performed for cations and neutral molecules separately, the relevance of the ligand charging is discussed.

Antagonism of immunostimulatory CpG-oligodeoxynucleotides by 4-aminoquinolines and other weak bases: mechanistic studies

Oligodeoxynucleotides with unmethylated CpG motifs are immunostimulatory. Chloroquine and a number of structural analogs specifically and powerfully inhibit this effect at nanomolar concentrations. We explored the mechanism of this inhibition, with 4-aminoquinolines, quinacrine, 9-aminoacridines, and novel dibasic analogs, many of which are fluorescent. WEHI 231 murine B-lymphoma cells accumulated analogs up to a concentration several hundredfold higher than the medium. Uptake was rapid, nonsaturable, reversible, and partially inhibited by monensin, an agent that collapses pH gradients within cells. Uptake did not correlate highly with efficacy as inhibitors of CpG-oligodeoxynucleotide (ODN)-induced effects, suggesting that analogs act by a specific action. Confocal microscopy revealed analogs concentrating in large peripheral organelles. CpG-ODN is taken up by cells into acidified, small, perinuclear vesicles. This uptake is thought to be necessary for immunostimulatory activity. Cellular uptake of fluorescent CpG-ODN was not inhibited by the analogs. The pH of intracellular CpG-ODN (6. 4) was not affected by analogs at the concentration required for inhibition, but pH was increased by higher concentrations. UV spectroscopy revealed no binding of analogs to CpG-ODN. Nuclear Overhauser effect spectroscopy revealed that an analog bound to phosphatidylcholine vesicles, with the ring structure of the analog buried within the lipid and the side chain facing the aqueous environment. We conclude that the analogs do not inhibit the action of CpG-ODN by preventing the uptake or acidification of CpG-ODN. It seems more likely that the analogs inhibit the efficacy of CpG-ODN by a specific action within acidified vesicles, possibly at the interface of a phospholipid membrane.

DNA triple helix stabilisation by covalent attachment of a triplex-specific ligand

We have prepared oligonucleotides with a naphthylquinoline triplex-binding ligand covalently tethered to the 5'-end and have used UV-melting and DNase I footprinting to examine the stability of intra- and inter-molecular triplexes containing this modification. We find that covalent attachment of the ligand increases the melting temperature of intramolecular 6-mer triplexes by about 14 K, and increases the binding of 9-mer oligonucleotides to their duplex target sites by about 60-fold.

Percutaneous penetration enhancement activity of aromatic S, S-dimethyliminosulfuranes

The activity of three series of iminosulfuranes (classes I-III) as potential transdermal penetration enhancers was investigated. These dimethyl sulfoxide (DMSO) related compounds were synthesized from activated DMSO by trifluoroacetic anhydride. Structure confirmation was accomplished by 1H NMR, and 13C NMR spectroscopy and elemental analysis prior to in vitro testing. Hydrocortisone (HC) was used as a model drug, and the effect of the iminosulfuranes on the penetration of HC through hairless mouse skin was evaluated. All enhancers tested were applied to the skin as saturated suspensions in propylene glycol to ensure their maximum thermodynamic activity. Three compounds, S,S-dimethyl-N-(4-bromobenzoyl)iminosulfurane (9), S,S-dimethyl-N-(5-nitro-2-pyridyl)iminosulfurane (13), and S, S-dimethyl-N-(4-phenylazaphenyl)iminosulfurane (16) showed statistically significant activity quantitated by amounts of model drug permeated through the skin in 24 h (Q(24)), and flux values, compared to control (propylene glycol without enhancer). Highest Q(24) and flux values were obtained for 9: 996.2+/-192.5 microg/cm(2) and 42.9+/-7.5 microg/cm(2) per h, respectively. All arylsulfonyl substituted compounds showed lower or similar enhancement activity when compared to control. S, S-dimethyl-N-(benzenesulfonyl)iminosulfurane (1), S, S-dimethyl-N-(2-methoxycarbonylbenzenesulfonyl)iminosulfurane++ + ( 7) and S,S-dimethyl-N-(4-chlorobenzenesulfonyl)iminosulfurane (8) decreased the permeation of HC significantly (P<0.05). It is possible that these agents work as retardants under these experimental conditions. None of the enhancers tested showed significant skin model drug retention, suggesting that these compounds could be useful for increasing systemic rather than local drug delivery.

Enhancement of bleomycin-induced micronucleus formation in V79 cells as a rapid and sensitive screen for non-covalent DNA-binding compounds

Non-covalent drug/DNA interactions are difficult to study and because of this, the significance of such interactions from a safety standpoint and their contribution to positive genetic toxicology test findings is poorly understood. It is shown in the present study that such interactions may be detected and quantified in Chinese hamster V79 cells by an adaptation of the bleomycin amplification assay. This assay measures the ability of a test compound to enhance the DNA damaging activity of the antibiotic bleomycin using micronucleus formation as an endpoint. Results are presented examining the bleomycin amplification activity of known intercalating agents, groove-binding agents and other structurally diverse classes of compounds for which intercalative status has not been reported. The assay reveals a strong and predictable SAR for amplification activity based on number and orientation of aromatic rings. Moreover, excellent correlations are observed between DNA binding (viscometric analyses) and DNA amplification in V79 cells for a series of seven experimental compounds. The assay is shown to be useful in understanding the genotoxicity of marketed antihistamines and to help explain genetic toxicology findings observed in a series of novel pharmaceutical entities. It is proposed that assessment of bleomycin amplification activity of novel compounds in early genotoxicity prescreening may provide important information upon which to base synthesis of compounds with minimal or no genotoxic liability.

Structure-activity relationship analysis of substituted 4-quinolinamines, antagonists of immunostimulatory CpG-oligodeoxynucleotides

On the basis of a systematic SAR analysis of substituted quinolines, a derivative 32 was synthesized that shows half-maximal inhibition of the immunostimulatory effect of CpG-oligodeoxynucleotides in vitro at the concentration of 0.24 nM.

Detection of biomolecules in the near-infrared spectral region via a fiber-optic immunosensor

The design, development, and application of a fluorescent fiber-optic immunosensor (FFOI) procedure for the detection of antibody/antigen binding within the near-infrared (NIR) spectral region is reported. The technique was developed through the combined use of fiber-optics, semiconductor laser excitation, fluorescence detection, NIR dye, and immunochemical techniques. The antibody is immobilized on the FFOI's sensing tip and utilized as a recognition component for trace amounts of specific antigen. The FFOI is constructed to utilize antibody sandwich technique. Three individual immunoassays are reported. The first two assays utilize the FFOI and NN382, a commercial NIR dye, for the detection of human immunoglobulin G (IgG). In these assays, goat anti-human IgG antibody (GAHG) is immobilized on the sensitive terminal of the FFOI followed by the exposure of the antibody-coated terminal to human IgG. The probe is then introduced to GAHG labeled with NN382, generating a signal. The third assay utilizes the FFOI for the detection of trace amounts of Legionella pneumophila serogroup 1 (LPS1). In this assay, rabbit anti-LPS1 antibody is immobilized on the sensitive terminal of the FFOI followed by exposure to LPS1. The antigen-coated probe is then treated with monoclonal anti-LPS1 antibody followed by incubation with GAHG labeled with NN382. The assays are optimized to detect the corresponding antigen via the NIR-FFOI. Typical measurements are performed in 10-15 min. A 780-nm semiconductor laser provides the excitation of the immune complex and the resulting emission is detected by a 820-nm silicon photodiode detector. The intensity of the resulting fluorescence is directly proportional to the concentration of the antigen. Solutions of IgG and LPS1 with concentrations as low as 10(-11) M and 0.5 ng/ml, respectively, have been detected with a minimum interference.

N-(4-bromobenzoyl)-S,S-dimethyliminosulfurane, a potent dermal penetration enhancer

N-Aroyl-, N-Arylsulfonyl-, and N-Aryl-S,S-dimethyliminosulfuranes have been synthesized and evaluated as potential dermal penetration enhancers. The title compound and Azone exhibit similar activities for permeation of hydrocortisone through hairless mouse skin.

DNA triple helix stabilisation by a naphthylquinoline dimer

We have used DNase I footprinting to examine the effect of a novel naphthylquinoline dimer, designed as a triplex-specific bis-intercalator, on the stability of intermolecular DNA triplexes. We find that this compound efficiently promotes triplex formation between the 9-mer oligonucleotide 5'-TTTTTTCTT and its oligopurine duplex target at concentrations as low as 0.1 microM, enhancing the triplex stability by at least 1000-fold. This compound, which is the first reported example of a triplex bis-intercalator, is about 30 times more potent than the simple monofunctional ligand.

Intercalation of ethidium and analogues with nucleic acids: a molecular orbital study

Semiempirical calculations suggest that the intercalation complexes of phenanthridinium cations 1-4 with G-C/C-G and 1 with A-U/U-A are stabilized by frontier orbital interactions between the LUMO of the intercalator and the HOMOs of the adjacent purine bases. The charge on the ring nitrogen of 1-4 appears to be necessary for the orbital interactions, lowering the LUMO, facilitating mixing of this orbital with the HOMOs of the adjacent purine bases to give an extended HOMO stabilizing the complex and resulting in the bathochromic shift in the electron absorption spectrum. Noncationic phenanthridine 5 shows no frontier orbital interactions in the forced intercalation complex with G-C/C-G. The results of the calculations parallel experimental T(m) values.

DNA sequence specificity of a naphthylquinoline triple helix-binding ligand

We have examined the effect of a naphthylquinoline triplex-binding ligand on the formation of intermolecular triplexes on DNA fragments containing the target sites A6G6xC6T6 and G6A6xT6C6. The ligand enhances the binding of T6C2, but not T2C6, to A6G6xC6T6 suggesting that it has a greater effect on TxAT than C+xGC triplets. The complex with T6C2 is only stable below pH 6.0, confirming the requirement for protonation of the third strand cytosines. Antiparallel triplexes with GT-containing oligonucleotides are also stabilised by the ligand. The complex between G5T5 and A6G6xC6T6 is stabilised by lower ligand concentrations than that between T5G5 and G6A6xC6T6. The ligand does not promote the interaction with GT-containing oligonucleotides which have been designed to bind in a parallel orientation. Although the formation of antiparallel triplexes is pH independent, we find that the ligand has a greater stabilising effect at lower pH, suggesting that the active species is protonated. The ligand does not promote the binding of antiparallel GA-containing oligonucleotides at pH 7.5 but induces the interaction between A5G5 and G6A6xT6C6 at pH 5.5. Ethidium bromide does not promote the formation of any of these triplexes and destabilises the interaction of acridine-linked pyrimidine-containing third strands with these target sites.

Synthesis and structure-DNA binding relationship analysis of DNA triple-helix specific intercalators

4-[N-(Aminoalkyl)amino]-2-arylquinolines with conformational freedom around positions 2 and 4 of the quinoline stabilize strongly poly(dT.dA.dT) (triplex DNA) and bind weakly to poly-(dA.dT) (duplex DNA). Basicity of N1 of the quinoline parallels the interaction strength of these compounds with the triple-helical DNA structure suggesting that N1 of the quinoline is protonated in the complex with the DNA triplex. The experimental results support the interaction model suggested previously.

Structure-activity relationship studies of CNS agents, Part 25. 4,6-di(heteroaryl)-2-(N-methylpiperazino)pyrimidines as new, potent 5-HT2A receptor ligands: a verification of the topographic model

A series of new 4,6-di(heteroaryl)pyrimidines containing an N-methylpiperazino group (6-13) or an ethylenediamine chain (15-20) in position 2 were synthesized and their 5-HT1A and 5-HT2A receptor affinities were determined. It was shown that the substituent effects on the 5-HT2A affinity are additive and could be described quantitatively. In a behavioral model it was also demonstrated that 6-11 are 5-HT2A receptor antagonists. The molecular modelling results suggested that the distances between the basic nitrogen atom and the two aromatic centers (d1 = 5.2-8.4 A, d2 = 5.7-8.5 A, and d3 = 4.6-7.3 A) define the molecular topography of the 5-HT2A receptor antagonists under study.

Footprinting studies on ligands which stabilize DNA triplexes: effects on stringency within a parallel triple helix

We have examined the effect of four triplex-binding ligands on the interaction of the oligodeoxynucleotides T8NT8 (N = A, G, C, T) with DNA fragments containing the sequences A8XA8.T8YT8 (X = G, C, T; Y = C, G, A) by DNase I footprinting. The ligands form a series of quinoline derivatives with an alkylamine chain in the 4-position and different aryl substituents in the 2-position. By themselves these compounds do not alter DNase I digestion of the DNA duplexes at concentrations up to 100 microM. At a concentration of 10 microM they potentiate triplex formation, lowering the concentration of oligonucleotide required to produce a clear footprint by as much as 100-fold. As well as stabilizing triplexes which consist of well-characterized DNA triplets, they also promote the formation of complexes which contain central triplet mismatches. This reduction in the stringency of triple helix formation may be used to broaden the range of triplex target sequences and enable recognition at sites which contain short regions for which there are no good triplet matches.

Effect of a triplex-binding ligand on parallel and antiparallel DNA triple helices using short unmodified and acridine-linked oligonucleotides

We have used DNase I footprinting to investigate the effect of a triplex-binding ligand on the formation of intermolecular DNA triple helices at target sites that have been cloned into longer DNA fragments. In the presence of a triplex-binding ligand (N-[2-(dimethylamino)ethyl]-2-(2-naphthyl)quinolin-4-ylamine ), the concentrations of T5C5 and C5T5 required to generate DNase I footprints at the target sites A6G6.C6T6 and G6A6.T6C6, respectively, are reduced by at least 100-fold. Complexes with the acridine-linked oligonucleotides Acr-T5C5 and Acr-C5T5 are stabilized to a much lesser extent and produce footprints at concentrations similar to those of the unmodified oligonucleotides in the presence of the ligand. The stabilizing effects of acridine modification or the addition of a triplex-binding ligand are not additive. The position and length of the footprints produced by Acr-T5C5 and T5C5 at the target sequence A6G6.C6T6 are unaffected by the ligand. In contrast, footprints at the target site G6A6.T6C6 appear 3-4 bases shorter in the presence of the ligand, when viewed from the pyrimidine strand, and 1-2 bases longer on the purine strand. These results are explained by suggesting that the compound binds at T.AT triplets and prevents the transmission of any DNA structural changes into the flanking duplex. The compound has a smaller stabilizing effect on short antiparallel triplexes consisting of G.GC and T.AT triplets. Binding of Acr-G5T5 to A6G6.C6T6 is enhanced slightly by the compound, which increases the apparent footprinting site, probably by preventing fraying at the 3'-end of the third strand. The compound does not promote the binding of G5T5 to A6G6.C6T6 or that of Acr-T5G5 and T5G5 to G6A6.T6C6.

Structure-activity relationship studies of CNS agents. Part 14: Structural requirements for the 5-HT1A and 5-HT2A receptor selectivity of simple 1-(2-pyrimidinyl)piperazine derivatives

The 5-HT1A and 5-HT2A receptor affinity of model 1-(2-pyrimidinyl)-piperazine derivatives 15-21 and 23-32 has been determined. 2-(N-Methylpiperazino)-4,6-di(2-thienyl)pyrimidine 26 is a new, highly active and selective 5-HT2A receptor ligand. The topography of a molecule and the stereoelectronic effects of the thiophene rings are the major factors responsible for the high affinity and selectivity of 26 towards 5-HT2A sites.

Instrument to detect near-infrared fluorescence in solid-phase immunoassay

The construction of a near-infrared (near-IR) fluorescence detector for measuring picomolar levels of near-IR laser dyes is described. The detector is designed for use in an immunoassay technique that employs antibodies labeled with near-IR polymethine cyanine dyes. These dyes possess spectral properties that are exclusive to the near-IR region (650-1100 nm). The instrumentation is characterized, including its hardware and data acquisition software components. The detector is capable of measuring fluorescence in both solution and solid-phase environments. Data on the detector's performance is presented.

The interaction of substituted 2-phenylquinoline intercalators with poly(A).poly(U): classical and threading intercalation modes with RNA

The interaction of a series of 2-phenylquinoline derivatives with RNA was investigated by means of viscometric, pKa, spectroscopic, binding, Tm, and kinetic methods. Compounds 1, 2, and 3 have a piperazyl substituent at the para, meta, or ortho position, respectively, while 4 has an unsubstituted phenyl ring. The pKa results suggest that 1 has three charges, 2 and 3 have more than two charges, and 4 has two charges at pH 6.2. Spectroscopic and Tm results indicate that 1 binds more strongly to RNA than 2-4. Kinetic and modeling results indicate that 1 is a threading intercalator while 2 and 4 are classical intercalators. All experimental results indicate that 3, which has a large twist between the phenyl and quinoline rings, binds weakly with RNA.

DNA triple-helix specific intercalators as antigene enhancers: unfused aromatic cations

Triple-helical structures involving the interaction of an oligonucleotide third strand with a duplex nucleic acid sequence have recently gained attention as a therapeutic strategy in the "antigene" approach [cf. Helene, C. (1991) Eur. J. Cancer 27, 1466-1471]. This method utilizes the triple helix formed from the cellular duplex and an added third strand to directly regulate the activity of a selected gene. The limited stability of nucleic acid triple-helical interactions, particularly if the third strand has backbone modifications such as methylphosphonate or phosphorothioate substitutions, is a limiting condition for the use of this approach. We have designed and synthesized compounds, on the basis of the following three criteria, that we feel should provide selective interactions and significant stabilization of triplexes: appropriate aromatic surface area for stacking with triplex bases in an intercalation complex, positive charge, and limited torsional freedom in the aromatic system to match the propeller twist of the triple-base interactions in the triplex. A series of quinoline derivatives with an alkylamine side chain at the 4-position and with different aryl substituents at the 2-position has been synthesized as our first compounds. A 2-naphthyl derivative provides significant and selective stabilization of the triplex. In a 0.2 M NaCl buffer, the naphthyl derivative increased the Tm for the triplex (triplex to duplex and third strand transition) by approximately 30 degrees C more than the Tm increase for the duplex (duplex to single strands transition). Spectral changes and energy-transfer results indicate that the naphthyl compound and related derivatives bind to the triplex by intercalation.(ABSTRACT TRUNCATED AT 250 WORDS)

The search for structure-specific nucleic acid-interactive drugs: effects of compound structure on RNA versus DNA interaction strength

The RNA genomes of a number of pathogenic RNA viruses, such as HIV-1, have extensive folded conformations with imperfect A-form duplexes that are essential for virus function and could serve as targets for structure-specific antiviral drugs. As an initial step in the discovery of such drugs, the interactions with RNA of a wide variety of compounds, which are known to bind to DNA in the minor groove, by classical or by threading intercalation, have been evaluated by thermal melting and viscometric analyses. The corresponding sequence RNA and DNA polymers, poly(A).poly(U) and poly(dA).poly(dT), were used as test systems for analysis of RNA binding strength and selectivity. Compounds that bind exclusively in the minor groove in AT sequences of DNA (e.g., netropsin, distamycin, and a zinc porphyrin derivative) do not have significant interactions with RNA. Compounds that bind in the minor grove in AT sequences of DNA but have other favorable interactions in GC sequences of DNA (e.q., Hoechst 33258, DAPI, and other aromatic diamidines) can have very strong RNA interactions. A group of classical intercalators and a group of intercalators with unfused aromatic ring systems contain compounds that intercalate and have strong interactions with RNA. At this time, no clear pattern of molecular structure that favors RNA over DNA interactions for intercalators has emerged. Compounds that bind to DNA by threading intercalation generally bind to RNA by the same mode, but none of the threading intercalators tested to date have shown selective interactions with RNA.

Comparison of covalent and noncovalent labeling with near-infrared dyes for the high-performance liquid chromatographic determination of human serum albumin

Noncovalent and covalent methods of labeling protein with near-infrared polymethine cyanine dyes were compared for use in analyzing human serum albumin (HSA) by high-performance liquid chromatography (HPLC) with near-infrared absorbance detection. While noncovalent labeling was faster than covalent labeling and took place in the physiological pH range, covalent labeling was more stable under conditions encountered in many of the widely used types of HPLC. Covalently labeled HSA protein peaks indicated uniform labeling of amino groups at both hydrophilic and hydrophobic binding sites, while noncovalent labeling showed a preference for hydrophobic binding sites.

Stereoelectronic factors in the interaction with DNA of small aromatic molecules substituted with a short cationic chain: importance of the polarity of the aromatic system of the molecule

We have performed a quantitative analysis of the interaction with DNA of several unfused aromatic compounds synthesized in our laboratory and substituted with one or two short cationic chains. These and similar literature compounds, for which DNA binding data are available, bind with DNA by partial intercalation of the aromatic system, groove interaction of the linker chain, and groove electrostatic interactions of the terminal cationic group. Several independent quantitative and qualitative approaches show consistently that the strength of the interaction of the aromatic unit of the molecule with DNA binding sites depends on the direction and magnitude of polarity of the aromatic system. The phenomenon is explained in terms of the greatest negative potential in the DNA grooves, a concept extensively elaborated by Pullman and Pullman [cf. Lavery, R. and Pullman, B. [(1985) J. Biomol. Struct. Dyn. 2, 1021-1032] and references therein]. Classical, fused-ring planar intercalators do not follow the polarity-DNA affinity correlation, presumably because the intercalative forces depend more strongly on polarizability than on polarity of the aromatic system.

Synthesis and quantitative structure-activity relationship analysis of 2-(aryl or heteroaryl)quinolin-4-amines, a new class of anti-HIV-1 agents

Thirty-eight 2-(aryl or heteroaryl)quinolin-4-amines, N,N-disubstituted, N-monosubstituted, and without a substituent at the amino group have been synthesized with use of novel chemistries developed by us recently. Some of these derivatives show anti-HIV-1 activity at a concentration level of 1 microM and low cell toxicity in vitro. The most active and least toxic compounds are derivatives of 2-(3-pyridyl)quinoline. The results of the quantitative structure-activity relationship analyses, including several classical, linear regression correlations and a Free-Wilson approach of de novo model, provide guidelines for the design of new active compounds of this class.

Quantitative structure-activity relationship analysis of cation-substituted polyaromatic compounds as potentiators (amplifiers) of bleomycin-mediated degradation of DNA

A set of 21 polyheteroaromatic compounds substituted with flexible cationic groups and of similar molecular size has been analyzed for binding with DNA and for effects of the bleomycin-mediated degradation of the DNA double helix. Increases in apparent rates of the DNA digestion were observed in all cases under the experimental conditions of noncompetitive binding of these compounds and bleomycin to DNA. Surprisingly, the quantitative structure-activity relationship analysis revealed two distinct correlations despite close structural similarities for the set of bleomycin amplifiers. These unusual results are explained in terms of the formation of two stereochemically different ternary complexes of activated bleomycin-DNA-amplifier. The relevance of this finding for the design of new bleomycin amplifiers is discussed.

DNA sequence dependent binding modes of 4',6-diamidino-2-phenylindole (DAPI)

The interactions of DAPI with natural DNA and synthetic polymers have been investigated by hydrodynamic, DNase I footprinting, spectroscopic, binding, and kinetic methods. Footprinting results at low ratios (compound to base pair) are similar for DAPI and distamycin. At high ratios, however, GC regions are blocked from enzyme cleavage by DAPI but not by distamycin. Both poly[d(G-C)]2 and poly[d(A-T)]2 induce hypochromism and shifts of the DAPI absorption band to longer wavelengths, but the effects are larger with the GC polymer. NMR shifts of DAPI protons in the presence of excess AT and GC polymers are significantly different, upfield for GC and mixed small shifts for AT. The dissociation rate constants and effects of salt concentration on the rate constants are also quite different for the AT and the GC polymer complexes. The DAPI dissociation rate constant is larger with the GC polymer but is less sensitive to changes in salt concentration than with the AT complex. Binding of DAPI to the GC polymer and to poly[d(A-C)].poly[d(G-T)] exhibits slight negative cooperativity, characteristic of a neighbor-exclusion binding mode. DAPI binding to the AT polymer is unusually strong and exhibits significant positive cooperativity. DAPI has very different effects on the bleomycin-catalyzed cleavage of the AT and GC polymers, a strong inhibition with the AT polymer but enhanced cleavage with the GC polymer. All of these results are consistent with two totally different DNA binding modes for DAPI in regions containing consecutive AT base pairs versus regions containing GC or mixed GC and AT base pair sequences. The binding mode at AT sites has characteristics which are similar to those of the distamycin-AT complex, and all results are consistent with a cooperative, very strong minor groove binding mode. In GC and mixed-sequence regions the results are very similar to those observed with classical intercalators such as ethidium and indicate that DAPI intercalates in DNA sequences which do not contain at least three consecutive AT base pairs.

The interaction with DNA of unfused aromatic systems containing terminal piperazino substituents. Intercalation and groove-binding

A number of unfused tricyclic aromatic intercalators have shown excellent activity as amplifiers of the anticancer activity of the bleomycins and the 4',6-diphenylpyrimidines, 2a and 2b, with terminal basic functions (4-methylpiperazino groups) have been synthesized to test the structural requirements for amplifier-DNA interactions. The terminal piperazine rings are bulky, have limited flexibility, and are twisted out of the phenyl ring plane in both 2a and 2b. With 2a the pyrimidine is unsubstituted at position 5 and the conformation predicted by molecular mechanics calculations has a 25-30 degrees twist between the phenyl and pyrimidine ring planes. With 2b the 5-position is substituted with a methyl group and this causes a larger twist angle (50-60 degrees) between the phenyl and pyrimidine planes. These conformational variations lead to markedly different DNA interactions for 2a and 2b. Absorption, CD and NMR spectral, viscometric, flow dichroism and kinetics results indicate that 2a binds strongly to DNA by intercalation while 2b binds more weakly in a groove complex. The general structure and conformation of 2a, a slightly twisted, unfused-aromatic system with terminal piperazino groups is more similar to groove-binding agents such as Hoechst 33258 than to intercalators. The fact that 2a forms a strong intercalation complex with DNA is unusual but in agreement with studies on other amplifiers of anticancer drug action. Molecular modeling studies provide a second unusual feature of the 2a intercalation complex. While most well-characterized intercalators bind with their bulky and/or cationic substitutents in the DNA minor groove, the cationic piperazino groups of 2a are too large to bind in the minor groove in an intercalation complex but can form strong interactions with DNA in the major groove. The tricyclic aromatic ring system of 2a stacks well with adjacent base-pairs in the major-groove complex and the piperazino groups have good electrostatic and van der Waals interactions with the DNA backbone.

The interaction of unfused polyaromatic heterocycles with DNA: intercalation, groove-binding and bleomycin amplification

A number of unfused-aromatic cations have been found to bind to DNA by intercalation and to amplify the bleomycin catalysed cleavage of DNA. These molecules are more similar in structure to unfused minor-groove binding compounds such as netropsin and DAPI than to fused-ring intercalators such as proflavine. An analysis of DAPI interactions with specific sequence DNA polymers has indicated that the binding modes for the molecule are sequence dependent: minor groove binding in sequences of three or more AT base pairs and intercalation in mixed or pure GC base pair sequences. As with other unfused intercalators which bind with their cationic side chains in the major groove, the amidinium groups of DAPI are in the major groove in the GC intercalation complex. DAPI is, thus, a good bleomycin amplifier in GC sequences but its minor-groove binding mode in AT sequences leads to bleomycin inhibition.

Long-acting contraceptive agents: testosterone esters of unsaturated acids

The synthesis of 13 new esters of testosterone is described, with the esterifying acids bearing acetylenic, olefinic, or polyunsaturated functions in the chain, for evaluation as long-acting androgens.

Molecular basis for potentiation of bleomycin-mediated degradation of DNA by polyamines. Experimental and molecular mechanical studies

The bleomycin-mediated degradation of DNA is stimulated (amplified) by certain DNA binding compounds, such as polyamines, that distort the double helix. Computer modelling studies suggest that putrescine (1), spermidine (2), and spermine (3) bind preferentially on the floor of the major groove of (dGdC)5.(dGdC)5. This interaction results in a bend of the oligomer helix toward the major groove and enlargement of the minor groove, both effects being in the order 1 less than 2 less than 3. These polyamine-induced distortions, as obtained from theoretical studies, parallel the experimental values of the amplification activities of 1-3 in the bleomycin-mediated degradation of poly(dGdC).poly(dGdC). The amplification mechanism of non-competitive binding of amplifier molecules in the major groove, and bleomycin in the minor groove, is proposed. It is suggested that the amplifier-induced conformational changes of the DNA helix increase affinity of the activated bleomycin complex toward the DNA minor groove and, consequently, result in an increased efficiency of the bleomycin-mediated degradation of the helix.

Interaction of unfused tricyclic aromatic cations with DNA: a new class of intercalators

Unfused tricyclic aromatic ring systems 1-6 with one or two cationic side chains have been synthesized and their interactions with DNA and synthetic polymers probed with a variety of techniques. Molecular mechanics calculations indicate that the torsional angle between ring planes in the minimum energy conformation of the tricyclic molecules can range from 0 degree to as high as 50 degrees depending on the type of rings and substituents. Viscometric titrations with linear and supercoiled DNA, linear dichroism, and NMR studies indicated that all compounds with torsional angles of approximately 20 degrees or less bind to DNA by intercalation. The more highly twisted intercalators caused significant perturbation of DNA structure. Unfused intercalators with twist angles of approximately 20 degrees have reduced binding constants, suggesting that they could not form an optimum interaction with the DNA base pairs. Unfused intercalators with twist less than 20 degrees formed strong complexes with DNA. The structures of these unfused intercalators are more analogous to typical groove-binding molecules, and an analysis of their interaction with DNA provides a better understanding of the subtle differences between intercalation and groove-binding modes for aromatic cations. The results indicate that intercalation and groove-binding modes should be viewed as two potential wells on a continuous energy surface. The results also suggest design strategies for intercalators that can optimally complement DNA base pair propeller twist or that can induce bends in DNA at the intercalation site.

A biphasic nature of the bleomycin-mediated degradation of DNA

The bleomycin-mediated digestion of DNA in the presence of ferrous ion, molecular oxygen, and dithiothreitol is characterized by a fast initial reaction, which is followed by a much slower process. The fast degradation is due to the fast activation of the bleomycin-Fe(II) complex and the subsequent fast reaction of the activated complex with DNA. The rate determining step for the slow process is reactivation of the bleomycin-Fe(III) complex. The apparent rate constants for both reactions increase with increasing ionic strength. The latter, unusual results are interpreted in terms of inhibition of bleomycin turnover by binding of cationic species with DNA at low ionic strength.

Amplification of bleomycin-mediated degradation of DNA by polyamines

The degradation of calf thymus DNA by a ferrous complex of bleomycin A2 or Blenoxane (a mixture consisting mainly of BLM-A2 and BLM-B2) is enhanced by polyamines higher than ethylenediamine. The QSAR analysis gave excellent correlation between the experimental amplification results and calculated valence molecular connectivity indices of the third order and path type for the protonated polyamines. A new amplifier of bleomycin activity has been synthesized and its interaction with DNA has been studied. This compound contains a DNA-intercalating moiety and a polyamine portion, two independent amplification systems in the same molecule. The role of the C-terminus of bleomycin as the intramolecular amplifier for the degradation of DNA is discussed.

Molecular basis for bleomycin amplification: conformational and stereoelectronic effects in unfused amplifiers

Sixteen unfused heterobiaromatic and biphenyl compounds substituted with an amino side chain (protonated in water) have been tested for (i) binding with DNA and (ii) their effect on the digestion of the DNA double helix by a bleomycin-iron complex. Only the DNA intercalating molecules amplify the digestion of DNA. One 2,2'-bipyridine derivative tested is an inhibitor of the bleomycin reaction because it removes ferrous ion from the bleomycin complex. Polarity of the intercalating unfused biaromatic system is of primary importance for effective binding of the molecule with native DNA and, at the same time, for its amplification activity. The molecules that have the biaromatic system polarized extensively in the direction of the side cationic chain, so that the intercalating sites constitutes a positive part of the dipole, show strong binding with DNA and good amplification activity. For strong intercalative forces that determine the amplification activity, it is important that both the heteroaromatic subsystems of the molecule have positive ends of their dipoles positioned away from the side chain. This work provides general guidelines for synthesis of new highly effective bleomycin amplifiers.

A non-classical intercalation model for a bleomycin amplifier

The bleomycin amplifier 1 is sterically hindered and twisted about the torsional bond joining the two aromatic rings. The intercalation of 1 and its sterically unhindered isomer 2 with DNA has been studied using n.m.r., viscometric titrations of superhelical and linear DNA, and flow dichroism. Based on the unusually strong interaction of 1 with DNA base pairs, a non-classical intercalation model for this compound is proposed. The intrinsic twists of both the unfused biaromatic system of 1 and the hydrogen-bonded DNA base pairs are retained in the intercalator-DNA complex, and the methyl group of 1 is accommodated between the hydrogen bonded bases. The complex of 1 is the first example found to date of this type of intercalation of the methyl group with DNA. The structure-activity relationships as bleomycin amplifiers for 1, 2 and similar derivatives is discussed.

Selective catalysis of A.T base pair proton exchange in DNA complexes: imino proton NMR analysis

Polyaromatic molecules with amino chain substituents, upon binding with DNA, selectively catalyze exchange of the A.T base pair protons with bulk water protons. The amine-catalyzed exchange is mediated by compounds which are A.T and G.C base sequence specific, intercalators, and outside binders. A mechanism for the selective exchange, involving transient opening and closing of individual A.T base pairs in the duplex, is discussed.

Amplification of bleomycin-mediated degradation of DNA

Three simple and independent tests have been introduced for studying the effect of DNA intercalating compounds on the bleomycin-mediated digestion of DNA in vitro. These methods are based on hyperchromic changes of DNA solution, changes in viscosity of DNA solution, and HPLC quantitative analysis of the four bases released from digested DNA. All three tests give comparable results. However, the viscometric method is technically the simplest and at the same time the most sensitive. The amplification of the bleomycin-mediated degradation of DNA by three unfused heteropolyaromatic intercalator molecules, namely N-[2''-(dimethylamino)ethyl]-4-thien-2'-ylpyrimidin-2-amine (1N), N,N-dimethyl-2-[(4'-thien-2''-ylpyrimidin-2'-yl)thio] ethylamine (1S), and newly synthesized 2,5-bis[2'-[[2''-(dimethylamino)ethyl]thio]pyrimidin-4'yl]thiophene (2) correlates well with the respective DNA binding constants for these compounds and is concentration dependent. The amplification activity of these compounds increases with increasing concentrations. The strongly binding compound 2 is the best amplifier of bleomycin in vitro found so far. Fused heteropolyaromatic systems, like ethidium bromide, are modest amplifiers of bleomycin at low concentrations but strongly inhibit the bleomycin chemistry at high concentrations.

Molecular basis for anticancer drug amplification: interaction of phleomycin amplifiers with DNA

The interaction of two phleomycin amplifiers, N,N-dimethyl-2-[[4'-(thien-2''-yl)pyrimidin-2'-yl]thio]ethylamine (1S, high activity) and N-[2''-(dimethylamino)ethyl]-4-(thien-2'-yl)pyrimidin-2-amine (1N, low activity) with DNA has been evaluated. The visible absorption bands of both compounds shift to longer wavelengths, and both exhibit hypochromicity on titration with DNA. The effects for 1S at low concentration are significantly greater than for 1N. 1S increases the DNA Tm by 2.5 degrees C while 1N causes only a 1.0 degree C increase under the same conditions. Spectrophotometric binding analysis of the interaction of 1S and 1N with calf thymus DNA indicates that 1S binds over 4 times more strongly to this DNA than 1N. Both compounds increase DNA viscosity, cause downfield shifts in DNA 31P NMR spectra, and shift the DNA imino base pair protons upfield, conclusively demonstrating that they bind to DNA by intercalation. Signals for the aromatic protons of 1S and 1N are shifted upfield on addition of DNA as expected for intercalation. The shifts for all aromatic protons are similar on 1S and on 1N, indicating that both the pyrimidine and thiophene are inserted between the DNA base pairs in the complex. NOE experiments demonstrate that the compounds are in the s-cis conformation both free in solution and in the DNA intercalation complex. Semiempirical INDO/S calculations indicate greater polarization of the pi-electron system of 1S than 1N. This greater polarization may account for the stronger interaction of 1S with DNA base pairs than 1N. The interaction of these compounds with DNA is strongly correlated with their biological amplification activity.

Unfused heterobicycles as amplifiers of phleomycin. VI. Some thienyl- and thiazolyl-pyrimidines with strongly basic side chains

2-Chloro-4-(thien-2'-yl)pyrimidine (2a) and its thiazol-2'-yl analogue (2d) are prepared by condensation of 2-chloropyrimidine with thien-2-yl- and thiazol-2-yl-lithium, followed by oxidation of the dihydro intermediates. 4-Chloro-6-methyl-2-(thien-2'-yl)pyrimidine (3b),its 2-(2',4'-dimethylthiazol-5'-yl) analogue (3f) and the 2-(2'-methylthiazol-4'-yl) analogue (4b) are made from the corresponding pyrimidinones, which are available by primary synthesis. Each chloro compound is converted by nucleophilic displacement into its β-dimethylaminoethylamino and β-dimethylaminoethylthio derivatives, for which activities as amplifiers of phleomycin are reported and discussed.