Structure–Activity Studies on the Fluorescent Indicator in a Displacement Assay for the Screening of Small Molecules Binding to RNA

A series of xanthone and thioxanthone derivatives with aminoalkoxy substituents were synthesized as fluorescent indicators for a displacement assay in the study of small‐molecule–RNA interactions. The RNA‐binding properties of these molecules were investigated in terms of the improved binding selectivity to the loop region in the RNA secondary structure relative to 2,7‐bis(2‐aminoethoxy)xanthone (X2S) by fluorimetric titration and displacement assay. An 11‐mer double‐stranded RNA and a hairpin RNA mimicking the stem loop IIB of Rev response element (RRE) RNA of HIV‐1 mRNA were used. The X2S derivatives with longer aminoalkyl substituents showed a higher affinity to the double‐stranded RNA than the parent molecule. Introduction of a methyl group on the aminoethoxy moiety of X2S effectively modulated the selectivity to the RNA secondary structure. Methyl group substitution at the C1′ position suppressed the binding to the loop regions. Substitution with two methyl groups on the amino nitrogen atom resulted in reducing the affinity to the double‐stranded region by a factor of 40 %. The effect of methyl substitution on the amino nitrogen atom was also observed for a thioxanthone derivative. Titration experiments, however, suggested that thioxanthone derivatives showed a more prominent tendency of multiple binding to RNA than xanthone derivatives. The selectivity index calculated from the affinity to the double‐stranded and loop regions suggested that the N,N‐dimethyl derivative of X2S would be suitable for the screening of small molecules binding to RRE.     

Optimisation of the derivatization in cellulose-type chiral selectors for enantioseparation by centrifugal partition chromatography

Cellulose was chemically modified with hydrophobic dodecanoyl groups followed by 3,5-dimethylphenylcarbamoyl substituents forming mixed ester/carbamate derivatives in order to improve the solubility in lipophilic solvents compared to the corresponding homosubstituted cellulose tris(3,5-dimethylphenylcarbamate). Two mixed derivatives of different degree of substitution were prepared, tested as chiral selectors (CSs) in counter-current chromatography (CCC) and compared to the homo-substituted derivative. Alternatively, cellulose tris(3,5-dichlorophenylcarbamate), was synthesised and tested with the same purpose. The racemic drugs pindolol and warfarin were used as test compounds. Biphasic organic/aqueous solvent systems, composed of methyl isobutyl ketone, t-butyl methyl ether or ethyl acetate and aqueous ammonium acetate or sodium phosphate buffer, were used. Centrifugal partition chromatography, a variety of CCC, in the classical elution mode and the pH-zone-refining displacement mode was applied. The enantioseparation of pindolol and warfarin was achieved in the latter conditions. The presence of dodecanoyl chains on the CS increased solubility in the organic solvents used. The selectivity of the mixed dodecanoyl/3,5-dimethylphenylcarbamoyl cellulose derivative with low degree of dodecanoyl groups (degree of substitution 0.3/degree of substitution 2.6, respectively) was similar to that of the homo-substituted derivative. Furthermore, the loading capacity for pindolol was increased by a factor of three compared to cellulose tris(3,5-dimethylphenylcarbamate). Nevertheless, the increasing degree of substitution with dodecanoyl groups on the CS, although improved solubility in the stationary phase, contributed negatively to the enantioselectivity, where warfarin was more affected than pindolol.     

Oligonucleotides Containing Novel 4′‐C‐ or 3′‐C‐(Aminoalkyl)‐Branched Thymidines

The synthesis of four novel 3′‐C‐branched and 4′‐C‐branched nucleosides and their transformation into the corresponding 3′‐O‐phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′‐C‐branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′‐O‐methyl and 2′‐deoxy‐2′‐fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′‐C‐(aminomethyl)‐2′‐O‐methyl monomer X and 4′‐C‐(aminomethyl)‐2′‐deoxy‐2′‐fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single‐stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′‐O‐methyl‐RNA oligonucleotide had a negative effect on the binding affinity of the 2′‐O‐methyl‐RNA oligonucleotide towards DNA and RNA. Starting from the 3′‐C‐allyl derivative 28 , 3′‐C‐(3‐aminopropyl)‐protected nucleosides and 3′‐O‐phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′‐C‐(3‐aminopropyl)thymidine monomer Z or the corresponding 3′‐C‐(3‐aminopropyl)‐2′‐O,5‐dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′‐deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′‐O‐methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).     

Targeted cleavage of HIV RRE RNA by Rev-coupled transition metal chelates

A series of compounds that target reactive metal chelates to the HIV-1 Rev response element (RRE) mRNA have been synthesized. Dissociation constants and chemical reactivity toward HIV RRE RNA have been determined and evaluated in terms of reduction potential, coordination unsaturation, and overall charge associated with the metal-chelate-Rev complex. Ethylenediaminetetraacetic acid (EDTA), nitrilotriacetic acid (NTA), diethylenetriaminepentaacetic acid (DTPA), and 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) were linked to a lysine side chain of a Rev-derived peptide by either EDC/NHS or isothiocyanate coupling. The resulting chelate-Rev (EDTA-Rev, DTPA-Rev, NTA-Rev, and DOTA-Rev) conjugates were used to form coordination complexes with Fe(2+), Co(2+), Ni(2+), and Cu(2+) such that the arginine-rich Rev peptide could mediate localization of the metal chelates to the Rev peptide's high-affinity mRNA binding partner, RRE stem loop IIB. Metal complexes of the extended peptides GGH-Rev and KGHK-Rev, which also contain N-terminal peptidic chelators (ATCUN motifs), were studied for comparison. A fluorescence titration assay revealed high-affinity RRE RNA binding by all 22 metal-chelate-Rev species, with K(D) values ranging from ~0.2 to 16 nM, indicating little to no loss of RNA affinity due to the coupling of the metal chelates to the Rev peptide. Dissociation constants for binding at a previously unobserved low-affinity site are also reported. Rates of RNA modification by each metal-chelate-Rev species were determined and varied from ~0.28 to 4.9 nM/min but were optimal for Cu(2+)-NTA-Rev. Metal-chelate reduction potentials were determined and varied from -228 to +1111 mV vs NHE under similar solution conditions, allowing direct comparison of reactivity with redox thermodynamics. Optimal activity was observed when the reduction potential for the metal center was poised between those of the two principal co-reagents for metal-promoted formation of reactive oxygen species: E°(ascorbate/ascorbyl radical) = -66 mV and E°(H(2)O(2)/hydroxyl radical) = 380 mV. Given the variety of oxidative activities of these metal complexes and their high-affinity binding to the targeted RRE mRNA following coupling to the Rev peptide, this class of metal-chelate-Rev derivatives constitutes a promising step toward development of multiple-turnover reagents for selective eradication of HIV-1 RRE mRNA.     

Derivatization procedures for the detection of beta(2)-agonists by gas chromatographic/mass spectrometric analysis

An evaluation of derivatization procedures for the detection of beta(2)-agonists is presented. The study was performed with the beta(2)-agonists bambuterol, clenbuterol, fenoterol, formoterol, salbutamol, salmeterol and terbutaline. Different derivatizating agents were employed, aiming to obtain derivatives with high selectivity to be used in the gas chromatographic/mass spectrometric analysis of beta(2)-agonists in biological samples. Trimethylsilylation was compared with different agents and the role of some catalysts was evaluated. Acylation, combined trimethylsilylation and acylation, and the formation of cyclic methylboronates were also studied. Sterical hindrance caused by different substituents at the nitrogen atom of the beta-ethanolamine lateral chain of beta(2)-agonist molecules is mainly responsible for differences in the abundances of the derivatives obtained. The use of catalysts produces an increase in the derivatization yield, especially for compounds with low steric hindrance (substituents with primary and secondary carbon atoms). The formation of trimethylsilyl (TMS) ethers is not influenced by structural molecular differences when only hydroxy groups are involved in derivatization. Combined trimethylsilylation and acylation showed that compounds with a secondary carbon atom linked to the nitrogen atom form mainly N-TFA-O-TMS derivatives, with a small amount of N-TMS-O-TMS derivatives. Compounds with tert-butyl substituents at the amino group (bambuterol, salbutamol and terbutaline) formed O-TMS derivatives as the main products, although a limited amount of trifluoroacylation at the nitrogen atom also occurred. Cyclic methylboronates were formed with bambuterol, clenbuterol, formoterol, salbutamol and salmeterol. Owing to hydroxy substituents in unsuitable positions for ring formation, this procedure was not effective for fenoterol and terbutaline. Mass spectra of different derivatives and tentative fragmentation profiles are also shown. For screening purpose (e.g. sports drug testing), derivatization with MSTFA or BSTFA alone is recommended as a comprehensive derivatization technique for beta(2)-agonists owing to minimal by-product formation; formation of cyclic methylboronates can be useful for confirmation purposes. Detection limits were obtained for the TMS and cyclic methylboronate derivatives using the derivatizing reagents MSTFA and trimethylboroxine, respectively. For most of the compounds, lower detection limits were found for the TMS derivatives.     

Semicarbazones and thiosemicarbazones of the heterocylic series XXXVIII. Aminohydrazone-iminohydrazine tautomerism of isatin 2-thiosemicarbazone and its alkyl derivatives

Isatin 2-thiosemicarbazone and its derivatives with one methyl group attached to the nitrogen atoms of the side chain exist in solution primarily in the iminohydrazine tautomeric form. Further substitution of the hydrogen atoms attached to the nitrogen atom in the primary thioamide group or replacement of the hydrogen atom attached to the sulfur atom by a methyl group promotes the formation of the aminohydrazone tautomer.See [1] for communication XXXVII.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 83–88, January, 1976.     

Factors governing the kinetic competition of nitrogen and sulfur ligands in cisplatin binding to biological targets

The kinetic competition of sulfur and nitrogen nucleophiles L in the substitution reactions of cisplatin derivatives, cis-[Pt(II)(NH(3))(2)(X)(OH(2))](n)(+) + L --> cis-[Pt(II)(NH(3))(2)(X)(L)](m)(+) + H(2)O (X = Cl(-), H(2)O), has been studied using density functional theory and continuum dielectric calculations. The calculations reveal an intrinsic kinetic preference of platinum(II) for nitrogen over sulfur ligands. However, biologically relevant substituents can mask this preference for nitrogen nucleophiles. Investigation of the activation free energies of the substitution reactions in dependence of the dielectric constant epsilon demonstrates the microenvironment to be crucial in the binding of cisplatin to its intracellular targets. The fused aromatic heterocycle of guanine stabilizes the transition state for platination at a smaller epsilon more efficiently than do the functional groups of amino acid residues. The results of this work suggest a relatively facile platination of guanine-N7 sites of DNA in regions of low epsilon, particularly in the proximity of histone cores.     

Experimental and theoretical approaches to the study of the reactivity and mechanism of the substitution of phenyl 1-(2,4-dinitronaphthyl) ether with anilines derivatives

Reactions of aniline derivatives in dimethyl sulfoxide with phenyl 1-(2,4-dinitronaphthyl) ether yield aryl 1-(2,4-dinitronaphthyl) amine, which results in substitution of the phenoxy groups at the naphthyl ipso carbon atom. Rate constants were measured spectrophotometrically, and reaction proton transfer was rate limiting. The values of the rate coefficients indicate a rate-limiting proton transfer mechanism with significant substituent effects. The calculated activation parameters were of regular variation with substituents in 4- and 3-position in the aniline nucleophile, and the reaction proceeded through a common mechanism. Hammett's reaction constant showed that the reaction rate constants depend on the electron density of the nitrogen atom of aniline derivative, whereas the coefficient value obtained from the Brönsted relation indicated that the reaction was significantly associative and quite zwitterion like. Computational studies of the substitution were carried out based on density functional theory, and theoretical to the experimental agreement was achieved.     

Intramolecular Nucleophilic Deselenenylation Reactions Promoted by Benzeneselenenyl Triflate. Stereospecific Synthesis of Vicinal Amino Alcohol Precursors

After activation with electrophilic selenenylating agents, the phenylseleno group of vicinal azido selenides, containing internal oxygen or nitrogen nucleophilic substituents, readily undergoes intramolecular nucleophilic displacement to afford azido-substituted heterocyclic compounds. This intramolecular substitution occurs with inversion of configuration at the carbon atom bearing the selenium atom. Starting from acetamido selenides and carbamato selenides, a stereocontrolled synthesis of the vicinal amino alcohol precursor oxazolines and oxazolidin-2-ones has been developed.     

A new sulfate-selective electrode and its use in analysis

The improvement of the steric accessibility of exchange centers of higher quaternary ammonium salts (QAS) by replacing several long-chain alkyl substituents at the nitrogen atom with methyl groups enhanced the selectivity of ion-selective electrodes (ISEs) based on the specified ion exchangers for the SO ₄ ^2? ion up to six orders of magnitude in the presence of singly charged anions. This can be qualitatively explained by the specific features of ion pair formation between quaternary ammonium cations and singly and doubly charged anions. The effect of the steric accessibility of the QAS exchange center on the selectivity of ISEs is partially retained in the presence of a neutral anion carrier, hexyl p-trifluoroacetylbenzoate (HTFAB), which is used for enhancing the selectivity for the sulfate ion in the presence of singly charged anions. A sulfate-selective electrode with a reasonable selectivity for practical purposes was proposed. It is based on the HTFAB-higher QAS ion pair bearing three methyl substituents at the nitrogen atom. The ISE was used in the analysis of natural water.     

Dithiane,Trithiane, and Dithiazane-Based Photolabile Scaffolds for Molecular Recognition: Mechanism and Efficiency of the Photoinduced Fragmentation in Aqueous Reductive Environments

Abstract

Photoinduced fragmentation in dithiane and trithiane adducts of aromatic ketones and aldehydes was studied in aqueous reductive environments. Density functional computations were carried out for thioxanthone derivatives bearing donor and acceptor substituents in the aromatic ring to identify the substitution pattern that is most promising for the productive irreversible electron transfer.     

Opioid ligands with mixed properties from substituted enantiomeric N-phenethyl-5-phenylmorphans. Synthesis of a micro-agonist delta-antagonist and delta-inverse agonists

Enantiomeric N-phenethyl-m-hydroxyphenylmorphans with various substituents in the ortho, meta or para positions of the aromatic ring in the phenethylamine side-chain (chloro, hydroxy, methoxy, nitro, methyl), as well as a pyridylethyl and a indolylethyl moiety on the nitrogen atom, were synthesized and their binding affinity to the mu-, delta-, and kappa-opioid receptors was examined. The higher affinity ligands were further examined in the [(35)S]GTPgammaS assay to study their function and efficacy. 3-((1R,5S)-(-)-2-(4-Nitrophenethyl)-2-aza-bicyclo[3.3.1]nonan-5-yl)phenol ((-)-) was found to be a mu-agonist and delta-antagonist in that functional assay and was about 50 fold more potent than morphine in vivo. 3-((1R,5S)-(-)-2-(4-Chlorophenethyl)-2-aza-bicyclo[3.3.1]nonan-5-yl)phenol ((-)-) and several other ligands displayed inverse agonist activity at the delta-opioid receptor. The absolute configuration of all of the reported compounds was established by chemical conversion of (-)- to 1R,5S-(-)-.HBr.     

Revealing Unexpected Mechanisms for Nucleophilic Attack on S?S and Se?Se Bridges

The reactivity of disulfide and diselenide derivatives towards F^? and CN^? nucleophiles has been investigated by means of B3PW91/6‐311+G(2df,p) calculations. This theoretical survey shows that these processes, in contrast with the generally accepted view of disulfide and diselenide linkages, do not always lead to S? S or Se? Se bond cleavage. In fact, S? S or Se? Se bond fission is the most favorable process only when the substituents attached to the S or the Se atoms are not very electronegative. Highly electronegative substituents (X) strongly favor S? X bond fission. This significant difference in the observed reactivity patterns is directly related to the change in the nature of the LUMO orbital of the disulfide or diselenide derivative as the electronegativity of the substituents increases. For weakly electronegative substituents, the LUMO is a σ‐type S? S (or Se? Se) antibonding orbital, but as the electronegativity of the substituents increases the π‐type S? X antibonding orbital stabilizes and becomes the LUMO. The observed reactivity also changes with the nature of the nucleophile and with the S or Se atom that undergoes the nucleophilic attack in asymmetric disulfides and diselenides. The activation strain model provides interesting insights into these processes. There are significant similarities between the reactivity of disulfides and diselenides, although some dissimilarities are also observed, usually related to the different interaction energies between the fragments produced in the fragmentation process.     

An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction

The interaction between the HIV-1 Rev protein and the Rev-Responsive Element (RRE) RNA is an attractive target for anti-viral therapy. We have designed alpha-helical peptidomimetics of Rev-like peptides using side chain-side chain macrolactam formation between positions i and i+4. One peptidomimetic having an appropriate location, orientation, and length of the macrolactam exhibited both significant helical character and specific RRE binding. This molecule displays 2-fold greater RNA specificity than the wild-type Rev peptide and more than 20-fold greater specificity than an uncyclized control peptide. Thus, specific, high affinity recognition of the RRE is feasible utilizing a small, relatively rigid peptidomimetic scaffold.     

Study on the second-order non-linear optical properties of 10-hydrocarbylacridones

Twenty 10-hydrocarbylacridones and 2-methylacridone, 1-hydroxyacridone were synthesized from acridone and characterized by mp, IR, UV, 1H NMR and MS. Using Nd:YAG as a laser source, the second-order harmonic generation (SHG) values of the acridone derivatives were measured in powder state as compared with urea powder. The results showed that the SHG values of some of 10-hydrocarbylacridones were higher than that of urea, while others were lower. Although the hydrocarbyl substituents (R) attached to nitrogen atom of acridone were different in size and electronegativity, they had a little effect on the SHG values of 10-hydrocarbylacridones. Substituents, such as methyl or hydroxy group connected to the phenyl ring, caused a little effect on the SHG values, too, compared with acridone. The ability of R to push electron toward the nitrogen atom or to pull electron from the nitrogen atom play an important role on the maximum wavelengthes of UV-visible absorption of acridone derivatives.     

X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno‐oncology.     

Substitution effect,absorption, and fluorescence behaviors of 11,12-benzo-1,7,10,13-tetraoxa-4-aza- cyclopentadec-11-ene (benzoaza-15-crown-5) derivatives upon cation complexation in solvent extraction

Substitution effect, absorption, and fluorescence behaviors of some benzoaza-15-crown-5 derivatives upon cation complexation in solvent extraction were studied. The introduction of a substituent on the nitrogen atom in benzoaza-15-crown-5 enhanced extractabilities in the solvent extraction of aqueous alkali metal picrates. The nondonating substituents raised the cation selectivity for Na(+) over K(+), but the donating substituents reduced the cation selectivity. The absorption and fluorescence spectral behavior was different with the alkali metal cations.     

Benzimidazole derivatives. 4. The recognition of the voluminous substituent attached to the basic amino group of 5-HT4 receptor antagonists

We report a structure-affinity analysis of an important element in the pharmacophore model for the recognition of 5-HT4 receptor antagonists: the voluminous substituent attached to the basic nitrogen of the ligand. We have designed, synthesized and pharmacologically evaluated a series of benzimidazole derivatives 1 containing a common molecular skeleton formed by N-[(4-piperidyl)methyl]-6-chlorobenzimidazole-4-carboxamide and four different substituents (R = butyl, 2-[(methylsulfonyl)amino]ethyl, 5-[(phenylacetyl)amino]pentyl, and 5-[(benzylsulfonyl)amino]pentyl). These compounds possess binding affinities in the nM range (Ki = 0.11-1.50 nM). Moreover, a ligand that contains a hydrogen atom attached to the basic nitrogen (R = H; Ki = 150 nM) is used as a control for structure-affinity relationships.     

Scanning conformational space with a library of stereo- and regiochemically diverse aminoglycoside derivatives: the discovery of new ligands for RNA hairpin sequences

A library of stereo- and regiochemically diverse aminoglycoside derivatives was screened at 1 microM using surface plasmon resonance (SPR) against RNA hairpin models of the bacterial A-site, and the HIV viral TAR and RRE sequences. In order to double the stereochemical diversity of the library, the compounds were screened against both enantiomers of each of these sequences. Remarkably, this initial screen suggested that the same four aminoglycoside derivatives bound most tightly to all three of the RNAs, suggesting that these compounds were good RNA binders which, nonetheless, discriminated poorly between the RNA sequences. The interactions between selected isomeric aminoglycoside derivatives and the RNA hairpins were then studied in more detail using an SPR assay. Three isomeric tight-binding aminoglycoside derivatives, which had been identified from the initial screen, were found to bind more tightly to the RNA hairpins (with K(D) values in the range 0.23 to 4.7 microM) than a fourth isomeric derivative (which had K(D) values in the range 6.0 to 30 microM). The magnitude of the tightest RNA-aminoglycoside interactions stemmed, in large part, from remarkably slow dissociation of the aminoglycosides from the RNA targets. The three tight-binding aminoglycoside derivatives were found, however, to discriminate rather poorly between alternative RNA sequences with, at best, around a twenty-fold difference in affinity for alternative RNA hairpin sequences. Within the aminoglycoside derivative library studied, high affinity for an RNA target was not accompanied by good discrimination between alternative RNA sequences.     

New Acridone- and (Thio)Xanthone-Derived 1,1-Donor–Acceptor-Substituted Alkenes: pH-Dependent Fluorescence and Unusual Photooxygenation Properties

A synthetic route to new heterocyclic 1,1-donor–acceptor-substituted alkenes starting with N-methyl-acridone, xanthone, and thioxanthone was investigated, leading to the acridone- and xanthone-derived products methyl 2-methoxy-2-(10-methylacridin-9 (10H)-ylidene)acetate (7) and methyl 2-methoxy-2-(9H-xanthen-9-ylidene)acetate (10) in low yields with the de-methoxylated product methyl 2-(10-methylacridin-9 (10H)-ylidene)acetate (8) and the reduced compound methyl 2-methoxy-2-(9H-xanthen-9-yl)acetate (11) as the major products from N-methyl acridone and xanthone. From thioxanthone, only the rearrangement and reduction products (14) and (15) resulted. The photophysical properties of compounds (7), (8), and (10) were investigated in the presence and absence of the Brønsted acid TFA by NMR, UV–VIS absorption, and fluorescence spectroscopy. Protonation of the acridone-derived alkenes (7) and (8) led to strong bathochromic and hyperchromic fluorescence shifts and a substantial increase in Stokes shift. The photooxygenation experiments with these substrates showed an unusual reactivity pattern in the singlet oxygen processes: whereas the electron-rich enolether (7) was chemically unreactive, (8) and (10) were oxidatively cleaved, presumably via intermediate 1,2-dioxetanes.