Enhanced stereoselectivity in internucleotidic bond formation by the use of the chiral ribose moiety of thymidine

This paper deals with the synthesis of new cyclic thymidine 3'-phosphoramidite building blocks having a covalent linker between the trityl type 5'-hydroxyl protecting group and the phosphorus atom attached to the 3'-hydroxyl group of thymidine. The ring structures were designed to reduce the conformational freedom around the phosphorus center so that the stereoselectivity in the internucleotide linkage formation would be improved. The linkers were also designed to be removed readily by treatment with aqueous ammonia. These building blocks were synthesized in good yield by one-pot cyclization of the diol precursors with dichloro(N,N-diisopropylamino)phosphine, despite their large-membered ring. Various activators having 1H-tetrazole, imidazole, and triazole structures were investigated to find the best selectivity in the synthesis of thymidylyl(5'-3')thymidine phosphorothioate. It turned out that our cyclic phosphoramidites gave preferentially the R(p) diastereoisomer in high coupling yield applicable to the solid-phase synthesis of oligodeoxynucleotides. It should be noted that high stereoselectivity was achieved without any chiral sources other than the 2'-deoxyribose moiety itself. The mechanistic studies revealed the importance of the steric bulk and the acidity of the activators. It was also found that the steric bulk of the alcoholic nucleophile was an important factor that determined the stereoselectivity in our systems.     

Synthesis of chalcone precursor via Cu(I) catalyzed 1,3-dipolar reaction of functionalized acetylene and pyrazole embedded dipole

A new class of functionalized pyrazole bearing 1,2,3-triazole has been synthesized via Cu(I) mediated 1,3-dipolar cycloaddition of pyrazole bearing azide with various aromatic/heteroaromatic bearing terminal dipolarophile (acetylene). Structures of the newly synthesized compounds were explicated by analytical and spectral analysis. All the newly synthesized compounds were evaluated for their in-vitro antibacterial and antioxidant activity. Among the synthesized compound, triazole bearing 2,5-thiazolidinone 5b (20 ± 0.70) and triazole bearing thiocarboamide 5e (19 ± 0.70) showed good antibacterial activity against Escherichia coli and Pseudomonas aeruginosa, respectively. The newly synthesized compounds further tested for their ability to bleach DPPH radical using DPPH scavenging assay. Among the synthesized compounds 1,2,3-triazole bearing 2,5-thiazolidinone 5b (58.81%) exhibited good DPPH scavenging activity compared to the rest of the compounds. From the X-ray and Hirshfield analysis, it was observed that compound 3 , crystallizes in a triclinic crystal system with a P-1 space group. The major intercontacts present in these molecules are H…H (39.7%), C…H (23.9%), N…H (20.3%).     

A redox-switchable alpha-cyclodextrin-based [2]rotaxane

A bistable [2]rotaxane comprising an alpha-cyclodextrin (alpha-CD) ring and a dumbbell component containing a redox-active tetrathiafulvalene (TTF) ring system within its rod section has been synthesized using the Cu(I)-catalyzed azide-alkyne cycloaddition, and the redox-driven movements of the alpha-CD ring between the TTF and newly formed triazole ring systems have been elucidated. Microcalorimetric titrations on model complexes suggested that the alpha-CD ring prefers to reside on the TTF rather than on the triazole ring system by at least an order of magnitude. The fact that this situation does pertain in the bistable [2]rotaxane has not only been established quantitatively by electrochemical experiments and backed up by spectroscopic and chiroptical measurements but also been confirmed semiquantitatively by the recording of numerous cyclic voltammograms which point, along with the use of redox-active chemical reagents, to a mechanism of switching that involves the oxidation of the neutral TTF ring system to either its radical cationic (TTF*+) or dicationic (TTF2+) counterparts, whereupon the alpha-CD ring, moves along the dumbbell to encircle the triazole ring system. Since redox control by both chemical and electrochemical means is reversible, the switching by the bistable [2]rotaxane can be reversed on reduction of the TTF*+ or TTF2+ back to being a neutral TTF.     

Directional Shuttling of a Stimuli‐Responsive Cone‐Like Macrocycle on a Single‐State Symmetric Dumbbell Axle

Rotaxane‐based molecular shuttles are often operated using low‐symmetry axles and changing the states of the binding stations. A molecular shuttle capable of directional shuttling of an acid‐responsive cone‐like macrocycle on a single‐state symmetric dumbbell axle is now presented. The axle contains three binding stations: one symmetric di(quaternary ammonium) station and two nonsymmetric phenyl triazole stations arranged in opposite orientations. Upon addition of an acid, the protonated macrocycle shuttles from the di(quaternary ammonium) station to the phenyl triazole binding station closer to its butyl groups. This directional shuttling presumably originates from charge repulsion and an orientational binding preference between the cone‐like cavity and the nonsymmetric phenyl triazole station. This mechanism for achieving directional shuttling by manipulating only the wheels instead of the tracks is new for artificial molecular machines.     

DNA binding properties of oligodeoxynucleotides containing pyrrolidino C-nucleosides

We have incorporated pyrrolidino-C-nucleosides (pyrrolidino-pseudonucleosides) containing the base uracil and N-1-methyl uracil into oligodeoxynucleotides and compared their thermal duplex and triplex stabilities with unmodified or pseudouridine-containing oligodeoxynucleotides. We find relative destabilizations of triplex formation by ca. -13 to -1 degrees C per modification (relative to thymidine) in a strongly sequence dependent mode. Duplex formation is less destabilizing and more homogeneous with -4 to -2 degrees C per modification.     

Novel 1,4-benzothiazine derivatives: synthesis,crystal structure,and anti-bacterial properties

In order to develop relatively small molecules as pharmacologically active molecules, novel 1,4-benzothiazine derivatives with triazole and oxazolidinone were synthesized. In this study, a series of 1,2,3-triazolylmethyl-1,4-benzothiazine derivatives were developed by exploiting a click chemistry reaction using a CuI-catalyzed Huisgen [3 + 2] cycloaddition. Starting from 2-(substituted)-3,4-dihydro-2H-1,4-benzothiazi-3-one, a number of 1,4-benzothiazine derivatives were also synthesized using different alkylating agents to give a 4-(substituted)-2-(substituted)-3,4-dihydro-2H-1,4-benzothiazi-3-one in good yields. The crystal and molecular structure of compound oxazolidin-2-one in basic benzothiazine was established by single-crystal X-ray diffraction. The newly synthesized products were subjected to in vitro biological evaluation. The result indicated that the compounds show convincing antibacterial activities against different microorganisms. All structures of the synthesized compounds were elucidated on the basis of spectral analyses and chemical reactions.     

Cooperative molecular recognition of dyes by dyad and triad cyclodextrin-crown ether conjugates

Three beta-cyclodextrin (beta-CyD) derivatives with crown ether units, that is N-(4'-benzo-15-crown-5)-6-imino-6-deoxy-beta-CyD (2), 6,6'-[N-(4,4'-dibenzo-18-crown-6)-imino]-bridged bis(beta-CyD)(3), and 2,2'-[O-(4',5'-benzo-15-crown-5)-ethyl]-bridged bis (beta-CyD)(5), were synthesized as cooperative recognition receptor models. Their molecular binding behavior with four representative fluorescent dyes, i.e., ammonium 8-anilino-1-naphthalenesulfonate (ANS), sodium-6-toluidino-2-naphthalene-sulfonate (TNS), Acridine Red (AR) and Rhodamine B (RhB), was investigated in buffer solutions (pH = 7.20) at 25 degreesC by means of circular dichroism, NMR and fluorescence spectroscopy. 2D-ROESY experiments showed that dyad host 2 and triad host 3 adopted a CyD-guest-crown ether binding mode, while triad host 5 adopted a CyD-guest-CyD binding mode, upon inclusion complexation with guest molecules. Therefore, hosts 2 and 3 showed high molecular recognition ability towards charged guests, giving an enhanced binding ability up to 115 times for ANS by 3 and fairly high molecular selectivity up to 1450 times for the ANS/AR pair by 2 as compared with native beta-CyD in an aqueous phosphate buffer solution. On the other hand, host 5 was found to be able to effectively recognize the shape of a guest molecule, showing significantly higher binding ability towards linear guests. The binding affinities and molecular recognition abilities of these CyD-crown ether conjugates towards guest molecules are discussed from the viewpoint of electrostatic and/or hydrophobic interactions, size/shape-fit concept, and multiple recognition mechanism between host and guest.     

Inhibition of Influenza Virus Replication in MDCK Cells by Circular Dumbbell RNA/DNA Chimeras with Closed Alkyl Loop Structures

We have demonstrated that a new type of circular dumbbell RNA/DNA chimeric oligonucleotide (CDRDON) with two closed nucleotide or alkyl loop structures (hexa‐ethylene glycol) inhibits influenza virus A replication in MDCK cells. The enzymatic synthesis of circular dumbbell RNA/DNA chimeric oligonucleotides was achieved by enzymatically ligating a self‐complementary phosphorylated oligonucleotide with T4‐RNA ligase. The CDRDON‐Al, with two closed alkyl loop structures, showed higher nuclease resistance, hybridization, and cellular uptake than the anti‐S‐ODN and the CDRDON, with two closed nucleotide hairpin‐loop structures. The circular dumbbell RNA/DNA chimeric oligonucleotide (CDRDON‐Al‐PB2‐as), containing an AUG initiation‐codon sequence as the target of PB2, showed highly inhibitory effects on influenza A virus RNA expression. The limited toxicity of unmodified phosphodiester oligonucleotides and the sequence‐specific binding to target mRNA indicate that circular dumbbell RNA/DNA chimeric phosphodiester oligonucleotides can be used with intact cells, and may prevent viral replication in culture.     

Anti-AIDS agents 88. Anti-HIV conjugates of betulin and betulinic acid with AZT prepared via click chemistry

In the present study, a new strategy to link AZT with betulin/betulinic acid (BA) by click chemistry was designed and achieved. This conjugation via a triazole linkage offers a new direction for modification of anti-HIV triterpenes. Click chemistry provides an easy and productive way for linking two molecules, even when one of them is a large natural product. Among the newly synthesized conjugates, compounds 15 and 16 showed potent anti-HIV activity with EC(50) values of 0.067 and 0.10 μM, respectively, which are comparable to that of AZT (EC(50): 0.10 μM) in the same assay.     

Synthesis,biological screening,in silico study and fingerprint applications of novel 1, 2, 4-triazole derivatives

A series of novel 1,2,4 triazole derivatives were synthesized by treating 4-bromo-2-(4H-1,2,4-triazole-3-yl)aniline (4) with different substituted benzene sulfonyl chlorides 5(a-f) and benzyl bromides 7(a-e) . IR, ¹H-NMR, ¹³C-NMR, and mass analysis confirmed the structures of the newly synthesized compounds. All derivatives were screened for their in vitro antibacterial activity against two bacterial strains viz Escherichia coli and Staphylococcus aureus, antifungal activity against Aspergillus flavus and Candida albicans, anthelmintic activity against Pheretima posthuma and also cytotoxicity activity against MDA-MB 231 and A375 cancer cell lines. It was found that some of the derivatives showed significant antibacterial, antifungal, anthelmintic, and cytotoxic activities when compared to respective standard drugs. Molecular docking studies have assisted the theoretical binding mode of the target molecules. Compounds were also explored for fingerprint application.     

Synthesis and Antimicrobial Activity of N‐Aryl‐4‐(cyano/alkoxycarbonyl)‐5‐(pyridin‐3‐yl)‐1H/3H‐1,2,3‐triazole Derivatives

A convenient synthesis of a new series of N‐aryl‐5‐(pyridin‐3‐yl)‐1H/3H‐1,2,3‐triazole‐4‐carbonitriles and alkyl N‐aryl‐5‐(pyridin‐3‐yl)‐1H/3H‐1,2,3‐triazole‐4‐carboxylic acid esters is reported. The newly synthesized 5‐(pyridin‐3‐yl)‐1,2,3‐triazole derivatives are evaluated for their antibacterial and antifungal activity. Some of these triazole derivatives have exhibited moderate antimicrobial activity.     

Squaryl group as a new mimic of phosphate group in modified oligodeoxynucleotides: synthesis and properties of new oligodeoxynucleotide analogues containing an internucleotidic squaryldiamide linkage

This paper describes the synthesis and properties of a new type of modified oligodeoxynucleotide containing a neutral but highly polarized squaryl group as a novel mimic of the phosphate group. A modified thymidine dimer derivative (TsqT) having a squaryldiamide linkage was synthesized in almost quantitative yield by a two-step substitution of diethyl squarate with 3'-amino-5'-O-(4,4'-dimethoxytrityl)-3'-deoxythymidine and 5'-amino-5'-deoxythymidine. The CD and UV studies of TsqT suggest that this dimer has basically a structure similar to that of TpT. The NMR studies of TsqT show a unique property, namely, that the squaryl group of TsqT is influenced by Mg2+ concentration. The ab initio calculations of TsqT showed a highly polarized structure resembling that of a phosphate group. This dimer structural motif was finally incorporated into oligodeoxynucleotides by use of the phosphoramidite approach. The hybridization affinity of these modified oligodeoxynucleotides for the complementary and mismatched oligodeoxynucleotides was studied in detail by using Tm experiments. Consequently, it turned out that in a matched duplex of 5'-d(CGCATsqTAGCC)-3'/5'-d(GGCTAATGCG)-3' the A-T base pairs at the modified site can be preserved, but instead thermal destabilization of the overall structure was observed. To estimate the structure of the duplex, two kinds of fluorescein chromophores (fluorescein (FL) and cyanine 3 (Cy3)) were introduced into the 5'-terminal site of 5'-d(GACGCATsqTAGCCGAT)-3' and 5'-d(ATCGGCTAATGCGTC)-3', respectively. The fluorescence resonance energy transfer experiments using these functionalized oligodeoxynucleotides suggest that the matched duplexes have a bent structure at the modified site. This conclusion was also strongly supported by computational MM and MD simulations.     

Probing the Binding of Syzygium-Derived α-Glucosidase Inhibitors with N- and C-Terminal Human Maltase Glucoamylase by Docking and Molecular Dynamics Simulation

Human maltase glucoamylase (MGAM) is a potent molecular target for controlling post prandial glucose surplus in type 2 diabetes. Binding of small molecules from Syzygium sp. with α-glucosidase inhibitory potential in MGAM has been investigated in silico. Our results suggest that myricetin was the most potent inhibitor with high binding affinity for both N- and C-terminals of MGAM. Molecular dynamics revealed that myricetin interacts in its stretched conformation through water-mediated interactions with C-terminal of MGAM and by normal hydrogen bonding with the N-terminal. W1369 of the extended 21 amino acid residue helical loop of C-terminal plays a major role in myricetin binding. Owing to its additional sugar sites, overall binding of small molecules favours C-terminal MGAM.     

Triazine-cored dendritic molecules containing multiple o-carborane clusters

A series of C₃-symmetricaltriazine-cored small dendritic molecules containing three to nine peripheral o-carborane clusters were synthesized through Cu(I)-catalyzedazide–alkyne cycloaddition reactions. The newly synthesized molecules containing multiple o-carborane moieties were characterized using nuclear magnetic resonance and matrix-assisted laser desorption/ionization-time of flight mass spectral analysis. The biological evaluation of these three to nine cage dendrimers was performed using breast cancer cells (Michigan Cancer Foundation 7). All these dendritic compounds showed cytotoxicity toward breast cancer cells, and the toxicity increased as the number of peripheral o-carboranes increased. The 9-cage molecule showed the highest cytotoxicity, and the half maximal inhibitory concentration (IC₅₀) value was found to be 80.67 ng/ml. Its cytotoxicity was significantly higher than the common chemotherapy agent cisplatin. As expected, the boron-richo-carborane-appended molecules showed high thermal stability. The thermal stability increased as the number of peripheral o-carborane moieties increased.     

Polybenzimidazoles tethered with N‐phenyl 1,2,4‐triazole units as polymer electrolytes for fuel cells

Polybenzimidazole (PBI) polymers tethered with N‐phenyl 1,2,4‐triazole (NPT) groups were prepared from a newly synthesized aromatic diacid, 3′‐(4‐phenyl‐4H‐1,2,4‐triazole‐3,5‐diyl) dibenzoic acid (PTDBA). The obtained polymers show superior thermal and chemical stability and good solubility in many aprotic solvents. The inherent viscosities of all polymers were around 1 dL/g. They exhibit high thermal stability with initial decomposition temperature ranging from 515 to 530 °C, high glass transition temperature ranging from 375 to 410 °C, and good mechanical properties with tensile stress in the range of 66–98 MPa and modulus 1897–2600 MPa. XRD analysis indicates that these polymers are amorphous in nature. Physicochemical properties such as water and phosphoric acid‐uptake, oxidative stability, and proton conductivity of membranes of these polymers have also been determined. The proton conductivity ranged from 4.7 × 10^?3 to 1.8 × 10^?2 S cm^?1 at 175 °C in dry conditions. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2289–2303, 2009     

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.     

Automated solid-phase synthesis and photophysical properties of oligodeoxynucleotides labeled at 5'-aminothymidine with Ru(bpy)2(4-m-4'-cam-bpy)2+

A facile and automated procedure for the incorporation of a derivatized Ru(bpy)3(2+) in an oligodeoxynucleotide is reported. The Ru(bpy)3(2+)-thymidine phosphoramidite is synthesized, and then incorporated in DNA using a standard protocol on an automated DNA solid-phase synthesizer. The structure of the DNA duplex is not altered after labeling with Ru(bpy)3(2+). Photophysical studies of the novel ruthenium trisdiimine thymidine complex as well as the corresponding labeled oligodeoxynucleotides demonstrate that the favorable properties associated with the ruthenium complex are retained after covalent attachment to the nucleoside and oligodeoxynucleotide.     

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.     

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations.

Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na(+) or K(+)). The simulations identify multiple nanosecond-scale stable arrangements of the thymidine loops present in the molecules investigated. In these thymidine loops, several structured pockets are identified capable of temporarily coordinating cations. However, no stable association of cations to a loop has been observed. The simulations reveal several paths through the thymidine loop regions that can be followed by the cations when exchanging between the central ion channel in the quadruplex stem and the surrounding solvent. We have carried out 20 independent simulations while the length of simulations reaches a total of 90 ns, rendering this study one of the most extensive MD investigations carried out on nucleic acids so far. The trajectories provide a largely converged characterization of the structural dynamics of these four-stranded G-DNA molecules.