Imidazo[1,2-a]-s-triazine nucleosides. Synthesis and antiviral activity of the N-bridgehead guanine, guanosine, and guanosine monophosphate analogues of imidazo[1,2-a]-s-triazine

Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-Aza-7-Deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet

The guanine derivative, 5-aza-7-deazaguanine (^5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art Extended Multi-State Complete Active Space Second-Order Perturbation Theory. It is demonstrated that excitation to the lowest energy ¹ ππ* state of ^5N7C G results in complex dynamics leading to ca. 10 to 30-fold slower relaxation (depending on solvent) compared to guanine. A significant conformational change occurs at the S₁ minimum, resulting in a 10-fold greater fluorescence quantum yield compared to guanine. The fluorescence quantum yield and S₁ decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S₁ minimum and the S₁ /S₀ conical intersection going from water to propanol. The longer lifetimes might make ^5N7C G more photochemical active to adjacent nucleobases than guanine or other nucleobases within DNA.

Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme

The Varkud satellite ribozyme catalyses site-specific RNA cleavage and ligation, and serves as an important model system to understand RNA catalysis. Here, we combine stereospecific phosphorothioate substitution, precision nucleobase mutation and linear free-energy relationship measurements with molecular dynamics, molecular solvation theory and ab initio quantum mechanical/molecular mechanical free-energy simulations to gain insight into the catalysis. Through this confluence of theory and experiment, we unify the existing body of structural and functional data to unveil the catalytic mechanism in unprecedented detail, including the degree of proton transfer in the transition state. Further, we provide evidence for a critical Mg²⁺ in the active site that interacts with the scissile phosphate and anchors the general base guanine in position for nucleophile activation. This novel role for Mg²⁺ adds to the diversity of known catalytic RNA strategies and unifies functional features observed in the Varkud satellite, hairpin and hammerhead ribozyme classes.

Anomeric 5-Aza-7-deaza-2'-deoxyguanosines in Silver-Ion-Mediated Homo and Hybrid Base Pairs: Impact of Mismatch Structure, Helical Environment, and Nucleobase Substituents on DNA Stability

Nucleoside configuration (α-d vs. β-d), nucleobase substituents, and the helical DNA environment of silver-mediated 5-aza-7-deazaguanine-cytosine base pairs have a strong impact on DNA stability. This has been demonstrated by investigations on oligonucleotide duplexes with silver-mediated base pairs of α-d and β-d anomeric 5-aza-7-deaza-2'-deoxyguanosines and anomeric 2'-deoxycytidines incorporated in 12-mer duplexes. To this end, a new synthetic protocol has been developed to access the pure anomers of 5-aza-7-deaza-2'-deoxyguanosine by glycosylation of either the protected nucleobase or its salt followed by separation of the glycosylation products by crystallization and chromatography. Thermal stability measurements were performed on duplexes with α-d/α-d and β-d/β-d homo base pairs or α-d/β-d and β-d/α-d hybrid pairs within two sequence environments, positions 6 or 7, of oligonucleotide duplexes. The respective T_m stability increases observed after silver ion addition differ significantly. Homo base pairs with β-d/β-d or α-d/α-d nucleoside combinations are more stable than α-d/β-d hybrid base pairs. The positional switch of silver-ion-mediated base pairs has a significant impact on stability. Nucleobase substituents introduced at the 5-position of the dC site of silver-mediated base pairs affect base pair stability to a minor extent. Our investigation might lead to applications in the construction of bioinspired nanodevices, in DNA diagnostics, or metal-DNA hybrid materials.

The surprising pairing of 2-aminoimidazo[1,2-a][1,3,5]triazin-4-one, a component of an expanded DNA alphabet

Synthetic biologists demonstrate their command over natural biology by reproducing the behaviors of natural living systems on synthetic biomolecular platforms. For nucleic acids, this is being done stepwise, first by adding replicable nucleotides to DNA, and then removing its standard nucleotides. This challenge has been met in vitro with `six-letter' DNA and RNA, where the Watson-Crick pairing `concept' is recruited to increase the number of independently replicable nucleotides from four to six. The two nucleobases most successfully added so far are Z and P, which present a donor-donor-acceptor and an acceptor-acceptor-donor pattern, respectively. This pair of nucleobases are part of an `artificially expanded genetic information system' (AEGIS). The Z nucleobase has been already crystallized, characterized, and published in this journal [Matsuura et al. (2016). Acta Cryst. C72, 952-959]. More recently, variants of Taq polymerase have been crystallized with the pair P:Z trapped in the active site. Here we report the crystal structure of the nucleobase 2-aminoimidazo[1,2-a][1,3,5]triazin-4-one (trivially named P) as the monohydrate, C₅H₅N₅O·H₂O. The nucleobase P was crystallized from water and characterized by X-ray diffraction. Interestingly, the crystal structure shows two tautomers of P packed in a Watson-Crick fashion that cocrystallized in a 1:1 ratio.

A multicomponent reaction of 2-aminoimidazoles: microwave-assisted synthesis of novel 5-aza-7-deaza-adenines

An efficient and highly selective multicomponent synthesis of 4-aminoimidazo[1,2-a]triazines, which are 5-aza-7-deaza-isosteres of adenine, was developed.

Ribonucleosides for an artificially expanded genetic information system

Rearranging hydrogen bonding groups adds nucleobases to an artificially expanded genetic information system (AEGIS), pairing orthogonally to standard nucleotides. We report here a large-scale synthesis of the AEGIS nucleotide carrying 2-amino-3-nitropyridin-6-one (trivially Z) via Heck coupling and a hydroboration/oxidation sequence. RiboZ is more stable against epimerization than its 2′-deoxyribo analogue. Further, T7 RNA polymerase incorporates ZTP opposite its Watson–Crick complement, imidazo[1,2-a]-1,3,5-triazin-4(8H)one (trivially P), laying grounds for using this “second-generation” AEGIS Z:P pair to add amino acids encoded by mRNA.

Novel anti-HIV-1 NNRTIs based on a pyrazolo[4,3-d]isoxazole backbone scaffold: design, synthesis and insights into the molecular basis of action

Design and synthesis of novel anti-HIV-1 NNRTIs based on a pyrazolo[4,3-d]isoxazole backbone scaffold.

Oligonucleotide probes containing pyrimidine analogs reveal diminished hydrogen bonding capacity of the DNA adduct O⁶-methyl-G in DNA duplexes

Oligonucleotide hybridization probes containing nucleoside analogs offer a potential strategy for binding specific DNA sequences that bear pro-mutagenic O(6)-G alkylation adducts. To optimize O(6)-Me-G-targeting probes, an understanding of how base pairs with O(6)-Me-G are stabilized is needed. In this study, we compared the ability of O(6)-Me-G and G to hydrogen bond with three pyrimidine-like nucleobases (Z, 4-thio-U, and 3-deaza-C) bearing varied hydrogen bond donor and acceptor groups. We found that duplexes containing the pyrimidine analog nucleoside:G pairs were more thermodynamically stable than those containing pyrimidine analog nucleoside:O(6)-alkyl-G pairs. Thus, hydrogen bonding alone was not sufficient to impart selectivity to probes that target O(6)-G alkylation adducts in DNA.

Synthesis of 7-aza-5-deazapurine analogues via copper(I)-catalyzed hydroamination of alkynes and 1-iodoalkynes

A new method for the synthesis of dihydroimidazo[1,2-a][1,3,5]triazin-4(6H)-ones via copper(I)-catalyzed hydroamination was developed. In addition, for the first time, iodoalkynes were shown to participate in the copper(I)-catalyzed intramolecular hydroamination reaction with exclusive formation of E-isomers.

Synthesis and cytotoxic activity of imidazo[1,2-a]-1,3,5-triazine analogues of 6-mercaptopurine

A series of 2-substituted imidazo[1,2-a]-1,3,5-triazines with various aliphatic and aromatic amines has been prepared and characterized by IR,1H-NMR, and elemental analysis. The initial in-vitro cytotoxicity studies with five human cancer cell lines showed that all but one of the compounds are without cytotoxic activity. The one active compound, 2-(indolin-1-yl)-7,8-dihydroimidazo[1,2-a]-1,3,5-triazine-4(6H)-thione 12, was tested on 12 human cancer cell lines. Of these, two lines, RT-4 and MCF-7, were the most sensitive to the compound, with IC50 values of 6.98 microM and 8.43 microM, respectively. When compared with the reference anticancer drug 6-mercaptopurine, only the RT-4 urinary bladder and KYSE-70 oesophagus cancer cell lines were more sensitive to the new compound. The antimetabolite thioguanine was more cytotoxic than 12 for all common cell lines tested.

Biocidal efficacy, biofilm-controlling function, and controlled release effect of chloromelamine-based bioresponsive fibrous materials

In this study, 2-amino-4-chloro-6-hydroxy-s-triazine (ACHT) was synthesized through controlled hydrolysis of 2-amino-4,6-dichloro-s-triazine (ADCT). A simple pad-dry-cure approach was employed to immobilize ACHT onto cellulosic fibrous materials. After treatment with diluted chlorine bleach, the covalently bound ACHT moieties were transformed into chloromelamines. The structures of the samples were fully characterized with NMR, UV/VIS, DSC, TG, iodometric titration and elemental analyses. The chloromelamine-based fibrous materials provided potent, durable, and rechargeable biocidal functions against bacteria (including multi-drug resistant species), yeasts, viruses, and bacterial spores. SEM studies demonstrated that the new fibrous materials could effectively prevent the formation of biofilms, and controlled release investigations in vitro suggested that the biocidal activities were bioresponsive. Biocidal mechanisms of the chloromelamine-based fibrous materials were further discussed.

Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern

To support efforts to develop a ‘synthetic biology’ based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1′-β-D-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson–Crick complement, the purine analog 2-amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where ‘py’ indicates a pyrimidine analog and ‘pu’ indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA.

Synthesis and biological evaluation of lisofylline (LSF) analogs as a potential treatment for Type 1 diabetes

Lisofylline (LSF, 1-(5-R-hydroxyhexyl)-3,7-dimethylxanthine) is an anti-inflammatory agent that protects beta-cells from Th1 cytokine-induced dysfunction and reduces the onset of Type 1 diabetes in non-obese diabetic (NOD) mice. Due to its low potency, poor oral bioavailability, and short half-life, the widespread clinical utility of LSF may be limited. Our goal has been to develop new agents based on the LSF structural motif that resolve the potency and pharmacokinetic liabilities of LSF. In this study, we have generated a focused library of LSF analogs that maintain the side chain (5-R-hydroxyhexyl) constant, while substituting a variety of nitrogen-containing heterocyclic substructures for the xanthine moiety of LSF. This library includes the xanthine-like (5-aza-7-deazaxanthine), as well as non-xanthine-like skeletons. The LSF analogs were evaluated in a pancreatic beta-cell line for the effects on apoptosis protection and insulin release. The metabolic stability of selected compounds was also tested.

Synthesis of 5-aza-7-deazaguanine nucleoside derivatives as potential anti-flavivirus agents

Coupling suitable sugars (D- or L-ribofuranose, 2' or 3-deoxysugar, branched sugars) with 2-aminoimidazo[1,2-a]-s-triazin-4-one was carried out using the different reaction conditions: 1) condensation in the presence of sodium hydride; or 2) condensation using Vorbrüggen's methods. The 5-aza- 7-deazaguanine nucleoside analogues obtained were evaluated in cell culture experiments for the inhibition of the replication of a number of RNA viruses, including BVDV, YFV, and WNV.

Broad-spectrum inhibitor of viruses in the Flaviviridae family

The viruses in the Flaviviridae family have been associated with human and animal diseases. In this report, we demonstrate that compound 2-amino-8-(beta-D-ribofuranosyl) imidazo [1,2-a]-s-triazine-4-one (ZX-2401) was capable of inhibiting the production in culture of at least five members of the Flaviviridae family with minimal cytotoxicity. This compound inhibited yellow fever virus, dengue virus, bovine viral diarrhea virus, banzi virus and West Nile virus with EC50 of 10, 10, 5, 5 and 3 microg/ml, respectively, and the CC50 in these experiments were greater than 1000 microg/ml. The activity of ZX-2401 is comparable to or better than the control drugs in these studies and was not affected by MOI variation. In addition, ZX-2401 inhibited HCV replication in a dose response fashion in the replicon assay system. Furthermore, ZX-2401 exhibited a synergistic antiviral activity in combination with IFN in tissue culture. The data described herein suggest that ZX-2401 is a broad-spectrum inhibitor of the RNA viruses, which has merit for development of treatments for the emerging infections caused by the viruses in the Flaviviridae family.

Mannich-Type C-Nucleosidations in the 5,8-Diaza-7,9-dicarba-purine Family1

[structure: see text] C-Nucleosidation with cyclic iminium salts occurring under mild reaction conditions and affording C-nucleosides that are isosteric with N-nucleosides of natural purines is shown to be a consistent property of the entire family of 2,6-(oxo or amino)-disubstituted 5,8-diaza-7,9-dicarba-purines.

Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern

6-Amino-3-(2'-deoxy-beta-D-ribofuranosyl)-5-nitro-1H-pyridin-2-one (4), a C-glycoside exhibiting the nonstandard pyDDA hydrogen-bonding pattern, was synthesized via Heck coupling. The nitro group greatly enhances the stability of the nucleoside toward acid-catalyzed epimerization without leading to significant deprotonation of the heterocycle at physiological pH. These results make nucleoside 4 a promising candidate for an expanded genetic alphabet.

Analogs of guanine nucleoside triphosphates for sequencing applications

We have synthesized more than 30 different deoxyribonucleosides and triphosphates with modifications either in the base or the phosphate moiety as analogs of 2'-dGTP for DNA sequencing applications. All the modified nucleoside triphosphates were tested as substrates for DNA polymerases, including Sequenase T7 DNA polymerase or Thermo Sequenase DNA polymerase. Two of the analogs, 7-ethyl-7-deaza-dGTP and 7-hydroxymethyl-7-deaza-dGTP meet our requirements as better sequencing reagents.

Conformation and structure of 2-amino-8-(beta-D-ribofuranosyl)imidazo [1,2-a]-s-triazin-4-one(5-aza-7-deaza guanosine), a potent antiviral nucleoside

The crystal and molecular structure of one imidazo[1,2-a]-s-triazine nucleoside and its antiviral activity are described. The crystal structure of 2-amino-8-(beta-D-ribofuranosyl)imidazo[1,2-a]-s-triazin-4-one monohydroate (C10H13N5O5.H2O) was solved by X-ray counter data. The compound crystallizes in the monoclinic space group P21 with cell dimensions a = 7.353 (1), b = 6.465 (1), c = 13.701 (1) A, B = 104.64 (1) degrees. The structure was solved by direct methods and refined by full matrix least-squares technique to a final value of the conventional R-factor of 0.049 using 1998 observed intensities. The orientation of the base relative to the sugar ring defined in terms of rotating about the C(1')-N(8) glycosyl bond is anti (47.8 degrees). The ribose moiety exhibits C(2')-endo, E conformation. The conformation around C(4')-C(5') is gauche-. Molecular packing is dominated by hydrogen bonds. Base stacking occurs long the b axis. 5-Aza-7-deazaguanosine has shown a marked antiviral activity in vitro against herpes simplex virus despite the fact that N(3) is effective as the hydrogen acceptor only.