Michal Hocek

C-Nucleosides: Synthetic Strategies and Biological Applications

While natural and synthetic N-nucleosides are vulnerable to enzymatic and acid-catalyzed hydrolysis of the nucleosidic bond, their C-analogues are much more stable. Several C-nucleosides are naturally occurring compounds, e.g., pseudouridine (isolated from the yeast t-RNA) and showdomycin (an antibiotic). Development of novel synthetic methodologies allowed the preparation of a large variety of synthetic analogues, which found numerous applications in medicinal chemistry and chemical biology. Most important biologically active C-nucleosides are the inhibitors of purine nucleosides phosphorylase or IMP dehydrogenase. A number of artificial aryl-C-nucleosides capable of π-stacking are being vigorously investigated as building blocks in chemical biology. In the past few years, several Artificial Expanded Genetic Information Systems (AEGIS)1 have been successfully developed as prime examples of synthetic biology, a newly emerging interdisciplinary area, with the ultimate goal to design systems where high-level behaviors of the living matter are mimicked by artificial chemical systems.2,3

Synthesis and Cytostatic Activity of Substituted 6-Phenylpurine Bases and Nucleosides: Application of the Suzuki−Miyaura Cross-Coupling Reactions of 6-Chloropurine Derivatives with Phenylboronic Acids

The Suzuki-Miyaura reaction of protected 6-chloropurine and 2-amino-6-chloropurine bases and nucleosides with substituted phenylboronic acids led to the corresponding protected 6-(substituted phenyl)purine derivatives 6-9. Their deprotection yielded a series of substituted 6-phenylpurine bases and nucleosides 10-13. Significant cytostatic activity (IC(50) 0.25-20 micromol/L) in CCRF-CEM, HeLa, and L1210 cell lines was found for several 6-(4-X-substituted phenyl)purine ribonucleosides 12 (X = H, F, Cl, and OR), while the 6-phenylpurine and 2-amino-6-phenylpurine bases 10 and 11, as well as 2-amino-6-phenylpurine ribosides 13, were entirely inactive against these cell lines.

Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids

Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.

Aminophenyl‐ and Nitrophenyl‐Labeled Nucleoside Triphosphates: Synthesis, Enzymatic Incorporation, and Electrochemical Detection

DNA biosensors and chips are broadly utilized in the life sciences. Electrochemical detection is a less expensive but comparatively sensitive alternative to common optical methods. Although nucleic acids are electroactive themselves, diverse electroactive tags are used to increase sensitivity and specificity. Besides widely used DNA tags based on metal complexes, quantum dots, or phenothiazine dyes, some simple organic derivatives (such as aromatic amines or nitro compounds) exhibit distinct electrochemical activity, thus making them candidates for nucleic acid labeling. In particular, the nitro group appears promising for sensitive detection because of the high number of electrons (four or six) collected per nitro group reduction. So far, neither amino nor nitro groups have been used as specific electroactive DNA markers. Some modified 2’-deoxyribonucleoside triphosphates (dNTPs) bearing substituents at the nucleobase can be enzymatically incorporated into DNA by polymerases. This approach has been used for the construction of functionalized nucleic acids bearing diverse functional groups. Recently, aqueous-phase cross-coupling reactions of unprotected halogenated nucleoside triphosphates with boronic acids or acetylenes were developed and used in combination with polymerase incorporation for the two-step construction of modified nucleic acids, including ferrocene-labeled oligonucleotides (ONs). Herein, we report the synthesis of nucleoside triphosphates bearing aminophenyl and nitrophenyl groups attached to a nucleobase, their enzymatic incorporation, and the preliminary electrochemical properties of the labeled ONs. We expected that the fully conjugated aromatic system would respond well to the electronic changes arising from incorporation into nucleic acids, and result in changes of the redox potential of the label. The modified dNTPs were prepared by the single-step aqueous-phase cross-coupling reactions of halogenated dNTPs, in analogy to our previously developed procedures. The Suzuki–Miyaura reaction of 7-iodo-7-deaza-2’-deoxyadenosine 5’-triphosphate (7-I-7-deaza-dATP), 5-iodo-2’deoxyuridine 5’-triphosphate (5-I-dUTP), or 5-iodo-2’-deoxycytidine 5’-triphosphate (5-I-dCTP) with either 3-aminophenylor 3-nitrophenylboronic acid (Scheme 1) gave the

Cross-coupling reactions of unprotected halopurine bases, nucleosides, nucleotides and nucleoside triphosphates with 4-boronophenylalanine in water. Synthesis of (purin-8-yl)- and (purin-6-yl)phenylalanines

An expeditious and highly efficient single-step methodology for the introduction of a phenylalanine moiety into position 8 and 6 of the purine scaffold was developed based on aqueous-phase Pd-catalysed Suzuki-Miyaura cross-coupling reactions of unprotected 4-boronophenylalanine with 8-bromo- or 6-chloropurines. The scope of the methodology was demonstrated by syntheses of unprotected (adenin-8-yl)phenylalanine base, nucleosides, nucleotides and nucleoside triphosphates as well as (purin-6-yl)phenylalanine base and nucleosides. All these products were obtained in high yields and in optically pure form.

6-(Het)aryl-7-Deazapurine Ribonucleosides as Novel Potent Cytostatic Agents

A series of novel 7-deazapurine ribonucleosides bearing an alkyl, aryl, or hetaryl group in position 6 and H, F, or Cl atom in position 7 has been prepared either by Pd-catalyzed cross-coupling reactions of the corresponding protected 6-chloro-(7-halogenated-)7-deazapurine ribonucleosides with alkyl- or (het)arylorganometallics followed by deprotection, or by single-step aqueous phase cross-coupling reactions of unprotected 6-chloro-(7-halogenated-)7-deazapurine ribonucleosides with (het)arylboronic acids. Significant cytostatic effect was detected with a substantial proportion of the prepared compounds. The most potent were 7-H or 7-F derivatives of 6-furyl- or 6-thienyl-7-deazapurines displaying cytostatic activity in multiple cancer cell lines with a geometric mean of 50% growth inhibition concentration ranging from 16 to 96 nM, a potency comparable to or better than that of the nucleoside analogue clofarabine. Intracellular phosphorylation to mono- and triphosphates and the inhibition of total RNA synthesis was demonstrated in preliminary study of metabolism and mechanism of action studies.

Synthesis and Photophysical Properties of Biaryl-Substituted Nucleos(t)ides. Polymerase Synthesis of DNA Probes Bearing Solvatochromic and pH-Sensitive Dual Fluorescent and 19F NMR Labels

The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.

Labelling of nucleosides and oligonucleotides by solvatochromic 4-aminophthalimide fluorophore for studying DNA–protein interactions

Solvatochromic fluorescent 4-aminophthalimide (API) and 4-(N,N-dimethylamino)phthalimide (DAPI) were attached covalently to 2′-deoxycytidine or -adenosine via a non-conjugated propargyl linker by Sonogashira cross-coupling reactions of N-propargylphthalimides with halogenated nucleosides. The nucleosides were phosphorylated to triphosphates and enzymatically incorporated into oligonucleotides by DNA polymerases. API-labelled DNA was used for the detection of DNA protein interactions with either the sequence-specific p53 protein or a non-specific single strand binding (SSB) protein. Both proteins changed the polarity around the fluorophore and increased (2–3 fold) the intensity of API fluorescence.

Intramolecular direct C-H arylation approach to fused purines. Synthesis of purino[8,9-f]phenanthridines and 5,6-dihydropurino[8,9-a]isoquinolines.

Intramolecular C-H arylations were employed as a key step in the synthesis of hitherto unknown fused purine systems: 13-substituted purino[8,9-f]phenanthridines and 11-substituted 5,6-dihydropurino[8,9-a]isoquinolines. The purino[8,9-f]phenanthridines were prepared in moderate yields by double C-H arylations of 9-phenylpurines with 1,2-diiodobenzene or, more efficiently, by consecutive Suzuki coupling of 9-(2-bromophenyl)purines with 2-bromophenylboronic acid followed by intramolecular C-H arylation. 5,6-Dihydropurino[8,9-a]isoquinolines were prepared in quantitative yields by intramolecular C-H arylations of 9-(2-chlorophenethyl)purines.

Synthesis and Significant Cytostatic Activity of 7-Hetaryl-7-deazaadenosines

A series of 7-aryl- and 7-hetaryl-7-deazaadenosines was prepared by the cross-coupling reactions of unprotected or protected 7-iodo-7-deazaadenosines with (het)arylboronic acids, stannanes, or zinc halides. Nucleosides bearing 5-membered heterocycles at the position 7 exerted potent in vitro antiproliferative effects against a broad panel of hematological and solid tumor cell lines. Cell cycle analysis indicated profound inhibition of RNA synthesis and induction of apoptosis in treated cells. Intracellular conversion to triphosphates has been detected with active compounds. The triphosphate metabolites showed only a weak inhibitory effect on human RNA polymerase II, suggesting potentially other mechanisms for the inhibition of RNA synthesis and quick onset of apoptosis. Initial in vivo evaluation demonstrated an effect of 7-(2-thienyl)-7-deazaadenine ribonucleoside on the survival rate in syngeneic P388D1 mouse leukemia model.