Efficient microwave-assisted synthesis, antibacterial activity and high fluorescence of 5 benzimidazolyl-2′-deoxyuridines

Microwave-assisted synthesis of base-modified fluorescent 1,4-dihydropyridine nucleosides: photophysical characterization and insights

A synthesis of a small library of fluorescent 1,4-dihydropyridine nucleoside analogues has been successfully carried out under solvent-free conditions via a one-pot three-component Hantzsch condensation reaction. The process involved a Ba(NO3)2 catalyzed solvent-free reaction between 3',5'-di-O-acetyl-5-formyl-2'-deoxyuridine, differently substituted β-keto ester and ammonium acetate under microwave irradiation. This facile methodology yielded the desired products with very high yields (86-96%) under solvent-free reaction conditions in a short reaction time, which was followed by a simple workup. Yields obtained under microwave and conventional heating were compared, with the microwave irradiation condition displaying superior results. The synthesized compounds were characterized by IR, 1H-NMR, 13C-NMR, 1H-1H COSY, 1H-13C HETCOR, 2D NOESY NMR and HRMS analysis. These nucleoside analogues exhibited significant fluorescence, with a prominent emission band around 460 nm (excitation at 235 nm). Photophysical studies revealed strong fluorescence intensity, excellent Stokes shifts (70-162 nm), and high quantum yields (0.022-0.579), outperforming other pyrimidine-based fluorescent nucleosides. Notably, 5-(diethyl 2'',6''-propyl-1'',4''-dihydropyridine-3'',5''-dicarboxylate)-4''-yl-2'-deoxyuridine demonstrated a quantum yield as high as 0.579 in DMSO during solvatochromic studies, highlighting their potential for probing local nucleic acid structure and dynamics. Additionally, we demonstrated the scalability of the synthesis protocol by producing one of the compounds on a gram scale, confirming its practical viability for large-scale production. This study underscores the potential of these fluorescent nucleoside analogues for various biochemical applications.

Recent Advances in the Green Synthesis of Active N-Heterocycles and Their Biological Activities

N-heterocyclic scaffolds represent a privileged architecture in the process of drug design and development. It has widespread occurrence in synthetic and natural products, either those that are established or progressing as potent drug candidates. Additionally, numerous novel N-heterocyclic analogues with remarkable physiological significance and extended pharmaceutical applications are escalating progressively. Hence, the classical synthetic protocols need to be improvised according to modern requirements for efficient and eco-friendly approaches. Numerous methodologies and technologies emerged to address the green and sustainable production of various pharmaceutically and medicinally important N-heterocyclic compounds in last few years. In this context, the current review unveils greener alternatives for direct access to categorically differentiated N-heterocyclic derivatives and its application in the establishment of biologically active potent molecules for drug design. The green and sustainable methods accentuated in this review includes microwave-assisted reactions, solvent-free approaches, heterogeneous catalysis, ultrasound reactions, and biocatalysis.

Synthesis and photophysical properties of 5-(3′′-alkyl/aryl-amino-1′′-azaindolizin-2′′-yl)-2′-deoxyuridines

The Groebke–Blackburn–Bienayame (GBB) reaction has been used for the efficient synthesis of novel fluorescent 5-azaindolizino-2′-deoxyuridines starting from commercially available thymidine following two strategies.

Design, synthesis, and evaluation of new α-aminonitrile-based benzimidazole biomolecules as potent antimicrobial and antitubercular agents

The study explores the one-pot synthesis of novel α-aminonitriles by reacting 4-[(1H-benzimidazol-2-yl)methoxy]benzaldehyde, substituted anilines and sodium cyanide using a catalytic amount of copper dipyridine dichloride (CuPy₂ Cl₂ ) and employing the Strecker reaction under mild conditions. All the synthesized compounds were screened for antimicrobial and antitubercular activity. The promising lead compounds 4d and 4e were identified, with MIC values ranging between 3.9 and 7.8 µg/mL against different bacterial strains. Compounds 4c-e and 4g also showed good antifungal activities against the tested fungal strain. Among those tested, compound 4e exhibited excellent antitubercular activity (MIC 0.05 μg/mL) with a low level of cytotoxicity, suggesting that compound 4e is a promising lead for subsequent investigations in search for new antitubercular agents.

Fluorogenic “photoclick” labelling of DNA using a Cy3 dye

Two 2′-deoxyuridines as new building blocks for automated DNA synthesis carry a small aryltetrazole as a “photoclickable” group at their 5-positions.

Fluorescent Wittig reagent as a novel ratiometric probe for the quantification of 5-formyluracil and its application in cell imaging

For the first time a Wittig reagent was introduced into the design of a fluorescent probe for the quantification of 5-formyluracil.

Synthetic Approaches for the Preparation of Phosphoramidate Prodrugs of 2'-Deoxypseudoisocytidine

A synthetic procedure for the preparation of phosphoramidate prodrugs of C-nucleosides is reported. Different phosphorochloridates were reacted with 3'-O-protected N-acetyl-2'-deoxypseudoisocytidine or 3'-O-protected 2'-deoxypseudoisocytidine, followed by acidic hydrolysis of the protecting group. In the presence of the N-acetyl moiety, the enolisable keto group of the nucleobase was able to react (like the 5'-OH) with the phosphorochloridates to give bisphosphorylated derivatives. Epimerisation (β to α) occurred if the amino group of the nucleobase was unprotected. These side reactions demonstrate the peculiar behaviour of C-nucleosides compared to their nucleoside analogues. It was demonstrated that the first enzymatic activation step for this new class of prodrugs can be mediated by carboxypeptidase and that it follows the same pathway and rate reported for ProTides of more conventional nucleoside analogues. These new phosphoramidate derivatives deserve further investigation for their therapeutic potential as anti-cancer agents.

Ultrasonic-assisted synthesis of 1,4-disubstituted 1,2,3-triazoles via various terminal acetylenes and azide and their quorum sensing inhibition

An efficient synthesis of 1,4-disubstituted 1,2,3-triazole derivatives was studied. 1,4-Disubstituted 1,2,3-triazoles containing isoxazole and thymidine structures were synthesized in 84-96% yields starting from various terminal isoxazole ether alkynes and β-thymidine azide derivatives via a 1,3-dispolar cycloaddition using copper acetate, sodium ascorbate as the catalyst under ultrasonic assisted condition. All the target compounds were characterized by HRMS, FT-IR, ¹H NMR and ¹³C NMR spectroscopy. Furthermore, the quorum sensing inhibitory activities of synthesized compounds were evaluated with Chromobacterium violaceum (C. Violaceum CV026) based on their inhibition of violacein production, with compound C₁₀-HSL as a positive control. The compounds 8a, 8c and 8f exhibited considerable levels of inhibitory activity against violacein production, and IC₅₀ values were 217±19, 223±20 and 42.8±4.5μM, respectively, which highlighted the potential of these compounds as lead structures for further research towards the development of novel QS inhibitors.

MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents

DNA accepts small substituents at the 5-position of 2′-deoxyuridine residues within mercury ion mediated dU–Hg^II–dU base pairs, while triple bonds interact with mercury ions and those with space demanding aromatic side chains block metal ion mediated base pair formation.

Therapeutic evolution of benzimidazole derivatives in the last quinquennial period

Benzimidazole, a fused heterocycle bearing benzene and imidazole has gained considerable attention in the field of contemporary medicinal chemistry. The moiety is of substantial importance because of its wide array of pharmacological activities. This nitrogen containing heterocycle is a part of a number of therapeutically used agents. Moreover, a number of patents concerning this moiety in the last few years further highlight its worth. The present review covers the recent work published by scientists across the globe during last five years.

Fluorogenic Labeling of 5-Formylpyrimidine Nucleotides in DNA and RNA

5-Formylcytosine (5fC) and 5-formyluracil (5fU) are natural nucleobase modifications that are generated by oxidative modification of 5-methylcytosine and thymine (or 5-methyluracil). Herein, we describe chemoselective labeling of 5-formylpyrimidine nucleotides in DNA and RNA by fluorogenic aldol-type condensation reactions with 2,3,3-trimethylindole derivatives. Mild and specific reaction conditions were developed for 5fU and 5fC to produce hemicyanine-like chromophores with distinct photophysical properties. Residue-specific detection was established by fluorescence readout as well as primer-extension assays. The reactions were optimized on DNA oligonucleotides and were equally suitable for the modification of 5fU- and 5fC-modified RNA. This direct labeling approach of 5-formylpyrimidines is expected to help in elucidating the occurrence, enzymatic transformations, and functional roles of these epigenetic/epitranscriptomic nucleobase modifications in DNA and RNA.

Novel 5-arylcarbamoyl-2-methylisoxazolidin-3-yl-3-phosphonates as nucleotide analogues

A series of 5-substituted 3-phosphonylated isoxazolidines have been obtained via cycloaddition of N-methyl-C-(diethoxyphosphoryl)nitrone with N-heteroaromatic acrylamides. Good trans/cis diastereoselectivities (d.e. 58-76%) of isomeric (3-diethoxyphosphoryl)isoxazolidines were observed. cis- and trans-Isoxazolidine phosphonates were evaluated for their antiviral activity against a broad range of DNA and RNA viruses but were found inactive. Their cytostatic activity toward L1210, CEM, and HeLa cells was also established, and compounds cis-12r and trans-11r having a 2,2-difluorobenzo[d][1,3]dioxole moiety slightly inhibited proliferation of HeLa cells at IC50 values of 186 and 179 μM, respectively.

Palladium-catalyzed direct arylation of 5-halouracils and 5-halouracil nucleosides with arenes and heteroarenes promoted by TBAF

The 1-N-benzyl-5-iodo(or bromo)uracil undergoes Pd-catalyzed [Pd₂(dba)₃] direct arylation with benzene and other simple arenes in the presence of TBAF in DMF without the necessity of adding any ligands or additives to give 5-arylated uracil analogues. The TBAF-promoted coupling also occurs efficiently with electron rich heteroarenes at 100 °C (1 h) even with only small excess of heteroarenes. The protocol avoids usage of the arylboronic acid or stannane precursors for the synthesis of 5-(2-furyl, or 2-thienyl, or 2-pyrrolyl)uracil nucleosides, which are used as important RNA and DNA fluorescent probes. The fact that 1-N-benzyl-3-N-methyl-5-iodouracil did not undergo the TBAF-promoted couplings with arenes or heteroarenes suggests that the C4-alkoxide (enol form of uracil) facilitates coupling by participation in the intramolecular processes of hydrogen abstraction from arenes. TBAF-promoted arylation was extended into the other enolizable heterocyclic systems such as 3-bromo-2-pyridone. The π-excessive heteroarenes also coupled with 5-halouracils in the presence of Pd(OAc)₂/Cs₂CO₃/PivOH combination in DMF (100 °C, 2 h) to yield 5-arylated uracils.

Synthesis of novel 2-(substituted amino)alkylthiopyrimidin-4(3H)-ones as potential antimicrobial agents

5-Alkyl-6-(substituted benzyl)-2-thiouracils 3a,c were reacted with (2-chloroethyl) diethylamine hydrochloride to afford the corresponding 2-(2-diethylamino)ethylthiopyrimidin- 4(3H)-ones 4a,b. Reaction of 3a-c with N-(2-chloroethyl)pyrrolidine hydrochloride and/or N-(2-chloroethyl)piperidine hydrochloride gave the corresponding 2-[2-(pyrrolidin-1-yl)ethyl]-thiopyrimidin-4(3H)-ones 5a-c and 2-[2-(piperidin-1-yl)ethyl]thiopyrimidin-4(3H)-ones 6a,b, respectively. Treatment of 3a-d with N-(2-chloroethyl)morpholine hydrochloride under the same reaction conditions formed the corresponding 2-[2-(morpholin-4-yl)ethyl]thiopyrimidines 6c-f. On the other hand, 3a,b were reacted with N-(2-bromoethyl)phthalimide and/or N-(3-bromopropyl)phthalimide to furnish the corresponding 2-[2-(N-phthalimido)ethyl]-pyrimidines 7a,b and 2-[3-(N-phthalimido)-propyl]pyrimidines 7c,d, respectively. Compounds 3a-d, 4a,b, 5a-c, 6a-f and 7a-d were screened against Gram-positive bacteria (Staphylococcus aureus ATCC 29213, Bacillus subtilis NRRL 4219 and Bacillus cereus), yeast-like pathogenic fungus (Candida albicans ATCC 10231) and a fungus (Aspergillusniger NRRL 599). The best antibacterial activity was displayed by compounds 3a, 3b, 4a, 5a, 5b, 6d, 6f, 7b and 7d, whereas compounds 4b, 5b, 5c, 6a, 6b and 6f exhibited the best antifungal activity.

Synthesis, single crystal and antitumor activities of benzimidazole-quinazoline hybrids

A series of novel regioisomeric hybrids of quinazoline/benzimidazole viz. (3-allyl-2-methyl-3H-benzimidazol-5-yl)-(2-substituted-quinazolin-4-yl)-amine and (1-allyl-2-methyl-1H-benzimidazol-5-yl)-(2-substituted-quinazolin-4-yl)-amine of biological interest were synthesized. All the synthesized compounds were well characterized by (1)H and (13)C NMR as well as mass spectroscopy. The newly synthesized compounds were screened for in vitro antitumor activities against 60 tumor cell lines panel assay. A significant inhibition for cancer cells were observed with compound 9 and also more active against known drug 5-fluorouracil (5-FU) in some tumor cell lines. Compound 9 displayed appreciable anticancer activity against leukemia, colon, melanoma, renal and breast cancer cell lines.

Postsynthetic on column RNA labeling via Stille coupling

Stille Coupling is a versatile C-C bond forming reaction with high functional group tolerance under mild conditions. Our on column synthesis concept for RNA modification is based on the incorporation of iodo substituted nucleotide precursors to RNA during automated standard solid phase synthesis via TBDMS-, TC-, and ACE- protecting group strategies. Subsequently, the RNA, still bound on solid support, is ready for orthogonal postsynthetic functionalization via Stille cross-couplings utilizing the advantages of solid phase synthesis. Several monomer test reactions were employed with 2-iodo adenosine and 5-iodo uridine and organostannanes as coupling partners under different conditions, changing the catalyst/ligand system, temperature, and reaction time as well as conventional heating and microwave irradiation. Finally, Stille cross-couplings under optimized conditions were transferred to fully protected 5-mer and 12-mer RNA oligonucleotides on-column. Deprotection and cleavage from solid support resulted in site-specifically labeled oligonucleotides. Derivatizations via Stille cross-couplings were performed initially with vinyltributylstannane as well as later with 2-furanyl-, 2-thiophene-, and benzothiophene-2-tributylstannanes yielding fluorescently functionalized RNA.