The chemistry and biochemistry of C-nucleosides and C-arylglycosides

Polycarcin V induces DNA-damage response and enables the profiling of DNA-binding proteins

To maintain genomic integrity and avoid diseases, the DNA-damage response (DDR) not only detects and repairs DNA lesions, but also contributes to the resistance to DNA-damaging chemotherapeutics. Targeting the DDR plays a significant role in drug discovery using the principle of synthetic lethality. The incomplete current knowledge of the DDR encouraged us to develop new strategies to identify and study its components and pathways. Polycarcin V, belonging to the C-aryl glycoside natural products, is a light-activatable DNA-intercalating agent that causes DNA damage by forming a covalent [2+2] cycloadduct with thymine residue under 365-450 nm of light irradiation in a DNA-sequence-independent manner. Taking advantage of the light-activatable feature and temporal control of DDR, we designed and synthesized polycarcin V-based bifunctional chemical probes, including one that cross-links DNA to DNA-binding protein to explore the DDR induced by polycarcin V and uncover novel DNA-protein interactions. Utilizing this chemical probe and activity-based protein profiling-stable isotope labeling with amino acids in cell culture, we identified 311 DNA-binding protein candidates, including known DDR factors and additional proteins that may be of interest in discovering new biology. We validated our approach by showing that our probe could specifically cross-link proteins involved in nucleotide excision repair (NER) that repair bulky DNA adducts. Our studies showed that the [2+2] cycloadduct formed by polycarcin V could indeed be repaired by NER in vivo. As a DNA-damaging agent, polycarcin V or its drug-like derivative plus blue light showed promising properties for psoriasis treatment, suggesting that it may itself hold promise for clinic applications.

Natural Products & Bioactivity Inspired Synthetic Pursuits Interfacing with Carbohydrates: Ongoing Journey with C-Glycosides

Natural products, remains the most important source for the discovery of new drugs for the treatment of human diseases. This has inspired the synthetic community to design and develop mimics of natural products either to answer important questions in biology or to explore their therapeutic potentials. Glycosides present themselves abundantly in nature, right from the cell surface receptors to natural products of any origin. The O-Glycosides are hydrolytically less stable compared to C-glycosides and this feature has presented a great opportunity for drug discovery. The discovery of Dapagliflozin, an SGLT inhibitor and C-glucoside, for the treatment of diabetes is one such example. Aryl acyl-anion chemistry has been explored for the synthesis of 2-deoxy-C-aryl furanoside/pyranoside/septanosides. Besides success, the studies have provided valuable insight into the natural propensities of the architectural framework for the cascade to furan derivatives. The aryl acyl-anion chemistry has also enabled the synthesis of biologically active diaryl heptanoids. Inspired from sucesss of Dapagliflozin, new analogues have been synthesized with pyridine and isocoumarin heterocycle as the proximal ring. C-glucosides of isoliquiritigenin have been synthesized for the first time and evaluated as an efficient aldose reductase inhibitor. The synthesis and evaluation of acyl-C-β-D-glucosides and benzyl-C-β-D-glucoside as glucose-uptake promoters has revealed promise in small molecules. The concept of building blocks has been used to obtain natural oxylipins, D-xylo and L-xylo-configured alkane tetrols and novel lipophilic ketones with erythro/threo configured trihydroxy polar head-group as possible anti-mycobacterial agents.

Synthesis of indole derivatives as prevalent moieties present in selected alkaloids

Indoles are a significant heterocyclic system in natural products and drugs. They are important types of molecules and natural products and play a main role in cell biology. The application of indole derivatives as biologically active compounds for the treatment of cancer cells, microbes, and different types of disorders in the human body has attracted increasing attention in recent years. Indoles, both natural and synthetic, show various biologically vital properties. Owing to the importance of this significant ring system, the investigation of novel methods of synthesis have attracted the attention of the chemical community. In this review, we aim to highlight the construction of indoles as a moiety in selected alkaloids.

Preparation and characterization of Pd supported on 5-carboxyoxindole functionalized cell@Fe3O4 nanoparticles as a novel magnetic catalyst for the Heck reaction

Pd supported on 5-carboxyoxindole functionalized cell@Fe₃O₄ nanoparticles (Pd@CAI@cell@Fe₃O₄), a new magnetic nanocatalyst, was prepared and characterized using inductively coupled plasma atomic emission spectroscopy, Fourier-transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, transmission electron microscopy, thermogravimetric analysis, and energy-dispersive X-ray spectroscopy techniques. The synthesized nanocatalyst (Pd@CAI@cell@Fe₃O₄) was employed for Heck-type arylation of different substituted maleimides with iodoarenes in good to excellent yields. This green catalyst was easily recovered and reused several times with no substantial loss of activity, providing a clean and efficient synthetic procedure with excellent yield and reduced time.

Reverse C-glycosidase reaction provides C-nucleotide building blocks of xenobiotic nucleic acids

C-Analogues of the canonical N-nucleosides have considerable importance in medicinal chemistry and are promising building blocks of xenobiotic nucleic acids (XNA) in synthetic biology. Although well established for synthesis of N-nucleosides, biocatalytic methods are lacking in C-nucleoside synthetic chemistry. Here, we identify pseudouridine monophosphate C-glycosidase for selective 5-β-C-glycosylation of uracil and derivatives thereof from pentose 5-phosphate (D-ribose, 2-deoxy-D-ribose, D-arabinose, D-xylose) substrates. Substrate requirements of the enzymatic reaction are consistent with a Mannich-like addition between the pyrimidine nucleobase and the iminium intermediate of enzyme (Lys166) and open-chain pentose 5-phosphate. β-Elimination of the lysine and stereoselective ring closure give the product. We demonstrate phosphorylation-glycosylation cascade reactions for efficient, one-pot synthesis of C-nucleoside phosphates (yield: 33 - 94%) from unprotected sugar and nucleobase. We show incorporation of the enzymatically synthesized C-nucleotide triphosphates into nucleic acids by RNA polymerase. Collectively, these findings implement biocatalytic methodology for C-nucleotide synthesis which can facilitate XNA engineering for synthetic biology applications.

Divergent synthesis of 1,3,5-tri and 1,3-disubstituted pyrazoles under transition metal-free conditions

Pyrazole cores are common structural motifs existing in various agrochemicals and pharmaceuticals. Herein, a transition metal-free, three-component reaction of arylaldehydes, ethyl acrylate and N-tosylhydrazones is described, which leads to the formation of 1,3,5-trisubstituted and 1,3-disubstituted pyrazoles divergently under slightly different conditions.

Total Synthesis of Alvaradoins E and F, Uveoside, and 10-epi-Uveoside

Concise total syntheses of the anthracenone C-glycosides alvaradoins E and F, uveoside, and 10-epi-uveoside (1-4) have been accomplished from chrysophanic acid 8 and bromosugar 9. Key steps in the syntheses include the DBU-induced coupling of 8 and 9 to produce β-C-glycoside 11, and a Pb(OAc)₄-mediated Kochi reaction to introduce the C-1' oxygen atom of the natural products. Isothermal titration calorimetry and fluorescence binding studies reveal that compounds 1 and 2 have good affinity for the plasma protein HSA.

Synthesis of Non-Classical Arylated C-Saccharides through Nickel/Photoredox Dual Catalysis

The development of synthetic tools to introduce saccharide derivatives into functionally complex molecules is of great interest, particularly in the field of drug discovery. Herein, we report a new route toward highly functionalized, arylated saccharides, which involves nickel-catalyzed cross-coupling of photoredox-generated saccharyl radicals with a range of aryl- and heteroaryl bromides, triggered by an organic photocatalyst. In contrast to existing methods, the mild reaction conditions achieve arylation of saccharide motifs while leaving the anomeric carbon available, thus providing access to a class of arylated glycosides that has been underexplored until now. To demonstrate the potential of this strategy in late-stage functionalization, a variety of structurally complex molecules incorporating saccharide moieties were synthesized.

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

C-nucleosides have intrigued biologists and medicinal chemists since their discovery in 1950's. In that regard, C-nucleosides and their synthetic analogues have resulted in promising leads in drug design. Concurrently, advances in chemical syntheses have contributed to structural diversity and drug discovery efforts. Convergent and modular approaches to synthesis have garnered much attention in this regard. Among them nucleophilic substitution at C1' has seen wide applications providing flexibility in synthesis, good yields, the ability to maneuver stereochemistry as well as to incorporate structural modifications. In this review, we describe recent reports on the modular synthesis of C-nucleosides with a focus on D-ribonolactone and sugar modifications that have resulted in potent lead molecules.

A Representative Synthetic Route for C5 Angucycline Glycosides: Studies Directed toward the Total Synthesis of Mayamycin

This study discloses an efficient synthetic route for the regiospecific construction of a C5 glycoside angucycline representative of mayamycin. The key steps are intramolecular aldol condensation and Hauser annulation, and the key precursor for the aldol reaction is accessible through utilization of α-lithiation of a vinyl ether.

The evolution of comprehensive strategies for furanoid glycal synthesis and their applications

Cyclic enol ether frameworks, especially stereochemically pure furanoid and pyranoid glycals are well known highly functionalized chiral building blocks.

Regioselective synthesis of naphthoquinone/naphthoquinol-carbohydrate hybrids by [4 + 2] anionic annulations and studies on their cytotoxicity

An efficient and regioselective synthetic route to naphthoquinone/naphthoquinol-carbohydrate hybrids has been developed. It is based upon anionic annulation of 3-nucleofugalphthalides with an acrylate appended sugar moiety. In each of the annulations studied, the arene-carbohydrate hybrids were obtained in good to excellent yields. The in vitro cytotoxic activity of the synthetic naphthoquinone/naphthonol-carbohydrate hybrids were evaluated against the human cervical cancer cell line (HeLa), and a few of them were found to exhibit potent anticancer activity against the cell line.

Total synthesis of mangiferin, homomangiferin, and neomangiferin

Efficient synthesis of natural C-glycosyl xanthone mangiferin, homomangiferin and neomangiferin based on their biosynthetic pathway.

Total synthesis of the antitumor natural product polycarcin V and evaluation of its DNA binding profile

The convergent total synthesis of polycarcin V, a gilvocarcin-type natural product that shows significant cytotoxicity with selectivity for nonsmall-cell lung cancer, breast cancer, and melanoma cells, has been achieved in 13 steps from 7, 8, and 22; the sequence features a stereoselective α-C-glycosylation reaction for the union of protected carbohydrate 7 and naphthol 8. The association constant for the binding of polycarcin V to duplex DNA is similar to that previously reported for gilvocarcin V.

Synthesis of 3,3'-di-O-methyl ardimerin and exploration of its DNA binding properties

The 3,3′-di-O-methyl derivative (15) of the bis-C-aryl glycoside natural product ardimerin (1) has been synthesized in 11 steps from 2,3,4,6-tetrabenzylglucose (2) and 1,2,3-trimethoxybenzene (3). Key steps in the synthesis involve a Lewis acid mediated Friedel–Crafts type glycosylation and a Yamaguchi lactonization under Yonemitsu conditions. 3,3′-Di-O-methyl ardimerin aggregates in aqueous solutions at concentrations greater than 1 μM, and both UV and fluorescence binding studies indicate that 15 has a low affinity for duplex DNA.

Synthesis of 2-deoxy-C-glycosides via Lewis acid-mediated rearrangement of 2,3-anhydro-1-thiopyranosides

The regio- and stereo-selective construction of 2-deoxy-C-glycosides via Lewis acid-mediated rearrangement of 2,3-anhydro-1-thiopyranosides is realized.

Design, synthesis, and biological evaluation of new 2'-deoxy-2'-fluoro-4'-triazole cytidine nucleosides as potent antiviral agents

A series of 4'-[1,2,3]triazole-2'-deoxy-2'-fluoro-β-d-arabinofuranosylcytosines (9-17) were prepared by Cu(I)-mediated [3 + 2] cycloaddition reactions (CuAAC) of 1-(4'-azido-2'-deoxy-2'-fluoro-β-d-arabinofuranosyl)cytosine (1) with appropriate alkynes in good yields. Their structures were fully established by (1)H NMR, (13)C NMR, HRMS, and elemental analysis. Most of these nucleoside analogs exhibited potent anti-HIV-1 activity with no cytotoxicity observed at the highest tested concentration up to 25 μM. Among them, compounds 9, 10 and 13 exhibited extremely potent antiviral activity, thus had a great potential for further development as novel nucleoside reverse transcriptase inhibitors (NRTIs) for the treatment of HIV-1 infection. Besides, the anti-HBV activity of compounds 10, 11 and 17 had been investigated.

Ultrasound-assisted one-pot synthesis of anti-CML nucleosides featuring 1,2,3-triazole nucleobase under iron-copper catalysis

A simple and efficient synthesis of modified 1,2,3-triazole nucleosides was developed. The strategy involved sequential one-pot acetylation-azidation-cycloaddition procedure and was found to be highly effective under a cooperative effect of ultrasound activation and iron/copper catalysis. The reactions were carried out under both conventional and ultrasonic irradiation conditions. In general, improvement in rates and yields were observed when reactions were carried out under sonication compared with conventional conditions. This one-pot procedure provides several advantages such as operational simplicity, high yield, safety and environment friendly protocol. The resulting substituted nucleosides were evaluated for their anticancer activity against K562 chronic myelogenous leukemia (CML) cell line.

Total synthesis of indole-3-acetonitrile-4-methoxy-2-C-β-D-glucopyranoside. Proposal for structural revision of the natural product

Indole-3-acetonitrile-4-methoxy-2-C-β-D-glucopyranoside (1), a novel C-glycoside from Isatis indigotica with important cytotoxic activity, has been prepared in ten steps from ethynyl-β-C-glycoside 3 and 2-iodo-3-nitrophenyl acetate 6. Key steps in the synthesis include a Sonogashira coupling and a CuI-mediated indole formation. NMR spectroscopic data for synthetic 1 differs from that reported for the natural product. A revised structure for the natural product, containing an alternate carbohydrate substituent, is proposed.

A sequential indium-mediated aldehyde allylation/palladium-catalyzed cross-coupling reaction in the synthesis of 2-deoxy-beta-C-aryl glycosides

Indium-mediated allylation of aldehydes with 2-chloro-3-iodopropene, followed by a palladium-catalyzed cross-coupling reaction with triarylindium reagents or arylboronic acids, leads to aryl-substituted homoallylic alcohols in good to excellent yields and diastereoselectivities. The products obtained from reactions conducted with d-glyceraldehyde acetonide can be transformed into 2-deoxy-beta-C-aryl ribofuranosides in high overall yields. Similarly, 2-deoxy-beta-C-aryl allopyranosides may be prepared efficiently from 2,4-O-benzylidene erythrose.

A review: synthesis of aryl C-glycosides via the heck coupling reaction

In this article, we focus on the synthesis of aryl C-glycosides via Heck coupling. It is organized based on the type of structures used in the assembly of the C-glycosides (also called C-nucleosides) with the following subsections: pyrimidine C-nucleosides, purine C-nucleosides, and monocyclic, bicyclic, and tetracyclic C-nucleosides. The reagents and conditions used for conducting the Heck coupling reactions are discussed. The subsequent conversion of the Heck products to the corresponding target molecules and the application of the target molecules are also described.