Nucleoside Conjugates Research Articles

Probing the Use of Triphenyl Phosphonium Cation for Mitochondrial Nucleoside Delivery.

Herein, we report the design, the synthesis, and the study of novel triphenyl phosphonium-based nucleoside conjugates. 2'-Deoxycytidine was chosen as nucleosidic cargo, as it allows the introduction of fluorescein on the exocyclic amine of the nucleobase and grafting of the vector was envisaged through the formation of a biolabile ester bond with the hydroxyl function at the 5'-position. Compound 3 was identified as a potential nucleoside prodrug, showing ability to be internalized efficiently into cells and to be co-localized with mitochondria.

Synthesis, characterization and photophysical studies of dual-emissive base-modified fluorescent nucleosides.

A straightforward and efficient methodology has been employed for the synthesis of a diverse set of base-modified fluorescent nucleoside conjugates via Cu(I)-catalysed cycloaddition reaction of 5-ethynyl-2',3',5'-tri-O-acetyluridine/3',5'-di-O-acetyl-2'-deoxyuridine with 4-(azidomethyl)-N9-(4'-aryl)-9,10-dihydro-2H,8H-chromeno[8,7-e][1,3]oxazin-2-ones in tBuOH to afford the desired 1,2,3-triazoles in 92-95% yields. Treatment with NaOMe/MeOH resulted in the final deprotected nucleoside analogues. The synthesized 1,2,3-triazoles demonstrated a significant emission spectrum, featuring two robust bands in the region from 350-500 nm (with excitation at 300 nm) in fluorescence studies. Photophysical investigations revealed a dual-emissive band with high fluorescence intensity, excellent Stokes shift (140-164 nm) and superior quantum yields (0.068-0.350). Furthermore, the electronic structures of the synthesized triazoles have been further verified by DFT studies. Structural characterization of all synthesized compounds was carried out using various analytical techniques, including IR, 1H-NMR, 13C-NMR, 1H-1H COSY, 1H-13C HETCOR experiments, and HRMS measurements. The dual-emissive nature of these nucleosides would be a significant contribution to nucleoside chemistry as there are limited literature reports on the same.

Synthesis and Photophysical Studies on N1‐(Coumarin‐4′′′‐yl)‐C4‐(2′,3′‐dideoxyuridin‐3′‐yl/3′‐deoxythymidin‐3′‐yl)‐oxymethyl‐1,2,3‐triazoles

AbstractA click chemistry‐based protocol has been utilized for the synthesis of a series of twelve novel tert‐butyldiphenylsilylated N1‐(coumarin‐4′′′‐yl)‐C4‐(2′,3′‐di‐deoxyuridin‐3′‐yl)‐oxymethyl‐1,2,3‐triazoles and N1‐(coumarin‐4′′′‐yl)‐C4‐(3′‐deoxythymin‐3′‐yl)‐oxymethyl‐1,2,3‐triazoles by utilising Cu(I)‐catalyzed azide‐alkyne cycloaddition reaction of 4‐azidocoumarins and 3′‐O‐(prop‐1‐yn‐3‐yl)‐5′‐O‐(tert‐butyldiphenylsilyl)‐2′,3′‐dideoxyuridin or 3′‐O‐(prop‐1‐yn‐3‐yl)‐5′‐O‐(tert‐butyldiphenylsilyl)‐3′‐deoxythymidin in 70–82 % and 68–82 % yields, respectively. The deprotection of resulted silylated uridine and thymidine conjugate with TBAF afforded title compounds in 81–91 % yield. The photophysical studies have been carried out on the synthesized coumarin‐triazolylmethyl nucleoside conjugates which revealed a very high Stokes shift value ranging from 82–215 nm.

Synthesis and Biological Evaluation of Novel Allobetulon/Allobetulin-Nucleoside Conjugates as AntitumorAgents.

Allobetulin is structurally similar tobetulinic acid, inducing the apoptosis of cancer cells with low toxicity. However, both of them exhibited weak antiproliferation against several tumor cell lines. Therefore, the new series of allobetulon/allobetulin–nucleoside conjugates 9a–10i were designed and synthesized for potency improvement. Compounds 9b, 9e, 10a, and 10d showed promising antiproliferative activity toward six tested cell lines, compared to zidovudine, cisplatin, and oxaliplatin based on their antitumor activity results. Among them, compound 10d exhibited much more potent antiproliferative activity against SMMC-7721, HepG2, MNK-45, SW620, and A549 human cancer cell lines than cisplatin and oxaliplatin. In the preliminary study for the mechanism of action, compound 10d induced cell apoptosis and autophagy in SMMC cells, resulting in antiproliferation and G0/G1 cell cycle arrest by regulating protein expression levels of Bax, Bcl-2, and LC3. Consequently, the nucleoside-conjugated allobetulin (10d) evidenced that nucleoside substitution was a viable strategy to improve allobetulin/allobetulon’s antitumor activity based on our present study.

Synthesis and Biological Evaluation of 5'-O-Fatty Acyl Ester Derivatives of 3'-Fluoro-2',3'-dideoxythymidine as Potential Anti-HIV Microbicides.

A number of 5′-O-fatty acyl derivatives of 3′-fluoro-2′,3′-dideoxythymidine (FLT, 1) were synthesized. These conjugates were evaluated for their potential as topical microbicides with anti-HIV activity against cell-free (X4 and R5), cell-associated, and multidrug-resistant viruses. Compared to FLT and 3′-azido-2′,3′-dideoxythymidine (AZT), 5′-O-(12-azidododecanoyl) (5), 5′-O-myristoyl (6), and 5′-O-(12-thioethyldodecanoyl) (8) derivatives of FLT were found to be more active against both cell-free viruses (lymphocytotropic and monocytotropic strains) with EC50 values of 0.4 μM, 1.1 μM, and <0.2 μM, respectively, as well as cell-associated virus with EC50 values of 12.6, 6.4, and 2.3 μM, respectively. Conjugates 5, 6, and 8 exhibited >4 and >30 times better antiviral index than FLT and AZT, respectively. Conjugates 5 and 8 were significantly more potent than FLT against many multidrug-resistant strains. A comparison of the anti-HIV activity with the corresponding non-hydrolyzable ether conjugates suggested that ester hydrolysis to FLT and fatty acids is critical to enable anti-HIV activity. Cellular uptake studies were conducted using fluorescent derivatives of FLT attached with 5(6)-carboxyfluorescein through either β-alanine (23) or 12-aminododecanoic acid (24) spacers. The lipophilic fluorescent analog with a long chain (24) showed more than 12 times higher cellular uptake profile than the fluorescent analog with a short chain (23). These studies further confirmed that the attachment of fatty acids improved the cellular uptake of nucleoside conjugates. In addition, 5, 6, and 8 were the least cytotoxic and did not alter vaginal cell and sperm viability compared to the positive control, a commercial topical spermicide (N-9), which significantly decreased sperm and vaginal cell viability inducing the generation of proinflammatory cytokines.

Effect of Stereochemistry and Hydrophobicity on the Self‐Assembly of Phe‐Phe‐Nucleoside Conjugates

AbstractMolecular self‐assembly of the minimal diphenylalanine (Phe‐Phe) peptide building block shows unique morphological organizations and potential utility in biochemistry and biomaterials applications. Furthermore, the molecular engineering of nucleoside‐conjugated Phe‐Phe scaffolds allows the formation of diverse architectures with tunable biophysical properties. While the self‐assembly of homochiral l‐dipeptides is well characterized, stereochemistry is known to determine the conformation, which also governs self‐assembly through molecular packing effects. Here, the effect of stereochemistry and hydrophobicity on Phe‐Phe nucleoside conjugates using all four diastereomers [(l)Phe‐(l)Phe, (d)Phe‐(dPhe, (l)Phe‐(d)Phe, and (d)Phe‐(l)Phe] of Phe‐Phe conjugates is systematically studied. The homochiral peptides form well‐defined nanorods while the heterochiral dipeptides do not form any regular structures. Since heterocyclic nucleobases can self‐assemble through hydrogen‐bonded complementary base‐pairing, the self‐assembly of chiral nucleoside‐conjugated Phe‐Phe peptides is examined. All conjugated Phe‐Phe peptides form seamless spherical particles. The completely or partially deprotected peptides do not assemble to any defined nanostructures suggesting that self‐assembly is governed by the precise hydrophobic/hydrophilic balance in the assembling units. Contact angle measurements of the diastereomeric peptides reveal a subtle difference in stereochemistry‐dependent molecular hydrophobicity. Taken together, it is revealed that the combination of chirality together with hydrophobic/hydrophilic balance within the peptides dictates the self‐assembly of Phe‐Phe dipeptide nucleoside conjugates.

Synthesis and Biological Evaluation of Novel Allobetulon/Allobetulin–Nucleoside Conjugates as AntitumorAgents

Synthesis and Biological Evaluation of Novel Allobetulon/Allobetulin–Nucleoside Conjugates as AntitumorAgents

Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs Against Human Coronavirus 229E (HCoV-229E).

Remdesivir is a nucleotide prodrug that is currently undergoing extensive clinical trials for the treatment of COVID-19. The prodrug is metabolized to its active triphosphate form and interferes with the action of RNA-dependent RNA polymerase of SARS-COV-2. Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. The anti-HIV nucleosides interfere with HIV RNA-dependent DNA polymerase and/or act as chain terminators. Normal human fibroblast lung cells (MRC-5) were used to determine the cytotoxicity of the compounds. The study revealed that remdesivir exhibited an EC50 value of 0.07 µM against HCoV-229E with TC50 of > 2.00 µM against MRC-5 cells. Parent NRTIs were found to be inactive against (HCoV-229E) at tested concentrations. Among all the NRTIs and 5′-O-fatty acyl conjugates of NRTIs, 5′-O-tetradecanoyl ester conjugate of FTC showed modest activity with EC50 and TC50 values of 72.8 µM and 87.5 µM, respectively. These data can be used for the design of potential compounds against other coronaviruses.

Design, Synthesis and Molecular Modeling Study of Conjugates of ADP and Morpholino Nucleosides as A Novel Class of Inhibitors of PARP-1, PARP-2 and PARP-3.

We report on the design, synthesis and molecular modeling study of conjugates of adenosine diphosphate (ADP) and morpholino nucleosides as potential selective inhibitors of poly(ADP-ribose)polymerases-1, 2 and 3. Sixteen dinucleoside pyrophosphates containing natural heterocyclic bases as well as 5-haloganeted pyrimidines, and mimicking a main substrate of these enzymes, nicotinamide adenine dinucleotide (NAD+)-molecule, have been synthesized in a high yield. Morpholino nucleosides have been tethered to the β-phosphate of ADP via a phosphoester or phosphoramide bond. Screening of the inhibiting properties of these derivatives on the autopoly(ADP-ribosyl)ation of PARP-1 and PARP-2 has shown that the effect depends upon the type of nucleobase as well as on the linkage between ADP and morpholino nucleoside. The 5-iodination of uracil and the introduction of the P–N bond in NAD+-mimetics have shown to increase inhibition properties. Structural modeling suggested that the P–N bond can stabilize the pyrophosphate group in active conformation due to the formation of an intramolecular hydrogen bond. The most active NAD+ analog against PARP-1 contained 5-iodouracil 2ʹ-aminomethylmorpholino nucleoside with IC50 126 ± 6 μM, while in the case of PARP-2 it was adenine 2ʹ-aminomethylmorpholino nucleoside (IC50 63 ± 10 μM). In silico analysis revealed that thymine and uracil-based NAD+ analogs were recognized as the NAD+-analog that targets the nicotinamide binding site. On the contrary, the adenine 2ʹ-aminomethylmorpholino nucleoside-based NAD+ analogs were predicted to identify as PAR-analogs that target the acceptor binding site of PARP-2, representing a novel molecular mechanism for selective PARP inhibition. This discovery opens a new avenue for the rational design of PARP-1/2 specific inhibitors.

Organoruthenium(ii) nucleoside conjugates as colon cytotoxic agents

Eleven organoruthenium(ii) nucleoside conjugates are reported, showing high cytotoxicity in HCT116 colon cancer cells and independent uptake of nucleoside transporters.

Synthesis and Evaluation of Novel Neamine-Nucleoside Conjugates as Potential Antibiotic Targets for Escherichia coli 16S Ribosomal RNA.

Based on the nucleobase rich character of the binding pocket of A-site 16S ribosomal RNA of Escherichia coli, it was proposed that the neamine moiety of synthesized Neamine-nucleoside conjugates could bind to the groove of RNA while the nucleobase moiety would bind specifically to the sequence of the 16S rRNA A-site fragment. Thus the designed conjugate compound 5 was found to have the same dissociation constant as neamine for binding to 16S rRNA and the neamine-amino acid substituted nucleoside conjugate 8 and 9 showed 6.3 and 4.8 times greater RNA binding affinity, respectively, as compared with neamine. The results obtained successfully demonstrate the need for chemically modifying neamine and probe the changes induced using NMR protocols to assist in the discovery of new aminoglycoside antibiotics.

Clickable conjugates of bile acids and nucleosides: Synthesis, characterization, in vitro anticancer and antituberculosis studies

A series of clickable bile acid-nucleosides conjugates linked directly or via amino acid linker were synthesized, and characterized by spectroscopic techniques such as 1H NMR, 13C NMR, FT-IR, HRMS and HPLC. The synthesized compounds 6a–p were screened for their in vitro anticancer property against a panel of three cancer cell lines (PC-3, MCF-7, IMR-32). In addition, the synthesized derivatives were also tested for their antimycobacterial activity against Mycobacterium tuberculosis H37Rv (ATCC 27294 strain). Among the screened compounds, cholic acid-uridine clicked conjugate (6c), and cholic acid-uridine clicked conjugate liked via phenylalanine moiety (6m) were found to be most active against MCF-7 and IMR-32 exhibiting an IC50 value of 8.084 and 8.71 µM, respectively. The antimycobacterial study of the synthesized conjugates revealed all the conjugates to be active with MIC values in the range of 4.09–15.41 µM. Deoxycholic acid-adenosine clicked conjugate (6b) showed most promising antituberculosis property with MIC value of 4.09 µM. Most of the synthesized conjugates were found to be safe at 50 µM against normal human embryonic kidney (HEK 293 T) cell line.

Advanced Prodrug Strategies in Nucleoside and Non-Nucleoside Antiviral Agents: A Review of the Recent Five Years.

Background: Poor pharmacokinetic profiles and resistance are the main two drawbacks from which currently used antiviral agents suffer, thus make them excellent targets for research, especially in the presence of viral pandemics such as HIV and hepatitis C. Methods: The strategies employed in the studies covered in this review were sorted by the type of drug synthesized into ester prodrugs, targeted delivery prodrugs, macromolecular prodrugs, other nucleoside conjugates, and non-nucleoside drugs. Results: Utilizing the ester prodrug approach a novel isopropyl ester prodrug was found to be potent HIV integrase inhibitor. Further, employing the targeted delivery prodrug zanamivir and valine ester prodrug was made and shown a sole delivery of zanamivir. Additionally, VivaGel, a dendrimer macromolecular prodrug, was found to be very efficient and is now undergoing clinical trials. Conclusions: Of all the strategies employed (ester, targeted delivery, macromolecular, protides and nucleoside analogues, and non-nucleoside analogues prodrugs), the most promising are nucleoside analogues and macromolecular prodrugs. The macromolecular prodrug VivaGel works by two mechanisms: envelope mediated and receptor mediated disruption. Nucleotide analogues have witnessed productive era in the recent past few years. The era of non-interferon based treatment of hepatitis (through direct inhibitors of NS5A) has dawned.

Synthesis and anti-HIV activities of unsymmetrical long chain dicarboxylate esters of dinucleoside reverse transcriptase inhibitors

A series of 11 unsymmetrical dicarboxylate conjugates of dinucleoside reverse transcriptase inhibitors were synthesized. Three dicarboxylic acids, succinic acid, suberic acid and 1,14-tetradecandioc acid, were diesterified with either 3′-azido-2′,3′-dideoxythymidine (AZT), 3′-fluoro-2′,3′-dideoxythymidine (FLT), 2′,3′-dideoxy-3′-thiacytidine (3TC), or 5-fluoro-2′,3′-dideoxy-3′-thiacytidine (FTC). The anti-HIV activity of synthesized compounds was evaluated against HIV-1 X4 (IIIB) and R5 (BaL) viral strains in single-round infection assays. Results indicated that the tetradecandioate esters of nucleosides were more active against HIV than the corresponding parent nucleosides and nucleoside conjugates. The tetradecandioate conjugate of FLT and FTC (5) was found to be the most potent compounds with EC50 values of 47 and 75nM against X4 and R5 HIV-1 strains, respectively, while the EC50 values for the parent analogs, FLT and FTC, ranged from 700 to 3300nM.

Disubstituted cobalt bis(1,2-dicarbollide)(-I) terminal alkynes: Synthesis, reactivity in the Sonogashira reaction and application in the synthesis of cobalt bis(1,2-dicarbollide)(-I) nucleoside conjugates

Reactions of [8-HCCCH2O-8′-I-3,3′-Co(1,2-C2B9H10)2]- ([2]Cs) with 5-iodo-2’-deoxyuridine under Sonogashira reaction conditions resulted in a cobalt bis(1,2-dicarbollide)(-I) 5-ethynyl-2'-deoxyuridine conjugate ([3]Cs) linked via short spacer. Its intramolecular cyclization led to furo [2,3-d]pyrimidin-2(3H)-one isomer ([4]Cs). Compounds [3]Cs and [4]Cs demonstrated moderate cytotoxicity, however they did not have antiviral activity against the viruses tested. A new terminal charge-compensated cobalt bis(1,2-dicarbollide)(-I) derivative with terminal alkyne group (5) was synthesized from 8,8’-μ-I-3,3′-Co(1,2-C2B9H10)2 and dimethylpropargyl amine. It was found that contrary to [2]Cs compound 5 did not react with 5-iodo-2’-deoxyuridine under Sonogashira reaction conditions. Total electrostatic potential (TEP) calculations gave explanation of this phenomenon.

2-Hydroxyethoxy-closo-undecahydrododecaborate(12)([B12H11CH2CH2OH]2−) as a new prospective reagent for the preparation of closo-dodecaborate building blocks and thymidine and 2-deoxyuridine conjugates linked via short spacer

Reaction of dioxonium derivative of closo-dodecaborate ([B12H11O+(CH2)4O]−) with an access of NaCN in boiling EtOH led to [B12H11OCH2CH2OH]2− with an excellent yield as a result of ring cleavage followed by elimination of acrylonitrile. The same entry in aprotic DMFA afforded regular ring cleavage product [B12H11OCH2CH2OCH2CH2CN]2. Subsequent work up of this nitrile with sodium methanolate in MeOH led to the alcohol ([B12H11OCH2CH2OH]2−) as well. The above alcohol was converted into new functionalized derivatives [B12H11OCH2CH2OMs]2− and [B12H11OCH2CH2N3]2− respectively using straightforward organic reactions. These new building blocks were employed for the preparation of novel closo-dodecaborate pyrimidine nucleoside conjugates.

Synthesis of Amino‐Acid–Nucleoside Conjugates

AbstractRepresentative derivatives of uridine‐conjugated amino acids that have been suitably protected for Fmoc solid‐phase chemistry have been prepared through efficient procedures that use “click” reactions as key steps, including thiol–ene radical reactions and copper‐catalyzed azide alkyne cycloaddition (CuAAC) reactions. Several linkers between the amino acid and nucleoside units, including alkyl chains and a triazole ring, have been successfully employed. Alkyl chains offer retention of flexibility, to allow the bisubstrate analogues to adopt an appropriate orientation, whilst the triazole ring can promote additional interactions at the active sites of target enzymes. Furthermore, a neutral surrogate of the pyrophosphate unit has been prepared by using a Staudinger–Vilarrasa reaction as a key step. Neutral analogues are promising surrogates for avoiding difficulties owing to cell‐membrane permeability.

Design, Synthesis, Antiviral Activity, and Pre-Formulation Development of Poly-L-Arginine-Fatty Acyl Derivatives of Nucleoside Reverse Transcriptase Inhibitors

GRAPHICAL ABSTRACT

Synthesis and biological evaluation of 5′-O-dicarboxylic fatty acyl monoester derivatives of anti-HIV nucleoside reverse transcriptase inhibitors

A number of 5′-O-dicarboxylic fatty acyl monoester derivatives of 3′-azido-3′-deoxythymidine (zidovudine, AZT), 2′,3′-didehydro-2′,3′-dideoxythymidine (stavudine, d4T), and 3′-fluoro-3′-deoxythymidine (alovudine, FLT) were synthesized to improve the lipophilicity and potentially the cellular delivery of parent polar 2′,3′-dideoxynucleoside (ddN) analogs. The compounds were evaluated for their anti-HIV activity. Three different fatty acids with varying chain length of suberic acid (octanedioic acid), sebacic acid (decanedioic acid), and dodecanedioic acid were used for the conjugation with the nucleosides. The compounds were evaluated for anti-HIV activity and cytotoxicity. All dicarboxylic ester conjugates of nucleosides exhibited significantly higher anti-HIV activity than that of the corresponding parent nucleoside analogs. Among all the tested conjugates, 5′-O-suberate derivative of AZT (EC50=0.10nM) was found to be the most potent compound and showed 80-fold higher anti-HIV activity than AZT without any significant toxicity (TC50 >500nM).

Hepatotoxicity of perfluorooctanoic acid in human hepatocytes using metabonomics

Ultra performance liquid chromatography coupled to orthogonal acceleration time-of-flight mass spectrometry was used to study metabolic profiling of L-02 human liver cell exposed to different doses of perfluorooctanoic acid (PFOA) for 72 h. Principle component analysis method was used for group differentiation and biomarker screening. Dose-dependent distribution of the treated samples with different doses could be observed in scores plots obtained under both positive and negative ionization modes. Furthermore, eighteen metabolites were identified as potential biomarkers which were closely related with the toxicity of PFOA. The identified biomarkers included carnitine and acylcarnitines, nucleosides and nucleoside conjugates, amino acids and amino acid conjugates etc. Among them, significant changes of carnitine and its metabolites were observed in the control group and dose groups, which play an important role in fatty acid metabolism. Meanwhile, some genes involved in cholesterol biosynthesis were upregulated dramatically using gene microarray analysis. The disturbance of cholesterol biosynthesis could have adverse impact on fatty acid metabolism, consequently induce the decrease of carnitine and increase of acylcarnitines in treated groups. Additionally, purine metabolism, tricarboxylic acid cycle, glycosphingolipid metabolism and amino acid metabolism may also be involved in the toxic response to PFOA.