Monocyclic L-nucleosides with type 1 cytokine-inducing activity

Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism

Accurate estimation of the synthetic accessibility of small molecules is needed in many phases of drug discovery. Several expert-crafted scoring methods and descriptor-based quantitative structure-activity relationship (QSAR) models have been developed for synthetic accessibility assessment, but their practical applications in drug discovery are still quite limited because of relatively low prediction accuracy and poor model interpretability. In this study, we proposed a data-driven interpretable prediction framework called GASA (Graph Attention-based assessment of Synthetic Accessibility) to evaluate the synthetic accessibility of small molecules by distinguishing compounds to be easy- (ES) or hard-to-synthesize (HS). GASA is a graph neural network (GNN) architecture that makes self-feature deduction by applying an attention mechanism to automatically capture the most important structural features related to synthetic accessibility. The sampling around the hypothetical classification boundary was used to improve the ability of GASA to distinguish structurally similar molecules. GASA was extensively evaluated and compared with two descriptor-based machine learning methods (random forest, RF; eXtreme gradient boosting, XGBoost) and four existing scores (SYBA: SYnthetic Bayesian Accessibility; SCScore: Synthetic Complexity score; RAscore: Retrosynthetic Accessibility score; SAscore: Synthetic Accessibility score). Our analysis demonstrates that GASA achieved remarkable performance in distinguishing similar molecules compared with other methods and had a broader applicability domain. In addition, we show how GASA learns the important features that affect molecular synthetic accessibility by assigning attention weights to different atoms. An online prediction service for GASA was offered at http://cadd.zju.edu.cn/gasa/.

Advances in Therapeutic L-Nucleosides and L-Nucleic Acids with Unusual Handedness

Nucleic-acid-based small molecule and oligonucleotide therapies are attractive topics due to their potential for effective target of disease-related modules and specific control of disease gene expression. As the non-naturally occurring biomolecules, modified DNA/RNA nucleoside and oligonucleotide analogues composed of L-(deoxy)riboses, have been designed and applied as innovative therapeutics with superior plasma stability, weakened cytotoxicity, and inexistent immunogenicity. Although all the chiral centers in the backbone are mirror converted from the natural D-nucleic acids, L-nucleic acids are equipped with the same nucleobases (A, G, C and U or T), which are critical to maintain the programmability and form adaptable tertiary structures for target binding. The types of L-nucleic acid drugs are increasingly varied, from chemically modified nucleoside analogues that interact with pathogenic polymerases to nanoparticles containing hundreds of repeating L-nucleotides that circulate durably in vivo. This article mainly reviews three different aspects of L-nucleic acid therapies, including pharmacological L-nucleosides, Spiegelmers as specific target-binding aptamers, and L-nanostructures as effective drug-delivery devices.

Mirror-Image Oligonucleotides: History and Emerging Applications

As chiral molecules, naturally occurring d-oligonucleotides have enantiomers, l-DNA and l-RNA, which are comprised of l-(deoxy)ribose sugars. These mirror-image oligonucleotides have the same physical and chemical properties as that of their native d-counterparts, yet are highly orthogonal to the stereospecific environment of biology. Consequently, l-oligonucleotides are resistant to nuclease degradation and many of the off-target interactions that plague traditional d-oligonucleotide-based technologies; thus making them ideal for biomedical applications. Despite a flurry of interest during the early 1990s, the inability of d- and l-oligonucleotides to form contiguous Watson-Crick base pairs with each other has ultimately led to the perception that l-oligonucleotides have only limited utility. Recently, however, scientists have begun to uncover novel strategies to harness the bio-orthogonality of l-oligonucleotides, while overcoming (and even exploiting) their inability to Watson-Crick base pair with the natural polymer. Herein, a brief history of l-oligonucleotide research is presented and emerging l-oligonucleotide-based technologies, as well as their applications in research and therapy, are presented.

Microwave promoted C–O coupling for synthesizing O-aryloxytriazole nucleoside analogues

A convenient and effective microwave-promoted synthesis of O-aryloxytriazole nucleosides was established, leading to an interesting candidate with anticancer activity.

In search of new inhibitors of HIV-1 replication: synthesis and study of 1-(2'-Deoxy-beta-D-Ribofuranosyl)-1,2,4-triazole-3-carboxamide as a selective viral mutagenic agent

With the emergence of HIV strains resistant or cross-resistant to nearly all antiretroviral regimen, novel therapy approaches have to be considered. As a part of our current work on viral mutagenic compounds, we prepared 1-(2' -deoxy-beta-D-ribofuranosyl)-1,2,4-triazole-3-carboxamide (2' -deoxy-ribavirin) and its 5' -triphosphate derivative. The nucleoside mutagenic activity was evaluated on HIV-1 NL4-3 in CEMx174 cell culture. After 2.5 months, no reduction on HIV-1 viability was observed. On the other hand, in vitro experiments with purified HIV-1 RT demonstrated that the triphosphate analog can be incorporated opposite to several natural nucleosides.

Interferon-based therapy of hepatitis C

In 2007, the world celebrated the 50th anniversary of the discovery of interferon (IFN). The first clinical trial of recombinant IFN-alpha in patients with chronic hepatitis C was published in 1986. This article reviews the classification of IFNs, IFN production during viral infections, IFN signaling pathways and the mechanisms of their antiviral and immunomodulatory properties. Hepatitis C virus infection treatment is currently based on the combination of pegylated IFN-alpha and ribavirin. The pegylated IFN-alpha molecules are described, as well as the putative mechanisms of action of ribavirin. Current treatment guidelines are discussed and new results suggesting that the treatment schedule should be tailored to the early virological response during therapy are presented. Finally, insights into new hepatitis C drug developments are given.

Analysis of ribavirin mutagenicity in human hepatitis C virus infection

The addition of ribavirin to alpha interferon therapy significantly increases response rates for patients with chronic hepatitis C virus (HCV) infection, but ribavirin's antiviral mechanisms are unknown. Ribavirin has been suggested to have mutagenic potential in vitro that would lead to "error catastrophe," i.e., the generation of nonviable viral quasispecies due to the increment in the number of mutant genomes, which prevents the transmission of meaningful genetic information. We used extensive sequence-based analysis of two independent genomic regions in order to test in vivo the hypothesis that ribavirin administration accelerates the accumulation of mutations in the viral genome and that this acceleration occurs only when HCV replication is profoundly inhibited by coadministered alpha interferon. The rate of variation of the consensus sequence, the frequency of mutation, the error generation rate, and the between-sample genetic distance were measured for patients receiving ribavirin monotherapy, a combination of alpha interferon three times per week plus ribavirin, or a combination of alpha interferon daily plus ribavirin. Ribavirin monotherapy did not increase the rate of variation of the consensus sequence, the mutation frequency, the error generation rate, or the between-sample genetic distance. The accumulation of nucleotide substitutions did not accelerate, relative to the pretreatment period, during combination therapy with ribavirin and alpha interferon, even when viral replication was profoundly inhibited by alpha interferon. This study strongly undermines the hypothesis whereby ribavirin acts as an HCV mutagen in vivo.

Recent advances in the chemistry of parainfluenza-1 (Sendai) virus inhibitors

Purine and pyrimidine derivatives, antioxidants, fusion inhibitors, statins, prostaglandins, antibiotic nucleosides, inhibitors of Ca(2+) homeostasis, carbohydrate derivatives, antisense polynucleotides and chimeras, are described as inhibitors of parainfluenza-1 (Sendai) viral infections.

Pleiotropic mechanisms of ribavirin antiviral activities

Renewed interest in the mechanism of action of ribavirin results from its synergistic enhancement of interferon therapy and the need to develop more efficacious agents to treat hepatitis C virus infection. Since the discovery of ribavirin over 30 years ago by scientists at ICN Pharmaceuticals, many mechanisms of action for ribavirin have been proposed. These include inhibition of host inosine monophosphate dehydrogenase by ribavirin monophosphate, inhibition of viral capping enzymes, inhibition of viral RNA synthesis by ribavirin triphosphate, lethal mutagenesis of viral RNA genomes resulting from promiscuous incorporation of ribavirin triphosphate by the viral RNA polymerase, and modulation of the host immune responses. In this article, we will briefly review the evidence for these mechanisms, emphasizing recent findings. In addition, we will discuss strategies for development of nucleoside analogs that may replace ribavirin in the future.

Ribavirin in cancer immunotherapies: controlling nitric oxide augments cytotoxic lymphocyte function

Either ribavirin (RBV) or cyclophosphamide (CY) can shift an immune response from Th2 toward a Th1 cytokine profile. CY is used in this role in various current cancer immunotherapy attempts but with mixed success. More potent and reliable immunoadjuvants and Th1 response biasing methods are needed. RBV is used today mainly to augment interferon-alpha treatment of hepatitis C. RBV shifts an immune response from Th2 toward Th1 more effectively than CY and may be a safe and useful adjuvant for current cancer immunotherapeutic efforts. RBV is thought to act by inhibition of tetrahydrobiopterin synthesis. Tetrahydrobiopterin is an essential cofactor for all known isoforms of nitric oxide synthase. Lowered nitric oxide favors Th1 development as high levels favor Th2 weighting.

Effect of ribavirin, levovirin and viramidine on liver toxicological gene expression in rats

The ribavirin/interferon-alpha combination is currently the standard therapy for patients with chronic hepatitis C. However, ribavirin causes hemolytic anemia as a significant side-effect. Levovirin, an L-enantiomer of ribavirin, possesses similar immunomodulatory activity to ribavirin but lacks direct antiviral activity or hemolytic anemia. Viramidine is a liver-targeting prodrug of ribavirin with much less potential for hemolytic anemia. The aim of the present study is to profile the hepatic toxicological gene response to ribavirin, levovirin and viramidine. Rats were dosed orally with 120 mg kg(-1) day(-1) of ribavirin and viramidine and 2000 mg kg(-1) day(-1) of levovirin for 8 days. Ribavirin did not cause any significant change (>threefold) in gene expression as analyzed by the Affymetrix GeneChip technique. Levovirin decreased the mRNA level of CYP7A1 by fourfold but did not affect the expression of CYP27/CYP7B1 that functions as an alternative pathway for cholesterol metabolism. Viramidine down-regulated both expressed sequence tag 233569 and heat shock protein 86 genes threefold. The changes at mRNA level of these genes were confirmed by the reverse transcription competitive polymerase chain reaction technique. None of the compounds changed the liver/body weight ratio, the major cytochrome P-450 protein levels or enzyme activities. The data indicated that a high dose of ribavirin, levovirin or viramidine did not cause significant change at the transcription level of most of the liver toxicological genes.

Specific, sensitive and accurate LC-MS/MS method for the measurement of levovirin in rat and monkey plasma

Levovirin is a guanosine nucleoside analogue and the L-enantiomer of ribavirin. Levovirin has a better safety profile than ribavirin, exerts similar immunomodulatory effects in a mouse efficacy model, and may provide a better therapeutic option than ribavirin in patients with chronic hepatitis C virus (HCV) infection. To facilitate pharmacokinetic studies, a LC-MS/MS method for the analysis of levovirin in rat and monkey plasma was developed and validated. The method involved adding ICN 10537 as an internal standard, protein precipitation with acetonitrile followed by separation on an Intersil Silica column, and quantification by a MS/MS system equipped with positive electrospray ionization (ESI) in the multiple reaction monitoring (MRM) mode. The MS/MS reaction was selected to monitor the 245-->113 and 259-->128 transitions for levovirin and internal standard, respectively. The calibration curve was linear over a concentration range of 10-5000 ng/ml. The limit of quantitation was 10 ng/ml, the coefficient of variation (CV) was 3-5%, and the bias was 3-6%. Intra- and inter-day analysis of QC samples at 30, 1500 and 3500 ng/ml indicated that the method was precise (CV<6%) and accurate (bias <9%). Levovirin in rat and monkey plasma was stable at 5 degrees C for at least 24 h, 0 degrees C for at least 4 h, and after three freeze-thaw cycles. This specific, accurate and precise assay is useful in the study the pharmacokinetic characteristics of this compound.

The ribavirin analog ICN 17261 demonstrates reduced toxicity and antiviral effects with retention of both immunomodulatory activity and reduction of hepatitis-induced serum alanine aminotransferase levels

The demonstrated utility of the nucleoside analog ribavirin in the treatment of certain viral diseases can be ascribed to its multiple distinct properties. These properties may vary in relative importance in differing viral disease conditions and include the direct inhibition of viral replication, the promotion of T-cell-mediated immune responses via an enhanced type 1 cytokine response, and a reduction of circulating alanine aminotransferase (ALT) levels associated with hepatic injury. Ribavirin also has certain known toxicities, including the induction of anemia upon chronic administration. To determine if all these properties are linked, we compared the D-nucleoside ribavirin to its L-enantiomer (ICN 17261) with regard to these properties. Strong similarities were seen for these two compounds with respect to induction of type 1 cytokine bias in vitro, enhancement of type 1 cytokine responses in vivo, and the reduction of serum ALT levels in a murine hepatitis model. In contrast, ICN 17261 had no in vitro antiviral activity against a panel of RNA and DNA viruses, while ribavirin exhibited its characteristic activity profile. Importantly, the preliminary in vivo toxicology profile of ICN 17261 is significantly more favorable than that of ribavirin. Administration of 180 mg of ICN 17261 per kg of body weight to rats by oral gavage for 4 weeks generated substantial serum levels of drug but no observable clinical pathology, whereas equivalent doses of ribavirin induced a significant anemia and leukopenia. Thus, structural modification of ribavirin can dissociate its immunomodulatory properties from its antiviral and toxicologic properties, resulting in a compound (ICN 17261) with interesting therapeutic potential.

Cytostatic 6-Arylpurine Nucleosides II. Synthesis of Sugar-Modified Derivatives: 9-(2-Deoxy-β-D-erythro-pentofuranosyl)-, 9-(5-Deoxy-β-D-ribofuranosyl)- and 9-(2,3-Dihydroxypropyl)-6-phenylpurines

9-(2-Deoxy-β-D-erythro-pentofuranosyl)-6-(4-substituted phenyl)purines, 9-(5-deoxy-β-D-ribofuranosyl)-6-(4-substituted phenyl)purines and 9-(2,3-dihydroxypropyl)-6-(4-substituted phenyl)purines were prepared by the Suzuki-Miyaura cross-coupling reactions of the corresponding protected 9-substituted 6-chloropurines with substituted phenylboronic acids followed by MeONa mediated deprotection. In contrast to the highly active 6-phenylpurine ribonucleosides, the title compounds did not show any considerable cytostatic activity.