Bicyclic Nucleoside Analogues Research Articles

The development of BVDU: An odyssey.

Brivudin, ((E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) can be considered the gold standard for the treatment of varicella-zoster virus (VZV) infections, such as herpes zoster (shingles). It is available for clinical use in most European countries (except for the UK) and over the whole world (except for the US and Canada). Besides VZV its activity spectrum also includes various other herpesviruses, such as herpes simplex virus type 1 (HSV-1). Its activity against VZV and HSV-1 depends on phosphorylation by the virus-encoded thymidine kinase (TK). In its active form (BVDU TP or BVDU 5'-triphosphate), it can act as both substrate and inhibitor of the viral (i.e., HSV-1) DNA polymerase. It has proven to be effective against herpes zoster, including post-herpetic neuralgia (PHN). It is contra-indicated in patients concomitantly treated by 5-fluorouracil (FU), since its degradation product, (E)-5-(2-bromovinyl)uracil, is inhibitory to the catabolism of FU, which may enhance the toxicity of the latter. A new compound, the bicyclic nucleoside analogue (BCNA) Cf-1743, has been described, which is a more potent inhibitor of VZV replication than BVDU and which does not interfere with the catabolism of FU. It is applicable orally, as its 5'-valine ester FV-100 (Fermavir), but has not (yet) been marketed for clinical use.

FV-100 for the Treatment of Varicella-Virus (VZV) Infections: Quo Vadis?

The bicyclic nucleoside analogue (BCNA) Cf1743 and its orally bioavailable prodrug FV-100 have unique potential as varicella-zoster virus (VZV) inhibitors to treat herpes zoster (shingles) and the therewith associated pain, including post-herpetic neuralgia (PHN). The anti-VZV activity of Cf1743 depends on a specific phosphorylation by the VZV-encoded thymidine kinase (TK). The target of antiviral action is assumed to be the viral DNA polymerase (or DNA synthesis in the virus-infected cells).

Novel Nucleoside Analogues as Effective Antiviral Agents for Zika Virus Infections.

Previously considered a neglected flavivirus, Zika virus has recently emerged as a public health concern due to its ability to spread rapidly and cause severe neurological disorders, such as microcephaly in newborn babies from infected mothers, and Guillain-Barré syndrome in adults. Despite extensive efforts towards the identification of effective therapies, specific antivirals are still not available. As part of ongoing medicinal chemistry studies to identify new antiviral agents, we screened against Zika virus replication in vitro in a targeted internal library of small-molecule agents, comprising both nucleoside and non-nucleoside agents. Among the compounds evaluated, novel aryloxyphosphoramidate prodrugs of the nucleosides 2′-C-methyl-adenosine, 2-CMA, and 7-deaza-2′C-methyl-adenosine, 7-DMA, were found to significantly inhibit the virus-induced cytopathic effect in multiple relevant cell lines. In addition, one of these prodrugs exhibits a synergistic antiviral effect against Zika virus when applied in combination with an indirect antiviral agent, a l-dideoxy bicyclic pyrimidine nucleoside analogue, which potently inhibits vaccinia and measles viruses in vitro by targeting a host pathway. Our findings provide a solid basis for further development of an antiviral therapy for Zika virus infections, possibly exploiting a dual approach combining two different agents, one targeting the viral polymerase (direct-acting antiviral), the second targeting a host-directed autophagy mechanism.

Electronic Structures of LNA Phosphorothioate Oligonucleotides.

Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules.

Synthesis of 1′-phenyl-2′-OMe ribose analogues connecting the thymine base at the 1′ position through a flexible linker for the formation of a stable anti-parallel triplex DNA

We have previously developed the innovative bicyclic nucleoside analogues (WNA) for the formation of the triplex DNA. The WNA analogue consists of an aromatic ring and a recognition base on the bicyclic skeleton, and the recognition of the CG or TA interrupting sites has been achieved by the WNA analogues. However, the stabilization ability of the WNA analogue is dependent on its neighboring nucleobases within the TFO. We hypothesized that the sequence dependency might arise from the fixed conformation of the bicyclic ring of the WNA. Thus, it was expected that an open-linker between the sugar part and the nucleobase might produce the flexibility and improve the stabilizing effect of the nucleobase analogues. We now report the design and synthesis of a new nucleoside analogue as an open-form of WNA-βT, the 1′-phenyl-2′-OMe-ribose derivative, connecting the thymine base to the ribose part through a methylene linker (1) or an ethylene linker (2). TFO containing the 3′-dA-1-dG context recognized the CG interrupting site, and that with the 3′-dG-1-dG context recognized the GC site. In contrast, 2 displayed a stabilizing effect on all four base pairs with some preferences for the TFO containing 3′-dA-2-dG and 3′-dG-2-dG. These results suggested that a flexible linker between the nucleobase and the ribose part may improve the sequence dependency for the triplex formation.

Preliminary validation of varicella zoster virus thymidine kinase as a novel reporter gene for PET

Imaging of gene expression with positron emission tomography (PET) has emerged as a powerful tool for biomedical research during the last decade. The prototypical herpes simplex virus type 1 thymidine kinase (HSV1-TK) PET reporter gene (PRG) is widely used and many other PRGs have also been validated. We investigated varicella zoster virus thymidine kinase (VZV-tk) as new PRG with radiolabeled bicyclic nucleoside analogues (BCNAs) as PET tracers. The uptake and washout of four different radiolabeled BCNAs was evaluated in cells expressing VZV-tk after lentiviral vector (LV) transduction and in control cells. Metabolism of the tracers was assayed by high pressure liquid chromatography (HPLC). Mice bearing VZV-TK expressing xenografts were imaged with PET. High uptake in VZV-tk expressing cells was seen for 3 of the 4 tracers tested. The uptake of the tracers could be blocked by the presence of excess thymidine in the incubation solution. Cellular retention was variable, with one tracer showing an acceptable half-life of ~1 hour. The amount of intracellular tracer correlated with the titer of LV used to transduce the cells. VZV-TK dependent conversion into metabolites was shown by HPLC. No specific accumulation was observed in cells expressing a fusion protein containing an HSV1-TK moiety. VZV-tk expression in xenografts resulted in a 60% increase in uptake in vivo as measured with PET. We have validated the combination of VZV-tk and radiolabeled BCNAs as new PRG/PRP system. Further optimization of the PRPs and the PRG are warranted to increase the signal.

Dipeptidyl Peptidase IV‐Activated Prodrugs of Anti‐Varicella Zoster Virus Bicyclic Nucleoside Analogues Containing Different Self‐Cleavage Spacer Systems

A new type of double prodrug of the antiviral family of bicyclic nucleoside analogues (BCNA) bearing cyclization self-cleavage spacers between the Val-Pro dipeptide sequence as well as the parent compound were synthesized and evaluated with regard to activation by the DPPIV/CD26 enzyme and for their stability in human and bovine serum. In buffer solution, carbamate and ester prodrugs were found to be chemically stable. Most prodrugs containing a dipeptidyl linker efficiently converted into the BCNA parent drug. In contrast, the Val-Pro alkyldiamino prodrugs converted predominantly into their alkyldiamino prodrug intermediates in the presence of CD26 and human serum. A marked increase in water solubility was observed for all prodrugs. In contrast to the parent compound, a tetrapeptide prodrug containing the Val-Val dipeptide as a self-cleavage spacer released substantial amounts of the BCNA parent drug at the basolateral side of Caco-2 cell cultures and exhibited 15- to 20-fold increased bioavailability in mice relative to the poorly bioavailable parent compound.

Efficient DNA Strand Displacement by a W‐Shaped Nucleoside Analogue (WNA‐βT) Containing an ortho‐Methyl‐Substituted Phenyl Ring

Molecules that can target duplex DNA with sequence selectivity have the potential to be useful tools in genomic research and also as therapeutic agents. Homopurine-homopyrimidine stretches in duplex DNA can be recognized by homopurine or homopyrimidine TFOs (triplex-forming oligonucleotides) through the formation of triplex DNA. We have previously developed bicyclic nucleoside analogues (WNAs) for the formation of stable triplexes in the formation of stable antiparallel triplexes containing a TA or a CG interrupting site. In this study, we investigated the effects on triplex DNA formation of ortho-, meta-, and para-methyl substituent groups on the aromatic ring of the WNA analogue. It was found that the homopurine TFO containing meta- and para-methyl-substituted WNA-βT (mMe-WNA-βT, pMe-WNA-βT) stabilized triplexes containing a TA interrupting site or a GC site, respectively. Interestingly, the ortho-methyl-substituted WNA-βT (oMe-WNA-βT) efficiently promoted DNA strand displacement to form the TFO/pyrimidine duplex. A detailed investigation showed that the duplex was in the antiparallel orientation and that its formation took place prior to triplex formation with the need for a magnesium cation. NOESY measurements indicated a significant difference in the rotation flexibilities of the phenyl rings of WNA-βTs: that is, the conformation of the ortho-methylated phenyl ring was stable in a temperature-independent manner. It was speculated that the initial formation of a ternary complex was followed by strand displacement and then the formation of the TFO/pyrimidine duplex together with the TFO(2)/pyrimidine triplex formation during the early stage, and that the equilibrium shifted to the triplex during the later stage. Although the detailed role is still uncertain, the fixed phenyl ring of oMe-WNA-βT might play a role in the displacement reaction.

Pharmacokinetics and safety of FV-100, a novel oral anti-herpes zoster nucleoside analogue, administered in single and multiple doses to healthy young adult and elderly adult volunteers.

FV-100 is the prodrug of the highly potent anti-varicella zoster virus bicyclic nucleoside analogue CF-1743. To characterize the pharmacokinetics and safety of oral FV-100, 3 randomized, double-blind, placebo-controlled clinical trials were conducted: (i) a single-ascending-dose study in 32 healthy subjects aged 18 to 55 years (100-, 200-, 400-, and 800-mg doses) with an evaluation of the food effect in the 400-mg group; (ii) a multiple-ascending-dose study in 48 subjects aged 18 to 55 years (100 mg once daily [QD], 200 mg QD, 400 mg QD, 400 mg twice a day, and 800 mg QD for 7 days); and (iii) a 2-part study in subjects aged 65 years and older with a single 400-mg dose in 15 subjects and a 400-mg QD dosing regimen for 7 days in 12 subjects. FV-100 was rapidly and extensively converted to CF-1743, the concentration of which remained above that required to reduce viral activity by 50% for the 24-hour dosing period. Renal excretion of CF-1743 was very low. A high-fat meal reduced exposure to CF-1743; a low-fat meal did not. Pharmacokinetic parameters for the elderly subjects were comparable to those for the younger subjects. FV-100 was well tolerated by all subjects. The pharmacokinetic and safety profiles of FV-100 support its continued investigation for the treatment of herpes zoster and prevention of postherpetic neuralgia with once-daily dosing and without dose modifications for elderly or renally impaired patients.

Dipeptidyl Peptidase IV Dependent Water-Soluble Prodrugs of Highly Lipophilic Bicyclic Nucleoside Analogues

We present the first report of the application of the dipeptidyl peptidase IV (DPPIV/CD26) based prodrug approach to hydroxy-containing drug derivatives. In particular, we applied this strategy to the highly lipophilic antiviral drug family of bicyclic furanopyrimidine nucleoside analogues (BCNA) in order to improve their physicochemical and pharmacokinetic properties. Our stability data demonstrated that the prodrugs efficiently release the parent BCNA drug upon selective conversion by purified DPPIV/CD26 and by soluble DPPIV/CD26 present in bovine, murine, and human serum. Vildagliptin, a specific inhibitor of DPPIV/CD26, was able to completely block the hydrolysis of the prodrugs in the presence of purified DPPIV/CD26 human, murine, and bovine serum. Several novel prodrugs showed remarkable increases in water solubility (up to more than 3 orders of magnitude) compared to the poorly soluble parent drug. We also demonstrated a markedly enhanced oral bioavailability of the prodrugs versus the parent drug in mice.

Evaluation of Novel Phosphoramidate ProTides of the 2′-Fluoro Derivatives of a Potent Anti-Varicella Zoster Virus Bicyclic Nucleoside Analogue

Recently, the synthesis and antiviral activity of a series of 2'-fluoro derivatives of the most potent anti-varicella zoster virus (VZV) agent reported to date, the bicyclic nucleoside analogue Cf1743, have been reported. Here, we present molecular modelling studies for the interaction of these compounds with VZV-encoded thymidine kinase (TK) and we report the synthesis of a series of phosphoramidate ProTides of these compounds designed to bypass the nucleoside kinase dependence of the parent nucleoside analogues. The phosphoramidate prodrugs were equally effective as their parent compounds against VZV in cell culture, but lost antiviral potency against TK-deficient VZV strains. ProTide-based kinase bypass is not successful in this case.

Synthesis, structure, and sugar dynamics of a 2′-spiroisoxazolidine thymidine analog

Abstract Bicyclic nucleoside analogs have shown promise in Antisense and RNA interference strategies. Ribofuranosyl ring conformation is a controlling factor in this regard. We have introduced a spiroisoxazolidine ring at the 2′-position of the sugar to gauge the effect it has on sugar dynamics. Proton relaxation measurements and coupling constant analysis indicate the sugar is locked in the North conformation with substantial sugar rigidity evident.

Synthesis and biological evaluation of acyclic nucleotide analogues with a furo[2,3-d]pyrimidin-2(3H)-one base

As a part of a broader structure–activity relationship (SAR) study of bicyclic nucleoside analogues (BCNAs) [anti-varicella-zoster virus (anti-VZV) and anti-human cytomegalovirus (anti-HCMV) agents], a novel series of 2-(phosphonomethoxy)ethyl (PME) substituted furo[2,3-d]pyrimidin-2(3H)-ones was synthesized. The target acyclic nucleotide analogues were prepared by Sonogashira coupling of protected 5-iodo-1-[2-(phosphonomethoxy)ethyl]uracil with various 1-alkynes, followed by in situ Cu(I)-promoted intramolecular cyclization and standard removal of the isopropyl ester groups. None of the prepared PME analogues were active at subtoxic concentrations against VZV thymidine kinase competent (TK+), VZV thymidine kinase deficient (TK–), HCMV, or any other viruses tested.

ChemInform Abstract: Facile Synthesis and Conformation of 3′-O,4′-C-Methyleneribonucleosides.

Bicyclic nucleoside analogues, 3′-O,4′-C-methyleneribonucleosides 1, including thymine, cytosine, adenine and guanine nucleobases, were conveniently synthesized from D-glucose, and the ribofuranose ring of 1 was found to exist predominantly in a S-conformation by means of 1H NMR and X-ray analysis.

ChemInform Abstract: Syntheses and Properties of Conformationally Restrained Nucleosides and Oligonucleotides Analogues

This review summarizes our efficient syntheses of novel bicyclic nucleoside analogues, 3'-O,4'-C-methyleneribonucleosides (1) (4-BC type nucleoside analogue), 2'-O,4'-C-methyleneribonucleosides (2) (5-BC), 3'-amino-3'-deoxy-3'-N,4'-C-methyleneribonucleosides (3) (aza 4-BC), and 3'-azido- and 3'-amino-3'-deoxy-2'-O,4'-C-methyleneribonucleosides (4, 5) (aza 5-BC). From 1H-NMR and X-ray crystallographic analyses, the 4-BC and aza 4-BC type nucleoside analogues (1, 3) were found to have a S-conformation predominantly, while the conformations of 5-BC and aza 5-BC type nucleoside analogues (2, 4, 5) were exclusively locked in N-form. The 4-BC and 5-BC type nucleoside analogues (1, 2) were effectively introduced into oligonucleotides using a DNA synthesizer. Furthermore, unprecedented hybridizing ability towards complementary RNA and DNA, RNA selectivity, potent triplex forming ability, and sufficient enzymatic stability of these modified oligonucleotides were also confirmed. These results should reveal a promising route to the development of antisense/antigene methodology.

FV100 as a new approach for the possible treatment of varicella-zoster virus infection

FV100 is a promising new agent with extreme potency and specificity for varicella-zoster virus (VZV). It is the valyl ester pro-drug of Cf1743, the lead clinical candidate among the highly lipophilic bicyclic nucleoside analogue (BCNA) family discovered in Cardiff/Leuven. Cf1743 is unique amongst antivirals in terms of its structure and lipophilicity. It is exquisitely potent and selective for human VZV. FV100 has recently entered a randomized, controlled Phase II clinical trial for the treatment of shingles, sponsored by Inhibitex.

Synthesis and Properties of CycloSal-phosphatetriesters of Fluorescent Bicyclic Nucleoside Analogues (BCNAS)

Synthesis and Properties of CycloSal-phosphatetriesters of Fluorescent Bicyclic Nucleoside Analogues (BCNAS)

Alkenyl substituted bicyclic nucleoside analogues retain nanomolar potency against Varicella Zoster Virus

Novel alkenyl substituted aryl bicyclic furano pyrimidines have been prepared and evaluated in vitro against Varicella Zoster Virus (VZV). The para-substituted analogues retain the nanomolar potency we have reported for p-alkyl analogues, while the ortho- and meta-alkenyl systems lose 3–4 orders of potency.

Antiviral drug discovery: Ten more compounds, and ten more stories (part B)

This review article that complements the previous review article on "The discovery of antiviral agents: ten different compounds, ten different stories" presents ten more compounds and ten more stories in which I have been closely involved at one or another point of my scientific career: (i) interferon (IFN) (in particular, IFN-beta); (ii) poly(I).poly(C); (iii) suramin; (iv) novel acyclic nucleoside phosphonates; (v) the double prodrug of [9-(2-phosphonomethoxyethyl)guanine]; (vi) cyclic nucleoside phosphonates; (vii) picornavirus inhibitors; (viii) human immunodeficiency virus (HIV) co-receptor inhibitors; (ix) nonimmunosuppressive cyclosporin A analogues; and (x) bicyclic (furanopyrimidine) nucleoside analogues. With the exception of the HIV co-receptor CCR5 inhibitor none of the compounds described here have already been marketed (for the indication they were initially developed). Successful antiviral drug development depends on the interplay of three disciplines, chemistry, biology/medicine, and industry, crucial factors being open mindedness for the unexpected, preparedness to explore serendipitous observations, and perseverance (in trying) to overcome the hurdles or setbacks inevitably compounding any drug development.

Synthesis of 2',3'-Cyclohexene Bicyclic Nucleoside Analogues as Antiviral Compounds

Chiral syntheses of a series of hexahydroisobenzofuran (HIBF) nucleosides have been accomplished via glycosylation of a stereo-defined (syn-isomer) sugar motif with the appropriate silylated bases. All nucleoside analogues were obtained in 52-71% yield as a mixture of alpha- and beta-anomeric products increasing the breadth of the novel nucleosides available for screening. Nucleoside derivatives were tested as inhibitor of HIV-1 in human peripheral blood mononuclear (PBM) cells.