Analogs of (A2'p)nA. Correlation of structure of analogs of ppp(A2'p)2A and (A2'p)2A with stability and biological activity

3-Deazaadenosine analogues of p5'A2'p5'A2'p5'A: synthesis, stereochemistry, and the roles of adenine ring nitrogen-3 in the interaction with RNase L

Sequence-specific 3-deazaadenosine (c(3)A)-substituted analogues of trimeric 2',5'-oligoadenylate, p5'A2'p5'A2'p5'A, were synthesized and evaluated for their ability to activate human RNase L (EC 3.1.2.6) aiming at the elucidation of the nitrogen-3 role in this biochemical process. Substitution of either 5'-terminal or 2'-terminal adenosine with c(3)A afforded the respective analogues p5'(c(3)A)2'p5'A2'p5'A and p5'A2'p5'A2'p5'(c(3)A) that were as effective as the natural tetramer itself as activators of RNase L (EC(50)=1nM). In contrast, p5'A2'p5'(c(3)A)2'p5'A showed diminished RNase L activation ability (EC(50)=10nM). The extensive conformational analysis of the c(3)A-substituted core trimers versus the parent natural core trimer by the (1)H and (13)C NMR, and CD spectroscopy displayed close stereochemical similarity between the natural core trimer and (c(3)A)2'p5'A2'p5'A and A2'p5'A2'p5'(c(3)A) analogues, thereby strong evidences for the syn base orientation about the glycosyl bond of the c(3)A residue of the latter were found. On the contrary, an analogue A2'p5'(c(3)A)2'p5'A displayed rather essential deviations from the spatial arrangement of the parent natural core trimer.

Dissection of the roles of adenine ring nitrogen (N-1) and exocyclic amino (N-6) moieties in the interaction of 2-5A with RNase L

To elucidate further the roles played by the adenine bases in the interaction of RNase L (EC 3.1.2.6) with the 2',5'-oligoadenylate 2-5A, p5'A2'(p5'A2')np5' A, a series of sequence-specific 1-deazaadenosine (c1A)-substituted analogues were synthesized and evaluated for their ability to bind to and activate human RNase L in comparison to earlier reported inosine-substituted congeners of 2-5A. Substitution of only the 5'-terminal adenosine of p5'A2'p5'A2 p5 A with c1A afforded an analogue with strongly diminished RNase L binding and activation ability, while replacement of the second or middle adenosine of p5 A2' p5'A2'p5' A had only a modest effect. In distinct contrast to p5'A2'p5'A2'p5'I, the c1A analogue with the third or 2'-terminal adenosine replacement approached parent p5' A2'p5'A2'p5' A in RNase L activation ability. These results permitted a further dissection of the role of various nucleotidic functional groups in the interaction of 2-5A with RNase L: specifically, that the 5'-terminal adenosine purine N-1 moiety is key for binding to RNase L, while the 2'-terminal adenosine N-6 exocyclic amino group is critical for RNase L activation.

Picornavirus inhibitors

Picornaviruses are among the best understood animal viruses in molecular terms. A number of important human and animal pathogens are members of the Picornaviridae family. The genome organization, the different steps of picornavirus growth and numerous compounds that have been reported as inhibitors of picornavirus functions are reviewed. The picornavirus particles and several agents that interact with them have been solved at atomic resolution, leading to computer-assisted drug design. Picornavirus inhibitors are useful in aiding a better understanding of picornavirus biology. In addition, some of them are promising therapeutic agents. Clinical efficacy of agents that bind to picornavirus particles has already been demonstrated.

Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Isotachophoretic determination of 2-5A phosphodiesterase

Together with 2-5A synthetase and ribonuclease L, 2-5A phosphodiesterase belongs to the 2-5A system, which plays an important role in the action of interferon. Analytical capillary isotachophoresis was used for the determination of 2-5A phosphodiesterase activity. Enzyme assay was optimized using snake venom phosphodiesterase as a source of 2-5A phosphodiesterase activity. The 2-5A trimer core was used as a substrate. Enzyme activity was determined in time- and concentration-dependent reactions. In addition, 2-5A phosphodiesterase activity was determined in lysates of mononuclear blood cells.

Mechanisms of degradation of 2'-5' oligoadenylates

We have studied the mechanisms of breakdown of 2'-5' oligoadenylates. We monitored the time-courses of degradation of ppp(A2'p5')nA (dimer to tetramer) and of 5'OH-(A2'p5')nA (dimer to pentamer) in unfractionated L1210 cell extract. The 5' triphosphorylated 2'-5' oligoadenylates are converted by a phosphatase activity. However, 2'-5' oligoadenylates are degraded mainly by phosphodiesterase activity which splits the 2'-5' phosphodiester bond sequentially at the 2' end to yield 5' AMP and one-unit-shorter oligomers. The nonlinear least-squares curve-fitting program CONSAM was used to fit these kinetics and to determine the degradation rate constant of each oligomer. Trimers and tetramers, whether 5' triphosphorylated or not, are degraded at the same rate, whereas 5' triphosphorylated dimer is rapidly hydrolyzed and 5'-OH dimer is the most stable oligomer. The interaction between degradation enzymes and the substrate strongly depends on the presence of a 5' phosphate group in the vicinity of the phosphodiester bond to be hydrolyzed; indeed, when this 5' phosphate group is present, as in pp/pA2'p5'A/or A2'/p5'A2'p5'A/, affinity is high and maximal velocity is low. Such a degradation pattern can control the concentration of 2'-5' oligoadenylates active on RNAse L either by limiting their synthesis (5' triphosphorylated dimer is the primer necessary for the formation of longer oligomers) and/or by converting them into inhibitory (e.g., monophosphorylated trimer) or inactive (e.g., nonphosphorylated oligomers) molecules.

Methylxanthine treatment of rats reduces 2,5-oligoadenylate synthesis in liver nuclei

The in vivo effects of methylxanthines on 2',5'-oligoadenylate (2,5An) synthetase activity, an interferon-inducible enzyme, were investigated in rat liver nuclei. Caffeine given at 50 mg/kg ip or theobromine given at 80 mg/kg sc twice daily for 5 d resulted in a 60% reduction (p less than 0.01 and p less than 0.05, respectively) of 2,5An synthetase activity in liver nuclei. Theophylline given at 80 mg/kg sc by the same regimen reduced the enzyme activity by 42% (p less than 0.05). Nuclear 2'-phosphodiesterase activity, which catalyzes the degradation of 2,5An, remained low and unchanged following the drug treatments. When animals receiving caffeine were also given the interferon inducer poly(I)poly(C) at 500 micrograms/kg ip once daily for the last 2 d of caffeine treatment, it resulted in the same fourfold increase in 2,5An synthetase activity as shown with poly(I)poly(C) alone. These results suggest that methylxanthines may interact with interferon-mediated actions. The reason for the inhibitory effect of methylxanthines on the basal but not on the induced 2,5An synthetase remains to be investigated.

Degradation by the 2',5'-phosphodiesterase activity of mouse cells requires the presence of a ribo hydroxyl group in the penultimate position of the oligonucleotide substrate

A series of 9-beta-D-xylofuranosyladenine (xyloA or xyloadenosine) substituted analogs of 2-5A core trimer and tetramer were examined for their ability to be degraded by the 2',5'-phosphodiesterase activity of cytoplasmic extracts of mouse L cells. Two distinct groups of xyloA-substituted analogs could be readily discriminated. The first group contained xyloadenosine at the 2'-termini and included A2'p5'A2'p5'(xyloA) and A2'p5'A2'p5'A2'p5'(xyloA). These oligomers behaved as did their parent oligoadenylates in that they were equally sensitive to degradation by the 2',5'-phosphodiesterase activity. The second group of oligonucleotides bore a xyloadenosine residue in the penultimate nucleotide residues of the oligomers and included A2'p5'(xyloA)2'p5'(xyloA), (xyloA)2'p5'(xyloA)2'p5'(xyloA), A2'p5'A2'p5'(xyloA)2'p5'(xyloA) and (xyloA)2'p5' (xyloA)2'p5'(xyloA)2'p5'(xyloA). This group was quite resistant to 2',5'-phosphodiesterase activity. In all, the findings demonstrate that the ribo configuration 3'-hydroxyl group in the penultimate nucleotide of the oligonucleotide substrate is a prerequisite for the 2',5'-phosphodiesterase activity.

2',5'-Phosphodiesterase activity depends upon the presence of a 3'-hydroxyl moiety in the penultimate position of the oligonucleotide substrate

3'-Deoxyadenosine (3'dA, cordycepin)-substituted analogs of 2-5A core 5'-monophosphate (p5'A2'p5'A2'p5'A) were examined for their sensitivity toward degradation by the 2'-phosphodiesterase activity in cytoplasmic extracts of mouse L cells. The analogs, p5'(3'dA)-2'p5'A2'p5'A, p5'(3'dA)2'p5'A2'p5'(3'dA) and p5'A2'p5'A2'p5'(3'dA) were degraded at a rate comparable to p5'A2'p5'A2'p5'A itself. On the other hand, under the assay conditions examined p5'A2'p5'(3'dA)2'p5'A, like p5'(3'dA)2'p5'(3'dA)2'p5'(3'dA), was completely resistant to degradation. The data imply that sensitivity to the 2',5'-phosphodiesterase activity of mouse L cells requires the presence of 3'-hydroxyl moiety in the penultimate nucleotide.

Antiviral activity of a chemically stabilized 2-5A analog upon microinjection into HeLa cells

2-5A[ppp(A2'p)n5'A] has been implicated as a mediator in the antiviral action of interferon. Its direct evaluation as an indicator of virus replication is hampered by two limitations: its inability to penetrate intact cells, and its rapid intracellular degradation by (2'-5')phosphodiesterase. These problems could be overcome by using a microinjection technique whereby a phosphodiesterase-resistant analog of 2-A, in which the 2'-terminals adenosine residue is replaced by 2-(9-adenyl)-6-hydroxy-methyl-4-hexylmorpholine, was injected into individual HeLa cells before infection with mengovirus or vesicular stomatitis virus (VSV). This comparative assay with two representatives of different virus classes in a single experimental system pointed to the high sensitivity of VSV to inhibition by 2-5A oligonucleotides, in contrast with the low sensitivity of mengovirus. Microinjection of the hexylmorpholine 2-5A analog led to a much greater reduction in mengovirus yield than did microinjection of 2-5A itself.

Antiviral activity in L1210 cells of liposome-encapsulated (2'-5')oligo(adenylate) analogues

Evidence is available for a role of a (2'-5')(A)n-activated endoribonuclease (RNase L) in the antiviral activity of interferon for several RNA viruses. (2'-5')(A)n and their analogues might thus provide an interesting alternative to exogenous interferons or their inducers in antiviral chemotherapy. In addition, the evaluation of the activity of (2'-5)(A)n as mediators of interferon's biological activities or as cell growth regulators requires biochemical studies using agonists or antagonists of the system. Non-disruptive techniques for the introduction of (2'-5')(A)n and their analogues into cell lines or tissues are required for these studies since these highly charged compounds are cell impermeable. (2'-5')(A)n oligomers and analogues of increased stability towards phosphodiesterases were derived by chemical modification of their 2' end and encapsulated in protein-A-bearing liposomes. The specific delivery of liposome contents into L1210 mouse leukemic cells was achieved with the help of monoclonal antibodies directed against the appropriate class I major histocompatibility complex-encoded proteins expressed by these cells. This intracellular delivery led to transient inhibition of protein synthesis and an antiviral activity, both compatible with activation of RNase L. This activity was enhanced for the analogues designed to resist degradation, with respect to the natural product.

New antiviral compounds

Several potent and selective antiviral agents against herpes virus infections have been developed. However, the majority of compounds against other viral diseases has not yet reached such high standard. Based on progress in molecular virology it can, however, be anticipated that similar concepts of selective inhibition will also be developed for other virus groups. In addition to virus-induced enzymes, viral proteins other than enzymes with specific activities will be identified. The identification of active sites will lead to the design of new and specific inhibitors. Moreover, studies on the mode of action of the huge number of known antiviral compounds may provide the basis for new and potent approaches to specific virus chemotherapy. New inhibitors of viral replication may also be derived from 2'-5'A and other mediators of the interferon induced antiviral state. However, since 2'-5'A does not enter cells, is rapidly degraded by phosphodiesterases, and affects viral and cellular protein synthesis, only analogs which do not have these disadvantages may qualify as antiviral drugs. In addition to refinements at the molecular level quantitative assays for a better evaluation of antiviral agents for clinical use are required. For clinical trials, rapid diagnosis, early initiation of treatment, and quantitative evaluation of the antiviral effects of a drug need to be developed. Moreover, new methods of drug delivery and/or drug targeting will improve potency and selectivity of antiviral compounds. Drug carriers have already successfully been used in cancer therapy (Poste and Fidler, 1981) they should be also applicable to virus chemotherapy. Finally, a better understanding of the pathogenesis and the natural course of viral diseases will contribute to the development of more effective and safe antiviral agents.

Influence of the xyloadenosine analogue of 2',5'-oligoriboadenylate on poly(A)-specific, 2',5'-oligoriboadenylate degrading 2',3'-exoribonuclease and further enzymes involved in poly(A)(+)mRNA metabolism

The homogeneous poly(A)-specific 2',3'-exoribonuclease from calf thymus gland, which cleaves both 3',5'- and 2',5'-linked oligoriboadenylates, does not degrade (xyloA2'p)2 xyloA, the xylofuranosyladenosine analogue of the 2-5A core. This oligonucleotide, which is supposed to enter intact cells rapidly, was found to possess an increased stability and an enhanced antiherpesvirus activity compared to the natural (A2'p)2A (Eppstein, D.A., Barnett, J.W., Marsh, Y.V., Gosselin, G. and Imbach, J.-L. (1983) Nature 302, 723-724). The poly(A) anabolic enzyme, poly(A) polymerase (Mn2+-dependent), from the same source, which is initiated by (A3'p)2A and its higher oligomers, does not accept 2-5A core and its xyloadenosine analogue as primer. Both oligonucleotides exert no influence on endoribonuclease IV and on the integrity of the poly(A)-ribonucleoprotein complex.

pppA2'p5A' blocks vesicular stomatitis virus replication in intact cells

pppA2'p5'A blocked the production of infectious vesicular stomatitis virus in HeLa cells. When this compound was present from the beginning of infection, a selective inhibitory effect was observed in viral protein synthesis. Thus, cellular translation was not affected even after 10 h of incubation with this compound, and the bulk of viral proteins was not synthesized. However, this effect was not observed with ATP, GTP, or the core A2'p5'A. The step blocked by pppA2'p5'A is located early during virus infection, but adsorption, entry, and virus uncoating seemed to be unaffected by this compound. Analysis of the antiviral spectrum of pppA2'p5'A indicated that it is active against poliovirus, encephalomyocarditis virus, and Semliki Forest virus and shows no effect against herpes simplex virus type 1 and adenovirus type 5.

Mechanism of inhibition of herpesvirus growth by 2'-5'-linked trimer of 9-beta-D-xylofuranosyladenine

The 2'-5'-linked trimer of 9-beta-D-xylofuranosyladenine (XyloA)3 is an extremely potent inhibitor of growth of herpes simplex viruses 1 and 2. Evidence is presented that in spite of its increased stability in cell-free extracts (D.A. Eppstein, Y.V. Marsh, B.B. Schryver, M.A. Larsen, J.W. Barnett, J.P.H. Verheyden, and E.J. Prisbe, J. Biol. Chem. 257, 13390-13397, 1982), intact (XyloA)3 was not detected in Vero cells, but instead was rapidly degraded in the medium to monomeric 9-beta-D-xylofuranosyladenine (XyloA). The XyloA thus formed was rapidly taken up by cells, phosphorylated to its triphosphate, and produced inhibition of RNA synthesis. The observed inhibition of DNA synthesis (D.A. Eppstein, Y.V. Marsh, B.B. Schryver, M.A. Larsen, J.W. Barnett, J.P.H. Verheyden, and E.J. Prisbe, J. Biol. Chem. 257, 13390-13397, 1982) and herpesvirus growth by (XyloA)3 (D.A. Eppstein, J.W. Barnett, Y.V. Marsh, G. Gosselin, and J.L. Imbach, Nature (London) 302, 723, 724, 1983) is most likely the result of inhibition of RNA synthesis by its degradation product XyloA.

Increased stability and antiviral activity of 2'-O-phosphoglyceryl derivatives of (2'-5')oligo(adenylate)

Metabolically stable analogues of (2'-5')oligo(adenylate), (2'-5')(A)n, might constitute a new class of antiviral agents as they mimic some of the effects of interferons. 2'-O-phosphoglyceryl derivatives of (2'-5')(A)n oligomers, (2'-5')(A)n-PGro have been synthesized by chemical modification of their terminal ribose residue. Such analogues are resistant to degradation by phosphodiesterases but remain sensitive to phosphatase activity, at least in cell-free extracts. In line with its increased stability, (2'-5')(A)n-PGro has a powerful antiviral activity against an RNA virus when microinjected with micropipettes into the cytoplasm of intact cells. This antiviral activity remains transient however, possibly as a consequence of degradation in intact cells. Since (2'-5')(A)n and its derivatives do not easily cross cell membranes, their possible use in antiviral chemotherapy is tightly linked with the development of vectors suitable for their administration in vivo.

Mechanism of antiviral activity of (XyloA2'p)2XyloA

(XyloA2'p)2xyloA, the xyloadenosine core analog of the interferon mediator 2-5A [ppp(A2'p)2A], was found to exhibit potent antiviral activity against herpes simplex viruses 1 and 2 (D. A. Eppstein, J. W. Barnett, Y. V. Marsh, G. Gosselin, and J. -L. Imbach (1983a) Nature (London) 302: 723-724). This xylo 2-5A core analog was over 100 times more stable to phosphodiester cleavage than was parent 2-5A core in cell-free extracts, which was originally thought to have contributed to its increased activity. However, we have now shown that the xylo 2-5A core does not activate the 2-5A-dependent endonuclease, and, additionally, that its mechanism of action is different from that of parent 2-5A core, even though it too does not activate the endonuclease. In fact, the mechanism of action of xylo 2-5A core apparently involves its degradation to monomer units, which then exert the antiviral effect. The enhanced antiviral activity of xylo 2-5A core (normalized to monomer-unit equivalents) as compared to that of xyloadenosine appears to be mediated through a slow release of xyloadenosine monomer units (i.e., xyloAMP). XyloAMP is resistant to inactivation by deamination, and thus intracellular xyloAMP should have increased antiviral activity compared to an equivalent concentration of xyloadenosine, which is subject to rapid inactivation by deamination.

Cordycepin analog of (A2'p)2A: evidence that it functions as a prodrug of cordycepin

The effect of the cordycepin trimer analog of (A2'p)2A on cell growth, cell viability and nucleic acid synthesis was assessed in human colon carcinoma cell line HT-29 in vitro. The cordycepin analog, (3'dA2'p)2(3)'dA reduced 24 hr cell growth by 50% at 10(-4)M and decreased cell viability by 98% under these conditions. The cytotoxicity and inhibitory effects of (3'dA2'p)2(3)'dA on DNA and RNA synthesis were potentiated 5-10-fold by the presence of the adenosine deaminase inhibitor, 2'-deoxycoformycin, and closely resembled those of the parent drug, cordycepin. Chromatographic analyses of the stability of (3'dA2'p)2(3)'dA in the tissue culture medium indicated that it was hydrolyzed to the dimer and monomer forms with a half life of approximately 2 hr. No intact (3'dA2'p)2(3)'dA was detectable intracellularly, but large concentrations of cordycepin nucleotide metabolites were formed, particularly in the presence of 2'-deoxycoformycin.

Xyloadenosine analogue of (A2'p)2A inhibits replication of herpes simplex viruses 1 and 2

Molecules of the structure ppp(A2'p)2A containing a 2' leads to 5' phosphodiester bond, commonly abbreviated as 2-5A, are synthesized in interferon-treated virally-infected cells and have been implicated in several systems as contributing to interferon's antiviral activity. The 2-5A binds to and subsequently activates an endogenous endonuclease, ultimately resulting in degradation of RNA. We have been interested in the use of 2-5A analogues to achieve antiviral activity without the use of interferon. For this approach to be successful, analogues must be synthesized with an increased stability (native 2-5A is rapidly degraded by cellular phosphodiesterases) and with increased ability to enter intact cells. Removal of the highly-negative charged 5' terminal phosphates from ppp(A2'p)2A results in formation of the 'core' species, (A2'p)2A, which should be able to penetrate intact cells more readily. While Kimchi et al. have shown that 2-5A core has an antimitogenic effect in mouse spleen lymphocytes and 3T3 fibroblasts, Williams and Kerr have reported lack of antiviral activity against Semliki Forest virus or encephalomyocarditis virus by exogenously-administered 2-5A core. We have previously determined that (xyloA2'p)2xyloA (abbreviated as xylo 2-5A core), the xyloadenosine analogue of the 5'-terminally dephosphorylated 2-5A core, is over 100 times more stable than the parent 2-5A core species. We now report that this xylo 2-5A core inhibits replication of herpes simplex viruses 1 and 2 in vitro, with greater than 100 times the activity of the parent 2-5A core. The mechanism of antiviral action of the 2-5A core analogue appears to involve a pathway different from that activated by the parent 5' triphosphorylated 2-5A species.

Partial dissociation of antiviral and antimitogenic activities of murine interferon after its incorporation into liposomes

Murine fibroblast interferon (MuIFN, 90% beta, 10% alpha) was associated with both positively and negatively charged liposomes formed by reverse-phase evaporation. This interferon-liposome association occurred predominantly in a manner that resulted in protection of a significant portion of the IFN's antiviral activity from trypsin digestion, yet also permitted biological expression of this activity without prior liposome disruption. A differential dissociation of antiviral and antimitogenic activities was observed with MuIFN associated with positively vs negatively charged liposomes, as reflected by differential sensitivities to trypsin inactivation. This may reflect either (1) differential associations of various molecular species of MuIFN with liposomes, or (2) that different portions of the IFN molecule are responsible for the antiviral and the antimitogenic activities.