RNA synthesis by ribonucleoprotein-polymerase complexes isolated from influenza virus

Prodrugs of the Phosphoribosylated Forms of Hydroxypyrazinecarboxamide Pseudobase T-705 and Its De-Fluoro Analogue T-1105 as Potent Influenza Virus Inhibitors

We here disclose chemical synthesis of ribonucleoside 5'-monophosphate (RMP), -diphosphate (RDP), and -triphosphate (RTP) and cycloSal-, Di PPro-, and Tri PPPro nucleotide prodrugs of the antiviral pseudobase T-1105. Moreover, we include one nucleoside diphosphate prodrug of the chemically less stable T-705. We demonstrate efficient T-1105-RDP and -RTP release from the Di PPro and Tri PPPro compounds by esterase activation. Using crude enzyme extracts, we saw rapid phosphorylation of T-1105-RDP into T-1105-RTP. In sharp contrast, phosphorylation of T-1105-RMP was not seen, indicating a yet unrecognized bottleneck in T-1105's metabolic activation. Accordingly, Di PPro and Tri PPPro compounds displayed improved cell culture activity against influenza A and B virus, which they retained in a mutant cell line incapable of activating the nucleobase parent. T-1105-RTP had a strong inhibitory effect against isolated influenza polymerase, and Di PPro-T-1105-RDP showed 4-fold higher potency in suppressing one-cycle viral RNA synthesis versus T-1105. Hence, our T-1105-RDP and -RTP prodrugs improve antiviral potency and achieve efficient metabolic bypass.

Distinct Effects of T-705 (Favipiravir) and Ribavirin on Influenza Virus Replication and Viral RNA Synthesis

T-705 (favipiravir) is a new antiviral agent in advanced clinical development for influenza therapy. It is supposed to act as an alternative substrate for the viral polymerase, causing inhibition of viral RNA synthesis or virus mutagenesis. These mechanisms were also proposed for ribavirin, an established and broad antiviral drug that shares structural similarity with T-705. We here performed a comparative analysis of the effects of T-705 and ribavirin on influenza virus and host cell functions. Influenza virus-infected cell cultures were exposed to T-705 or ribavirin during single or serial virus passaging. The effects on viral RNA synthesis and infectious virus yield were determined and mutations appearing in the viral genome were detected by whole-genome virus sequencing. In addition, the cellular nucleotide pools as well as direct inhibition of the viral polymerase enzyme were quantified. We demonstrate that the anti-influenza virus effect of ribavirin is based on IMP dehydrogenase inhibition, which results in fast and profound GTP depletion and an imbalance in the nucleotide pools. In contrast, T-705 acts as a potent and GTP-competitive inhibitor of the viral polymerase. In infected cells, viral RNA synthesis is completely inhibited by T-705 or ribavirin at ≥50 μM, whereas exposure to lower drug concentrations induces formation of noninfectious particles and accumulation of random point mutations in the viral genome. This mutagenic effect is 2-fold higher for T-705 than for ribavirin. Hence, T-705 and ribavirin both act as purine pseudobases but profoundly differ with regard to the mechanism behind their antiviral and mutagenic effects on influenza virus.

Identification of N-Hydroxamic Acid and N-Hydroxyimide Compounds that Inhibit the Influenza Virus Polymerase

The RNA-dependent RNA polymerase of influenza virus transcribes messenger RNA through a unique cap-scavenging mechanism. The polymerase binds to the cap structure at the 5′ ends of host mRNAs, which are then cleaved and used as primers for viral mRNA synthesis. In an effort to discover antiviral compounds against this target, an in-vitro transcription assay was utilized to screen a proprietary chemical collection. Results of this screening effort identified an N-hydroxamic acid structure as an inhibitor of the capped RNA-dependent transcriptase activity. Subsequent sub-structure searching and screening based upon this pharmacophore identified two related N-hydroxyimide compounds as specific inhibitors. These compounds were found to inhibit the cap-scavenging mechanism through inhibition of the endonuclease function of the polymerase.

Influenza virus endoribonuclease

The influenza virus polymerase complex contains two associated enzymatic activities, an endoribonuclease and a RNA-dependent RNA polymerase activity. Both activities have so far been observed only with the complete polymerase complex consisting of three subunits, PB1, PB2, and PA. This chapter describes a robust and optimized procedure for the purification of active influenza virus polymerase in complex with genomic RNA and the single-stranded RNA-binding protein nucleoprotein from influenza virus particles. It also explains the synthesis of capped RNA molecules as substrates of the influenza virus endonuclease. The enzymatic properties of influenza virus-derived endoribonuclease activity have been characterized with a model RNA substrate of 20-nucleotide length, termed G20 RNA. The rate of RNA cleavage under steady state conditions appears to be limited by product dissociation. Therefore conditions have been optimized to study the chemical step of RNA cleavage under single turnover conditions. The enzyme requires divalent metal ions for activity and can use Mn(II), Co(II), and Fe(II) efficiently at pH 7, Mg(II) with intermediate efficiency, and Ni(II) and Zn(II) with lower efficiency. The reaction progress curves show slow binding of Zn(II) and Ni(II) to the protein, suggesting a conformational change of the active site as a prerequisite for endonuclease activity in the presence of these two metal ions. Low concentrations of the detergent DOC inhibit the activity and also disrupt the trimeric polymerase complex, whereas other detergents do not have a significant effect on the activity.

Differential effect of modified capped RNA substrates on influenza virus transcription

The RNA-dependent RNA polymerase of influenza virus transcribes messenger RNA through a unique cap scavenging mechanism. Viral enzyme binds to the cap structure of host mRNA, cleaves the molecule 9-15 bases downstream of the cap, and uses the short capped oligonucleotide as a primer for mRNA synthesis. Previously, we have shown that the viral polymerase can efficiently bind capped RNAs shorter than 9 nucleotides in length, but the viral enzyme can not utilize these RNAs as primers. For this reason, these short capped oligonucleotides are potent inhibitors of influenza virus transcription. In these studies, it is now shown that short capped oligomers inhibit capped-RNA dependent transcription at the initial step of cap binding. In contrast, low concentrations of these short capped RNAs can actually stimulate viral transcription primed with high concentrations of the dinucleotide ApG. Another capped RNA derivative containing phosphorothioate oligonucleotides was also investigated as a potential polymerase inhibitor. This longer capped RNA was able to bind to the polymerase, but could not be cleaved to primer length by the enzyme associated endonuclease. Thus, the capped phosphorothioate RNA inhibited cap-primed transcription at the step of cap binding. However, in contrast to the short capped oligonucleotide, it also inhibited ApG primed viral transcription.

Effect of M1 protein and low pH on nuclear transport of influenza virus ribonucleoproteins

Influenza virus enters its host cell by receptor-mediated endocytosis followed by acid-activated membrane fusion in endosomes. The viral ribonucleoprotein particles (vRNPs) delivered into the cytosol then dissociate from the matrix protein, M1, and from each other, after which they are individually imported into the nucleus via the nuclear pores. For some time, it has been believed that the low pH in endosomes may, in some way, trigger the capsid disassembly events necessary for nuclear transport. This report provides direct evidence that the association of M1 with vRNPs is sensitive to mildly acidic pH within the infected cell. Recombinant M1, expressed in cultured cells, was found to associate with vRNPs and inhibit their nuclear import. Brief acidification of the cytosolic compartment eliminated the interfering activity and allowed the incoming vRNPs to enter the nucleus. Newly assembled progeny M1-vRNP complexes in the cytosol of infected cells were also dissociated by brief acidification. Acidic pH was thus found to serve as a switch that allowed M1 to carry out its multiple functions in the uncoating, nuclear transport, and assembly of vRNPs.

Monoclonal antibodies against influenza virus PB2 and NP polypeptides interfere with the initiation step of viral mRNA synthesis in vitro

Two panels of monoclonal antibodies (MAbs) specific for the influenza A virus PA and PB2 polypeptides have been obtained from mice immunized with denatured proteins produced in Escherichia coli. All MAbs (13 specific for the PA polypeptide and 8 specific for the PB2 protein) reacted to the corresponding influenza virus protein in Western blotting (immunoblotting), immunoprecipitation, and immunofluorescence assays. To gain information about the roles of the nucleoprotein (NP) and PB2 and PA proteins during viral mRNA synthesis, the 21 anti-P antibodies and 3 anti-NP antibodies (J. A. López, M. Guillen, A. Sánchez-Fauquier, and J. A. Melero, J. Virol. Methods 13:255-264, 1986) were purified and tested for their ability to inhibit the transcriptase activity associated with viral cores purified from virions. Four of the antibodies (one anti-PB2 and the three anti-NP MAbs) inhibited transcription by more than 50% compared with unrelated control antibodies. The inhibitory effect was not due to a nonspecific effect of the antibody preparations, because these MAbs did not inhibit transcription when tested on influenza B virus nucleocapsids, which are not recognized by the antibodies. To determine whether the antibodies were acting on an early transcription step, transcription reactions were carried out in the presence of globin mRNA (a mixture of alpha- and beta-globin chains) and only one labeled nucleoside triphosphate (either GTP or CTP). The results obtained showed that MAbs to the PB2 and NP polypeptides interfered with the initiation step of mRNA-primed transcription. The implications of these results regarding initiation of viral mRNA synthesis are discussed.

Biochemical studies on capped RNA primers identify a class of oligonucleotide inhibitors of the influenza virus RNA polymerase

A synthetic 67-nt RNA substrate, containing a 32P-labeled cap-1 structure (m7G32pppGm) was specifically cleaved by the influenza virus RNA polymerase (EC 2.7.7.48) to yield a single capped 11-nt fragment capable of directly priming transcription. An analysis of systematic truncations of this RNA substrate demonstrated that an additional nucleotide beyond this cleavage site was required for cleavage. The minimal RNA chain length required for priming activity was found to be 9 nt, while in contrast an RNA chain length of at least 4 nt was required for efficient binding to the viral polymerase. On the basis of these chain length requirements we show that a pool of capped oligonucleotides too short to prime transcription, but long enough to bind with high affinity to the viral polymerase, are potent inhibitors of cap-dependent transcription in vitro.

Solubilization of matrix protein M1/M from virions occurs at different pH for orthomyxo- and paramyxoviruses

Enveloped viruses, of which the orthomyxo- and paramyxoviruses are members, are known to be uncoated by nonionic detergents in a salt concentration-dependent manner. In this study we have shown that detergent uncoating of myxoviruses depends not only on salt concentration but also on pH. Treatment of orthomyxoviruses with Nonidet-P40 or Triton N-101 at low salt concentrations results in solubilization of surface virion glycopolypeptides in alkaline and neutral pH (9.0-6.5), but in acidic pH (6.0-5.0) the viral matrix protein M1 is also removed, and the viral ribonucleoprotein complex is released. Conversely, the paramyxovirus matrix protein M is more completely solubilized in alkaline pH (pH 9.0) than in neutral and acidic pH 7.4-5.0. The described pH-dependent differences are discussed in terms of orthomyxo- and paramyxovirus uncoating in target cells.

Promoter analysis of influenza virus RNA polymerase

Influenza virus polymerase, which was prepared depleted of viral RNA, was used to copy small RNA templates prepared from plasmid-encoded sequences. Template constructions containing only the 3' end of genomic RNA were shown to be efficiently copied, indicating that the promoter lay solely within the 15-nucleotide 3' terminus. Sequences not specific for the influenza virus termini were not copied, and, surprisingly, RNAs containing termini identical to those from plus-sense cRNA were copied at low levels. The specificity for recognition of the virus sense promoter was further defined by site-specific mutagenesis. It was also found that increased levels of viral protein were required in order to catalyze both the cap endonuclease-primed and primer-free RNA synthesis from these model templates, as well as from genomic-length RNAs. This finding indicates that the reconstituted system has catalytic properties very similar to those of native viral ribonucleoprotein complexes.

Complementation and analysis of an NP mutant of influenza virus

Cell lines were constructed so as to express the influenza A virus nucleoprotein (NP) at levels approximating 5% of the total NP made throughout virus infection. Two types of cell lines were analyzed. One cell line (NP-5) expresses only the NP while another cell line was constructed which expresses the three viral polymerase proteins in addition to the NP (3PNP-4). Both cell lines were able to complement the growth of an NP mutant, ts56, at the non-permissive temperature. The 3PNP-4 cell line, constructed by transfecting a cell line already expressing the three polymerase proteins, continued to be able to complement viral PB2 mutants. In addition, sequence analysis was performed on the NP gene segment of A/WSN/33 and ts56 viruses. This analysis revealed that the mutant phenotype exhibited by ts56 at non-permissive temperature is due to a single serine to asparagine change (at codon 332) within the protein.

Viral RNA polymerases

Recent progress in molecular biological techniques revealed that genomes of animal viruses are complex in structure, for example, with respect to the chemical nature (DNA or RNA), strandedness (double or single), genetic sense (positive or negative), circularity (circle or linear), and so on. In agreement with this complexity in the genome structure, the modes of transcription and replication are various among virus families. The purpose of this article is to review and bring up to date the literature on viral RNA polymerases involved in transcription of animal DNA viruses and in both transcription and replication of RNA viruses. This review shows that the viral RNA polymerases are complex in both structure and function, being composed of multiple subunits and carrying multiple functions. The functions exposed seem to be controlled through structural interconversion.

Effect of ribavirin triphosphate on primer generation and elongation during influenza virus transcription in vitro

These studies examine the effect of ribavirin triphosphate (RTP) on two replicative functions associated with influenza virus nucleocapsids, primer generation and its subsequent elongation. To study primer generation influenza virus cores were added to beta-globin mRNA in the presence of only [32P]GTP. To examine elongation, ATP and CTP were added to the reaction mixture to permit limited elongation, and products from both reactions were separated on polyacrylamide gels and quantified. Under these conditions, the 50% inhibitory concentration of RTP for primer generation was 3.0 mM, and the 50% inhibitory concentration for elongation was 0.6 mM. RNA polymerase activity associated with cores isolated from clinical strains of influenza A and B viruses reacted as did the laboratory strain of influenza virus and was equally susceptible to inhibition by RTP.

Complete nucleotide sequence of the nucleoprotein gene of influenza B virus

A DNA copy of influenza B/Singapore/222/79 viral RNA segment 5, containing the gene coding for the nucleoprotein (NP), has been cloned in Escherichia coli plasmid pBR322, and its nucleotide sequence has been determined. The influenza B NP gene contains 1,839 nucleotides and codes for a protein of 560 amino acids with a molecular weight of 61,593. Comparison of the influenza B NP amino acid sequence with that of influenza A NP (A/PR/8/34) reveals 37% direct homology in the aligned regions, indicating a common ancestor. However, influenza B NP has an additional 50 amino acids at its N-terminal end. As is the case with influenza A NP, influenza B NP is a basic protein, with its charged residues relatively evenly distributed rather than clustered. The structural homology suggests functional similarity between the NP of influenza A and B viruses.

Molecular model of a eucaryotic transcription complex: functions and movements of influenza P proteins during capped RNA-primed transcription

We present a model for the functions and movements of the influenza virus P proteins (PB1, PB2, and PA) as they transcribe the virion RNAs (vRNAs) into messenger RNAs (mRNAs). Using ultraviolet-light-induced crosslinking, we show that the P proteins as a complex move from the 3' ends of the vRNA templates down the elongating mRNAs. PB2 binds the cap 1 structure of heterologous RNAs, which are cleaved to generate capped primer fragments. PB1, initially found at the first residue added onto the primer, moves to the 3' ends of the growing mRNA chains, indicating that it most likely catalyzes each nucleotide addition. PA and PB2 move down the growing chains in concert with PB1. PB2 is also associated with the cap during the first 11-15 nucleotides of chain growth, but then dissociates from the cap as the P protein complex moves further down the mRNA chains.

The sequence of RNA segment 1 of influenza virus A/NT/60/68 and its comparison with the corresponding segment of strains A/PR/8/34 and A/WSN/33

The complete nucleotide sequence of RNA segment 1 of influenza virus A/NT/60/68, corresponding to the PB2 protein, has been determined. It is 2341 nucleotides long, encoding a predicted product of 759 amino acids with a net charge of +27 1/2 at neutral pH. The predicted amino acid sequence has been compared to the equivalent sequences in influenza viruses A/PR/8/34 and A/WSN/33. Evolutionary divergence, assuming a direct lineage from A/PR/8/34 and allowing for "laboratory drift", is 0.08% per year. The alignment of RNA segment 10 of A/NT/60/68 with segments 1 and 3 is completed, confirming that it is a mosaic of regions from these two segments.

Interaction of polymerases with 2'-deoxyuridine-5'-triphosphate spin-labeled at the 5-position

2'-Deoxyuridine-5'-triphosphate spin-labeled at the 5-position with N-[1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl]-O- was found to be an inhibitor of some DNA and RNA polymerases including avian myeloblastosis virus reverse transcriptase. Furthermore, the spin-labeled nucleotide was found to be incorporated internally into polydeoxythymidylic acid via reverse transcriptase to an extent of 1.0 spin-labeled base per 10(3) bases. The incorporation, monitored by electron spin resonance, is analogous to some other nucleotide inhibitors of polymerases, and the results indicate that it may be feasible to obtain sequence specific, spin-labeled DNA, enzymatically.

Influenza virus temperature-sensitive cap (m7GpppNm)-dependent endonuclease

The first step in influenza viral mRNA synthesis is the endonucleolytic cleavage of heterologous RNAs containing cap 1 (m(7)GpppNm) structures to generate capped primers that are 10 to 13 nucleotides long, which are then elongated to form the viral mRNA chains. We examined the temperature sensitivity of these steps in vitro by using two WSN virus temperature-sensitive mutants, ts1 and ts6, which have a defect in the genome RNA segment coding for the viral PB2 protein. For these experiments, it was necessary to employ purified viral cores rather than detergent-treated virions to catalyze transcription, as preparations of detergent-treated virions contain destabilizing or inhibitory activities which render even the transcription catalyzed by wild-type virus temperature sensitive. Using purified wild-type viral cores, we found that the rates of endonucleolytic cleavage of capped primers and of overall transcription were similar at 39.5 and 33 degrees C, the in vivo nonpermissive and permissive temperatures, respectively. In contrast, the activities of the cap-dependent endonucleases of ts1 and ts6 viral cores at 39.5 degrees C were only about 15% of those at 33 degrees C. The steps in transcription after endonucleolytic cleavage of the capped RNA primer were largely, if not totally, temperature insensitive, indicating that the mutations in the PB2 protein found in ts1 and ts6 virions affect only the endonuclease step. The temperature-sensitive defect is most likely in the recognition of the 5'-terminal cap 1 structure that occurs as a required first step in the endonuclease reaction: the cap-dependent binding of a specific capped primer fragment to ts1 viral cores was temperature sensitive under conditions in which binding to wild-type viral cores was not affected by increasing the temperature from 33 to 39.5 degrees C. Thus, our results establish that the viral PB2 protein functions in cap recognition during the endonuclease reaction.

The influenza virus nucleoprotein synthesized from cloned DNA in a simian virus 40 vector is detected in the nucleus

We obtained DNA sequences coding for the nucleoprotein (NP) of an influenza A virus by reverse transcription of virion RNA with synthetic oligonucleotide primers. Terminal sequence analysis showed that the cloned gene contained a full-length copy of the virion RNA segment. The NP-specific DNA was inserted into the late region of a simian virus 40 vector, and the DNA recombinant was propagated in the presence of an early simian virus 40 temperature-sensitive mutant helper. Infection of African green monkey kidney cells with the recombinant produced a polypeptide immunoprecipitable with NP-specific antisera. The polypeptide product had a molecular weight of 56,000, identical to that of the nucleoprotein of influenza virus as estimated on polyacrylamide gels. The putative NP was detected in the nucleus of infected primate cells by an immunofluorescence assay. This nuclear localization of NP from recombinant DNA was similar to that seen during influenza virus infection.

Role of two of the influenza virus core P proteins in recognizing cap 1 structures (m7GpppNm) on RNAs and in initiating viral RNA transcription

Purified influenza viral cores catalyze the entire process of viral RNA transcription, which includes the endonucleolytic cleavage of heterologous RNAs containing cap 1 (m(7)GpppNm) structures to generate capped primers 10-13 nucleotides long, the initiation of transcription via the incorporation of a guanosine residue onto the primers, and elongation of the viral mRNAs [Plotch, S. J., Bouloy, M., Ulmanen, L & Krug, R. M. (1980) Cell 23, 847-858]. To identify which viral core protein (nucleocapsid protein, P1, P2, or P3) recognizes the cap 1 structure on the RNA primer, we irradiated (UV) endonuclease reactions carried out by viral cores in the absence of ribonucleoside triphosphates, with a primer RNA labeled in its cap 1 structure with (32)P. The labeled cap was crosslinked to a protein that had a mobility similar to that of the P3 protein, the smaller of the two basic P proteins, in both one- and two-dimensional gel electrophoresis. This strongly suggests that this crosslinked protein is the viral P3 protein. Competition experiments with unlabeled RNAs containing or lacking a cap 1 structure established that this protein recognizes the cap 1 structure on RNAs. This protein remained associated with the cap throughout the transcription reaction, even after the viral mRNA molecules were elongated. To identify the viral core protein that catalyzes the initiation of transcription via the incorporation of a guanosine residue onto primer fragments, we irradiated transcription reactions carried out by viral cores in the presence of [alpha-(32)P]GTP as the only ribonucleoside triphosphate with an unlabeled primer RNA. A labeled guanosine residue was crosslinked to a protein that had a mobility similar to that of the P1 protein, the larger of the two basic P proteins, in both one-and two-dimensional gel electrophoresis. The transcription reaction conditions required to bring this protein in close association with a labeled guanosine residue so that crosslinking could occur indicated that this association most likely occurred coincident with the guanosine residue's being incorporated onto the primer. These results suggest that the viral P1 protein catalyzes this incorporation and hence initiates transcription.

Monoclonal antibodies to the influenza A virus nucleoprotein affecting RNA transcription

Monoclonal antibodies were used to map the antigenic domains of the A/WSN/33 (HoN1) influenza virus nucleoprotein. Three nonoverlapping antigenic regions of the nucleoprotein were identified by using competitive-binding enzyme-linked immunosorbent assays. Monoclonal antibodies to two nucleoprotein domains inhibited in vitro transcription of viral RNA, suggesting that these specific regions of the nucleoprotein are topographically or functionally involved in RNA transcription.

The coupling of transcription from influenza virions to translation in vitro

The optimum conditions for the coupling of fowl plague virus (FPV) transcription to an in vitro reticulocyte translation system have been established and shown to be close to those required for maximum RNA synthesis by purified FPV virions. Products have been characterized by the peptides they yield on limited proteolysis in SDS and it has been shown that virus nucleoprotein (NP) and matrix (M) protein are made. The smallest virus coded polypeptide, the non-structural protein (NS), is made in only small amounts in the coupled system although it is a major virus coded product of infected cells early in infection.

Host range mutants of an influenza A virus

Temperature-sensitive (ts) mutants of fowl plague virus with a ts-lesion in segment 1 (ts 3, polymerase 1 gene) or segment 2 (ts 90, transport gene) do not form plaques on MDCK cells at the permissive temperature, while the wild type and ts-mutants of other groups are able to do so. This property is correlated with the ts-lesion, since revertants for the ts-lesion of ts 3 and ts 90 again form plaques on MDCK cells. The block on MDCK cells--at least for ts3--may be located in a late function, since viral RNA polymerase and hemagglutinin are formed in almost normal yields. MDCK cells infected with ts 3 or ts 90 exhibit a retarded cytopathic effect at 33 degrees C, but no cytopathic effect at 39 degrees C, at which temperature the infected cells can be passaged and super-infected with the wild type strain. Cells surviving the infection with ts 90 at 33 degrees C sometimes grow out again to a normal monolayer. It is suggested that the spread of virus is inhibited under these conditions.

Cell-free coupling of influenza virus RNA transcription and translation

A cell-free coupled system for the transcription and translation of fowl plague virus RNA is described. The system utilizes a new nuclease-preincubated rabbit reticulocyte lysate that has a high sensitivity to exogenous mRNA and a very low level of nuclease activity. Translation of the viral proteins in the coupled system is strictly dependent upon the viral transcriptase activity. In the coupled system the optimal concentration of magnesium is intermediate between the optimum for transcription and that for translation. Translation of the viral proteins seems faithful. The products represent the major viral peptides M and NP and two peptides with the same electrophoretic mobility as HA and P2. Viron NA is not resolved in the kind of polyacrylamide gels described. Proteins M and NP were immunoprecipitable with monospecific antisera. It is concluded that the virion-associated RNA polymerase transcribes the negative-stranded segments of the viral genome coding for these major structural proteins into fully functional mRNA's.