# Patent

## Title
Sequences encoding hepatitis C virus glycoproteins

## Abstract

The present invention concerns a modified nucleic acid molecule comprising a nucleotide sequence coding for a full length hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, this molecule having at least one nucleotide alteration, wherein, due to this alteration, at least one RNA splice site selected from the group consisting of RNA splice acceptor and RNA splice donor sites is eliminated from the coding sequence. The invention is also directed to methods for expressing on the surface of a cell and a pseudovirion an HCV glycoprotein, wherein the majority of the glycoprotein is full length. The invention further provides a cell and a pseudovirion expressing such glycoprotein. The invention still further provides a method for determining whether an agent inhibits HCV fusion with and entry into a target cell. The invention also provides an agent that inhibits HCV fusion with and entry into a target cell. The invention further provides methods for treating a subject afflicted with an HCV-associated disorder, for preventing an HCV infection in a subject, and for inhibiting in a subject the onset of an HCV-associated disorder.

## Background
This application claims the benefit of U.S. Provisional Application No. 60/519,536, filed Nov. 12, 2003, the contents of which are incorporated herein by reference.


The invention disclosed herein was made with United States Government support under grant number AI051134 from the National Institutes of Health, U.S. Department of Health and Human Services. Accordingly, the United States Government has certain rights in this invention.


Throughout this application, various publications are referenced in parentheses by author name and date. Full citations for these publications may be found at the end of the specification immediately preceding the claims. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art as known to those skilled therein as of the date of the invention described and claimed herein. However, the citation of a reference herein should not be construed as an acknowledgement that such reference is prior art to the present invention.
BACKGROUND OF THE INVENTION
Hepatitis C virus (HCV) was first recognized in 1989. It infects the liver and is responsible for the majority of cases of non-A, non-B hepatitis (Alter and Seef, 1993). Infections are typically chronic and lifelong; many infected individuals are healthy and unaffected for decades, whereas others develop chronic hepatitis or liver cirrhosis, the latter often leading to hepatocellular carcinoma (Fry and Flint, 1997; Lauer and Walker, 2001). While screening of the blood supply has drastically reduced new transmissions of the virus, there exists a large cohort of infected individuals who will require treatment in the coming decades. Some reports estimate that nearly 3% of the world's population or about 170 million people worldwide, including about 4 million people in the U.S.A., are infected with HCV (Anon, 1999).
HCV infection and its clinical sequelae are the leading causes of liver transplantation in the U.S.A. No vaccine is currently available, and the two licensed therapies, interferon alpha and ribavirin, which are both non-specific anti-viral agents with incompletely understood mechanisms of action, are only modestly efficacious (McHutchison et al., 1998). Thus, whereas the best long-term response rates are obtained with a combination of interferon alpha-2b and ribavirin, only a minority of subjects treated with this combination achieves the desired result of no detectable serum HCV RNA six months after stopping treatment (McHutchison et al., 1998). Moreover, these drugs exhibit severe, life-threatening toxicities, including neutropenia, hemolytic anemia and severe depression. There is therefore an urgent need for the development of new therapeutic approaches and agents to combat HCV infection.
The development of new treatments for HCV infection would be facilitated by a detailed knowledge of how the virus attaches to and fuses with cell membranes, enters target cells, replicates therein, infects neighboring cells and induces disease symptoms. However, even a basic understanding of HCV replication and pathogenesis remains poor, primarily due to a lack of experimental models and key reagents. An important step, therefore, is the development of better model systems that will facilitate the elucidation of the mechanisms underlying various aspects of the viral life cycle and disease causation.
The HCV genome is a 9.6 kb positive-sense, single-stranded RNA molecule that replicates exclusively in the cytoplasm of infected cells (Rice, 1996). The genomic RNA encodes a  ̃3000 amino acid polyprotein that is processed to generate at least ten proteins termed C, E1, E2, p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B (Grakoui et al., 1993; Rice, 1996; Lauer and Walker, 2001). The C protein constitutes the nucleocapsid; E1 and E2 are transmembrane envelope glycoproteins; p7 is a membrane spanning protein of unknown function; and the various non-structural (NS) proteins have replication functions (Bartenschlager and Lohmann, 2000; Op De Beeck et al., 2001).
The envelope glycoproteins are thought to play a crucial role in viral infectivity through their direct effect on various processes including the packaging of virions, the attachment of virions to target cells, fusion with and entry into these cells, and the budding of viruses from cell membranes before another round of cell infection can be initiated. HCV entry into target cells is a particularly attractive target for antiviral therapy because entry inhibitors do not need to cross the plasma membrane nor be modified intracellularly. In addition, viral entry is generally a rate-limiting step that is mediated by conserved structures on the viral envelope and cell membrane. Consequently, inhibitors of viral entry can provide potent and durable suppression of viral replication.
HCV entry into host cells requires attachment of the viral particle to the cell surface, followed by fusion of the viral envelope with the cellular membrane. The HCV envelope glycoproteins, E1 and E2, are thought to be involved in mediating virus entry into susceptible target cells. In mammalian cell-based expression systems, the molecular weight of mature, full length E1 is  ̃35 kD and that of E2 is  ̃72 kD (Grakoui et al., 1993; Matsuura et al., 1994; Spaete et al., 1992). E1 and E2 are present as a non-covalently associated heterodimer, hereinafter referred to as E1/E2, on the virus surface and undergo extensive posttranslational modification by N-linked glycosylation (Lauer and Walker, 2001).
Entry of the HCV structural proteins, C-E1-E2-p7, into the cell is followed by translocation into the endoplasmic reticulum (ER), which is accompanied by cleavage of internal signal sequences by ER-resident signal peptidases (Bartenschlager and Lohmann, 2000; Op De Beeck et al., 2001; Reed and Rice, 2000). It is assumed that HCV buds into the ER and matures by passage through cytoplasmic vesicles (Pettersson, 1991). Studies of the subcellular localization of HCV envelope glycoproteins and particles in cells transfected or infected in vitro suggest vesicle-based morphogenesis of HCV (Dash et al., 1997; Egger et al., 2002; Greive et al., 2002; Iocovacci et al., 1997; Pietschmann et al., 2002; Serafino et al., 1997; Shimizu et al., 1996). However, HCV-like particles have been detected in the cytoplasm of hepatocytes from infected patients, which suggests budding at the plasma membrane (DeVos et al., 2002), though the budding and maturation process of HCV have not yet been delineated.
The two most common experimental models of viral entry are cell-cell membrane fusion between receptor- and envelope glycoprotein-expressing cells, and entry of “reporter” viruses pseudotyped with heterologous envelope glycoproteins. Both systems rely on cell surface-associated expression of functional envelope glycoproteins. However, achieving expression of E1 and E2 on the surface of cells has proven to be elusive, and various studies have suggested that modification of the TM domains may be required. Two groups (Lagging et al., 1998; Takikawa et al., 2000) have described fusion and entry mediated by E1 and E2 ectodomains fused to the TM domain of the VSV G envelope glycoprotein. However, the TM domain of VSV G has no known dimerization function, and E1 and E2 were expressed from separate mRNAs, further minimizing their potential to form native heterodimers. It is unclear from these reports whether fusion and entry events were actually mediated by E1 and E2, because key controls demonstrating specificity were omitted.
There has also been some inconsistency in the results reported: one group showed that pH-independent entry of viral pseudotypes was mediated by either E1 or E2 (Lagging et al., 1998; Meyer et al., 2000; Lagging et al., 2002), whereas the other showed that pH-dependent fusion required both glycoproteins (Takikawa et al., 2000; Matsuura et al., 2001). Moreover, a more recent report that HCV-VSV chimeric envelope glycoproteins are not functional (Buonocore et al., 2002), contradicts the results of the earlier studies. It therefore appears that the chimeric VSV G system does not reproducibly model HCV envelope glycoprotein-mediated cell fusion and entry.
The apparent absence of E1/E2 heterodimers on the cell surface and the lack of N-glycan modifications by Golgi enzymes have led to suggestions that HCV envelope glycoproteins are retained in the ER (Duvet et al., 1998; Martire et al., 2001; Michalak et al., 1997; Patel et al., 2001; Selby et al., 1994). Both ER retention of E1/E2 and the heterodimerization of these glycoproteins are thought to be mediated by the TM domains of E1 and E2 (Cocquerel et al., 1999; Cocquerel et al., 1998; Cocquerel et al., 2000; Flint and McKeating, 1999; Flint et al., 1999; (Deleersnyder et al., 1997; Dubuisson et al., 1994; Op De Beeck et al., 2000; Patel et al., 1999; Ralston et al., 1993; Selby et al., 1994), and this has made it difficult to generate cell surface-expressed E1/E2 heterodimers. However, an experimental system for generating such surface-expressed E1/E2 heterodimers would be very valuable, with applications in, for example, the development of assays for measuring the extent of cell membrane fusion and pseudovirion entry and for identifying agents that inhibit HCV entry into susceptible cells, as well as the production of monoclonal antibodies and vaccines.
SUMMARY OF THE INVENTION
The present invention provides a modified nucleic acid comprising consecutive nucleotides having a nucleotide sequence coding for a full length hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, this nucleic acid having at least one nucleotide alteration, wherein, due to this alteration, at least one RNA splice site selected from the group consisting of RNA splice acceptor and RNA splice donor sites is eliminated from the coding sequence.
This invention also provides a modified nucleic acid comprising consecutive nucleotides having a nucleotide sequence encoding a truncated hepatitis C virus (HCV) E1 glycoprotein, wherein nucleotides extending from nucleotide positions 675 to 887 inclusive in a coding sequence coding for E1 are deleted, these nucleotide positions being numbered by reference to SEQ ID NO:2.
This invention further provides an expression vector comprising any one of the modified nucleic acids described herein.
This invention still further provides a host cell containing therein the expression vector described above. This invention also provides a method for expressing on a cell surface a hepatitis C virus (HCV) glycoprotein, selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length, which method comprises transfecting a cell with an expression vector comprising a modified HCV coding sequence, selected from the group consisting of the E1 and E1-E2 coding sequences, wherein at least one nucleotide alteration in the modified coding sequence eliminates at least one RNA splice site selected from the group consisting of RNA splice acceptor and RNA splice donor sites so as to reduce the extent of excision of an intron from the modified coding sequence, under conditions suitable for nuclear transcription of the modified coding sequence, such that the glycoprotein is expressed on the cell surface.
This invention further provides a cell expressing on a surface thereof a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the glycoprotein is expressed from a modified HCV coding sequence according to any of the methods described herein.
This invention additionally provides a cell-surface-localized hepatitis C virus (HCV) glycoprotein, selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the glycoprotein is expressed from a modified HCV coding sequence according to any of the methods described herein.
This invention also provides a method for making a pseudovirion expressing on a surface thereof a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length, which method comprises (a) co-transfecting a cell with (1) at least one vector which provides virion packaging functions and expresses a reporter gene, and (2) a vector construct comprising a modified HCV coding sequence, selected from the group consisting of E1 and E1-E2 coding sequences, wherein at least one nucleotide alteration in the coding sequence eliminates at least one RNA splice site selected from the group consisting of RNA splice acceptor and RNA splice donor sites from the modified HCV coding sequence so as to reduce the extent of excision of an intron from the modified coding sequence; and (b) collecting viral supernatant containing pseudovirions.
This invention further provides a pseudovirion expressing on its surface a hepatitis C virus (HCV) glycoprotein, selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length.
This invention still further provides an immunogen comprising any one of the hepatitis C virus (HCV) pseudovirions described herein.
This invention also provides a pharmaceutical composition comprising any one of the hepatitis C virus (HCV) pseudovirions described herein and a pharmaceutically acceptable carrier.
This invention further provides a method for producing a polyclonal antibody that specifically binds to hepatitis C virus (HCV) comprising: (a) injecting into a subject an immunogen comprising an HCV pseudovirion to induce a primary immune response in said subject; (b) administering at least one booster injection of pseudovirion to the subject; and (c) purifying from the subject's serum a polyclonal antibody that binds specifically to HCV.
This invention still further provides a polyclonal antibody that specifically binds to HCV.
This invention also provides a method for producing a monoclonal antibody that specifically binds to hepatitis C virus (HCV) comprising: (a) injecting into a subject an immunogen comprising an HCV pseudovirion to induce a primary immune response in the subject; (b) administering at least one booster injection of pseudovirion to the subject; (c) harvesting antibody-producing lymphatic cells from the subject; (d) generating hybridomas by fusing single antibody-producing cells obtained in (c) with myeloma cells; and (e) screening hybridoma supernatants from these hybridomas to identify at least one monoclonal antibody that specifically binds to HCV.
This invention further provides a monoclonal antibody that specifically binds to HCV.
This invention still further provides a nucleic acid molecule encoding a monoclonal antibody or fragment thereof that specifically binds to HCV.
In addition, this invention provides a method for expressing in a cell a modified hepatitis C virus (HCV) glycoprotein selected from the group consisting of modified E1 glycoprotein and modified E1/E2 glycoprotein heterodimer, wherein the glycoprotein produced is homogeneously truncated by a deletion of amino acid residues 226 to 296 inclusive, these amino acid residues being numbered by reference to SEQ ID NO:3, which method comprises transfecting a cell with an expression vector comprising a modified coding sequence, wherein a nucleotide sequence corresponding to a putative intron between nucleotide positions 675 and 887 inclusive is deleted, these nucleotide positions being numbered by reference to SEQ ID NO:2, under conditions suitable for expression of vector-encoded glycoprotein, so as to express a homogeneously truncated glycoprotein lacking amino acid residues 226 to 296 inclusive, these amino acid residues being numbered by reference to SEQ ID NO:3.
This invention also provides a modified hepatitis C virus (HCV) glycoprotein, selected from the group consisting of modified E1 glycoprotein and modified E1/E2 glycoprotein heterodimer, wherein the modified glycoprotein is homogeneously truncated by a deletion of amino acid residues 226 to 296 inclusive, these amino acid residues being numbered by reference to SEQ ID NO:3.
This invention further provides a method for determining whether an agent inhibits fusion of hepatitis C virus (HCV) to a target cell capable of fusing with HCV, which method comprises (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of an agent under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the agent, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; and (c) determining whether there is a reduction of resonance energy transfer in the presence of the agent compared with the resonance energy transfer in the absence of the agent; wherein a reduction in resonance energy transfer in the presence of the agent indicates that the agent inhibits fusion of HCV to the target cell.
This invention still further provides a method for screening a plurality of agents, not known to inhibit fusion of hepatitis C virus (HCV) to a target cell capable of fusing with this virus, to identify at least one agent that inhibits such fusion, which method comprises (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of a plurality of agents under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the plurality of agents, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; (c) determining whether there is a reduction of resonance energy transfer in the presence of the plurality of agents compared with the resonance energy transfer in the absence of the plurality of agents; and (d) if the resonance energy transfer is reduced in the presence of the plurality of agents, separately determining which of the agents present in the plurality of agents causes a reduction in resonance energy transfer, so as to thereby identify at least one agent that inhibits fusion of HCV to a target cell.
The present invention additionally provides an agent that inhibits fusion of hepatitis C virus (HCV) to a target cell capable of fusing with HCV.
This invention also provides a pharmaceutical composition comprising any of the agents described herein and a pharmaceutically acceptable carrier.
This invention further provides a method for determining whether an agent inhibits entry of hepatitis C virus (HCV) into a target cell susceptible to infection by HCV, comprising (a) separately contacting (1) a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein a majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using at least one vector which provides virion packaging functions and expresses a reporter gene, with (2) a target cell in the presence and absence of an agent under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the agent; and (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the agent compared with reporter gene activity in the absence of the agent; wherein a reduction in reporter gene activity in the presence of the agent indicates that the agent inhibits entry of HCV into the target cell.
This invention still further provides a method for screening a plurality of agents, not known to inhibit entry of hepatitis C virus (HCV) into a target cell susceptible to infection by HCV, to identify at least one agent that inhibits such entry, which method comprises (a) separately contacting (1) a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein a majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using at least one vector which provides virion packaging functions and expresses a reporter gene, with (2) a target cell in the presence and absence of a plurality of agents under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the plurality of agents; (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the plurality of agents compared with the reporter gene activity in the absence of the plurality of agents; and (c) if the reporter gene activity is reduced in the presence of the plurality of agents, separately determining which of the agents present in the plurality of agents causes a reduction in reporter gene activity, so as to thereby identify at least one agent that inhibits entry of HCV into a target cell.
Additionally, this invention provides an agent that inhibits entry of hepatitis C virus (HCV) into a target cell susceptible to infection by HCV.
This invention also provides a pharmaceutical composition comprising any of the agents described herein and a pharmaceutically acceptable carrier.
This invention further provides a method for treating a subject afflicted with a hepatitis C virus (HCV)-associated disorder, which treatment is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit fusion of HCV to a target cell capable of fusing with HCV using a method comprising (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of the agent under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the agent, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; and (c) determining whether there is a reduction of resonance energy transfer in the presence of the agent compared with the resonance energy transfer in the absence of the agent; wherein a reduction in resonance energy transfer in the presence of the agent indicates that the agent inhibits fusion of HCV to the target cell, and (2) administered in a therapeutically effective amount to treat the subject.
This invention still further provides a method for treating a subject afflicted with a hepatitis C virus (HCV)-associated disorder, which treatment is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit entry of HCV into a target cell using a method comprising: (a) separately contacting a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein the majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using a packaging vector that expresses a reporter gene, with a target cell in the presence and absence of the agent under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the agent; and (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the agent compared with the reporter gene activity in the absence of the agent; wherein a reduction in reporter gene activity in the presence of the agent indicates that the agent inhibits entry of HCV into the target cell; and (2) administered in a therapeutically effective amount to treat the subject.
This invention additionally provides a method for preventing a hepatitis C virus (HCV) infection in a subject, the prevention of which is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit fusion of HCV to a target cell capable of fusing with HCV using a method comprising: (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of the agent under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the agent, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; and (c) determining whether there is a reduction of resonance energy transfer in the presence of the agent compared with the resonance energy transfer in the absence of the agent; wherein a reduction in resonance energy transfer in the presence of the agent indicates that the agent inhibits fusion of HCV to the target cell; and (2) administered in a prophylactically effective amount to prevent an HCV infection in the subject.
This invention also provides a method for inhibiting in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit fusion of HCV to a target cell capable of fusing with HCV using a method comprising (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of the agent under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the agent, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; and (c) determining whether there is a reduction of resonance energy transfer in the presence of the agent compared with the resonance energy transfer in the absence of the agent; wherein a reduction in resonance energy transfer in the presence of the agent indicates that the agent inhibits fusion of HCV to the target cell; and (2) administered in a prophylactically effective amount to have a prophylactic effect in the subject.
This invention further provides a method for preventing a hepatitis C virus (HCV) infection in a subject, the prevention of which is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit entry of HCV into a target cell using a method comprising: (a) separately contacting a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein the majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using a packaging vector that expresses a reporter gene, with a target cell in the presence and absence of the agent under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the agent; and (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the agent compared with the reporter gene activity in the absence of the agent; wherein a reduction in reporter gene activity in the presence of the agent indicates that the agent inhibits entry of HCV into the target cell; and (2) administered in a prophylactically effective amount to prevent an HCV infection in the subject.
This invention still further provides a method for inhibiting in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit entry of HCV into a target cell using a method comprising: (a) separately contacting a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein the majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using a packaging vector that expresses a reporter gene, with a target cell in the presence and absence of the agent under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the agent; and (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the agent compared with the reporter gene activity in the absence of the agent; wherein a reduction in reporter gene activity in the presence of the agent indicates that the agent inhibits entry of HCV into the target cell; and (2) administered in a prophylactically effective amount to have a prophylactic effect in the subject.
The present invention also provides a method for preventing a hepatitis C virus (HCV) infection in a subject, the prevention of which is effected by immunizing the subject, which method comprises: (a) injecting into the subject a pharmaceutical composition comprising an HCV pseudovirion expressing on its surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length; and thereby (b) eliciting a protective HCV immune response in the subject.
This invention further provides a method for inhibiting in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by immunizing the subject, which method comprises: (a) injecting into the subject a pharmaceutical composition comprising an HCV pseudovirionexpressing on its surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length; and thereby (b) eliciting a protective HCV immune response in the subject.
This invention still further provides a diagnostic kit comprising an antibody as described herein and instructions for using this antibody to detect hepatitis C virus (HCV) in human tissue.
This invention also provides an article of manufacture comprising a packaging material containing therein a modified nucleic acid molecule as described herein and a label providing instructions for using this modified nucleic acid to express on a cell surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the expressed glycoprotein is full length.
This invention further provides an article of manufacture comprising a packaging material containing therein a modified nucleic acid molecule as described herein and a label providing instructions for using the modified nucleic acid to generate a pseudovirion expressing on its surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the expressed glycoprotein is full length.
This invention still further provides an article of manufacture comprising a packaging material containing therein a cell expressing on the cell surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length, and a label providing instructions for using the cell to identify an agent that inhibits fusion of HCV to a target cell capable of fusing with this virus.
Additionally, this invention provides an article of manufacture comprising a packaging material containing therein a pseudovirion expressing on its surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length, and a label providing instructions for using the pseudovirion to identify an agent that inhibits entry of HCV into a target cell susceptible to infection by this virus.
This invention also provides an article of manufacture comprising a packaging material containing therein an agent as described herein and a label providing instructions for using this agent to treat a subject afflicted with a hepatitis C virus (HCV)-associated disorder, treatment to which is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus.
This invention further provides an article of manufacture comprising a packaging material containing therein an agent as described herein and a label providing instructions for using this agent to treat a subject afflicted with a hepatitis C virus (HCV)-associated disorder, treatment to which is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus.
This invention still further provides an article of manufacture comprising a packaging material containing therein an agent as described herein and a label providing instructions for using this agent to inhibit in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus.
This invention also provides an article of manufacture comprising a packaging material containing therein an agent as described herein and a label providing instructions for using this agent to inhibit in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Full length consensus sequence of the HCV genome. The genomic sequence (SEQ ID NO:1) shown in (a)-(c) is taken from Yanagi et al. (1997) (Genbank Accession #AF011751). Noncoding sequences are underlined.
FIG. 2. Consensus sequence coding for HCV structural proteins. This sequence (SEQ ID NO:2) encodes the C, E1, E2 and p7 proteins. The first nucleotide in the translation initiation codon of the sequence encoding the C (capsid) protein is numbered 1.
FIG. 3. Full length HCV consensus amino acid sequence. This sequence (SEQ ID NO:3) shown in (a) and (b) is the amino acid sequence deduced from the coding region of consensus HCV genome sequence (SEQ ID NO:1).
FIG. 4. Nucleotide sequence of the 5′-HindIII-C-E1-E2-p7-XbaI-3′ construct. Restriction sites are shown in italics, whereas the translation start and stop codons are in bold and underlined. The sequence shown is designated SEQ ID NO:4.
FIG. 5. Nucleotide sequence of the 5′-HindIII-C-E1-E2-XbaI-3′ construct. Restriction sites are shown in italics, whereas the translation start and stop codons are in bold and underlined. The sequence shown is designated SEQ ID NO:5.
FIG. 6. Nucleotide sequence of the 5′-HindIII-ΔC-E1*-E2*-XbaI-3′ construct. This construct contains a sequence encoding an N-terminally truncated portion (ΔC) of the wild type HCV core protein that serves as a signal sequence (described in PCT International Publication WO 204/024904), and modified E1 and E2 genes (indicated by “*”) with mutations of the putative splice sites at positions 675, 887 and 2183. The wild type HCV signal sequence from the core protein is thought to be required for proper folding of the E1/E2 proteins. Restriction sites are shown in italics, whereas the translation start and stop codons are in bold and underlined. The sequence shown is designated SEQ ID NO:6.
FIG. 7. Nucleotide sequence of the 5′-HindIII-E1-E2-p7-XbaI-3′ construct. Restriction sites are shown in italics, whereas the translation start and stop codons are in bold and underlined. The sequence shown is designated SEQ ID NO:7.
FIG. 8. Nucleotide sequence of the 5′-HindIII1-E1-E2-XbaI-3′ construct. Restriction sites are shown in italics, whereas the translation start and stop codons are in bold and underlined. The sequence shown is designated SEQ ID NO:8.
FIG. 9. Nucleotide sequence of the 5′-HindIII-E1-E2-p7-XbaI-3′ construct containing A866C and A2183T double mutations. Restriction sites are shown in italics. The translation start and stop codons as well as nucleotides altered by site-specific mutagenesis are in bold and underlined. The sequence shown is designated SEQ ID NO:9.
FIG. 10. Nucleotide sequence of the 5′-HindIII-E1-XbaI-3′ construct with the putative intron deleted. Restriction sites are shown in italics whereas the translation start and stop codons are in bold and underlined. The sequence shown is designated SEQ ID NO:10.
FIG. 11. Cell surface expression of E1 and E2. Unmodified HCV envelope glycoprotein genes were transiently expressed in HeLa cells using either a vaccinia virus vector system (a-d) or lipofection with plasmid DNA constructs (e-h), and protein expression was analyzed 24 h post-infection. Cells were fixed in 3% formaldehyde for 20 min at room temperature (c, d, g, h) or fixed/permeabilized with methanol for 20 min at −20° C. (a, b, e, f). E1 and E2 expression on the cell surface was detected by incubation with the anti-E1 monoclonal antibody (MAb), A4 (a, c, e, g), or the anti-E2 MAb, H53 (b, d, f, h), and visualized by chemifluorescence under a fluorescence microscope (see Methods for details).
FIG. 12. Characterization of E1 and E2 proteins. Unmodified HCV envelope glycoprotein genes (E1, E2 and E1-E2) were expressed in HeLa cells with a vaccinia-(a, c) or a plasmid-based system (b, d), and protein expression was analyzed by immunoblotting of cell lysates with anti-E2 MAb A11 (a, b) or anti-E1 MAb A4 (c, d) (see Methods for details). M, molecular weight markers showing sizes in kDa; 3.1, cell lysate from cells transfected with the expression vector, pcDNA3.1+ (Invitrogen, Carlsbad, Calif.); endoH, endoglycosidase H-treated lysate. Arrowheads indicate the positions of E1 and E2 proteins on the blots.
FIG. 13. Excision of a putative intron in E1 mRNA generates a deleted protein. The HCV genome was analyzed with a splice site prediction neural network. (a) Sequences in the E1-E2-p7 coding region having >80% probability of being functional splice donor (SD) and acceptor (SA) sites are indicated. Splicing occurs between nucleotide positions 675 and 887 generating an E1 protein with a deletion spanning amino acids 230 to 292. (b) Unmodified E1 (E1), E1 with a mutated splice acceptor site (E1*), or E1 lacking a putative intron (E1ΔHCV) were transiently expressed in HeLa cells by lipofection and analyzed by immunoblotting with anti-E1 MAb A4. The black arrowhead indicates the position of full length E1 and the white arrowhead indicates the position of the deleted E1 protein species.
FIG. 14. Stable expression of E1 and E2 lacking putative splice acceptor sites. Proteins from whole cell lysates of HeLa cells, stably transfected with different constructs comprising modified E1, E2 or E1-E2 genes (indicated by “*”), were analyzed by immunoblotting with anti-E2 MAb A11 (a) or anti-E1 MAb A4 (b). M, molecular weight markers showing sizes in kDa. Arrowheads indicate the positions of full-length E1 and E2 proteins.
FIG. 15. Cell surface expression of E1 and E2 lacking putative splice acceptor sites. (a) Cell surface proteins of HeLa cells stably expressing modified E1*, E1*-E2* and E1*-E2*-p7 were tagged with biotin before lysis. After cell lysis, the biotinylated proteins were immunoblotted with anti-E1 MAb A4. The arrowhead indicates the position of E1 proteins. (b) Cell surface-associated E2 proteins generated by stable expression of E1*-E2* and E1*-E2*-p7 were detected by flow cytometry analyses after labeling of cells with five different anti-E2 MAbs, H2, H52, H53, H60 and 091b-5 or a control mouse IgG. (c) Cell surface-associated E2 proteins, generated by stable expression of E1*-E2* and E1*-E2*-p7 in NKNT3 cells, were detected by anti-E2 MAb H53.
FIG. 16. Heterodimerization of E1 and E2 on the cell surface. HeLa cells stably expressing modified HCV envelope glycoproteins were incubated with the anti-E2 MAb H53, lysed and incubated with protein G-coupled agarose beads. Lysates from cells treated with a mouse immunoglobulin (mIgG), but not H53, were used as a control. E1 was detected by immunoblotting with anti-E1 MAb A4 (a), whereas E2 was detected by immunoblotting with anti-E2 MAb A11 (b). Arrowheads indicate the positions of full-length E1* and E2* proteins.



DETAILED DESCRIPTION OF THE INVENTION
Definitions
As used in this application, except as otherwise expressly provided herein, each of the following terms shall have the meaning set forth below.
“Administering” shall mean delivering in a manner which is effected or performed using any of the various methods and delivery systems known to those skilled in the art. Administering can be performed, for example, topically, intravenously, pericardially, orally, parenterally, via implant, trans-mucosally, transdermally, intradermally, intramuscularly, subcutaneously, intraperitoneally, intrathecally, intralymphatically, intra-lesionally, or epidurally. An agent or composition may also be administered in an aerosol, such as for pulmonary and/or intranasal delivery. Administering can also be performed, for example, once, a plurality of times, and/or over one or more extended periods.
“Attachment” of HCV or a pseudovirion to a target cell shall mean the process that is mediated by the binding of the HCV envelope glycoprotein to a ligand, e.g., L-SIGN, present on the surface of a cell susceptible to HCV infection. This process is distinguished from the fusion of HCV or a pseudovirion with, and entry into a target cell. “Fusion” shall mean the joining or union of the lipid bilayer membranes found on mammalian cells or viruses such as HCV. The fusion of the cell membrane of a cell susceptible to HCV infection with an HCV envelope glycoprotein+ cell membrane shall mean the hydrophobic joining and integration of the cell membrane of the infection-susceptible cell with the HCV envelope glycoprotein+ membrane to form a hybrid membrane comprising components of both cell membranes. In one embodiment, the host cell is a bodily cell from a subject, such as from a human subject. “Entry” shall mean the process whereby viral genetic information is introduced into a host cell. HCV entry into a host cell requires prior attachment of the viral particle to the cell surface, followed by fusion of the viral envelope with the cellular membrane. The overall process of HCV attachment, fusion and entry results in “HCV infection” of a host cell. Infection is usually but not necessarily accompanied by the induction of disease symptoms in a subject.
A “cell” includes a biological cell, e.g., a HeLa cell, and a non-biological cell, e.g., a phospholipid vesicle or virion. A “cell susceptible to HCV infection” may also be referred to as a “target cell” and includes cells capable of being infected by or fusing with HCV or HCV-infected cells.
A “full length” hepatitis C virus (HCV) glycoprotein is one which is identical in amino acid length and sequence to that of a polypeptide encoded by a corresponding unmodified HCV envelope glycoprotein coding sequence. In particular, such full length HCV glycoprotein is not truncated as a result of the excision of any putative intron sequence from a corresponding unmodified HCV envelope glycoprotein coding sequence.
A “fully human” antibody shall mean an antibody wherein all of the amino acids correspond to amino acids in human immunoglobulin molecules.
A “humanized” antibody shall mean an antibody wherein some, most or all of the amino acids outside the complementarity determining regions (CDRs) are replaced with corresponding amino acids derived from human immunoglobulin molecules.
“HCV” shall mean the hepatitis C virus without limitation to strain, subtype or genotype, such as are disclosed in U.S. Pat. Nos. 6,572,864 and 5,882,852. HCV includes but is not limited to extracellular virus particles and the forms of HCV associated with and/or found in HCV-infected cells.
An “immunogenically effective amount” of an immunogen, such as a pseudovirion, is an amount sufficient to elicit a protective immune response in a subject.
“Inhibiting fusion” of HCV, an HCV pseudovirion or a HCV envelope glycoprotein+ cell with a cell susceptible to HCV infection shall mean (a) reducing the rate of fusion of a cell membrane of a cell susceptible to HCV infection with an HCV envelope, an HCV pseudovirion or a cell membrane of an HCV envelope glycoprotein+ cell by at least 5%, preferably by at least 50%, more preferably by at least 75%, and/or (b) reducing by at least 5%, preferably by at least 50%, more preferably by at least 75%, the total amount of fusion of a cell membrane of a cell susceptible to HCV infection with an HCV envelope, an HCV pseudovirion or an HCV envelope glycoprotein+ cell membrane occurring by the endpoint of fusion. The rate of cell membrane fusion means the total quantity of cell membrane fused per unit of time. The endpoint of fusion means the point in time at which all fusion of cell membranes of cells susceptible to HCV infection with HCV envelope glycoprotein+ cell membrane capable of occurring has occurred.
“Inhibiting entry” of HCV or an HCV pseudovirion into a host cell shall mean reducing the amount of viral genetic information introduced into the host cell as compared to the amount that would be introduced without, for example, an inhibiting agent. In one embodiment, “inhibiting” means that the amount of viral genetic information introduced into the host cell is reduced at least 50%, preferably at least 75%. In a preferred embodiment, the amount of viral genetic information introduced into the host cell is reduced 100%.
A “majority” of a hepatitis C virus (HCV) glycoprotein being full length shall mean that greater than fifty percent of the glycoprotein consists of full length molecules.
“Pharmaceutically acceptable carriers” are well known to those skilled in the art and include, but are not limited to, 0.01-0.1 M and preferably 0.05 M phosphate buffer or 0.8% saline. Additionally, such pharmaceutically acceptable carriers can be aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions and suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's and fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers such as those based on Ringer's dextrose, and the like. Solid compositions may comprise nontoxic solid carriers such as, for example, glucose, sucrose, mannitol, sorbitol, lactose, starch, magnesium stearate, cellulose or cellulose derivatives, sodium carbonate and magnesium carbonate. For administration in an aerosol, such as for pulmonary and/or intranasal delivery, an agent or composition is preferably formulated with a nontoxic surfactant, for example, esters or partial esters of C6 to C22 fatty acids or natural glycerides, and a propellant. Additional carriers such as lecithin may be included to facilitate intranasal delivery. In addition to carriers described above, a vaccine may further include carriers known in the art such as, for example, thyroglobulin, albumin, tetanus toxoid, polyamino acids such as polymers of D-lysine and D-glutamate, inactivated influenza virus and hepatitis B recombinant protein(s). The vaccine may also include any well known adjuvants such as incomplete Freund's adjuvant, alum, aluminum phosphate, aluminum hydroxide, monophosphoryl lipid A (MPL, GlaxoSmithKline), saponins including QS21 (GlaxoSmithKline), CpG oligonucleotides (Krieg et al., 1995), montanide, vitamin E and various water-in-oil emulsions prepared from biodegradable oils such as squalene and/or tocopherol, Quil A, Ribi Detox, CRL-1005, L-121 and combinations thereof. Preservatives and other additives, such as, for example, antimicrobials, antioxidants, chelating agents, inert gases, and the like may also be included with all the above carriers.
A “prophylactically effective amount” is any amount of an agent which, when administered to a subject prone to suffer from a disorder, inhibits the onset of the disorder. “Inhibiting” the onset of a disorder means either lessening the likelihood of the disorder's onset, or preventing the onset of the disorder entirely. In the preferred embodiment, inhibiting the onset of a disorder means preventing its onset entirely.
A “protective immune response” against hepatitis C virus (HCV) shall mean an immune response that prevents infection or inhibits the spread of infection from cell to cell after an initial exposure of a subject to the virus. Such immune response, elicited, for example, by administration of an HCV pseudovirion, may include generation of anti-HCV antibodies and/or generation of a cellular immune response (e.g., activation of cytotoxic T lymphocytes).
“Subject” means any animal, such as a mammal or a bird, including, without limitation, a human, a non-human primate, a cow, a horse, a sheep, a pig, a dog, a cat, a rabbit, a rodent such as a mouse, rat or guinea pig, a turkey or a chicken. In a preferred embodiment, the subject is a human being.
A “therapeutically effective amount” is any amount of an agent which, when administered to a subject afflicted with a disorder against which the agent is effective, causes the subject to be treated. With regards to administration of a hepatitis C virus (HCV) pseudovirion immunogen, a therapeutically effective amount shall mean any amount of pseudovirion that is effective in inhibiting spread of HCV (e.g., to limit a chronic infection) and thus alleviates symptoms or prevents further deterioration of liver tissue.
“Treating” a subject afflicted with a disorder shall mean causing the subject to experience a reduction, remission or regression of the disorder and/or its symptoms. In one embodiment, recurrence of the disorder and/or its symptoms is prevented. In the preferred embodiment, the subject is cured of the disorder and/or its symptoms.
“Suitable conditions” shall have a meaning dependent on the context in which this term is used. Generally, it means conditions that permit an agent, capable of doing something, to do that intended thing. In one embodiment, the term “suitable conditions” as used herein means physiological conditions.
“Unmodified” HCV envelope glycoprotein coding sequences shall mean the C, E1, E2 and p7 consensus gene sequences as they occur in the wild-type HCV genome. “Modified” HCV glycoprotein gene sequences shall refer to the in vitro-mutagenized HCV H77 gene sequences containing conservative mutations that remove splice acceptor sites in E1 (A886C and or G888T; modified sequence designated E1*) and E2 (A2183T; modified sequence designated E2*), or a deletion mutation that removes the putative intron in E1 between nucleotide positions 675 and 887 (modified sequence designated E1Δ). Nucleotide positions and mutations are numbered by reference to SEQ ID NO:2. Constructs for expressing these genes in transfected cells may contain modified or unmodified HCV glycoprotein gene sequences singly or in various combinations.
Embodiments of the Invention
Studies on fundamental aspects of HCV replication and infection of susceptible cells have been stymied by a lack of key reagents and experimental systems. The virus replicates poorly or not at all in vitro, and the apparent retention of HCV envelope glycoproteins in the ER has hindered efforts to develop membrane fusion and pseudovirion entry assays which rely on expression of functional envelope glycoproteins on the cell surface. The present invention helps to overcome these obstacles by providing systems for expression of full-length HCV glycoproteins on the cell surface. As described herein, these systems have in turn enabled the development of HCV fusion and entry assays as well as assays for identifying chemical agents that inhibit HCV fusion with and entry into target cells.
Specifically, this invention provides a modified nucleic acid comprising consecutive nucleotides having a nucleotide sequence coding for a full length hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, this nucleic acid having at least one nucleotide alteration, wherein, due to this alteration, at least one RNA splice site selected from the group consisting of RNA splice acceptor and RNA splice donor sites is eliminated from the coding sequence. In one embodiment, the modified nucleic acid is an isolated nucleic acid. In another embodiment, elimination of at least one RNA splice acceptor site or splice donor site reduces an extent to which an intron is excised from the coding sequence. In a preferred embodiment, elimination of at least one RNA splice acceptor site or splice donor site prevents excision of an intron from the coding sequence.
In another embodiment of this modified nucleic acid, the alteration comprises an A886C mutation in the HCV E1 coding sequence, this mutation being numbered by reference to SEQ ID NO:2, such that a splice-acceptor site at nucleotide position 887 in SEQ ID NO:2 is eliminated. In a further embodiment, the alteration comprises a G888T mutation in the HCV E1 coding sequence, this mutation being numbered by reference to SEQ ID NO:2, such that a splice-acceptor site at nucleotide position 887 in SEQ ID NO:2 is eliminated. In a still further embodiment, the alteration comprises a G675A mutation in the HCV E1 coding sequence, this mutation being numbered by reference to SEQ ID NO:2, such that a splice donor site at nucleotide position 675 in SEQ ID NO:2 is eliminated. In another embodiment, the alteration comprises an A886C mutation and a G888T mutation in the HCV E1 coding sequence, these mutations being numbered by reference to SEQ ID NO:2, such that a splice-acceptor site at nucleotide position 887 in SEQ ID NO:2 is eliminated. In yet another embodiment, the alteration comprises an A2183T mutation in the E2 coding sequence, this mutation being numbered by reference to SEQ ID NO:2, such that a splice-acceptor site at nucleotide position 2183 in SEQ ID NO:2 is eliminated. In a further embodiment, the alteration comprises an A886C mutation in the HCV E1 coding sequence and an A2183T mutation in the E2 coding sequence, these mutations being numbered by reference to SEQ ID NO:2, such that splice-acceptor sites at nucleotide positions 887 and 2183 in SEQ ID NO:2 are eliminated. In a still further embodiment, the alteration comprises a G888T mutation in the HCV E1 coding sequence and an A2183T mutation in the E2 coding sequence, these mutations being numbered by reference to SEQ ID NO:2, such that splice-acceptor sites at nucleotide positions 887 and 2183 in SEQ ID NO:2 are eliminated. In another embodiment, the alteration comprises an A886C mutation and a G888T mutation in the HCV E1 coding sequence and an A2183T mutation in the E2 coding sequence, these mutations being numbered by reference to SEQ ID NO:2, such that splice-acceptor sites at nucleotide positions 887 and 2183 in SEQ ID NO:2 are eliminated.
This invention also provides a modified nucleic acid comprising consecutive nucleotides having a nucleotide sequence encoding a truncated hepatitis C virus (HCV) E1 glycoprotein, wherein nucleotides extending from nucleotide positions 675 to 887 inclusive in a coding sequence coding for E1 are deleted, these nucleotide positions being numbered by reference to SEQ ID NO:2. In one embodiment, the modified nucleic acid is an isolated nucleic acid molecule. In another embodiment, the modified nucleic acid molecule further comprises a nucleotide sequence encoding an HCV E2 gene and including an alteration comprising an A2183T mutation such that a splice-acceptor site at nucleotide position 2183 in the E2 coding sequence is eliminated, this nucleotide position being numbered by reference to SEQ ID NO:2.
This invention further provides an expression vector comprising any one of the modified nucleic acid molecules described herein.
This invention still further provides a host cell containing therein the expression vector described above.
This invention also provides a method for expressing on a cell surface a hepatitis C virus (HCV) glycoprotein, selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length, which method comprises transfecting a cell with an expression vector comprising a modified HCV coding sequence, selected from the group consisting of the E1 and E1-E2 coding sequences, wherein at least one nucleotide alteration in the modified coding sequence eliminates at least one RNA splice site selected from the group consisting of RNA splice acceptor and RNA splice donor sites so as to reduce the extent of excision of an intron from the modified coding sequence, under conditions suitable for nuclear transcription of the modified coding sequence, such that the glycoprotein is expressed on the cell surface. In one embodiment, a splice-acceptor site at nucleotide position 887 in the HCV E1 coding sequence is eliminated by introduction of an A886C mutation, this nucleotide position and mutation being numbered by reference to SEQ ID NO:2. In another embodiment, a splice-acceptor site at nucleotide position 887 in the HCV E1 coding sequence is eliminated by introduction of a G888T mutation, this nucleotide position and mutation being numbered by reference to SEQ ID NO:2. In a further embodiment, a splice donor site at nucleotide position 675 in the HCV E1 coding sequence is eliminated by introduction of a G675A mutation, this nucleotide position and mutation being numbered by reference to SEQ ID NO:2. In a still further embodiment, a splice-acceptor site at nucleotide position 887 in the HCV E1 coding sequence is eliminated by introduction of an A886C mutation and a G888T mutation, these nucleotide position and mutations being numbered by reference to SEQ ID NO:2. In an additional embodiment, splice-acceptor sites at nucleotide positions 887 in the HCV E1 coding sequence and 2183 in the E2 coding sequence are eliminated by introduction of an A886C mutation and an A2183T mutation, respectively, these nucleotide positions and mutations being numbered by reference to SEQ ID NO:2. In yet another embodiment, splice-acceptor sites at nucleotide positions 887 in the HCV E1 coding sequence and 2183 in the E2 coding sequence are eliminated by introduction of a G888T mutation and an A2183T mutation, respectively, these nucleotide positions and mutations being numbered by reference to SEQ ID NO:2. In a further embodiment, splice-acceptor sites at nucleotide positions 887 in the HCV E1 coding sequence and 2183 in the E2 coding sequence are eliminated by introduction of an A886C mutation, a G888T mutation and an A2183T mutation, respectively, these nucleotide position and mutations being numbered by reference to SEQ ID NO:2.
In another embodiment of the instant invention, intron excision from the modified HCV coding sequence is sufficiently reduced such that greater than 70% of the glycoprotein is full length. In a further embodiment, intron excision from the modified HCV coding sequence is sufficiently reduced such that greater than 90% of the glycoprotein is full length.
This invention still further provides a cell expressing on a surface thereof a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the glycoprotein is expressed from a modified HCV coding sequence according to any of the methods described herein.
This invention additionally provides a cell-surface-localized hepatitis C virus (HCV) glycoprotein, selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the glycoprotein is expressed from a modified HCV coding sequence according to any of the methods described herein.
This invention further provides a method for making a pseudovirion expressing on a surface thereof a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length, which method comprises (a) co-transfecting a cell with (1) at least one vector which provides virion packaging functions and expresses a reporter gene, and (2) a vector construct comprising a modified HCV coding sequence, selected from the group consisting of E1 and E1-E2 coding sequences, wherein at least one nucleotide alteration in the coding sequence eliminates at least one RNA splice site selected from the group consisting of RNA splice acceptor and RNA splice donor sites from the modified HCV coding sequence so as to reduce the extent of excision of an intron from the modified coding sequence; and (b) collecting viral supernatant containing pseudovirions.
In one embodiment of this method, intron excision from the modified HCV coding sequence is sufficiently reduced such that greater than 70% of the glycoprotein is full length. In another embodiment, intron excision from the modified HCV coding sequence is sufficiently reduced such that greater than 90% of the glycoprotein is full length.
In one embodiment, the packaging vector is preferably a retroviral packaging vector such as one of the vectors described in PCT International Publication No. WO 2004/024904. In a further embodiment, the at least one vector which provides virion packaging functions and expresses a reporter gene is derived from human immunodeficiency virus type 1 (HIV-1). In a still further embodiment, a single packaging vector provides virion packaging functions and expresses a reporter gene. In yet another embodiment, the packaging vector expresses a luciferase, a green fluorescent protein, a yellow fluorescent protein or a beta-galactosidase reporter gene. In a preferred embodiment, the packaging vector is pNL4.3-Luc+env-, wherein pNL4.3-Luc+env- expresses a luciferase reporter gene.
In an additional embodiment, the at least one vector which provides virion packaging functions and expresses a reporter gene is derived from human T-cell leukemia virus type 1 (HTLV-1). In another embodiment, a packaging vector provides virion packaging functions and a separate transfer vector expresses a reporter gene. In yet another embodiment, the transfer vector expresses a luciferase, a green fluorescent protein, a yellow fluorescent protein or a beta-galactosidase reporter gene. In a preferred embodiment, the packaging vector is pCMV-HT1 or PCMV-HT-Δenv. In another preferred embodiment, the transfer vector is pHTC-luc, pHTC-luc-tsa, pHTC-eYFP or pHTC-eYFP-tsa.
In another embodiment, the at least one vector which provides virion packaging functions and expresses a reporter gene is derived from an avian C-type retrovirus. In a preferred embodiment, the packaging vector is pRD136. In another preferred embodiment, the transfer vector is pCXL.
In a further embodiment, the cell is a 293T cell.
This invention also provides a pseudovirion expressing on its surface a hepatitis C virus (HCV) glycoprotein, selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length. In one embodiment, greater than 70% of the glycoprotein is full length. In another embodiment, greater than 90% of the glycoprotein is full length.
This invention additionally provides an immunogen comprising any one of the hepatitis C virus (HCV) pseudovirions described herein.
The present invention also provides a pharmaceutical composition comprising any one of the hepatitis C virus (HCV) pseudovirions described herein and a pharmaceutically acceptable carrier. In one embodiment, this pharmaceutical composition further comprises an adjuvant.
The pseudovirion of the present invention may be used to produce antibodies useful for binding to HCV or producing a protective immune response in humans. Anti-HCV antibodies useful for diagnostic kits to detect HCV in human tissues can also be readily produced in animals such as a mouse, rat, rabbit, goat, sheep or horse using well known techniques. It will be understood that human antibodies that bind to pseudovirion can be similarly raised by immunizing a human patient or volunteer.
Accordingly, this invention provides a method for producing a polyclonal antibody that specifically binds to hepatitis C virus (HCV) comprising: (a) injecting into a subject an immunogen comprising an HCV pseudovirion to induce a primary immune response in said subject; (b) administering at least one booster injection of pseudovirion to the subject; and (c) purifying from the subject's serum a polyclonal antibody that binds specifically to HCV.
Pseudovirion are used to immunize the subject generally using a procedure where about 10 to 100 μg, preferably about 50 μg, of the particles are initially administered to the animal to induce a primary immune response followed by one to about five booster injections of about 10 to 100 μg of pseudovirion over a period of about two weeks to twelve months. Depending on the size of the animal to which the pseudovirion are administered, the dosage may vary, as may be readily determined by those skilled in the art. The timing and dosage of the booster injections in particular are determined based on the immune response detected in the animal, using methods well known to those skilled in the art. The pseudovirion are preferably administered subcutaneously as a suspension that includes an adjuvant such as Freund's complete or incomplete adjuvant, although a wide variety of available adjuvants are also suitable. Polyclonal antibodies induced after the primary response to pseudovirion are generally IgM whereas those produced following booster injections are generally IgG, generally reaching levels of 1 to 10 mg/ml of serum.
This invention also provides a polyclonal antibody that specifically binds to HCV. In one embodiment, the antibody neutralizes HCV. In another embodiment, the antibody inhibits HCV fusion with and entry into a target cell. In a further embodiment, the antibody inhibits transinfection. In a still further embodiment, the antibody binds to E1, E2 or E1/E2 and reduces viral load in a cell infected with HCV. In yet another embodiment, the antibody binds to E1, E2 or E1/E2 expressed from any of the modified nucleic acids described herein.
Methods for producing monoclonal antibodies are well known in the art (see, e.g., Kohler and Milstein, 1975). This invention further provides a method for producing a monoclonal antibody that specifically binds to hepatitis C virus (HCV) comprising: (a) injecting into a subject an immunogen comprising an HCV pseudovirion to induce a primary immune response in the subject; (b) administering at least one booster injection of pseudovirion to the subject; (c) harvesting antibody-producing lymphatic cells from the subject; (d) generating hybridomas by fusing single antibody-producing cells obtained in (c) with myeloma cells; and (e) screening hybridoma supernatants from these hybridomas to identify at least one monoclonal antibody that specifically binds to HCV.
This invention still further provides a monoclonal antibody that specifically binds to HCV. In one embodiment, the antibody neutralizes HCV. In another embodiment, the antibody inhibits HCV fusion with and entry into a target cell. In a further embodiment, the antibody inhibits transinfection. In a still further embodiment, the antibody binds to E1, E2 or E1/E2 and reduces viral load in a cell infected with HCV. In yet another embodiment, the antibody binds to E1, E2 or E1/E2 expressed from any of the modified nucleic acids described herein.
In one embodiment, the antibody is humanized. In a further embodiment, the antibody is a human antibody.
In one embodiment of the humanized form of the antibody, some, most or all of the amino acids outside the CDR regions have been replaced with amino acids from human immunoglobulin molecules whereas some, most or all amino acids within one or more CDR regions are unchanged. Small additions, deletions, insertions, substitutions or modifications of amino acids are permissible as long as they do not abrogate the ability of the antibody to bind a given antigen. Suitable human immunoglobulin molecules include IgG1, IgG2, IgG3, IgG4, IgA and IgM molecules. A humanized antibody retains a similar antigenic specificity as the original antibody, i.e., in the present invention, the ability to bind to HCV, inhibit fusion of HCV to or entry into cells so as to inhibit or prevent infection of these cells.
One skilled in the art would know how to make the humanized antibodies of the subject invention. Various publications, several of which are hereby incorporated by reference into this application- also describe how to make humanized antibodies. For example, the methods described in U.S. Pat. No. 4,816,567 enable the production of chimeric antibodies having a variable region of one antibody and a constant region of another antibody. U.S. Pat. No. 5,225,539 describes another approach for the production of a humanized antibody. In this approach, recombinant DNA technology is used to produce a humanized antibody wherein the CDRs of a variable region of one immunoglobulin are replaced with the CDRs from an immunoglobulin with a different specificity such that the humanized antibody would recognize the desired target but would not be recognized in a significant way by the human subject's immune system. Specifically, site directed mutagenesis is used to graft the CDRs onto the framework.
Other approaches for humanizing an antibody are described in U.S. Pat. Nos. 5,585,089 and 5,693,761 and WO 90/07861 which describe methods for producing humanized immunoglobulins. These have one or more CDRs and possible additional amino acids from a donor immunoglobulin and a framework region from an accepting human immunoglobulin. These patents describe a method to increase the affinity of an antibody for the desired antigen. Some amino acids in the framework are chosen to be the same as the amino acids at those positions in the donor rather than in the acceptor. Specifically, these patents describe the preparation of a humanized antibody that binds to a receptor by combining the CDRs of a mouse monoclonal antibody with human immunoglobulin framework and constant regions. Human framework regions can be chosen to maximize homology with the mouse sequence. A computer model can be used to identify amino acids in the framework region which are likely to interact with the CDRs or the specific antigen and then mouse amino acids can be used at these positions to create the humanized antibody.
The variable regions of the humanized antibody may be linked to at least a portion of an immunoglobulin constant region of a human immunoglobulin. In one embodiment, the humanized antibody contains both light chain and heavy chain constant regions. The heavy chain constant region usually includes CH1, hinge, CH2, CH3 and sometimes, CH4 region.
Fully human monoclonal antibodies also can be prepared by immunizing mice transgenic for large portions of human immunoglobulin heavy and light chain loci (see, e.g., U.S. Pat. Nos. 5,591,669; 5,598,369; 5,545,806; 5,545,807; 6,150,584 and references cited therein, the contents of which are incorporated herein by reference). These animals have been genetically modified such that there is a functional deletion in the production of endogenous (e.g., murine) antibodies. These animals are further modified to contain all or a portion of the human germ-line immunoglobulin gene locus such that immunization of these animals results in the production of fully human antibodies. Following immunization of these mice (e.g., XenoMouse®, Abgenix, Fremont, Calif.; HuMab-Mouse®, Medarex/GenPharm, Princeton, N.J.), monoclonal antibodies are prepared according to standard hybridoma technology (e.g., Kohler and Milstein, 1975).
This invention additionally provides a nucleic acid molecule encoding a monoclonal antibody or fragment thereof that specifically binds to HCV. In one embodiment, the encoded monoclonal antibody or fragment thereof is humanized. In another embodiment, the encoded monoclonal antibody or fragment thereof is fully human.
The nucleic acid molecule can be RNA, DNA or cDNA. In one embodiment, the nucleic acid molecule encodes the light chain. In another embodiment, the nucleic acid molecule encodes the heavy chain. In a further embodiment, the nucleic acid encodes both the heavy and light chains. In a still further embodiment, one or more nucleic acid molecules encode the Fab portion. In an additional embodiment, one or more nucleic acid molecules encode CDR portions. In another embodiment, the nucleic acid molecule encodes the variable domain. In a further embodiment, the nucleic acid molecule encodes the variable domain and one or more constant domains.
In addition, this invention provides a method for expressing in a cell a modified hepatitis C virus (HCV) glycoprotein selected from the group consisting of modified E1 glycoprotein and modified E1/E2 glycoprotein heterodimer, wherein the glycoprotein produced is homogeneously truncated by a deletion of amino acid residues 226 to 296 inclusive, these amino acid residues being numbered by reference to SEQ ID NO:3, which method comprises transfecting a cell with an expression vector comprising a modified coding sequence, wherein a nucleotide sequence corresponding to a putative intron between nucleotide positions 675 and 887 inclusive is deleted, these nucleotide positions being numbered by reference to SEQ ID NO:2, under conditions suitable for expression of vector-encoded glycoprotein, so as to express a homogeneously truncated glycoprotein lacking amino acid residues 226 to 296 inclusive, these amino acid residues being numbered by reference to SEQ ID NO:3.
This invention also provides a modified hepatitis C virus (HCV) glycoprotein, selected from the group consisting of modified E1 glycoprotein and modified E1/E2 glycoprotein heterodimer, wherein the modified glycoprotein is homogeneously truncated by a deletion of amino acid residues 226 to 296 inclusive, these amino acid residues being numbered by reference to SEQ ID NO:3.
This invention further provides a method for determining Whether an agent inhibits fusion of hepatitis C virus (HCV) to a target cell capable of fusing with HCV, which method comprises (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of an agent under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the agent, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; and (c) determining whether there is a reduction of resonance energy transfer in the presence of the agent compared with the resonance energy transfer in the absence of the agent; wherein a reduction in resonance energy transfer in the presence of the agent indicates that the agent inhibits fusion of HCV to the target cell. In one embodiment of the instant method, the agent is not previously known to inhibit fusion of HCV to the target cell.
This invention still further provides a method for screening a plurality of agents, not known to inhibit fusion of hepatitis C virus (HCV) to a target cell capable of fusing with this virus, to identify at least one agent that inhibits such fusion, which method comprises (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of a plurality of agents under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the plurality of agents, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; (c) determining whether there is a reduction of resonance energy transfer in the presence of the plurality of agents compared with the resonance energy transfer in the absence of the plurality of agents; and (d) if the resonance energy transfer is reduced in the presence of the plurality of agents, separately determining which of the agents present in the plurality of agents causes a reduction in resonance energy transfer, so as to thereby identify at least one agent that inhibits fusion of HCV to a target cell.
In one embodiment of the above methods, the agent is added to the cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, the target cell, or both the target cell and the cell expressing HCV E1/E2 glycoprotein heterodimer on its surface. In another embodiment, the target cell is a liver cell selected from the group consisting of Huh-7, PLC/PRF/5, Hep 3B, HepG2, Caco-2, HT1080, HT-29, LoVo, MCF-7, U118, 293T, and Vero cells. In a further embodiment, the target cell is a fresh or cryopreserved human hepatocyte, isolated from an adult human liver biopsy. In another embodiment, the first dye is a rhodamine moiety-containing molecule and the second dye is a fluorescein moiety-containing molecule. In a further embodiment, the rhodamine moiety-containing molecule is octadecyl rhodamine B chloride and the fluorescein moiety-containing molecule is fluorescein octadecyl ester. In a still further embodiment, the first dye is a fluorescein moiety-containing molecule and the second dye is a rhodamine moiety-containing molecule. In yet another embodiment, the rhodamine moiety-containing molecule is octadecyl rhodamine B chloride and the fluorescein moiety-containing molecule is fluorescein octadecyl ester.
The present invention additionally provides an agent that inhibits fusion of hepatitis C virus (HCV) to a target cell capable of fusing with HCV. In one embodiment, the agent is an antibody or fragment thereof. In another embodiment, the antibody is a monoclonal antibody. In yet another embodiment, the antibody is a polyclonal antibody. In a further embodiment, the antibody is a humanized antibody or fragment thereof. In a still further embodiment, the antibody is a human antibody or fragment thereof. In one embodiment, the fragment of the antibody comprises a light chain of an antibody. In another embodiment, the fragment of the antibody comprises a heavy chain of an antibody. In yet another embodiment, the fragment of the antibody comprises an Fab fragment of an antibody. In a further embodiment, the fragment of the antibody comprises an F(ab′)2 fragment of an antibody. In a still further embodiment, the fragment of the antibody comprises an Fd fragment of an antibody. In one embodiment, the fragment of the antibody comprises an Fv fragment of an antibody. In another embodiment, the fragment of the antibody comprises a variable domain of an antibody. In a further embodiment, the fragment of the antibody comprises one or more CDR domains of an antibody.
In another embodiment, the agent is a peptide. In yet another embodiment, the agent comprises a peptide bond. In a further embodiment, the agent is a non-peptidyl agent. In a still further embodiment, the agent is a small molecule or a low molecular weight molecule. In another embodiment, the molecule has a molecular weight less than 500 daltons.
The designing and synthesizing of chemical agents described herein that bind to surface components of HCV or a cell and inhibit fusion of HCV with the cell membrane or inhibit HCV entry into the cell may be facilitated by experimental approaches that are well known in the art, including traditional medicinal chemistry and the newer technology of combinatorial chemistry, both of which may be supported by computer-assisted molecular modeling. With such approaches, chemists and pharmacologists use their knowledge of the structures of surface molecules, e.g., the E1/E2 glycoprotein heterodimer, and agents determined to bind such molecules to design and synthesize a variety of additional agents that will bind to the surface molecules.
Combinatorial chemistry involves automated synthesis of a variety of novel agents by assembling them using different combinations of chemical building blocks. The use of this technique greatly accelerates the process of generating agents. The resulting arrays of agents are called libraries and are used to screen for agents (“lead agents”) that demonstrate a sufficient level of binding at molecules of interest. Using combinatorial chemistry it is possible to synthesize “focused” libraries of agents anticipated to be highly biased toward the target molecule.
Once lead agents are identified, whether through the use of combinatorial chemistry or traditional medicinal chemistry or otherwise, a variety of homologs and analogs are prepared to facilitate an understanding of the relationship between chemical structure, binding affinity for the target molecule, and biological or functional activity, which in the methods described herein is the ability of an agent to inhibit the fusion of HCV to a target cell or inhibit HCV entry into the cell. These studies define structure activity relationships (SARs) which are then used to design drugs with improved potency, selectivity and pharmacokinetic properties. Combinatorial chemistry is also used to rapidly generate a variety of structures for lead optimization. Traditional medicinal chemistry, which involves the synthesis of agents one at a time, is also used for further refinement and to generate agents not synthesizable by automated techniques. Once such drugs are defined, production is scaled up using standard chemical manufacturing methodologies utilized throughout the pharmaceutical and chemical industries.
Numerous non-peptidyl small molecules are available from a variety of commercial sources for screening for agents having desired functional properties. For example, ChemDiv (San Diego, Calif.) has an International Diversity collection of small molecules comprising over 150,000 small molecules selected from more than 3,500,000 chemical agents, and a CombiLab set of over 2,000 libraries of “probe” agents. Each library is represented by the validated template, a set of corresponding building blocks, substituents for SAR synthesis, the off-shelf probe compound set and complete synthetic protocol. Every template is prone.
The total feasible chemistry space of CombiLab's libraries is over 10,000,000,000 structures, with 250,000 of these being represented by probe sets. The major emphases of these libraries are on chemical novelty, drug- and lead-likeness, particular protein families identified as potential therapeutic target, favorable predicted absorption, distribution, metabolism, and excretion (ADME) and toxicity properties, and synthetic feasibility and cost. All compounds are produced in >150 mg quantities by liquid-phase parallel synthesis and individually purified to meet a >90% purity threshold. Every final compound and all key intermediates are analyzed by LC-MS or NMR at 400 Mhz.
ChemDiv has a large number of small molecules that are usable as building blocks for identifying and optimizing the chemical structures of agents in the screening methods described herein. The following are examples of building block molecules available for custom synthesis:




    
    
        S00501, S00503, S00504: R1=H, CH3, Cl, CF3, and other; R2=alkyl, aryl, hetaryl, and other; R2+R3=(CH2)m; R4, R5=H, alkyl, aryl, heterocyclyl, and other; m=0, 1-4; n=1-3.
        S00507, S00508: R═H, alkyl, alkoxy, Cl and other.
    
    


The library of building blocks contains scaffolds with several reaction centers, of which the following are examples:




    
    
        S00104: R1, R2=H, alkyl, aryl, heterocyclyl, and other; n=0, 1-5; R1—N—(CH2)n—R2=heterocycle.
        S00105: R═H, alkyloxyalkyl, alkylthioalkyl, aryl, heterocyclyl, and other.
        S00106: R═H, alkyl, alkyloxy, F, Cl, and other.
    
    






Each of these scaffolds may be used for generating a series of different combinatorial libraries. For example, the scheme below depicts some agents belonging to various combinatorial libraries, which can be produced with the scaffolds containing the fluoronitrobenzene moiety.




    
    
        Compound I is described by Ouyang et al. (1999a), VII by Ouyang et al. (1999b) and VIII by Ouyang et al. (1999c). Compound II is described by Wei et al. (1998). Compounds III is described by Kiselyov et al. (1999a); IV by Kiselyov et al. (1998) and VI by Kiselyov et al. (1999b). Compound V is described by Goldberg et al. (1999).
    
    


Libraries of nonpeptidyl small molecule agents for use in the present invention are also commercially available from Chembridge Collections (ChemBridge Corp., San Diego, Calif.). One ChemBridge library, PHARMACOphore diverse combination library, has over 60,000 compounds comprising multiple, chemically diverse libraries/templates. The average number of compounds per library/template is less than 2,000 with multiple chemical motifs inside each individual library. Another library available from ChemBridge includes DIVERSet which contains 50,000 compounds.
This invention also provides a pharmaceutical composition comprising any of the agents described herein and a pharmaceutically acceptable carrier. In one embodiment, the pharmaceutical composition further comprises at least one conventional antiviral agent. In a further embodiment, the antiviral agent includes but is not limited to the group consisting of interferon-alpha, interferon-alpha-2B and ribavirin.
Pharmaceutically acceptable carriers are well known to those skilled in the art and include, but are not limited to, 0.01-0.1 M and preferably 0.05 M phosphate buffer or 0.8% saline. Additionally, such pharmaceutically acceptable carriers can be aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions and suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's and fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers such as those based on Ringer's dextrose, and the like. Solid compositions may comprise nontoxic solid carriers such as, for example, glucose, sucrose, mannitol, sorbitol, lactose, starch, magnesium stearate, cellulose or cellulose derivatives, sodium carbonate and magnesium carbonate. For administration in an aerosol, such as for pulmonary and/or intranasal delivery, an agent or composition is preferably formulated with a nontoxic surfactant, for example, esters or partial esters of C6 to C22 fatty acids or natural glycerides, and a propellant. Additional carriers such as lecithin may be included to facilitate intranasal delivery. In addition to carriers described above, a vaccine may further include carriers known in the art such as, for example, thyroglobulin, albumin, tetanus toxoid, polyamino acids such as polymers of D-lysine and D-glutamate, inactivated influenza virus and hepatitis B recombinant protein(s). The vaccine may also include any well known adjuvants such as incomplete Freund's adjuvant, alum, aluminum phosphate, aluminum hydroxide, monophosphoryl lipid A (MPL, GlaxoSmithKline), saponins including QS21 (GlaxoSmithKline), CpG oligonucleotides (Krieg et al., 1995), montanide, vitamin E and various water-in-oil emulsions prepared from biodegradable oils such as squalene and/or tocopherol, Quil A, Ribi Detox, CRL-1005, L-121 and combinations thereof. Preservatives and other additives, such as, for example, antimicrobials, antioxidants, chelating agents, inert gases, and the like may also be included with all the above carriers.
This invention further provides a method for determining whether an agent inhibits entry of hepatitis C virus (HCV) into a target cell susceptible to infection by HCV, comprising (a) separately contacting (1) a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein a majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using at least one vector which provides virion packaging functions and expresses a reporter gene, with (2) a target cell in the presence and absence of an agent under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the agent; and (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the agent compared with reporter gene activity in the absence of the agent; wherein a reduction in reporter gene activity in the presence of the agent indicates that the agent inhibits entry of HCV into the target cell. In one embodiment of the instant method, the agent is not previously known to inhibit entry of HCV into the target cell.
This invention still further provides a method for screening a plurality of agents, not known to inhibit entry of hepatitis C virus (HCV) into a target cell susceptible to infection by HCV, to identify at least one agent that inhibits such entry, which method comprises (a) separately contacting (1) a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein a majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using at least one vector which provides virion packaging functions and expresses a reporter gene, with (2) a target cell in the presence and absence of a plurality of agents under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the plurality of agents; (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the plurality of agents compared with the reporter gene activity in the absence of the plurality of agents; and (c) if the reporter gene activity is reduced in the presence of the plurality of agents, separately determining which of the agents present in the plurality of agents causes a reduction in reporter gene activity, so as to thereby identify at least one agent that inhibits entry of HCV into a target cell.
In one embodiment of the above methods, the agent is added to the target cell, the pseudovirion or both the target cell and the pseudovirion. In another embodiment, the agent is added after the target cell is contacted with the pseudovirion but prior to viral entry. In a further embodiment, the target cell is selected from a group of liver cells consisting of Huh-7, PLC/PRF/5, Hep 3B, HepG2, Caco-2, HT1080, HT-29, LoVo, MCF-7, U118, 293T, and Vero cells. In another embodiment, the target cell is a fresh or cryopreserved human hepatocyte, isolated from an adult human liver biopsy.
In one embodiment, the packaging vector is preferably a retroviral packaging vector such as one of the vectors described in PCT International Publication No. WO 2004/024904. In a further embodiment, the at least one vector which provides virion packaging functions and expresses a reporter gene is derived from human immunodeficiency virus type 1 (HIV-1). In a still further embodiment, a single packaging vector provides virion packaging functions and expresses a reporter gene.
In one embodiment, the packaging vector expresses a luciferase, a green fluorescent protein, a yellow fluorescent protein or a beta-galactosidase reporter gene.
In a preferred embodiment, the packaging vector is pNL4.3-Luc+env-, wherein pNL4.3-Luc+env- expresses a luciferase reporter gene.
In another embodiment, the at least one vector which provides virion packaging functions and expresses a reporter gene is derived from human T-cell leukemia virus type 1 (HTLV-1). In a further embodiment, a packaging vector provides virion packaging functions and a separate transfer vector expresses a reporter gene. In yet another embodiment, the transfer vector expresses a luciferase, a green fluorescent protein, a yellow fluorescent protein or a beta-galactosidase reporter gene. In a preferred embodiment, the packaging vector is pCMV-HT1 or PCMV-HT-Δenv. In another preferred embodiment, the transfer vector is pHTC-luc, pHTC-luc-tsa, pHTC-eYFP or pHTC-eYFP-tsa.
In an additional embodiment, the at least one vector which provides virion packaging functions and expresses a reporter gene is derived from an avian C-type retrovirus. In a preferred embodiment, the packaging vector is pRD136. In another preferred embodiment, the transfer vector is pCXL.
Additionally, this invention provides an agent that inhibits entry of hepatitis C virus (HCV) into a target cell susceptible to infection by HCV. In one embodiment, the agent is an antibody or fragment thereof. In another embodiment, the antibody is a monoclonal antibody. In yet another embodiment, the antibody is a polyclonal antibody. In a further embodiment, the antibody is a humanized antibody or fragment thereof. In a still further embodiment, the antibody is a human antibody or fragment thereof. In one embodiment, the fragment of the antibody comprises a light chain of an antibody. In another embodiment, the fragment of the antibody comprises a heavy chain of an antibody. In yet another embodiment, the fragment of the antibody comprises an Fab fragment of an antibody. In a further embodiment, the fragment of the antibody comprises an F(ab′)2 fragment of an antibody. In a still further embodiment, the fragment of the antibody comprises an Fd fragment of an antibody. In one embodiment, the fragment of the antibody comprises an Fv fragment of an antibody. In another embodiment, the fragment of the antibody comprises a variable domain of an antibody. In a further embodiment, the fragment of the antibody comprises one or more CDR domains of an antibody.
In another embodiment, the agent is a peptide. In yet another embodiment, the agent comprises a peptide bond. In a further embodiment, the agent is a non-peptidyl agent. In a still further embodiment, the agent is a small molecule or a low molecular weight molecule. In another embodiment, the molecule has a molecular weight less than 500 daltons.
This invention also provides a pharmaceutical composition comprising any of the agents described herein and a pharmaceutically acceptable carrier. In one embodiment, the pharmaceutical composition further comprises at least one conventional antiviral agent. In a further embodiment, the antiviral agent includes but is not limited to the group consisting of interferon-alpha, interferon-alpha-2B and ribavirin.
In various methods described herein, agents identified to inhibit HCV fusion with or entry into target cells are used in therapeutically or prophylactically effective amounts respectively to treat a subject afflicted with a pathogen-related disorder or to inhibit the onset of such a disorder. Specifically, the present invention provides a method for treating a subject afflicted with a hepatitis C virus (HCV)-associated disorder, which treatment is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit fusion of HCV to a target cell capable of fusing with HCV using a method comprising (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of the agent under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the agent, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; and (c) determining whether there is a reduction of resonance energy transfer in the presence of the agent compared with the resonance energy transfer in the absence of the agent; wherein a reduction in resonance energy transfer in the presence of the agent indicates that the agent inhibits fusion of HCV to the target cell, and (2) administered in a therapeutically effective amount to treat the subject.
This invention also provides a method for treating a subject afflicted with a hepatitis C virus (HCV)-associated disorder, which treatment is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit entry of HCV into a target cell using a method comprising: (a) separately contacting a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein the majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using a packaging vector that expresses a reporter gene, with a target cell in the presence and absence of the agent under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the agent; and (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the agent compared with the reporter gene activity in the absence of the agent; wherein a reduction in reporter gene activity in the presence of the agent indicates that the agent inhibits entry of HCV into the target cell; and (2) administered in a therapeutically effective amount to treat the subject.
This invention further provides a method for preventing a hepatitis C virus (HCV) infection in a subject, the prevention of which is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit fusion of HCV to a target cell capable of fusing with HCV using a method comprising: (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of the agent under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the agent, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; and (c) determining whether there is a reduction of resonance energy transfer in the presence of the agent compared with the resonance energy transfer in the absence of the agent; wherein a reduction in resonance energy transfer in the presence of the agent indicates that the agent inhibits fusion of HCV to the target cell; and (2) administered in a prophylactically effective amount to prevent an HCV infection in the subject.
This invention still further provides a method for inhibiting in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit fusion of HCV to a target cell capable of fusing with HCV using a method comprising (a) separately contacting a target cell, which is labeled with a first dye, with a cell expressing HCV E1/E2 glycoprotein heterodimer on its surface, which HCV glycoprotein-expressing cell is labeled with a second dye, in the presence and absence of the agent under conditions which would normally permit fusion of the target cell to the cell expressing HCV E1/E2 glycoprotein dimer on its surface in the absence of the agent, wherein the first and second dyes are selected so as to allow resonance energy transfer between the dyes; (b) exposing the contacted cells to conditions which would result in resonance energy transfer if fusion has occurred; and (c) determining whether there is a reduction of resonance energy transfer in the presence of the agent compared with the resonance energy transfer in the absence of the agent; wherein a reduction in resonance energy transfer in the presence of the agent indicates that the agent inhibits fusion of HCV to the target cell; and (2) administered in a prophylactically effective amount to have a prophylactic effect in the subject.
This invention additionally provides a method for preventing a hepatitis C virus (HCV) infection in a subject, the prevention of which is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit entry of HCV into a target cell using a method comprising: (a) separately contacting a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein the majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using a packaging vector that expresses a reporter gene, with a target cell in the presence and absence of the agent under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the agent; and (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the agent compared with the reporter gene activity in the absence of the agent; wherein a reduction in reporter gene activity in the presence of the agent indicates that the agent inhibits entry of HCV into the target cell; and (2) administered in a prophylactically effective amount to prevent an HCV infection in the subject.
This invention also provides a method for inhibiting in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus, which method comprises administering to the subject an agent, wherein this agent is (1) determined to inhibit entry of HCV into a target cell using a method comprising: (a) separately contacting a pseudovirion expressing HCV E1/E2 glycoprotein heterodimer on its surface, wherein the majority of the E1/E2 glycoprotein is full length, which pseudovirion was produced using a packaging vector that expresses a reporter gene, with a target cell in the presence and absence of the agent under conditions which would normally permit entry of the pseudovirion into the target cell in the absence of the agent; and (b) lysing the contacted target cell and determining whether there is a reduction in reporter gene activity in the presence of the agent compared with the reporter gene activity in the absence of the agent; wherein a reduction in reporter gene activity in the presence of the agent indicates that the agent inhibits entry of HCV into the target cell; and (2) administered in a prophylactically effective amount to have a prophylactic effect in the subject.
Determining a therapeutically or prophylactically effective amount of the agents and compositions described herein can be done based on animal data using routine computational methods. The effective amount is based upon, among other things, the size, form, biodegradability, bioactivity and bioavailability of the agent. By way of illustration, if the agent does not degrade quickly, is bioavailable and highly active, a smaller amount will be required to be effective.
In one embodiment of the instant method, the therapeutically or prophylactically effective amount contains between about 0.000001 mg/kg body weight and about 1000 mg/kg body weight of polypeptide or non-peptidyl agent. In another embodiment, the effective amount contains between about 0.0001 mg/kg body weight and about 250 mg/kg body weight of polypeptide or non-peptidyl agent. In a further embodiment, the effective amount contains between about 0.001 mg/kg body weight and about 50 mg/kg body weight of polypeptide or non-peptidyl agent. In a still further embodiment, the effective amount contains between about 0.01 mg/kg body weight and about 10 mg/kg body weight of polypeptide or non-peptidyl agent. In another embodiment, the effective amount contains between about 0.05 mg/kg body weight and about 2.5 mg/kg body weight of polypeptide or non-peptidyl agent. In yet another embodiment, the effective amount contains between about 0.1 mg/kg body weight and about 0.5 mg/kg body weight of polypeptide or non-peptidyl agent.
Embodiments of methods described above for treating a subject afflicted with a hepatitis C virus (HCV)-associated disorder and methods for inhibiting in a subject the onset of a hepatitis C virus (HCV)-associated disorder further comprise administration of at least one conventional antiviral agent. In further embodiments, the antiviral agent includes but is not limited to the group consisting of interferon-alpha, interferon-alpha-2B and ribavirin.
Treatment of hepatitis C virus (HCV) infection may also be accomplished using pharmaceutical compositions comprising pseudovirion. Suitable formulations for delivery of pseudovirion are found in Remington's Pharmaceutical Sciences (1985). These pharmaceutical compositions are suitable for use in a variety of drug delivery systems (se Langer, 1990). Pseudovirion in compositions are suitable for single administration or in a series of inoculations (e.g., an initial immunization followed by subsequent inoculations to boost the anti-HCV immune response). The pharmaceutical compositions are intended for parenteral, topical or oral administration. Parenteral administration is preferably by intravenous, subcutaneous, intradermal, intraperitoneal or intramuscular administration. Parenteral administration may be preferentially directed to the patient's liver such as by catheterization to hepatic arteries or into a bile duct. For parenteral administration, the compositions can include pseudovirion suspended in a suitable sterile carrier such as water, aqueous buffer, 0.4% saline solution, 0.3% glycine, hyaluronic acid or emulsions of nontoxic nonionic surfactants as is well known in the art. The compositions may further include substances to approximate physiological conditions such as buffering agents and wetting agents such as NaCl, KCl, CaCl2, sodium acetate and sodium lactate. Aqueous suspensions of pseudovirion can be lyophilized for storage and can be suitably recombined with sterile water before administration. Solid compositions including pseudovirion in conventional nontoxic solid carriers may be used. For oral administration of solid compositions, the pseudovirion preferably comprise 10% to 95%, and more preferably 25% to 75% of the composition.
Pseudovirion, formulated with a nontoxic surfactant, a propellant and possibly other carriers well known in the art, can also be administered in an aerosol such as for pulmonary and/or intranasal delivery
Pseudovirion can be used prophylactically as a vaccine to prevent HCV infection. Accordingly, this invention also provides a method for preventing a hepatitis C virus (HCV) infection in a subject, the prevention of which is effected by immunizing the subject, which method comprises: (a) injecting into the subject a pharmaceutical composition comprising an HCV pseudovirion expressing on its surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length; and thereby (b) eliciting a protective HCV immune response in the subject.
This invention further provides a method for inhibiting in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by immunizing the subject, which method comprises: (a) injecting into the subject a pharmaceutical compositions comprising an HCV pseudovirion; thereby (b) eliciting a protective immune response in the subject. One embodiment of the instant immunization methods further comprises injecting into the subject a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein, E1/E2 glycoprotein heterodimer and immunogenic fragments thereof. In another embodiment, the methods further comprise injecting into the subject a nucleic acid vector capable of expressing an HCV glycoprotein selected from the group consisting of E1 glycoprotein, E1/E2 glycoprotein heterodimer and immunogenic fragments thereof. In an additional embodiment, the methods further comprise administration of at least one conventional antiviral agent. In yet another embodiment, the antiviral agent includes but is not limited to the group consisting of interferon-alpha, interferon-alpha-2B and ribavirin.
A vaccine containing pseudovirion contains an immunogenically effective amount of the particles admixed with a pharmaceutically acceptable carrier such as those described above. The vaccine may further include carriers known in the art such as, for example, thyroglobulin, albumin, tetanus toxoid, polyamino acids such as polymers of D-lysine and D-glutamate, inactivated influenza virus and hepatitis B recombinant protein(s). The vaccine may also include any well known adjuvants such as incomplete Freund's adjuvant, alum, aluminum phosphate, aluminum hydroxide, monophosphoryl lipid A (MPL, GlaxoSmithKline), saponins including QS21 (GlaxoSmithKline), CpG oligonucleotides. (Krieg et al., 1995), montanide, vitamin E and various water-in-oil emulsions prepared from biodegradable oils such as squalene and/or tocopherol, Quil A, Ribi Detox, CRL-1005, L-121 and combinations thereof. The immune response generated to the pseudovirion may include generation of anti-HCV antibodies and/or generation of a cellular immune response (e.g., activation of cytotoxic T lymphocytes or CTL).
A vaccine composition containing a HCV pseudovirion is administered to a patient in an immunogenically effective amount to elicit a protective immune response against HCV. The immunogenically effective amount will vary depending on the composition of the vaccine (e.g., whether or not it contains adjuvant), the manner of administration, the weight and general health of the patient and the judgment of the prescribing health care provider. For initial vaccination, the general range of pseudovirion in the administered vaccine is about 100 μg to about 1 μm per 70 kg patient; subsequent inoculations to boost the immune response include pseudovirion in the range of 100 μg to about 1 μm per 70 kg patient. Single or multiple boosting immunizations are administered over a period of about two weeks to about six months from the initial vaccination. The prescribing health care provider may determine the number and timing of booster immunizations based on well known immunization protocols and the individual patient's response to the immunizations (e.g., as monitored by assaying for anti-HCV antibodies).
For treatment of a patient infected with HCV, the amount of pseudovirion to be delivered will vary with the method of delivery, the number of administrations and the state of the person receiving the composition (e.g., age, weight, severity of HCV infection, active or chronic status of HCV infection and general health status). Before therapeutic administration, the patient will already have been diagnosed as HCV-infected and may or may not be symptomatic. Generally, a therapeutically effective amount of pseudovirion will be in the range of about 1 mg to about 10 gm per day, preferably about 50 mg to about 5 gm per day, and most preferably about 100 mg to 1 gm per day for a 70 kg patient. The pseudovirion may be administered as a prime and/or boost, alone or in various prime/boost combinations with E1 glycoprotein, E1/E2 glycoprotein dimer or immunogenic portions thereof, or nucleic acid molecules encoding such glycoproteins as described above.
This invention further provides a diagnostic kit comprising an antibody as described herein and instructions for using this antibody to detect hepatitis C virus (HCV) in human tissue. In one embodiment, the instructions describe use of the antibody for an immunoassay. In another embodiment, the antibody is immobilized on a solid support. In a further embodiment, the solid support is selected from the group consisting of polysaccharide polymers (see U.S. Pat. No. 3,642,852), filter paper, nitrocellulose membrane, polyethylene, polystyrene and polypropylene.
This invention also provides an article of manufacture comprising a packaging material containing therein a modified nucleic acid molecule as described herein and a label providing instructions for using this modified nucleic acid to express on a cell surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the expressed glycoprotein is full length.
This invention further provides an article of manufacture comprising a packaging material containing therein a modified nucleic acid molecule as described herein and a label providing instructions for using the modified nucleic acid to generate a pseudovirion expressing on its surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the expressed glycoprotein is full length.
This invention still further provides an article of manufacture comprising a packaging material containing therein a cell expressing on the cell surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length, and a label providing instructions for using the cell to identify an agent that inhibits fusion of HCV to a target cell capable of fusing with this virus.
Additionally, this invention provides an article of manufacture comprising a packaging material containing therein a pseudovirion expressing on its surface a hepatitis C virus (HCV) glycoprotein selected from the group consisting of E1 glycoprotein and E1/E2 glycoprotein heterodimer, wherein the majority of the glycoprotein is full length, and a label providing instructions for using the pseudovirion to identify an agent that inhibits entry of HCV into a target cell susceptible to infection by this virus.
This invention also provides an article of manufacture comprising a packaging material containing therein an agent as described herein and a label providing instructions for using this agent to treat a subject afflicted with a hepatitis C virus (HCV)-associated disorder, treatment to which is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus.
This invention further provides an article of manufacture comprising a packaging material containing therein an agent as described herein and a label providing instructions for using this agent to treat a subject afflicted with a hepatitis C virus (HCV)-associated disorder, treatment to which is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus.
This invention still further provides an article of manufacture comprising a packaging material containing therein an agent as described herein and a label providing instructions for using this agent to inhibit in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by inhibiting fusion of HCV to a target cell capable of fusing with this virus.
This invention also provides an article of manufacture comprising a packaging material containing therein an agent as described herein and a label providing instructions for using this agent to inhibit in a subject the onset of a hepatitis C virus (HCV)-associated disorder, the inhibition of which is effected by inhibiting entry of HCV into a target cell susceptible to infection by this virus.
EXPERIMENTAL DETAILS
The following Experimental Details are set forth to aid in an understanding of the invention, and are not intended, and should not be construed, to limit in any way the invention set forth in the claims which follow thereafter.
It should also be understood that the HCV isolates used as examples to provide nucleotide and amino acid sequences in the present invention are not intended to limit the scope of the invention, and that any HCV isolate from type 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or any other new genotype of HCV is a suitable source of E1 and/or E2 sequence for the practice of the present invention. Analysis of the entire HCV sequence from any genotype of HCV by a splice site neural network (http://www.fruitfly.org/seq tools/splice.html) is used to identify the presence of a splice donor site and/or splice acceptor site, and conservative mutagenesis is performed to generate the modified nucleic acid molecules of the present invention.
Materials and Methods
DNA constructs for expression of HCV envelope glycoproteins The sequences used to construct vectors for expression of different combinations of HCV envelope glycoproteins were derived from the full length HCV consensus sequence (Yanagi et al., 1997; Genbank Accession #AF011751). The genomic sequence (SEQ ID NO:1) is shown in FIGS. 1a-c, the sequence (SEQ ID NO:2) encoding the HCV structural proteins is shown in FIG. 2, and the deduced amino acid sequence (SEQ ID NO:3) of the HCV polyprotein is shown in FIGS. 3a and b. The pBR cloning vector derivative, p90/HCV FL-long pU, expressing a full-length cDNA of the consensus HCV H77 (1a genotype) sequence (Koykhalov et al., 1997), is available from the NIH AIDS Research & Reference Reagent Program (Catalog #7672). PCR cloning was used to insert translation initiation and stop codons near the ends of the HCV inserts in each construct, and flanking HindIII and XbaI restriction enzyme site at the 5′ and 3′ termini respectively. The following primer pairs, showing HindIII and XbaI restriction enzyme sites in bold, were used to generate the PCR fragments encompassing the sequences encoding unmodified HCV structural proteins:







Upstream (U) and downstream (D) primers


used for construction of the 5′-HindIII-



C-E1-E2-p7-XbaI-3′ sequence (FIG. 4):








(SEQ ID NO:11)









U: 5′-aaaaaaaagcttatgagcacgaatcctaaacctc-3′









(SEQ ID NO:12)









D: 5′-aaaaaatctagattatgcgtatgcccgctgaggca-3′



 


Primers used for construction of 5′-HindIII-C-E1-


E2-XbaI-3′ sequence (FIG. 5):








(SEQ ID NO:13)









U: 5′-aaaaaaaagcttatgagcacgaatcctaaacctc-3′









(SEQ ID NO:14)









D: 5′-aaaaaatctagattacgcctccgcttg-3′



 


Primers used for construction of 5′-HindIII-ΔC-


E1*-E2*-XbaI-3′ sequence (FIG. 6):








(SEQ ID NO:15)









U: 5′-aaaaaaaagcttatggacctcatggggtacata-3′









(SEQ ID NO:16)









D: 5′-aaaaaatctagattacgcctccgcttg-3′



 


Primers used for construction of 5′-HindIII-E1-


E2-p7-XbaI-3′ sequence (FIG. 7):








(SEQ ID NO:17)









U: 5′-aaaaaaaagcttatgggttgctctttctctatc-3′









(SEQ ID NO:18)









D: 5′-aaaaaatctagattatgcgtatgcccgctgaggca-3′



 


Primers used for construction of 5′-HindIII-E1-E2-


XbaI-3′ sequence (FIG. 8):








(SEQ ID NO:19)









U: 5′-aaaaaaaagcttatgggttgctctttctctatc-3′









(SEQ ID NO:20)









D: 5′-aaaaaatctagattacgcctccgcttg-3′







Fragments encoding unmodified HCV glycoprotein sequences with HindIII and XbaI sticky ends at the 5′ and 3′ termini respectively were generated by double digestion with HindIII and XbaI, and ligated into HindIII/XbaI-doubly digested pcDNA3.1+expression vector (Invitrogen). Ligation products were transformed into MAX Efficiency® DH5αTM chemically competent cells (Invitrogen). Ampicillin resistant clones were selected and plasmid DNA was purified using a QIAprep® Spin Miniprep Kit (Qiagen, Valencia, Calif.). Recombinant vector constructs were verified by DNA sequencing.
Putative splice donor and/or splice acceptor sites in E1 and E2 sequences (nucleotide positions 887, 888 and 2182 in SEQ ID NO:1) were modified by conservative mutagenesis (A886→C886 and A2183→T2183 substitutions) using the QuickChange® Mutagenesis Kit (Stratagene, La Jolla, Calif.). As an example, the sequence (SEQ ID NO:9) of the 5′-HindIII-E1-E2-p7-XbaI-3′ construct with A886C and A2183T double mutations is shown in FIG. 9. The predicted intron in E1 (between nucleotide positions 673 and 887 in SEQ ID NO:1) was excised with restriction enzymes following PCR generation of restriction sites flanking the sequence to be deleted. The sequence (SEQ ID NO:10) of the 5′-HindIII-E1-XbaI-3′ construct with the intron deleted is shown in FIG. 10. The same nucleotide substitutions and intron deletion modifications were introduced into constructs encoding E1/E2 with or without C and p7 as described above.
Extraction of Viral RNA from Cells
Viral RNA was extracted from cells using a QIAmp Viral RNA Mini Spin Kit (Qiagen) with modifications. Briefly, two extractions with 280 μl of lysis buffer were performed per well and transferred to a 1.7-ml tube. The empty plate was washed with 140 μl of Dulbecco's phosphate-buffered saline containing calcium and magnesium, and pooled into the same tube. RNA extraction and binding to spin columns were carried out according to the manufacturer's instructions. Following a wash with wash buffer, contaminating DNA on the column was removed by treatment with RNase-free DNase (Qiagen) according to the manufacturer's instructions. The bound RNA was washed and eluted from the column in two steps using 30 μl and 40 μl of elution buffer respectively, and the eluates were combined.
Reverse Transcriptase-polymerase Chain Reaction (RT-PCR)
Total RNA was isolated from cells using an RNeasy® Protect Mini Kit (Qiagen) according to the manufacturer's instructions. The RNA was used in a one-tube RT-PCR reaction using a SensiscriptTM Reverse Transcriptase Kit (Qiagen) according to the manufacturer's instructions.
A primer pair comprising SEQ ID NOS: 19 and 20 was used in a PCR reaction to specifically amplify DNA encoding the HCV E1/E2 envelope glycoproteins, thereby placing a HindIII site and an Xba1 site at the 5′ and 3′ ends, respectively, of the amplified DNA (see FIG. 8), and facilitating cloning into HindIII/Xba1-doubly digested pcDNA-3.1+(Invitrogen) as described.
Transient Expression of HCV Envelope Glycoproteins in HeLa Cells
HeLa cells were seeded overnight on glass coverslips and infected with 5 plaque forming units per cell of a recombinant T7 polymerase-expressing vaccinia virus vector, vTF7.3 (Earl and Moss, 1991), for 1 h at 37° C., followed by lipofection (Invitrogen) with the E1-E2 gene construct. Alternatively, cells were lipofected with plasmid vector containing the E1-E2 construct. Following each of these procedures, protein expression was analyzed 24 h post-infection by immunofluorescent staining using anti-E1 or anti-E2 MAbs. Cells were either fixed in 3% formaldehyde for 20 min at room temperature or fixed/permeabilized with methanol for 20 min at −20° C., followed by washing with 2% gelatin in phosphate-buffered saline (PBS). The fixed cells were then incubated with the anti-E1 MAb, A4 (1:100; provided by Dr. Jean Dubuisson), or the anti-E2, MAb H53 (1:100; provided by Dr. Jean Dubuisson), washed and incubated with a phycoerythrin (PE)-labeled goat anti-mouse IgG secondary antibody (1:100, Pierce, Rockford, Ill.). Coverslips were mounted on slides with Moviol (Calbiochem-Novabiochem Corp., La Jolla, Calif.) and observed under a fluorescence microscope.
Stable Expression of HCV Envelope Glycoproteins in Mammalian Cells
HeLa cells were lipofected with different recombinant plasmid vectors containing HCV envelope glycoprotein gene constructs and placed in medium containing 1 mg/ml G418 (Sigma Chemical, St. Louis, Mo.). G418-resistant cells were pooled and labeled with anti-E2 MAb H53. The 10% most strongly labeled cells were sorted using the FACS Vantage SE (Becton Dickinson, San Jose, Calif.) and subcloned by limiting dilution in order to generate clonal populations. For E1-expressing stable cell lines, cells were subcloned directly after G418 selection and individual clones were tested for E1 expression by immunoblotting. Proteins from whole cell lysates were analyzed by immunoblotting with anti-E2 MAb A11 or anti-E1 MAb A4.
Immunoblot Analysis of HCV Proteins Expressed in Cells
HCV envelope glycoproteins were expressed in HeLa cells with a vaccinia- or a plasmid-based expression system. Cells were lysed in a 1% Nonidet® P40 (NP40), 150 mM NaCl, 50 mM Tris-HCl pH 7.5, 1 mM EDTA buffer containing a protease inhibitor cocktail (Roche, Indianapolis, Ind.). A fraction of the cell lysates was treated with 0.25 units/ml of endoglycosidase H (Boehringer, Indianapolis, Ind.) overnight at 37° C. Proteins were separated by 10% or 12% SDS-PAGE (BioRad, Hercules, Calif.) followed by transfer to Trans-Blot nitrocellulose membranes (BioRad). Membranes were probed either with anti-E2 MAb A11 (1:1000) or anti-E1 MAb A4 (1:1000), followed by horseradish peroxidase (HRP)-labeled goat anti-mouse IgG (1:10,000, Amersham, Piscataway, N.J.) and incubation with a chemifluorescent substrate (Vistra ECFTM, Amersham).
Biotinylation and Streptavidin Capture of Cell Surface-localized HCV Envelope Glycoproteins
Cell surface proteins of HeLa cells stably expressing HCV envelope glycoproteins were tagged with EZ-Link Sulfo-NHS-LC-Biotin (Pierce) before cell lysis as described by Lu and Kielian (2000). Biotinylated proteins were recovered by incubation of lysates with streptavidin-coupled agarose beads (Molecular Probes, Eugene, Oreg.) for 1 h at 4° C. followed by three washes with the lysis buffer. For detection of E1 proteins, recovered proteins were immunoblotted with anti-E1 MAb A4. Surface-associated E2 proteins in HeLa or NKNT3 cells were detected by flow cytometry analyses after labeling of cells with different anti-E2 MAbs as indicated.
Protein G Immunoprecipitation of Cell Surface-localized E1/E2 Heterdiomers
HeLa cells were stably transfected with constructs for expression of modified HCV envelope glycoproteins. Intact transfected cells were incubated with the anti-E2 MAb H53 (1:100), lysed and incubated with protein G-coupled agarose beads (Oncogene Research Products, San Diego, Calif.) overnight at 4° C., followed by three washes with the lysis buffer. The presence of E1 was detected by immunoblotting with anti-E1 MAb A4 and the presence of E2 was detected by immunoblotting with anti-E2 MAb A11.
Generation of HCV Pseudovirions Expressing Modified HCV Glycoprotein Genes
HCV pseudotyped particles were generated in 293T cells by co-transfection with an HCV envelope glycoprotein vector construct and an HIV-1-based packaging vector, pNL4.3-Luc+env-, expressing a luciferase reporter gene, as described (Bartosch et al., 2003; Hsu et al., 2003). Briefly, 293T cells were plated the day before transfection at a confluence of 1.5 million cells per 10 cm plate. Cells were transfected using the standard calcium phosphate precipitation method with a mix of 15 μg of a pcDNA-3.1-HCV-envelope glycoprotein construct and 5 μg of pNL-Luc+env- DNA per plate. The following day, the medium was replaced with 7 ml of fresh medium and the cells were incubated for another 24 h. Viral supernatant was collected, centrifuged for 10 min at 4,000 rpm or filtered through a 0.2 μm membrane, and either frozen at −70° C. or used directly to infect target cells.
A human T-cell leukemia virus type 1 (HTLV-1)-based packaging system (e.g., Derse et al., 2001) can also be used for preparing HCV pseudotyped particles. Examples of vectors used in this system are described in detail by Derse et al. (2001). Briefly, an initial packaging plasmid, pCMVHT1, encoding Gag-Pol and other HTLV-1 accessory proteins under the control of a cytomegalovirus (CMV) promoter, was constructed from an infectious clone of HTLV-1 (pCS-HTLV; Derse et al., 1995) by replacing the 5′-LTR and 5′-untranslated region with a CMV promoter linked to a fragment from the R region of the LTR. pCMVHT1 lacks the minus-strand primer binding site and virion RNA-packaging elements are absent. Derivatives of pCMVHT1 include pCMVHT-Δenv, generated by deletion of the XhoI fragment (positions 5779 to 6497) in the env gene of pCMVHT1, and pCMVHT-Int− which was derived from pCMVHT-Δenv by site-directed mutagenesis to create a stop codon (nucleotide position 4700) in the integrase-coding region. A transfer vector, pHTC-luc, containing the 5′ and 3′ LTR, the psi encapsidation element and the firefly luciferase reporter gene under the control of a CMV promoter, was derived from pCS-HTLV by replacing sequences between the NcoI and MluI sites at positions 1232 and 7482, respectively, with a cassette containing the CMV immediate early promoter joined to the luciferase gene. A modified version of this vector, pHTC-luc-tsa, was generated by inserting a fragment containing the HTLV-1 tax/rex splice acceptor site (positions 6731 to 7436) immediately upstream of the CMV promoter. pHTC-luc-tsa seems to give better transduction efficiency due the presence of the splice acceptor site upstream from the CMV promoter. Other transfer vectors, pHTC-eYFP and pHTC-eYFP-tsa, were derived from pHTC-luc and pHTC-luc-tsa, respectively, by replacing the luciferase gene with the enhanced yellow fluorescent protein (eYFP) gene (Derse et al., 2001).
HCV pseudotyped particles are generated by co-transfecting 293T cells, seeded at 3 million cells in 10-cm plates the previous day, with 10 μg each of any of the HCV envelope glycoprotein-expressing vectors described herein, pCMVHT1, pCMVHT-Δenv, or a similar packaging vector encoding Gag-Pol and other HTLV-1 accessory proteins, and pHTC-luc, pHTC-luc-tsa, pHTC-eYFP, pHTC-eYFP-tsa or a similar transfer vector containing at least the 5′ and 3′ LTR, the psi encapsidation element and a reporter gene. Cells are transfected by calcium phosphate precipitation. The medium is changed 16 h after co-transfection, and virus-containing supernatant is collected 12 h later. Viral supernatant is cleared by low-speed centrifugation and filtered through a 0.45 μm filter.
Another retroviral packaging system that can be used to prepare HCV pseudotyped particles is derived from spleen necrosis virus (SNV), an avian C-type retrovirus (Parveen et al., 2000). This packaging system employs a transfer vector, pCXL, which is a SNV vector containing 5′ and 3′ LTRs, an encapsidation sequence and the bacterial β-galactosidase (lacZ) reporter gene inserted in place of the retroviral protein coding sequences. A packaging vector, pRD136, expresses the SNV wild-type Gag-Pol genes from the murine leukemia virus (MLV) U3 promoter and contains the adenovirus tripartite leader sequence (AVtl) downstream of the promoter for enhanced gene expression. Polyadenylation is mediated by the simian virus 40 (SV40) polyadenylation signal sequence (Parveen et al., 2000). HCV pseudotyped particles are generated by essentially as described above for the HIV-1- and HTLV-1-based packaging systems by co-transfecting 293T cells with any of the HCV envelope glycoprotein-expressing vectors disclosed herein, pRD136 or a similar packaging vector encoding Gag-Pol, and pCXL or a similar transfer vector containing a reporter gene.
Infection of Cells with HCV Pseudovirions
One day prior to infection, target cells were plated in 24-well plates at a confluence of 40,000 cells per well. On the day of infection, viral supernatant (500 μl) was applied directly onto the cells and incubated overnight at 37° C. The medium was then changed and cells were incubated for another 24 h. Cells were lysed and luciferase activity quantified using the Luciferase Assay System (Promega, Madison, Wis.) according to the manufacturer's recommendations.
Assay for Identification of Inhibitors of HCV Fusion to Target Cells
The resonance energy transfer (RET) technique (Litwin et al., 1996) may be used to quantify HCV envelope glycoprotein-mediated membrane fusion and to identify inhibitors of HCV fusion to target cells. Briefly, one fusion partner (e.g., an E1/E2-expressing cell line) is labeled with a fluorescent dye such as octadecyl fluorescein (F18; Molecular Probes, Eugene, Oreg.), and the other fusion partner (e.g., a target cell capable of fusing with HCV) is labeled with a dye such as octadecyl rhodamine (R18; Molecular Probes, Eugene, Oreg.). The octadecyl versions of these probes spontaneously insert into the plasma membranes of cells using the labeling protocol described by Litwin et al. (1996). The fluorochromes are chosen such that the emission spectrum of one (F18) overlaps the excitation spectrum of the second (R18).
F18 or R18 is dissolved in ethanol at 5-10 mg/ml and diluted approximately 1000-fold into the appropriate cell culture medium. The exact concentration in the medium is adjusted to bring the OD to 0.34 at 506 nm (F18) or 1.04 at 565 nm (R18). The labeled cells are then contacted under conditions that permit cell fusion. Monolayers of cells are incubated with the appropriate medium overnight, then washed and counted. 100,000 cells of each type are mixed together in wells of a 24-well tissue culture plate and incubated at 37° C. At intervals after mixing, the cells are removed with EDTA, washed and placed in a fluorometer cuvette.
Upon cell fusion, the F18 and R18 associate together closely enough that stimulation of F18 results in resonance energy transfer to R18 and emission at the R18 emission wavelengths. The dyes are excited at the wavelengths indicated in Table 1, and fluorescence measured at the indicated emission wavelengths (Table 1) using a LS50 fluorometer (Perkin-Elmer).







TABLE 1







Excitation and emission wavelengths used in RET assay.











Excitation
Emission




Wavelength (nm)
Wavelength (nm)
Measurement obtained







450
530
Total F18 fluorescence



557
590
Total R18 fluorescence



450
590
RET*







*The calculation of RET requires first subtracting the fluorescence due to direct F18 and R18 fluorescence following excitation at 450 nm and emission at 590 nm. The fluorescence measurements are determined by measuring the fluorescence of cells labeled with each dye separately. The RET value, calculated as described by Litwin et al. (1996), is divided by the total R18 fluorescence to give a % RET value.






Assay for Identification of Inhibitors of HCV Entry Into Target Cells

HCV pseudovirions expressing modified HCV glycoproteins are used to infect target cells as described above. A panel of liver target cells lines, available from the ATCC (Catalog #CRL-HB-8065) and including HepG2 human hepatocellular carcinoma cells, is used. Alternatively, fresh or cryopreserved human hepatocytes, isolated from adult human liver biopsies (available from Cambrex/Clonetics, San Diego, Calif.), may be used. Duplicate infections are performed in the presence and absence respectively of the agent being assayed for entry inhibitory activity. The agent is added to the target cells, pseudovirions or both and incubated for 0-4 h. Alternatively, the agent is added after contacting the target cells with the pseudovirions but prior to viral entry. The degree of inhibition is quantified as a decrease in the level of luciferase activity measured in the presence of an inhibitory agent compared to the level observed in the absence of that agent.
Results
Plasmid-based Expression Causes Cell Surface Localization of E1 and E2
Constructs were generated for expression of full-length unmodified HCV E1 (E1), E2 (E2) and E1/E2 (E1-E2), using HCV envelope glycoprotein gene sequences derived by PCR amplification of p90/HCV FL-long pU which contains a cDNA insert corresponding to the full-length genome of an infectious HCV isolate, H77 (Kolykhalov et al., 1997). The first nucleotide of the capsid (C) start codon is defined as position +1 in the HCV genome (SEQ ID NO:1; see FIG. 1). Therefore, C extends from nucleotides +1 to 510 inclusive, E1 extends from nucleotides 511 to 1149, E2 extends from nucleotides 1111 to 2238, E1-E2 extends from nucleotides 511 to 2238, and p7 extends from nucleotides 2238 to 2427.
Transient expression of HCV envelope glycoproteins was achieved by lipofection of the different expression plasmids into HeLa cells. Alternatively, HeLa cells were infected with vTF7.3, a vaccinia virus vector expressing T7 polymerase, followed by lipofection with HCV E1/E2-expression plasmids (resulting in cytoplasmic transcription from the T7 promoter in pcDNA3.1+).
Intracellular but not cell surface-associated E1 and E2 were detected by immunofluorescence after vaccinia virus-driven expression of E1-E2 (FIGS. 11a-d). In contrast, E1 and E2 were detected both intracellularly and on the cell surface following plasmid-based expression of the E1-E2 construct (FIGS. 11e-h). Intracellular staining of envelope glycoproteins was comparable in the two expression systems (FIGS. 11a, b, e, f), indicating that similar levels of E1 and E2 expression were achieved in both systems but that transport to the cell surface was not occurring in the vaccinia-based expression system. Differences in expression levels were not observed between envelope glycoproteins expressed as single proteins (E1 and E2) or as part of an E1-E2 polyprotein (E1-E2, data not shown). Similar expression patterns were obtained after transient expression of E1 and E2 by vaccinia- and plasmid-based systems in a hepatoma cell line, HepG2 (data not shown).
Size Heterogeneity of HCV Envelope Glycoproteins Expressed in HeLa Cells
Vaccinia vector- and plasmid vector-based expression of unmodified E2 and E1-E2 constructs HCV invariably generated a major E2 protein species with an apparent molecular weight of 62 kDa (FIGS. 12a, b). However, vaccinia expression of unmodified E1 and E1-E2 constructs generated four E1 protein species of 18, 21, 24 and 27 kDa apparent molecular weights (FIG. 12c). Treatment of cell lysates with endoglycosidase H generated a single low molecular weight band corresponding to the deglycosylated E1 protein core (FIG. 12c). The 27 kDa species therefore corresponds to the fully glycosylated E1 protein, whereas the lower molecular weight species correspond to incomplete glycosylation products. By contrast, plasmid-based expression of E1-E2 generated E1 proteins of 27 and 20 kDa apparent molecular weights (FIG. 12d). The 20 kDa E1 species was not the result of hypoglycosylation because two E1 protein species were still present after endoglycosidase H treatment of cell lysates (FIG. 12d, see below).
A Putative Intron is Excised from the E1 Gene Transcribed in Cell Nuclei
Vaccinia virus-based expression of heterologous genes depends on transcription in the cytoplasm. By contrast, transient and stable expression from plasmid vectors requires transcription in the nucleus, followed by mRNA maturation and transport to the cytoplasm. It appeared likely that mRNA modifications accounted for the different E1 species expressed by plasmid vectors. RT-PCR was therefore performed on RNA extracts of HeLa cells stably expressing E1. Sequence analyses of the PCR products detected a deletion between nucleotides 675 and 887 (inclusive), which preserves the E1 reading frame but results in a protein with a 71 amino acid deletion (FIG. 13a and data not shown). This deletion was not present in PCR products derived by amplification of genomic DNA containing the integrated E1 construct (data not shown).
Analysis of the entire HCV genomic sequence by a splice site prediction neural network (available at http://www.fruitfly.org/seq_tools/splice.html) revealed the presence of a putative splice donor site at position 675 of E1, whereas putative splice acceptor sites were found at positions 887 of E1 and 2183 of E2 (see FIG. 14a). These findings suggested that putative intron splicing between positions 675 and 887 resulted in expression of a truncated E1 protein, corresponding to the 20 kDa species observed after transient expression of E1 and E1-E2 constructs. The absence of a larger deletion corresponding to nucleotides between positions 675 and 2183 suggests that the splice acceptor at position 2183 is not functional.
Nature of E1 Proteins Expressed from Modified E1 Genes
E1-expression constructs were generated wherein the splice acceptor site in E1 was removed by conservative substitution of A886GG to C886GT (E1*), or the sequence encoding the putative intron between positions 675 and 887 was deleted (E1Δ). Transient, plasmid-based expression of both E1 and E1Δ generated a single 20 kDa protein species (FIG. 13b). A single, 27 kDa protein species was generated by E1*, wherein the splice acceptor site was mutated (FIG. 13b). The 2.0 kDa protein species generated by unmodified E1 is therefore the result of E1 mRNA splicing, whereas the 27 kDa protein species corresponds to full-length E1. Secondary structure may partially obstruct splice sites in E1-E2 mRNA leading to expression of full-length (27 kDa) as well as truncated (20 kDa) forms of E1 (cf. E1-E2 lane in FIG. 12d).
The putative splice acceptor site in position 887 was also eliminated by conservative mutagenesis in all constructs to ensure that splicing would not occur. To guard against the splice acceptor site at position 2183 in E2 becoming functional in the absence of the upstream splice acceptor eliminated from position 887, that putative splice acceptor site was also modified by a conservative A2183→T2183 substitution. Constructs expressing modified E1, E2 or E1-E2 (indicated by “*”, i.e., E1*, E2* or E1*-E2*) were stably transfected into HeLa cells. Stable clones were also generated with constructs expressing E1/E2 in conjunction with p7 (extending from nucleotides 511 to 2427), an HCV structural protein of unknown function. RT-PCR analyses of RNA extracts showed that the length of transcripts matched the full-length of the coding sequences, indicating that putative intron splicing was no longer occurring (data not shown). E2* and E1*-E2* expression generated a major 62 kDa protein corresponding to E2 (FIG. 14a). Immunoblotting demonstrated that E1 was now expressed as a single 27 kDa species by E1* and E1*-E2* constructs (FIG. 14b).
Immunological Detection of Cell Surface-localized E1 and E2
Cell surface-associated E1 protein could not be detected in any of the stable HeLa clones by flow cytometry using two different anti-E1 MAbs, A4 (Dubuisson et al., 1994) and 081-5 (Austral Biologicals, San Ramon, Calif.) (data not shown). This suggests that the E1 epitopes recognized by these MAbs may not be accessible in the full-length protein. Cell surface-associated E1 was readily detected, however, by cell surface biotinylation followed by streptavidin capture and immunoblotting of E1*-E2* and E1*-E2*-p7-expressing cells with an anti-E1 MAb (FIG. 15a). When E1 was expressed alone, it was not detectable on the cell surface, suggesting that coexpression of E2 is required for efficient transport of E1 to the plasma membrane (FIG. 15a).
Cell surface-associated E2 was detected in stable HeLa clones by flow cytometry after labeling with four different anti-E2 MAbs of E2*-, E1*-E2*- as well as E1*-E2*-p7-expressing cells (FIG. 15b and data not shown). MAb H2, which has been reported to recognize E1/E2 heterodimers, did not recognize cell surface E2, but this antibody is also not reactive with HCV particles in patient sera (Deleersnyder et al., 1997). E1*-E2* and E1*-E2*-p7 were also stably expressed in hepatic NKNT3 cells. These cells display morphological characteristics of liver parenchyma cells, express key genes of liver metabolism, and are not tumorigenic in SCID mice (Kobayashi et al., 2000; 2001). E2 was readily detected on the surface of NKNT3 cells, suggesting that plasma membrane localization is an inherent property of HCV envelope glycoproteins rather than of the cell line in which they are expressed (FIG. 15c). Coexpression of E1/E2 with p7 did not appear to influence the processing and cell surface localization of the envelope glycoproteins.
E1 and E2 Form Non-covalent Heterodimers in Cell Membranes
Cell surface-associated E1 and E2 were analyzed for their ability to form non-covalent heterodimers. HeLa cells stably expressing different combinations of E1, E2 and p7 were preincubated with an anti-E2 MAb, and protein-antibody complexes were recovered by immunoprecipitation of cell lysates with G protein-coupled agarose beads. In this manner, cell surface-associated envelope glycoproteins were selected for analysis by SDS-PAGE and immunoblotting with an anti-E1 MAb. E1 readily coimmunoprecipitated with E2 only in cells expressing E1*-E2*, and only if the cells were preincubated with an anti-E2 MAb (FIG. 16a). Similarly, E2 was detected in cells expressing E2*, E1*-E2* or E1*-E2*-p7, only if the cells were preincubated with an anti-E2 MAb (FIG. 16b). E1 and E2 proteins associated with the plasma membrane therefore also form non-covalent heterodimers.
Preliminary Evaluation of Pseudovirions Expressing Modified HCV Glycoproteins
Envelope constructs with mutated E1-E2 splice acceptor sites generated higher concentrations of HCV pseudovirions than non-mutated E1-E2 sequences (data not shown). This is an important finding because the E1 and E2 proteins used for pseudotyping, though translated from modified nucleotide sequences, are of identical length and amino acid sequence as the native HCV glycoproteins. However, homogeneous proteins are generated when the modified gene sequences are expressed from DNA plasmids. Therefore, the nucleic acid modifications in E1 and E2 may induce more efficient folding of the encoded protein, thereby enhancing the packaging, assembly, budding and ultimately stability of the pseudovirions. The inclusion of all or part of the capsid, C, further enhanced pseudoparticle production, suggesting that the C region may stabilize protein folding. Importantly, these pseudoparticles were found to be fusion-competent and were demonstrated to enter hepatic cell lines with high efficiency. They therefore provide powerful tools to help elucidate the molecular mechanisms underlying HCV attachment to, fusion with and entry into cells, and other aspects of HCV pathogenesis. These pseudovirions can also be used in assays for identifying inhibitors of HCV entry.
Discussion
HCV envelope glycoproteins, E1 and E2, have previously been described to form membrane-anchored, non-covalent heterodimers that are retained in the ER, where HCV budding is believed to occur (Op De Beeck et al., 2001). The colocolization of heterodimerization and ER retention signals to residues in the TM domains of E1 and E2 suggested that the two functions cannot be dissociated (Op De Beeck et al., 2001). Thus, it has been difficult to generate cell surface-associated variants of E1/E2 heterodimers which would be invaluable for developing cell fusion and entry assays and generating virus pseudotypes. Attempts to create such variants have hitherto focused on fusing E1 and E2 ectodomains to the TM domains of Vesicular Stomatitis Virus (VSV) G or influenza HA envelope glycoproteins, which have no known dimerization function (Flint et al., 1999; Lagging et al., 1998; Takikawa et al., 2000). Additionally, in these previous studies, chimeric E1 and E2 proteins were translated from separate mRNAs, which may have further minimized their potential to form native heterodimers. Even though E2-HA chimeras underwent pH-dependent conformational changes and were incorporated into influenza virus particles, they did not induce fusion with target cells (Flint et al., 1999). HCV-VSV chimeric envelope glycoproteins also did not appear to reproducibly model HCV fusion and entry (cf. Buonocore et al., 2002; Lagging et al., 1998; Lagging et al., 2002; Matsuura et al., 2001; Meyer et al., 2000; Takikawa et al., 2000).
The initial goal of the present study was to create chimeric HCV envelope glycoproteins that would be expressed on the cell surface as E1/E2 heterodimers and that would be incorporated onto pseudovirions and mediate entry into HCV target cells. A strategy was therefore chosen wherein the ectodomains of HCV E1 and E2 were fused to the TM domains of E1 and E2 from a related alphavirus, the Semliki Forest virus (SFV). The SFV envelope glycoproteins form cell surface-associated heterodimers that efficiently pseudotype heterologous viral nucleocapsids in order to mediate their entry into host cells. It was found that chimeric HCV-SFV envelope glycoproteins were expressed on the cell surface and resembled unmodified HCV envelope glycoproteins in size and post-translational processing. However, a surprising finding, and one that changed the focus the study, was the expression of unmodified HCV E1 and E2 on the cell surface.
E2 was detected on the cell surface by flow cytometry with four different anti-E2 MAbs. Cell surface-associated E2 expression was also detected in a hepatic cell line and was not influenced by the presence of p7. By biotin-tagging cell surface proteins, it was demonstrated that full-length E1 was also associated with the plasma membrane. Most importantly, it was found that E1 protein could be specifically coimmunoprecipitated with an anti-E2 MAb, thus demonstrating that cell surface-associated E1 and E2 form non-covalent heterodimers.
One of the complicating factors in identifying properly folded and functional E1 and E2 has been the multitude of expression systems used to study these proteins, and a careful survey of the literature reveals significant diversity in the number and size of protein species corresponding to E1 and E2. In the present study, unmodified and chimeric envelope glycoproteins were generated using two different expression systems. The use of vaccinia-based expression is justifiable on the premise that it circumvents the nucleus, just as HCV replication does. In this expression system, E1 and E2 remain intracellular. Vaccinia replication, however, is known to modify internal cellular membranes as well as the translation machinery (Person-Fernandez and Beaud, 1986; Ploubidou et al., 2000; Rice and Roberts, 1983; Risco et al., 2002: Rodriguez et al., 1997; Sanger et al., 2001), and the apparent trapping of HCV envelope glycoproteins inside the cell may be an artifact of these vaccinia-induced modifications. Indeed, vaccinia-based expression has been shown to cause ER retention of other viral envelope glycoproteins (Sanger et al., 2001; Szepanski et al., 1994).
The observation that vaccinia-based expression generates hypoglycosylated E1 proteins prompted the use of an alternative, plasmid-based system for expressing HCV envelope glycoproteins. Plasmid-based expression of proteins typically does not adversely affect cellular protein synthesis but does involve nuclear transcription, which is not a natural part of HCV replication. Indeed, it was clearly demonstrated that plasmid-based expression of HCV envelope glycoproteins results in putative intron excision in E1 mRNA that is subsequently translated to give a truncated protein. This finding highlights an inherent complication in expressing RNA virus proteins by DNA-based expression systems.
To circumvent the problem of excision of the potential intron from the E1 gene, which results in the production of heterogeneous E1 proteins, site-specific mutagenesis was used to introduce conservative mutations in the E1 and E2 coding sequences. These mutations eliminated putative intron acceptor sites and prevented intron excision but did not alter the sequence of the encoded E1 and E2 proteins. Thus, E1 and E2 proteins identical to the native HCV glycoproteins were expressed in cells, and these proteins were found to be localized in the plasma membrane. The modified nucleic acid molecules encoding HCV glycoproteins have several potential applications. First, for example, although the envelope glycoproteins translated from the mutated constructs have identical amino acid sequences to native HCV envelope glycoproteins, the translation of the mRNA and co-translational folding of the protein may be different from unmodified HCV glycoproteins. Moreover, the homogeneity of the envelope proteins produced from modified DNA sequences may be advantageous, compared to the synthesis of a mixture of full length and truncated proteins from unmodified coding sequences. These differences may enable more efficient heterodimerization of E1 and E2, and lead to enhanced packaging of virions. Alternatively, interactions with other components (C, p7) of the HCV envelope complex may be more efficient with the envelope glycoproteins synthesized from modified coding sequences than from native HCV coding sequences.
Second, the modified nucleic acids encoding the envelope proteins may allow more efficient production of virus pseudotype particles in transient expression systems or in packaging cell lines. They may also be able to package HCV replicons (Blight et al., 2000) or be useful in the culture of infectious, replication-competent HCV. Further, they may facilitate the manufacture of vaccines using nucleic acid vectors (DNA, RNA, viruses) or proteins.
Third, modified HCV glycoprotein sequences could be invaluable in developing novel HCV fusion and entry assays, including the use of pseudovirion systems and resonance energy transfer (RET) assays, as well as in studying of viral budding from membranes and viral particle formation. They may have further utility in developing novel virus replicon packaging systems with HCV or non-structural protein vectors from other viruses.
Fourth, the production of homogeneous HCV envelope glycoproteins may be useful in vaccine design or in generating monoclonal antibodies to HCV as these glycoproteins may contain epitopes that are capable of eliciting neutralizing antibodies to native HCV.
Fifth, these novel systems for expressing cell surface-localized, full length HCV envelope glycoproteins enable the design of screening assays to identify agents that inhibit HCV fusion and entry into cells.
Recently, two groups reported that HCV envelope glycoproteins are able to pseudotype retroviral particles and mediate their entry into target cells (Bartosch et al., 2003; Hsu et al., 2003). Both groups used plasmid vectors to express E1/E2 from unmodified coding sequences, and thus the pseudoviral envelopes likely contained both full-length and truncated E1 proteins. The present study has confirmed that unmodified HCV envelope glycoproteins are able to mediate entry of retroviral pseudotypes into several hepatic and non-hepatic cell lines as well as primary hepatocytes. Studies are underway to determine how the presence of truncated E1 species in pseudoviral envelopes affects entry into different target cells. These studies will permit optimization of pseudovirion entry mediated by HCV envelope glycoproteins, which will facilitate structure/function studies of HCV envelope glycoproteins as well as the identification of HCV receptors and target cells.
It remains to be determined whether cell surface-associated E1/E2 heterodimers have any physiological relevance in the viral replication cycle. The observation that HCV envelope glycoproteins are expressed on the surface of cells that closely resemble primary hepatocytes implies that there is no specific retention mechanism for HCV envelope glycoproteins in liver cells. The postulated HCV replication cycle is based on analogies to the closely related flavi- and pestiviruses and it is generally assumed that flaviviridae bud into the endoplasmic reticulum and mature by passage into cytoplasmic vesicles (Pettersson, 1991). Thus far, the cellular localization of HCV envelope glycoproteins and particles has mostly been studied in cells transfected or infected in vitro. Virus-like particles mostly occurred in cytoplasmic vesicles, suggesting vesicle-based morphogenesis of HCV (Dash et al., 1997; Egger et al., 2002; Greive et al., 2002; Iacovacci et al., 1997; Pietschmann et al., 2002; Serafino et al., 1997; Shimizu et al., 1996). No study to date, however, has clearly documented the budding and maturation process of HCV, probably because they do not occur in currently available experimental systems though it is also possible that budding of HCV is an extremely rare event that is difficult to detect by standard techniques. Ongoing studies will address these questions by expressing E1/E2 envelope glycoproteins in human primary hepatocytes.
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## Claims

1. A nucleic acid comprising consecutive nucleotides, the sequence of which corresponds to a sequence encoding a hepatitis C virus (HCV) E1 glycoprotein in which (a) at least one nucleotide has been altered to eliminate a RNA splice acceptor site or a RNA splice donor site, wherein the altered nucleotide is (i) an A886C mutation, (ii), a G888T mutation, or (iii) a G675A mutation, or (b) nucleotides 675-887 have been deleted, wherein the positions of the mutation and the deleted nucleotides are numbered by reference to SEQ ID NO:2.

2. The nucleic acid of claim 1, wherein at least one nucleotide has been altered to eliminate a RNA splice acceptor site and the altered nucleotide is an A886C mutation.

3. The nucleic acid of claim 1, wherein at least one nucleotide has been altered to eliminate a RNA splice acceptor site and the altered nucleotide is a G888T mutation.

4. The nucleic acid of claim 1, wherein at least one nucleotide has been altered to eliminate a RNA splice donor site and the altered nucleotide is a G675A mutation.

5. The nucleic acid of claim 1, wherein nucleotides 675-887 have been deleted.

6. The nucleic acid of any of claims 1-5 comprising further consecutive nucleotides, the sequence of which corresponds to a sequence encoding HCV E2 glycoprotein, wherein the sequence encoding HCV E2 glycoprotein has at least one nucleotide that has been altered to eliminate a RNA splice acceptor site, and wherein the altered nucleotide in the sequence encoding HCV E2 glycoprotein is an A2183T mutation, the position of the mutation being numbered by reference to SEQ ID NO:2.

7. An isolated host cell which comprising a vector comprises a nucleic acid comprising consecutive nucleotides, the sequence of which corresponds to a sequence encoding a hepatitis C virus (HCV) E1 glycoprotein in which (a) at least one nucleotide has been altered to eliminate a RNA splice acceptor site or a RNA splice donor site, wherein the altered nucleotide is (i) an A886C mutation, (ii) a G888T mutation, or (iii) a G675A mutation, or (b) nucleotides 675-887 have been deleted, wherein the positions of the mutation and the deleted nucleotides are numbered by reference to SEQ ID NO:2.

8. The isolated host cell of claim 7, wherein the nucleic acid comprises further consecutive nucleotides, the sequence of which corresponds to a sequence encoding HCV E2 glycoprotein, wherein the sequence encoding HCV E2 glycoprotein has at least one nucleotide that has been altered to eliminate a RNA splice acceptor site, and wherein the altered nucleotide in the sequence encoding HCV E2 glycoprotein is an A2183T mutation, the position of the mutation being numbered by reference to SEQ ID NO:2.

9. The isolated host cell of claim 7, wherein the isolated host cell is a cultured cell.

10. The isolated host cell of claim 9, wherein the cultured cell is a mammalian cell.

11. A method for expressing on a cell surface an altered hepatitis C virus (HCV) glycoprotein which comprises transfecting a cell with a vector which comprises a nucleic acid comprising consecutive nucleotides, the sequence of which corresponds to a sequence encoding a hepatitis C virus (HCV) E1 glycoprotein in which (a) at least one nucleotide has been altered to eliminate a RNA splice acceptor site or a RNA splice donor site, wherein the altered nucleotide is (i) an A886C mutation, (ii) a G888T mutation, or (iii) a G675A mutation, or (b) nucleotides 675-887 have been deleted, wherein the positions of the mutation and the deleted nucleotides are numbered by reference to SEQ ID NO:2, under conditions which permit expression of the nucleic acid such that the altered HCV glycoprotein is expressed on the surface of a cell.

12. The method of claim 11, wherein greater than 70% of the altered HCV glycoprotein expressed on the surface of the cell is a full length HCV glycoprotein.

13. The method of claim 11, wherein greater than 90% of the altered HCV glycoprotein expressed on the surface of the cell is a full length HCV glycoprotein.

14. A method for making a pseudovirion expressing on its surface an altered hepatitis C virus (HCV) glycoprotein which comprises:
(a) co-transfecting a cell with (i) at least one packaging vector which expresses a reporter gene, and (ii) a vector which comprises a nucleic acid comprising consecutive nucleotides, the sequence of which corresponds to a sequence encoding a hepatitis C virus (HCV) E1 glycoprotein in which (a) at least one nucleotide has been altered to eliminate a RNA splice acceptor site or a RNA splice donor site, wherein the altered nucleotide is (i) an A886C mutation, (ii) a G888T mutation, or (iii) a G675A mutation, or (b) nucleotides 675-887 have been deleted, wherein the positions of the mutation and the deleted nucleotides are numbered by reference to SEQ ID NO:2, under conditions which permit transcription of the nucleic acid, thereby making a pseudovirion expressing on its surface a altered HCV glycoprotein.

15. The method of claim 14, wherein greater than 70% of the altered HCV glycoprotein expressed on the surface of the pseudovirion is a full length HCV glycoprotein.

16. The method of claim 14, wherein greater than 90% of the altered HCV glycoprotein expressed on the surface of the pseudovirion is a full length HCV glycoprotein.

17. The method of claim 14, wherein the packaging vector expresses a luciferase, a green fluorescent protein or a beta-galactosidase reporter gene.

18. The method of 14, wherein the packaging vector is pNL4.3-Luc+env- and expresses a luciferase.

19. The method of claim 14, where the cell is a 293T cell.