An amphipathic helix at the approximate N-terminus of Hepatitis C virus (HCV) nonstructural proteins mediates the association of these proteins with cytoplasmic membranes in infected cells. This association is essential for replication. Thus, assessing the ability of compounds or protocols to disrupt the association of such helices with cytoplasmic membranes permits identification of compounds and protocols which are useful in the treatment of HCV infection. Also useful in the invention are mimics, or function-disrupting ligands, of an amphipathic helix of the nonstructural proteins described herein and antibodies and fragments thereof immunoreactive with said helix.

Description of the Invention

The Hepatitis C virus has been well studied and the genome has been completely sequenced. The genome of HCV is a single-stranded RNA of 9.6 kb that encodes a single approximately 3,010 amino acid polyprotein. This polyprotein is proteolytically processed into structural proteins and nonstructural proteins. HCV, like other positive strand RNA viruses, is thought to replicate in association with cytoplasmic membranes; and the approximately 447 amino acid nonstructural protein, NS5A is known to associate with host cell membranes. This protein is thus believed to play a key role in replication. The discovery of alternative treatments has been hampered by the lack of a cell culture model for HCV. The present invention overcomes this problem, and provides a convenient assay for identifying agents that can directly and specifically curtail the course of HCV infection. As noted above, the present invention resides in the discovery of a mechanism to disrupt association between certain nonstructural proteins of the virus and cytoplasmic membranes.

Administration of peptides and proteins intracellularly has been limited by the lack of consistent and efficient uptake across the cell membrane. However, various membrane translocation sequences (MTS) have been identified which allow the transduction of peptides across the plasma membrane (for example, References 10, 13, 14, 16, 17, 20, 21 and 22). While unknown, it is hypothesized that the mechanism of the transduction is that an MTS is able to transport both peptides and full-length proteins into the cytoplasm of cells. It is believed that the separate peptides form a noncovalent complex in solution that is then transported into the cell.

It has now been found that an amphipathic helix consisting of about 20-25 amino acids is critical to the association of NS5A with cytoplasmic membranes, for example endoplasmic reticulum (ER), as are similar helices found in NS4B and NS5B. As shown below, when the amphipathic nature of the helix is disrupted, NS5A no longer associates with cell membranes; in addition, the helix when coupled to other substances, including other proteins, effects association of the carried component to the cell's cytoplasmic membranes. As used herein, "cytoplasmic membrane" refers to a structure contained in the cellular cytoplasm, which can generally be recognized as a membrane structure for example, membranes of the endoplasmic reticulum (ER). The membranes may include protein receptors or other elements in addition to the more hydrophobic portions of the membrane per se which may account at least in part for the association of the amphipathic helix to the "cytoplasmic membrane". No theory is advanced as to the mechanism whereby the amphipathic helix associates itself with the cytoplasmic membrane, and thus the precise elements contained in the membrane, which are responsible for this association, are not defined. The observations related to the screening methods described below are not dependent on any definition: intracellular embodiments of these assays rely on direct observation of the cellular distribution of the helix and its label and studies which involve membrane preparations ex vivo employ compositions of cytoplasmic membranes as conventionally prepared, without regard to substructure. This amphipathic helix feature is found in nonstructural proteins of isolates of many strains of HCV of various geographical origins. It is also demonstrated below that disruption of the amphipathic nature of the helix of NS5A prevents replication of HCV RNA.

FIG. 1 (see Original Patent) shows the amino acid sequences of the amphipathic helices that have been found near to the N-terminus of three nonstructural proteins from prototype genotype 1a representing amino acids 7-34 of NS4B (SEQ ID NO: 1), amino acids 5-26 of NS5A (SEQ ID NO: 2), and two amphipathic helical regions of NS5B, amino acids 65-87 (SEQ ID NO: 3) and 107-125 (SEQ ID NO: 4). This figure also shows the relevant sequences in NS5A for additional genotypes 1b (acc. No. P26663) (SEQ ID NO: 5); 2a (acc. No. P26660) (SEQ ID NO: 6); 2b (acc. No. AB030907) (SEQ ID NO: 7); 3a-K (acc. No. D28917) (SEQ ID NO: 8); 3a-NZL (acc. No. D17763) (SEQ ID NO: 9); 3b (acc. No. D49374) (SEQ ID NO: 10); 4a (acc. No. Y11604) (SEQ ID NO: 11); 10a (acc. No. D63821) (SEQ ID NO: 12); and 11a (acc. No. D63822) (SEQ ID NO: 13). The sequences listed in FIG. 1 are not an exhaustive list of the amino acid sequences of amphipathic helices of these three nonstructural proteins. NS4B and NS5B may be expanded similarly to NS4A in FIG. 1. Although the sequences per se are not completely homologous, they are all capable of forming amphipathic helices. (See FIGS. 2A-2J (see Original Patent) which show these helices from the NS5A proteins.) Thus, it is clear that the presence of the N-terminal amphipathic helix, containing a sequence of approximately 20-25 amino acids is widespread in the nonstructural proteins of HCV and in various isolates.

As used herein, the term "HCV nonstructural protein amphipathic helix" refers to a sequence of at least 15 amino acids, preferably at least 20 amino acids and preferably not more than 30, more preferably not more than 25 amino acids which has the amino acid sequence selected from the group consisting of those set forth in FIG. 1, or which is at least 80% homologous, preferably at least 90% homologous and more preferably at least 95% homologous to at least one of said sequences and which retains the ability to form an amphipathic helix. While it is known that certain amino acid substitutions will result in peptides, which, while they retain the required degree of homology (sequence identity), will disrupt the formation of the helix, the nature of these substitutions is already understood by those of ordinary skill and can be avoided, or purposefully used, as desired. Insertion of, for example, disruptive proline residues, is understood to be undesirable. Thus, it is well within ordinary skill to substitute one or more amino acids in these sequences to obtain substitute helices with the required degree or homology, avoiding unsuccessful substitutions.

It should be noted that in certain embodiments of the invention, the amphipathic helix may be other than a peptide; for example, it may constitute a pseudopeptide where the native peptide linkages are substituted by isosteres as is understood in the art. Similarly, alternative polymeric structures can be designed which mimic the charge and shape distribution of these amphipathic helices and mutants and variants thereof. These homologs and analogs are included within the scope of the invention and are useful both in therapeutic protocols and in assay systems for ascertaining alternative compounds and protocols which will be useful in treating HCV infection.

As used herein, the term "amino acid" is applicable not only to cell membrane-permeant peptides, but also to amphipathic helices and anti-HCV peptides useful as pharmaceutical agents, i.e., all the individual components of the present compositions.

The term "amino acid" is used herein in its broadest sense, and includes naturally occurring amino acids as well as non-naturally occurring amino acids, including amino acid analogs and derivatives. The latter includes molecules containing an amino acid moiety. One skilled in the art will recognize, in view of this broad definition, that reference herein to an amino acid includes, for example, naturally occurring proteogenic L-amino acids; D-amino acids; chemically modified amino acids such as amino acid analogs and derivatives; naturally occurring non-proteogenic amino acids such as norleucine, .beta.-alanine, ornithine, etc.; and chemically synthesized compounds having properties known in the art to be characteristic of amino acids. As used herein, the term "proteogenic" indicates that the amino acid can be incorporated into a peptide, polypeptide, or protein in a cell through a metabolic pathway.

The incorporation of non-natural amino acids, including synthetic non-native amino acids, substituted amino acids, or one or more D-amino acids into the present anti-HCV peptides of the present invention is advantageous in a number of different ways. D-amino acid-containing peptides exhibit increased stability in vitro or in vivo compared to L-amino acid-containing counterparts. Thus, the construction of peptides incorporating D-amino acids can be particularly useful when greater intracellular stability is desired or required. More specifically, D-peptides, etc., are resistant to endogenous peptidases and proteases, thereby providing improved bioavailability of the molecule, and prolonged lifetimes in vivo when such properties are desirable. When it is desirable to allow the peptide, etc., to remain active for only a short period of time, the use of L-amino acids therein will permit endogenous peptidases, proteases, etc., in a cell to digest the molecule in vivo, thereby limiting the cell's exposure to the molecule. Additionally, D-peptides, etc., cannot be processed efficiently for major histocompatibility complex class II-restricted presentation to T helper cells, and are therefore less likely to induce humoral immune responses in the whole organism.

One factor that can be considered in making such changes is the hydropathic index of amino acids. The importance of the hydropathic amino acid index in conferring interactive biological function on a protein has been discussed by Kyte and Doolittle (1982, J. Mol. Biol., 157: 105-132). It is accepted that the relative hydropathic character of amino acids contributes to the secondary structure of the resultant protein. This, in turn, affects the interaction of the protein with molecules such as enzymes, substrates, receptors, DNA, antibodies, antigens, etc.

Based on its hydrophobicity and charge characteristics, each amino acid has been assigned a hydropathic index as follows: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate/glutamine/aspartate/asparagine (-3.5); lysine (-3.9); and arginine (-4.5).

As is known in the art, certain amino acids in a peptide, polypeptide, or protein can be substituted for other amino acids having a similar hydropathic index or score and produce a resultant peptide, etc., having similar biological activity, i.e., which still retains biological functionality. In making such changes, it is preferable that amino acids having hydropathic indices within .+-.2 are substituted for one another. More preferred substitutions are those wherein the amino acids have hydropathic indices within .+-.1. Most preferred substitutions are those wherein the amino acids have hydropathic indices within .+-.0.5.

Like amino acids can also be substituted on the basis of hydrophilicity. U.S. Pat. No. 4,554,101, herein incorporated by reference, discloses that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with a biological property of the protein. The following hydrophilicity values have been assigned to amino acids: arginine/lysine (+3.0); aspartate/glutamate (+3.0.+-.1); serine (+0.3); asparagine/glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5.+-.1); alanine/histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine/isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); and tryptophan (-3.4). Thus, one amino acid in a peptide, polypeptide, or protein can be substituted by another amino acid having a similar hydrophilicity score and still produce a resultant peptide, etc., having similar biological activity, i.e., still retaining correct biological function. In making such changes, amino acids having hydropathic indices within .+-.2 are preferably substituted for one another, those within .+-.1 are more preferred, and those within .+-.0.5 are most preferred.

As outlined above, amino acid substitutions in the anti-HCV peptides of the present invention can be based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, etc. Exemplary substitutions that take various of the foregoing characteristics into consideration in order to produce conservative amino acid changes resulting in silent changes within the present peptides, etc., can be selected from other members of the class to which the naturally occurring amino acid belongs. Amino acids can be divided into the following four groups: (1) acidic amino acids; (2) basic amino acids; (3) neutral polar amino acids; and (4) neutral non-polar amino acids. Representative amino acids within these various groups include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, cystine, tyrosine, asparagine, and glutamine; and (4) neutral non-polar amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine.

It should be noted that changes which are not expected to be advantageous can also be useful if these result in the production of functional sequences. Since small peptides, etc., can be easily produced by conventional solid phase synthetic techniques, the present invention includes peptides, etc., such as those discussed herein, containing the amino acid modifications discussed above, alone or in various combinations. To the extent that such modifications can be made while substantially retaining the activity of the peptide, they are included within the scope of the present invention. The utility of such modified peptides, etc., can be determined without undue experimentation by, for example, the methods described herein.

Based on the present discoveries, various methods to identify agents and protocols which would be effective in treating HCV are made possible. In their simplest form, since binding between the helix and the cytoplasmic membrane is a necessary condition for association of the nonstructural protein with the membrane and is required for the virus to replicate, compounds which simply bind the helix compete with the cellular membranes for this association. When the helix is contained in a substantially larger molecule, such as existing in the context of a significantly longer amino acid sequence, it is possible that the remaining portion of the molecule or amino acid sequence may itself contain elements that are capable of affecting binding. Thus, in the assays of the invention, appropriate controls may be required to ensure that it is the interaction of the helix with the compounds tested or the membranes tested that is being measured. Compounds that bind to the helix would inhibit the required cellular binding, and by identifying compounds that bind with high affinity to the helix compounds that would be successful in interfering with the binding will be found. By "high affinity" is meant binding with a dissociation constant of <10.sup.-4, preferably <10.sup.-6, and more preferably <10.sup.-8. Dissociation constants can be determined using methods generally known in the art; for example the helix could be bound to solid support and labeled compound at varying concentrations supplied wherein the amount of label coupled to solid support can be readily determined.

Alternatively, the peptide comprising the helix can be displayed using standard phage display techniques and the phage tested for ability to bind to compounds that are coupled to solid supports. Phage display is also utilized to screen random peptides to screen for competitive inhibitors of the amphipathic helix. Such peptides would block virus from binding to the receptor.

There are a variety of techniques well known in the art for assessing binding of compounds to targets. A wide variety of detectable labels can be used, and the assays can be conducted in heterogeneous or homogeneous formats. For example, the compound itself can be labeled for detection of its ability to transport label to solid support, to which solid support has been bound the amphipathic helix or, vice versa, the amphipathic helix can be labeled and the compound to be tested can be coupled to solid support. The assay can also be conducted in a homogeneous format using fluorescence techniques, for example, where the fluorescence of a fluorescent label attached to the compound is altered by virtue of its binding to a peptide the size of the amphipathic helix or larger.

The amphipathic helix itself can be supplied in the context of the nonstructural protein or fragment thereof or can be supplied per se or as a fusion protein that contains a label, such as green fluorescent protein.

In a variation of this extracellular format, the effect of individual compounds or mixtures of compounds on the binding of the amphipathic helix or a protein containing it with a membrane preparation can be evaluated. Techniques similar to those described above may be used--e.g., the membrane preparation may be labeled and the amphipathic helix or protein containing it coupled to solid support or displayed using phage. The coupling of the label to solid support containing the helix or relevant protein or to the phage displayed helix in the presence and absence of compound or mixtures of compounds can be determined. These assays can be conducted in homogeneous format by using fluorescence labeling, for example, of the amphipathic helix. A wide variety of such protocols is known in the art, and the essential feature is determination of the effect of the compound or a mixture of compounds on the binding of the amphipathic helix or a protein containing it and the membrane preparation. Perhaps a particularly convenient embodiment of this method would involve a fusion between the amphipathic helix and green fluorescent protein which could be produced very conveniently using recombinant techniques; assessment of the binding of this fusion to the membrane preparation either in a heterogeneous or homogeneous format can then be performed.

As further described below, in Example 3, an assay for binding of the amphipathic helix to the microsomal membrane can be performed by treating a microsomal or cytoplasmic membrane preparation in vitro with a peptide containing the helix and distributing the contents of the reaction mixture in a sedimentation gradient. The helix coupled to membrane will reside in a relatively low density portion of the gradient and is thus separated from mere debris that is found at the bottom of the gradient. The floated helix can be detected in the appropriate gradient fraction using polyacrylamide gel electrophoresis. The helix may be labeled for example, with a radioisotope or a coupled fluorescent label such as green fluorescent protein used in a fusion. This assay can be used to screen for compounds or protocols that disrupt binding to the microsomal membrane by conducting the assay in the presence and absence of the protocols or compounds and comparing the results.

In addition to the above-described methods that can be conducted extracellularly, the effect of various protocols and compounds or mixtures of compounds on the behavior in terms of binding to cytoplasmic membranes of the relevant amphipathic helix can be determined in a variety of intracellular assays. Any eukaryotic cells may be used, but typically and most conveniently, mammalian cells or yeast cells are used in these assays.

Intracellular assays can be performed by generating desired peptide constructs intracellularly from recombinant expression systems. Alternatively, the assays can be conducted by first preparing the labeled amphipathic helix or protein containing said helix and introducing the derivatized helix into the cells using cell-penetrating peptides. The compounds to be tested may be introduced in the same manner. Such cell-penetrating peptides are described, for example, in a review article by Lindgrin, M., et al., in TiPS (2000) 21:99-103, the contents of which are incorporated herein by reference to describe an exemplary list of such cell-penetrating peptides. These peptides can be coupled to any substance to facilitate the entry of said substance into a eukaryotic cell.

In another embodiment, MTS is able to transport both peptides and full-length proteins into the cytoplasm of cells with or without covalent linkage or crosslinking. (For example, Reference 14.) It is believed that the separate peptides form a noncovalent complex in solution that is then transported into the cell. In one embodiment, the peptides are NS4B or NS5A.

The ability to deliver peptides and proteins into the intracellular milieu for investigational studies or therapeutic applications has previously been limited by the lack of consistent and efficient uptake across the cell membrane. However, a number of reports in the last couple of years have identified various membrane translocation sequences (For example, see references 10, 13, 14, 16, 17, 20, 21, 22) that allow the transduction of peptides across the plasma membrane. The mechanism of transduction is not yet clear, but it has been shown that it is not due to receptor-mediated uptake, or in conjunction with a known transport mechanism. In the initial reports, the MTS was covalently linked to the peptide or protein that was to be delivered into the cell, but recently an MTS was identified that was able to transport both peptides and full-length proteins into the cytoplasm of cells in the absence of covalent linkage or crosslinking (14). Apparently, the separate peptides form a noncovalent complex in solution that is then transported into the cell.

In the most direct forms of such assays, the change in intracellular distribution of the labeled amphipathic helix either supplied per se or in the context of a larger protein can be determined. A wide variety of labels can be used; perhaps the most convenient is a fusion with green fluorescent protein, or simple coupling of the amphipathic helix or the protein containing it to a detectable fluorescent label. The location of the labeled helix or protein containing it can then be observed by a variety of methods including direct observation and histological techniques. Thus, in one example, the effect of a candidate compound or protocol directly on the ability of the helix to bind to cellular membranes can be assessed by coupling the helix to a reporter which is detectable; most convenient are labels which are fusion proteins formed with the helix, such as green fluorescent protein. The intracellular locations of the reporter in the presence and absence of the candidate protocol compound can then be compared. The corresponding labeled helix, which has been mutated to disrupt the amphipathic helical conformation, can conveniently be used as a control. Compounds or protocols that are able to disrupt the binding of the helix with the membrane can readily be identified when their presence results in less label associated with cell membranes.

If histological techniques are used, the label can be less direct; for example, the helix might be fused to a protein that can be detected with a labeled antibody or may be fused to an enzyme that can be detected in the presence of a substrate. Once the cells are fixed histologically, the supplementary reagents can be added for detection.

Another embodiment of this uses cells harboring a vector or plasmid expression NS5A or HCV replicon with a wild-type amphipathic helix in NS5A. The cells are exposed to a control or candidate inhibitor. At the end of the assay, the cells are fixed and stained for NS5A by indirect immunofluorescence. A compound is deemed inhibitory if it alters the normal membrane associated staining of NS5A.

Test compounds that appear to interrupt the ability of the amphipathic helix to bind to the cellular membranes, or which are shown to disrupt the normal binding pattern of the amphipathic helix can be confirmed as anti-HCV agents in a standard colony formation assay. In this assay, an HCV replicon is supplied with a drug resistance marker, such as neomycin resistance. When neomycin-sensitive cells are infected with the replicon and grown on neomycin-containing medium or G418, for example, only cells wherein replication can occur will be able to form colonies. The diagnostic replicon can be used to infect neomycin-sensitive cells in the presence and absence of the compound that has been shown to disrupt the amphipathic helix/membrane binding, and such compounds result in destroying or decreasing the ability of the infected cells to form colonies. Alternatively, RNA replicon levels can be measured to identify the effect of the compound.

When intracellular formats are used, in addition to testing compounds and mixtures of compounds, as noted above, it is possible to test the effect of protocols which involve various regimes of treatment, including, in addition to providing compounds, various antisense techniques, and various forms of environmental stress such as pH changes, temperature changes, mechanical disturbances and the like.

In addition to the foregoing, somewhat more sophisticated methods to assess the impact of compounds and protocols on the intracellular location of substances containing the amphipathic helices derived from Hepatitis C nonstructural proteins can be employed. For example, it is demonstrated below that disruption of the amphipathic helix in NS5A, in addition to causing the protein to fail to associate with cytoplasmic membranes, directs this protein to the nucleus. Therefore, the assay methods can include features in the substance containing the amphipathic helix that act as nuclear localization signals (NLS), many of which are well known in the art. Under these conditions the label can constitute a functionality which exerts its effect in the nucleus, and the disruption of binding of the amphipathic helix with the cytoplasmic membrane can be detected by a reporter function associated with the helix which exerts its effects in the nucleus. Such effects would be, for example, enhancement or repression of the expression of a detectable protein; this would involve including transactivators, transcription factors, or repressors in the construct containing the helix and the NLS. Of course, the nuclear localization signal--derived constructs can also be detected in the nucleus directly, using a direct detectable label of the sort described above--e.g., GFP, a partner in an antibody/antigen interaction, or an enzymatic activity, or a radiolabel.

For example, in one preferred format, the amphipathic helix or a larger protein comprising said helix is coupled to a nuclear localization signal and to a transactivator. The host cell is modified to contain an expression system for a detectable protein, for example, green fluorescent protein in its genome. The transactivator then can effect the expression of the green fluorescent protein under conditions wherein the protocol or compound to be tested disrupts the binding of the amphipathic helix with the cytoplasmic membrane, thus permitting the nuclear localization signal to transport the construct to the nucleus where the transactivator can effect expression of the GFP. Alternative proteins whose expression can be detected are those, such as GFP, that are detectable per se or may be detectable by virtue of their effects on cellular growth, such as his3, leu2, .beta.-galactosidase, .beta.-glucoronidase, SV40T antigen, chloramphenicol acetyl transferase (CAT), hygromycin B phosphotransferase, SEAP or cell surface antigens such as CD4. In addition to transactivators, transcription factors which enhance expression include derivatives of lexa, cI, or gal4 DNA binding domains fused to activation domains of B42, VP16 and the like.

Again, the essential feature is the detection of the effect of the proposed protocol, compounds or mixtures of compounds on the interaction of the amphipathic helix, whether supplied per se or in the context of a larger protein, with the cytoplasmic membranes. The foregoing suggested assay formats are merely exemplary and a wide variety of such formats will be apparent to one of skill in the art. Any such assay method is appropriate; the design of such assays and forms of label draws on a wide literature available to the practitioner.

By conducting the foregoing assays, compounds and/or protocols are identified which will be effective in treating HCV infection. By "treating" is meant both therapeutic and prophylactic treatment, and refers to a desirable effect on viral load, or symptomology, or any desirable outcome which mitigates the negative consequences of the typical progress of HCV infection. The term "treat" is not to be construed to imply absolute cure or absolute prevention. Any helpful amelioration or repression of the infection is sufficient to meet this definition.

Compounds thus identified can be administered in conventional ways using standard pharmaceutical formulations such as those set forth in Remington's Pharmaceutical Sciences, latest edition, Mack Publishing Co., Easton, Pa., incorporated herein by reference. (See also, References 23-33.) Various enteral or parenteral routes of administration may be used, including administering by injection, such as intravenous, intramuscular, subcutaneous and the like, or by oral administration or by suppository. In addition, sustained release compositions can also be used.

The terms "an effective amount," "an anti-HCV effective amount," or a "pharmaceutically effective amount" of a peptide of the present invention as applied to such molecules refers to an amount of a peptide, or combination of two or more peptides as disclosed herein, effective in reducing or ameliorating conditions, symptoms, or disorders associated with HCV infection or associated pathogenesis in patients, and/or in reducing viral levels in vitro or in vivo.

Effective amounts of peptides for the treatment or prevention of HCV infections, delivery vehicles containing peptides or constructs encoding the same, agonists, and treatment protocols, can be determined by conventional means. For example, the medical practitioner can commence treatment with a low dose of one or more peptides in a subject or patient in need thereof, and then increase the dosage, or systematically vary the dosage regimen, monitor the effects thereof on the patient or subject, and adjust the dosage or treatment regimen to maximize the desired therapeutic effect. Further discussion of optimization of dosage and treatment regimens can be found in Benet et al., in Goodman & Gilman's The Pharmacological Basis of Therapeutics, Ninth Edition, Hardman et al., Eds., McGraw-Hill, New York, (1996), Chapter 1, pp. 3-27, and L. A. Bauer, in Pharmacotherapy, A Pathophysiologic Approach, Fourth Edition, DiPiro et al., Eds., Appleton & Lange, Stamford, Conn., (1999), Chapter 3, pp. 21-43, and the references cited therein, to which the reader is referred.

The dosage levels and mode of administration will be dependent on the nature of the compound identified and the particular situation of the subject. Optimization of routes of administration, dosage levels, and adjustment of protocols, including monitoring systems to assess effectiveness of the treatment are routine matters well within ordinary skill. Protocols which are identified using the intracellular assays set forth above must, of course, be modified in the context of treatment of subjects, and this, too, falls within the skill of the practitioner.

Typically, the compounds that are identified by the methods of the invention will be "small molecules"--i.e., synthetic organic structures typical of pharmaceuticals. Examples of such "small molecules" are found, for example, in the Physicians' Desk Reference (with respect to approved drugs), the Merck Index, and the U.S. Pharmacopoeia. However, such compounds may also include peptides, peptidomimetics, nucleic acids, peptide nucleic acids, carbohydrates, lipids, and the like. As noted above, the HCV nonstructural protein amphipathic helix used in these assays may be the native helix, both alone and in the context of a larger protein and the assays may also utilize a homologous form of the helix included within the definition above which retains the spatial and charge configuration of the native form.

In addition to compounds identified by means of the foregoing assays, protocols and substances useful in treating HCV infection can be formulated and utilized a priori. For example, the helix itself, or a functional fragment thereof can readily be used in treatment by virtue of its ability to bind the helix as it resides in an HCV non-structural protein itself or to compete with the helix as it resides in an HCV non-structural protein itself for sites on the cytoplasmic membrane to which the helix will bind. Thus, formulations of the HCV nonstructural protein amphipathic helix or functional fragment thereof can be used directly to treat HCV infection. Typically, these formulations will contain peptides bearing the helix of less than 60 amino acids, in another embodiment less than 50 amino acids, in another embodiment less than 30 amino acids, and, in yet another embodiment less than 25 amino acids in another embodiment, not be less than 4 amino acids, and may, in addition to the peptide region bearing the helix, further contain components to enhance membrane penetration. The peptides comprising the helix may be as short as 10-15 amino acids, 6-9 amino acids or 4-6 amino acids, so long as functionality in terms of competitive binding, or inhibition of binding, is retained. Methods to synthesize such peptides are, of course, well known, both direct and recombinant methods may be used. Thus, a peptide useful in the method of the invention as to its helix-based antiviral activity will typically contain from about 4 to 60 amino acids, and certainly far less than the several hundred amino acids contained in the native viral protein from which it can be derived. This relatively short peptide may optionally be coupled to additional sequence either for labeling, or, more typically, for conferring the ability to enter cells. Such membrane penetration facilitators are known, for example, the HIV-tat peptide or MTSs described herein, are able to introduce non-native proteins into cells. The peptides to be administered will thus contain a portion comprising the amphipathic helix and a heterologous portion for facilitating cellular entry. Entry can also be facilitated by liposomes or cationic polymers, for example. However, wild type NS5A is able to cross the membrane without the assistance of a facilitator. Wild type NS5A is capable of entering the cell without any previously described MTS peptide or other facilitator.

As used herein "functional" refers to a protein, peptide, helix or antibody, or fragment thereof, which possesses the ability to inhibit the binding of a nonstructural HCV protein, for example, NS4B or NS5A, to a cell membrane.

The peptides useful in the methods of the invention can also be generated in the subject to be treated by virtue of administering expression systems for those peptides consisting entirely of gene-encoded amino acids. These expression systems may be introduced as naked DNA, as expression vectors suitable for transfection of mammalian cells, or preferably using adenoviral or retroviral or other suitable viral vectors.

As described above, however, these competitor peptides need not be the native sequences per se and need not even be peptides per se, but may contain isosteric linkages or other polymeric features that result in similar charge/shape features as compared to the native helices.

Peptides, or compounds with similar charge/shape features and having the activity of the peptides described herein, can be identified by phage display using wild-type amphipathic helix and a mutant amphipathic helix peptides as positive and negative selectors, respectively.

The compositions or agents of the invention may comprise, consist essentially of, or consist of the peptide sequences disclosed herein. The phrase "consists essentially of or consisting essentially of" or the like, when applied to anti-HCV peptides encompassed by the present invention refers to peptide sequences like those disclosed herein, but which contain additional amino acids (or analogs or derivatives thereof as discussed above). Such additional amino acids, etc., however, do not materially affect the basic and novel characteristic(s) of these peptides in modulating, attenuating, or inhibiting HCV infection, replication, and/or pathogenesis, including the specific quantitative effects of these peptides, compared to those of the corresponding peptides disclosed herein.

In one approach, the agent may be a transdominant inhibitor of the membrane association function whereby forms of the amphipathic helix that interfere with the ability of the helix to form oligomers can be used. Thus, by generating or providing a mutant form of the helix containing one or more amino acid substitutions, this form may associate with the native helix to provide an inactive form or rendering it unable to dimerize or oligomerize with additional native forms. In one approach, the decoy peptide is mutated to convert hydrophobic amino acids to hydrophilic ones thus destroying the hydrophobic face of the helix. For example, mutated versions of the peptide sequence for NS5A strains would include

In another approach, the agent is a competitive inhibitor of the amphipathic helix. These competitive inhibitors may interrupt the binding between the helix and the membrane, achieving the desired effect. Such inhibitors may be fragments of the wild type sequence of the amphipathic sequence or variants or mutants thereof. Fragments of the HCV nonstructural proteins that may be used as competitive inhibitors may include, but are not limited to:

Another competitive inhibitor of NS5A would include: SGSWLRDVWDWICTVLTDFKTWLQSKL (SEQ ID NO:14) and variants and mutants thereof. Variants and mutants of this peptide would include a peptide with one or more of the following amino acid substitutions: substitute of L at amino acid 16 by A or K; or substitution of the T at amino acid 17 by A; or substitution of the D at amino acid 18 by A; or substitution of the F at amino acid 19 by A; or substitution of the K at amino acid 20 by A; or substitution of the W at amino acid 22 by A; or substitution of the L at amino acid 23 by K, and derivatives thereof. Another such mutant of HS5A is -- see Original Patent.

A mutant and competitive inhibitor, of NS4B may include the sequence -- see Original Patent.

While the majority of the above mutations and substitutions are conservative (i.e. wild type hydrophobic residues are substituted with additional hydrophobic residues (for example, A to F), charged residues are substituted with similarly charged residues, etc.), it is noted that nonconservative substitutions may also be performed. For example, where a wild type hydrophobic residue is substituted with a hydrophilic residue, or a negatively charged residue (for example, D) is substituted with a positively charged residue (for example, K).

Where the agent is a competitive inhibitor, some of the above mutations would enhance the inhibitory activity of the peptide, others would completely or partially abolish the inhibitory activity of the peptide. Mutations may be observed alone or in combination, for example, any one substitution, X.sub.1-28, occurs within the context of the wild type sequence at any one time, a combination of two mutations such as: X.sub.2 and X.sub.5, X.sub.2 and X.sub.19, or X.sub.5 and X.sub.19 or three mutations are found in the same peptide, X.sub.2, with X.sub.5, and X.sub.19.

In another embodiment, the agent may be a complementary peptide to the helix. Complementary peptides may interrupt the binding between the helix and the membrane, achieving the desired effect. Such complementary peptides may also inhibit the formation of the amphipathic helix, may interact or bind to the helix to inhibit binding of the helix to cellular membranes, or may otherwise inhibit the amphipathic helices.

For example, the HCV genomic RNA sequence that codes for the NS4B amphipathic helix in the HCV genotype 1A sequence is -- see Original Patent.

(Kolykhalov, A. A. and Rice, C. M., Science 277 (5325), 570-574 (1997); GenBank Accession No.: AF009606.) The protein translation of the above sequence is: YIEQGMMLAEQFKQKALGLLQTASRQAE (SEQ ID NO: 18). The reverse complement cDNA sequence corresponding to the HCV genomic RNA sequence that codes for the NS4B amphipathic helix (GenBank Accession No.: AF009606) is -- see Original Patent.

The complementary peptide translated from the reverse complement sequence is: LCLAGRGLQEAEGLLLELLSEHHPLLDV (SEQ ID NO: 20).

This complementary peptide, as a whole, or in part, may be active as an HCV antiviral or may be useful in the prediction of small molecules that are HCV antivirals. In one embodiment a fragment of this complementary peptide comprising 6-27 amino acids may be used in the discovery of HCV antivirals. Table 1 (see Original Patent) sets forth exemplary peptides (SEQ ID NOS: 21-295) of this embodiment.

In a particular embodiment, the complementary peptides of the invention are used, in whole or in part, in the prediction of small molecules that are HCV antivirals. "Small molecule" as defined above, may include synthetic organic structures typical of pharmaceuticals, and may also include peptides, nucleic acids, peptide nucleic acids, carbohydrates, lipids, and the like. Additionally, small molecules, as used herein, may include chemically synthesized peptidomimetics of the 6-mer to 9-mer peptides of the invention.

Additionally, the HCV genomic RNA sequence that codes for the NS5A amphipathic helix in the HCV genotype 1A sequence is -- see Original Patent.

The peptides that mimic the helices and functional fragments thereof are administered in formulations and by routes well understood. A variety of methods for introducing such substances are known, typically, by injection, aerosol administration, suppository, and, with proper design, oral administration. This general statement is true as well with respect to providing expression systems for peptides represented by the helix mimics.

In addition to the peptides or other compounds of the invention, combination therapies including known HCV inhibitors can be utilized in the present invention. For example, it may be desirable to administer both a peptide or peptides of the invention in combination with interferon to a subject infected with HCV. Other drugs or compounds known in the art to be effective against HCV, can also be used.

In one embodiment, the invention provides a method of screening compounds, to identify those that selectively inhibit the binding of HCV nonstructural proteins (for example, NS4B or NS5A) and cellular membranes. Methods known to those of skill in the art, can be readily adapted to detect interference with the binding of these components. The method of screening may involve high-throughput techniques. For example, to screen for compounds that selectively inhibit the binding of HCV nonstructural proteins and cellular membranes, a synthetic reaction mix, a viral fragment or component, or a preparation of any thereof, comprising an HCV nonstructural protein and a labeled substrate or ligand of such polypeptide is incubated in the absence or the presence of a candidate molecule that may inhibit the binding of the HCV nonstructural proteins and the cellular membrane. The ability of the candidate molecule to inhibit the binding of the HCV nonstructural protein and the cellular membrane is reflected in decreased binding of the labeled ligand or decreased production of product from such substrate.

In another aspect, the screening can be performed by adding the candidate compound to intact cells that have been infected by HCV, or that contain an HCV replicon, and then examining the component of interest to demonstrate the effect on this component, or the effect on viral or replicon replication. An exemplary cell-based in vitro assay for this purpose is disclosed in PCT International Publication WO 02/18369. Alternatively, the screening can be performed by adding the test agent to in vitro translation reactions and then proceeding with the established analysis. As another alternative, purified or partially purified components which have been determined to interact with one another by the methods described above can be placed under conditions in which the interaction between them would normally occur, with and without the addition of the candidate compound, and the procedures previously established to analyze the interaction can be used to assess the impact of the candidate compound. However their anti-HCV activity is initially assayed, peptide or other inhibitors of the present invention should cause inhibition of infection, replication, or pathogenesis of Hepatitis C Virus in vitro or in vivo when introduced into a host cell containing the virus, and exhibit an IC.sub.50 in the range of from about 0.0001 nM to 100 .mu.M in an in vitro assay for at least one step in infection, replication, or pathogenesis of HCV, more preferably from about 0.0001 nM to 75 .mu.M, more preferably from about 0.0001 nM to 50 .mu.M, more preferably from about 0.0001 mM to 25 .mu.M, more preferably from about 0.0001 nM to 10 .mu.M, and even more preferably from about 0.0001 nM to 1 .mu.M.

In another embodiment of the invention, the method of screening may be by phage display. A method of obtaining selective ligands that bind a chosen target is to select from a library of proteins or peptides displayed on phage. In order to obtain a novel binding protein against a chosen target, such as an amphipathic helix region of an HCV component, DNA molecules, each encoding a protein or peptide fragment thereof, and a structural signal calling for the display of the protein on the outer surface of a chosen genetic package (bacterial cell, bacterial spore or phage) are introduced into a genetic package. The protein is expressed and the potential binding domain is displayed on the outer surface of the package. The package is then exposed to the target. If the genetic package binds to the target, then it is confirmed that the corresponding binding domain is indeed displayed by the genetic package. Packages which display the binding domain (and thereby bind the target) are separated from those which do not. For example, in the present invention, the target may be the amphipathic helix or a mutated amphipathic helix. Potential peptides, which may then be used as anti-HCV agents, are screened by determination of which will bind to the amphipathic helix or a mutated amphipathic helix. Preferred peptides are those that not only bind to the amphipathic helix, but in addition, block or inhibit the amphipathic helix from binding to its receptor or binding site, thereby inhibiting infectivity. Examples of peptides identified by phage display are set forth in Table 3 (see Original Patent).

In all of the embodiments of the invention, the active agent which will interact, generally, either with the sites on the cytoplasmic membrane to which the amphipathic helix binds or will interact with the amphipathic helix itself, may be derivatized or coupled to additional components. By "derivatives" of these agents is meant modifications thereof that do not interfere with their ability to interact with the sites or the helix, but may optionally confer some additional useful property. One particularly useful property is the ability to penetrate cell membranes, and preferred among the derivatives or conjugated forms are those coupled to such facilitators. An additional desired coupled component may be a labeling component such as a fluorescent dye, an enzyme, or a radioisotope. One particularly useful label is, for example, green fluorescent protein in any of its many colors and forms. Green fluorescent protein thus, includes, not only forms of this fluorescent protein that fluoresce green, but also those that fluoresce various other colors such as red and blue. These forms of the protein are commercially available as are recombinant materials for their production.

The compositions of the invention can be administered as conventional HCV therapeutics. The compositions of the invention may include more than one ingredient which interrupts the binding of the amphipathic helix to the membranes and more than one peptide of the invention.

The precise formulations and modes of administration of the anti-HCV compositions of the invention will depend on the nature of the anti-HCV agent, the condition of the subject, and the judgment of the practitioner. Design of such administration and formulation is routine optimization generally carried out without difficulty by the practitioner.

In addition to the assay methods, methods to identify compounds or protocols against HCV infection, and methods to treat HCV infections as set forth above, the invention provides compositions which are effective to elicit immunological responses to HCV in appropriate subjects, such as humans or other animals subject to HCV infection.

Administration may be performed using conventional methods, typically by injection. The elicited immunological response is helpful in general HCV prophylaxis.
 

Claim 1 of 17 Claims

1. A method for assessing activity of a candidate compound in interfering with binding of a Hepatitis C virus (HCV) nonstructural protein with a eukaryotic cell cytoplasmic membrane, comprising: assessing, in the presence and absence of a candidate compound, binding of a polypeptide comprising an amphipathic helix of an N-terminal region of an HCV nonstructural protein with cytoplasmic membranes of a eukaryotic cell, wherein the non-structural protein is NS4B or NS5A; wherein reduced binding in the presence of the candidate compound relative to a level of binding in the absence of the candidate compound indicates activity of the candidate compound in interfering with binding of HCV nonstructural protein to the cytoplasmic membranes.

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