U.S. patent application number 12/229436 was filed with the patent office on 2009-08-20 for flavivirus fusion inhibitors.
Invention is credited to David H. Coy, Srikanta Dash, Robert F. Garry, Jane A. McKeating.
Application Number | 20090209464 12/229436 |
Document ID | / |
Family ID | 32312869 |
Filed Date | 2009-08-20 |
United States Patent
Application |
20090209464 |
Kind Code |
A1 |
Garry; Robert F. ; et
al. |
August 20, 2009 |
Flavivirus fusion inhibitors
Abstract
The present invention relates to peptides and methods of
inhibiting fusion between the virion envelope of Flaviviruses and
membranes of the target cell, the process that delivers the viral
genome into the cell cytoplasm. The invention provides for methods
which employ peptides or peptide derivatives to inhibit
Flavivirus:cell fusion. The present invention is based in part on
the discovery that E1 envelope glycoprotein of hepaciviruses and E2
envelope glycoprotein of pestivirus have previously undescribed
structures, truncated class II fusion proteins. The present
invention provides peptides and methods of treatment and
prophylaxis of diseases induced by Flaviviruses.
Inventors: |
Garry; Robert F.; (New
Orleans, LA) ; Dash; Srikanta; (New Orleans, LA)
; Coy; David H.; (New Orleans, LA) ; McKeating;
Jane A.; (Birmingham, GB) |
Correspondence
Address: |
Olson & Cepuritis, LTD.
20 NORTH WACKER DRIVE, 36TH FLOOR
CHICAGO
IL
60606
US
|
Family ID: |
32312869 |
Appl. No.: |
12/229436 |
Filed: |
August 22, 2008 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10532480 |
Apr 22, 2005 |
7416733 |
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PCT/US2003/035666 |
Nov 7, 2003 |
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12229436 |
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60424746 |
Nov 8, 2002 |
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Current U.S.
Class: |
514/4.3 ;
530/324 |
Current CPC
Class: |
Y02A 50/30 20180101;
C12N 2770/24022 20130101; C12N 2770/36122 20130101; C12N 2770/24222
20130101; A61P 1/16 20180101; C07K 14/005 20130101; A61P 31/12
20180101; C12N 2770/24322 20130101; A61K 39/00 20130101; A61K
38/162 20130101; A61P 31/14 20180101; Y02A 50/394 20180101; C12N
2770/24122 20130101 |
Class at
Publication: |
514/12 ;
530/324 |
International
Class: |
A61K 38/16 20060101
A61K038/16; C07K 14/00 20060101 C07K014/00; A61P 31/12 20060101
A61P031/12 |
Claims
1. (canceled)
2. A pharmaceutical composition comprising at least one isolated
peptide selected from the following: a) a peptide having SEQ ID
NO:25, wherein the peptide's N-terminal chemical moiety is an amino
group and the peptide's C-terminal chemical moiety is a carboxyl
group; b) a peptide having SEQ ID NO:25, wherein the peptide's
N-terminal chemical moiety is selected from the group consisting of
an acetyl group, a hydrophobic group, a carbobenzoxyl group, a
dansyl group, a t-butyloxycarbonyl group, and a macromolecular
group; or wherein the peptide's C-terminal chemical moiety is
selected from the group consisting of an amido group, a hydrophobic
group, a t-butyloxycarbonyl group and a macromolecular group; c) a
peptide having SEQ ID NO:25, wherein at least one bond linking
adjacent amino acid residues of the peptide is a non-peptide bond;
d) a peptide having SEQ ID NO:25, wherein at least one amino acid
residue of the peptide is in the D-isomer configuration; e) a
peptide as in part "a)" or "b)" except that at least one amino acid
of the peptide has been substituted for by a different amino acid;
or f) a functional fragment of a peptide as set out in any of parts
"a)" to "e)", having at least 3 contiguous amino acids of SEQ ID
NO:25.
3-14. (canceled)
15. The composition of claim 2, wherein the selected peptide
comprises SEQ ID NO:25, and wherein the peptide's N-terminal
chemical moiety is an amino group and the peptide's C-terminal
chemical moiety is a carboxyl group.
16. The composition of claim 2, wherein the peptide's N-terminal
chemical moiety is an acetyl group, a hydrophobic group, a
carbobenzoxyl group, a dansyl group, a t-butyloxycarbonyl group, or
a macromolecular group; or wherein the peptide's C-terminal
chemical moiety is a hydrophobic group, a t-butyloxycarbonyl group
or a macromolecular group.
17. The composition of claim 16, wherein the peptide's N-terminal
chemical moiety is a macromolecular group selected from a lipid
conjugate, polyethylene glycol, or a carbohydrate; or wherein the
peptide's C-terminal chemical moiety is a macromolecular group
selected from a lipid conjugate, polyethylene glycol, or a
carbohydrate.
18. The composition of claim 15, wherein at least one bond of the
peptide is a non-peptide bond selected from the group consisting of
an imido bond, an ester bond, a hydrazine bond, a semicarbazoide
bond and an azo bond.
19. The composition of claim 15, wherein at least one amino acid of
the peptide is a D-isomer amino acid.
20-27. (canceled)
28. A method of treating or preventing a Flavivirus infection
comprising administering to a patient an effective amount of a
pharmaceutical composition according to claim 2.
29-30. (canceled)
31. The method of claim 28, wherein the selected peptide consists
of SEQ ID NO:25.
32. The method of claim 31, wherein the peptide's N-terminal
chemical moiety is an amino group and the peptide's C-terminal
chemical moiety is a carboxyl group.
33. The method of claim 28, wherein the Flavivirus is West Nile
virus.
34. A method of inhibiting infection of a cell by a Flavivirus,
wherein the method comprises exposing said cell or Flavivirus to a
pharmaceutical composition according to claim 2.
35. The method of claim 34, wherein the selected peptide consists
of SEQ ID NO:25.
36. The method of claim 35, wherein the peptide's N-terminal
chemical moiety is an amino group and the peptide's C-terminal
chemical moiety is a carboxyl group.
37. The method of claim 34, wherein the Flavivirus is West Nile
virus.
38. The composition of claim 2, wherein the selected peptide
consists of SEQ ID NO:25.
39. The composition of claim 38, wherein the peptide's N-terminal
chemical moiety is an amino group and the peptide's C-terminal
chemical moiety is a carboxyl group.
Description
[0001] This Application claims the Benefit of U.S. Provisional
Application Ser. No. 60/424,746, filed Nov. 8, 2002, which is
incorporated by reference, in its entirety.
1. FIELD OF THE INVENTION
[0002] The present invention relates to peptides and methods of
inhibiting cell infection and/or virion:cell fusion by members of
the Flaviviridae family.
2. BACKGROUND OF THE INVENTION
[0003] 2.1. Entry of enveloped animal viruses requires fusion
between the viral membrane and a cellular membrane, either the
plasma membrane or an internal membrane. Class I fusion proteins
possess a "fusion peptide" at or near the amino terminus, a pair of
extended .alpha. helices and, generally, a cluster of aromatic
amino acids proximal to a hydrophobic transmembrane anchoring
domain (Carr and Kim, 1993; Suarez et al., 2000; Wilson, Skehel,
and Wiley, 1981). Several otherwise disparate viruses, including
orthomyxoviruses, paramyxoviruses, retroviruses, arenaviruses, and
filoviruses encode class I fusion proteins varying in length and
sequence, but highly similar in overall structure (Gallaher, 1996;
Gallaher et al., 1989). X-ray crystallography of the E glycoprotein
(E-protein) of tick-borne encephalitis virus (TBEV), a member of
the genus flavivirus of the Flaviviridae family, revealed a
structure for this fusion protein distinct from other fusion
proteins (Rey et al., 1995). E-protein possesses an internal fusion
peptide stabilized by dicysteine linkages and three domains (I-III)
comprised mostly of antiparallel .beta. sheets. In the slightly
curved rod-like configuration of the E-protein present in the
virion, the fusion peptide is located at the tip of domain II, the
furthest point distal from the C-terminal transmembrane anchor.
Examination by Lescar and coworkers (2001) of E1, the fusion
protein of the Togavirus Semliki Forest virus (SFV), revealed a
remarkable fit to the scaffold of TBEV E. Recently, the
E-glycoprotein of dengue virus, a medically important flavivirus,
was also shown to have a class II structure (Kuhn et al.,
2002).
[0004] 2.2. The Flaviviridae family consists of three genera,
flaviviruses, hepaciviruses and pestiviruses. In the United States
alone, 4 million people are infected with a member of the
hepacivirus genus, hepatitis C virus (HCV). This is four times the
number infected by HIV. Each year in the US, 30-50,000 new HCV
infections occur, and about 15-20,000 people die. These numbers are
expected to increase dramatically. The infection is spread
primarily through needle sharing among drug users, although there
is some risk from accidental needle sticks, blood products before
1992, chronic blood dialysis, and frequent sexual contact. Current
treatments for HCV using ribavirin and interferon cost $8,000 to
$20,000 per year, and help about half of patient only partly. End
stage HCV disease is the most frequent indication for liver
transplants and this costs $250,000 to $300,000. Better drugs to
treat HCV infection and an effective vaccine to prevent HCV
infection are urgently needed. Members of the flavivirus genus,
dengue virus, Japanese encephalitis virus, yellow fever virus, and
West Nile virus, cause important human diseases world-wide.
Pestiviruses, such as bovine viral diarrhea virus and border
disease virus, cause significant veterinary illnesses.
3. SUMMARY OF THE INVENTION
[0005] Based on sequence similarities, it is likely that the E
glycoproteins of other members of the flavivirus genus within the
family Flaviviridae, including West Nile virus, are also class II
fusion proteins. Analyses presented herein indicate that
glycoproteins of viruses from members of the other two genera of
the Flaviviridae family, hepaciviruses and pestiviruses, have
previously undescribed structures. The envelope glycoprotein E1 of
hepatitis C virus, a hepacivirus, and the envelope glycoprotein E2
of pestiviruses have novel structures, resembling a truncated
version of a class II fusion protein. No viral protein has
previously been identified with this structure. Our observations
were unexpected and contrast with published studies. Hepatitis C
virus encodes two envelope glycoproteins, E1 (gp35) and E2 (gp70),
both with C-terminal transmembrane anchor domains. Prior studies
indicated that another HCV protein, E2, has a class II structure.
The structural determinations of the hepacivirus and pestivirus
fusion proteins allow the identification of several heretofore
unknown features of Flavivirus fusion proteins for drug and vaccine
development.
[0006] Thus, the instant invention teaches that HCV envelope
glycoprotein E1 has a previously unknown structure, a truncated
class II fusion protein. This structure identifies regions of HCV
E1 and other class II viral fusion proteins important for
virus:cell fusion. This invention also teaches that peptides can be
designed to inhibit viruses, including HCV and other members of the
Flaviviridae family, that have fusion peptides with a class II
structure.
[0007] Structural features of Flavivirus envelope glycoproteins
identified herein provide surprising guidance for the development
of vaccines and/or drugs to prevent or treat Flavivirus infections.
Prior to the availability of X-ray structural data (Wild,
Greenwell, and Matthews, 1993; Wild et al., 1994), several potent
HIV-1 TM inhibitors were developed based on the Gallaher HIV-1 TM
fusion protein model (Gallaher et al., 1989). DP178 (T20) peptide
(FIG. 5A) has been shown to substantially reduce HIV-1 load in AIDS
patients in preliminary results from phase III clinical trials.
(Hoffman-La Roche and Trimeris, 2002). Peptide drugs should be
relatively easy to develop, based on our structures. Once an
effective peptide inhibitor is described a non-peptide drug can be
developed.
[0008] More specifically, the present invention provides for
methods of inhibiting viral infection by Flaviviruses and/or fusion
between the virion envelope of Flaviviruses and membranes of the
target cell (the process that delivers the viral genome into the
cell cytoplasm). The invention is related to the discovery, as
described herein, that hepacivirus envelope glycoprotein E1 and
pestivirus E2 glycoprotein have novel structures. The invention
provides for methods that employ peptides or peptide derivatives to
inhibit Flavivirus:cell fusion. The present invention provides for
methods of treatment and prophylaxis of diseases induced by
Flaviviruses.
[0009] Various embodiments of the instant invention provide for
pharmaceutical compositions comprising one or more peptides
selected from one or more of the following groups.
A) Peptides having the sequence of any of SEQ ID NO:1 to SEQ ID
NO:36; B) Peptides homologous to any one of SEQ ID NO:1 to SEQ ID
NO:36, except that they are from a different flavivirus. C)
Peptides that are functionally equivalent to any one of SEQ ID NO:1
to SEQ ID NO:36, wherein the functionally equivalent peptide is
identical to at least one of SEQ ID NO:1 to SEQ ID NO:36 except
that one or more amino acid residues has been substituted with a
homologous amino acid, resulting in a functionally silent change,
or one or more amino acids has been deleted.
[0010] Various aspects of this embodiment of the invention provide
for compositions that comprise one or more peptides selected from
the following.
A) Peptides having the amino acid sequence one or more of SEQ ID
NO:1 to SEQ ID NO:36, wherein the N-terminal "Xaa" is an amino
group and the C-terminal "Xaa" is a carboxyl group. B) Peptides
having the sequence of any of SEQ ID NO:1 to SEQ ID NO:36, wherein
the N-terminal "Xaa" is not an amino group and/or the C-terminal
"Xaa" is not a carboxyl group, wherein the N-terminal "Xaa" is
selected from the group consisting of: an acetyl group, a
hydrophobic group, carbobenzoxyl group, dansyl group, a
t-butyloxycarbonyl group, or a macromolecular carrier group, and/or
wherein the C-terminal "Xaa" is selected from the group consisting
of an amido group, a hydrophobic group, t-butyloxycarbonyl group or
a macromolecular group. C) Peptides having the sequence of any of
SEQ ID NO:1 to SEQ ID NO:36 except that at least one bond linking
adjacent amino acid residues is a non-peptide bond. D) Peptides
having the sequence of any of SEQ ID NO:1 to SEQ ID NO:36, except
that at least one amino acid residue is in the D-isomer
configuration. E) Peptides as in groups "A)" or "B)" except that at
least one amino acid has been substituted for by a different amino
acid (whether a conservative or non-conservative change). F)
Peptides that are a functional fragment of a peptide as set out in
any of groups "A)" to "E)", above, where the peptides have at least
3 contiguous nucleotides of any one of SEQ ID NO:1 to SEQ ID
NO:36.
[0011] The instant invention also provides for substantially
purified antibodies that specifically react with one or more of the
peptides described above.
[0012] The instant invention also provides for methods for treating
or preventing viral infections in an animal where the method
comprises administering to an animal or human peptides and/or
antibodies as described above.
[0013] 3.1. Abbreviations [0014] HIV--human immunodeficiency virus
[0015] TBEV--tick-borne encephalitis virus [0016] DV--dengue virus
[0017] WNV--West Nile virus [0018] HCV--hepatitis C virus [0019]
GBV--hepatitis GB virus [0020] CSFV--classical swine fever virus
[0021] BVDV--bovine viral diarrhea virus [0022] BD--border disease
virus [0023] HSA--human serum albumen
4. BRIEF DESCRIPTION OF THE DRAWINGS
[0024] FIG. 1. Alignments of tick-borne encephalitis virus E,
hepatitis C virus E1 and classical swine fever virus E2
glycoproteins. Panel A: Amino acids are numbered from the beginning
of the TBEV, HCV and CSFV polyproteins in this and subsequent
figures. Bracketed HCV insert sequences are wrapped and do not
represent an alignment comparison. "(:)" refers to identical amino
acids. "(.)" refers to chemically similar amino acids. Panel B:
Linear arrangement of the domain structure of TBEV E as determined
by Rey et al. (1995). Regions of significant sequence similarities
to TBEV E in HCV E1 and E2 and CSFV E2 as determined by the PRSS3
sequence alignment program are indicated. Probabilities (p-values)
are based on 1000 shuffles.
[0025] FIG. 2. Structures of hepacivirus E1 and pestivirus E2
glycoproteins. Panel A. Structure of TBEV E as determined by Rey et
al. (1995) is shown schematically (traced from a RasMac molecular
visualization software rendering). Panel B: Structure of HCV E1.
HCV E1 sequences with similarity to TBEV E sequences are enclosed
in quotation marks. Panel C: Structure of CSFV E2.
[0026] FIG. 3. Alignments of the precursor of tick-borne
encephalitis virus small membrane protein, prM, and classical swine
fever virus E1. Panel A: alignments were constructed as detailed in
the text. Panel B: Linear arrangement of TBEV prM and CSFV E1 with
a region of sequence similarity determined by the PPSS3 algorithm
indicted.
[0027] FIG. 4. Common order of proteins in Flaviviridae
polyproteins. Proteins or portions of proteins with similar
functions are located in similar locations along the polyproteins
of members of the Flaviviridae. Hydrophobic domains were predicted
using TMpred.
[0028] FIG. 5. Comparison of human immunodeficiency virus
transmembrane glycoprotein (TM) with hepatitis C virus envelope
glycoprotein 1 (E1). Panel A: an updated structure of HIV-1 TM from
Gallaher et al. (1989) with structural motifs indicated in rainbow
order. Amino acids are numbered from the beginning of the Env
polyprotein. HIV-1 TM is truncated after the transmembrane domain.
The precise ends of the TM N- and C-helices are unclear because of
conflicting structural data. No attempt was made to align the N-
and C-helices, although points of contact are solved in the
coiled-coil formations. Positions of known neutralizing epitopes on
TM are indicated, as well as sequences corresponding to peptides
CS3 and DP178 (T20) (Qureshi et al., 1990; Wild et al., 1994) that
inhibit HIV-1 infectivity. Panel B: Structure of HCV E1 with motifs
that are shared with HIV-1 TM. Boxed arrows are predicted beta
sheet structures that are similar to the indicated .beta. sheets of
TBEV E. Predicted .alpha. helical structures are outlined. Arrows
denote directions that the HCV E1 structure could fold in three
dimensions.
5. DETAILED DESCRIPTION OF THE INVENTION
[0029] The present invention relates to methods of inhibiting
Flavivirus infection that comprises inhibiting the fusion between
the virion envelope and a cell membrane, the process that delivers
the viral genome into the cell cytoplasm. For purposes of clarity
of disclosure, and not by way of limitation, the description of the
present invention will be divided into the following
subsections:
(i) peptides of the invention (ii) utility of the invention
[0030] 5.1. Peptides of the Invention
[0031] Any peptide or protein which inhibits the fusion between the
Flavivirus virion envelope and a cell membrane, including those of
Flaviviruses which infect human as well as nonhuman hosts, may be
used according to the invention. In various embodiments of the
invention, these inhibitors may include, but are not limited to
peptides related to several membrane-interactive domains of
Flavivirus fusion proteins.
[0032] Flavivirus inhibitory peptides are, according to the instant
invention, identical or homologous to the amino acid sequences HCV
Fusion Inhibitory Protein 1, X-YQVRNSSGLYHVTNDCPNSSIVYEAADAIL-Z
(SEQ ID NO:1); HCV Fusion Inhibitory Protein 2,
X-CSALYWVGDLCGSVFLVGQLFTFSPRRHWTTQDC-Z (SEQ ID NO:2); HCV Fusion
Inhibitory Protein 3, X-SPRRHWTTQDCNCSIYPGHITGHRMAWDMMMNWSPT-Z (SEQ
ID NO:3); or HCV Fusion Inhibitory Protein 4,
X-MMMNWSPTAALLRIPQAIMDMIAGAHWGVLAGIKYFSMVGNW-Z (SEQ ID NO:4), or
portions thereof or, alternatively, to a homologous peptide
sequence associated with another Flavivirus, including, but not
limited to, HGB, DV, JEV, YFV, WNV, CSFV, BVDV, or BDV as provided
below in tables 1 through 4.
[0033] As used herein the term "homologous peptide" preferably
refers to similar peptides from other strains of a given virus or,
alternatively from related viruses.
[0034] As used herein the term "similar peptides" refers to those
peptides having at least 70% identical or chemically similar amino
acids. More preferably, it refers to peptides having 75%, 80%, 85%,
90%, 95%, or greater identical and/or chemically equivalent amino
acid resides.
[0035] As used herein the terms "portion thereof" refers to the
peptide resulting from the removal of from one or more amino acids
from either or both ends of the listed peptide, i.e. a truncated
peptide. The number of amino acids removed may vary from 1-10 so
long as the remaining fragment is "functional". As defined herein
the term "functional fragment" refers to a fragment capable of
inhibiting virus:cell fusion, inhibiting viral infectivity, capable
of eliciting an antibody capable of recognizing and specifically
binding to non-truncated peptide and/or interfering with Flavivirus
envelope protein-mediated cell infection.
TABLE-US-00001 TABLE 1 Flavivirus fusion inhibitory peptide 1
PROTEIN SEQUENCE HCV E1 X-YQVRNSSGLYHVTNDCPNSSIVYEAADAIL-Z (SEQ ID
NO:1) HGB E1 X-RVTDPDTNTTILTNCCQRNQVIYCSPSTCL-Z (SEQ ID NO:5) DV E
X-RDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDF-Z (SEQ ID NO:6) JEV E
X-RDFIEGASGATWVDLVLEGDSCLTIMANDKPTLDV-Z (SEQ ID NO:7) YFV E
X-RDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDI-Z (SEQ ID NO:8) WNV E
X-RDFLEGVSGATWVDLVLEGDSCVTIMSKDKPTIDV-Z (SEQ ID NO:9) CSFV E2
X-GQLACKEDYRYAISSTNEIGLLGAGGLTTTWKEYN-Z (SEQ ID NO:10) BVDV E2
X-GHLDCKPEFSYAIAKDERIGQLGAEGLTTTWKEYS-Z (SEQ ID NO:11) BDV E2
X-GEFACREDHRYALAKTKETGPLGAESLTTTWTDYQ-Z (SEQ ID NO:12)
TABLE-US-00002 TABLE 2 Flavivirus fusion inhibitory peptide 2
PROTEIN SEQUENCE HCV E1 X-CSALYWVGDLCGSVFLVGQLFTFSPRRHWTTQDC-Z (SEQ
ID NO:2) HGB E1 X-TCDALDIGELCGACVLVGDWLVRHWLIHIDLNET-Z (SEQ ID
NO:13) DV E X-KRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTC-Z (SEQ ID NO:14)
JEV E X-SSYVCKQGFTDRGWGNGCGLFGKGSIDTCAKFSC-Z (SEQ ID NO:15) YFV E
X-GDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTC-Z (SEQ ID NO:16) WNV E
X-PAFVCRQGVVDRGWGNGCGLFGKGSIDTCAKFAC-Z (SEQ ID NO:17) CSFV E2
X-KGKYNTTLLNGSAFYLVCPIGWTGVIECTAVSPT-Z (SEQ ID NO:18) BVDV E2
X-RGKFNTTLLNGPAFQMVCPIGWTGTVSCTSFNMD-Z (SEQ ID NO:19) BDV E2
X-RGKYNATLLNGSAFQLVCPYEWTGRVECTTISKS-Z (SEQ ID NO:20)
TABLE-US-00003 TABLE 3 Flavivirus fusion inhibitory peptide 3
PROTEIN SEQUENCE HCV E1 X-SPRRHWTTQDCNCSIYPGHITGHRMAWDMMMNWSPT-Z
(SEQ ID NO:3) HGB E2 X-IHIDLNETGTCYLEVPTGIDPGFLGFIGWMAGKVEA-Z (SEQ
ID NO:21) DV E X-MVLLQMEDKAWLVHRQWFLDLPLPWLPGADTQGSNW-Z (SEQ ID
NO:22) JEV E X-FYVMTVGSKSFLVHREWFHDLALPWTSPSSTAWRNR-Z (SEQ ID
NO:23) YFV E X-SYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREM-Z (SEQ ID
NO:24) WNV E X-YYVMTVGTKTFLVHREWFMDLNLPWSSAGSTVWRNR-Z (SEQ ID
NO:25) CSFV E2 X-TLRTEVVKTFRRDKPFPHRMDAVTTTVENEDLFY-Z (SEQ ID
NO:26) BVDV E2 X-TLATEVVKIYKRTKRFRSGLVATHTTIYEEDLYH-Z (SEQ ID
NO:27) BDV E2 X-TLATTVVRTYRRSKPFPHRQGAITQKNLGEDLH-Z (SEQ ID
NO:28)
TABLE-US-00004 TABLE 4 Flavivirus fusion inhibitory peptide 4
PROTEIN SEQUENCE HCV E1
X-MMMNWSPTAALLRIPQAIMDMIAGAHWGVLAGIKYFSMVGNW-Z (SEQ ID NO:4) HGB E1
X-WMAGKVEAVIFLTKLASQVPYAIATMFSSVHYLAVGALIYYS-Z (SEQ ID NO:29) DV E
X-MAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSW-Z (SEQ ID NO:30) JEV E
X-LAALGDTAWDFGSIGGVFNSIGKAVHQVFGGAFRSLFGGMSW-Z (SEQ ID NO:31) YFV E
X-LAVMGDTAWDFSSAGGFFTSVGKGIHTVFGSAFQGLFGGLNW-Z (SEQ ID NO:32) WNV E
X-LAALGDTAWDFGSVGGVFTSVGKAVHQVFGGAFRSLFGGMSW-Z (SEQ ID NO:33) CSFV
E2 X-QQYMLKGEYQYWFDLDVTDRHSDYFAEFVVLVVVALLGGRYI-Z (SEQ ID NO:34)
BVDV E2 X-QQYMLKGEYQYWFDLEVTDHHRDYFAESILVVVVALLGGRYV-Z (SEQ ID
NO:35) BDV E2 X-QQYMLKGQYQYWFDLEVISSTHQIDLTEFIMLAVVALLGGRYV-Z (SEQ
ID NO:36)
[0036] According to the instant invention peptides related to the
Flavivirus fusion inhibitory peptides (FIP) preferably comprise at
least three contiguous residues of the FIP peptides, or a
homologous peptide, more preferably they comprise 4, 5, 6, or 7
contiguous residues. Even more preferably they comprise at least 8,
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, or 30 contiguous residues, and most preferably all
residues of these sequences. As used herein the term Flavivirus
inhibitory peptides preferably means peptides having a sequence
identical to the corresponding portion of the Flavivirus inhibitory
protein and peptides in which one or more amino acids are
substituted by functionally equivalent amino acids (see infra). The
term also refers to derivatives of these peptides, including but
not limited to benzylated derivatives, glycosylated derivatives,
and peptides which include enantiomers of naturally occurring amino
acids. In other embodiments of the invention, the Flavivirus
inhibitory peptides, related peptides or derivatives are linked to
a carrier molecule such as a protein. Proteins contemplated as
being useful according to this embodiment of the invention, include
but are not limited to, (human serum albumen). Flavivirus
inhibitory peptide-related peptides comprising additional amino
acids are also contemplated as useful according to the
invention.
[0037] Peptides may be produced from naturally occurring or
recombinant viral proteins, or may be produced using standard
recombinant DNA techniques (e.g. the expression of peptide by a
microorganism which contains recombinant nucleic acid molecule
encoding the desired peptide, under the control of a suitable
transcriptional promoter, and the harvesting of desired peptide
from said microorganism). Preferably, the peptides of the invention
may be synthesized using any methodology known in the art,
including but not limited to, Merrifield solid phase synthesis
(Clark-Lewis et al., 1986, Science 231:134-139).
[0038] The FIP, or fragments or derivatives thereof, of the
invention include, but are not limited to, those containing, as a
primary amino acid sequences the amino acid sequence HCV Fusion
Inhibitory Protein 1, X-YQVRNSSGLYHVTNDCPNSSIVYEAADAIL-Z (SEQ ID
NO:1); HCV is Fusion Inhibitory Protein
2X-CSALYWVGDLCGSVFLVGQLFTFSPRRHWTTQDC-Z (SEQ ID NO:2); HCV Fusion
Inhibitory Protein 3, X-SPRRHWTTQDCNCSIYPGHITGHRMAWDMMMNWSPT-Z (SEQ
ID NO:3); or HCV Fusion Inhibitory Protein 4,
X-MMMNWSPTAALLRIPQAIMDMIAGAHWGVLAGIKYFSMVGNW-Z (SEQ ID NO:4), or a
functional portion or functional portions thereof. Also
contemplated are homologous peptide sequences associated with
another Flaviviruses, including, but not limited to, HGB, DV, JEV,
YFV, WNV, CSFV, BVDV, or BDV. Also contemplated are altered
sequences (i.e. altered from any of the sequences referred to
herein) in which functionally equivalent amino acid residues are
substituted for residues within the sequence, resulting in a
functionally silent change. For example, one or more amino acid
residues within the sequence can be substituted by replacing the
original amino acid with another amino acid, of a similar polarity,
that acts as a functional equivalent, resulting in a functionally
silent alteration. Substitutes for an amino acid within the
sequence may be selected from other members of the class to which
the amino acid belongs. For example, the nonpolar (hydrophobic)
amino acids include alanine, leucine, isoleucine, valine, proline,
phenylalanine, tryptophan and methionine. The polar neutral amino
acids include glycine, serine, threonine, cysteine, tyrosine,
asparagine, and glutamine. The positively charged (basic) amino
acids include arginine, lysine and histidine. The negatively
charged (acidic) amino acids include aspartic acid and glutamic
acid. For example, and not by way of limitation, such peptides may
also comprise one or more D-amino acids. Furthermore, in any of the
embodiments of the instant invention the peptide may comprise an
inefficient carrier protein, or no carrier protein at all.
[0039] 5.3. Utility of the Invention
[0040] The Flavivirus inhibitory peptides of the instant invention
may be utilized to inhibit Flavivirus virion:cell fusion and may,
accordingly, be used in the treatment of Flavivirus infection and
also in prophylaxis against Flavivirus infection. The peptides of
the invention may be administered to patients in any sterile,
biocompatible pharmaceutical carrier, including, but not limited
to, saline, buffered saline, dextrose, and water. Methods for
administering peptides to patients are well known to those of skill
in the art; they include, but are not limited to, intradermal,
intramuscular, intraperitoneal, intravenous, subcutaneous, oral,
and intranasal. In addition, it may be desirable to introduce the
pharmaceutical compositions of the invention into the central
nervous system by any suitable route, including intraventricular
and intrathecal injection.
[0041] The instant invention provides for pharmaceutical
compositions comprising Flavivirus inhibitory peptides, peptide
fragments, or derivatives (as described supra) administered via
liposomes, microparticles, or microcapsules. Various embodiments of
the invention, contemplate the use of such compositions to achieve
sustained release of Flavivirus inhibitory peptides. Other
embodiments contemplate the administration of the FIP or
derivatives thereof, linked to a molecular carrier (e.g. HSA).
[0042] Various embodiments of the instant invention provide for
administration of the Flavivirus inhibitory peptides and/or
antibodies specific for the these peptides to human or animal
subjects who suffer from Flavivirus infection (e.g. dengue
hemorrhagic fever, West Nile disease, hepatitis C or classical
swine fever). In any embodiment the peptides and/or antibodies are
typically substantially purified (as used herein the term
"substantially purified" refers to a peptide, peptide analog, or
antibody that is greater than about 80% pure. More preferably,
"substantially purified" refers to a peptide, peptide analog, or
antibody that is greater than about 90% or greater than about 95%
pure. Most preferably it refers to a peptide, peptide analog, or
antibody that is greater than 99% pure. Functionally,
"substantially purified" means that it is free from contaminants to
a degree that that makes it suitable for the purposes provided
herein. Other embodiments provide for the prophylactic
administration of the peptides to those at risk for Flavivirus
infection.
[0043] Other embodiments of the instant invention provide for
methods for identifying the structure of truncated Flavivirus
fusion proteins which involved in virion:cell fusion by members of
the Flaviviridae family and for the structures themselves.
[0044] Other embodiments of the invention provide for a peptide
having a formula selected from one or more of the following.
A. Various embodiments of the invention provide for hepatitis C
virus Fusion Inhibitory Peptides: hepatitis C virus Fusion
Inhibitory Protein 1, X-YQVRNSSGLYHVTNDCPNSSIVYEAADAIL-Z (SEQ ID
NO:1); HCV Fusion Inhibitory Protein 2,
X-CSALYWVGDLCGSVFLVGQLFTFSPRRHWTTQDC-Z (SEQ ID NO:2); HCV Fusion
Inhibitory Protein 3, X-SPRRHWTTQDCNCSIYPGHITGHRMAWDMMMNWSPT-Z (SEQ
ID NO:3); or HCV Fusion Inhibitory Protein 4,
X-MMMNWSPTAALLRIPQAIMDMIAGAHWGVLAGIKYFSMVGNW-Z (SEQ ID NO:4) B.
Other embodiments of the invention provide for a peptide or peptide
homolog wherein the Flavivirus is member or tentative member of the
hepacivirus genus. A preferred embodiment of this invention is
drawn to a peptide or peptide analog wherein the tentative member
of the hepacivirus genus is hepatitis G virus and peptides are
selected from the group consisting of: hepatitis G virus Fusion
Inhibitory Peptides: hepatitis G virus Fusion Inhibitory Protein 1,
X-RVTDPDTNTTILTNCCQRNQVIYCSPSTCL-Z (SEQ ID NO:5); hepatitis G virus
Fusion Inhibitory Protein 2, X-TCDALDIGELCGACVLVGDWLVRHWLIHIDLNET-Z
(SEQ ID NO:13); hepatitis G virus Fusion Inhibitory Protein 3,
X-IHIDLNETGTCYLEVPTGIDPGFLGFIGWMAGKVEA-Z (SEQ ID NO:21); or
hepatitis G virus Fusion Inhibitory Protein 4,
X-WMAGKVEAVIFLTKLASQVPYAIATMFSSVHYLAVGALIYYS-Z (SEQ ID NO:29) C.
Other embodiments of the invention provide for a peptide or peptide
homolog from the flavivirus genus. In a preferred aspect of this
embodiment, the peptide or peptide analog is from dengue virus and
the peptides are selected from the group consisting of: dengue
virus Fusion Inhibitory Peptides: dengue virus Fusion Inhibitory
Protein 1, X-RDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDF-Z (SEQ ID NO:6);
dengue virus Fusion Inhibitory Protein 2,
X-KRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTC-Z (SEQ ID NO:14); dengue virus
Fusion Inhibitory Protein 3,
X-MVLLQMEDKAWLVHRQWFLDLPLPWLPGADTQGSNW-Z (SEQ ID NO:22); or dengue
virus Fusion Inhibitory Protein 4,
X-MAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSW-Z (SEQ ID NO:30). D.
Other embodiments of the invention provide for peptides or peptide
homolog from flavivirus genus member, Japanese encephalitis virus.
In preferred aspects of these embodiments the peptides and
or/peptide analogs are selected from the group consisting of:
Japanese encephalitis virus Fusion Inhibitory Peptides: Japanese
encephalitis virus Fusion Inhibitory Protein 1,
X-RDFIEGASGATWVDLVLEGDSCLTIMANDKPTLDV-Z (SEQ ID NO:7); Japanese
encephalitis virus Fusion Inhibitory Protein 2,
X-SSYVCKQGFTDRGWGNGCGLFGKGSIDTCAKFSC-Z (SEQ ID NO:15); Japanese
encephalitis virus Fusion Inhibitory Protein 3,
X-FYVMTVGSKSFLVHREWFHDLALPWTSPSSTAWRNR-Z (SEQ ID NO:23); or
Japanese encephalitis virus Fusion Inhibitory Protein 4,
X-LAALGDTAWDFGSIGGVFNSIGKAVHQVFGGAFRTLFGGMSW-Z (SEQ ID NO:31). E.
Other embodiments of the invention provide for peptides and/or
peptide homologs wherein the member of the flavivirus genus is
yellow fever virus and the peptides are selected from the group
consisting of: yellow fever virus Fusion Inhibitory Peptides:
yellow fever virus Fusion Inhibitory Protein 1,
X-RDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDI-Z (SEQ ID NO:8); yellow fever
virus Fusion Inhibitory Protein 2,
X-GDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTC-Z (SEQ ID NO:16); yellow fever
virus Fusion Inhibitory Protein 3,
X-SYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREM-Z (SEQ ID NO:24); or yellow
fever virus Fusion Inhibitory Protein 4,
X-LAVMGDTAWDFSSAGGFFTSVGKGIHTVFGSAFQGLFGGLNW-Z (SEQ ID NO:32). F.
Other embodiments of the invention provide for peptides and/or
peptide homologs of wherein the member of the flavivirus genus is
West Nile virus and the peptides are selected from the group
consisting of: West Nile virus Fusion Inhibitory Peptides: West
Nile virus Fusion Inhibitory Protein 1,
X-RDFLEGVSGATWVDLVLEGDSCVTIMSKDKPTIDV-Z (SEQ ID NO:9); West Nile
virus Fusion Inhibitory Protein 2,
X-PAFVCRQGVVDRGWGNGCGLFGKGSIDTCAKFAC-Z (SEQ ID NO:17); West Nile
virus Fusion Inhibitory Protein 3,
X-YYVMTVGTKTFLVHREWFMDLNLPWSSAGSTVWRNR-Z (SEQ ID NO:25); or West
Nile virus Fusion Inhibitory Protein 4,
X-LAALGDTAWDFGSVGGVFTSVGKAVHQVFGGAFRSLFGGMSW-Z (SEQ ID NO:33). G.
Other embodiments of the instant invention provide for peptides
and/or peptide homologs wherein the Flavivirus is a member of the
pestivirus genus. In various aspects of these embodiments the
peptides or homologs thereof the member of the pestivirus genus is
classical swine fever virus and the peptides are selected from the
group consisting of: classical swine fever virus Fusion Inhibitory
Peptides: classical swine fever virus Fusion Inhibitory Protein 1,
X-GQLACKEDYRYAISSTNEIGLLGAGGLTTTWKEYN-Z (SEQ ID NO:10); classical
swine fever virus Fusion Inhibitory Protein 2,
X-KGKYNTTLLNGSAFYLVCPIGWTGVIECTAVSPT-Z (SEQ, ID NO:18); or
classical swine fever virus Fusion Inhibitory Protein 3,
X-TLRTEVVKTFRRDKPFPHRMDAVTTTVENEDLFY-Z (SEQ ID NO:26); or classical
swine fever virus Fusion Inhibitory Protein 4,
X-QQYMLKGEYQYWFDLDVTDRHSDYFAEFVVLVVVALLGGRYI-Z (SEQ ID NO:34). H.
Other embodiments of the instant invention provide for peptides and
peptide homologs wherein the member of the pestivirus genus is
bovine viral diarrhea virus and the peptides are selected from the
group consisting of: bovine viral diarrhea virus Fusion Inhibitory
Peptides: bovine viral diarrhea virus Fusion Inhibitory Protein 1,
X-GHLDCKPEFSYAIAKDERIGQLGAEGLTTTWKEYS-Z (SEQ ID NO:11); bovine
viral diarrhea virus Fusion Inhibitory Protein 2,
X-RGKFNTTLLNGPAFQMVCPIGWTGTVSCTSFNMD-Z (SEQ ID NO:19); or bovine
viral diarrhea virus Fusion Inhibitory Protein 3,
X-TLATEVVKIYKRTKRFRSGLVATHTTIYEEDLYH-Z (SEQ ID NO:27); or bovine
diarrhea virus Fusion Inhibitory Peptide 4,
X-QQYMLKGEYQYWFDLEVTDHHRDYFAESILVVVVALLGGRYV-Z (SEQ ID NO:35). I.
Other embodiments of the instant invention provide for peptides and
peptide homologs wherein the member of the pestivirus genus is
border disease virus and the peptides are selected from the group
consisting of: border disease virus Fusion Inhibitory Peptides:
classical swine fever virus Fusion Inhibitory Protein 1,
X-GEFACREDHRYALAKTKEIGPLGAESLTTTWTDYQ-Z (SEQ ID NO:12); border
disease virus Fusion Inhibitory Protein 2,
X-RGKYNATLLNGSAFQLVCPYEWTGRVECTTISKS-Z (SEQ ID NO:20); or border
disease virus Fusion Inhibitory Protein 3,
X-TLATTVVRTYRRSKPFPHRQGAITQKNLGEDLH-Z (SEQ ID NO:28); or border
disease virus Fusion Inhibitory Peptide 4,
X-QQYMLKGQYQYWFDLEVISSTHQIDLTEFIMLAVVALLGGRYV-Z (SEQ ID NO:36)
[0045] In any of the foregoing groups the amino acids are
represented by the single letter code. In various aspects of these
embodiments "X" comprises an amino group, an acetyl group, a
hydrophobic group or a macromolecular carrier group; "Z" comprises
a carboxyl group, an amido group a hydrophobic group or a
macromolecular carrier group. In other aspects of this embodiment
of the invention, X is a hydrophobic group, a carbobenzoxyl group,
a dansyl group, t-butyloxycarbonyl group, a lipid conjugate, a
polyethylene glycol group, or a carbohydrate. In any aspect of this
embodiment Z may be a t-butyloxycarbonyl group, a lipid conjugate,
a polyethylene glycol group, or a carbohydrate.
[0046] Moreover, aspects of this embodiment also include peptides
wherein at least one bond linking adjacent amino acids residues is
a non-peptide bond. In particularly preferred aspects of this
embodiment the non-peptide bond is an imido, ester, hydrazine,
semicarbazoide or azo bond.
[0047] Other aspects of this embodiment provide for peptides
wherein at least one amino acid is a D-isomer amino acid.
[0048] Additional aspects of this embodiment of the invention
provide for peptides wherein compromising at least one amino acid
substitution has been made so that a first amino acid residue is
substituted for a second, different amino acid residue. These
substitutions may be conservative or non-conservative. So long as
the peptide is still functional according to the instant
invention.
[0049] Other aspects of this embodiment of the invention provide
for peptides wherein at least one amino acid has been deleted. As
noted, supra, the peptides according to this embodiment of the
invention must comprise at least 3 contiguous amino acids of one of
the SEQ ID NOs indicated above and must be a functional
segment.
[0050] It is noted that any combination of the modifications listed
above is considered as part of the instant invention.
6. EXAMPLE
Hepatitis C Virus E1 is a Truncated Class II Fusion Protein
[0051] Proteomics computational tools were used to fit HCV E1
protein to the scaffold of TBEV E, the prototypic class II fusion
protein. Because HCV E1 is shorter than TBEV E, we reasoned that
the former might contain several "deletions" relative to the
latter. The HCV E1 fusion peptide (Flint et al., 1999) was assumed
to be located at the end of the molecule furthest from the carboxyl
terminal (C-terminal) transmembrane anchor domain, and, like other
class II fusion proteins to be comprised mostly of antiparallel
.beta.-sheets. This latter assumption was supported by Chou-Fasman
(Chou and Fasman, 1974) and Robson-Garnier (Biou et al., 1988)
analyses, the most commonly applied secondary structure prediction
algorithms.
[0052] The fusion peptide of HCV (amino acids [aa] 272 to 281 of
the full-length polyprotein) was aligned with the fusion peptide of
TBEV E (aa 385-396) (FIG. 1A). Both TBEV E and HCV E1 fusion
peptides have cysteine residues at either end and contain a core of
mostly aromatic and hydrophobic amino acids (FIG. 1A). Another
domain readily identifiable in HCV E1 is the transmembrane domain.
Amino acids 361 to 381 of the hydrophobic sequence near the
carboxyl terminus of E1 were predicted to form a transmembrane
helix by TMpred (transmembrane prediction software, see
ch.embnet.org) (TMpred score 1308, >500 is statistically
significant).
[0053] Several regions of predicted .beta. sheets and .alpha.
helices in HCV E1 showed similarities to sequences known to assume
those secondary structures in TBEV E (FIG. 1A). Beginning from the
amino terminus, the first similarity of HCV E1 begins in .beta.
sheet D.sub.o of TBEV E and extends through the fusion peptide.
PRSS3, a sequence alignment algorithm, was used to confirm that
there is a significant similarity (p<0.025) between amino acids
246-281 of HCV E1 and amino acids 350-396 of TBEV E (FIG. 1B). The
fusion peptide is flanked by .beta. sheets in class II fusion
proteins and predicted .beta. sheets with similarities to the b and
c .beta. sheets of TBEV E are indeed predicted to be present on
either side of the putative HCV E1 fusion peptide by Chou-Fasman
and Robson-Garnier analysis. HCV E1 also has an extended region of
similarity with the amino acid sequence between the two longest
helices in TBEV E, .alpha.A and .alpha.B. There is a statistically
significant (P<0.025) alignment of amino acids 316-356 of HCV E1
with amino acids 496-544 of TBEV E (FIG. 1B).
[0054] To determine the plausibility of these alignments, a
three-dimensional model of HCV E1 was scaffolded on domain II of
TBEV E (FIG. 2A). Similar sequences/structures were drawn in
similar locations. Reorienting the "b" sheet in E1 is the only
change relative to E required to bring the eight cysteine residues
into close proximity. The four dicysteines of HCV E1 potentially
form a "zipper" down the center of the molecule like the three
dicysteines in domain II of TBEV E (FIG. 2B). This model locates
the five HCV E1 glycosylation sites so they are surface accessible.
Additionally, most of the hydrophobic residues are present in a
region on one side of E1 between the fusion peptide and the
transmembrane anchor (see below, FIG. 5).
[0055] Each of the HCV E1 structures drawn in FIG. 2B conforms to
both Chou-Fasman and Robson-Garnier predictions, with the exception
of the region from "i" to ".alpha.B". The structures designated "i"
and "j" were predicted to be .beta. sheets by Chou-Fasman analysis,
but .alpha. helical by Robson-Garnier analysis. The structure
designated ".alpha.B" was predicted to be a .beta. sheet by
Chou-Fasman analysis, but .alpha. helical by Robson-Garnier
analysis. HCV E1 appears to be missing, relative to TBEV E, much of
the portion of the molecule prior to the transmembrane helix
(pre-anchor). This region of TBEV E follows the trypsin cleavage
site at amino acid 395 used to generate that portion of the
ectodomain of E examined by X-ray crystallography, and therefore,
the TBEV E pre-anchor (stem) structure is uncertain. The pre-anchor
of TBEV E has been predicted to form an amphipathic .alpha. helix
(Allison et al., 1999). A sequence (aa 693-721) of the pre-anchor
domain in TBEV E has the characteristics of a leucine zipper, i.e.
leucine or another hydrophobic amino acid in the first and fourth
(a and d) positions of a seven amino acid periodicity (FIG. 1A).
The pre-anchor sequence of HCV E1 was also predicted to be an
.alpha. helix with characteristics of a "leucine zipper"
(Charloteaux et al., 2002). Because of the significant amino acid
sequence similarity with TBEV E, the HCV E1 secondary structures
between ".alpha.A" and ".alpha.B" were depicted as in TBEV E. There
are several possible alternatives to the 3D model of HCV E1 drawn
in FIG. 2B, and it is possible that the secondary structures change
on interaction with membranes.
[0056] In contrast to HCV E1, our analyses did not reveal any
sequences of HCV E2 with significant similarity to any sequence in
domains I or II of TBEV E or any other flavivirus E protein
(representatives of each of the four major serogroups were
examined). Most of the N-terminal half of HCV E2, which include
hypervariable region I (HVR 1), is without any sequence similarity
to TBEV E. However, we detected a significant alignment
(p<0.025) of the C-terminal half of HCV E2 (aa 549-726) with the
region of TBEV E (aa 590-763) from domain III through the first of
two predicted transmembrane spanning domains of TBEV E (FIG. 1,
TBEV E TM1, amino acids 448-469, TMpred: 1496; TM2, amino acids
474-496, TMpred: 1962). As discussed above, the pre-anchor region
of TBEV E has a sequence (aa 693-721) with features of a "leucine
zipper; a similar motif (aa 675-703) is found in the HCV E2
pre-anchor (FIG. 1). In addition, the carboxyl (C) terminus of HCV
E2, like that of TBEV E, contains a stretch of hydrophobic amino
acids that potentially could span the membrane twice. The
transmembrane anchor(s) of HCV E2 (TMpred score: 1364) is
interrupted by charged amino acids like TM1 of TBEV E. Thus, by
sequence alignments and structural predictions there are
demonstrable similarities between the C-terminal portions of HCV E2
and TBEV E.
[0057] Significant alignments of E1 of hepatitis GB virus (GBV-B)
with HCV E1, indicate that this unclassified member of the
Flaviviridae family also encodes a truncated class II fusion
protein.
[0058] 6.1. Materials and Methods
[0059] Prototype strains of representatives of the Flaviviridae
were used for sequence and structural comparisons. The strains
examined include TBEV strain Neudoerf1 (accession number: P14336);
and the human prototype strain H (subtype 1a) of hepatitis C virus
(P27958), Some comparisons used representatives of the major
serogroups of flaviviruses, including Japanese encephalitis virus,
strain JaOARS982 (P32886), yellow fever virus, strain 17D-204
(P19901), dengue virus type 2, strain PR-159/S1 (P12823), and West
Nile virus, strain NY 2000-crow3356 (AF404756). We also compared
HCV sequences to those of GB virus-B virus (AAC54059), an
unassigned member of the Flaviviridae.
[0060] MACMOLLY.RTM., protein analysis software (Soft Gene GmbH,
Berlin), was used to locate areas of limited sequence similarity
and to perform Chou-Fasman and Robson-Garnier analyses. PRSS3, a
program derived from rdf2 (Pearson and Lipman, 1988), which uses
the Smith-Waterman sequence alignment algorithm (Smith and
Waterman, 1981), was used to determine the significance of protein
alignments. PRSS3 is part of the FASTA package of sequence analysis
programs available by anonymous ftp from ftp.virginia.edu. Default
settings for PRSS3 were used, including the blosum50 scoring
matrix, gap opening penalty of 12, and gap extension penalty of 2.
The alignments presented are those that produced the highest
alignment scores, rather than the longest sequences that produced
significant scores. Chou-Fasman and Robson-Garnier algorithms
predict protein structures in an aqueous environment, but they
cannot predict protein structures in a lipid bilayer. Domains with
significant propensity to form transmembrane helices were
identified with TMpred (ExPASy, Swiss Institute of Bioinformatics).
TMpred is based on a statistical analysis of TMbase, a database of
naturally occurring transmembrane glycoproteins (Hofman and
Stoffel, 1993). RasMac, developed by Roger Sayle, was used to
render 3D models of TBEV E.
[0061] 6.2. Results and Discussion
[0062] The results indicate that the ectodomain of hepaciviruses is
a truncated version of the class II fusion protein structure. The
ectodomain of HCV E1 is roughly equivalent to the part of TBEV E
from the "hinge" region to the fusion peptide (FIG. 2). Our
conclusions contrast with those of Yagnik et al. (2000), who
predicted that HCV E2 fits the scaffold of a complete class II
fusion protein. These models were not previously described. Yagnik
et al. (2000), taught that HCV E2 fits the scaffold of a complete
class II fusion protein. Lescar and co-workers (2001) stated that
their structural determinations of SFV E1, which established the
existence of a second class of fusion proteins, "indeed support the
proposed model of the hepatitis C virus envelope protein E2 which
was based on the 3D structure of the flavivirus envelope protein
E." In contrast our model indicated that HCV E1 is class II
although not similar to that previously described. Although there
are sequence and structural similarities between HCV E2 and TBEV E,
these similarities are limited to the C-terminal portions of these
proteins, and are different than those proposed previously (Yagnik
et al., 2000).
7. EXAMPLE
Pestivirus E2 is a Truncated Class II Fusion Protein
[0063] To provide additional evidence for the HCV E1 class II
fusion protein model, we determined whether the fusion proteins of
the third Flaviviridae genus, pestiviruses, might share
structural/sequential similarities with fusion proteins of members
of the flavivirus and hepacivirus genera. Pestiviruses encode three
envelope glycoproteins, E.sup.rns, E1 and E2. E.sup.rns, a secreted
protein with RNAse activity, does not have a hydrophobic
transmembrane anchor domain. E.sup.rns does possess a C-terminal
charged amphipathic segment that can mediate translocation of
E.sup.rns across bilayer membranes (Langedijk, 2002). Pestivirus E1
and E2 both have C-terminal hydrophobic domains that could function
as transmembrane anchors. Therefore, we postulated that either
pestivirus E1 or E2 must be the pestivirus fusion protein.
[0064] A putative fusion peptide (aa 818-828) is present in CSFV
E2, containing a consensus sequence with aromatic and hydrophobic
amino acids located between two cysteine residues (FIG. 1). The
cysteine residues as well as the sequences in between are highly
conserved among pestiviruses, as is true of fusion peptides from
other enveloped RNA viruses of class I and II (not shown). Although
statistically significant alignments were not detected between the
N-terminus of CSFV E2 and TBEV E (or between other flaviviruses), a
significant alignment (p<0.01) was detected between CSFV E2 (aa
792-835) and HCV E1 (aa 253-294) in this region (FIG. 1B).
Furthermore, sequences flanking the putative fusion peptide were
predicted to form .beta. sheets by both Chou-Fasman and
Robson-Garnier analyses (supplemental data). A significant
alignment (p<0.05) between CSFV E2 (aa 841-913) and HCV E1 (aa
301-383) was also determined. By extension, the central portion of
CSFV E2 is predicted to structurally resemble domain II of TBEV E.
A significant alignment (p<0.005) was detected between amino
acids 914-1018 of CSFV E2 and a sequence in domain III of TBEV E
(aa 587-685) (FIG. 1B). There was also a significant similarity
(p<0.005) of this region of CSFV E2 (aa 914-1123) with a
sequence (aa 549-743) in the region of HCV E2 that aligns with TBEV
domain III. In addition, TMpred confirmed that the hydrophobic
C-terminal domain of CSFV E2 has a high propensity to span the
lipid bilayer (score: 1137). Like the transmembrane domains of HCV
E1/E2 and TBEV TM1, the putative transmembrane anchor of CSFV E2
has a central positive charge.
[0065] On the basis of the regions of significant sequence
similarities between CSFV E2, HCV E1/E2 and TBEV E, coupled with
the internal location of a possible fusion peptide, we conclude
that relative to TBEV E, CSFV E2 is lacking a portion of domain I
including segments corresponding to .beta. sheets E.sub.o through
I.sub.o. CSFV E2 also appears to contain a somewhat shorter segment
relative to TBEV E in the pre-anchor domain, i.e. the sequence
between the alignment with TBEV E domain III and the transmembrane
domain (FIG. 1B). No leucine zipper is evident in the pre-anchor of
CSFV E2. A three dimensional model of CSFV E2 (FIG. 2C) confirms
that the alignment in FIG. 1 is plausible. Each of the cysteine
residues is in proximity to other cysteine residues and potentially
form dicysteine bridges. Like HCV E1, CSFV E2 conforms to the
structure of a truncated class II fusion protein, albeit with fewer
truncations relative to flavivirus E than HCV E1. Because E2 is
conserved among the pestivirus genus, the similarities of CSFV E2
with TBEV E extend to other pestiviruses.
[0066] None of the E1 envelope glycoproteins of any pestivirus bear
any significant sequence similarities to any sequenced flavivirus E
protein. Immature flavivirus virions contain a precursor, prM, to
the small membrane protein M. prM is cleaved in the endoplasmic
reticulum by furin or by a furin-like protease during virus release
to produce the mature M protein localized on the surface of
flavivirus virions (Stadler et al., 1997). A sequence (amino acids
173-256) of CSFV E1 has similarity (p=0.030) to amino acids 583-654
of TBEV prM (FIG. 3A). CSFV E1 does not contain the sequence RXR/KR
(SEQ ID NO:37), the furin consensus cleavage site. CSFV E1 also
does not contain an identifiable fusion peptide, although TMpred
predicts a significant transmembrane spanning domain in the first
third of CSFV E1. Like the transmembrane domains of TBEV E, HCV E1
and E2 and CSFV E2, and TBEV prM (TMpred score=1828), the
C-terminus of CSFV E1 is predicted to form a membrane spanning
domain (TMpred score=1884) with a central positive charge.
[0067] 7.1. Materials and Methods
[0068] The Alfort 187 strain of classical swine fever virus, aka
hog cholera virus (CAA61161) was used as the prototype of the
pestivirus genus of the family Flaviviridae. Type species of other
pestiviruses, including bovine viral diarrhea virus (BVDV) genotype
1, aka pestivirus type 1, strain NADL (CAB91847) and border disease
virus strain BD31 (AAB37578), were used in other comparisons.
Proteomics computational methods were as described in 6.1.
[0069] 7.2. Results and Discussion
[0070] Pestivirus E2 proteins are truncated class II fusion
proteins, although with fewer truncations relative to flavivirus E
than hepacivirus E1.
8. EXAMPLE
Gene Order of Flaviviridae Genomes
[0071] Genes that encode proteins with similar functions may be
present in similar locations in genomes of different members of the
Flaviviridae family. The positive-polarity single-stranded RNA
genomes of all members of the Flaviviridae are translated into a
single large polyprotein that is subsequently cleaved by viral and
cellular proteases into functional proteins. The order (from N to C
terminus) of proteins in the polyproteins of TBEV and other members
of the flavivirus genus is C-prM-E-nonstructurals (C: capsid), and
the order of proteins in the polyproteins of hepaciviruses is
C-E1-E2-p7-nonstructurals (FIG. 4). The 5' portion of the
flavivirus E gene encodes the fusion peptide in domain II of the E
protein, whereas the receptor binding domain of E is probably
located in domain III encoded by the 3' portion of the E gene
(Crill and Roehrig, 2001; Mandl et al., 2000). Fusion and receptor
functions may reside in two different HCV proteins, E1 and E2
respectively, occurring in the same order as the domains of
flavivirus E that carry out these functions (FIG. 4). Hepacivirus
E1 and E2 may have arisen by insertion of a transmembrane anchor
and variable domains, including hypervariable region 1 (HVR-1, FIG.
1), into the ancestral E gene. Alternatively, HCV E1 could have
evolved into a separate fusion protein from an ancestral prM, with
concurrent lost of the fusion peptide and fusion functions in E2.
The sequence similarities between TBEV E and HCV E1 and E2,
however, do not favor this latter possibility.
[0072] The order of proteins in pestivirus polyproteins is
Npro-C-Erns-E1-E2-p7-nonstructurals. Pestiviruses encode two
proteins, Npro and E.sup.rns, with no obvious homologs among
members of the other two Flaviviridae genera. Pestivirus E1 and E2
are similar in sequence to flavivirus M and E, respectively. Like
TBEV E, pestivirus E2 may serve both as fusion protein and receptor
binding protein. These functions are carried out by TBEV E domains
II and III that appear to be represented by similar structures in
pestivirus E2 (FIG. 4). TBEV PrM/M functions to protect internal
cellular membranes from fusion mediated by E2, and it is possible
that pestivirus E1 serves the same function for E2, the
fusion/receptor protein. Excepting Npro and E.sup.rns, the order of
structural proteins with sequence and other similarities is
analogous in pestiviruses and flavivirus polyproteins.
[0073] TBEV E has two hydrophobic C-terminal transmembrane domains,
TM1 and TM2 (FIG. 1). Hepaciviruses and pestiviruses encode a small
hydrophobic peptide, "p7", which could associate with cellular or
viral membranes. The cleavage that produces p7 is inefficient and
delayed, and therefore much of HCV E2 and pestivirus E2 are present
in the cell as uncleaved E2-p7 precursors (Harada, Tautz, and
Thiel, 2000). The p7 gene is located in a similar genomic location
and could have evolved from the sequence encoding the second
transmembrane domain, TM2, of flavivirus E (FIG. 4). The consensus
Flaviviridae genome can therefore be represented as
X1-C-X2-M-fusion-binding-TM1-TM2-nonstructurals-3', where X 1 and
X2 represents inserted sequences in pestiviruses, N.sup.pro and
E.sup.rns, respectively, M represents flavivirus prM/M-pestivirus
E1 and TM2 is the second transmembrane domain of flaviviruses and
p7 of hepaciviruses and pestiviruses. These similarities in gene
order and functions support the hypothesis that E1 is the fusion
protein of HCV.
[0074] 8.1. Materials and Methods
[0075] Prototype strains of representatives of the Flaviviridae as
described in 6.1 and 7.1 were used for sequence comparisons.
[0076] 8.2. Results and Discussion
[0077] Hepaciviruses, like alphaviruses, appear to use one envelope
protein for attachment (E2) and another for fusion (E1). In
contrast, E glycoproteins of TBEV, dengue virus, and other members
of the flavivirus genus mediate both receptor binding and membrane
fusion functions. E2 functions as one of the pestivirus
receptor-binding protein (Hulst and Moormann, 1997), and if the
current analysis is correct also carries out the virion:cell fusion
function. In addition to E, flaviviruses encode a membrane protein
prM whose functions may include shielding of cellular membranes
from the fusion peptide of E (Kuhn et al., 2002). Functions of the
flavivirus small membrane protein may be vested in E1 of
pestiviruses, which has significant sequence similarity with
flavivirus prM. Mature flavivirus virions contain prM that has been
cleaved to M. Unlike M, pestivirus E1 does not associate with the
virion envelope as a precursor protein and lacks a furin cleavage
site.
[0078] The Flavivirus fusion protein structures and functional
domains described here are supported by the observations that
envelope glycoproteins with significant sequence similarities, HCV
E1/2, TBEV E and pestivirus E2 and TBEV prM and pestivirus E1 are
in analogous locations in the polyproteins encoded by the three
genera of the Flaviviridae. These results suggest that members of
the Flavivirus family may have a common ancestor. Divergence of the
genes for the fusion proteins within the three genera of this
family may have occurred either through acquisition of sequences
and/or lose of sequences in a cassette manner constrained by the
domain organization of class II fusion proteins.
9. EXAMPLE
Membrane Interfacial Domains in a Class I Fusion Protein and HCV
E1
[0079] Although the overall structures of class I and II fusion
proteins are distinct, they may share structural/functional
characteristics in the parts of the molecules that interact with
and disrupt bilayer membranes. It is well established that class I
fusion proteins have a fusion peptide at the amino terminus of the
molecule that is critical for fusion (Gallaher, 1987; Gallaher,
1996; Gallaher et al., 1989; Gallaher, DiSimone, and Buchmeier,
2001). Class II fusion proteins have an internal fusion peptide
that are located after secondary structural folding at distal
locations from the transmembrane anchor (Kuhn et al., 2002; Lescar
et al., 2001; Rey et al., 1995). To provide further support for the
proposed models of HCV E1 and pestivirus E2, we used another
proteomics computational tool to compare other potential membrane
interactive domains in the proteins with the HIV-1 transmembrane
glycoprotein (TM), a class I fusion protein. Besides fusion
peptides, another motif in class I fusion proteins that can be
important in virus:cell fusion is an aromatic amino acid rich motif
proximal to the anchor (FIG. 5A, amino acids 667-683) (Suarez et
al., 2000). The pre-anchor domains of class I fusion proteins are
not highly hydrophobic according to the Kyte-Doolittle hydropathy
prediction algorithm, however, these domains have a tendency to
partition into bilayer membranes, as revealed by analyses using the
Wimley-White interfacial hydrophobicity scale (Suarez et al., 2000;
Wimley and White, 1996). HCV E1 contains three domains that produce
significant Wimley-White partition scores using Membrane Protein
eXplorer (Jaysinghe, Hristova, and White, 2000). One of these is
the transmembrane anchor (aa 361-372). The other two sequences with
significant Wimley-White partition scores are located immediately
following the fusion peptide (aa 284-300) and at a location (aa
321-340) that the model in FIG. 2B predicts to be near the bilayer
membrane (FIG. 5B).
[0080] 9.1. Materials and Methods
[0081] Sequences with a propensity to partition into the lipid
bilayer were identified with Membrane Protein eXplorer from the
Stephen White laboratory (Jaysinghe, Hristova, and White, 2000)
using default settings.
[0082] 9.2. Results and Discussion
[0083] These two HCV E1 domains, in conjunction with the fusion
peptide and the transmembrane anchor, potentially form a continuous
track of membrane interactive regions that could channel the
movement of lipids during virion:cell fusion. These Wimley-White
partition analyses thus provide additional support for the proposal
that E1 is the fusion protein of HCV.
10. EXAMPLE
Identification of Peptides that Inhibit Fusion/Infectivity Mediated
by HCV Envelope Proteins
[0084] The membrane fusogenic envelope glycoproteins of
Flaviviruses share several common structural features, including
"fusion peptides" and globular domain structures consisting mostly
of antiparallel .beta. sheets. Furthermore, the E1 protein of HCV
and the E proteins of DEN, WNV and YFV each have several motifs
with a high propensity to interact with bilayer membranes as
revealed by algorithms employing the Wimley-White interfacial
hydrophobicity scale. These structural features and membrane
interfacial motifs are presumably important in Flavivirus fusion,
entry and infection and may represent targets to develop peptide
drugs against Flavivirus infection.
[0085] 10.1. Materials and Methods
[0086] To overcome the lack of a conventional cell culture system
for the propagation of HCV, infectious pseudotype viruses
expressing HCV envelope glycoproteins have been generated (Hsu et
al., 2003). Pseudotypes with HIV core proteins and HCV envelope
proteins were generated by cotransfection of 293-T cells with equal
amounts of plasmids expressing HCV E1 and E2 of strain H77 and the
HIV envelope-defective proviral genome, pNL4.3.Luc.R.sup.-E.sup.-
(Pohlmann et al., 2003). Peptides from an 18mer peptide set,
overlapping by 7-10 amino acids and representing the entire amino
acid sequence of E1 of HCV strain H77, were solubilized in 20%
DMSO, diluted (final DMSO concentration <2%). Peptides were
incubated on ice for 30 minutes with p24 antigen-normalized HCV
pseudotype viral supernatants. The average concentration of
peptides was .about.25 .mu.M, however, actual concentrations of
some peptides in solution were 10 .mu.M or less due to low
solubility in DMSO (marked by asterisk in Table 5). Supernatants
were also treated with DMSO vehicle alone or with a Mab (monoclonal
antibody) to HCV E2 known to neutralize pseudotype infectivity. HCV
peptides, vehicle, and anti-E2 MAb were also incubated with
pseudotypes expressing murine leukemia virus (MLV) envelope
proteins and HIV capsid proteins to control for cytotoxicity.
Peptide treated and control HCV and MLV pseudotypes were added to
cells, which were incubated at 37.degree. C. for 72 h. Cell lysates
were then tested for luciferase activity as described (Hsu et al.,
2003).
[0087] 10.2. Results and Discussion
[0088] Four HCV E1 peptides demonstrated greater than 70%
inhibition of HCV pseudotype infectivity, with one (peptide 54)
reducing HCV pseudotype infectivity by >99.9% (Table 5, FIG.
5B). Two of the peptides (66 and 70) correspond to sequences with a
high propensity to interact with the surface of bilayer membranes,
as determined by application of the Wimley-White interfacial
hydrophobicity scale. Peptide 66 also inhibited infection by the
HIV(MLV) pseudotype by greater that 50% suggesting either that this
peptide is a general inhibitor of viral fusion or that it is
cytotoxic. The other two inhibitory peptides (54 and 74) represent
sequences of HCV E1 predicted to "fold" over and interact with the
portion of E1 displaying high Wimley-White interfacial
hydrophobicity scores (FIG. 5B). The postulated folding over of
these domains was marked by arrows in the original published figure
(FIG. 5 of Garry and Dash, 2003). These results demonstrate the
potential of peptides as antiHCV drugs, and indicate that similar
strategies can identify peptides that inhibit fusion and
infectivity of other Flaviviruses.
TABLE-US-00005 TABLE 5 Identification of lead peptides that inhibit
infectivity mediated by HCV envelope proteins. Peptide Percent
Percent number .sup..dagger-dbl.H77-E1E2.dagger. inhibition
.sup..sctn.MLV.dagger. inhibition 52 133,259 -17.16 533,179 -21.4
53 113,469 0.23 443,528 -9.95 54 74 99.93 280,113 36.22 55 112,470
1.12 447,957 -2.00 56 65,612 42.32 433,459 1.30 57 169,860 -49.35
331,852 24.44 58 118,767 -4.42 329,895 24.98 59 91,794 19.29
446,063 -1.57 60 98,766 13.16 340,384 22.49 61 148,796 -30.83
423,925 3.47 62 115,966 -1.96 415,014 5.50 63 57,915 49.08 438,440
0.16 64 113,108 0.55 316,948 27.83 65* 87,726 22.87 491,789 -11.98
66 23,387 79.46 189,683 56.81 67 64,601 43.20 357,577 28.58 68
79,297 31.28 498,991 -13.62 69* 196,922 -73.14 354,027 19.39 70
15,717 86.19 553,120 -25.95 71 83,489 26.60 533,765 -21.54 72
75,763 33.39 392,680 10.58 73 100,666 11.49 433,001 1.40 74 32,888
71.09 467,876 -6.54 75 113,359 0.32 420,026 4.36 76 96,283 15.34
473,757 -7.88 77 56,425 50.39 321,076 26.89 78* 137,700 -21.07
402,953 8.24 79 101,702 10.58 740,034 -68.51 Vehicle 113,733 --
439,158 -- anti-E2 73 99.93 349,113 21.50 .sup..dagger-dbl.H77-E1E2
is the pseudotype expressing envelope glycoproteins E1 and E2 of
the H77 strain of HCV. .sup..sctn.MLV is a similar pseudotype
expressing the envelope glycoprotein of murine leukemia virus and
serves as a peptide control. .dagger.The numbers represent the
number of luciferase units (lumens) produced after infection by
either the HCV or the MLV pseudotype in the presence of the peptide
at a concentration of ~25 .mu.M.
TABLE-US-00006 TABLE 6 Sequence and Location of peptides shown in
Table 5. Peptide Peptide Number Location Amino acid sequence FIP
overlap 52 183-200 SCLTVPASAYQVRNSSGL (SEQ ID NO:38) 53 190-207
SAYQVRNSSGLYHVTNDC (SEQ ID NO:39) HCV E1 FIP1 54 197-214
SSGLYHVTNDCPNSSIVY (SEQ ID NO:40) HCV E1 FIP1 55 204-221
TNDCPNSSVVYEAADAIL (SEQ ID NO:41) HCV E1 FIP1 56 211-228
SIVYEAADAILHTPGCVP (SEQ ID NO:42) 57 218-235 DAILHTPGCVPCVREGNA
(SEQ ID NO:43) 58 225-242 GCVPCVREGNASRCWVAV (SEQ ID NO:44) 59
232-249 WVAVTPTVATRDGKLPTT (SEQ ID NO:45) 60 239-256
WVAVTPTVATRDGKLPTT (SEQ ID NO:46) 61 246-263 VATRDGKLPTTQLRRHID
(SEQ ID NO:47) 62 253-270 LPTTQLRRHIDLLVGSAT (SEQ ID NO:48) 63
260-277 RHIDLLVGSATLCSALYV (SEQ ID NO:49) 64 267-284
GSATLCSALYVGDLCGSV (SEQ ID NO:)50 HCV E1 FIP2 65 274-291
ALYVGDLCGSVFLVGQLF (SEQ ID NO:51) HCV E1 FIP2 66 281-298
CGSVFLVGQLFTFSPRHH (SEQ ID NO:52) HCV E1 FIP2/3 67 288-305
GQLFTFSPRHHWTTQDCN (SEQ ID NO:53) HCV E1 FIP3 68 295-312
PRHHWTTQDCNCSIYPGH (SEQ ID NO:54) HCV E1 FIP3 69 302-319
QDCNCSIYPGHITGHRMA (SEQ ID NO:55) HCV E1 FIP3 70 309-326
YPGHITGHRMANMMMNW (SEQ ID NO:56) HCV E1 FIP3/4 71 316-333
HRMANMMMNWSPTAALV (SEQ ID NO:57) HCV E1 FIP3/4 72 323-340
MMNWSPTAALVVAQLLRI (SEQ ID NO:58) HCV E1 FIP4 73 330-347
AALVVAQLLRIPQAIMDM (SEQ ID NO:59) HCV E1 FIP4 74 337-354
LLRIPQAIMDMIAGAHWG (SEQ ID NO:60) HCV E1 FIP4 75 344-361
IMDMIAGAHWGVLAGIKY (SEQ ID NO:61) HCV E1 FIP4 76 351-368
AHWGVLAGIKYFSMVGNW (SEQ ID NO:62) HCV E1 FIP4 77 359-375
GIKYFSMVGNWAKVLVVL (SEQ ID NO:63) 75 365-382 VGNWAKVLVVLLLFAGVD
(SEQ ID NO:64) 79 372-389 LVVLLLFAGVDAETHVTG (SEQ ID NO:65)
[0089] The present invention is not to be limited in scope by the
specific embodiments described herein. Indeed, various
modifications of the invention in addition to those described
herein will become apparent to those skilled in the art from the
foregoing description and accompanying figures. Such modifications
are intended to fall within the scope of the claims. Various
publications are cited herein, the disclosures of each of which is
incorporated by reference in its entirety. Citation or
identification of any reference in any section of this application
shall not be construed as an admission that such reference is
available as prior art to the present invention.
REFERENCES
[0090] Each of the following is herein incorporated by reference in
its entirety. [0091] CHAN, D. C., FASS, D., BERGER, J. M., and KIM,
P. S. (1997). Core structure of gp41 from the HIV envelope
glycoprotein. Cell 89, 263-73. [0092] FLINT, M., THOMAS, J. M.,
MAIDENS, C. M., SHOTTON, C., LEVY, S., BARCLAY, W. S., and
MCKEATING, J. A. (1999). Functional analysis of cell
surface-expressed hepatitis C virus E2 glycoprotein. J Virol 73,
6782-90. [0093] GALLAHER, W. R. (1987). Detection of a fusion
peptide sequence in the transmembrane protein of human
immunodeficiency virus. Cell 50, 327-8. [0094] GALLAHER, W. R.
(1996). Similar structural models of the transmembrane
glycoproteins of Ebola and avian sarcoma viruses. Cell 85, 1-2.
[0095] GALLAHER, W. R., BALL, J. M., GARRY, R. F., GRIFFIN, M. C.,
and MONTELARO, R. C. (1989). A general model for the transmembrane
proteins of HIV and other retroviruses. AIDS Res Hum Retro 5,
431-40. [0096] GALLAHER, W. R., DISIMONE, C., and BUCHMEIER, M. J.
(2001). The viral transmembrane superfamily: possible divergence of
Arenavirus and Filovirus glycoproteins from a common RNA virus
ancestor. BMC Microbiol 1, 1. [0097] GARRY, R. F. and DASH S.
(2003). Proteomics computational analysis suggest that hepatitis C
virus E1 and pestivirus E2 envelope glycoproteins are truncated
class II fusion proteins. Virology 307, 255-65. [0098] HOFFMAN-LA
ROCHE, and TRIMERIS. (2002). Roche and Trimeris announce 24-week
results from second pivotal study of HIV fusion inhibitor T-20.
trimeris.com/news/pr/2002/020516.html. [0099] HSU, M., ZHANG, J.,
FLINT, M., LOGVINOFF, C., CHENG-MAYER, C., RICE, C. M., AND
MCKEATING, J. A. (2003). Hepatitis C virus glycoproteins mediate
pH-dependent cell entry of pseudotyped retroviral particles. Proc
Natl Acad Sci USA 100, 7271-6. [0100] JAYSINGHE, S., HRISTOVA, K.,
and WHITE, S. H. (2000). Membrane Protein Explorer.
http://blanco.biomol.uci.edu/mpex. [0101] KUHN, R. J., ZHANG, W.,
ROSSMANN, M. G., PLETNEV, S. V., CORVER, J., LENCHES, E., JONES, C.
T., MUKHOPADHYAY, S., CHIPMAN, P. R., STRAUSS, E. G., BAKER, T. S.,
and STRAUSS, J. H. (2002). Structure of dengue virus: implications
for flavivirus organization, maturation, and fusion. Cell 108,
717-25. [0102] LESCAR, J., ROUSSEL, A., WIEN, M. W., NAVAZA, J.,
FULLER, S. D., WENGLER, G., and REY, F. A. (2001). The fusion
glycoprotein shell of Semliki Forest virus: an icosahedral assembly
primed for fusogenic activation at endosomal pH. Cell 105, 137-48.
[0103] MALASHKEVICH, V. N., SCHNEIDER, B. J., MCNALLY, M. L.,
MILHOLLEN, M. A., PANG, J. X., and KIM, P. S. (1999). Core
structure of the envelope glycoprotein GP2 from Ebola virus at
1.9-A resolution. Proc Natl Acad Sci USA 96, 2662-7. [0104]
QURESHI, N., COY, D., GARRY, R., and HENDERSON L A (1990).
Characterization of a putative cellular receptor for HIV-1
transmembrane glycoprotein using synthetic peptides. AIDS 4,
553-558. [0105] REY, F. A., HEINZ, F. X., MANDL, C., KUNZ, C., and
HARRISON, S. C. (1995). The envelope glycoprotein from tick-borne
encephalitis virus at 2 A resolution. Nature 375, 291-8. [0106]
SUAREZ, T., GALLAHER, W. R., AGIRRE, A., GONI, F. M., and NIEVA, J.
L. (2000). Membrane interface-interacting sequences within the
ectodomain of the human immunodeficiency virus type 1 envelope
glycoprotein: putative role during viral fusion. J Virol 74,
8038-47. [0107] WEISSENHORN, W., CARFI, A., LEE, K. H., SKEHEL, J.
J., and WILEY, D. C. (1998). Crystal structure of the Ebola virus
membrane fusion subunit, GP2, from the envelope glycoprotein
ectodomain. Mol Cell 2, 605-16. [0108] WEISSENHORN, W., WHARTON, S.
A., CALDER, L. J., EARL, P. L., MOSS, B., ALIPRANDIS, E., SKEHEL,
J. J., and WILEY, D. C. (1996). The ectodomain of HIV-1 env subunit
gp41 forms a soluble, alpha-helical, rod-like oligomer in the
absence of gp120 and the N-terminal fusion peptide. EMBO J 15,
1507-14. [0109] WILD, C., GREENWELL, T., and MATTHEWS, T. (1993). A
synthetic peptide from HIV-1 gp41 is a potent inhibitor of
virus-mediated cell-cell fusion. AIDS Res Hum Retro 9, 1051-3.
[0110] WILD, C. T., SHUGARS, D. C., GREENWELL, T. K., MCDANAL, C.
B., and MATTHEWS, T. J. (1994). Peptides corresponding to a
predictive alpha-helical domain of human immunodeficiency virus
type 1 gp41 are potent inhibitors of virus infection. Proc Natl
Acad Sci USA 91, 9770-4. [0111] WILSON, I. A., SKEHEL, J. J., and
WILEY, D. C. (1981). Structure of the haemagglutinin membrane
glycoprotein of influenza virus at 3 A resolution. Nature 289,
366-73. [0112] YAGNIK, A. T., LAHM, A., MEOLA, A., ROCCASECCA, R.
M., ERCOLE, B. B., NICOSIA, A., and TRAMONTANO, A. (2000). A model
for the hepatitis C virus envelope glycoprotein E2. Proteins 40,
355-66
Sequence CWU 1
1
75130PRTArtificial SequenceSynthetic Peptide 1Tyr Gln Val Arg Asn
Ser Ser Gly Leu Tyr His Val Thr Asn Asp Cys1 5 10 15Pro Asn Ser Ser
Ile Val Tyr Glu Ala Ala Asp Ala Ile Leu20 25 30234PRTArtificial
SequenceSynthetic Peptide 2Cys Ser Ala Leu Tyr Trp Val Gly Asp Leu
Cys Gly Ser Val Phe Leu1 5 10 15Val Gly Gln Leu Phe Thr Phe Ser Pro
Arg Arg His Trp Thr Thr Gln20 25 30Asp Cys336PRTArtificial
SequenceSynthetic Peptide 3Ser Pro Arg Arg His Trp Thr Thr Gln Asp
Cys Asn Cys Ser Ile Tyr1 5 10 15Pro Gly His Ile Thr Gly His Arg Met
Ala Trp Asp Met Met Met Asn20 25 30Trp Ser Pro
Thr35442PRTArtificial SequenceSynthetic Peptide 4Met Met Met Asn
Trp Ser Pro Thr Ala Ala Leu Leu Arg Ile Pro Gln1 5 10 15Ala Ile Met
Asp Met Ile Ala Gly Ala His Trp Gly Val Leu Ala Gly20 25 30Ile Lys
Tyr Phe Ser Met Val Gly Asn Trp35 40530PRTArtificial
SequenceSynthetic Peptide 5Arg Val Thr Asp Pro Asp Thr Asn Thr Thr
Ile Leu Thr Asn Cys Cys1 5 10 15Gln Arg Asn Gln Val Ile Tyr Cys Ser
Pro Ser Thr Cys Leu20 25 30635PRTArtificial SequenceSynthetic
Peptide 6Arg Asp Phe Val Glu Gly Val Ser Gly Gly Ser Trp Val Asp
Ile Val1 5 10 15Leu Glu His Gly Ser Cys Val Thr Thr Met Ala Lys Asn
Lys Pro Thr20 25 30Leu Asp Phe35735PRTArtificial SequenceSynthetic
Peptide 7Arg Asp Phe Ile Glu Gly Ala Ser Gly Ala Thr Trp Val Asp
Leu Val1 5 10 15Leu Glu Gly Asp Ser Cys Leu Thr Ile Met Ala Asn Asp
Lys Pro Thr20 25 30Leu Asp Val35835PRTArtificial SequenceSynthetic
Peptide 8Arg Asp Phe Ile Glu Gly Val His Gly Gly Thr Trp Val Ser
Ala Thr1 5 10 15Leu Glu Gln Asp Lys Cys Val Thr Val Met Ala Pro Asp
Lys Pro Ser20 25 30Leu Asp Ile35935PRTArtificial SequenceSynthetic
Peptide 9Arg Asp Phe Leu Glu Gly Val Ser Gly Ala Thr Trp Val Asp
Leu Val1 5 10 15Leu Glu Gly Asp Ser Cys Val Thr Ile Met Ser Lys Asp
Lys Pro Thr20 25 30Ile Asp Val351035PRTArtificial SequenceSynthetic
Peptide 10Gly Gln Leu Ala Cys Lys Glu Asp Tyr Arg Tyr Ala Ile Ser
Ser Thr1 5 10 15Asn Glu Ile Gly Leu Leu Gly Ala Gly Gly Leu Thr Thr
Thr Trp Lys20 25 30Glu Tyr Asn351135PRTArtificial SequenceSynthetic
Peptide 11Gly His Leu Asp Cys Lys Pro Glu Phe Ser Tyr Ala Ile Ala
Lys Asp1 5 10 15Glu Arg Ile Gly Gln Leu Gly Ala Glu Gly Leu Thr Thr
Thr Trp Lys20 25 30Glu Tyr Ser351235PRTArtificial SequenceSynthetic
Peptide 12Gly Glu Phe Ala Cys Arg Glu Asp His Arg Tyr Ala Leu Ala
Lys Thr1 5 10 15Lys Glu Ile Gly Pro Leu Gly Ala Glu Ser Leu Thr Thr
Thr Trp Thr20 25 30Asp Tyr Gln351334PRTArtificial SequenceSynthetic
Peptide 13Thr Cys Asp Ala Leu Asp Ile Gly Glu Leu Cys Gly Ala Cys
Val Leu1 5 10 15Val Gly Asp Trp Leu Val Arg His Trp Leu Ile His Ile
Asp Leu Asn20 25 30Glu Thr1434PRTArtificial SequenceSynthetic
Peptide 14Lys Arg Phe Val Cys Lys His Ser Met Val Asp Arg Gly Trp
Gly Asn1 5 10 15Gly Cys Gly Leu Phe Gly Lys Gly Gly Ile Val Thr Cys
Ala Met Phe20 25 30Thr Cys1534PRTArtificial SequenceSynthetic
Peptide 15Ser Ser Tyr Val Cys Lys Gln Gly Phe Thr Asp Arg Gly Trp
Gly Asn1 5 10 15Gly Cys Gly Leu Phe Gly Lys Gly Ser Ile Asp Thr Cys
Ala Lys Phe20 25 30Ser Cys1634PRTArtificial SequenceSynthetic
Peptide 16Gly Asp Asn Ala Cys Lys Arg Thr Tyr Ser Asp Arg Gly Trp
Gly Asn1 5 10 15Gly Cys Gly Leu Phe Gly Lys Gly Ser Ile Val Ala Cys
Ala Lys Phe20 25 30Thr Cys1734PRTArtificial SequenceSynthetic
Peptide 17Pro Ala Phe Val Cys Arg Gln Gly Val Val Asp Arg Gly Trp
Gly Asn1 5 10 15Gly Cys Gly Leu Phe Gly Lys Gly Ser Ile Asp Thr Cys
Ala Lys Phe20 25 30Ala Cys1834PRTArtificial SequenceSynthetic
Peptide 18Lys Gly Lys Tyr Asn Thr Thr Leu Leu Asn Gly Ser Ala Phe
Tyr Leu1 5 10 15Val Cys Pro Ile Gly Trp Thr Gly Val Ile Glu Cys Thr
Ala Val Ser20 25 30Pro Thr1934PRTArtificial SequenceSynthetic
Peptide 19Arg Gly Lys Phe Asn Thr Thr Leu Leu Asn Gly Pro Ala Phe
Gln Met1 5 10 15Val Cys Pro Ile Gly Trp Thr Gly Thr Val Ser Cys Thr
Ser Phe Asn20 25 30Met Asp2034PRTArtificial SequenceSynthetic
Peptide 20Arg Gly Lys Tyr Asn Ala Thr Leu Leu Asn Gly Ser Ala Phe
Gln Leu1 5 10 15Val Cys Pro Tyr Glu Trp Thr Gly Arg Val Glu Cys Thr
Thr Ile Ser20 25 30Lys Ser2136PRTArtificial SequenceSynthetic
Peptide 21Ile His Ile Asp Leu Asn Glu Thr Gly Thr Cys Tyr Leu Glu
Val Pro1 5 10 15Thr Gly Ile Asp Pro Gly Phe Leu Gly Phe Ile Gly Trp
Met Ala Gly20 25 30Lys Val Glu Ala352236PRTArtificial
SequenceSynthetic Peptide 22Met Val Leu Leu Gln Met Glu Asp Lys Ala
Trp Leu Val His Arg Gln1 5 10 15Trp Phe Leu Asp Leu Pro Leu Pro Trp
Leu Pro Gly Ala Asp Thr Gln20 25 30Gly Ser Asn
Trp352336PRTArtificial SequenceSynthetic Peptide 23Phe Tyr Val Met
Thr Val Gly Ser Lys Ser Phe Leu Val His Arg Glu1 5 10 15Trp Phe His
Asp Leu Ala Leu Pro Trp Thr Ser Pro Ser Ser Thr Ala20 25 30Trp Arg
Asn Arg352436PRTArtificial SequenceSynthetic Peptide 24Ser Tyr Ile
Ala Glu Met Glu Thr Glu Ser Trp Ile Val Asp Arg Gln1 5 10 15Trp Ala
Gln Asp Leu Thr Leu Pro Trp Gln Ser Gly Ser Gly Gly Val20 25 30Trp
Arg Glu Met352536PRTArtificial SequenceSynthetic Peptide 25Tyr Tyr
Val Met Thr Val Gly Thr Lys Thr Phe Leu Val His Arg Glu1 5 10 15Trp
Phe Met Asp Leu Asn Leu Pro Trp Ser Ser Ala Gly Ser Thr Val20 25
30Trp Arg Asn Arg352634PRTArtificial SequenceSynthetic Peptide
26Thr Leu Arg Thr Glu Val Val Lys Thr Phe Arg Arg Asp Lys Pro Phe1
5 10 15Pro His Arg Met Asp Ala Val Thr Thr Thr Val Glu Asn Glu Asp
Leu20 25 30Phe Tyr2734PRTArtificial SequenceSynthetic Peptide 27Thr
Leu Ala Thr Glu Val Val Lys Ile Tyr Lys Arg Thr Lys Arg Phe1 5 10
15Arg Ser Gly Leu Val Ala Thr His Thr Thr Ile Tyr Glu Glu Asp Leu20
25 30Tyr His2833PRTArtificial SequenceSynthetic Peptide 28Thr Leu
Ala Thr Thr Val Val Arg Thr Tyr Arg Arg Ser Lys Pro Phe1 5 10 15Pro
His Arg Gln Gly Ala Ile Thr Gln Lys Asn Leu Gly Glu Asp Leu20 25
30His2942PRTArtificial SequenceSynthetic Peptide 29Trp Met Ala Gly
Lys Val Glu Ala Val Ile Phe Leu Thr Lys Leu Ala1 5 10 15Ser Gln Val
Pro Tyr Ala Ile Ala Thr Met Phe Ser Ser Val His Tyr20 25 30Leu Ala
Val Gly Ala Leu Ile Tyr Tyr Ser35 403042PRTArtificial
SequenceSynthetic Peptide 30Met Ala Ile Leu Gly Asp Thr Ala Trp Asp
Phe Gly Ser Leu Gly Gly1 5 10 15Val Phe Thr Ser Ile Gly Lys Ala Leu
His Gln Val Phe Gly Ala Ile20 25 30Tyr Gly Ala Ala Phe Ser Gly Val
Ser Trp35 403142PRTArtificial SequenceSynthetic Peptide 31Leu Ala
Ala Leu Gly Asp Thr Ala Trp Asp Phe Gly Ser Ile Gly Gly1 5 10 15Val
Phe Asn Ser Ile Gly Lys Ala Val His Gln Val Phe Gly Gly Ala20 25
30Phe Arg Thr Leu Phe Gly Gly Met Ser Trp35 403242PRTArtificial
SequenceSynthetic Peptide 32Leu Ala Val Met Gly Asp Thr Ala Trp Asp
Phe Ser Ser Ala Gly Gly1 5 10 15Phe Phe Thr Ser Val Gly Lys Gly Ile
His Thr Val Phe Gly Ser Ala20 25 30Phe Gln Gly Leu Phe Gly Gly Leu
Asn Trp35 403342PRTArtificial SequenceSynthetic Peptide 33Leu Ala
Ala Leu Gly Asp Thr Ala Trp Asp Phe Gly Ser Val Gly Gly1 5 10 15Val
Phe Thr Ser Val Gly Lys Ala Val His Gln Val Phe Gly Gly Ala20 25
30Phe Arg Ser Leu Phe Gly Gly Met Ser Trp35 403442PRTArtificial
SequenceSynthetic Peptide 34Gln Gln Tyr Met Leu Lys Gly Glu Tyr Gln
Tyr Trp Phe Asp Leu Asp1 5 10 15Val Thr Asp Arg His Ser Asp Tyr Phe
Ala Glu Phe Val Val Leu Val20 25 30Val Val Ala Leu Leu Gly Gly Arg
Tyr Ile35 403542PRTArtificial SequenceSynthetic Peptide 35Gln Gln
Tyr Met Leu Lys Gly Glu Tyr Gln Tyr Trp Phe Asp Leu Glu1 5 10 15Val
Thr Asp His His Arg Asp Tyr Phe Ala Glu Ser Ile Leu Val Val20 25
30Val Val Ala Leu Leu Gly Gly Arg Tyr Val35 403643PRTArtificial
SequenceSynthetic Peptide 36Gln Gln Tyr Met Leu Lys Gly Gln Tyr Gln
Tyr Trp Phe Asp Leu Glu1 5 10 15Val Ile Ser Ser Thr His Gln Ile Asp
Leu Thr Glu Phe Ile Met Leu20 25 30Ala Val Val Ala Leu Leu Gly Gly
Arg Tyr Val35 40375PRTArtificial SequenceSynthetic Peptide 37Arg
Xaa Arg Lys Arg1 53818PRTArtificial SequenceSynthetic Peptide 38Ser
Cys Leu Thr Val Pro Ala Ser Ala Tyr Gln Val Arg Asn Ser Ser1 5 10
15Gly Leu3918PRTArtificial SequenceSynthetic Peptide 39Ser Ala Tyr
Gln Val Arg Asn Ser Ser Gly Leu Tyr His Val Thr Asn1 5 10 15Asp
Cys4018PRTArtificial SequenceSynthetic peptide 40Ser Ser Gly Leu
Tyr His Val Thr Asn Asp Cys Pro Asn Ser Ser Ile1 5 10 15Val
Tyr4118PRTArtificial SequenceSynthetic peptide 41Thr Asn Asp Cys
Pro Asn Ser Ser Val Val Tyr Glu Ala Ala Asp Ala1 5 10 15Ile
Leu4218PRTArtificial SequenceSynthetic peptide 42Ser Ile Val Tyr
Glu Ala Ala Asp Ala Ile Leu His Thr Pro Gly Cys1 5 10 15Val
Pro4318PRTArtificial SequenceSynthetic peptide 43Asp Ala Ile Leu
His Thr Pro Gly Cys Val Pro Cys Val Arg Glu Gly1 5 10 15Asn
Ala4418PRTArtificial SequenceSynthetic peptide 44Gly Cys Val Pro
Cys Val Arg Glu Gly Asn Ala Ser Arg Cys Trp Val1 5 10 15Ala
Val4518PRTArtificial SequenceSynthetic peptide 45Trp Val Ala Val
Thr Pro Thr Val Ala Thr Arg Asp Gly Lys Leu Pro1 5 10 15Thr
Thr4618PRTArtificial SequenceSynthetic peptide 46Trp Val Ala Val
Thr Pro Thr Val Ala Thr Arg Asp Gly Lys Leu Pro1 5 10 15Thr
Thr4718PRTArtificial SequenceSynthetic peptide 47Val Ala Thr Arg
Asp Gly Lys Leu Pro Thr Thr Gln Leu Arg Arg His1 5 10 15Ile
Asp4818PRTArtificial SequenceSynthetic peptide 48Leu Pro Thr Thr
Gln Leu Arg Arg His Ile Asp Leu Leu Val Gly Ser1 5 10 15Ala
Thr4918PRTArtificial SequenceSynthetic peptide 49Arg His Ile Asp
Leu Leu Val Gly Ser Ala Thr Leu Cys Ser Ala Leu1 5 10 15Tyr
Val5018PRTArtificial SequenceSynthetic peptide 50Gly Ser Ala Thr
Leu Cys Ser Ala Leu Tyr Val Gly Asp Leu Cys Gly1 5 10 15Ser
Val5118PRTArtificial SequenceSynthetic peptide 51Ala Leu Tyr Val
Gly Asp Leu Cys Gly Ser Val Phe Leu Val Gly Gln1 5 10 15Leu
Phe5218PRTArtificial SequenceSynthetic peptide 52Cys Gly Ser Val
Phe Leu Val Gly Gln Leu Phe Thr Phe Ser Pro Arg1 5 10 15His
His5318PRTArtificial SequenceSynthetic peptide 53Gly Gln Leu Phe
Thr Phe Ser Pro Arg His His Trp Thr Thr Gln Asp1 5 10 15Cys
Asn5418PRTArtificial SequenceSynthetic peptide 54Pro Arg His His
Trp Thr Thr Gln Asp Cys Asn Cys Ser Ile Tyr Pro1 5 10 15Gly
His5518PRTArtificial SequenceSynthetic peptide 55Gln Asp Cys Asn
Cys Ser Ile Tyr Pro Gly His Ile Thr Gly His Arg1 5 10 15Met
Ala5617PRTArtificial SequenceSynthetic peptide 56Tyr Pro Gly His
Ile Thr Gly His Arg Met Ala Asn Met Met Met Asn1 5 10
15Trp5717PRTArtificial SequenceSynthetic peptide 57His Arg Met Ala
Asn Met Met Met Asn Trp Ser Pro Thr Ala Ala Leu1 5 10
15Val5818PRTArtificial SequenceSynthetic peptide 58Met Met Asn Trp
Ser Pro Thr Ala Ala Leu Val Val Ala Gln Leu Leu1 5 10 15Arg
Ile5918PRTArtificial SequenceSynthetic peptide 59Ala Ala Leu Val
Val Ala Gln Leu Leu Arg Ile Pro Gln Ala Ile Met1 5 10 15Asp
Met6018PRTArtificial SequenceSynthetic peptide 60Leu Leu Arg Ile
Pro Gln Ala Ile Met Asp Met Ile Ala Gly Ala His1 5 10 15Trp
Gly6118PRTArtificial SequenceSynthetic peptide 61Ile Met Asp Met
Ile Ala Gly Ala His Trp Gly Val Leu Ala Gly Ile1 5 10 15Lys
Tyr6218PRTArtificial SequenceSynthetic peptide 62Ala His Trp Gly
Val Leu Ala Gly Ile Lys Tyr Phe Ser Met Val Gly1 5 10 15Asn
Trp6318PRTArtificial SequenceSynthetic peptide 63Gly Ile Lys Tyr
Phe Ser Met Val Gly Asn Trp Ala Lys Val Leu Val1 5 10 15Val
Leu6418PRTArtificial SequenceSynthetic peptide 64Val Gly Asn Trp
Ala Lys Val Leu Val Val Leu Leu Leu Phe Ala Gly1 5 10 15Val
Asp6518PRTArtificial SequenceSynthetic peptide 65Leu Val Val Leu
Leu Leu Phe Ala Gly Val Asp Ala Glu Thr His Val1 5 10 15Thr
Gly66496PRTTick borne encephalitis virus 66Ser Arg Cys Thr His Leu
Glu Asn Arg Asp Phe Val Thr Gly Thr Gln1 5 10 15Gly Thr Thr Arg Val
Thr Leu Val Leu Glu Leu Gly Gly Cys Val Thr20 25 30Ile Thr Ala Glu
Gly Lys Pro Ser Met Asp Val Trp Leu Asp Ala Ile35 40 45Tyr Gln Glu
Asn Pro Ala Lys Thr Arg Glu Tyr Cys Leu His Ala Lys50 55 60Leu Ser
Asp Thr Lys Val Ala Ala Arg Cys Pro Thr Met Gly Pro Ala65 70 75
80Thr Leu Ala Glu Glu His Gln Gly Gly Thr Val Cys Lys Arg Asp Gln85
90 95Ser Asp Arg Gly Trp Gly Asn His Cys Gly Leu Phe Gly Lys Gly
Ser100 105 110Ile Val Ala Cys Val Lys Ala Ala Cys Glu Ala Lys Lys
Lys Ala Thr115 120 125Gly His Val Tyr Asp Ala Asn Lys Ile Val Tyr
Thr Val Lys Val Glu130 135 140Pro His Thr Gly Asp Tyr Val Ala Ala
Asn Glu Thr His Ser Gly Arg145 150 155 160Lys Thr Ala Ser Phe Thr
Ile Ser Ser Glu Lys Thr Ile Leu Thr Met165 170 175Gly Glu Tyr Gly
Asp Val Ser Leu Leu Cys Arg Val Ala Ser Gly Val180 185 190Asp Leu
Ala Gln Thr Val Ile Leu Glu Leu Asp Lys Thr Val Glu His195 200
205Leu Pro Thr Ala Trp Gln Val His Arg Asp Trp Phe Asn Asp Leu
Ala210 215 220Leu Pro Trp Lys His Glu Gly Ala Gln Asn Trp Asn Asn
Ala Glu Arg225 230 235 240Leu Val Glu Phe Gly Ala Pro His Ala Val
Lys Met Asp Val Tyr Asn245 250 255Leu Gly Asp Gln Thr Gly Val Leu
Leu Lys Ala Leu Ala Gly Val Pro260 265 270Val Ala His Ile Glu Gly
Thr Lys Tyr His Leu Lys Ser Gly His Val275 280 285Thr Cys Glu Val
Gly Leu Glu Lys Leu Lys Met Lys Gly Leu Thr Tyr290 295 300Thr Met
Cys Asp Lys Thr Lys Phe Thr Trp Lys Arg Ile Ala Thr Asp305 310 315
320Ser Gly His Asp Thr Val Val Met Glu Val Thr Phe Ser Gly Thr
Lys325 330 335Pro Cys Arg Ile Pro Val Arg Ala Val Ala His Gly Ser
Pro Asp Val340
345 350Asn Val Ala Met Leu Ile Thr Pro Asn Pro Thr Ile Glu Asn Asn
Gly355 360 365Gly Gly Phe Ile Glu Met Gln Leu Pro Pro Gly Asp Asn
Ile Ile Tyr370 375 380Val Gly Glu Leu Ser His Gln Trp Phe Gln Lys
Gly Ser Ser Ile Gly385 390 395 400Arg Val Phe Gln Lys Thr Arg Lys
Gly Ile Glu Arg Leu Thr Val Ile405 410 415Gly Glu His Ala Trp Asp
Phe Gly Ser Ala Gly Gly Phe Leu Ser Ser420 425 430Ile Gly Lys Ala
Val His Thr Val Leu Gly Gly Ala Phe Asn Ser Ile435 440 445Phe Gly
Gly Val Gly Phe Leu Pro Lys Leu Leu Leu Gly Val Ala Leu450 455
460Ala Trp Leu Gly Leu Asn Met Arg Asn Pro Thr Met Ser Met Ser
Phe465 470 475 480Leu Leu Ala Gly Gly Leu Val Leu Ala Met Thr Leu
Gly Val Gly Ala485 490 49567168PRTHepatitis C virus 67Tyr Gln Val
Arg Asn Ser Ser Gly Leu Tyr His Val Thr Asn Asp Cys1 5 10 15Pro Asn
Ser Ser Val Val Tyr Glu Ala Ala Asp Ala Ile Leu His Thr20 25 30Pro
Gly Cys Val Pro Cys Val Arg Glu Gly Asn Ala Ser Arg Cys Trp35 40
45Val Ala Val Thr Pro Thr Val Ala Thr Arg Gly Lys Leu Pro Thr Thr50
55 60Gln Leu Arg Arg His Ile Asp Leu Leu Val Gly Ser Ala Thr Leu
Cys65 70 75 80Ser Ala Leu Tyr Val Gly Asp Leu Cys Gly Ser Val Phe
Leu Val Gly85 90 95Gln Leu Phe Thr Phe Ser Pro Arg His His Trp Thr
Thr Gln Asp Cys100 105 110Asn Cys Ser Ile Tyr Pro Gly His Ile Thr
Gly His Arg Met Ala Trp115 120 125Asn Met Met Met Asn Trp Ser Pro
Thr Ala Ala Leu Val Val Ala Gln130 135 140Leu Leu Arg Ile Pro Gln
Ala Ile Met Asp Met Ile Ala Gly Ala His145 150 155 160Trp Gly Val
Leu Ala Gly Ile Lys16568366PRTClassical swine fever virus 68Gly Gln
Leu Ala Cys Lys Glu Asp Tyr Arg Tyr Ala Ile Ser Ser Thr1 5 10 15Asn
Glu Ile Gly Leu Leu Gly Ala Gly Gly Leu Thr Thr Thr Trp Lys20 25
30Glu Tyr Asn Asp Leu Gln Leu Asn Asp Gly Thr Val Lys Ile Cys Val35
40 45Ala Gly Ser Phe Lys Val Thr Ala Leu Asn Val Val Ser Arg Arg
Tyr50 55 60Val Leu Ala Ser Leu His Lys Lys Ala Leu Pro Ile Ser Val
Thr Phe65 70 75 80Glu Leu Leu Phe Asp Gly Thr Asn Pro Ser Thr Glu
Glu Met Glu Asp85 90 95Asp Phe Gly Phe Gly Leu Cys Pro Phe Asp Thr
Ser Pro Val Val Lys100 105 110Gly Lys Tyr Asn Thr Thr Leu Leu Asn
Gly Ser Ala Phe Tyr Leu Val115 120 125Cys Pro Ile Gly Trp Thr Gly
Val Ile Glu Cys Thr Ala Val Ser Pro130 135 140Thr Thr Leu Arg Thr
Glu Val Val Lys Thr Phe Arg Arg Asp Lys Pro145 150 155 160Phe Pro
His Arg Met Asp Cys Val Thr Thr Thr Val Glu Asn Glu Asp165 170
175Leu Phe Tyr Cys Lys Leu Gly Gly Asn Trp Thr Cys Val Lys Gly
Glu180 185 190Pro Val Val Tyr Thr Gly Gly Val Val Lys Gln Cys Arg
Trp Cys Gly195 200 205Phe Asp Phe Asn Glu Pro Asp Gly Leu Pro His
Tyr Pro Ile Gly Lys210 215 220Cys Ile Leu Ala Asn Glu Thr Gly Tyr
Arg Ile Val Asp Ser Thr Asp225 230 235 240Cys Asn Arg Asp Gly Val
Val Ile Ser Thr Glu Gly Ser His Glu Cys245 250 255Leu Ile Gly Asn
Thr Thr Val Lys Val His Ala Ser Asp Glu Arg Leu260 265 270Gly Pro
Met Pro Cys Arg Pro Lys Glu Ile Val Ser Ser Ala Gly Pro275 280
285Val Arg Lys Thr Ser Cys Thr Phe Asn Tyr Ala Lys Thr Leu Lys
Asn290 295 300Lys Tyr Tyr Glu Pro Arg Asp Ser Tyr Phe Gln Gln Tyr
Met Leu Lys305 310 315 320Gly Glu Tyr Gln Tyr Trp Phe Asp Leu Asp
Val Thr Asp Arg His Ser325 330 335Asp Tyr Phe Ala Glu Phe Val Val
Leu Val Val Val Ala Leu Leu Gly340 345 350Gly Arg Tyr Ile Leu Trp
Leu Ile Val Thr Tyr Ile Val Leu355 360 3656990PRTHepatitis C virus
69Tyr Phe Ser Met Val Gly Asn Trp Ala Lys Val Leu Val Val Leu Leu1
5 10 15Leu Phe Ala Gly Val Asp Ala Glu Thr His Val Thr Gly Gly Asn
Ala20 25 30Gly Arg Thr Thr Ala Gly Leu Val Gly Leu Leu Thr Pro Gly
Ala Lys35 40 45Gln Asn Ile Gln Leu Ile Asn Thr Asn Gly Ser Trp His
Ile Asn Ser50 55 60Thr Ala Leu Asn Cys Asn Glu Ser Leu Asn Thr Gly
Trp Leu Ala Gly65 70 75 80Leu Phe Tyr Gln His Lys Phe Asn Ser Ser85
907089PRTHepatitis C virus 70Gly Cys Pro Glu Arg Leu Ala Ser Cys
Arg Arg Leu Thr Asp Phe Ala1 5 10 15Gln Gly Trp Gly Pro Ile Ser Tyr
Ala Asn Gly Ser Gly Leu Asp Glu20 25 30Arg Pro Tyr Cys Trp His Tyr
Pro Pro Arg Pro Cys Gly Ile Val Pro35 40 45Ala Lys Ser Val Cys Gly
Pro Val Tyr Cys Phe Thr Pro Ser Val Val50 55 60Val Gly Thr Thr Asp
Arg Ser Gly Ala Pro Thr Tyr Ser Trp Gly Ala65 70 75 80Asn Asp Thr
Asp Val Phe Val Leu Asn8571195PRTHepatitis C virus 71Trp Phe Gly
Cys Thr Trp Met Asn Ser Thr Gly Phe Thr Lys Val Cys1 5 10 15Gly Ala
Pro Pro Cys Val Ile Gly Gly Val Gly Asn Asn Thr Leu Leu20 25 30Cys
Pro Thr Asp Cys Phe Arg Lys Tyr Pro Glu Ala Thr Tyr Ser Arg35 40
45Cys Gly Ser Gly Pro Arg Ile Thr Pro Arg Cys Met Val Asp Tyr Pro50
55 60Tyr Arg Leu Trp His Tyr Pro Cys Thr Ile Asn Tyr Thr Ile Phe
Lys65 70 75 80Val Arg Met Tyr Val Gly Gly Val Glu His Arg Leu Glu
Ala Ala Cys85 90 95Asn Trp Thr Arg Gly Glu Arg Cys Asp Leu Glu Asp
Arg Asp Arg Ser100 105 110Glu Leu Ser Pro Leu Leu Leu Ser Thr Thr
Gln Trp Gln Val Leu Pro115 120 125Cys Ser Phe Thr Thr Leu Pro Ala
Leu Ser Thr Gly Leu Ile His Leu130 135 140His Gln Asn Ile Val Asp
Val Gln Tyr Ile Tyr Gly Val Gly Ser Ser145 150 155 160Ile Ala Ser
Trp Ala Ile Lys Trp Glu Tyr Val Val Leu Leu Phe Leu165 170 175Leu
Leu Ala Asp Ala Arg Val Cys Ser Cys Leu Trp Met Met Leu Leu180 185
190Ile Ser Gln19572167PRTTick borne encephalitis virus 72Thr Leu
Ala Ala Thr Val Arg Lys Glu Arg Asp Gly Ser Thr Val Ile1 5 10 15Arg
Ala Glu Gly Lys Asp Ala Ala Thr Gln Val Arg Val Glu Asn Gly20 25
30Thr Cys Val Ile Leu Ala Thr Asp Met Gly Ser Trp Cys Asp Asp Ser35
40 45Leu Ser Tyr Glu Cys Val Thr Ile Asp Gln Gly Glu Glu Pro Val
Asp50 55 60Val Asp Cys Phe Cys Arg Asn Val Asp Gly Val Tyr Leu Glu
Tyr Gly65 70 75 80Arg Cys Gly Lys Gln Glu Gly Ser Arg Thr Arg Arg
Ser Val Leu Ile85 90 95Pro Ser His Ala Gln Gly Glu Leu Thr Gly Arg
Gly His Lys Trp Leu100 105 110Glu Gly Asp Ser Leu Arg Thr His Leu
Thr Arg Val Glu Gly Trp Val115 120 125Trp Lys Asn Lys Leu Leu Ala
Leu Ala Met Val Thr Val Val Trp Leu130 135 140Thr Leu Glu Ser Val
Val Thr Arg Val Ala Val Leu Val Val Leu Leu145 150 155 160Cys Leu
Ala Pro Val Tyr Ala16573194PRTClassical swine fever virus 73Leu Ser
Pro Tyr Cys Asn Val Thr Ser Lys Ile Gly Tyr Ile Trp Tyr1 5 10 15Thr
Asn Asn Cys Thr Pro Ala Cys Leu Pro Lys Asn Thr Lys Ile Ile20 25
30Gly Pro Gly Lys Phe Asp Thr Asn Ala Glu Asp Gly Lys Ile Leu His35
40 45Glu Met Gly Gly His Leu Ser Glu Phe Leu Leu Leu Ser Leu Val
Val50 55 60Leu Ser Asp Phe Ala Pro Glu Thr Ala Ser Ala Leu Tyr Leu
Ile Phe65 70 75 80His Tyr Val Ile Pro Gln Ser His Glu Glu Pro Glu
Gly Cys Asp Thr85 90 95Asn Gln Leu Asn Leu Thr Val Glu Leu Arg Thr
Glu Asp Val Ile Pro100 105 110Ser Ser Val Trp Asn Val Gly Lys Tyr
Val Cys Val Arg Pro Asp Trp115 120 125Trp Pro Tyr Glu Thr Lys Val
Ala Leu Leu Phe Glu Glu Ala Gly Gln130 135 140Val Val Lys Leu Ala
Leu Arg Ala Leu Arg Asp Leu Thr Arg Val Trp145 150 155 160Asn Ser
Ala Ser Thr Thr Ala Phe Leu Ile Cys Leu Ile Lys Val Leu165 170
175Arg Gly Gln Ile Val Gln Gly Val Ile Trp Leu Leu Leu Val Thr
Gly180 185 190Ala Gln74198PRTHuman immunodeficiency virus 74Ala Val
Gly Ile Gly Ala Leu Phe Leu Gly Phe Leu Gly Ala Ala Gly1 5 10 15Ser
Thr Met Gly Ala Ala Ser Met Thr Leu Thr Val Gln Ala Arg Gln20 25
30Ile Leu Ser Gly Ile Val Gln Gln Gln Asn Asn Leu Leu Arg Ala Ile35
40 45Glu Ala Gln Gln His Leu Leu Gln Leu Thr Val Trp Gly Ile Lys
Gln50 55 60Leu Gln Ala Arg Ile Leu Ala Val Glu Arg Tyr Leu Lys Asp
Gln Gln65 70 75 80Leu Leu Gly Ile Trp Gly Cys Ser Gly Lys Leu Ile
Cys Thr Thr Ala85 90 95Val Pro Trp Asn Ala Ser Trp Ser Asn Lys Ser
Leu Glu Gln Ile Trp100 105 110Asn His Thr Thr Trp Met Glu Trp Asp
Arg Glu Ile Asn Asn Tyr Thr115 120 125Ser Leu Ile His Ser Leu Ile
Glu Glu Ser Gln Asn Gln Gln Glu Lys130 135 140Asn Glu Gln Glu Leu
Leu Glu Leu Asp Lys Trp Ala Ser Leu Trp Asn145 150 155 160Trp Phe
Asn Ile Thr Asn Trp Leu Trp Tyr Ile Leu Phe Ile Met Ile165 170
175Val Gly Gly Leu Val Gly Leu Arg Ile Val Phe Ala Val Leu Ser
Ile180 185 190Val Asn Arg Val Arg Gln19575190PRTHepatitis C virus
75Tyr Gln Val Arg Asn Ser Ser Gly Leu Tyr His Val Thr Asn Asp Cys1
5 10 15Pro Asn Ser Ser Val Val Tyr Glu Ala Ala Asp Ala Ile Leu His
Thr20 25 30Pro Gly Cys Val Pro Cys Val Arg Glu Gly Asn Ala Ser Arg
Cys Trp35 40 45Val Ala Thr Pro Thr Val Ala Thr Arg Asp Gly Lys Leu
Pro Thr Thr50 55 60Gln Leu Arg Arg His Ile Asp Leu Leu Val Gly Ser
Ala Thr Leu Cys65 70 75 80Ser Ala Leu Tyr Trp Val Gly Asp Leu Cys
Gly Ser Val Phe Leu Val85 90 95Gly Gln Leu Phe Thr Phe Ser Pro Arg
His His Trp Thr Thr Gln Asp100 105 110Cys Asn Cys Ser Ile Tyr Pro
Gly His Ile Thr Gly His Arg Met Ala115 120 125Trp Asn Met Met Met
Asn Trp Ser Pro Thr Ala Ala Val Val Ala Gln130 135 140Leu Leu Arg
Ile Pro Ala Ile Met Asp Met Ile Ala Gly Ala His Trp145 150 155
160Gly Val Leu Ala Gly Ile Lys Tyr Phe Ser Met Val Gly Asn Trp
Ala165 170 175Lys Val Leu Val Val Leu Leu Leu Phe Ala Gly Val Asp
Ala180 185 190
* * * * *
References