WO2008039983A2 - Methods and compositions using mutant gp120 - Google Patents

Abstract

Compositions and methods for eliciting an immune response against HIV and/or SIV are provided. Isolated gpl20 proteins having two or more amino acids deleted from their β3-β5 loop regions and isolated nucleic acid sequences encoding a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region are also provided.

Description

PATENT ATTORNEY DOCKET NO. 10498-00152

METHODS AND COMPOSITIONS USING MUTANT gpl20

RELATED APPLICATION

[001] This application claims priority from U.S. provisional patent application number 60/847,738, filed September 28, 2006, which is hereby incorporated herein by reference in its entirety for all purposes.

STATEMENT OF GOVERNMENT INTERESTS

[002] This invention was made with U.S. Government support under grant number AI069972, awarded by the National Institutes of Health. The Government has certain rights in the invention.

BACKGROUND OF THE INVENTION

[003] Infection by enveloped viruses, such as influenza virus, human immunodeficiency virus (HIV), and simian immunodeficiency virus (SIV), begins with fusion of viral and cellular membranes. The membrane fusion reaction is facilitated by the viral envelope glycoproteins (Harrison (2005) Adv. Virus Res. 64:231). The HIV or SIV envelope glycoprotein is synthesized as a precursor, gpl60, and cleaved by a furin-like protease after trimerization (Allan et al. (1985) Science 228:1091; Veronese et al. (1985) Science, 229:1402). The two fragments produced by the cleavage, gpl20 and gp41, form a non-covalently associated heterodimer, three of which make up the mature viral spike (Center et al. (2002) J. Virol. 76:7863; Center et al. (2001) Proc. Natl. Acad. Sci. U.S.A. 98:14877; Zhu et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100:15812). The interaction between gpl20 and gp41 is relatively weak, and gpl20 spontaneously dissociates from mature virions (shedding), especially in some laboratory-adapted strains (Moore et al. (1990) J. Virol. 66:235). Sequential binding of gpl20 to viral receptor CD4 and co-receptor (e.g., CCR5 or CXCR4) triggers a cascade of conformational changes within both gpl20 and gp41 (Harrison (2005) Adv. Virus Res. 64:231; Wyatt and Sodroski (1998) Science 280:1884). It is generally believed that refolding of gp41 pulls viral and cellular membranes together (Chan et al. (1997) Cell, 89:263; Weissenhorn et al. (1997) Nature 387:426). Changes in gpl20 that accompany CD4 and co-receptor binding must somehow liberate gp41 to undergo the fusion-inducing, refolding process, either by dissociating from it or by releasing conformational constraints.

[004] CD4 binding is the first step in viral entry. A large body of evidence derived from biochemical and thermodynamic experiments supports the notion that some major conformational changes take place in gpl20 upon binding to CD4 (Myszka et al. (2000) Proc. Natl. Acad. Sci. U.S.A. 97:9026; Sattentau and Moore (1991) J. Exp. Med. 174:407; Sattentau et al. (1993) J. Virol. 67:7383). CD4 binding has a number of consequences: It leads to formation of the co-receptor binding site (Rizzuto et al. (1998) Science, 280:1949; Trkola et al. (1996) Nature, 384:184; Wu et al. (1996) Nature, 384:179); to formation of binding sites (epitopes) for so-called CD4i (CD4 induced) antibodies, such as 17b and 48d (Sullivan et al. (1998) J. Virol. 72:4694; Thali et al. (1993) J. Virol. 67:3978); to enhanced exposure of the V1V2 and V3 variable loops in the context of the gpl60 trimer (Wyatt et al. (1995) J. Virol. 69:5723); to exposure of the gp41 HRl region in the trimer (Furuta et al. (1998) Nat. Str. Biol. 5:276; Gallo et al. (2004) Biochem. 43:8230); and to dissociation (shedding) of gpl20 from gp41, especially in some laboratory-adapted strains (Moore et al. (1992) J. Virol. 66:235; Moore et al. (1990) Science 250:1139). Crystal structures of gpl20 in both CD4-bound and unliganded conformations have recently allowed the visualization of these changes in considerable detail (Chen et al. (2005) Nature 433:834; Kwong et al. (1998) Nature 393:648).

[005] Fragments of gpl20 and gp41, truncated to facilitate structural studies, have been crystallized and have yielded atomic structures. The gpl20 "core" - that is, gpl20 stripped of non-essential variable regions and also of N- and C- terminal segments - has been crystallized in two forms: In an unliganded and fully glycosylated state (from SIV mac32H) (Chen et al. (2005) Nature 433:834) and in a CD4-bound form (from HIV-I HXBc2 and YU2) in complex with the Fab from mAb 17b (Kwong et al. (2000) Struct. Fold Des. 8:1329; Kwong et al. (1998) Nature 393:648). The latter is the receptor-induced conformation. It has been described as two closely associated domains, named "inner" and "outer" (Kwong et al. (1998) supra). The relative orientations of the two domains are fixed by a four- strand β- sheet, termed the "bridging sheet," which is formed by two β hairpins, the base of the V1V2 variable loop from the inner domain and a hairpin that projects from the outer domain. CD4 makes direct contacts with both domains as well as with the bridging sheet. The bridging sheet and the V3 variable loop together contribute to the binding site for co-receptor (Rizzuto and Sodroski (2000) Retroviruses 16:741; Rizzuto et al. (1998) Science 280:1949). Comparison of the liganded and unliganded core structures shows that CD4 binding results in large rearrangements of the inner domain as well as formation of the bridging sheet (Chen et al. (2005) Nature 433:834). The latter constitutes at least part of the binding sites for both co-receptor and antibody 17b. These structural rearrangements are consistent with the observation that unusually large negative entropy changes accompany CD4 binding (Myszka et al., supra).

[006] Eliciting broadly neutralizing antibodies against HIV-I remains the most elusive goal for AIDS vaccine development as illustrated by the many failed strategies for envelope-based immunogen design (Burton et al. (2004) Nat. Immunol. 5:233). Most efforts have used recombinant, cell-associated, or virion-associated envelope glycoproteins, known to be structurally heterogeneous. For instance, recombinant, uncleaved HIV-I gpl40 is often a mixture of monomer, dimer, trimer and higher-order oligmers, the conformations of which are difficult to define (Jeffs et al. (2004) Vaccine 22:1032). Using such preparations as immunogen may distract the immune system with irrelevant decoys, contributing to production of non-effective antibody responses. Lack of adequate high-resolution structural information on the envelope glycoprotein, has impeded efforts to make Env immunogens with well- defined conformations.

BRIEF SUMMARY OF THE INVENTION

[007] The present invention overcomes the difficulties in developing an envelope- based immunogen against HIV and/or SIV. The present invention is based in part on the discovery that deletions in the β3-β5 loop of HIV-I gpl20 weakened the interaction with CD4 and blocked formation of the mAb 17b epitope. Altering amino acid residues present the β3-β5 loop represents a simple strategy for producing a gpl20 immunogen locked in its pre-fusion conformation.

[008] Accordingly, embodiments of the present invention are directed to methods of inducing an immune response against HIV in a subject including administering to the subject pharmaceutical composition including a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region, such that an immune response against HIV is induced. In certain aspects, the subject is infected with HIV and the subject is therapeutically treated. In other aspects, the subject is prophylactically treated. In still other aspects, the gpl20 protein has three, four, five, six, seven, eight or nine amino acids deleted from its β3-β5 loop region.

[009] Other embodiments of the present invention are directed to methods of treating a subject infected with HIV including administering to the subject an antibody specific against a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region, such that the subject is treated.

[010] Still other embodiments are directed to vaccines against HIV including an expression vector having a nucleic acid sequence encoding a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region.

[011] Other embodiments of the present invention are directed to isolated nucleic acid sequences which encode a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region, and isolated polypeptides including a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region.

[012] Further features and advantages of certain embodiments of the present invention will become more fully apparent in the following description of the embodiments and drawings thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[013] The patent or application file contains at least one drawing executed in color.

Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. The foregoing and other features and advantages of the present invention will be more fully understood from the following detailed description of illustrative embodiments taken in conjunction with the accompanying drawings in which:

[014] Figures 1A-1C schematically depict the location of the β3-β5 loop in the gpl20 structures. (A) shows the structure of the unliganded SIV gpl20 core. The disordered segment (residues 220 to 228; the β3-β5 loop) is evident as a dashed, purple line. The β3-β5 loop connects the inner domain β-sheet in cyan and the V1V2 stem in red. (B) shows the structure of CD4-bound HIV gpl20 core. The β3-β5 loop is a well-ordered strand shown in purple. (C) shows a proposed gpl20 trimer structure, based on the unliganded gpl20 core structure (Chen et al. (2005) Nature 433:834). Note that the three 220-228 loops from the three gpl20 subunits, shown in red, green and blue respectively, project around the three-fold axis towards gp41.

[015] Figures 2A-2B depict protein production of HIV-I gpl20 core and its loop- deletion variants. (A) shows schematic representations of HIV-I gpl20 protein and its loop-deletion variants. HIV gpl20, the surface subunit of the envelope glycoprotein; N-linked glycans are represented by tree-like symbols; various segments of gpl20 are designated as follows: C1-C5 in light blue, conserved regions 1-5; V1-V5 in yellow, variable regions 1-5. HIV92ug, HIV-I gpl20 core, the protein is truncated the same way as described in Chen at al. (2005) Structure (Camb.) 13:197 for crystallographic studies. HIV92ugD5, gpl20 core with five residues deleted from the β3-β5 loop. HIV92ugD9GG, gpl20 core with the entire β3-β5 loop replaced by a short linker GG. The location of the β3-β5 loop is highlighted in red. The actual residues in the loop are shown beneath each construct. All gpl20 core proteins have a His-tag (in grey) at the N-terminus to facilitate protein purification. (B) HIV-I gpl20 core protein and its loop-deletion variants were purified from supernatants of insect cell culture, and then resolved by gel-filtration chromatography using a Superdex 200 column. The traces are shown in red for HIV92ug, blue for HIV92ugD5 and green for HIVug92D9GG. The apparent molecular masses were calculated based on a standard curve using the following known standards: thyoglobulin (670 kDa), γ- globulin (158 kDa), and ovalbumin (44 kDa), myoglobin (17 kDa) and vitamin Bi₂ (1.4 kDa). Peak fractions were pooled and analyzed by Coomassie stained SDS- PAGE (inset). Lane 1, HIV92ug; lane 2, HIV92ugD5; lane 3, HIV92ugD9GG.

[016] Figure 3 graphically depicts Kinetic analysis of binding of mAb 2Gl 2 to

HIV-I gpl20 core proteins. mAb 2G12 was immobilized on a CM-5 chip, and various concentrations of gpl20 were passed over the chip surface as described further herein. All injections were carried out in duplicate, which gave essentially identical results. Binding kinetics were evaluated using BiaEvaluation software (Biacore) using a 1 : 1 Langmuir binding model. The recorded sensorgrams are shown in black (one of the duplicates) and the calculated curves in red. The residues in the β3-β5 loop are also shown for each protein at the bottom.

[017] Figure 4 graphically depicts binding of soluble CD4 to HIV-I gpl20 core proteins. Soluble 4-domain CD4 was immobilized on a CM-5 chip, and various concentrations of gpl20 were passed over the chip surface. All injections were carried out in duplicate, which gave essentially identical results. Binding kinetics was evaluated using BiaEvaluation software (Biacore) using a two-step binding model. The recorded sensorgrams are shown in black (one of the duplicates) and the calculated curves in red. The residues in the β3-β5 loop are also shown for each protein at the bottom. The two-step model includes formation of the encounter complex [gpl20/CD4]* and, after conformational changes, formation of docking complex gpl20/CD4. Rate constants and equilibrium dissociation constants derived from the fits are also summarized.

[018] Figure 5 graphically depicts binding of mAb 17b to HIV-I gpl20 core proteins in the absence or presence of CD4. mAb 17b was immobilized on a CM5 chip, and various gpl20 proteins at 500 nM were passed over the chip surface with or without pre-incubation with equimolar amounts of 2-domain soluble CD4. All injections were carried out in duplicate, which gave essentially identical results. The recorded sensorgrams for binding in the presence of CD4 are shown in black, and those for binding in the absence of CD4, in cyan (one of the duplicates). The residues in the β3-β5 loop are also shown for each protein at the bottom.

[019] Figures 6A-6B depict fusion activity of mutant envelope glycoproteins in a cell-cell fusion assay and spontaneous dissociation of gpl20 from the cell surface. (A) cell-cell fusion assays were carried out in triplicate for each construct as described previously (Ferrer et al. (1999) Nat. Struct. Biol. 6:953). The readouts of the assay were normalized based on the activity of the wild-type Env (100) to give the relative fusion activity of the mutant Envs. WT: wild-type Env transfected into effector cell; NOCR: chemokine receptor, CCR5, omitted from target cell; NOENV: Env construct omitted from effector cell. NOCR and NOENV are negative controls. The standard deviations derived from the three measurements for each construct are indicated by the error bars. The experiment was repeated twice using independent transfections, which gave similar results. (B) Wild-type and mutant Env expression constructs were trans fected into 293 T cells. Expression and distribution of gpl20 were monitored by western blot using monoclonal antibodies KKl 9 and SIV-101, specific for SIV gpl20. Mutations are indicated at the top; S, cell supernatants; C, cell-associated. Equal volumes for all supernatants or cell lysates were loaded in each lane. The equal intensity of a very abundant protein (NS) from the medium recognized non-specifically by the antibodies indicates uniform sample loading. The experiment was repeated four times, using independent transfections. The same result was obtained each time.

DETAILED DESCRIPTION

[020] The principles of the present invention may be applied with particular advantage to generate novel viral deletion proteins (e.g., gpl20 deletion proteins) that are capable of eliciting an immunogenic response against wild-type gpl20 in an organism and/or for generating therapeutic antisera specific against wild-type gpl20. The novel viral deletion proteins of the invention are also useful for preventing infection by and/or reducing one or more cytopathic effects of a retrovirus (e.g., HIV, SIV) by reducing or inhibiting membrane fusion mediated by the virus or cell infected with the virus.

[021] As used herein, the term "gpl20 deletion protein" refers to a gpl20 protein sequence, or portion thereof, having a deletion of one or more amino acid residues in the nine residue β3-β5 loop region that is present in the wild-type gpl20 protein. Accordingly, a gpl20 deletion protein of the present invention has one, two, three, four, five, six, seven, eight or nine of its amino acids in the β3-β5 loop deleted. A gpl20 deletion protein of the present invention also includes an amino acid substitution at one, two, three, four, five, six, seven, eight or nine positions in the β3- β5 loop. A gpl20 deletion protein of the present invention further includes various combinations of amino acid deletions and/or substitutions. Gp 120 deletion proteins of the present invention also include truncations in which the gpl20 deletion protein has been truncated at an amino acid N-terminal to the furin cleavage site. Gp 120 proteins of the present invention also include proteins having amino acid additions to the β3-β5 loop such that it is longer than nine amino acids in length. [022] One aspect of the invention pertains to isolated gpl20 deletion proteins and/or portions thereof suitable for use as immunogens to raise anti-gpl20 deletion protein antibodies. In one embodiment, gpl20 deletion proteins are produced by recombinant DNA techniques. Alternative to recombinant expression, a gpl20 deletion proteins and/or portions thereof can be synthesized chemically using standard peptide synthesis techniques.

[023] An "isolated" or "purified" protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the gpl20 deletion protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language "substantially free of cellular material" includes preparations of gpl20 deletion protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced.

[024] The language "substantially free of chemical precursors or other chemicals" includes preparations of a gpl20 deletion protein in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein.

[025] The gpl20 deletion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject in vivo. Accordingly, the gpl20 deletion proteins of the invention can be used as immunogens to produce anti- gpl20 deletion protein antibodies in a subject, to inhibit or prevent infection by HIV and/or to inhibit or prevent the spread of HIV in an infected individual..

[026] A gpl20 deletion protein, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that bind wild-type gpl20 using standard techniques for polyclonal and monoclonal antibody preparation. A full-length gpl20 deletion protein can be used or, alternatively, the invention provides antigenic portions of a gpl20 deletion protein for use as immunogens.

[027] A gpl20 deletion protein immunogen typically is used to prepare antibodies by immunizing a suitable subject, (e.g., rabbit, goat, mouse or other mammal) with the immunogen. An appropriate immunogenic preparation can contain, for example, recombinantly expressed gpl20 deletion protein or a chemically synthesized gpl20 deletion protein. The preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent. Immunization of a suitable subject with an immunogenic gpl20 deletion protein preparation induces a polyclonal anti-gpl20 antibody response, i.e., an anti-HIV antibody response.

[028] Accordingly, another aspect of the invention pertains to anti-gpl20 deletion protein antibodies. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site which specifically binds (immunoreacts with) an antigen, such as gpl20. Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin. The invention provides polyclonal and monoclonal antibodies that bind gpl20. The term "monoclonal antibody" or "monoclonal antibody composition," as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of gpl20. A monoclonal antibody composition thus typically displays a single binding affinity for a particular gpl20 protein with which it immunoreacts.

[029] Polyclonal anti-gpl20 antibodies can be prepared as described above by immunizing a suitable subject with a gpl20 deletion protein immunogen. The anti- gpl20 antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized gpl20. If desired, the antibody molecules directed against gpl20 can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as protein A chromatography to obtain the IgG fraction. At an appropriate time after immunization, e.g., when the anti-gpl20 antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497) (see also, Brown et al. (1981) J. Immunol. 127:539-46; Brown et al. (1980) J. Biol. Chem. 255:4980-83; Yeh et al. (1976) Proc. Natl. Acad. Sci. USA 76:2927-31; and Yeh et al. (1982) Int. J. Cancer 29:269-75), the more recent human B cell hybridoma technique (Kozbor et al. (1983) Immunol Today 4:72), the EBV-hybridoma technique (Cole et al. (1985), Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques. The technology for producing monoclonal antibody hybridomas is well known (see generally R. H. Kenneth, in Monoclonal Antibodies: A New Dimension In Biological Analyses, Plenum Publishing Corp., New York, N.Y. (1980); E. A. Lerner (1981) Yale J. Biol. Med., 54:387-402; M. L. Gefter et al. (1977) Somatic Cell Genet. 3:231-36). Briefly, an immortal cell line (typically a myeloma) is fused to lymphocytes (typically splenocytes) from a mammal immunized with a gpl20 deletion protein immunogen as described above, and the culture supernatants of the resulting hybridoma cells are screened to identify a hybridoma producing a monoclonal antibody that binds gpl20. Any of the many well known protocols used for fusing lymphocytes and immortalized cell lines can be applied for the purpose of generating an anti-gpl20 monoclonal antibody (see, e.g., G. Galfre et al. (1977) Nature 266:55052; Gefter et al. Somatic Cell Genet., cited supra; Lerner, Yale J. Biol. Med., cited supra; Kenneth, Monoclonal Antibodies, cited supra). Moreover, the ordinarily skilled worker will appreciate that there are many variations of such methods which also would be useful. Typically, the immortal cell line (e.g., a myeloma cell line) is derived from the same mammalian species as the lymphocytes. For example, murine hybridomas can be made by fusing lymphocytes from a mouse immunized with an immunogenic preparation of the present invention with an immortalized mouse cell line. Particularly suitable immortal cell lines are mouse myeloma cell lines that are sensitive to culture medium containing hypoxanthine, aminopterin and thymidine ("HAT medium"). Any of a number of myeloma cell lines can be used as a fusion partner according to standard techniques, e.g., the P3-NSl/l-Ag4-l, P3-x63-Ag8.653 or Sp2/O-Agl4 myeloma lines. These myeloma lines are available from ATCC. Typically, HAT-sensitive mouse myeloma cells are fused to mouse splenocytes using polyethylene glycol ("PEG"). Hybridoma cells resulting from the fusion are then selected using HAT medium, which kills unfused and unproductively fused myeloma cells (unfused splenocytes die after several days because they are not transformed). Hybridoma cells producing a monoclonal antibody of the invention are detected by screening the hybridoma culture supernatants for antibodies that bind gpl20 deletion proteins, e.g., using a standard ELISA assay. [031] Alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal anti-gpl20 antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with a gpl20 deletion protein to thereby isolate immunoglobulin library members that bind gpl20. Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SURFZAP™ Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, Ladner et al. U.S. Pat. No. 5,223,409; Kang et al. PCT International Publication No. WO 92/18619; Dower et al. PCT International Publication No. WO 91/17271; Winter et al. PCT International Publication WO 92/20791; Markland et al. PCT International Publication No. WO 92/15679; Breitling et al. PCT International Publication WO93/01288; McCafferty et al. PCT International Publication No. WO 92/01047; Garrard et al. PCT International Publication No. WO 92/09690; Ladner et al. PCT International Publication No. WO 90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBO J., 12:725-734; Hawkins et al. (1992) J. MoI. Biol. 226:889-896; Clarkson et al. (1991) Nature 352:624-628; Gram et al. (1992) Proc. Natl. Acad. Sci. USA 89:3576-3580; Garrad et al. (1991) Bio/Technology 9:1373-1377; Hoogenboom et al. (1991) Nuc. Acid Res. 19:4133-4137; Barbas et al. (1991) Proc. Natl. Acad. Sci. USA 88:7978-7982; and McCafferty et al. (1990) Nature 348:552-554.

[032] Additionally, recombinant anti-gpl20 antibodies, such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in Robinson et al. International Application No. PCT/US86/02269; Akira, et al. European Patent Application 184,187; Taniguchi, M., European Patent Application 171,496; Morrison et al. European Patent Application 173,494; Neuberger et al. PCT International Publication No. WO 86/01533; Cabilly et al. U.S. Pat. No. 4,816,567; Cabilly et al. European Patent Application 125,023; Better et al. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439- 3443; Liu et al. (1987) J. Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al. (1987) Cane. Res. 47:999-1005; Wood et al. (1985) Nature 314:446-449; and Shaw et al. (1988) J. Natl. Cancer Inst. 80:1553-1559); Morrison, S. L. (1985) Science 229:1202-1207; Oi et al. (1986) BioTechniques 4:214; Winter U.S. Pat. No. 5,225,539; Jones et al. (1986) Nature 321 :552-525; Verhoeyan et al. (1988) Science 239:1534; and Beidler et al. (1988; J. Immunol. 141 :4053-4060.

[033] Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding a gpl20 deletion protein (or a portion thereof). As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid," which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "expression vectors." In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, "plasmid" and "vector" can be used interchangeably. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno- associated viruses), which serve equivalent functions.

[034] The recombinant expression vectors of the invention comprise a nucleic acid of the invention (e.g., a nucleic acid sequence encoding a gpl20 deletion protein or a portion thereof) in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term "regulatory sequence" is intended to includes promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or portions thereof, including fusion proteins or portions thereof, encoded by nucleic acids as described herein (e.g., gpl20 deletion proteins).

[035] The recombinant expression vectors of the invention can be designed for expression of gpl20 deletion proteins in prokaryotic or eukaryotic cells. For example, gpl20 deletion proteins can be expressed in bacterial cells such as E. coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

[036] Expression of proteins in prokaryotes is most often carried out in E. coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non- fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein. Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S.

(1988) Gene 67:31-40); pMAL (New England Biolabs, Beverly, MA); and pRIT5 (Pharmacia, Piscataway, N.J.) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.

[037] In another embodiment, the gpl20 deletion protein expression vector is a yeast expression vector. Examples of vectors for expression in yeast S. cerevisiae include pYepSecl (Baldari, et. al, (1987) EMBO J. 6:229-234); pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943); pJRY88 (Schultz et al., (1987) Gene 54:113- 123); pYES2 (Invitrogen Corporation, San Diego, Calif); and picZ (InVitrogen Corp, San Diego, CA).

[038] Alternatively, gpl20 deletion proteins can be expressed in insect cells using baculo virus expression vectors. Baculo virus vectors available for expression of proteins in cultured insect cells (e.g., Sf9 cells) include the pAc series (Smith et al. (1983) MoI. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers

(1989) Virology 170:31-39).

[039] In yet another embodiment, a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman et al. (1987) EMBO J. 6:187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus and simian virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 1989.

[040] In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific, Pinkert et al. (1987) Genes Dev. 1 :268), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J. 8:729) and immunoglobulins (Banerji et al. (1983) Cell 33:729; Queen and Baltimore (1983) Cell 33:741), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. U.S.A. 86:5473), pancreas-specific promoters (Edlund et al. (1985) Science 230:912), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374) and the (α-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537).

[041] Another aspect of the invention pertains to host cells into which a recombinant expression vector of the invention has been introduced. The terms "host cell" and "recombinant host cell" are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

[042] A host cell can be any prokaryotic or eukaryotic cell. For example, a gpl20 deletion protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.

[043] Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection" are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. {Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 1989), and other laboratory manuals.

[044] Nucleic acid sequences encoding a gpl20 deletion proteins, gpl20 deletion proteins, and anti-gpl20 deletion protein antibodies (also referred to herein as "active compounds") of the invention can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier. As used herein the language "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.

[045] A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerin, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.

[046] Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, CREMOPHOR EL™ (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.

[047] Sterile injectable solutions can be prepared by incorporating the active compound (e.g., a gpl20 deletion protein or an anti-gpl20 deletion protein antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. [048] Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: A binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic, acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant: such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.

[049] In one embodiment, the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These may be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.

[050] Nasal compositions generally include nasal sprays and inhalants. Nasal sprays and inhalants can contain one or more active components and excipients such as preservatives, viscosity modifiers, emulsifϊers, buffering agents and the like. Nasal sprays may be applied to the nasal cavity for local and/or systemic use. Nasal sprays may be dispensed by a non-pressurized dispenser suitable for delivery of a metered dose of the active component. Nasal inhalants are intended for delivery to the lungs by oral inhalation for local and/or systemic use. Nasal inhalants may be dispensed by a closed container system for delivery of a metered dose of one or more active components.

[051] In one embodiment, nasal inhalants are used with an aerosol. This is accomplished by preparing an aqueous aerosol, liposomal preparation or solid particles containing the compound. A non-aqueous (e.g., fluorocarbon propellant) suspension could be used. Sonic nebulizers may be used to minimize exposing the agent to shear, which can result in degradation of the compound.

[052] Ordinarily, an aqueous aerosol is made by formulating an aqueous solution or suspension of the agent together with conventional pharmaceutically acceptable carriers and stabilizers. The carriers and stabilizers vary with the requirements of the particular compound, but typically include nonionic surfactants (T weens, Pluronics, or polyethylene glycol), innocuous proteins like serum albumin, sorbitan esters, oleic acid, lecithin, amino acids such as glycine, buffers, salts, sugars or sugar alcohols. Aerosols generally are prepared from isotonic solutions.

[053] Systemic administration can also be by transmucosal or transdermal means.

For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.

[054] The compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.

[055] In one embodiment, the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.

[056] It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.

[057] Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.

[058] The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

[059] One embodiment of the present invention involves a method for treatment of a viral infection, e.g., an HIV infection which includes the step of administering a therapeutically effective amount of an agent which inhibits one or more activities of HIV to a subject. As defined herein, a therapeutically effective amount of agent (i.e., an effective dosage) ranges from about 0.001 to 30 mg/kg body weight, preferably about 0.01 to 25 mg/kg body weight, more preferably about 0.1 to 20 mg/kg body weight, and even more preferably about 1 to 10 mg/kg, 2 to 9 mg/kg, 3 to 8 mg/kg, 4 to 7 mg/kg, or 5 to 6 mg/kg body weight. The skilled artisan will appreciate that certain factors may influence the dosage required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present. Moreover, treatment of a subject with a therapeutically effective amount of an inhibitor can include a single treatment or, preferably, can include a series of treatments. It will also be appreciated that the effective dosage of inhibitor used for treatment may increase or decrease over the course of a particular treatment. Changes in dosage may result from the results of diagnostic assays as described herein.

[060] The nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Pat. No. 5,328,470) or by stereotactic injection (see e.g., Chen et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91 :3054). The pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system. [061] The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.

[062] The gpl20 deletion proteins, nucleic acids encoding gpl20 deletion proteins and antisera against gpl20 deletions proteins described herein can be used in combination with one or more anti-viral treatments to prophylactically and/or therapeutically treat one or more viral infections. Anti-viral treatments are well know in the art and include, but are not limited to: antiviral pharmaceuticals, e.g., nucleoside/nucleotide reverse transcriptase inhibitors such as AZT (zidovudine, Retrovir), ddl (didanosine, Videx), 3TC (lamivudine, Epivir), d4T (stavudine, Zerit), abacavir (Ziagen), and FTC (emtricitabine, Emtriva), tenofovir (Viread), AZT/3TC combination (Combivir), AZT/3TC/abacavir combination (Trizivir), AZT/abacavir combination (Kivexa); non-nucleoside reverse transcriptase inhibitors such as efavirenz (Sustiva) and nevirapine (Viramune); protease inhibitors such as lopinavir/ritonavir (Kaletra), indinavir (Crixivan), ritonavir (Norvir), nelfmavir (Viracept), saquinavir hard gel capsules (Invirase), atazanavir (Reyataz), amprenavir (Agenerase), fosamprenavir (Telzir), tipranavir (Aptivus); fusion inhibitors such as enfuvirtide (Fuzeon); antiviral vaccines; and the like.

[063] It is to be understood that the embodiments of the present invention which have been described are merely illustrative of some of the applications of the principles of the present invention. Numerous modifications may be made by those skilled in the art based upon the teachings presented herein without departing from the true spirit and scope of the invention. The contents of all references, patents and published patent applications cited throughout this application are hereby incorporated by reference in their entirety for all purposes.

[064] The following examples are set forth as being representative of the present invention. These examples are not to be construed as limiting the scope of the invention as these and other equivalent embodiments will be apparent in view of the present disclosure, figures, tables, and accompanying claims. EXAMPLE I

Conservation of the β3-β5 Loop in the Inner Domain The β3-β5 loop (residues 220 to 228 in SIVmac 32H) connecting the V1V2 stem and the inner-domain β-sheet is in conserved region C2. It immediately follows a conserved cysteine in the protein sequence, so the sequence alignment in this region is indisputable. Table 1, which depicts the sequences of β3-β5 loops and gp41 C-C loops from various HIV and SIV strains, demonstrates that the β3-β5 loop is highly conserved in strains among HIV-1/SIVcpz (residues 206 - 214, HXBc2 numbering) and among HIV-2/SIV, but differs between these two groups. The only invariant residue among all viruses is a lysine at the second position of the loop. A similar pattern of conservation is also true for the C-C loop and HRl of gp41, as expected for interacting segments that must co-evolve to maintain optimal fit (Douglas et al. (1997) J. MoI. Biol. 273:122; Leitner (2003) HIV Sequence Compendium LA-UR 04- 7420).

Table 1. EXAMPLE II Production of gpl20 Core Proteins with Loop Deletions

[066] The β3-β5 loop is flexible (hence disordered) in the unliganded gpl20 structure, but extends into a well-ordered strand upon CD4 binding. Loop deletions in the SIV gpl20 core were designed based on our crystal structure of the unliganded protein. Because the two ordered residues (219 and 229 in SIV) that flank the β3-β5 loop are about 15 A apart (Ca positions) but might tolerate some degree of flexibility, two constructs were generated: One with deletion of five residues in the middle of the loop and another with the entire 9-residue loop replaced by two glycine residues. When introduced into insect cells, both constructs yielded secreted gpl20 core proteins that could be purified using a 17Al 1 antibody column. The antibody 17Al 1 recognized a conformation-dependent epitope close to the co-receptor binding site (Edinger et al. (2000) J. Virol. 74:7922). A mono-disperse protein preparation could be obtained by further purification using size-exclusion chromatography. These observations indicate that the deletions in the β3-β5 loop did not affect protein folding.

[067] Taking advantage of the many well-studied reagents available for characterizing HIV-I gpl20, similar constructs were made for HIV-I. A primary isolate, 92UG037.8, from clade A was chosen (Figure 2A). The wild-type gpl20 core (here designated HIV92ug) was generated as described previously (Chen et al. (2005) Structure (Camb.) 13:197) and a His-tag was added to the N-terminus for purification. This HIV-I gpl20 core still contained 17 N-linked glycosylation sites. Construct HIV92ugD5 had five residues deleted in the middle of the β3-β5 loop, and HIV92ugD9GG contained a short linker GG replacing the entire β3-β5 loop. The proteins were expressed in insect cells and purified by metal-chelate affinity chromatography with Ni-NTA agarose resin using cell supernatants, followed by gel- filtration. All three proteins eluted from a Superdex 200 column as a sharp peak, with a size corresponding to a 60 kDa globular protein (Figure 2B). This was consistent with the calculated mass for the monomeric gpl20 core, which contains polypeptide chains of about 36 kDa and 17 N-linked glycans. The proteins migrated as a single, but diffuse protein band with an average molecular mass of 64 kD, as expected for a heavily glycosylated species. [068] Binding of these proteins to some well-characterized monoclonal antibodies was examined by surface plasmon resonance (SPR) biosensor analysis. mAb 2Gl 2 is a broadly neutralizing antibody that recognizes a glycan- and conformation-dependent epitope in the outer domain of gpl20 (Trkola et al. (1996) J. Virol. 70:1100). To measure the binding kinetics of various gpl20 core proteins to 2Gl 2, the intact IgG was immobilized on a CM5 chip, and gpl20 at different molar concentrations was passed over the surface of the chip. In Figure 3, the sensorgrams for binding of 2Gl 2 to the HIV92ug protein and its two loop deletion variants, HIV92ugD5 and HIV92ugD9GG, were almost identical. The data were analyzed with a 1 : 1 Langmuir binding model. The kinetic binding constants are listed in Table 2. The on- and off- rate constants and the Kd, were essentially identical for all three proteins, indicting that the loop deletions did not affect the conformation of the 2Gl 2 epitope.

[069] Binding of the three proteins to another broadly neutralizing antibody, bl2, which recognizes an epitope that overlaps the CD4 binding site (CD4 BS) (Burton et al. (1994) Science 266:1024) was also tested. Among all CD4 BS antibodies, bl2 was the only one with potent, broadly neutralizing activity. Unlike many other CD4 BS antibodies, its association with gpl20 did not appear to require a large, entropically costly conformational change (Kwong et al. (2002) Nature 420:678). The sensorgrams for b 12 binding were very similar for all three proteins, and the kinetic data, derived from a 1 : 1 Langmuir binding model, are summarized in Table 2, which depicts the rate constants for binding the gpl20 core and its loop-deletion variants with the broadly neutralizing antibodies. Although bl2 bound to the gpl20 core of this particular HIV-I strain from clade A with relatively low affinity (Kd = 1.42 μM), the rate constants for two deletion variants, HIV92ugD5 and HIV92ugD9GG, did not differ significantly (within a factor of 1.6) from that of the wild-type core, HIV92ug. It was concluded from the antibody binding studies and from the data described above that the deletions introduced into the β3-β5 loop did not have deleterious effects on the conformation or stability of gpl20.

Table 2.

EXAMPLE III CD4 Binding to HIV-I gpl20 Core Proteins

[070] Kinetics of CD4 binding to HIV92ug and its loop deletion variants, HIV92ugD5 and HIV92ugD9GG, were analyzed using SPR. Soluble, four-domain CD4 was immobilized on a chip, and solutions of gpl20 at various concentrations were allowed to flow over the surface. As shown in Figure 4, all three proteins had similar rate constants for the initial, rapid encounter step (both k_on and k_off), but quite different rate constants for the tight-binding step. Both loop-deletion variants had association rate constants three to four times lower than did wild-type gpl20, and dissociation rate constants 15-20 times greater. The equilibrium dissociation constants (at 25 ⁰C) derived from these data were 13.9 nM for wild-type HIV92ug, 228 nM for HIV92ugD5, and 1.0 μM for HIV92ugD9GG. The same experiment was also carried out at 10⁰C with similar results.

EXAMPLE IV niAb 17b Binding Site is Not Formed When the β3-β5 Loop is Deleted

[071] SPR biosensor analysis was used to investigate binding of the three gpl20 core proteins to mAb 17b in presence or absence of soluble CD4. 17b IgG molecules were immobilized on a CM5 chip and various gpl20 proteins were passed over the chip surface with or without pre-incubation with two- domain soluble CD4. Wild- type gpl20 core (HIV92ug) did not bind to the 17b surface in the absence of CD4 (Figure 5, sensorgram in cyan) but did so in complex with soluble CD4 (Figure 5, sensorgram in black). In contrast, the two variants with deletions in the β3-β5 loop (HIV92ugD5 and HIV92ugD9GG) failed to bind the 17b surface, regardless of whether they had been pre-incubated with CD4 or not. Shortening the β3-β5 loop thus blocked formation of the 17b epitope.

[072] Without intending to be bound by scientific theory, several observations ruled out the possibility that mAb 17b failed to bind the loop- deletion variants because the excised residues were part of its epitope. In the high resolution structure of the ternary complex of gpl20, CD4 and 17b, none of residues in the β3-β5 loop makes a direct contact with 17b (Kwong et al. (1998), supra). The closest distance between an atom of a β3-β5 loop residue and an atom in 17b is greater than 8 A. Moreover, HIV92ugD5, which has the same properties as the full deletant, has only five residues eliminated from the middle of the loop, and these residues are even more distant (greater than 15 A) from the 17b binding site in the CD4-bound conformation. Finally, mutation of residues in the β3-β5 loop published by other groups does not significantly affect 17b binding (Rizzuto et al. (1998), supra).

EXAMPLE V

The β3-β5 Loop Helps Anchor gpl20 to gp41

[073] To test the hypothesis that that the β3-β5 loop participates in the gpl20/gp41 interaction (Figure 1C), the loop residues (220-228) in SIV Env were systematically mutated and these mutants were examined for induction of cell-cell fusion and spontaneous shedding of gpl20. The envelope protein from SIV was chosen because SIV gpl20 sheds from the Env trimer much less readily than does HIV-I gpl20 (Sattentau et al. (1993), supra). Each residue in the loop was replaced with alanine by PCR-based site-directed mutagenesis, and the mutations were confirmed by DNA sequencing. All mutant Env proteins were tested first for membrane fusion activity by a cell-cell fusion assay based on a reporter gene activation technique (Ferrer et al. (1999), supra). As shown in Figure 6 A, all the mutant Env proteins supported membrane fusion at a level similar to that of the wild-type, regardless of the nature of the substitution. For example, D220A, K221A, D225A and R228A are all non- conservative substitutions that eliminate one charged side chain at a time, and Y223A and W224A replaced bulky side chains with smaller ones. Mutants K221A and T226A had significantly higher levels of cell-associated gpl20 than did wild-type, probably due to more efficient processing of gpl60 (Figure 6B). Without intending to be bound by theory, these two mutants may therefore be more strongly fusogenic than the wild type. Thus, a single change in this region did not seem to affect either folding or functionality of the protein.

[074] The stability of the association of gpl20 and gp41 was then examined by monitoring the distribution of gpl20 between cell and supernatant. All mutated Env constructs were transfected into 293T cells. Both supernatants and cell lysates were harvested and analyzed by western blot using a mixture of monoclonal antibodies, KK19 and SIV-101 (Kent et al. (1991)). Figure 6B shows that the antibodies detected dissociated gpl20 in cell supernatants (S) and both gpl20 and gpl60 in cell pellets (C). In addition, they also detected a strong band of a very abundant protein migrating around 60 kD from supernatants, presumably by non-specific binding, as the same band was detected from a mock transfection. Sample loading was normalized by volume, and the non-specific band showed the same intensity throughout, indicating the differences among dissociated gpl20 mutant proteins in the supernatants were not due to variations in sample loading. All mutants except R228A showed a significant increase in the ratio between shed gpl20 and cell-associated gpl20. Mutation of residues between 220 to 225 increased the amount of free gpl20, while the amount of cell-associated gpl20 decreased. In contrast, the change R228A produced an Env protein very similar to the wild-type in its gpl20 dissociation properties. Without intending to be bound by theory, these results are consistent with residues in the β3-β5 loop, disordered in the unliganded conformation, contributing to anchoring gpl20 to gp41.

EXAMPLE VI Discussion

[075] CD4 binding to the HIV-I envelope glycoprotein induces large structural rearrangements in gpl20. These changes lead to formation of the co-receptor binding site and may prime the protein for further changes triggered by the co-receptor interaction. In the absence of CD4, various structural elements of gpl20 may be relatively flexible, allowing it to be present in a range of conformations. Thus, "conformational masking" of the CD4 binding site is believed to be among the viral strategies for immune evasion (Kwong et al. (2002), supra). Monomeric gpl20 has failed to elicit a protective immune response against HIV infection (Maek et al. (2003) AIDS Alert 18:41, 43). We have derived a simple strategy to lock gpl20 in its unliganded, prefusion conformation. Comparison of the unliganded and CD4-bound gpl20 core structures showed that the β3-β5 loop connecting the V1V2 stem and the inner domain β-sheet is disordered in the unliganded gpl20 structure, but stretches into a well-ordered strand upon CD4 binding. Deletions in the β3-β5 loop prevented the docking (tight-binding) step of CD4 association, but did not prevent formation of a weaker encounter complex. Moreover, deletion of just five residues in the β3-β5 loop completely abolished the formation of 17b binding site, and likely also the co- receptor binding site, even in the presence of CD4. Thus, deleting the β3-β5 loop in the inner domain represents a simple strategy for producing a gpl20 immunogen restrained in the unliganded conformation.

[076] Neutralizing antibodies must bind a relevant, functional conformation of Env.

Many antibodies recognize epitopes near the receptor binding site (CD4 BS), but among well-studied CD4 BS antibodies, only bl2 has potent, broadly neutralizing activity that inhibits viral infection by a variety of HIV-I strains (Burton et al. (1994)). Another CD4 BS antibody, b6, is non-neutralizing, but it has essentially the same affinity for gpl20 as does bl2 (Pantophlet et al. (2003) J. Virol. 77:642). Thermodynamic studies show that binding of b6 to gpl20 produces a large negative entropy change and therefore seems to induce major conformational changes (Kwong et al. (2002), supra). The corresponding entropy change for b 12 binding is relatively small, suggesting that bl2 recognizes the unliganded conformation of gpl20. Id. The data in Table 2 are consistent with this conclusion, as bl2 binding is unaffected by deletion of the β3-β5 loop. The bl2 binding data also indicate that the conformation of unliganded, free gpl20, as seen in the SIV gpl20 crystal structure, closely resembles its structure when part of trimeric gpl20/gp41 on the surface of a virion (Chen et al. (2005) Nature 433:834).

[077] The spatially adjacent β3-β5 loop of gpl20 can interact directly with gp41

(Figure 1C). The data presented herein supports this (e.g., Figure 6), as mutations in the β3-β5 loop weaken the gpl20 : gp41 interaction and enhance gpl20 shedding. Comparison of the unliganded and liganded conformations of gpl20 further indicate how CD4 (and co-receptor) binding could trigger fusion. In the CD4-bound conformation of gpl20, the β3-β5 loop interacts with other parts of the gpl20 inner domain. Thus, without intending to be bound by theory, CD4 binding will peel the loop away from gp41 and release constraints that hold it in a pre-fusion configuration. The interaction between the β3-β5 loop and gp41 detected by our experiments intervenes directly in the cascade of conformational changes that ultimately leads to membrane fusion and viral entry.

EXAMPLE VII Materials and Methods

Expression and Purification of gpl20 Core Protein and its Deletion Variants Expression constructs pHIV92ug, pHIV92ugD5 and pHIV92ugD9GG were generated by standard PCR techniques. For gpl20 core, residues were deleted from the N- and C-termini of gpl20, and short linkers were substituted for the V1-V2 and V3 loops as described. A His-tag was added to the N-terminus to facilitate purification. Two additional residues (His-Met) were introduced by the restriction site (Nde Y) at the N-terminus. pHIV92ugD5 and pHIV92ugD9GG were derived from pHIV92ug with five residues deleted from the β3-β5 loop and a short linker, GG, replacing the entire nine-residue β3-β5 loop, respectively. Both restriction digestion and DNA sequencing verified the expression constructs. The proteins were expressed using the Bac-to-Bac system (Invitrogen, Carlsbad, CA). Sf9 insect cells were used for large-scale protein production and that the cell supernatant was harvested 84 hours post-infection. Gp 120 core proteins were purified by metal chelate affinity chromatography with NTA-nickel resin (Qiagen, Hilden, Germany). The protein was eluted with 300 mM imidazole, and the fractions containing gpl20 core protein were pooled, concentrated, and further purified by gel filtration chromatography on Superdex 200 (GE Healthcare, Piscataway, NJ) with a buffer containing 25 mM Tris- HCl (pH 8.0) and 150 mM NaCl. The protein was concentrated and stored at -80 ⁰C. His-tagged 2 domain soluble CD4 was also expressed in insect cells and purified by a similar protocol. Surface Plasmon Resonance Binding Assays

[079] All experiments were performed in duplicate with a Biacore 3000 instrument

(Biacore Inc, Piscataway NJ) at 20 ⁰C in HBS-EP running buffer (10 mM HEPES pH 7.4, 150 mM NaCl, 3 mM EDTA, 0.005% surfactant P20). Immobilization of ligands, 4 domain sCD4 (Protein Sciences, Meriden, CT), 2Gl 2 (Polymun Scientific Inc, Vienna, Austria), bl2 (a gift from Dr. Dennis Burton), 17b (hybridoma was provided by Dr. James Robinson), to CM5 chips (Biacore) was performed following the standard amine coupling procedure. Briefly, carboxyl groups were activated by injection of 50 μl of EDC:NHS (200 mM l-ethyl-3 [3 -dimethyl aminopropyl] carbodiimide hydrochloride, 50 mM N-hydroxysuccinimide) at a flow rate of 5 μl/min (10 min contact time). Ligand (20 μg/ml in 10 mM Na Acetate pH 5.0) was passed over the activated surface until the desired immobilization level was reached. Excess carboxyl groups were blocked with 1 M ethanolamine (35 μl at a flow rate of 5 μl/min). A reference surface was prepared by activating and blocking a flow cell in the absence of ligand. The final immobilization levels for CD4 was 800 response units (RUs), for 2G12, 1200 RUs, for bl2, 950 RUs, and for 17b, 900 RUs. For kinetic measurements of gpl20 binding to immobilized CD4, sensorgrams were obtained by passing various concentrations (10 nM-1.0 μM) of gpl20 over the ligand surface at a flow rate of 50 μl/min using a 2 min association phase and 5 min dissociation phase. The sensor surface was regenerated between each experiment using a single injection (3 sec) of 35 mM NaOH, 1.3 M NaCl at a flow rate of 100 μl/min. Identical injections over blank surfaces were subtracted from the data for kinetic analysis. All injections were carried out in duplicate, and the results of the duplicate measurements were essentially identical. Binding kinetics was evaluated using BiaEvaluation software (Biacore) using a two-state reaction model. Kinetic measurements of gpl20 to IgGs were performed in an identical manner, with the exception that regeneration was achieved using a single injection (3 sec) of 10 mM HCl and a flow rate of 100 μl/min. Binding kinetics were evaluated using BiaEvaluation software (Biacore) using 1 : 1 Langmuir binding model. Cell-Cell Fusion Assay

[080] Each residue was replaced with alanine by PCR-based site-directed mutagenesis, and the mutations were confirmed by DNA sequencing. All mutant Envs were tested for membrane fusion activity by a cell-cell fusion assay based on reporter gene activation. Briefly, 293 T cells were co-transfected by the calcium phosphate method with equal amounts of an SIV gpl60 expression construct and a plasmid expressing T7 polymerase, and these were designated effector cells. CD4- and CCR5 -expressing cells with a luciferase reporter gene under the control of a T7 promoter were designated target cells. The two types of cells were resuspended and mixed 40 hours post-transfection, followed by incubation at 37 ⁰C for another 8 hr. Fusion activity was measured by a luciferase assay (Promega, Madison, WI) following protocols recommended by the manufacturer.

Gp 120 Shedding Assay by Western Blot

[081] The stability of the association of gpl20 and gp41 was examined by monitoring the distribution of gpl20 between cell and supernatant. Transfected 293 T cells were harvested 40 hours post-transfection. After a clarifying spin, supernatants were separated from cell pellets. Cells were then resuspended in the same volume of PBS and lysed by mixing with an equal volume of 2x lysis buffer [100 mM Tris pH 7.5, 300 mM NaCl, 1% NP-40, 0.2% SDS, 0.25 mM MgCl₂, 0.02 mg/ml RNase A (Sigma, St. Louis, MO) and 2,000 units/ml DNase I (Sigma)]. Both supernatants and lysates were then boiled with SDS-loading buffer and resolved in a 6% SDS polyacrylamide gel. Proteins were transferred to PVDF membrane (Millipore, Billerica, MA) and detected by a mixture of monoclonal antibodies, KKl 9 and SIV- 101 and an ECL Plus western blotting detection kit (GE Healthcare). EXAMPLE VIII

References

Binley et el. (200O) J. Virol. 74:627

Chen et al. (200O) J. Biol. Chem. 275:34946

Edwards et al. (2001) J. Virol. 75:5230

Helseth et al. (1991) J. Virol. 65:2119

Ho et al. (2006) J. Virol. 80:4017

Jacobs et al. (2005) J. Biol. Chem. 280:27284

Kent et al. (1991) Λzώ 5:829

Lin et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100:11013

Maerz et al. (2001) J. Virol. 75:6635

Skehel et al. (2000) Ann. Rev. ofBiochem. 69

Wang et al. (2003) J. Med. Chem. 46:4236

Wilson et al. (1981) Nature 289:366

Wyatt et al. (1997) J. Virol. 71 :9722

York et al. (2004) J. Virol. 78:4921

Zhang et al. (2001) Biochemistry 40:1662

EXAMPLE IX Immunogenic Assays

[082] The gpl20 deletion proteins of the present invention and nucleic acid sequences encoding these proteins will be used in immunogenic assays, such as those described in Kothe et al. (2006) Virology 352:438.

Guinea Pig Immunization and Serum Collection

[083] Female Hartley guinea pigs (Harlan Sprague, Indianapolis, IN) will be immunized intramuscularly three times at three week intervals with 400 μg plasmid DNA. Two weeks following the last immunization, 5 mL of blood will be collected from each animal via the cranial vena cava. Sera will be obtained by tabletop centrifugation using Beckton Dickinson SST tubes (BD, Franklin Lakes, NJ) as directed by the manufacturer. Samples will be stored at -20 ⁰C until analysis. Endpoint Binding Titer ELISA

[084] Guinea pig sera will be tested for binding antibodies to a gpl20 deletion protein and/or wild-type gpl20 by enzyme linked immunosorbent assay (ELISA). Microtiter plates will be coated with gpl20 deletion protein and/or wild-type gpl20 (0.5 μg/mL in PBS), washed, and blocked with 200 μl/well 5% nonfat milk in PBS-T. Serial five-fold dilutions will be made of each guinea pig serum, added to individual wells, and set to incubate for one hour at 37 ⁰C. Following a wash, 100 μl of HRP- conjugated goat anti-guinea pig antibody (ICN Pharmaceuticals, Costa Mesa, CA) diluted 1 :50,000 in blocking buffer will be added to each well. After an additional one hour incubation at 37 ⁰C, 100 ml of liquid TMB (3,3',5,5'-tetramethylbenzidine) will be added to each well. Reactions will be stopped by the addition of 100 μl of 4N sulfuric acid. Absorbances will be read at 405 nm. Endpoint titers will be determined as the serum titer at which the absorbance value is 2x the mean OD of the negative serum control.

Immunization of Mice and Splenocvtes Isolation

[085] Female BALB/c mice will be purchased from Charles River Laboratories

(Raleigh, NC). Four mice per group will be immunized intramuscularly in the quadriceps with plasmid DNA encoding a gpl20 deletion protein four times at three week intervals. Two weeks after the fourth DNA immunization, mice will be euthanized and spleens will be collected. Spleens from individual mice will be minced and forced through a 70-μm nylon cell strainer (BD Labware, Franklin Lakes, NJ). Splenocytes will then be washed, treated with ACK lysis buffer and will be resuspended in HEPE S -buffered complete RPMI medium with 10% fetal bovine serum, gentamicin (50 μg/mL), 10 mM non-essential amino acids and 0.053 mM β- mercaptethanol.

Enzyme Linked Immune Spot (ELISpof) Assay

[086] Single-cell suspensions of mouse splenocytes will be plated in 96-well polyvinylidene difluoride -backed plates (MultiScreen-IP, Millipore, Billerica, MA) coated with 50 μl of anti-mouse IFN-γ Mab ANl 8 (5 μg/mL; Mabtech, Stockholm, Sweden) overnight at 4 ⁰C. The plates will be blocked with HEPES-buffered complete RPMI medium at 37 ⁰C for two hours. Equal volumes (50 μl) of each splenocytes-stimulating peptide pool and splenocytes (10⁷ cells/mL) will be added to the plates in duplicate. Wells containing cells and complete RPMI medium will serve as negative controls, whereas wells containing cells and concavalin A (5 μg/mL) (Sigma, St, Louis, MO) will serve as positive controls. Plates will be incubated overnight (14 - 16 hours) at 37 ⁰C with 5% CO₂. After the plates are washed six times with phosphate buffered saline (PBS), 50 μl of l :1000-diluted biotinylated anti- mouse IFN-γ mAb (Mabtech) will be added to each well. Plates will then be incubated at room temperature for two hours, washed three times with PBS, and 50 μl of streptavidin-alkaline phosphatase conjugate (1 :1000 dilution, Mabtech) will be added to each well. After incubation for one hour at room temperature, plates will be washed five times with PBS-T, and 100 μl of BCIP/NBT (Plus) alkaline phosphatase substrate (Moss, Pasadena, CA) will be added to each well. Following an incubation for ten minutes at room temperature and a final wash with water, plates will be air- dried. Spots will be counted using an automated ELISpot plate reader (Immunospot counting system, CTL Analyzers, Cleveland, OH) and expressed as spot-forming cells (SFC) per 10⁶ splenocytes. Responses will be considered positive if the number of spots is four times greater than the negative control and at least 50 SFC/10⁶ cells/well.

Claims

What is claimed is:

1. A method of inducing an immune response against HIV in a subject comprising: administering to the subject pharmaceutical composition including a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region, such that an immune response against HIV is induced.

2. The method of claim 1, wherein the gpl20 protein has five or more amino acids deleted from its β3-β5 loop region.

3. The method of claim 1 , wherein the subject is infected with HIV.

4. The method of claim 3, wherein the subject is therapeutically treated.

5. The method of claim 1 , wherein the subject is prophylactically treated.

6. A method of treating a subject infected with HIV comprising: administering to the subject an antibody specific against a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region, such that the subject is treated.

7. A vaccine against HIV comprising: an expression vector comprising a nucleic acid sequence encoding a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region.

8. An isolated nucleic acid sequence which encodes a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region.

9. An isolated polypeptide comprising a gpl20 protein having two or more amino acids deleted from its β3-β5 loop region.