WO2003060067A2 - P85-alpha nucleic acids, polypeptides and related methods - Google Patents

Abstract

The present application provides compositions and methods for inhibiting viral infections and/or viral maturation. The application also provides screening assays to identify small molecules for treating such viral infections. The present application also provides compositions of protein complexes containing p85 and p85-associating proteins.

Description

P85-ALPHA NUCLEIC ACIDS, POLYPEPTIDES AND RELATED

METHODS

BACKGROUND Viral maturation requires the proteolytic processing of the Gag proteins and the activity of the host proteins. It is believed that cellular machineries for exo/endocytosis and for ubiquitin conjugation may be involved in the maturation. In particular, the assembly and subsequent budding of retro viruses, rhabdoviruses, and filoviruses depends on the Gag polyprotein. After its synthesis, Gag is targeted to the plasma membrane where it induces budding of nascent virus particles.

The role of ubiquitin in virus assembly was suggested by Dunigan et al. (1988, Virology 165, 310, Meyers et al. 1991, Virology 180, 602), who observed that mature virus particles were enriched in unconjugated ubiquitin. More recently, it was shown that proteasome inhibitors suppress the release of HIV- 1, HIV-2 and virus-like particles derived from SIV and RSV Gag. Also, inhibitors affect Gag processing and maturation into infectious particles (Schubert et al 2000, PNAS 97, 13057, Harty et al. 2000, PNAS 97, 13871, Strack et al. 2000, PNAS 97, 13063, Patnaik et al. 2000, PNAS 97, 13069).

It is well known in the art that ubiquitin-mediated proteolysis is the major pathway for the selective, controlled degradation of intracellular proteins in eukaryotic cells. Ubiquitin modification of a variety of protein targets within the cell appears to be important in a number of basic cellular functions such as regulation of gene expression, regulation of the cell-cycle, modification of cell surface receptors, biogenesis of ribosomes, and DNA repair. One major function of the ubiquitin-mediated system is to control the half-lives of cellular proteins. The half-life of different proteins can range from a few minutes to several days, and can vary considerably depending on the cell-type, nutritional and environmental conditions, as well as the stage of the cell-cycle.

Targeted proteins undergoing selective degradation, presumably through the actions of a ubiquitin-dependent proteosome, are covalently tagged with ubiquitin through the formation of an isopeptide bond between the C-terminal glycyl residue

8870445 4 DOC of ubiquitin and a specific lysyl residue in the substrate protein. This process is catalyzed by a ubiquitin-activating enzyme (El) and a ubiquitin-conjugating enzyme (E2), and in some instances may also require auxiliary substrate recognition proteins (E3s). Following the linkage of the first ubiquitin chain, additional molecules of ubiquitin may be attached to lysine side chains of the previously conjugated moiety to form branched multi-ubiquitin chains.

The conjugation of ubiquitin to protein substrates is a multi-step process. In an initial ATP requiring step, a thioester is formed between the C-terminus of ubiquitin and an internal cysteine residue of an El enzyme. Activated ubiquitin is then transferred to a specific cysteine on one of several E2 enzymes. Finally, these E2 enzymes donate ubiquitin to protein substrates. Substrates are recognized either directly by ubiquitin-conjugated enzymes or by associated substrate recognition proteins, the E3 proteins, also known as ubiquitin ligases.

In addition to the membrane reorganization required for release of viral particles, viral maturation involves substantial coordination and assembly of host and viral proteins at the plasma membrane. Phosphatidylinositol-3-kinase (PI3K) is a heteromultimeric enzyme that phosphorylates the membrane lipid phosphatidylinositol. When the lipid is phosphorylated at the 3 position on the inositol ring, it interacts with a wide range of proteins involved in processes such as cytoskeletal rearrangement, membrane dynamics, signal transduction, etc. PI3Ks typically consist of a 110 kDa catalytic subunit (pi 10) and one or more regulatory subunits that range in approximate molecular weight from 50 to 85 kDa. The 85 kDa regulatory subunits are termed p85. The 110 kDa subunits typically include an N-terminal region that interacts with regulatory protein subunits, a domain that binds a small G protein Ras, a PIK domain and a C- terminal catalytic subunit. The two primary p85 isoforms are p85-alpha and p85-gamma. These subunits do not have a lipid kinase activity but do contain SH2 and SH3 domains that allow the proteins to interact with tyrosine kinase receptors and then transduce the signal to the catalytic subunit. The gene coding for p85-alpha gives rise to splice variants termed p50- alpha and p55-alpha, which also regulate PI3K activity.

8870445 4 DOC — 2 — SUMMARY OF THE INVENTION

It is proposed that a variety of proteins, including ubiquitin protein ligases and proteins involved in membrane trafficking, are recruited to the site of viral budding by direct or indirect interaction with viral proteins, for example Gag proteins. The ligase then ubiquitinates viral and/or cellular proteins that that are part of the membrane remodeling machinery. For example, two Gag protein motifs, PxxP and PPxY, are known to recruit proteins involved in viral budding.

To this end, the invention provides p85-alpha (hereinafter referred to as simply "p85") nucleic acid sequences and proteins encoded thereby. In certain embodiments p85 proteins play a role in viral maturation. In cells infected with viruses that utilize a Gag-dependent pathway for budding and release, p85 acts in the assembly of complexes that mediate release. p85 complexes may stimulate, for example, phosphorylation of membrane lipids, ubiquitylation of certain proteins or stimulate membrane fusion, or all of these. As one of skill in the art can readily appreciate, a p85 protein may form multiple different complexes at different times. In certain embodiments, p85 interacts directly or indirectly with a Gag protein and/or a protein comprising a sequence motif of RXXPXXP. In further embodiments, p85, through its interaction with a Gag protein, recruits the PI3K enzyme to the site of viral budding. In certain embodiments, the localized activity of PI3K assists in the transport of viral proteins and/or assemblies thereof from endosomes to the plasma membrane.

In some aspects, the invention provides nucleic acid sequences and proteins encoded thereby, as well as probes derived from the nucleic acid sequences, antibodies directed to the encoded proteins, and diagnostic methods for detecting cells infected with a virus, preferably an RNA virus and particulalry a retrovirus. In one aspect, the invention provides an isolated nucleic acid comprising a nucleotide sequence which hybridizes under stringent conditions to a sequence of SEQ ID NOS: 1 and/or 3 or a sequence complementary thereto. In a related embodiment, the nucleic acid is at least about 60%, 70%, 80%, 90%, 95%, or 97- 98%, or 100% identical to a sequence corresponding to at least about 12, at least about 15, at least about 25, at least about 40, at least about 100, at least about 300, at least about 500, at least about 1000, or at least about 2000 consecutive nucleotides

887044₅ 4.DOC -- 3 — up to the full length of SEQ ID NO: 1 and/or 3, or a sequence complementary thereto.

In other embodiments, the invention provides a nucleic acid comprising a nucleotide sequence which hybridizes under stringent conditions to a sequence of SEQ ID NOS. 1 and/or 3, or a nucleotide sequence that is at least about 60%, 70%, 80%, 90%, 95%, or 97-98%, or 100% identical to a sequence corresponding to at least about 12, at least about 15, at least about 25, at least about 40, at least about 100, at least about 300, at least about 500, at least about 1000, or at least about 2000 consecutive nucleotides up to the full length of SEQ ID NO: 1 and/or 3, or a sequence complementary thereto, and a transcriptional regulatory sequence operably linked to the nucleotide sequence to render the nucleotide sequence suitable for use as an expression vector. In another embodiment, the nucleic acid may be included in an expression vector capable of replicating in a prokaryotic or eukaryotic cell. In a related embodiment, the invention provides a host cell transfected with the expression vector.

In yet another embodiment, the invention provides a substantially pure nucleic acid which hybridizes under stringent conditions to a nucleic acid probe corresponding to at least about 12, at least about 15, at least about 25, or at least about 40 consecutive nucleotides up to the full length of SEQ ID NO:l and/or 3, or a sequence complementary thereto or up to the full length of the gene of which said sequence is a fragment. The invention also provides an antisense oligonucleotide analog which hybridizes under stringent conditions to at least 12, at least 25, or at least 50 consecutive nucleotides up to the full length of SEQ ID NO:l, or a sequence complementary thereto. In a further embodiment, the invention provides a nucleic acid comprising a nucleic acid encoding an amino acid sequence as set forth in SEQ LO NO:2, or a nucleic acid complement thereof. In a related embodiment, the encoded amino acid sequence is at least about 60%, 70%, 80%, 90%, 95%, or 97-98%, or 100% identical to a sequence corresponding to at least about 12, at least about 15, at least about 25, or at least about 40, at least about 100, at least about 200, at least about 300, at least about 400 or at least about 500 consecutive amino acids up to the full length of SEQ ID NO:2.

8870445 4.DOC — 4 — In another embodiment, the invention provides a probe/primer comprising a substantially purified oligonucleotide, said oligonucleotide containing a region of nucleotide sequence which hybridizes under stringent conditions to at least about 12, at least about 15, at least about 25, or at least about 40 consecutive nucleotides of sense or antisense sequence selected from SEQ ID NO: 1 and/or 3, or a sequence complementary thereto. In preferred embodiments, the probe selectively hybridizes with a target nucleic acid. In another embodiment, the probe may include a label group attached thereto and able to be detected. The label group may be selected from radioisotopes, fluorescent compounds, enzymes, and enzyme co-factors. The invention further provides arrays of at least about 10, at least about 25, at least about 50, or at least about 100 different probes as described above attached to a solid support.

In another aspect, the invention provides polypeptides. In one embodiment, the invention pertains to a polypeptide including an amino acid sequence encoded by a nucleic acid comprising a nucleotide sequence which hybridizes under stringent conditions to a sequence of SEQ ID NO:l and/or 3, or a sequence complementary thereto, or a fragment comprising at least about 25, or at least about 40 amino acids thereof.

In a preferred embodiment, the p85 polypeptide comprises a sequence that is identical with or homologous to SEQ ID NO:2. For instance, a p85 polypeptide preferably has an amino acid sequence at least 60% homologous to a polypeptide represented by SEQ ID NO:2 and polypeptides with higher sequence homologies of, for example, 60%, 70%, 80%, 90% or 95% are also contemplated. The ρ85 polypeptide can comprise a full length protein, such as represented in the sequence listings, or it can comprise a fragment of, for instance, at least 5, 10, 20, 50, 100, 150, 200, 250, 300, 400 or 500 or more amino acids in length. In certain embodiments, the p85 polypeptide interacts with a viral Gag protein.

In another preferred embodiment, the invention features a purified or recombinant polypeptide fragment of a p85 polypeptide, which polypeptide has the ability to modulate, e.g., mimic or antagonize, an activity of a wild-type p85 protein. Preferably, the polypeptide fragment comprises a sequence identical or homologous to an amino acid sequence designated in SEQ ID NO:2.

₈₈₇0445 4.DOC ~ 5 — Moreover, as described below, the p85 polypeptide can be either an agonist (e.g. mimics), or alternatively, an antagonist of a biological activity of a naturally occurring form of the protein, e.g., the polypeptide is able to modulate the intrinsic biological activity of a p85 protein or a p85 complex, such as an enzymatic activity, binding to other cellular components, cellular compartmentalization, membrane reorganization and the like.

The subject proteins can also be provided as chimeric molecules, such as in the form of fusion proteins. For instance, the p85 polypeptide can be provided as a recombinant fusion protein which includes a second polypeptide portion, e.g., a second polypeptide having an amino acid sequence unrelated (heterologous) to p85, e.g. the second polypeptide portion is glutathione-S-transferase, e.g. the second polypeptide portion is an enzymatic activity such as alkaline phosphatase, e.g. the second polypeptide portion is an epitope tag, etc.

Yet another aspect of the present invention concerns an immunogen comprising a p85 polypeptide in an immunogenic preparation, the immunogen being capable of eliciting an immune response specific for the p85 polypeptide; e.g. a humoral response, e.g. an antibody response; e.g. a cellular response. In preferred embodiments, the immunogen comprises an antigenic determinant, e.g. a unique determinant, from a protein represented by SEQ ID NO:2. In yet another aspect, this invention provides antibodies immunoreactive with one or more p85 polypeptides. In one embodiment, antibodies are specific for an SH3 domain or an SH2 domain derived from a p85 polypeptide. In a more specific embodiment, the domain is part of an amino acid sequence set forth in SEQ ID NO:2. In a set of exemplary embodiments, an antibody binds to an SH3 domain represented by amino acids 3-79 of SEQ ID NO:2. In another exemplary embodiment, an antibody binds to one or more SH2 domains represented by amino acids 333-428 and 624-718 of SEQ ID NO:2. In another embodiment, the antibodies are immunoreactive with one or more proteins having an amino acid sequence that is at least 60%, 70%, or 80% identical, at least 90% identical or at least 95% identical to an amino acid sequence as set forth in SEQ ID NO:2. In other embodiments, an antibody is immunoreactive with one or more proteins having an

8870445 4.DOC — 6 — amino acid sequence that is 85%, 90%, 95%, 98%, 99% or identical to an amino acid sequence as set forth in SEQ ID NO:2.

In certain embodiments, the subject p85 nucleic acids will include a transcriptional regulatory sequence, e.g. at least one of a transcriptional promoter or transcriptional enhancer sequence, which regulatory sequence is operably linked to the p85 sequence. Such regulatory sequences can be used to render the p85 sequence suitable for use as an expression vector.

In yet another aspect, the invention provides an assay for screening test compounds for inhibitors, or alternatively, potentiators, of an interaction between a p85 polypeptide and a p85-associated protein (p85-AP) such as a late domain region of an RNA virus such as a retrovirus. An exemplary method includes the steps of (i) combining p85-AP, a p85 polypeptide, and a test compound, e.g., under conditions wherein, but for the test compound, the p85 polypeptide and p85-AP are able to interact; and (ii) detecting the formation of a complex which includes the p85 polypeptide and a p85-AP. A statistically significant change, such as a decrease, in the formation of the complex in the presence of a test compound (relative to what is seen in the absence of the test compound) is indicative of a modulation, e.g., inhibition, of the interaction between the p85 polypeptide and p85-AP.

In yet another aspect, the invention provides cells carrying a recombinant form of a p85 nucleic acid, often included on a vector. In further embodiments, cells carry a recombinant form of p85 and a recombinant form of a Gag protein and/or a polypeptide comprising an RXXPXXP motif. In certain aspects, the cells are bacterial, and in other aspects the cells are eukaryotic cells, preferrably a mammalian cell line. The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Patent No: 4,683,195; Nucleic Acid Hybridization (B.

8870445_4 DOC — 7 — D. Hames & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).

Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 : Nucleic acid sequence encoding human p85-alpha (SEQ ID NO:l).

Figure 2: Amino acid sequence of human p85-alpha (SEQ ED NO:2).

Figure 3: Nucleic acid cDNA sequence encoding human p85-alpha (SEQ ED NO:3). Figure 4: p85 crosslinks and co-immunoprecipitates with p24 Gag in HIV- transfected cells. Immunoprecipitation was performed using anti-p24 sheep polyclonal antibody.

4A: Silver stain of immuno-precipitated proteins from HIV transfected and non- transfected cell lysates. 4B: Western blot of Gag protein using rabbit anti-p24 polyclonal antibody (55kD and 24 kD). 4C: Western blot of PI3K (85kD). Figure 5: Reciprocal co-immunoprecipitation of p85 with p24 Gag in HIV- transfected cells. 5 A: Western blot of Gag protein using rabbit anti-p24 polyclonal antibody (55kD and 24 kD). For each lane from left to right, immunoprecipitation was performed using anti-p24 sheep polyclonal antibody, anti-PI3k antibody, and anti-p24 sheep polyclonal antibody, respectively. 5B: Western blot of PI3K (85kD). For each lane from left to right, immunoprecipitation was performed using anti-p24

8870445 4 DOC ~ 8 — sheep polyclonal antibody, anti-PI3k antibody, and anti-p24 sheep polyclonal antibody, respectively, nt: non-transfected; wt: with HIV-transfection. Figure 6: PI3K inhibitor LY inhibitor inhibits the release of virus-like-particles (VLP). Posphohimages of SDS-PAGE gels of immunoprecipitations of 35S pulse- chase labeled Gag proteins are presented for cell and viral lysates from transfected HeLa cells that where either untreated (control) or treated with LY. The time during the chase period (1, 2, 3, 4 and 5 after the pulse) are presented from left to right for control and for LY-treated samples.

DETAILED DESCREPTION OF THE INVENTION 1. Definitions

The term "binding" refers to a direct association between two molecules, due to, for example, covalent, electrostatic, hydrophobic, ionic and/or hydrogen-bond interactions under physiological conditions.

"Cells," "host cells" or "recombinant host cells" are terms 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. A "chimeric protein" or "fusion protein" is a fusion of a first amino acid sequence encoding a polypeptide with a second amino acid sequence defining a domain foreign to and not substantially homologous with any domain of the first amino acid sequence. A chimeric protein may present a foreign domain which is found (albeit in a different protein) in an organism which also expresses the first protein, or it may be an "interspecies", "intergenic", etc. fusion of protein structures expressed by different kinds of organisms.

The terms "compound", "test compound" and "molecule" are used herein interchangeably and are meant to include, but are not limited to, peptides, nucleic acids, carbohydrates, small organic molecules, natural product extract libraries, and

8870445 4.DOC — 9 — any other molecules (including, but not limited to, chemicals, metals and organometallic compounds).

The phrase "conservative amino acid substitution" refers to grouping of amino acids on the basis of certain common properties. A functional way to define common properties between individual amino acids is to analyze the normalized frequencies of amino acid changes between corresponding proteins of homologous organisms (Schulz, G. E. and R. H. Schirmer., Principles of Protein Structure,

Springer- Verlag). According to such analyses, groups of amino acids may be defined where amino acids within a group exchange preferentially with each other, and therefore resemble each other most in their impact on the overall protein structure (Schulz, G. E. and R. H. Schirmer., Principles of Protein Structure,

Springer- Verlag). Examples of amino acid groups defined in this manner include:

(i) a charged group, consisting of Glu and Asp, Lys, Arg and His,

(ii) a positively-charged group, consisting of Lys, Arg and His, (iii) a negatively-charged group, consisting of Glu and Asp,

(iv) an aromatic group, consisting of Phe, Tyr and Trp,

(v) a nitrogen ring group, consisting of His and Trp,

(vi) a large aliphatic nonpolar group, consisting of Val, Leu and He,

(vii) a slightly-polar group, consisting of Met and Cys, (viii) a small-residue group, consisting of Ser, Thr, Asp, Asn, Gly, Ala, Glu, Gin and Pro,

(ix) an aliphatic group consisting of Val, Leu, He, Met and Cys, and

(x) a small hydroxyl group consisting of Ser and Thr.

In addition to the groups presented above, each amino acid residue may form its own group, and the group formed by an individual amino acid may be referred to simply by the one and/or three letter abbreviation for that amino acid commonly used in the art.

A "conserved residue" is an amino acid that is relatively invariant across a range of similar proteins. Often conserved residues will vary only by being replaced with a similar amino acid, as described above for "conservative amino acid substitution".

8870445 4 DOC — 10 — The term "domain" as used herein refers to a region of a protein that comprises a particular structure and/or performs a particular function.

A "HECT domain" is a protein domain involved in E3 ubiquitin ligase activity. Certain HECT domains are 100 - 400 amino acids in length and comprise an amino acid sequence as set forth in the following consensus sequence: Pro Xaa3 Thr Cys Xaa2-4 Leu Xaa Leu Pro Xaa Tyr.

Preferred HECT domains of the invention have ubiquitin ligase activity. Preferably, the conserved Cys of a HECT domain forms a thioester with a ubiquitin. E6-AP is the best characterized E3 ligase of the Hect-domain class of proteins. E6- AP was originally identified through its interaction with the E6 oncoprotein of the cancer-associated human papillomavirus types 16 and 18. The E6/E6-AP complex specifically binds to the tumor suppressor protein p53 and induces its ubiquitination and subsequent degradation. The cysteine residue necessary for thioester formation of E6-AP with ubiquitin is conserved among all of the Hect-domain class proteins. Because of this similarity these proteins have been termed Hect proteins, for 'Homologous to E6-AP C Terminus (HECT) (Huibregtse et al. (1995) PNAS 92:2563-2567).

"Homology" or "identity" or "similarity" refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology and identity can each be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When an equivalent position in the compared sequences is occupied by the same base or amino acid, then the molecules are identical at that position; when the equivalent site occupied by the same or a similar amino acid residue (e.g., similar in steric and/or electronic nature), then the molecules can be referred to as homologous (similar) at that position. Expression as a percentage of homology/similarity or identity refers to a function of the number of identical or similar amino acids at positions shared by the compared sequences. A sequence which is "unrelated" or "non-homologous" shares less than 40% identity, though preferably less than 25% identity with a sequence of the present invention. In comparing two sequences, the absence of residues (amino acids or nucleic acids) or presence of extra residues also decreases the identity and homology/similarity.

8870445 4.DOC — 1 1 -- The term "homology" describes a mathematically based comparison of sequence similarities which is used to identify genes or proteins with similar functions or motifs. The nucleic acid and protein sequences of the present invention may be used as a "query sequence" to perform a search against public databases to, for example, identify other family members, related sequences or homologs. Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J Mol. Biol. 215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to nucleic acid molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Res. 25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and BLAST) can be used. See http://www.ncbi.nlm.nih.gov.

As used herein, "identity" means the percentage of identical nucleotide or amino acid residues at corresponding positions in two or more sequences when the sequences are aligned to maximize sequence matching, i.e., taking into account gaps and insertions. Identity can be readily calculated by known methods, including but not limited to those described in (Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; and Carillo, H., and Lipman, D., SEAM J. Applied Math., 48: 1073 (1988). Methods to determine identity are designed to give the largest match between the sequences tested. Moreover, methods to determine identity are codified in publicly available computer programs. Computer program methods to determine identity between two sequences include, but are not limited to, the GCG program package (Devereux, J., et al., Nucleic Acids Research

8870445 4 DOC — 12 -- 12(1): 387 (1984)), BLASTP, BLASTN, and FASTA (Altschul, S. F. et al., J. Molec. Biol. 215: 403-410 (1990) and Altschul et al. Nuc. Acids Res. 25: 3389-3402 (1997)). The BLAST X program is publicly available from NCBI and other sources (BLAST Manual, Altschul, S., et al., NCBI NLM NIH Bethesda, Md. 20894; Altschul, S., et al., J. Mol. Biol. 215: 403-410 (1990). The well known Smith Waterman algorithm may also be used to determine identity.

The term "intron" refers to a portion of nucleic acid that is intially transcribed into RNA but later removed such that it is not, for the most part, represented in the processed mRNA. Intron removal occurs through reactions at the 5' and 3' ends, typically referred to as 5' and 3' splice sites, respectively. Alternate use of different splice sites results in splice variants. An intron is not necessarily situated between two "exons", or portions that code for amino acids, but may instead be positioned, for example, between the promoter and the first exon. An intron may be self-splicing or may require cellular components to be spliced out of the mRNA. A "heterologous intron" is an intron that is inserted into a coding sequence that is not naturally associated with that coding sequence. In addition, a heterologous intron may be a genrally natural intron wherein one or both of the splice sites have been altered to provide a desired quality, such as increased or descreased splice efficiency. Heterologous introns are often inserted, for example, to improve expression of a gene in a heterologous host, or to increase the production of one splice variant relative to another. As an example, the rabbit beta-globin gene may be used, and is commercially available on the pCI vector from Promega Inc. Other exemplary introns are provided in Lacy-Hulbert et al. (2001) Gene Ther 8(8):649- 53. The term "isolated", as used herein with reference to the subject proteins and protein complexes, refers to a preparation of protein or protein complex that is essentially free from contaminating proteins that normally would be present with the protein or complex, e.g., in the cellular milieu in which the protein or complex is found endogenously. Thus, an isolated protein complex is isolated from cellular components that normally would "contaminate" or interfere with the study of the complex in isolation, for instance while screening for modulators thereof. It is to be understood, however, that such an "isolated" complex may incorporate other

8870445 4. DOC — 13 — proteins the modulation of which, by the subject protein or protein complex, is being investigated.

The term "isolated" as also used herein with respect to nucleic acids, such as DNA or RNA, refers to molecules in a form which does not occur in nature. Moreover, an "isolated nucleic acid" is meant to include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state.

The term "LY294002" or "L", as used herein, refers to the phosphatidylinositol 3-kinase inhibitor, 2-(4-Morpholinyl)-8-phenyl-4 H-l- benzopyran-4-one; as described by Vlahos, et al. (1994) J. Biol., Chem., 269(7) 5241-5248, and is available from Calbiochem Corp., La Jolla Calif.

As used herein, the term "nucleic acid" refers to polynucleotides such as deoxyribonucleic acid (DNA), and, where appropriate, ribonucleic acid (RNA). The term should also be understood to include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs, and, as applicable to the embodiment being described, single-stranded (such as sense or antisense) and double-stranded polynucleotides.

The term "maturation" as used herein refers to the processing of viral proteins leading to the pinching off of nascent virion from the cell membrane. A "membrane associated protein" is meant to include proteins that are integral membrane proteins as well as proteins that are stably associated with a membrane.

The term "p6" or pόgag" is used herein to refer to a protein comprising a viral L domain. Antibodies that bind to a p6 domain are referred to as "anti-p6 antibodies". p6 also refers to proteins that comprise artificially engineered L domains including, for example, L domains comprising a series of L motifs. The term "Gag protein" or "Gag polypeptide" refers to a polypeptide having Gag activity and preferably comprising an L (or late) domain. Exemplary Gag proteins include a motif such as PXXP, PPXY, RXXPXXP, RPDPTAP, RPLPVAP, RPEPTAP, and/or RPEPTAPPEE. HIV p24 is an exemplary Gag polypeptide.

8870445 4.DOC — 14 — "p85" unless otherwise specified relates to p85-alpha. If it is intended to refer to another p85, such as p85-gamma, this will be specified.

A "p85 nucleic acid" is a nucleic acid comprising a sequence as represented in SEQ ID NO:l or 3, as well as any of the variants described herein. Exemplary p85 nucleic acids include but are not limited to the following NCBI database entries: AK000121, BF670313, BF966441, BF338662, AI860800, AI571125, AI679268, AI679842, R54049, R54050 and AI613450.

A "p85 polypeptide" or "p85 protein" is a polypeptide comprising a sequence as represented in SEQ ED NO:2 as well as any of the variations described herein. Exemplary p85 polypeptides include, but are not limited to, M. musculus p85 (P26450), R. norvegicus p85 (Q63787) and C. elegans protein C38D4.5 (T19825).

A "p85 complex" as used herein includes a p85 polypeptide and at least one one the following polypeptides A "p85-associated protein" or "p85-AP" refers to a protein capable of interacting with and/or binding to a p85 polypeptide. Generally, the p85-AP may interact directly or indirectly with the p85 polypeptide. Exemplary p85-APs are provided throughout.

The term "PI3K" refers to a phosphatidylinositol (PI) 3 '-kinase, a family of proteins that phosphorylate the inositol ring of PI in the D-3 position. The canonical mammalian PI3K is a heterodimeric complex that contains p85 and a 110-Kd protein (ρl 10) (Carpenter et al. (1990) J. Biol. Chem. 265, 19704). The purified p85 subunit has a regulatory role while the 110-Kd subunit harbors the catalytic activity.

The "PI3K pathway" refers to the collection of molecular actors that are influenced by the primary effects of PI3K activity. It is understood that a cellular signaling event, such as an increase in the activation of a PI3K, will generally produce effects that occur independent of any changes in gene expression, referred to herein as "primary" effects, such as certain changes in protein-protein interactions, certain changes in protein activities and certain changes in post- translational modifications. The term "PI3K pathway" is not intended to encompass the vast array of actors that become involved only as a result of changes in gene expression.

8870445_4 DOC — 15 — A "PI3K pathway inhibitor" includes any substance or mixture of substances that decreases a cellular activity that is increased in response to PI3K activity. A PI3K pathway inhibitor may be a "PI3K inhibitor".

A "PI3K inhibitor" includes any substance or mixture of substances that act in any one of the following ways, such as decreasing PI3K activity, acting on the catalytic or regulatory subunits of p85, or on the interactions between the catalytic and regulatory subunits with each other, with a substrate, or with another protein. Alternatively, a PI3K pathway inhibitor may act by affecting a part of the PI3K pathway. Exemplary PI3K pathway inhibitors include LY294002, a PI3K-targeted RNAi, etc.

A "profile" is used herein to indicate an aggregate of information regarding a preparation of cell or membrane surface proteins. A profile will comprise, at minimum, information regarding the presence or absence of such proteins. More typically, a profile will comprise information regarding the presence or absence of a plurality of such proteins. In addition, a profile may contain other information about each identified protein, such as relative or absolute amount of protein present, the degree of post-translational modification, membrane topology, three-dimensional structure, isoelectric point, molecular weight, etc. A "test profile" is a profile obtained from a subject of unknown diagnostic state. A "reference profile" is a profile obtained from subject known to be infected or uninfected.

The terms peptides, proteins and polypeptides are used interchangeably herein.

The term "purified protein" refers to a preparation of a protein or proteins which are preferably isolated from, or otherwise substantially free of, other proteins normally associated with the protein(s) in a cell or cell lysate. The term

"substantially free of other cellular proteins" (also referred to herein as "substantially free of other contaminating proteins") is defined as encompassing individual preparations of each of the component proteins comprising less than 20% (by dry weight) contaminating protein, and preferably comprises less than 5% contaminating protein. Functional forms of each of the component proteins can be prepared as purified preparations by using a cloned gene as described in the attached examples. By "purified", it is meant, when referring to component protein preparations used to

8870445 4 DOC — 16 — generate a reconstituted protein mixture, that the indicated molecule is present in the substantial absence of other biological macromolecules, such as other proteins (particularly other proteins which may substantially mask, diminish, confuse or alter the characteristics of the component proteins either as purified preparations or in their function in the subject reconstituted mixture). The term "purified" as used herein preferably means at least 80% by dry weight, more preferably in the range of 85% by weight, more preferably 95-99% by weight, and most preferably at least 99.8% by weight, of biological macromolecules of the same type present (but water, buffers, and other small molecules, especially molecules having a molecular weight of less than 5000, can be present). The term "pure" as used herein preferably has the same numerical limits as "purified" immediately above.

An "RCC1 domain" is a domain that interacts with small GTPases to promote loss of GDP and binding of GTP. Certain RCC1 domains are about 50-60 amino acids in length. Often RCC1 domains are found in a series of repeats. The first RCC 1 domain was identified in a protein called "Regulator of Chromosome Condensation" (RCC1), which interacts with the small GTPase Ran. In the RCC1 protein, a series of seven tandem repeats of a domain of about 50 - 60 amino acids fold to form a beta-propeller structure (Renault et al. Nature 1998 392:9-101). RCC1 domains are known to interact with other types of small GTPases including members of the Arf, Rab, Rac and Rho families.

A "receptor" or "protein having a receptor function" is a protein that interacts with an extracellular ligand or a ligand that is within the cell but in a space that is topologically equivalent to the extracellular space (eg. inside the Golgi, inside the endoplasmic reticulum, inside the nuclear membrane, inside a lysosome or transport vesicle, etc.). Exemplary receptors are identified herein by annotation as such in various public databases. Receptors often have membrane domains. A "recombinant nucleic acid" is any nucleic acid that has been placed adjacent to another nucleic acid by recombinant DNA techniques. A "recombined nucleic acid" also includes any nucleic acid that has been placed next to a second nucleic acid by a laboratory genetic technique such as, for example, tranformation and integration, transposon hopping or viral insertion. In general, a recombined nucleic acid is not naturally located adjacent to the second nucleic acid.

8870445 4.DOC ~ 17 ~ The term "recombinant protein" refers to a protein of the present invention which is produced by recombinant DNA techniques, wherein generally DNA encoding the expressed protein is inserted into a suitable expression vector which is in turn used to transform a host cell to produce the heterologous protein. Moreover, the phrase "derived from", with respect to a recombinant gene encoding the recombinant protein is meant to include within the meaning of "recombinant protein" those proteins having an amino acid sequence of a native protein, or an amino acid sequence similar thereto which is generated by mutations including substitutions and deletions of a naturally occurring protein. A "RING domain" or "Ring Finger" is a zinc-binding domain with a defined octet of cysteine and histidine residues. Certain RING domains comprise the consensus sequences as set forth below: Cys Xaa Xaa Cys XaalO - 20 Cys Xaa His Xaa2-5 Cys Xaa Xaa Cys Xaal3-50 Cys Xaa Xaa Cys or Cys Xaa Xaa Cys XaalO - 20 Cys Xaa His Xaa2-5 His Xaa Xaa Cys Xaal3-50 Cys Xaa Xaa Cys. Preferred RING domains of the invention bind to various protein partners to form a complex that has ubiquitin ligase activity. RING domains preferably interact with at least one of the following protein types: F box proteins, E2 ubiquitin conjugating enzymes and cullins.

"Small molecule" as used herein, is meant to refer to a composition, which has a molecular weight of less than about 5 kD and most preferably less than about 2.5 kD. Small molecules can be nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic (carbon containing) or inorganic molecules. Many pharmaceutical companies have extensive libraries of chemical and/or biological mixtures comprising arrays of small molecules, often fungal, bacterial, or algal extracts, which can be screened with any of the assays of the invention.

An "SH2" or "Src Homology 2" domain is a protein domain of generally about 100 amino acid residues. SH2 domains function as regulatory modules of intracellular signalling cascades by interacting with high affinity to phosphotyrosine- containing target peptides in a sequence-specific and phosphorylation-dependent manner. Exemplary SH2 domains are represented by amino acids 333-428 and 624- 718 of SEQ ED NO:2.

₈₈70445 4.DOC — 18 — An "SH3" or "Src Homology 3" domain is a protein domain of generally about 60 amino acid residues first identified as a conserved sequence in the non- catalytic part of several cytoplasmic protein tyrosine kinases (e.g. Src, Abl, Lck). SH3 domains mediate assembly of specific protein complexes via binding to proline-rich peptides. An exemplary SH3 domain is represented by amino acids 3- 79 of SEQ ID NO:2. In certain embodiments, an SH3 domain interacts with a consensus sequence of RXaaXaaPXaaX6P (where X6, as defined in table 1 below, is a hydrophobic amino acid). In certain embodiments, an SH3 domain interacts with one or more of the following sequences: RPEPTAP, RQGPKEP, RQGPKEPFR, RPEPTAPEE and RPLPVAP.

As used herein, the term "specifically hybridizes" refers to the ability of a nucleic acid probe/primer of the invention to hybridize to at least 12, 15, 20, 25, 30, 35, 40, 45, 50 or 100 consecutive nucleotides of a target gene sequence, or a sequence complementary thereto, or naturally occurring mutants thereof, such that it has less than 15%, preferably less than 10%, and more preferably less than 5% background hybridization to a cellular nucleic acid (e.g., mRNA or genomic DNA) other than the target gene. A variety of hybridization conditions may be used to detect specific hybridization, and the stringency is determined primarily by the wash stage of the hybridization assay. Generally high temperatures and low salt concentrations give high stringency, while low temperatures and high salt concentrations give low stringency. Low stringency hybridization is achieved by washing in, for example, about 2.0 x SSC at 50 °C, and high stringency is acheived with about 0.2 x SSC at 50 °C. Further descriptions of stringency are provided below. As applied to polypeptides, "substantial sequence identity" means that two peptide sequences, when optimally aligned, such as by the programs GAP or BESTFIT using default gap which share at least 90 percent sequence identity, preferably at least 95 percent sequence identity, more preferably at least 99 percent sequence identity or more. Preferably, residue positions which are not identical differ by conservative amino acid substitutions. For example, the substitution of amino acids having similar chemical properties such as charge or polarity are not

8870445 4.DOC — 19 — likely to effect the properties of a protein. Examples include glutamine for asparagine or glutamic acid for aspartic acid.

"Transcriptional regulatory sequence" is a generic term used throughout the specification to refer to DNA sequences, such as initiation signals, enhancers, and promoters, which induce or control transcription of protein coding sequences with which they are operably linked. In preferred embodiments, transcription of a recombinant protein gene is under the control of a promoter sequence (or other transcriptional regulatory sequence) which controls the expression of the recombinant gene in a cell-type in which expression is intended. It will also be understood that the recombinant gene can be under the control of transcriptional regulatory sequences which are the same or which are different from those sequences which control transcription of the naturally-occurring form of the protein. 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 preferred vector is an episome, i.e., a nucleic acid capable of extra-chromosomal replication. Preferred vectors are those capable of autonomous replication and/expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA techniques are often in the form of "plasmids" which refer to circular double stranded DNA loops which, in their vector form are not bound to the chromosome. In the present specification, "plasmid" and "vector" are used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors which serve equivalent functions and which become known in the art subsequently hereto.

A "virion" is a complete viral particle; nucleic acid and capsid (and a lipid envelope in some viruses.

A "WW Domain" is a small functional domain found in a large number of proteins from a variety of species including humans, nematodes, and yeast. WW domains are approximately 30 to 40 amino acids in length. Certain WW domains may be defined by the following consensus sequence (Andre and Springael, 1994, Biochem. Biophys. Res. Comm. 205: 1201-1205): Trp Xaa6-9 Gly Xaal-3 X4 X4

8870445 4 DOC — 20 — Xaa4-6 XI X8 Trp Xaa2 Pro. In certain instances a WW domain will be flanked by stretches of amino acids rich in histidine or cysteine. In some cases, the amino acids in the center of WW domains are quite hydrophobic. Preferred WW domains bind to the L domains of retroviral Gag proteins.

Table 1: Abbreviations for classes of amino acids*

* Abbreviations as adopted from http://smart.embl- heidelberg.de/SMART_DATA/alignments/consensus/grouping.html.

8870445 4.DOC - 21 - 2. Exemplary Nucleic Acids and Expression Vectors

In certain aspects the invention provides nucleic acids encoding p85 polypeptides, such as, for example, SEQ ID NO:2. Nucleic acids of the invention are further understood to include nucleic acids that encode variants of SEQ ID NO:l. Variant nucleotide sequences include sequences that differ by one or more nucleotide substitutions, additions or deletions, such as allelic variants; and will, therefore, include coding sequences that differ from the nucleotide sequence of the coding sequence designated in SEQ ID NO:l e.g., due to the degeneracy of the genetic code. In other embodiments, variants will also include sequences that will hybridize under highly stringent conditions to a nucleotide sequence of a coding sequence designated in SEQ ID NO:l.

One of ordinary skill in the art will understand readily that appropriate stringency conditions which promote DNA hybridization can be varied. For example, one could perform the hybridization at 6.0 x sodium chloride/sodium citrate (SSC) at about 45 °C, followed by a wash of 2.0 x SSC at 50 °C. For example, the salt concentration in the wash step can be selected from a low stringency of about 2.0 x SSC at 50 °C to a high stringency of about 0.2 x SSC at 50 °C. In addition, the temperature in the wash step can be increased from low stringency conditions at room temperature, about 22 °C, to high stringency conditions at about 65 °C. Both temperature and salt may be varied, or temperature or salt concentration may be held constant while the other variable is changed. In one embodiment, the invention provides nucleic acids which hybridize under low stringency conditions of 6 x SSC at room temperature followed by a wash at 2 x

SSC at room temperature.

Isolated nucleic acids which differ from SEQ ID NO:l due to degeneracy in the genetic code are also within the scope of the invention. For example, a number of amino acids are designated by more than one triplet. Codons that specify the same amino acid, or synonyms (for example, CAU and CAC are synonyms for histidine) may result in "silent" mutations which do not affect the amino acid

8870445 4 DOC — 22 — sequence of the protein. However, it is expected that DNA sequence polymorphisms that do lead to changes in the amino acid sequences of the subject proteins will exist among mammalian cells. One skilled in the art will appreciate that these variations in one or more nucleotides (up to about 3-5% of the nucleotides) of the nucleic acids encoding a particular protein may exist among individuals of a given species due to natural allelic variation. Any and all such nucleotide variations and resulting amino acid polymorphisms are within the scope of this invention.

Another aspect of the invention relates to the use of the isolated nucleic acid in "antisense" therapy. As used herein, antisense therapy refers to administration or in situ generation of oligonucleotide probes or their derivatives which specifically hybridize (e.g. binds) under cellular conditions with the cellular mRNA and/or genomic DNA encoding one of the subject p85 polypeptides so as to inhibit expression of that protein, e.g. by inhibiting transcription and/or translation. The binding may be by conventional base pair complementarity, or, for example, in the case of binding to DNA duplexes, through specific interactions in the major groove of the double helix. In general, antisense therapy refers to the range of techniques generally employed in the art, and includes any therapy which relies on specific binding to oligonucleotide sequences. An antisense construct of the present invention can be delivered, for example, as an expression plasmid which, when transcribed in the cell, produces RNA which is complementary to at least a unique portion of the cellular mRNA which encodes a p85 polypeptide. Alternatively, the antisense construct is an oligonucleotide probe which is generated ex vivo and which, when introduced into the cell causes inhibition of expression by hybridizing with the mRNA and/or genomic sequences encoding a p85 polypeptide. Such oligonucleotide probes are preferably modified oligonucleotide which are resistant to endogenous nucleases, e.g. exonucleases and/or endonucleases, and is therefore stable in vivo. Exemplary nucleic acid molecules for use as antisense oligonucleotides are phosphoramidate, phosphothioate and methylphosphonate analogs of DNA (see also U.S. Patents 5,176,996; 5,264,564; and 5,256,775). Additionally, general approaches to constructing oligomers useful in antisense therapy have been reviewed, for example,

8870445 4.DOC — 23 — by van der Krol et al., (1988) Biotechniques 6:958-976; and Stein et al., (1988) Cancer Res 48:2659-2668

Accordingly, the modified oligomers of the invention are useful in therapeutic, diagnostic, and research contexts. In therapeutic applications, the oligomers are utilized in a manner appropriate for antisense therapy in general.

Another aspect of the invention relates to the use of RNA interference (RNAi) to effect knockdown of p85 genes. RNAi constructs comprise double stranded RNA that can specifically block expression of a target gene. "RNA interference" or "RNAi" is a term initially applied to a phenomenon observed in plants and worms where double-stranded RNA (dsRNA) blocks gene expression in a specific and post-transcriptional manner. Without being bound by theory, RNAi appears to involve mRNA degradation, however the biochemical mechanisms are currently an active area of research. Despite some mystery regarding the mechanism of action, RNAi provides a useful method of inhibiting gene expression in vitro or in vivo.

RNAi constructs can comprise either long stretches of double stranded RNA identical or substantially identical to the target nucleic acid sequence or short stretches of double stranded RNA identical to substantially identical to only a region of the target nucleic acid sequence. Exemplary methods of making and delivering either long or short RNAi constructs can be found, for example, in WOOl/68836 and WOO 1/75164.

Exemplary RNAi constructs that specifically recognize a particular gene, or a particular family of genes can be selected using methodology outlined in detail above with respect to the selection of antisense oligonucleotide. Similarly, methods of delivery RNAi constructs include the methods for delivery antisense oligonucleotides outlined in detail above.

Ribozymes molecules designed to catalytically cleave an mRNA transcripts can also be used to prevent translation of mRNA (See, e.g., PCT International

Publication WO90/11364, published October A, 1990; Sarver et al., 1990, Science 247:1222-1225 and U.S. Patent No. 5,093,246). While ribozymes that cleave mRNA at site-specific recognition sequences can be used to destroy particular mRNAs, the

8870445 4 DOC — 24 — use of hammerhead ribozymes is preferred. Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA. The sole requirement is that the target mRNA have the following sequence of two bases: 5'-UG-3'. The construction and production of hammerhead ribozymes is well known in the art and is described more fully in Haseloff and Gerlach, 1988, Nature, 334:585-591.

The ribozymes of the present invention also include RNA endoribonucleases (hereinafter "Cech-type ribozymes") such as the one which occurs naturally in Tetrahymena thermophila (known as the IVS, or L-19 IVS RNA) and which has been extensively described by Thomas Cech and collaborators (Zaug, et al., 1984, Science, 224:574-578; Zaug and Cech, 1986, Science, 231 :470-475; Zaug, et al., 1986, Nature, 324:429-433; published International patent application No. WO88/04300 by University Patents Inc.; Been and Cech, 1986, Cell, 47:207-216). The Cech-type ribozymes have an eight base pair active site that hybridizes to a target RNA sequence whereafter cleavage of the target RNA takes place. The invention encompasses those Cech-type ribozymes that target eight base-pair active site sequences.

As in the antisense approach, the ribozymes can be composed of modified oligonucleotides (e.g., for improved stability, targeting, etc.) and can be delivered to cells that in vitro or in vivo. A preferred method of delivery involves using a DNA construct "encoding" the ribozyme under the control of a strong constitutive pol III or pol II promoter, so that transfected cells will produce sufficient quantities of the ribozyme to destroy targeted messages and inhibit translation. Because ribozymes unlike antisense molecules, are catalytic, a lower intracellular concentration is required for efficiency.

A further aspect of the invention relates to the use of DNA enzymes to inhibit expression of p85 gene. DNA enzymes incorporate some of the mechanistic features of both antisense and ribozyme technologies. DNA enzymes are designed so that they recognize a particular target nucleic acid sequence, much like an antisense oligonucleotide, however much like a ribozyme they are catalytic and specifically cleave the target nucleic acid.

8870445 4.DOC — 25 — There are currently two basic types of DNA enzymes, and both of these were identified by Santoro and Joyce (see, for example, US Patent No. 6110462). The 10-23 DNA enzyme (shown schematically in Figure 1) comprises a loop structure which connect two arms. The two arms provide specificity by recognizing the particular target nucleic acid sequence while the loop structure provides catalytic function under physiological conditions.

Briefly, to design an ideal DNA enzyme that specifically recognizes and cleaves a target nucleic acid, one of skill in the art must first identify the unique target sequence. This can be done using the same approach as outlined for antisense oligonucleotides. Preferably, the unique or substantially sequence is a G/C rich of approximately 18 to 22 nucleotides. High G/C content helps insure a stronger interaction between the DNA enzyme and the target sequence.

When synthesizing the DNA enzyme, the specific antisense recognition sequence that will target the enzyme to the message is divided so that it comprises the two arms of the DNA enzyme, and the DNA enzyme loop is placed between the two specific arms. Schematic representation of DNA enzymes are provided in Figures 1 and 2. Additionally, Figure 3 provides the sequence of a specific DNA enzyme - an XT-I DNA enzyme.

Methods of making and administering DNA enzymes can be found, for example, in US 6110462. Similarly, methods of delivery DNA ribozymes in vitro or in vivo include methods of delivery RNA ribozyme, as outlined in detail above. Additionally, one of skill in the art will recognize that, like antisense oligonucleotide, DNA enzymes can be optionally modified to improve stability and improve resistance to degradation. In another aspect of the invention, the subject nucleic acid is provided in an expression vector comprising a nucleotide sequence encoding a subject p85 polypeptide and operably linked to at least one regulatory sequence. Regulatory sequences are art-recognized and are selected to direct expression of the p85 polypeptide. Accordingly, the term regulatory sequence includes promoters, enhancers and other expression control elements. Exemplary regulatory sequences are described in Goeddel; Gene Expression Technology: Methods in Enzymology,

8870445 4 DOC — 26 — Academic Press, San Diego, CA (1990). For instance, any of a wide variety of expression control sequences that control the expression of a DNA sequence when operatively linked to it may be used in these vectors to express DNA sequences encoding a p85 polypeptide. Such useful expression control sequences, include, for example, the early and late promoters of SV40, tet promoter, adenovirus or cytomegalovirus immediate early promoter, the lac system, the trp system, the TAC or TRC system, T7 promoter whose expression is directed by T7 RNA polymerase, the major operator and promoter regions of phage lambda , the control regions for fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase, e.g., Pho5, the promoters of the yeast -mating factors, the polyhedron promoter of the baculovirus system and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells or their viruses, and various combinations thereof. It should be understood that the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to be expressed. Moreover, the vector's copy number, the ability to control that copy number and the expression of any other protein encoded by the vector, such as antibiotic markers, should also be considered.

As will be apparent, the subject gene constructs can be used to cause expression of the subject p85 polypeptides in cells propagated in culture, e.g. to produce proteins or polypeptides, including fusion proteins or polypeptides, for purification.

This invention also pertains to a host cell transfected with a recombinant gene including a coding sequence for one or more of the subject p85 polypeptides. The host cell may be any prokaryotic or eukaryotic cell. For example, a polypeptide of the present invention may be expressed in bacterial cells such as E. coli, insect cells (e.g., using a baculovirus expression system), yeast, or mammalian cells. Other suitable host cells are known to those skilled in the art.

Accordingly, the present invention further pertains to methods of producing the subject p85 polypeptides. For example, a host cell transfected with an expression vector encoding a p85 polypeptide can be cultured under appropriate

8870445 4 DOC — 27 — conditions to allow expression of the polypeptide to occur. The polypeptide may be secreted and isolated from a mixture of cells and medium containing the polypeptide. Alternatively, the polypeptide may be retained cytoplasmically and the cells harvested, lysed and the protein isolated. A cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art. The polypeptide can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins, including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffmity purification with antibodies specific for particular epitopes of the polypeptide. In a preferred embodiment, the p85 polypeptide is a fusion protein containing a domain which facilitates its purification, such as a p85-GST fusion protein, p85-intein fusion protein, p85-cellulose binding domain fusion protein, p85- polyhistidine fusion protein etc.

A nucleotide sequence encoding a p85 polypeptide can be used to produce a recombinant form of the protein via microbial or eukaryotic cellular processes.

Ligating the polynucleotide sequence into a gene construct, such as an expression vector, and transforming or transfecting into hosts, either eukaryotic (yeast, avian, insect or mammalian) or prokaryotic (bacterial) cells, are standard procedures.

A recombinant p85 nucleic acid can be produced by ligating the cloned gene, or a portion thereof, into a vector suitable for expression in either prokaryotic cells, eukaryotic cells, or both. Expression vehicles for production of a recombinant p85 polypeptides include plasmids and other vectors. For instance, suitable vectors for the expression of a p85 polypeptide include plasmids of the types: pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prokaryotic cells, such as E. coli.

A number of vectors exist for the expression of recombinant proteins in yeast. For instance, YEP24, YEP5, YEP51, YEP52, pYES2, and YRP17 are cloning and expression vehicles useful in the introduction of genetic constructs into S. cerevisiae (see, for example, Broach et al., (1983) in

Experimental Manipulation of Gene Expression, ed. M. Inouye Academic Press, p.

8870445 4.DOC — 28 — 83, incorporated by reference herein). These vectors can replicate in E. coli due the presence of the pBR322 ori, and in S. cerevisiae due to the replication determinant of the yeast 2 micron plasmid. In addition, drug resistance markers such as ampicillin can be used. The preferred mammalian expression vectors contain both prokaryotic sequences to facilitate the propagation of the vector in bacteria, and one or more eukaryotic transcription units that are expressed in eukaryotic cells. The pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, pko-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells. Some of these vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells. Alternatively, derivatives of viruses such as the bovine papilloma virus (BPV-1), or Epstein-Barr virus (pHEBo, pREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells. Examples of other viral (including retroviral) expression systems can be found below in the description of gene therapy delivery systems. The various methods employed in the preparation of the plasmids and transformation of host organisms are well known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells, as well as general recombinant procedures, see Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press, 1989) Chapters 16 and 17. In some instances, it may be desirable to express the recombinant p85 polypeptide by the use of a baculovirus expression system. Examples of such baculovirus expression systems include pVL-derived vectors (such as pVL1392, pVL1393 and ρVL941), pAcUW-derived vectors (such as pAcUWl), and pBlueBac-derived vectors (such as the β-gal containing pBlueBac III).

It is well known in the art that a methionine at the N-terminal position can be enzymatically cleaved by the use of the enzyme methionine aminopeptidase (MAP). MAP has been cloned from E. coli (Ben-Bassat et al., (1987) J. Bacteriol. 169:751-

757) and Salmonella typhimurium and its in vitro activity has been demonstrated on recombinant proteins (Miller et al., (1987) PNAS USA 84:2118-1122). Therefore,

8870445_4.DOC — 29 ~ removal of an N-terminal methionine, if desired, can be achieved either in vivo by expressing such recombinant polypeptides in a host which produces MAP (e.g., E. coli or CM89 or S. cerevisiae), or in vitro by use of purified MAP (e.g., procedure of Miller et al.). Alternatively, the coding sequences for the polypeptide can be incorporated as a part of a fusion gene including a nucleotide sequence encoding a different polypeptide. This type of expression system can be useful under conditions where it is desirable, e.g., to produce an immunogenic fragment of a p85 polypeptide. For example, the VP6 capsid protein of rotavirus can be used as an immunologic carrier protein for portions of polypeptide, either in the monomeric form or in the form of a viral particle. The nucleic acid sequences corresponding to the portion of the p85 polypeptide to which antibodies are to be raised can be incorporated into a fusion gene construct which includes coding sequences for a late vaccinia virus structural protein to produce a set of recombinant viruses expressing fusion proteins comprising a portion of the protein as part of the virion. The Hepatitis B surface antigen can also be utilized in this role as well. Similarly, chimeric constructs coding for fusion proteins containing a portion of a p85 polypeptide and the poliovirus capsid protein can be created to enhance immunogenicity (see, for example, ΕP Publication NO: 0259149; and Evans et al.„ (1989) Nature 339:385; Huang et al., (1988) J. Virol. 62:3855; and Schlienger et al., (1992) J. Virol. 66:2).

The Multiple Antigen Peptide system for peptide-based immunization can be utilized, wherein a desired portion of a p85 polypeptide is obtained directly from organo-chemical synthesis of the peptide onto an oligomeric branching lysine core (see, for example, Posnett et al., (1988) JBC 263:1719 and Nardelli et al., (1992) J. Immunol. 148:914). Antigenic determinants of a p85 polypeptide can also be expressed and presented by bacterial cells.

In another embodiment, a fusion gene coding for a purification leader sequence, such as a poly-(His)/enterokinase cleavage site sequence at the N- terminus of the desired portion of the recombinant protein, can allow purification of the expressed fusion protein by affinity chromatography using a Ni2+ metal resin. The purification leader sequence can then be subsequently removed by treatment

8870445 4 DOC — 30 — with enterokinase to provide the purified p85 polypeptide (e.g., see Hochuli et al., (1987) J. Chromatography Al 1 :177; and Janknecht et al., PNAS USA 88:8972).

Techniques for making fusion genes are well known. Essentially, the joining of various DNA fragments coding for different polypeptide sequences is performed in accordance with conventional techniques, employing blunt-ended or stagger- ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al., John Wiley & Sons: 1992).

3. Exemplary Polypeptides

The present invention also makes available isolated and/or purified forms of the subject p85 polypeptides, which are isolated from, or otherwise substantially free of, other intracellular proteins which might normally be associated with the protein or a particular complex including the protein. In certain embodiments, polypeptides of the invention have an amino acid sequence that is at least 60% identical to an amino acid sequence as set forth in SEQ ID NO:2. In other embodiments, the polypeptide has an amino acid sequence at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to an amino acid sequence as set forth in SEQ ED NO:2. Preferred p85 polypeptides of the invention interact with a viral Gag protein, and preferably through one or more SH3 domain. While not wishing to be bound to theory, it is expected that p85 polypeptides affect viral maturation after being recruited to the site of budding by direct or indirect interaction with a Gag protein. It is further expected that p85 polypeptides recruit a PI3K catalytic domain, such as a pi 10, that participates in viral maturation.

8870445 4.DOC — 31 — In another aspect, the invention provides polypeptides that are agonists or antagonists of a p85 polypeptide. Variants and fragments of a p85 polypeptide may have a hyperactive or constitutive activity, or, alternatively, act to prevent p85 polypeptides from performing one or more functions. For example, a truncated form lacking one or more domain may have a dominant negative effect.

Another aspect of the invention relates to polypeptides derived from a full- length p85 polypeptide. Isolated peptidyl portions of the subject proteins can be obtained by screening polypeptides recombinantly produced from the corresponding fragment of the nucleic acid encoding such polypeptides. In addition, fragments can be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry. For example, any one of the subject proteins can be arbitrarily divided into fragments of desired length with no overlap of the fragments, or preferably divided into overlapping fragments of a desired length. The fragments can be produced (recombinantly or by chemical synthesis) and tested to identify those peptidyl fragments which can function as either agonists or antagonists of the formation of a specific protein complex, or more generally of a p85 complex, such as by microinjection assays.

It is also possible to modify the structure of the subject p85 polypeptides for such purposes as enhancing therapeutic or prophylactic efficacy, or stability (e.g., ex vivo shelf life and resistance to proteolytic degradation in vivo). Such modified polypeptides, when designed to retain at least one activity of the naturally-occurring form of the protein, are considered functional equivalents of the p85 polypeptides described in more detail herein. Such modified polypeptides can be produced, for instance, by amino acid substitution, deletion, or addition. For instance, it is reasonable to expect, for example, that an isolated replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar replacement of an amino acid with a structurally related amino acid (i.e. conservative mutations) will not have a major effect on the biological activity of the resulting molecule. Conservative replacements are those that take place within a family of amino acids that are related in their side chains. Genetically encoded amino acids are can be divided into four families: (1) acidic = aspartate, glutamate; (2) basic = lysine, arginine, histidine; (3) nonpolar =

8870445 4 DOC — 32 — alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar = glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. In similar fashion, the amino acid repertoire can be grouped as (1) acidic = aspartate, glutamate; (2) basic = lysine, arginine histidine, (3) aliphatic = glycine, alanine, valine, leucine, isoleucine, serine, threonine, with serine and threonine optionally be grouped separately as aliphatic-hydroxyl; (4) aromatic = phenylalanine, tyrosine, tryptophan; (5) amide = asparagine, glutamine; and (6) sulfur -containing = cysteine and methionine. (see, for example, Biochemistry, 2nd ed., Ed. by L. Stryer, W.H. Freeman and Co., 1981). Whether a change in the amino acid sequence of a polypeptide results in a functional homolog can be readily determined by assessing the ability of the variant polypeptide to produce a response in cells in a fashion similar to the wild-type protein. For instance, such variant forms of a p85 polypeptide can be assessed, e.g., for their ability to bind to another polypeptide, e.g., another p85 polypeptide or another protein involved in viral maturation. Polypeptides in which more than one replacement has taken place can readily be tested in the same manner.

This invention further contemplates a method of generating sets of combinatorial mutants of the subject p85 polypeptides, as well as truncation mutants, and is especially useful for identifying potential variant sequences (e.g. homologs) that are functional in binding to a p85 polypeptide. The purpose of screening such combinatorial libraries is to generate, for example, p85 homologs which can act as either agonists or antagonist, or alternatively, which possess novel activities all together. Combinatorially-derived homologs can be generated which have a selective potency relative to a naturally occurring p85 polypeptide. Such proteins, when expressed from recombinant DNA constructs, can be used in gene therapy protocols.

Likewise, mutagenesis can give rise to homologs which have intracellular half-lives dramatically different than the corresponding wild-type protein. For example, the altered protein can be rendered either more stable or less stable to proteolytic degradation or other cellular process which result in destruction of, or otherwise inactivation of the p85 polypeptide of interest. Such homologs, and the

8870445 4.DOC — 33 ~ genes which encode them, can be utilized to alter p85 levels by modulating the half- life of the protein. For instance, a short half-life can give rise to more transient biological effects and, when part of an inducible expression system, can allow tighter control of recombinant p85 levels within the cell. As above, such proteins, and particularly their recombinant nucleic acid constructs, can be used in gene therapy protocols.

In similar fashion, p85 homologs can be generated by the present combinatorial approach to act as antagonists, in that they are able to interfere with the ability of the corresponding wild-type protein to function. In a representative embodiment of this method, the amino acid sequences for a population of p85 homologs are aligned, preferably to promote the highest homology possible. Such a population of variants can include, for example, homologs from one or more species, or homologs from the same species but which differ due to mutation. Amino acids which appear at each position of the aligned sequences are selected to create a degenerate set of combinatorial sequences. In a prefened embodiment, the combinatorial library is produced by way of a degenerate library of genes encoding a library of polypeptides which each include at least a portion of potential p85 sequences. For instance, a mixture of synthetic oligonucleotides can be enzymatically ligated into gene sequences such that the degenerate set of potential p85 nucleotide sequences are expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g. for phage display).

There are many ways by which the library of potential homologs can be generated from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be carried out in an automatic DNA synthesizer, and the synthetic genes then be ligated into an appropriate gene for expression. The purpose of a degenerate set of genes is to provide, in one mixture, all of the sequences encoding the desired set of potential p85 sequences. The synthesis of degenerate oligonucleotides is well known in the art (see for example, Narang, SA (1983) Tetrahedron 39:3; Itakura et al., (1981) Recombinant DNA, Proc. 3rd

Cleveland Sympos. Macromolecules, ed. AG Walton, Amsterdam: Elsevier pp273- 289; Itakura et al., (1984) Annu. Rev. Biochem. 53:323; Itakura et al., (1984)

₈870445 4 DOC — 34 — Science 198:1056; Ike et al., (1983) Nucleic Acid Res. 11 :477). Such techniques have been employed in the directed evolution of other proteins (see, for example, Scott et al., (1990) Science 249:386-390; Roberts et al., (1992) PNAS USA 89:2429-2433; Devlin et al., (1990) Science 249: 404-406; Cwirla et al., (1990) PNAS USA 87: 6378-6382; as well as U.S. Patent Nos: 5,223,409, 5,198,346, and 5,096,815).

Alternatively, other forms of mutagenesis can be utilized to generate a combinatorial library. For example, p85 homologs (both agonist and antagonist forms) can be generated and isolated from a library by screening using, for example, alanine scanning mutagenesis and the like (Ruf et al., (1994) Biochemistry 33:1565- 1572; Wang et al., (1994) J. Biol. Chem. 269:3095-3099; Balint et al., (1993) Gene 137:109-118; Grodberg et al., (1993) Eur. J. Biochem. 218:597-601; Nagashima et al., (1993) J. Biol. Chem. 268:2888-2892; Lowman et al., (1991) Biochemistry 30:10832-10838; and Cunningham et al., (1989) Science 244:1081-1085), by linker scanning mutagenesis (Gustin et al., (1993) Virology 193:653-660; Brown et al., (1992) Mol. Cell Biol. 12:2644-2652; McKnight et al., (1982) Science 232:316); by saturation mutagenesis (Meyers et al., (1986) Science 232:613); by PCR mutagenesis (Leung et al., (1989) Method Cell Mol Biol 1:11-19); or by random mutagenesis, including chemical mutagenesis, etc. (Miller et al., (1992) A Short Course in Bacterial Genetics, CSHL Press, Cold Spring Harbor, NY; and Greener et al., (1994) Strategies in Mol Biol 7:32-34). Linker scanning mutagenesis, particularly in a combinatorial setting, is an attractive method for identifying truncated (bioactive) forms of p85 polypeptides.

A wide range of techniques are known in the art for screening gene products of combinatorial libraries made by point mutations and truncations, and, for that matter, for screening cDNA libraries for gene products having a certain property. Such techniques will be generally adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of p85 homologs. The most widely used techniques for screening large gene libraries typically comprises cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates relatively easy isolation

8870445 4.DOC -- 35 ~ of the vector encoding the gene whose product was detected. Each of the illustrative assays described below are amenable to high through-put analysis as necessary to screen large numbers of degenerate sequences created by combinatorial mutagenesis techniques. In an illustrative embodiment of a screening assay, candidate combinatorial gene products of one of the subject proteins are displayed on the surface of a cell or virus, and the ability of particular cells or viral particles to bind a p85 polypeptide is detected in a "panning assay". For instance, a library of p85 variants can be cloned into the gene for a surface membrane protein of a bacterial cell (Ladner et al.„ WO 88/06630; Fuchs et al., (1991) Bio/Technology 9:1370-1371; and Goward et al.,

(1992) TEBS 18:136-140), and the resulting fusion protein detected by panning, e.g. using a fluorescently labeled molecule which binds the p85 polypeptide, to score for potentially functional homologs. Cells can be visually inspected and separated under a fluorescence microscope, or, where the morphology of the cell permits, separated by a fluorescence-activated cell sorter.

In similar fashion, the gene library can be expressed as a fusion protein on the surface of a viral particle. For instance, in the filamentous phage system, foreign peptide sequences can be expressed on the surface of infectious phage, thereby conferring two significant benefits. First, since these phage can be applied to affinity matrices at very high concentrations, a large number of phage can be screened at one time. Second, since each infectious phage displays the combinatorial gene product on its surface, if a particular phage is recovered from an affinity matrix in low yield, the phage can be amplified by another round of infection. The group of almost identical E. coli filamentous phages Ml 3, fd, and fl are most often used in phage display libraries, as either of the phage gill or gVIII coat proteins can be used to generate fusion proteins without disrupting the ultimate packaging of the viral particle (Ladner et al., PCT publication WO 90/02909; Garrard et al., PCT publication WO 92/09690; Marks et al., (1992) J. Biol. Chem. 267:16007-16010; Griffiths et al., (1993) EMBO J. 12:725-734; Clackson et al., (1991) Nature 352:624-628; and Barbas et al., (1992) PNAS USA 89:4457-4461). The invention also provides for reduction of the subject p85 polypeptides to generate mimetics, e.g. peptide or non-peptide agents, which are able to mimic

8870445 4 DOC — 36 — binding of the authentic protein to another cellular partner. Such mutagenic techniques as described above, as well as the thioredoxin system, are also particularly useful for mapping the determinants of a p85 polypeptide which participate in protein-protein interactions involved in, for example, binding of proteins involved in viral maturation to each other. To illustrate, the critical residues of a p85 polypeptide which are involved in molecular recognition of a substrate protein can be determined and used to generate p85 polypeptide-derived peptidomimetics which bind to the substrate protein, and by inhibiting p85 binding, act to inhibit its biological activity. By employing, for example, scanning mutagenesis to map the amino acid residues of a p85 polypeptide which are involved in binding to another polypeptide, peptidomimetic compounds can be generated which mimic those residues involved in binding. For instance, non-hydrolyzable peptide analogs of such residues can be generated using benzodiazepine (e.g., see Freidinger et al., in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al., in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gamma lactam rings (Garvey et al., in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), keto- methylene pseudopeptides (Ewenson et al., (1986) J. Med. Chem. 29:295; and Ewenson et al., in Peptides: Structure and Function (Proceedings of the 9th

American Peptide Symposium) Pierce Chemical Co. Rockland, IL, 1985), b-turn dipeptide cores (Nagai et al., (1985) Tetrahedron Lett 26:647; and Sato et al., (1986) J Chem Soc Perkin Trans 1 :1231), and b-aminoalcohols (Gordon et al., (1985) Biochem Biophys Res Cornmun 126:419; and Dann et al., (1986) Biochem Biophys Res Commun 134:71).

4. Antibodies and Uses Therefor

Another aspect of the invention pertains to an antibody specifically reactive with a p85 polypeptide. For example, by using immunogens derived from a p85 polypeptide, e.g., based on the cDNA sequences, anti-protein/anti-peptide antisera or monoclonal antibodies can be made by standard protocols (See, for example, Antibodies: A Laboratory Manual ed. by Harlow and Lane (Cold Spring Harbor

8870445 4 DOC -- 37 — Press: 1988)). A mammal, such as a mouse, a hamster or rabbit can be immunized with an immunogenic form of the peptide (e.g., a p85 polypeptide or an antigenic fragment which is capable of eliciting an antibody response, or a fusion protein as described above). Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art. An immunogenic portion of a p85 polypeptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassays can be used with the immunogen as antigen to assess the levels of antibodies. In a preferred embodiment, the subject antibodies are immunospecific for antigenic determinants of a p85 polypeptide of a mammal, e.g., antigenic determinants of a protein set forth in SEQ ED NO:2.

In one embodiment, antibodies are specific for an SH2 domain or an SH3 domain, and preferably the domain is part of a p85 polypeptide. In a more specific embodiment, the domain is part of an amino acid sequence set forth in SEQ ID NO:2. In a set of exemplary embodiments, an antibody binds to one or more SH2 domains represented by amino acids 333-428 of SEQ ID NO:2, and/or amino acids 624-718 of SEQ ED NO:2. In another exemplary embodiment, an antibody binds to an SH3 domain represented by amino acids 3-79 of SEQ ED NO:2. In another embodiment, the antibodies are immunoreactive with one or more proteins having an amino acid sequence that is at least 80% identical to an amino acid sequence as set forth in SEQ ID NO:2. In other embodiments, an antibody is immunoreactive with one or more proteins having an amino acid sequence that is 85%, 90%, 95%, 98%, 99% or identical to an amino acid sequence as set forth in SEQ ID NO:2. In further embodiments, an antibody of the invention disrupts the interaction between a p85 polypeptide and a p85-AP, such as, for example, a Gag protein or a pi 10 catalytic subunit.

Following immunization of an animal with an antigenic preparation of a p85 polypeptide, anti-p85 antisera can be obtained and, if desired, polyclonal anti-p85 antibodies isolated from the serum. To produce monoclonal antibodies, antibody- producing cells (lymphocytes) can be harvested from an immunized animal and fused by standard somatic cell fusion procedures with immortalizing cells such as

8870445 4 DOC — 38 -- myeloma cells to yield hybridoma cells. Such techniques are well known in the art, and include, for example, the hybridoma technique (originally developed by Kohler and Milstein, (1975) Nature, 256: 495-497), the human B cell hybridoma technique (Kozbar et al., (1983) Immunology Today, 4: 72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., (1985) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. pp. 77-96). Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with a mammalian p85 polypeptide of the present invention and monoclonal antibodies isolated from a culture comprising such hybridoma cells. In one embodiment anti-human p85 antibodies specifically react with the protein encoded by a nucleic acid having SEQ ID NO:2.

The term antibody as used herein is intended to include fragments thereof which are also specifically reactive with one of the subject p85 polypeptides. Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above for whole antibodies. For example, F(ab)2 fragments can be generated by treating antibody with pepsin. The resulting F(ab)2 fragment can be treated to reduce disulfide bridges to produce Fab fragments. The antibody of the present invention is further intended to include bispecific, single-chain, and chimeric and humanized molecules having affinity for a p85 polypeptide conferred by at least one CDR region of the antibody. In preferred embodiments, the antibodies, the antibody further comprises a label attached thereto and able to be detected, (e.g., the label can be a radioisotope, fluorescent compound, enzyme or enzyme co-factor).

Anti-p85 antibodies can be used, e.g., to monitor p85 polypeptide levels in an individual, particularly the presence of p85 at the plasma membrane for determining whether or not said patient is infected with a virus such as an RNA virus, or allowing determination of the efficacy of a given treatment regimen for an individual afflicted with such a disorder. In addition, p85 polypeptides are expected to localize, occasionally, to the released viral particle. Viral particles may be collected and assayed for the presence of a p85 polypeptide. The level of p85 polypeptide may be measured in a variety of sample types such as, for example, cells and/or in bodily fluid, such as in blood samples.

8870445 4.DOC — 39 — Another application of anti-p85 antibodies of the present invention is in the immuno logical screening of cDNA libraries constructed in expression vectors such as gtl l, gtl8-23, ZAP, and ORF8. Messenger libraries of this type, having coding sequences inserted in the correct reading frame and orientation, can produce fusion proteins. For instance, gtl 1 will produce fusion proteins whose amino termini consist of β-galactosidase amino acid sequences and whose carboxy termini consist of a foreign polypeptide. Antigenic epitopes of a p85 polypeptide, e.g., other orthologs of a particular protein or other paralogs from the same species, can then be detected with antibodies, as, for example, reacting nitrocellulose filters lifted from infected plates with the appropriate anti-p85 antibodies. Positive phage detected by this assay can then be isolated from the infected plate. Thus, the presence of p85 homologs can be detected and cloned from other animals, as can alternate isoforms (including splice variants) from humans.

5. Homology Searching of Nucleotide and Polypeptide Sequences The nucleotide or amino acid sequences of the invention may be used as query sequences against databases such as GenBank, SwissProt, BLOCKS, and Pima II. These databases contain previously identified and annotated sequences that can be searched for regions of homology (similarity) using BLAST, which stands for Basic Local Alignment Search Tool (Altschul S F (1993) J Mol Evol 36:290-300; Altschul, S F et al (1990) J Mol Biol 215:403-10).

BLAST produces alignments of both nucleotide and amino acid sequences to determine sequence similarity. Because of the local nature of the alignments, BLAST is especially useful in determining exact matches or in identifying homologs which may be of prokaryotic (bacterial) or eukaryotic (animal, fungal or plant) origin. Other algorithms such as the one described in Smith, R. F. and T. F. Smith (1992; Protein Engineering 5:35-51), incorporated herein by reference, can be used when dealing with primary sequence patterns and secondary structure gap penalties. As disclosed in this application, sequences have lengths of at least 49 nucleotides and no more than 12% uncalled bases (where N is recorded rather than A, C, G, or T).

8870445 4. DOC ~ 40 The BLAST approach, as detailed in Karlin and Altschul (1993; Proc Nat Acad Sci 90:5873-7) and incorporated herein by reference, searches matches between a query sequence and a database sequence, to evaluate the statistical significance of any matches found, and to report only those matches which satisfy the user-selected threshold of significance. Preferably the threshold is set at 10-25 for nucleotides and 3-15 for peptides.

6. Diagnostic Assays

A further aspect of the invention includes diagnostic assays for determining whether a cell is infected with a virus and for characterizing the nature, progression and/or infectivity of the infection.

In one embodiment, it is contemplated that p85 polypeptides and certain associated proteins localize to different regions of the cell depending on the function being performed. In the course of normal activities, it is expected that p85 polypeptides will be free in the cytoplasm or associated with an intracellular organelle, such as the nucleus, the Golgi network, etc. During a viral infection, p85 polypeptides are recruited to the cell membrane to participate in viral maturation, including ubiquitination and/or membrane fusion. As a result, the detection of p85 polypeptide associated with the plasma membrane fraction is indicative of a viral infection. Additionally, the presence of p85 polypeptide at the plasma membrane would suggest that the infective virus is in the process of reproducing and is therefore actively engaged in infective or lytic activity (versus a lysogenic or otherwise dormant state).

Association of the proteins of the invention with the plasma membrane may be detected using a variety of techniques known in the art. For example, membrane preparations may be prepared by breaking open the cells (via sonication or detergent lysis) and then separating the membrane components from the cytosolic fraction via centrifugation. Segregation of proteins into the membrane fraction can be detected with antibodies specific for the protein of interest, for example by using Western blot analysis or ELISA techniques. Plasma membranes may be separated from intracellular membranes on the basis of density using density gradient centrifugation. Alternatively, plasma membranes may be obtained by chemically or

8870445 4 DOC — 41 ~ enzymatically modifying the surface of the cell and affinity purifying the plasma membrane by selectively binding the modifications. An exemplary modification includes non-specific biotinylation of proteins at the cell surface. Plasma membranes may also be selected for by affinity purifying for abundant plasma membrane proteins.

Localization of the proteins of the invention may also be determined using histochemical techniques. For example, cells may be fixed and stained with a fluorescently labeled antibody specific for the protein of interest. The stained cells may then be examined under the microscope to determine the subcellular localization of the antibody bound proteins.

In addition, as noted above, p85 polypeptides may localize to released or budding viral particles. The presence of these proteins in viral particles may be determined by a variety of methods. For example, viral particles may be enriched and analyzed by Western blot or ELISA. As another example, viral particles or cells having budding viroids ay be examined by electron microscopy. Immunogold labeling, for example, is useful for localizing p85 polypeptides by electron microscopy.

Samples to be used for diagnostic assays may include essentially any sample comprising cells and/or viral particles or a sample prepared from a cellular sample. Exemplary samples would include fluid samples (eg. blood, urine, saliva, mucus, broncheoalveolar lavage, cerebrospinal fluid etc.). Other fluids comprising cells and/or viral particles are well known to those of skill in the art. Other sample types include stool samples, tissue biopsies and any processed or purified form of the above.

7. Drug Screening Assays

The present invention also provides assays for identifying therapeutics which either interfere with or promote viral maturation, particularly by affecting p85 function. In one embodiment, the assay detects agents which inhibit interaction of one or more subject p85 polypeptides with a p85-AP. In another embodiment, the assay detects agents which modulate the intrinsic biological activity of a p85 polypeptide or p85 complex, such as an enzymatic activity, binding to other cellular

8870445 4.DOC — 42 — components, cellular compartmentalization, and the like. Such modulators can be used, for example, in the treatment of viral infections and/or particularly viral infections by a virus that uses a Gag-dependent maturation system (eg. retrovirus, rhabdovirus, filovirus).

In one aspect, the invention provides methods and compositions for the identification of compositions that interfere with the function of p85 polypeptides. Given the role of p85 polypeptides in virion release, compositions that perturb the formation or stability of the protein-protein interactions between p85 polypeptides and the proteins that they interact with, such as p85-APs are candidate pharmaceuticals for the treatment of viral infections.

While not wishing to be bound to mechanism, it is postulated that p85 polypeptides promote the assembly of protein complexes that are important in release of virions. Complexes of the invention may include a combination of a p85 polypeptide and one or more of the following: a p85-AP; a Gag; a GTPase; an E2 enzyme; a cullin; a clathrin; AP-1; AP-2; a pi 10 catalytic subunit.

The type of complex formed by a p85 polypeptide will depend upon the domains present in the protein. While not intended to be limiting, exemplary domains of potential interacting proteins are provided below. An SH2 domain is expected to interact with phosphotyrosine residues, such as, for example, might be found on any of a variety of activated receptors, such as Src, ErbB, PDGFR, etc. An SH3 domain may interact with Gag L domains and other proteins having the sequence motif PXXP, PPXY or RXXPXXP, such as, for example, the HIV Gag (p24) sequence RQGPKEPFR.

A variety of assay formats will suffice and, in light of the present disclosure, those not expressly described herein will nevertheless be comprehended by one of ordinary skill in the art. Assay formats which approximate such conditions as formation of protein complexes, enzymatic activity, and even a p85 polypeptide- mediated membrane reorganization activity, can be generated in many different forms, and include assays based on cell-free systems, e.g. purified proteins or cell lysates, as well as cell-based assays which utilize intact cells. Simple binding assays

8870445 4.DOC — 43 — can also be used to detect agents which, by disrupting the binding of p85 polypeptide to interacting protein, or the binding of a p85 polypeptide or complex to a substrate, can inhibit viral maturation. Agents to be tested for their ability to act as viral maturation inhibitors can be produced, for example, by bacteria, yeast or other organisms (e.g. natural products), produced chemically (e.g. small molecules, including peptidomimetics), or produced recombinantly. In a preferred embodiment, the test agent is a small organic molecule, e.g., other than a peptide or oligonucleotide, having a molecular weight of less than about 2,000 daltons.

In many drug screening programs which test libraries of compounds and natural extracts, high throughput assays are desirable in order to maximize the number of compounds surveyed in a given period of time. Assays of the present invention which are performed in cell-free systems, such as may be developed with purified or semi-purified proteins or with lysates, are often preferred as "primary" screens in that they can be generated to permit rapid development and relatively easy detection of an alteration in a molecular target which is mediated by a test compound. Moreover, the effects of cellular toxicity and/or bioavailability of the test compound can be generally ignored in the in vitro system, the assay instead being focused primarily on the effect of the drug on the molecular target as may be manifest in an alteration of binding affinity with other proteins or changes in enzymatic properties of the molecular target.

In preferred in vitro embodiments of the present assay, a reconstituted p85 complex comprises a reconstituted mixture of at least semi-purified proteins. By semi-purified, it is meant that the proteins utilized in the reconstituted mixture have been previously separated from other cellular or viral proteins. For instance, in contrast to cell lysates, the proteins involved in p85 complex formation are present in the mixture to at least 50% purity relative to all other proteins in the mixture, and more preferably are present at 90-95% purity. In certain embodiments of the subject method, the reconstituted protein mixture is derived by mixing highly purified proteins such that the reconstituted mixture substantially lacks other proteins (such as of cellular or viral origin) which might interfere with or otherwise alter the ability to measure p85 complex assembly and/or disassembly.

8870445 4. DOC ~ 44 — Assaying p85 complexes, in the presence and absence of a candidate inhibitor, can be accomplished in any vessel suitable for containing the reactants. Examples include microtitre plates, test tubes, and micro-centrifuge tubes.

In one embodiment of the present invention, drug screening assays can be generated which detect inhibitory agents on the basis of their ability to interfere with assembly or stability of the p85 complex. In an exemplary binding assay, the compound of interest is contacted with a mixture comprising a p85 polypeptide and at least one interacting polypeptide. Detection and quantification of p85 complexes provides a means for determining the compound's efficacy at inhibiting (or potentiating) interaction between the two polypeptides. The efficacy of the compound can be assessed by generating dose response curves from data obtained using various concentrations of the test compound. Moreover, a control assay can also be performed to provide a baseline for comparison. In the control assay, the formation of complexes is quantitated in the absence of the test compound.

Complex formation between the p85 polypeptides and a substrate polypeptide may be detected by a variety of techniques, many of which are effectively described above. For instance, modulation in the formation of complexes can be quantitated using, for example, detectably labeled proteins (e.g. radiolabeled, fluorescently labeled, or enzymatically labeled), by immunoassay, or by chromatographic detection. Surface plasmon resonance systems, such as those available from BiaCore, Inc., may also be used to detect protein-protein interaction

Often, it will be desirable to immobilize one of the polypeptides to facilitate separation of complexes from uncomplexed forms of one of the proteins, as well as to accommodate automation of the assay. In an illustrative embodiment, a fusion protein can be provided which adds a domain that permits the protein to be bound to an insoluble matrix. For example, GST-p85 fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtitre plates, which are then combined with a potential interacting protein, e.g. an 35S-labeled polypeptide, and the test compound and incubated under conditions conducive to complex formation . Following incubation, the beads are

8870445 4 DOC — 45 — washed to remove any unbound interacting protein, and the matrix bead-bound radiolabel determined directly (e.g. beads placed in scintillant), or in the supernatant after the complexes are dissociated, e.g. when microtitre plate is used. Alternatively, after washing away unbound protein, the complexes can be dissociated from the matrix, separated by SDS-PAGE gel, and the level of interacting polypeptide found in the matrix-bound fraction quantitated from the gel using standard electrophoretic techniques.

In yet another embodiment, the p85 polypeptide and potential interacting polypeptide can be used to generate an interaction trap assay (see also, U.S. Patent NO: 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J Biol Chem 268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; and Iwabuchi et al. (1993) Oncogene 8:1693-1696), for subsequently detecting agents which disrupt binding of the proteins to one and other.

In particular, the method makes use of chimeric genes which express hybrid proteins. To illustrate, a first hybrid gene comprises the coding sequence for a DNA-binding domain of a transcriptional activator can be fused in frame to the coding sequence for a "bait" protein, e.g., a p85 polypeptide of sufficient length to bind to a potential interacting protein. The second hybrid protein encodes a transcriptional activation domain fused in frame to a gene encoding a "fish" protein, e.g., a potential interacting protein of sufficient length to interact with the p85 polypeptide portion of the bait fusion protein. If the bait and fish proteins are able to interact, e.g., form a p85 complex, they bring into close proximity the two domains of the transcriptional activator. This proximity causes transcription of a reporter gene which is operably linked to a transcriptional regulatory site responsive to the transcriptional activator, and expression of the reporter gene can be detected and used to score for the interaction of the bait and fish proteins.

In accordance with the present invention, the method includes providing a host cell, preferably a yeast cell, e.g., Kluyverei lactis, Schizosaccharomyces pombe, Ustilago maydis, Saccharomyces cerevisiae, Neurospora crassa, Aspergillus niger, Aspergillus nidulans, Pichia pastoris, Candida tropicalis, and Hansenula

8870445 4 DOC — 46 — polymorpha, though most preferably S cerevisiae or S. pombe. The host cell contains a reporter gene having a binding site for the DNA-binding domain of a transcriptional activator used in the bait protein, such that the reporter gene expresses a detectable gene product when the gene is transcriptionally activated. The first chimeric gene may be present in a chromosome of the host cell, or as part of an expression vector. Interaction trap assays may also be performed in mammalian and bacterial cell types.

The host cell also contains a first chimeric gene which is capable of being expressed in the host cell. The gene encodes a chimeric protein, which comprises (i) a DNA-binding domain that recognizes the responsive element on the reporter gene in the host cell, and (ii) a bait protein, such as a p85 polypeptide sequence.

A second chimeric gene is also provided which is capable of being expressed in the host cell, and encodes the "fish" fusion protein. In one embodiment, both the first and the second chimeric genes are introduced into the host cell in the form of plasmids. Preferably, however, the first chimeric gene is present in a chromosome of the host cell and the second chimeric gene is introduced into the host cell as part of a plasmid.

Preferably, the DNA-binding domain of the first hybrid protein and the transcriptional activation domain of the second hybrid protein are derived from transcriptional activators having separable DNA-binding and transcriptional activation domains. For instance, these separate DNA-binding and transcriptional activation domains are known to be found in the yeast GAL4 protein, and are known to be found in the yeast GCN4 and ADRl proteins. Many other proteins involved in transcription also have separable binding and transcriptional activation domains which make them useful for the present invention, and include, for example, the LexA and VP16 proteins. It will be understood that other (substantially) transcriptionally-inert DNA-binding domains may be used in the subject constructs; such as domains of ACE1, lcl, lac repressor, jun or fos. In another embodiment, the DNA-binding domain and the transcriptional activation domain may be from different proteins. The use of a LexA DNA binding domain provides certain

8870445 4 DOC -- 47 — advantages. For example, in yeast, the LexA moiety contains no activation function and has no known effect on transcription of yeast genes. In addition, use of LexA allows control over the sensitivity of the assay to the level of interaction (see, for example, the Brent et al. PCT publication WO94/10300).

In preferred embodiments, any enzymatic activity associated with the bait or fish proteins is inactivated, e.g., dominant negative or other mutants of a p85 polypeptide can be used.

Continuing with the illustrated example, the p85 polypeptide-mediated interaction, if any, between the bait and fish fusion proteins in the host cell, therefore, causes the activation domain to activate transcription of the reporter gene. The method is carried out by introducing the first chimeric gene and the second chimeric gene into the host cell, and subjecting that cell to conditions under which the bait and fish fusion proteins and are expressed in sufficient quantity for the reporter gene to be activated. The formation of a p85 - p85-AP complex results in a detectable signal produced by the expression of the reporter gene. Accordingly, the level of formation of a complex in the presence of a test compound and in the absence of the test compound can be evaluated by detecting the level of expression of the reporter gene in each case. Various reporter constructs may be used in accord with the methods of the invention and include, for example, reporter genes which produce such detectable signals as selected from the group consisting of an enzymatic signal, a fluorescent signal, a phosphorescent signal and drug resistance.

One aspect of the present invention provides reconstituted protein preparations including a p85 polypeptide and one or more interacting polypeptides.

In still further embodiments of the present assay, the p85 complex is generated in whole cells, taking advantage of cell culture techniques to support the subject assay. For example, as described below, the p85 complex can be constituted in a eukaryotic cell culture system, including mammalian and yeast cells. Often it will be desirable to express one or more viral proteins (eg. Gag or Env) in such a cell along with a subject p85 polypeptide. It may also be desirable to infect the cell with a virus of interest. Advantages to generating the subject assay in an intact cell

8870445 4.DOC — 48 — include the ability to detect inhibitors which are functional in an environment more closely approximating that which therapeutic use of the inhibitor would require, including the ability of the agent to gain entry into the cell. Furthermore, certain of the in vivo embodiments of the assay, such as examples given below, are amenable to high through-put analysis of candidate agents.

The components of the p85 complex can be endogenous to the cell selected to support the assay. Alternatively, some or all of the components can be derived from exogenous sources. For instance, fusion proteins can be introduced into the cell by recombinant techniques (such as through the use of an expression vector), as well as by microinjecting the fusion protein itself or mRNA encoding the fusion protein.

In any case, the cell is ultimately manipulated after incubation with a candidate drug and assayed for a p85 activity. p85 activities may include, without limitation, complex formation, ubiquitination and membrane fusion events (eg. release of viral buds or fusion of vesicles). p85 complex formation may be assessed by immunoprecipitation and analysis of co-immunoprecipiated proteins or affinity purification and analysis of co-purified proteins. Fluorescence Resonance Energy Transfer (FRET)-based assays may also be used to determine complex formation. Fluorescent molecules having the proper emission and excitation spectra that are brought into close proximity with one another can exhibit FRET. The fluorescent molecules are chosen such that the emission spectrum of one of the molecules (the donor molecule) overlaps with the excitation spectrum of the other molecule (the acceptor molecule). The donor molecule is excited by light of appropriate intensity within the donor's excitation spectrum. The donor then emits the absorbed energy as fluorescent light. The fluorescent energy it produces is quenched by the acceptor molecule. FRET can be manifested as a reduction in the intensity of the fluorescent signal from the donor, reduction in the lifetime of its excited state, and/or re- emission of fluorescent light at the longer wavelengths (lower energies) characteristic of the acceptor. When the fluorescent proteins physically separate, FRET effects are diminished or eliminated. (U.S. Patent No. 5,981,200).

8870445 4. DOC — 49 — For example, a cyan fluorescent protein is excited by light at roughly 425 - 450 nm wavelength and emits light in the range of 450 - 500 nm. Yellow fluorescent protein is excited by light at roughly 500 - 525 nm and emits light at 525 - 500 nm. If these two proteins are placed in solution, the cyan and yellow fluorescence may be separately visualized. However, if these two proteins are forced into close proximity with each other, the fluorescent properties will be altered by FRET. The bluish light emitted by CFP will be absorbed by YFP and re-emitted as yellow light. This means that when the proteins are stimulated with light at wavelength 450 nm, the cyan emitted light is greatly reduced and the yellow light, which is not normally stimulated at this wavelength, is greatly increased. FRET is typically monitored by measuring the spectrum of emitted light in response to stimulation with light in the excitation range of the donor and calculating a ratio between the donor-emitted light and the acceptor-emitted light. When the donor: acceptor emission ratio is high, FRET is not occurring and the two fluorescent proteins are not in close proximity. When the donor: acceptor emission ratio is low, FRET is occurring and the two fluorescent proteins are in close proximity. In this manner, the interaction between a first and second polypeptide may be measured. The occurrence of FRET also causes the fluorescence lifetime of the donor fluorescent moiety to decrease. This change in fluorescence lifetime can be measured using a technique termed fluorescence lifetime imaging technology (FLIM) (Verveer et al. (2000) Science 290: 1567-1570; Squire et al. (1999) J. Microsc. 193: 36; Verveer et al. (2000) Biophys. J. 78: 2127). Global analysis techniques for analyzing FLEM data have been developed. These algorithms use the understanding that the donor fluorescent moiety exists in only a limited number of states each with a distinct fluorescence lifetime. Quantitative maps of each state can be generated on a pixel-by-pixel basis.

To perform FRET-based assays, the p85 polypeptide and the interacting protein of interest are both fluorescently labeled. Suitable fluorescent labels are, in view of this specification, well known in the art. Examples are provided below, but suitable fluorescent labels not specifically discussed are also available to those of skill in the art. Fluorescent labeling may be accomplished by expressing a polypeptide as a fusion protein with a fluorescent protein, for example fluorescent

8870445 4.DOC ~ 50 — proteins isolated from jellyfish, corals and other coelenterates. Exemplary fluorescent proteins include the many variants of the green fluorescent protein (GFP) of Aequoria victoria. Variants may be brighter, dimmer, or have different excitation and/or emission spectra. Certain variants are altered such that they no longer appear green, and may appear blue, cyan, yellow or red (termed BFP, CFP, YFP and RFP, respectively). Fluorescent proteins may be stably attached to polypeptides through a variety of covalent and noncovalent linkages, including, for example, peptide bonds (eg. expression as a fusion protein), chemical cross-linking and biotin-streptavidin coupling. For examples of fluorescent proteins, see U.S. Patents 5,625,048; 5,777,079; 6,066,476; 6,124,128; Prasher et al. (1992) Gene, 111:229-233; Heim et al. (1994) Proc. Natl. Acad. Sci., USA, 91 :12501-04; Ward et al. (1982) Photochem. Photobiol, 35:803-808 ; Levine et al. (1982) Comp. Biochem. Physiol, 72B:77-85; Tersikh et al. (2000) Science 290: 1585-88.

Other exemplary fluorescent moieties well known in the art include derivatives of fluorescein, benzoxadioazole, coumarin, eosin, Lucifer Yellow, pyridyloxazole and rhodamine. These and many other exemplary fluorescent moieties may be found in the Handbook of Fluorescent Probes and Research Chemicals (2000, Molecular Probes, Inc.), along with methodologies for modifying polypeptides with such moieties. Exemplary proteins that fluoresce when combined with a fluorescent moiety include, yellow fluorescent protein from Vibrio fischeri (Baldwin et al. (1990) Biochemistry 29:5509-15), peridinin-chlorophyll a binding protein from the dinoflagellate Symbiodinium sp. (Morris et al. (1994) Plant Molecular Biology 24:673:77) and phycobiliproteins from marine cyanobacteria such as Synechococcus, e.g., phycoerythrin and phycocyanin (Wilbanks et al. (1993) J. Biol Chem. 268:1226-35). These proteins require flavins, peridinin-chlorophyll a and various phycobilins, respectively, as fluorescent co-factors.

FRET-based assays may be used in cell-based assays and in cell-free assays. FRET-based assays are amenable to high-throughput screening methods including Fluorescence Activated Cell Sorting and fluorescent scanning of microtiter areays. In certain aspects the invention provides inhibitors of a p85-regulated activity. For example, wortmannin, LY294002 and demefhoxyviridin are inhibitors of PI3K activity.

8870445 4.DOC — 51 — 8. Methods and Compositions for Treatment of Viral Disorders

In a further aspect, the invention provides methods and compositions for treatment of viral disorders, and particularly disorders caused by RNA viruses, including but not limited to retroviruses, rhabdoviruses and filoviruses. Preferred therapeutics of the invention function by disrupting the biological activity of a p85 polypeptide or p85 complex in viral maturation.

Exemplary therapeutics of the invention include antisense therapies, polypeptides, peptidomimetics, antibodies and small molecules.

Antisense therapies -of the invention include methods of introducing antisense nucleic acids to disrupt the expression of p85 polypeptides or proteins that are necessary for p85 function.

Therapeutic polypeptides may be generated by designing polypeptides to mimic certain protein domains important in the formation of p85 complexes, such as, for example SH3 or SH2 domains. For example, a polypeptide comprising a p85 SH3 domain will compete for binding to a p85 SH3 domain and will therefore act to disrupt binding of a partner protein, such as Gag for example, to the p85 complex. Likewise, a polypeptide that resembles an L domain may disrupt recruitment of Gag to the p85 complex.

In other embodiments the application provides compositions and methods for inhibiting viral infections and/or viral maturation by administering an effective amount of a PI3K inhibitors. A variety of PI3K pathway inhibitors may be employed in the methods disclosed herein, including direct inhibitors that act directly on a PI3K subunit and pathway inhibitors that affect one or more other molecular actors in the PI3K pathway. PI3K pathway inhibitors may have both direct and indirect actions.

Phosphatidylinositol 3-kinase, has been found to phosphorylate the 3- position of the inositol ring of phosphatidylinositol (PI) to form phosphatidylinositol 3-phosphate (PI-3P) (Whitman et al.(1988) Nature, 322: 664-646). In addition to PI,

8870445 4 DOC ~ 52 — this enzyme also can phosphorylate phosphatidylinositol 4-phosphate and phosphatidylinositol 4,5-bisphosphate to produce phosphatidylinositol 3,4- bisphosphate and phosphatidylinositol 3,4,5-trisphosphate (PEP3), respectively (Auger et al. (1989) Cell, 57: 167-175). Direct PI3K inhibitors include materials that reduce or eliminate either or both of these activities of P3 K. Such inhibitors include direct PI3K inhibitors such as Ly294002 (Calbiochem Corp., La Jolla, Calif.) and wortmannin (Sigma Chemical Co., St. Louis Mo. The chemical properties of Ly294002 are described in detail in J. Biol, Chem., (1994) 269: 5241-5248.

Other inhibitors of PI3K include viridin, viridiol, demethoxyviridin, and demethoxyviridiol (see, U.S. Pat. No. 5,276,167). Once viridin, viridiol, demethoxyviridin, and demethoxyviridiol, or other PI3K inhibitors are isolated and purified, analogs of each may be prepared via well known methods to provide generally known compounds such as those illustrated by formula I of U.S. Pat. No. 5,276,167 (see, also, Grove et al. (1965) J. Chem. Soc, June: 3803-3811, Hanson et al. (1985) J Chem. Soc. Perkin Trans. I: 1311-1314. Aldridge et al. (1975) J. Chem. Soc. Perkin Trans. I: 943-945 (1975), and Blight et al. J. Chem. Soc. Perkin Trans I: 1317-1322).

Suitable derivatives and analogues include, but are not limited to alpha/beta- viridin, 1-acetylviridin, 1-methylether of viridin, demethoxyviridin, demethoxyviridin mono-acetate, dehydroxyviridin, demethoxyviridin mono- methanesulfonate, diacetyldemethoxyviridol OAc, viridiol, 1 -O-acetylviridiol, l-O- methyl-mefhylefher of viridiol, demethoxyviridiol, 1-acetyldemethoxyviridiol, l-O- methylether dimethoxyviridiol (see, U.S. Pat. No. 5,276,167). Other derivatives include, but are not limited to Wortmannin stereochemical alcohol and ester derivatives, such as 11 -substituted, 17-substituted and 11, 17 disubstituted derivatives of wortmannin (see, U.S. Pat. No. 5,480,906), and the like.

The functionality of a PI3K inhibitor may be assessed according to any of a variety of art-recognized assays. In general, the assays for direct PI3K inhibitors involve comparing the activity of PI3K in the presence and absence of the putative inhibitor. Examples of such assays are described in detail in U.S. Pat. No. 5,480,906.

PI3K activity may be measured as described by Matter et al. (1992) Biochem.

8870445 4.DOC — 53 — Biophys. Res. Comm., 186: 624-631. Briefly, inhibitor candidates are initially dissolved, e.g., in DMSO and then diluted e.g., 10-fold with 50 mM of HEPES buffer, pH 7.5, containing 15 mM of MgC12 and 1 mM of EGTA. Ten microliters of this solution are incubated with purified PI3K and phosphatidylinositol in 50 mM of HEPES buffer, pH 7.5, containing 1 mM of EGTA. Reactants are preincubated 10 minutes at ambient temperature and then the enzyme reaction is started upon addition of 32P-ATP (2 mCi/mL, 500 mu M of stock solution; 0.08 mCi/mL, 20 mu M of final concentration; Dupont New England Nuclear, Boston, Mass.). The reaction is allowed to proceed for 10 minutes at ambient temperature with frequent mixing, after which time the reaction is quenched by addition of 40 mu L of IN HCI. Lipids are extracted with addition of 80 μl L CHC13 :MeOH (1 :1, v:v). The samples are mixed and centrifuged, and the lower organic phase is applied to a silica gel TLC plate (EM Science, Gibbstown, N.J.), which is developed in CHC13 :MeOH:H2O:NH4OH (45:35:8.5:1.5, v:v). Plates are dried, and the kinase reaction visualized by autoradiography. The phosphatidylinositol 3-monophosphate region is scraped from the plate and quantitated using liquid scintillation spectroscopy with ReadyProtein (Beckman Instruments, Inc., Fullerton, Calif.) used as the scintillation cocktail. The level of inhibition for the putative inhibitor is determined as the percentage of 32P-counts per minute compared to controls. The activity of a candidate PI3K inhibitor may also be assessed by testing its effect on expression of a PI3K-responsive gene in a cell, particularly where the promoter of the PI3K-responsive gene is linked to a reporter gene.

Any of the various PI3K inhibitors described herein may be replaced with functional analogs. A functional analog is a structurally similar molecule having at least 10%, and preferably at least 50%, of an activity of the inhibitor in an assay designed to test PI3K activity. In the case of polypeptide factors, a functional analog may be simply a version using one or more modified amino acids but retaining the same sequence, or a functional analog may be a polypeptide having at least 80% amino acid sequence identity to the polypeptide factor, and preferably at least 90% or 95% sequence identity. Functional analogs may be identified from combinatorial libraries by the use of high-throughput screens. A combinatorial chemical library is a collection of diverse chemical compounds. Such libraries may be generated by

8870445 4 DOC — 54 — chemical synthesis or biological synthesis by combining a number of simpler chemical subunits. For example, a linear combinatorial chemical library such as a polypeptide library is formed by combining a set of amino acids in as many ways as possible for a given polypeptide length. The functionality of a candidate functional analog may be evaluated by using a published assay for the activity of the agent to be replaced. Millions of chemical compounds can be synthesized through such combinatorial mixing of subunits. Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Pat. No. 5,010,175, Furka (1991) Int. J. Pept. Prot. Res., 37: 487-493, Houghton et al. (1991) Nature, 354: 84-88). Peptide synthesis is by no means the only approach envisioned and intended for use with the present invention. Other chemistries for generating chemical diversity libraries can also be used. Such chemistries include, but are not limited to: peptoids (PCT Publication No WO 91/19735, Dec. 26, 1991), encoded peptides (PCT Publication WO 93/20242, Oct. 14, 1993), random bio- oligomers (PCT Publication WO 92/00091, Jan. 9, 1992), benzodiazepines (U.S. Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., (1993) Proc. Nat. Acad. Sci. USA 90: 6909-6913), vinylogous polypeptides (Hagihara et al. (1992) J. Amer. Chem. Soc. 114: 6568), nonpeptidal peptidomimetics with a .beta.-D-Glucose scaffolding (Hirschmann et al., (1992) J. Amer. Chem. Soc. 114: 9217-9218), analogous organic syntheses of small compound libraries (Chen et al. (1994) J. Amer. Chem. Soc. 116: 2661), oligocarbamates (Cho, et al., (1993) Science 261:1303), and/or peptidyl phosphonates (Campbell et al., (1994) J Org. Chem. 59: 658). See, generally, Gordon et al., (1994) J. Med. Chem. 37:1385, nucleic acid libraries (see, e.g.,

Strategene, Corp.), peptide nucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083) antibody libraries (see, e.g., Vaughn et al. (1996) Nature Biotechnology, 14(3): 309- 314), and PCT US96/ 10287), carbohydrate libraries (see, e.g., Liang et al. (1996) Science, 274: 1520-1522, and U.S. Pat. No. 5,593,853), and small organic molecule libraries (see, e.g., benzodiazepines, Baum (1993) C&EN, January 18, page 33, isoprenoids U.S. Pat. No. 5,569,588, thiazolidinones and metathiazanones U.S. Pat. No. 5,549,974, pyrrolidines U.S. Pat. Nos. 5,525,735 and 5,519,134, morpholino

8870445 4 DOC — 55 -- compounds U.S. Pat. No. 5,506,337, benzodiazepines U.S. Pat. No. 5,288,514, and the like).

In view of the specification, methods for generating antibodies directed to epitopes of p85 and p85 -interacting proteins are known in the art. Antibodies may be introduced into cells by a variety of methods. One exemplary method comprises generating a nucleic acid encoding a single chain antibody that is capable of disrupting a p85 complex. Such a nucleic acid may be conjugated to antibody that binds to receptors on the surface of target cells. It is contemplated that in certain embodiments, the antibody may target viral proteins that are present on the surface of infected cells, and in this way deliver the nucleic acid only to infected cells. Once bound to the target cell surface, the antibody is taken up by endocytosis, and the conjugated nucleic acid is transcribed and translated to produce a single chain antibody that interacts with and disrupts the targeted p85 complex. Nucleic acids expressing the desired single chain antibody may also be introduced into cells using a variety of more conventional techniques, such as viral transfection (eg. using an adenoviral system) or liposome-mediated transfection.

Small molecules of the invention may be identified for their ability to modulate the formation of p85 complexes, as described above.

In view of the teachings herein, one of skill in the art will understand that the methods and compositions of the invention are applicable to a wide range of RNA viruses including retroviruses. While not intended to be limiting, relevant retroviruses include: C-type retrovirus which causes lymphosarcoma in Northern Pike, the C-type retrovirus which infects mink, the caprine lentivirus which infects sheep, the Equine Infectious Anemia Virus (EIAV), the C-type retrovirus which infects pigs, the Avian Leukosis Sarcoma Virus (ALSV), the Feline Leukemia Virus (FeLV), the Feline Aids Virus, the Bovine Leukemia Virus (BLV), the Simian Leukemia Virus (SLV), the Simian Immuno-deficiency Virus (SIV), the Human T- cell Leukemia Virus type-I (HTLV-I), the Human T-cell Leukemia Virus type-II (HTLV-II), Human Immunodeficiency virus type-2 (HIV-2) and Human Immunodeficiency virus type- 1 (HIV-1). Other RNA viruses include picomaviruses

8870445 4. DOC — 56 — such as enterovirus, poliovirus, coxsackievirus and hepatitis A virus, the caliciviruses, including Norwalk-like viruses, the rhabdoviruses, including rabies virus, the togaviruses including alphaviruses, Semliki Forest virus, denguevirus, yellow fever virus and rubella virus, the orthomyxoviruses, including Type A, B, and C influenza viruses, the bunyaviruses, including the Rift Valley fever virus and the hantavirus, the filoviruses such as Ebola virus and Marburg virus, and the paramyxoviruses, including mumps virus and measles virus.

9. Effective Dose

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 induces 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.

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

8870445 4.DOC — 57 — can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

10. Formulation and Use

Pharmaceutical compositions for use in accordance with the present invention may be formulated in conventional manner using one or more physiologically acceptable carriers or excipients. Thus, the compounds and their physiologically acceptable salts and solvates may be formulated for administration by, for example, injection, inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral or rectal administration.

For such therapy, the compounds of the invention can be formulated for a variety of loads of administration, including systemic and topical or localized administration. Techniques and formulations generally may be found in Remmington's Pharmaceutical Sciences, Meade Publishing Co., Easton, PA. For systemic administration, injection is preferred, including intramuscular, intravenous, intraperitoneal, and subcutaneous. For injection, the compounds of the invention can be formulated in liquid solutions, preferably in physiologically compatible buffers such as Hank's solution or Ringer's solution. In addition, the compounds may be formulated in solid form and redissolved or suspended immediately prior to use. Lyophilized forms are also included.

For oral administration, the pharmaceutical compositions may take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl mefhylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulphate). The tablets may be coated by methods well known in the art. Liquid preparations for oral administration may take the form of, for example, solutions, syrups or suspensions, or they may be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations may be prepared by

8870445 4 DOC — 58 — conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., ationd oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The preparations may also contain buffer salts, flavoring, coloring and sweetening agents as appropriate.

Preparations for oral administration may be suitably formulated to give controlled release of the active compound. For buccal administration the compositions may take the form of tablets or lozenges formulated in conventional manner. For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromefhane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

The compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.

The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides. In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or

8870445 4 DOC — 59 — by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt. 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 bile salts and fusidic acid derivatives, in addition, detergents may be used to facilitate permeation. Transmucosal administration may be through nasal sprays or using suppositories. For topical administration, the oligomers of the invention are formulated into ointments, salves, gels, or creams as generally known in the art. A wash solution can be used locally to treat an injury or inflammation to accelerate healing. The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. For therapies involving the administration of nucleic acids, the oligomers of the invention can be formulated for a variety of modes of administration, including systemic and topical or localized administration. Techniques and formulations generally may be found in Remmington's Pharmaceutical Sciences, Meade Publishing Co., Easton, PA. For systemic administration, injection is preferred, including intramuscular, intravenous, intraperitoneal, intranodal, and subcutaneous for injection, the oligomers of the invention can be formulated in liquid solutions, preferably in physiologically compatible buffers such as Hank's solution or Ringer's solution. In addition, the oligomers may be formulated in solid form and redissolved or suspended immediately prior to use. Lyophilized forms are also included.

Systemic administration can also be by transmucosal or transdermal means, or the compounds can be administered orally. For transmucosal or transdermal

8870445_4.DOC -- 60 — 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 bile salts and fusidic acid derivatives. In addition, detergents may be used to facilitate permeation. Transmucosal administration may be through nasal sprays or using suppositories. For oral administration, the oligomers are formulated into conventional oral administration forms such as capsules, tablets, and tonics. For topical administration, the oligomers of the invention are formulated into ointments, salves, gels, or creams as generally known in the art.

EXEMPLIFICATION

The invention now being generally described, it will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the invention.

11. Examples

1. p8δ Interaction with HIV Gag

HeLa cells were grown and transfected with HIV. Cell were harvested and subjected to an in vivo cross linking procedure. Cell lysates were incubated over night with p24 sheep polyclonal antibody (Serumun) conjugated to protein G beads (SP-30-005). Immunoprecipitates from cell lysates, were resolved by 10% Tris glycine gel, and analyzed by immuno-blotting with p24 rabbit polyclonal antibody (Seramun Lot #A023b), and rabbit anti-PI3K (p85) polyclonal antibody. Results, shown in Figure 4 and Figure 5, demonstrate that p24 and p85 form a complex in HIV-transfected cells.

2. Effect ofLY (PI3K inhibitor) on viruses release-Kinetics

A. TRANSFECTION

8870445 4.DOC -- 61 ~ HeLa cells, plated a day before at a concentration of 1x10 cells/plate in 15cm plate, were grown and transfected with HIV according to SP 30-012.

B. LABELING

1. Take out starvation medium, thaw and place at 37 C.

2. Scrape cells in growth medium and transfer gently into 15 ml conical tube.

3. Centrifuge to pellet cells at 1800rpm for 5 minutes at room temperature.

4. Aspirate supernatant and let tube stand for 10 sec. Remove the rest of the supernatant with a 200μl pipetman.

8870445 4. DOC - 62 5. Gently add 10ml warm starvation medium with and without 43μg/ml LY and resuspend carefully with a 10ml pipette, up and down, just turning may not resolve the cell pellet).

6. Place in the incubator for 60 minutes. Set an Eppendorf thermo mixer to 37°C.

7. Centrifuge to pellet cells at 1800rpm for 5 minutes at room temperature.

8. Aspirate supernatant and let tube stand for 10 sec. Remove the rest of the supernatant with a 200 μl pipetman.

9. Cut a 200μl tip from the end and resuspend cells (~ 1.5xl0⁷ cells in 150μl RPEM without Met, but try not to go over 250μl if you have more cells) gently in

150μl starvation medium with and without 43μg/ml LY (LY-294002, catalog number cat 440202 by Calbiochem, Mega Pharm). Transfer cells to an Eppendorf tube and place in the thermo mixer. Wait 10 sec and transfer the rest of the cells from the 10 ml tube to the Eppendorf tube, if necessary add another 50 μl to splash the rest of the cells out (all specimens should have the same volume of labeling reaction!).

10. Pulse: Add 50μl of ³⁵S-methionine (specific activity 14.2μCi/μl), tightly cup tubes and place in thermo mixer. Set the mixing speed to the lowest possible (700 rpm) and incubate for 25 minutes.

11. Stop the pulse by adding 1ml ice-cold chase/stop medium. Shake tube very gently three times and pellet cells at όOOOrpm for 6 sec.

12. Remove supernatant with a 1ml tip. Add gently 1ml ice-cold chase/stop medium with and without 43μg/ml LY to the pelleted cells and invert gently to resuspend.

13. Chase: Transfer all tubes to the thermo mixer and incubate for the required chase time (1,2,3,4 and 5 hours). Add every hour LY to the require concentration (43μg/ml.

8870445 4.DOC — 63 — 14. At the end of total chase time, place tubes on ice, add 1ml ice-cold chase/stop and pellet cells for 1 minute at 14,000 rpm. Remove supernatant and transfer supernatant to a second eppendorf tube. The cell pellet freeze at -80 C, until all tubes are ready.

15. Centrifuge supernatants for 2 hours at 14,000rpm, 4°C. Remove the supernatant very gently, leave 20 μl in the tube (labeled as V).

*** All steps are done on ice with ice-cold buffers

16. When the time course is over, remove all tubes form -80°C. Lyse VLP pellet (from step 15) and cell pellet (step 14) by adding 500 μl of lysis buffer (see solutions), resuspend well by pipeting up and down three times. Incubate on ice for 15 minutes, and spin in an eppendorf centrifuge for 15 minutes at 40°C, 14,000 rpm. Remove supernatant to a fresh tube, discard pellet.

17. (A) Perform EP with anti-p24 sheep for all samples (conjugation done by Shmulik).

(B) Take out 20μl from each sample for IB with anti-phospho AKT.

C. IMMUNOPRECIPITATION

1. Preclearing: add to all samples 15μl LmmunoPure PlusG (Pierce). Rotate for 1 hour at 4°C in a cycler, spin 5 min at 4°C, and transfer to a new tube for EP.

2. Add to all samples 15μl of p24-protein G conjugated beads and incubate 4 hours in a cycler at 4°C.

3. Post immunoprecipitations, transfer all immunoprecipitations to a fresh tube.

4. Wash beads twice with high salt buffer, once with medium salt buffer and once with low salt buffer. After each spin don't remove all solution, but leave ~50μl solution on the beads. After the last spin remove supernatant carefully with a loading tip and leave ~10 μl solution.

5. Add to each tube 15μl 2x SDS sample buffer. Heat to 70°C for 10 minutes.

8870445 4.DOC ~ 64 — 6. Samples were separated on 10% SDS-PAGE. Before loading the samples centrifuge for 5 minutes at 14000rpm.

7. Fix gel in 25% ethanol and 10% acetic acid for 15 minutes.

8. Pour off the fixation solution and soak gels in Amplify solution (NAMP 100 Amersham) for 15 minutes.

9. Dry gels on warm plate (60-80 °C) under vacuum.

10. Expose gels to screen for 4 hours and scan.

Results, as shown in Figure 6, demonstrate that treating HIV-infected cells with PI3K inhibitor LY inhibits HIV release.

INCORPORATION BY REFERENCE

All publications and patents mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.

EQUIVALENTS

While specific embodiments of the subject invention have been discussed, the above specification is illustrative and not restrictive. Many variations of the invention will become apparent to those skilled in the art upon review of this specification and the claims below. The full scope of the invention should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations.

8870445 4 DOC — 65 —

Claims

WHAT IS CLAIMED:

I. A method of inhibiting viral infections comprising administering an effective amount of a PI3K pathway inhibitor to a subject in need thereof.

2. A method of inhibiting viral maturation comprising administering an effective amount of a PI3K pathway inhibitor to a subject in need thereof.

3. A method of any one of claims 1 or 2, wherein the PI3K pathway inhibitor inhibits the interaction between PI3K and PI3K-AP.

4. The method of claim any one of claims 1 or 2, wherein the viral infection is a retroviral infection.

5. The method of claim 4, wherein the infection is HIV infection.

6. The method of claim 5, wherein the infection is HIV1 infection.

7. The method of claim 1, wherein the PI3K Pathway inhibitor is a PI3K inhibitor.

8. The method of claim 7, wherein the PI3K inhibitor is selected from the group consisting of a small molecule, an antibody, a peptide and a polynucleotide.

9. The method of claim 8, wherein the PI3K inhibitor is a small molecule.

10. The method of claim 7, wherein the PI3K inhibitor is selected from the group consisting of LY294002, wortmannin, Quercetin, demethoxyviridin, Myricetin, Staurosporine, and a PI3K-targeted RNAi.

I I. The method of claim 10, wherein the PI3K inhibitor is LY294002.

12. The method of claim 7, wherein the PI3K inhibitor is a structural analog of any one of wortmannin, LY294002, demethoxyviridin, Myricetin, and Staurosporine.

8870445 4.DOC — 66 —

13. An isolated protein complex having a p85 polypeptide and at least one polypeptide selected from the group comprising:

—a polypeptide comprising at least one HECT domain and a ww domain; —a polypeptide comprising at least one RCC1 domain and at least one HECT domain;

— a polypeptide comprising at least one Ring finger domain and at least one SH3 domain;

-a p85-AP; —an E2 enzyme;

—a cullin;

—a clathrin;

—a Gag protein;

—a Gag late domain; and -POSH protein.

14. The complex of claim 13, further comprising one or more of the following proteins:

—a Nef protein; -a p21 -activated kinase (PAK); —a Vav protein; — Rac; and -Cdc42.

15. The complex of claim 13, further comprising a pi 10 catalytic subunit.

16. An isolated protein complex having a p85 polypeptide, a gag protein, and at least one polypeptide selected from the group comprising: —a polypeptide comprising at least one HECT domain and a ww domain; —a polypeptide comprising at least one RCC1 domain and at least one HECT domain;

8870445 4 DOC — 67 — — a polypeptide comprising at least one Ring finger domain and at least one SH3 domain;

-a p85-AP;

—an E2 enzyme; —a cullin;

~a clathrin;

—a Gag protein;

—a Gag late domain;

-POSH protein; -a Nef protein;

-a p21 -activated kinase (PAK);

-a Vav protein;

-Rac; and

-Cdc42.

17. An assay for identifying a test compound which inhibits or potentiates the stability of a p85 complex, comprising:

(a) forming a reaction mixture including:

(i) an isolated protein complex of claim 13; (ii) a test compound; and

(b) detecting the presence of p85 polypeptide in the complex; wherein a change in the presence of p85 polypeptide in the complex in the presence of the test compound, relative to the presence of p85 polypeptide in the complex in the absence of the test compound, indicates that said test compound potentiates or inhibits the stability of said p85 complex.

18. An assay for identifying a test compound which inhibits or potentiates the stability of a p85 complex, comprising:

(a) forming a reaction mixture including: (i) an isolated protein complex comprising a p85 polypeptide and a Gag protein; and (ii) a test compound; and

8870445 4 DOC — 68 ~ (b) detecting the association between the p85 polypeptide and the Gag protein; wherein a change in the association between the p85 polypeptide and the Gag protein in the presence of the test compound, relative to the association between the p85 polypeptide and the Gag protein in the absence of the test compound, indicates that said test compound potentiates or inhibits the stability of said p85 complex.

19. The method of claim 18, wherein the p85 polypeptide is at least 90% identical to SEQ D NO:2.

20. The method of claim 18, wherein the Gag protein is HIV p24.

21. The method of claim 18, wherein the Gag protein comprises a sequence motif RXXPXXP.

22. A method for identifying modulators of protein complexes, comprising: (i) forming a reaction mixture comprising:

(i) a p85 polypeptide; (ii) a p85-AP; and (iii) a test compound;

(ii) contacting the reaction mixture with a test agent, and

(iii) determining the effect of the test agent for one or more activities selected from the group comprising (a) a change in the level of the protein complex, (b) a change in the enzymatic activity of the complex, (c) where the reaction mixture is a whole cell, a change in the plasma membrane localization of the complex or a component thereof or (d) a change in the interaction between the p85 polypeptide and the p85- AP.

23. A screening assay to identify agents that inhibit or potentiate the interaction of a p85 polypeptide and a p85-AP, comprising providing a two-hybrid assay system including a first fusion protein comprising a p85 polypeptide portion, and a second fusion protein comprising a p85-AP portion, under conditions wherein said two

8870445 4 DOC — 69 — hybrid assay is sensitive to interactions between the p85 polypeptide portion of said first fusion protein and said p85-AP portion of said second polypeptide; ii. measuring a level of interactions between said fusion proteins in the presence and in the absence of a test agent; and iii. comparing the level of interaction of said fusion proteins, wherein a decrease in the level of interaction is indicative of an agent that will inhibit the interaction between a p85 polypeptide and a p85-AP.

24. The method of claim 23, wherein p85-AP is selected from the group consisting of

—a polypeptide comprising at least one HECT domain and a ww domain;

—a polypeptide comprising at least one RCC1 domain and at least one HECT domain;

— a polypeptide comprising at least one Ring finger domain and at least one SH3 domain;

-a p85-AP;

—an E2 enzyme;

—a cullin;

—a clathrin; —a Gag protein;

—a Gag late domain;

—a Nef protein;

—a p21 -activated kinase (PAK);

—a Vav protein; -Rac;

-Cdc42; and

—Posh Protein.

25. The screening assay of claim 23, wherein the p85 polypeptide is at least 90% identical to SEQ ID NO:2.

8870445 4 DOC — 70 —

26. The screening assay of claim 23, wherein the p85-AP comprises a sequence motif of RXXPXXP.

27. An assay for screening test compounds for an inhibitor of an interaction of a p85 polypeptide with a p85-AP, comprising:

(i) providing a two hybrid assay system including a host cell comprising: (a) a reporter gene operably linked to a transcriptional regulatory sequence, said regulatory sequence including a DNA sequence which binds to a DNA binding domain, (b) a first chimeric gene comprising a sequence encoding the p85 polypeptide and the DNA binding domain, and (c) a second chimeric gene comprising a sequence encoding the p85- AP and a transcriptional activation domain, wherein said p85 polypeptide interacts with said p85-AP protein and increases expression of the reporter gene relative to its expression in the absence of the interaction; (ii) measuring expression of said reporter gene in the absence of a test compound;

(iii) contacting said two hybrid assay system with a test compound; and (iv) measuring expression of said reporter gene in the presence of the test compound; wherein a decrease in expression of the reporter gene in the presence of the test compound relative to its expression in the absence of the test compound indicates that the test compound is an inhibitor of the interaction between the p85 polypeptide and the p85-AP.

28. A method for inhibiting infection in a subject in need thereof, comprising administering an effective amount of an agent that inhibits the interaction of a p85 polypeptide to a p85-AP.

29. The method of claim 28, wherein said agent is selected from the group comprising a small molecule, a antibody, a polynucleotide, and a peptide.

8870445 4 DOC — 71 —

30. The method of claim 28, wherein the p85-AP is selected from the group consisting of a Gag polypeptide, p24, POSH, and a polypeptide comprising at least one HECT domain and a ww domain.

31. The method of claim 30, wherein the Gag polypeptide is HEV p24.

32. The method of claim 29, wherein said polynucleotide is selected from the group consisting of an RNAi construct, a ribozyme, antisense oligonucleotide, and a DNA enzyme.

33. A method of identifying small molecules effective in inhibiting viral infections, comprising: identifying a structural analog of a PI3K pathway inhibitor, and determining its effect in inhibiting the activity of said PI3K pathway inhibitor in inhibiting viral infections.

34. A method of identifying small molecules effective in inhibiting viral maturation, comprising: identifying a structural analog of a PI3K pathway inhibitor, and determining its effect in inhibiting the activity of said PI3K pathway inhibitor in inhibiting viral maturation.

35. The method of claim 34, wherein the structural analogs of the PI3K pathway inhibitor are identified by screening a small molecule libraries.

36. The method of claim 34, wherein the PI3K Pathway inhibitor is a PI3K inhibitor.

37. The method of claim 36, wherein the PI3K inhibitor is a small molecule.

8870445 4 DOC — 72 —

38. The method of claim 37, wherein the PI3K inhibitor is selected from the group consisting of LY294002, wortmannin, demethoxyviridin, Quercetin, Myricetin, Staurosporine, and a PI3K-targeted RNAi.

39. The method of claim 37, wherein the PI3K inhibitor is a structural analog of any one of wortmannin, LY294002, demethoxyviridin, Quercetin, Myricetin, and Staurosporine.

40. The method of claim 38, wherein the PI3K inhibitor is LY294002.

41. The method of claim 33, wherein the viral infection is retroviral infection.

42. The method of claim 41, wherein the retroviral infection is HIV infection.

43. The method of claim 42, wherein the HIV infection is HIV1 infection.

44. The method of claim 41, wherein the retroviral infection is Ebola virus infection.

45. An isolated antibody, or fragment thereof, specifically immunoreactive with an epitope of SEQ ID NO:2, which disrupts the interaction between SEQ ED NO:2 and a p85-AP.

46. The antibody of claim 45, which disrupts the interaction between SEQ ID NO:2 and a Gag polypeptide.

47. The antibody of claim 45, which disrupts the interaction between SEQ ID NO:2 and a Gag late domain.

48. The antibody of any one of claims 45-47, wherein said antibody is a monoclonal antibody.

8870445 4 DOC — 73 —

49. The antibody of any one of claims 45-47, wherein said antibody is a Fab fragment.

50. The antibody of any one of claims 45-47, wherein said antibody is labeled with a detectable label.

51. A host cell comprising a first nucleic acid and a second nucleic acid, wherein the first nucleic acid comprises a recombinant p85 nucleic acid, and wherein the second nucleic acid comprises a recombinant nucleic acid encoding a late domain of a Gag polypeptide.

52. The host cell of claim 51, wherein the p85 nucleic acid encodes polypeptide comprising a polypeptide sequence at least 90% identical to SEQ ID NO:2 and wherein the encoded polypeptide forms a complex with a Gag polypeptide.

53. A host cell comprising a first nucleic acid and a second nucleic acid, wherein the first nucleic acid comprises a recombinant p85 nucleic acid, and wherein the second nucleic acid comprises a recombinant nucleic acid encoding a Gag polypeptide.

8870445 4.DOC — 74