Definitions

• Integrins are heterodimeric receptors that mediate a wide variety of important interactions both between cells and between cells and the extracellular matrix via ligand binding. All integrins have an ⁇ subunit and a ⁇ subunit. Within the ⁇ subunit a region referred to as the A domain (or I domain) is known to be an important mediator of ligand binding. A similar region, the A-like domain, is present in many ⁇ subunits. Many integrins are thought to exist in two conformations, a low affinity state (the "closed” or “unliganded” conformation") and a high affinity state (the "open” or "Iiganded” conformation), the later of which is responsible for high affinity ligand binding.
• Integrins transduce signals that mediate the effects of the matrix on the physiological activity of cells (e.g., motility, proliferation, and differentiation). Moreover, integrins play a role in inflammation and in oncogenic cell transformation, metastasis, and apoptosis. Thus, there is considerable interest in identifying compounds that can activate or inhibit the activity of one or more integrins. In order for an efficient integrin-ligand binding to occur, it is thought that the integrin must be in its high affinity configuration. It appears that inside-out signals generated when cells are activated by a variety of stimuli switch integrins from a low affinity state to a high affinity state.
• This functional upregulation is associated with conformational changes in the extracellular regions of integrins that include the A domain of the ⁇ subunit and the A-like domain of the ⁇ subunit (Smith et al. 1988 J. Biol. Chem. 263 : 18726).
• the integrin A-domain assumes a dinocleotide-binding fold (Lee et al. 1995 Cell 80:631; Emsley et al. 1997 J Biol. Chem..272:28512; Li et al. 1998 J. Cell Biol. 143:1523; Nolte et al. 1999 FEBSLett. 452:379; and Legge et al. 2000 J. Mol. Biol. 295:1251) with a metal ion dependent adhesion site (MJJDAS) on its top, and it is connected through a C- terminal ⁇ 7 helix at its bottom to the body of the integrin.
• MJJDAS metal ion dependent adhesion site
• MIDAS and its surrounding exposed side-chains form the binding site for physiologic ligands (Li et al., supra; Michishita et al., Cell 72:857-867, 1993; Kamata et al., J. Biol. Chem. 269:26006-26010, 1994; Kern et al., J. Biol. Chem. 269:22811-6, 1994; Edwards et al., JBiol Chem. 273:28937-44, 1998; Zhang et al., Biochemistiy 38:8064-71, 1999) and certain antagonists (Rieu et al., JBiol Chem. 271:15858-15861, 1996).
• the invention features polypeptides comprising all or part of a variant integrin ⁇ subunit A domain or a variant integrin ⁇ subunit A-like domain.
• an important isoleucine (He) residue (described in greater detail below) is absent.
• the isoleucine can be either deleted or replaced with different amino acids residue, preferably a smaller or less hydrophobic amino acid residue, e.g., alanine or glycine.
• the variant integrin polypeptides of the invention tend to exist in solution in a high affinity conformation, they are useful in screening assays for the identification of molecules that bind to (and/or modulate the activity of) an integrin. They are also useful for generating antibodies, e.g., monoclonal antibodies, which selectively bind to the high affinity form of an integrin. Some such antibodies recognize an epitope that is either not present or not accessible on an integrin that is in a lower affinity conformation. Thus, the invention features antibodies which bind with greater affinity to a variant integerin of the invention than to corresponding wild-type integrin.
• the variant integrin polypeptides of the invention can be derived from any integrin ⁇ subunit or any integrin ⁇ subunit.
• the variant integrin polypeptides preferably include a ligand-binding portion of an A-domain or an A-like domain.
• the invention also features methods for identifying a compound that binds to a variant integrin polypeptide of the invention.
• screening methods can entail exposing the polypeptide to a test compound of interest and determining whether the compound binds to the polypeptide.
• the assay can be a simple binding assay (e.g., where binding of the compound is measured only in the absence of the ligand) or a competitive binding assay (e.g., where binding of the compound is measured in the presence of the ligand).
• the invention also features methods for identifying a compound that interferes with the binding of an integrin ligand to an integrin by measuring the binding of an integrin ligand to a variant integrin polypeptide in the presence and absence of a test compound.
• the ability of a test compound to interfere with the binding of an integrin ligand to an integrin may also be tested.
• the binding specificity of a compound can be assessed by measuring the binding of the integrin ligand to a second integrin (or measuring the binding of a second ligand to the integrin) in the presence and absence of the test compound.
• the invention also features methods for interfering with the binding of an integrin to an integrin ligand by administering a variant integrin polypeptide of the invention or an antibody that selectively binds to a variant integrin polypeptide of the invention.
• the invention also features methods of administering a variant integrin polypeptide of the invention or an antibody that selectively binds to a variant integrin polypeptide of the invention for the purpose of identifying the presence of a ligand which binds to an active integrin.
• assays are useful for diagnosing inflammation, e.g., occult inflammation (e.g. an abscess or an active atherosclerotic lesion).
• Compounds that bind to a variant A domain or A-like domain of the invention are candidate compounds for the treatment of inflammatory disorders mediated by an integrin, e.g., a disorder mediated by CDl lb, CDl la, or CDl lc.
• the invention further features nucleic acid molecules (e.g., mRNA and DNA) encoding a polypeptide of the invention or a polypeptide which includes a polypeptide of the invention.
• the invention also includes nucleic acid molecule encoding a fusion polypeptide comprising a polypeptide of the invention and a second polypeptide, e.g., an immunoglobulin constant domain.
• variant CDl lb involves deletion or substitution of an invariable He residue. Deletion or substitution of the He residue confers a high affinity phenotype in isolated CDl lb A domain as well as in the intact CDl lb integrin. Moreover, the He- modified A-domain can be crystallized in the "open" conformation. Thus, without being bound by any particular theory, it appears that an lie-based allosteric switch controls affinity and conformation in the integrin A-domain. Accordingly, variant, high affinity forms of other integrin ⁇ subunits (and ⁇ subunits) can be created by deleting or substituting the corresponding highly conserved He residue.
• Figures 1A and IB depict a surface representation of the CDl IbA domain crystal structure in its "closed” ( Figure 1 A) and “open” ( Figure IB) states, with the C-terminal ⁇ 7 helix outlined as a gray ribbon, the isoleucine (1332) residue in black. An arrow points to the MIDAS face. MIDAS and SILEN (socket for isoleucine) lie on almost opposite ends of the A-domain structure. Note that the amino acids in these figures are number based on the number of the mature protein.
• the CDllb ⁇ subunit has a 16 amino acid signal sequence. Thus, 1332 in the immature protein corresponds to 1316 in the mature protein.
• Figures IC and ID depict magnified face views of SELEN residues (1151, L180, 1252, Y283, lying within 4A radius from 1332) in the "closed” ( Figure IC) and “open” (Figure ID) conformations.
• 1332 sidechain is wedged in SILEN, and L328 is seen on top. L328 moves to cover SILEN in the "open” structure ( Figure ID).
• Figures 1 A- ID were built using GRASP (Barry Honig, Columbia University, NY). Note that the amino acids in these figures are number based on the number of the mature protein.
• the CDllb ⁇ subunit has a 16 amino acid signal sequence.
• 1332 in the immature protein corresponds to 1316 in the mature protein.
• Figures IE and IF depict stereo views of the 1332 coordination socket in the "closed” ( Figure IE) and “open” ( Figure IF) conformations.
• SILEN residues and 1332 and L328 are labeled. Note that the amino acids in these figures are number based on the number of the mature protein.
• the CDllb ⁇ subunit has a 16 amino acid signal sequence.
• 1332 in the immature protein corresponds to 1316 in the mature protein.
• Figures 2 A and 2B depict 2F 0 -Fc electron density maps of the C-terminal portions of ⁇ 7 from 1 IbA " ( Figure 2 A) and lib A ' structures. The maps were contoured at 1. l ⁇ , and made with O. Note that the amino acids in these figures are number based on the number of the mature protein.
• the CDllb ⁇ subunit has a 16 amino acid signal sequence. Thus, 1332 in the immature protein corresponds to 1316 in the mature protein.
• Figures 2C and 2D depict ribbon diagrams showing the complete superimposition of the llbA 139"337 (Figure 2C) and llbA 139'331 (Figure 2D) structures on the reported "closed” ( Figure 2C) and "open” ( Figure 2D) forms of the CDllb A domain, respectively.
• the metal ion is shown as a sphere.
• the amino acids in these figures are number based on the number of the mature protein.
• the CDllb ⁇ subunit has a 16 amino acid signal sequence.
• 1332 in the immature protein corresponds to 1316 in the mature protein.
• Figures 2E and 2F depict stereo views of MED AS in the llbA 139"337 ( Figure 2E) and llbA 139'331 ( Figure 2F) structures.
• the direct D258-metal bond, and indirect T225-water- metal bond (Figure 2E) are characteristic of the "closed” conformation.
• the metal ion in this case is Mn 2+ .
• the MIDAS conformation (a direct T225-metal bond, indirect D258-water- metal bond, and a pseudo ligand glutamate, occupying the active site, shown in green, and directly coordinating the metal ion (Ca 2+ ) are those of the "open” conformation).
• the amino acids in these figures are number based on the number of the mature protein.
• the CDllb ⁇ subunit has a 16 amino acid signal sequence.
• 1332 in the immature protein corresponds to 1316 in the mature protein.
• Figures 3A-3J depict the results of functional analysis of llbA E"G and llbA 139"331 A- domains using BIAcoreTM for recording the interactions of llbA E"G ( Figures 3A-3E) and llbA 139"331 ( Figures 3F-3J) with the activation-dependent ligands iC3b ( Figures 3 A and 3F), fibrinogen ( Figures 3B and 3G) or CD54 ( Figures 3C and 3H). All three ligands bound to 1 IbA 139"331 , but not to 1 IbA 139"337 .
• Figure 4 A depicts the results of an analysis of the binding of llbA 1 ⁇ G to iC3b.
• the dotted line represents the lack of binding of llbA to the same ligand.
• Figure 5 depicts an alignment of the A domains of nine alpha integrin ⁇ subunit (CDllb, CDllc, CDlld, CDlla, alpha 1, alpha 2, alpha 10, alpha 11, and alpha E).
• the invariant He 1332 in CDllb ⁇ subunit is indicated by an arrow.
• Figure 6 shows that an I to G mutation of the invariant isoleucine in CDlla A domain induces an activated domain in this integrin, underscoring the applicability of the findings in the CDllb A domain to other integrin A-domains.
• Figure 7 is an alignment of the A-like domains of eight integrin ⁇ subunits. In this alignment, the residue corresponding to the invariant He in ⁇ subunits is indicated by an arrow.
• Example 1 Generation of a stable, high affinity CDl lb variant A-domain by deletion
• CDllb ⁇ domain is for the immature protein, including the 16 amino acid signal sequence).
• This variant A domain was characterized and compared to a CDl lb A domain consisting of amino acids E 139 to G 337 (1 IbA 139"337 ; also referred to as 1 lbA E" °).
• a variant A domain with a He to Gly change at residue 332 (1 lbA I ⁇ G ) was also created. All three proteins were expressed as GST fusion proteins that were cleaved to release the protein of interest.
• the variant polypeptides were created using standard recombinant techniques. Restriction and modification enzymes were purchased from New England Biolabs, Inc. (Beverly, MA), Boehringer Mannheim (Germany), or GTBCO BRL (Gaithersburd, MD). Site-directed mutagenesis was carried out in pGEX-4T-l vector as described (Rieu et al. 1996 JBiol Chem 271 : 15858). The following mutagenic primers were used.
• IFAdel Fwd 5'-TATAGGATCCGAGGCCCTCCGAGGGAGTCCTCAAGAGGATAG-3'; Reverse: 5'- CTACTCGAGTTACTTCTCCCGAAGCTGGTTCTGAATGGTC-3'; I-G reverse: 5'- CTACTCGAGTTAACCCTCGATCGCAAAGCCCTTCTC-3'. Introduction of the respective mutation was confirmed by direct DNA sequencing.
• the PvuI-BspEI-restricted cDNA fragment of the A-domain containing the mutation was subcloned into the Pvul- BspEI-restricted CDllb cDNA, cloned into pcDNA3 plasmid, which containing full-length human CDl lb (Rieu et al 1996 JBiol Chem 271: 15858).
• l ib A 139"337 and llbA 139"331 and 1 lbA 1 ⁇ G A-domains were expressed as GST fusion proteins in Escherichia coli (Michishita et al.
• a single llbA " crystal was used to collect a 2.3 A resolution data set, at 100 K, on beamline XI 2B of the National Synchrotron Light Source at the Brookhaven National
• the preliminary rigid body refinements were performed using X-plor, with the diffraction data range from 8.0 to 3.0 A resolution with 5% of reflections for R-free calculation.
• the phases were gradually extended to high resolution and the structures were refined by several cycles of alternating torsion- angle dynamics and restrained individual isotropic B factor refinement protocols with all diffraction data between 8.0 and 2.6 A, and 8.0 and 2.3 A resolution, for llbA 139"337 and llbA " structures, respectively (Table 1).
• Model inspection and manual adjustments were made on SGI graphics workstations using O (Jones et al. 1991 Ada Crystallogr 47:110).
• the addition of solvent molecules was based on the suitable peaks in difference maps, reasonable hydrogen bond and refined temperature factors of less than 50 A 2 .
• the addition of solvent molecules was based on the suitable peaks in difference maps, reasonable hydrogen bond and refined temperature factors of less than 50 A 2 .
• the structure was refined to a final R factor of 20.3% (R-free: 25.6%) for the llbA 139"321 structure, and 21.9% (R-free: 30.0%) for the llbA " structure.
• the final models comprises all nonhydrogen atoms of residues D148 to K331, 30 water molecules, and one Ca 2+ ion for llbA 139"331 , and residues D148 to G337, 44 water molecules and one Mn 2+ ions for llbA 139"337 . Crystallographic data is presented in Table 1.
• ligand binding properties of llbA " and 1 IbA " were determined using surface plasmon resonance as previously described (Li et al, supra) on a BIAcore (BIAcore AB, Uppsala, Sweden).
• IC3b, fibrinogen or CD54 each was covalently couples via primary amine groups to the dextran matrix of a separate CM5 sensor chip (BIAcore AB).
• BSA immobilized in the same way was used as a control surface.
• 1 IbA " , 1 IbA ' and 1 lbA I ⁇ G A-domains were flowed over the chip at 5 ml/min at different times.
• TBS (20 mM Tris-HCl, pH 8.0, 150 mM NaCl) with 2 mM MgC 1 2 and 0.005% P20 (BIAcore AB) was used as the running buffer. 1 M NaCl in 20 mM Tris-HCl, pH 8.0, was used to remove the bound proteins and to regenerate the surface. Binding was measured as a function of time. The binding data (after subtracting background binding to BSA-coated chip) were analyzed using Scatchard plots as described (Dall'Acqua et al. 1996 Biochemstiy 35:9667-9676).
• COS M7 simian fibroblastoid cells at -70% confluence were transfected with supercoiled cDNAs encoding WT or CDl lb I ⁇ G together with full-length CD18 as described (Michishita et al, supra)
• Transfected COS cells were grown for 24 h in Iscove's modified Dulbecco's medium (BioWhittaker, Inc., Walkersville, MD) supplemented with 10% FBS, 2 mM glutamine, 50 IU/ml penicillin and streptomycin at 37°C.
• CR3 ⁇ G was expressed as a percentage of binding to wild type, after correcting for the degree of surface expression using binding of mAb904 (Rieu et al. 1996 JBiol Chem 271:15858).
• He 332 is invariable in all integrin alpha A-domains cloned to date ( Figure 5).
• An A- domain with an He to glycine substitution (1 lbA I ⁇ G ) exhibited a "high affinity” state ( Figure 4A).
• the same substitution created in the holoreceptor dramatically increased its ligand binding activity (Figure 4B).
• the crystal structure 1 lbA I ⁇ G was identical to that of the "open” 1 IbA 139"331 form.
• SILEN hydrophobic intramolecular socket
• I is replaced by L in the "open” structure
• Figures 1 A and IF A conserved hydrophobic intramolecular socket
• SILEN is formed by the hydrophobic side chains of I 151 , L 180 , I 252 , and Y 283 both in the "closed” and "open” conformations.
• Figures IC and ID In several integrins, certain mutations that lie outside MIDAS produce gain-of function effects in the holoreceptor, and are believed to act allosterically (Zhang et al, supra; Oxvig et al, supra; Zhang et al., supra).
• N-terminal extension facilitates A-domain switching into the less favored high-affinity state (Li et al, supra).
• the underlying structural basis for this effect is unknown, since none of the residues in the N-terminal extension are included in the derived 3-D structures. It has been observed however that residues within this extension regulate ligand binding in A-domains.
• residues within this extension regulate ligand binding in A-domains.
• synthetic peptide from the N-terminal extension inhibited CD 11 a-dependent adhesion. Structural data from the
• CD49b A-domain also show that three residues that extend beyond the ⁇ 7 helix can pack into a crevice formed in part by residues in the N-terminal extension, bringing the N and C termini into very close proximity (Emsley et al, supra). Flexibility of the C-terminal residues in ⁇ 7 has also been observed in the crystal and NMR structures of the CDl la A- domain. Taken together, these data suggest the N-terminal extension may offer an alternative by imperfect "competitive" surface for luring He away from SJLEN, allowing some molecules to exist in the "open” form. The present data suggest that such a mechanism may operate in the holoreceptor, providing a mechanistic basis for integrin activation by inside-out signals.
• FIG. 5 is an alignment of the C-terminal ⁇ 7 helix of the A domains of nine integrin ⁇ subunits (CDllb, CD lie, CD lid, CDlla, alpha 1, alpha 2, alpha 10, alpha 11, and alpha E).
• the present invention features variant integrin ⁇ subunit polypeptides in which the invariant He (listed in Table 2) is substituted by Gly, Ala or some amino acid other than He (e.g., Val).
• the polypeptide can include part or all of the indicated A domain, e.g., 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 contiguous amino acids of the A domain that includes the position of the invariant He.
• the invention also includes variant integrin ⁇ subunits in which the He has been deleted.
• polypeptides comprising the entire A domain of an integrin ⁇ except for the invariant He (e.g., amino acids 144-132 of CDllb, amino acids 145-332 of CDllc, amino acids 144-331 of CDlld, amino acids 150-330 of CDlla), but does not include the remainder of the integrin ⁇ subunit.
• the invention also features polypeptides comprising the A domain of an integrin ⁇ subunit up to but not including the invariant He and further lacking the 5 amino acids following the invariant He (e.g., amino acids 144-331, but not 332-336 of CDllb; amino acids 145-332, but not 333-337 of CDllc; amino acids 144-331, but not 332-336 of CDlld; amino acids 150-330, but not 331-335 of CDlla; amino acids 139-330, but not 331- 335 of human alpha 1; amino acids 169-360, but not 361-335 of human alpha 2; amino acids 57-248, but not 249-253 of human alpha 10; amino acids 159-348, but not 349-353 of human alpha 11; or amino acids 196-384, but not 385-389 of human alpha E).
• amino acids 144-331, but not 332-336 of CDllb amino acids 145-332, but not 333-337 of CDllc
• variant integrin in which a change (substitution or deletion) of the He corresponding to He 332 of CDl lb ⁇ subunit is combined with one or more other activating mutations, e.g., an L 180 -F substitution or a mutation at E 147 , D 148 , K 247 orF 250 .
• the portion of the integrin ⁇ subunit (or the A-like domain of the subunit) that includes the conserved He (or Leu) and all amino acid residues C terminal to the invariant He can be deleted.
• the invention features isolated or purified nucleic acid molecules that encodes a variant integrin polypeptide, e.g., a full-length variant integrin subunit or a fragment thereof (e.g., in which the invariant He is deleted or substituted), e.g., a biologically active variant integrin polypeptide.
• a variant integrin polypeptide e.g., a full-length variant integrin subunit or a fragment thereof (e.g., in which the invariant He is deleted or substituted), e.g., a biologically active variant integrin polypeptide.
• an isolated nucleic acid molecule of the invention includes the nucleotide sequence encoding amino acids 139-321 of the CDl lb ⁇ subunit (SEQ ID NO:l) or a portion thereof.
• the nucleic acid molecules can include non-coding sequences or sequences encoding all or a portion of a protein other than an integrin.
• an isolated nucleic acid molecule of the invention includes a nucleic acid molecule which is a complement of the nucleotide sequence encoding amino acids 139-321 of the CDl lb ⁇ subunit.
• a nucleic acid molecule of the invention can include only a portion of the nucleic acid sequence of SEQ ID NO: 1.
• such a nucleic acid molecule can include a fragment which encodes all or a portion (e.g., an immunogenic or biologically active portion) or an integrin A domain or A-like domain.
• the present invention also includes variant integrin polypeptides.
• Such polypeptides can be produced using recombinant DNA methods, by chemical synthesis or using other techniques.
• the polypeptides can be used as immunogens or antigens generate antibodies that bind the active form of an integrin A-domain or A-like domain.
• the polypeptide can be post-translationally modified, e.g., glycosylated.
• a variant integrin polypeptide can be part of a fusion protein that includes all or a portion of a second polypeptide that is not a variant integrin polypeptide. This second polypeptide can be fused to the C-terminus or the N-terminus of the variant integrin polypeptide. All or part of a third peptide may also be present.
• a variant integrin polypeptide can be fused to, e.g., GST, an immunoglobulin constant region, a heterologous signal sequence.
• the variant integrin polypeptide fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject in vivo.
• the variant integrin polypeptides can be used to reduce skeletal muscle injury.
• Isolated CDl lb A domain has already been found to reduce damage in an animal model of this type of injury.
• purified recombinant rat CDl lb A-domain was administered intravenously in a single dose (lmg/kg) to seven groups of Lewis rats (5 per group), 30 minutes before inducing mechanically skeletal muscle injury. Equal numbers of rats were treated with a function- blocking anti-CDllb/CD18 mAb (1 mg/kg). Quantitative histological examination of the wounded area in controlled rats (treated with PBS), showed edema, myofiber disruption, necrosis and erythrocytes extravasation. Influx of neutrophils was detected 30 minutes post wound, followed by a second wave 3 hours later.
• variant integrin polypeptide fusion proteins can be used to affect the bioavailability of a variant integrin polypeptide ligand.
• variant integrin polypeptide fusion proteins may be useful therapeutically for the treatment of disorders caused by, for example, ischemia-reperfusion injury (Stroke 30:134- 9,1999), immune complexes (JExpMed 186:1853-63,1997), restenosis, and parasitic diseases (e.g. Ancylostoma spp; see J Cell Biol 127:2081-91, 1994).
• variant integrin polypeptide-fusion proteins of the invention can be used as immunogens to produce anti-variant integrin polypeptide antibodies in a subject, to purify variant integrin polypeptide ligands and in screening assays to identify molecules that inhibit the interaction of variant integrin polypeptide with an variant integrin polypeptide ligand.
• Expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide).
• a variant integrin polypeptide-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the variant integrin polypeptide protein.
• Variant integrin polypeptides can be produced using an expression vectors (e.g., a plasmid vector or a viral vector).
• the vector can be autonomously replicating or integrated in to the host genomes.
• the expression vector can include at least one regulatory sequence
• the expression vector can be designed for expression in prokaryotic or eukaryotic cells, e.g., plant cell, insect cells, yeast cells, mammalian cells, and E coli. Depending on the host cells used to express the variant integrin polypeptide, it may be desirable to encode the polypeptide using codons optimized for the host cell. In some cases it may be desirable to employ an expression vector capable of directing tissue-specific expression.
• the invention also features host cells or recombinant cells harboring a nucleic acid molecule encoding a variant integrin polypeptide.
• the nucleic acid molecule can be integrated into the host cells genome or present in an autonomously replicating vector.
• a host cell can be any prokaryotic or eukaryotic cell, e.g., E. coli, an insect cell, yeast or a mammalian cell.
• the nucleic acid molecules can be introduced into the host cells through transformation or transfection techniques.
• a host cell of the invention can be used to produce (i.e., express) a variant integrin polypeptide by culturing the host cell under conditions such that the polypeptide is produced and then isolating the polypeptide from the cells or the culture medium.
• the invention also features antibodies directed against a variant integrin polypeptide.
• Such antibodies bind to the variant polypeptide with greater affinity than they bind to the corresponding wild-type integrin polypeptide.
• the antibodies can be generated using standard methods and can be screened by comparing the binding of the antibody to the variant integrin polypeptide to binding of the antibody to the corresponding wild-type polypeptide.
• antibody refers to an immunoglobulin molecule or immunologically active portion thereof, i.e., an antigen-binding portion.
• immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin.
• the antibody can be a polyclonal, monoclonal, recombinant, e.g., a chimeric or humanized, fully human, non- human, e.g., murine, or single chain antibody. In a preferred embodiment it has effector function.
• the antibody can be coupled to a toxin or imaging agent for use in diagnosis of occult inflammation (e.g. in abscess or active atherosclerotic plaques).
• Chimeric, humanized, but most preferably, completely human antibodies are desirable for applications which include repeated administration, e.g., therapeutic treatment (and some diagnostic applications) of human patients.
• the anti- variant integrin polypeptide antibody can be a single chain antibody which can be optionally dimerized or multimerized to generate multivalent antibodies.
• the antibody can be designed to have little or no ability to bind to an Fc receptor.
• the antibodies of the invention can be used to detect or purify integrin subunits that are in the active conformation. Thus, they can be used to evaluate the abundance and pattern of expression of an active form of an integrin as part of a clinical testing procedure. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance (i.e., antibody labeling).
• detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials (e.g., horseradish peroxidase, alkaline phosphatase, ⁇ - galactosidase, acetylcholinesterase, streptavidin/biotin and avidin/biotin, umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescent, dansyl chloride or phycoerythrin, luminol, luciferase, luciferin, aequorin, I, I, S and 3 H).
• radioactive materials e.g., horseradish peroxidase, alkaline phosphatase, ⁇ - galactosidase, acetylcholinesterase, streptavidin/biotin and avidin/biotin, umbelliferone, fluorescein
• the invention features methods for evaluating a compound for the ability to bind to a variant integrin polypeptide or inhibit the ability of an integrin ligand (e.g., a naturally- occurring integrin ligand) to bind to a variant integrin polypeptide.
• the methods can include contacting the compound with the variant integrin polypeptide in the presence or absence of a ligand and measuring the ability of the compound or the ligand to bind to the variant polypeptide.
• the methods can be performed in vitro, e.g., in a cell free system, or in vivo, e.g., in a two-hybrid interaction trap assay.
• the method can be used to identify naturally- occurring molecules which interact with an integrin. It can also be used to find natural or synthetic inhibitors of the interaction between an integrin and an integrin ligand.
• the compounds tested can be, e.g., proteins, peptides, peptidomimetics, peptoids, and small molecules.
• the test compounds can be obtained from combinatorial libraries including: biological libraries; peptoid libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; "one-bead one- compound” libraries.
• the screening assay can be a cell-based assay in which a cell which expresses an variant integrin polypeptide protein or biologically active portion thereof is contacted with a test compound, and the ability of the test compound to modulate variant integrin polypeptide activity is determined.
• Determining the ability of the test compound to modulate variant integrin polypeptide activity can be accomplished by monitoring, for example, the ability to bind an integrin ligand.
• the ability of the test compound to modulate variant integrin polypeptide binding to a compound, e.g., an integrin ligand or to bind to variant integrin polypeptide can also be evaluated. This can be accomplished, for example, by coupling the compound, e.g., the substrate, with a radioisotope or enzymatic label such that binding of the compound, e.g., the substrate, to variant integrin polypeptide can be determined by detecting the labeled compound, e.g., substrate, in a complex.
• a variant integrin polypeptide or the integrin ligand can be coupled with a radioisotope or enzymatic label to monitor the ability of a test compound to modulate variant integrin polypeptide binding to an integrin ligand.
• compounds can be labeled with I, S, C, or H, either directly or indirectly, and the radioisotope detected by direct counting of radioemmission or by scintillation counting.
• compounds can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product.
• a cell-free assay in which an variant integrin polypeptide or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the variant integrin polypeptide or biologically active portion thereof is evaluated.
• Preferred biologically active portions of the variant integrin polypeptide to be used in assays of the present invention include fragments that bind an integrin ligand.
• Soluble and/or membrane-bound forms of isolated proteins e.g., variant integrin polypeptide proteins or biologically active portions thereof
• membrane-bound forms of the protein it may be desirable to utilize a solubilizing agent.
• solubilizing agents include non- ionic detergents such as n-octylglucoside, n-dodecylglucoside, n-dodecylmaltoside, octanoyl- N-methylglucamide, decanoyl-N-methylglucamide, Triton® X-100, Triton® X-l 14,
• Cell-free assays involve preparing a reaction mixture of the target gene protein and the test compound under conditions and for a time sufficient to allow the two components to interact and bind, thus forming a complex that can be removed and/or detected.
• FET fluorescence energy transfer
• a fluorophore label on the first, 'donor' molecule is selected such that its emitted fluorescent energy will be absorbed by a fluorescent label on a second, 'acceptor' molecule, which in turn is able to fluoresce due to the absorbed energy.
• the 'donor' protein molecule may simply utilize the natural fluorescent energy of tryptophan residues.
• Labels are chosen that emit different wavelengths of light, such that the 'acceptor' molecule label may be differentiated from that of the 'donor'. Since the efficiency of energy transfer between the labels is related to the distance separating the molecules, the spatial relationship between the molecules can be assessed.
• the fluorescent emission of the 'acceptor' molecule label in the assay should be maximal.
• An FET binding event can be conveniently measured through standard fluorometric detection means well known in the art (e.g., using a fluorimeter).
• determining the ability of the variant integrin polypeptide protein to bind to a target molecule can be accomplished using real- time Biomolecular Interaction Analysis (BIA) as described above (see, e.g., Sjolander and Urbaniczky (1991) Anal. Chem. 63:2338-2345 and Szabo et al (1995) Curr. Opin. Struct. Biol. 5:699-705).
• Biomolecular Interaction Analysis e.g., Sjolander and Urbaniczky (1991) Anal. Chem. 63:2338-2345 and Szabo et al (1995) Curr. Opin. Struct. Biol. 5:699-705.
• "Surface plasmon resonance" or "BIA” detects biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore).
• the polypeptide or the test compound is anchored onto a solid phase.
• the polypeptide/test compound complexes anchored on the solid phase can be detected at the end of the reaction.
• the polypeptide can be anchored onto a solid surface, and the test compound, (which is not anchored), can be labeled, either directly or indirectly, with a detectable labels.
• Binding of a test compound to a variant integrin polypeptide protein, or interaction of an variant integrin polypeptide protein with a target molecule in the presence and absence of a candidate compound can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and micro-centrifuge tubes.
• a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matrix.
• glutathione-S-transferase/variant integrin polypeptide fusion proteins or glutathione-S- transferase/target fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtiter plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or variant integrin polypeptide protein, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH).
• the beads or microtiter plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above.
• the complexes can be dissociated from the matrix, and the level of variant integrin polypeptide binding or activity determined using standard techniques.
• Biotinylated variant integrin polypeptide or target molecules can be prepared from biotin-NHS (N- hydroxy-succinimide) using techniques known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, JL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).
• the non-immobilized component is added to the coated surface containing the anchored component. After the reaction is complete, unreacted components are removed (e.g., by washing) under conditions such that any complexes formed will remain immobilized on the solid surface.
• the detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the previously non- immobilized component is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed.
• an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the immobilized component (the antibody, in turn, can be directly labeled or indirectly labeled with, e.g., a labeled anti-Ig antibody).
• this assay is performed utilizing antibodies reactive with variant integrin polypeptide or target molecules but which do not interfere with binding of the variant integrin polypeptide to its target molecule.
• Such antibodies can be derivatized to the wells of the plate, and unbound target or variant integrin polypeptide protein trapped in the wells by antibody conjugation.
• Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with the variant integrin polypeptide or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the variant integrin polypeptide or target molecule.
• cell free assays can be conducted in a liquid phase.
• the reaction products are separated from unreacted components, by any of a number of standard techniques, including chromatography, electrophoresis and immunoprecipitation.
• the assay includes contacting the variant integrin polypeptide or biologically active portion thereof with a known compound which binds variant integrin polypeptide to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with an variant integrin polypeptide protein, wherein determining the ability of the test compound to interact with an variant integrin polypeptide includes determining the ability of the test compound to preferentially bind to variant integrin polypeptide or biologically active portion thereof, or to modulate the activity of a target molecule, as compared to the known compound.
• a reaction mixture containing the variant integrin polypeptide and the ligand is incubated, under conditions and for a time sufficient, to allow the two products to form complex.
• the reaction mixture is provided in the presence and absence of the test compound.
• the test compound can be initially included in the reaction mixture, or can be added at a time subsequent to the addition of the target gene and its cellular or extracellular binding partner. Control reaction mixtures are incubated without the test compound or with a placebo. The formation of any complexes between the variant integrin polypeptide and integrin ligand is then detected.
• reaction mixtures containing the test compound and variant integrin polypeptide can also be compared to complex formation within reaction mixtures containing the test compound and the corresponding wild-type integrin polypeptide.
• assays can be conducted in a heterogeneous or homogeneous format. Heterogeneous assays involve anchoring either the variant integrin polypeptide or the binding partner (i.e., the integrin ligand) onto a solid phase, and detecting complexes anchored on the solid phase at the end of the reaction. In homogeneous assays, the entire reaction is carried out in a liquid phase.
• test compounds that interfere with the interaction between the variant integrin polypeptides and the binding partner e.g., an integrin ligand
• the binding partner e.g., an integrin ligand
• test compounds that disrupt preformed complexes e.g., compounds with higher binding constants that displace one of the components from the complex
• either the variant integrin polypeptide or the integrin ligand is anchored onto a solid surface (e.g., a microtiter plate), while the non-anchored species is labeled, either directly or indirectly.
• the anchored species can be immobilized by non-covalent or covalent attachments.
• an immobilized antibody specific for the species to be anchored can be used to anchor the species to the solid surface.
• the partner of the immobilized species is exposed to the coated surface with or without the test compound. After the reaction is complete, unreacted components are removed (e.g., by washing) and any complexes formed will remain immobilized on the solid surface.
• the detection of label immobilized on the surface indicates that complexes were formed.
• an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the initially non-immobilized species (the antibody, in turn, can be directly labeled or indirectly labeled with, e.g., a labeled anti-Ig antibody).
• test compounds that inhibit complex formation or that disrupt preformed complexes can be detected.
• the reaction can be conducted in a liquid phase in the presence or absence of the test compound, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for one of the binding components to anchor any complexes formed in solution, and a labeled antibody specific for the other partner to detect anchored complexes.
• test compounds that inhibit complex or that disrupt preformed complexes can be identified.
• a homogeneous assay can be used.
• a preformed complex of the variant integrin polypeptide and the integrin ligand is prepared in that either the variant integrin polypeptide or the integrin ligand is labeled, but the signal generated by the label is quenched due to complex formation (see, e.g., U.S. Patent No. 4,109,496 that utilizes this approach for immunoassays).
• the addition of a test substance that competes with and displaces one of the species from the preformed complex will result in the generation of a signal above background. In this way, test substances that disrupt variant integrin polypeptide-binding partner interaction can be identified.
• the variant integrin polypeptide proteins can be used as "bait proteins" in a two-hybrid assay or three-hybrid assay (see, e.g., 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; Barrel et al (1993) Biotechniques 14:920-924; Iwabuchi et al. (1993) Oncogene 8: 1693- 1696; and Brent WO94/10300), to identify other proteins, which bind to or interact with variant integrin polypeptide.
• a two-hybrid assay can be carried out using a variant A domain as the bait protein. Briefly, the variant A domain is fused to the LexA DNA binding domain and used as bait.
• the prey is an aptamer library cloned into the active site loop of TrxA expression as a fusion protein with an N-terminal nuclear localization signal, a LexA activation domain, and an epitope tag (Colas et al 1996 Nature 380:548; and Gyuris et al. Cell 1993 75:791). Yeast cells are transformed with bait and prey genes. If an aptamer binds to variant A domain, the LexA activation domain is brought into proximity with the LexA DNA binding domain and expression of genes having an appropriately positioned LexA binding site increases.
• yeast strain EGY48 was transformed with the bait plasmid and pSH18-34 (a URA3, 2 ⁇ m plasmid containing the GALl promoter fused to lacZ, in which the GALl enhancer- like Upstream Activating Sequence (UASG) has been replaced with binding sites for eight LexA dimers).
• the yeast strain contains two reporter genes, LexAop- LEU2 (replaces the yeast chromosomal LEU2 gene) and LexAop-lacZ, carried on a 2 ⁇ m
• HIS3 + plasmid HIS3 + plasmid
• Transformed cells were plated on medium containing X-gal The presence of the bait did not cause the expression of ⁇ -galactosidase.
• the bait by itself also did not activate the LexAop-Leu2 gene in EGY48, since the transformed cells did not grow on Leu deficient plates.
• nuclear transport of the bait was assessed using the bait plasmid and a pJKlOl reporter in a repression type assay. In this assay DNA binding by transcriptionally inert LexA fusion proteins can be detected.
• the pJKlOl reporter is a URA3, 2 ⁇ m plasmid containing most of the UASG.
• CDl IbA-LexA bait impaired the galactosidase activity of yeast harboring the pJKlOl plasmid when grown on galactose medium, indicating that this bait enters the nucleus.
• An aptamer library was introduced into the Leu and lacZ reporter-containing yeast cells. Synthesis of library proteins was induced by growing the yeast in galactose medium.
• yeast cells does not grow on Leu" medium and have no ⁇ -galactosidase activity.
• a cell expressing a suitable prey will form colonies on Leu medium and have ⁇ -galactosidase activity.
• Selective galactose (but not glucose) inducible expression allows the Leu and LacZ phenotypes to be unambiguously ascribed to the library protein, diminishing the number of library plasmids that must be excluded by subsequent analysis. Plasmids from positive colonies (i.e., colonies able to grow on galactose, Ura", Tip" His" Leu” plates) were rescued (Hoffman et al. 1987 Gene 57:267).
• the specificity of their interaction with the bait was tested. This was done by showing that they do not interact with unrelated or nonfunctional baits (e.g., a CDl la A-domain-lexA and 1 lbA-D242A-lexA respectively), with the DNA-binding domain portion of the bait or nonspecifically with the promoters or other elements of the transcription machinery.
• the library plasmids were rescued from the galactose-dependent Leu+ lacZ+ yeast and re-introduced into the original selection strain and into other strains containing different baits.
• compositions The variant integrin polypeptides, fragments thereof, as well as anti- variant integrin polypeptide antibodies (also referred to herein as "active compounds") of the invention can be incorporated into pharmaceutical compositions.
• Such compositions typically include the protein or antibody and a pharmaceutically acceptable carrier.
• pharmaceutically acceptable carrier includes solvents, dispersion media, coatings, antibacterial and anti-fungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Supplementary active compounds can also be incorporated into the compositions.
• a pharmaceutical composition is formulated to be compatible with its intended route of administration.
• routes of administration include parenteral, intravenous, intradermal, subcutaneous, oral, inhalation, transdermal, transmucosal, and rectal administration.
• Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
• the parenteral preparation can be enclosed in
• compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
• suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, NJ) or phosphate buffered saline (PBS).
• the composition must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
• the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof.
• the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
• Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
• isotonic agents for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition.
• Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
• Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
• dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above.
• the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
• Oral compositions generally include an inert diluent or an edible carrier.
• the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, e.g., gelatin capsules.
• Oral compositions can also be prepared using a fluid carrier for use as a mouthwash.
• Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition.
• the tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
• a binder such as microcrystalline cellulose, gum tragacanth or gelatin
• an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch
• a lubricant such as magnesium stearate or Sterotes
• a glidant such as colloidal silicon dioxide
• the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
• a suitable propellant e.g., a gas such as carbon dioxide, or a nebulizer.
• Systemic administration can also be by transmucosal or transdermal means.
• penetrants appropriate to the barrier to be permeated are used in the formulation.
• penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
• Transmucosal administration can be accomplished through the use of nasal sprays or suppositories.
• the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
• the compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
• suppositories e.g., with conventional suppository bases such as cocoa butter and other glycerides
• retention enemas for rectal delivery.
• the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
• a controlled release formulation including implants and microencapsulated delivery systems.
• Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc.
• Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S.
• Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. 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.
• 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 ED 50 with little or no toxicity.
• the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
• 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 IC 50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans.
• a therapeutically effective amount of protein or polypeptide ranges from about 0.001 to 30 mg/kg body weight, preferably about 0.01 to 25 mg/kg body weight, more preferably about 0.1 to 20 mg/kg body weight, and even more preferably about 1 to 10 mg/kg, 2 to 9 mg/kg, 3 to 8 mg/kg, 4 to 7 mg/kg, or 5 to 6 mg/kg body weight.
• the protein or polypeptide can be administered one time per week for between about 1 to 10 weeks, preferably between 2 to 8 weeks, more preferably between about 3 to 7 weeks, and even more preferably for about 4, 5, or 6 weeks.
• treatment of a subject with a therapeutically effective amount of a protein, polypeptide, or antibody can include a single treatment or, preferably, can include a series of treatments.
• the preferred dosage is 0.1 mg/kg of body weight (generally 10 mg/kg to 20 mg/kg). If the antibody is to act in the brain, a dosage of 50 mg/kg to 100 mg/kg is usually appropriate. Generally, partially human antibodies and fully human antibodies have a longer half-life within the human body than other antibodies. Accordingly, lower dosages and less frequent administration is often possible. Modifications such as lipidation can be used to stabilize antibodies and to enhance uptake and tissue penetration (e.g., into the brain). A method for lipidation of antibodies is described by Cruikshank et al ((1997) J. Acquired Immune Deficiency Syndromes and Human Retrovirology 14:193).
• An agent may, for example, be a small molecule.
• small molecules include, but are not limited to, peptides, peptidomimetics (e.g., peptoids), amino acids, amino acid analogs, polynucleotides, polynucleotide analogs, nucleotides, nucleotide analogs, organic or inorganic compounds (i.e,.
• heteroorganic and organometallic compounds having a molecular weight less than about 10,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 5,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 1,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 500 grams per mole, and salts, esters, and other pharmaceutically acceptable forms of such compounds.
• Exemplary doses include milligram or microgram amounts of the small molecule per kilogram of subject or sample weight (e.g., about 1 microgram per kilogram to about 500 milligrams per kilogram, about 100 micrograms per kilogram to about 5 milligrams per kilogram, or about lmicrogram per kilogram to about 50 micrograms per kilogram.
• a small molecule depend upon the potency of the small molecule with respect to the expression or activity to be modulated.
• a physician, veterinarian, or researcher may, for example, prescribe a relatively low dose at first, subsequently increasing the dose until an appropriate response is obtained.
• the specific dose level for any particular animal subject will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, gender, and diet of the subject, the time of administration, the route of administration, the rate of excretion, any drug combination, and the degree of expression or activity to be modulated.
• An antibody (or fragment thereof) may be conjugated to a therapeutic moiety such as a cytotoxin, a therapeutic agent or a radioactive metal ion.
• a cytotoxin or cytotoxic agent includes any agent that is detrimental to cells.
• Examples include taxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin and analogs or homologs thereof.
• Therapeutic agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6- thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (H) (DDP) cisplatin), anthracyclines (e.g., daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin), bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents (e.g.
• the conjugates of the invention can be used for modifying a given biological response, the drug moiety is not to be construed as limited to classical chemical therapeutic agents.
• the drug moiety may be a protein or polypeptide possessing a desired biological activity.
• proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin or a protein such as a cytokine or interleukin.
• an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Patent No. 4,676,980.
• the nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors.
• Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Patent 5,328,470) or by stereotactic injection (see e.g., Chen et al (1994) Proc. Natl. Acad. Sci. USA 91:3054-3057).
• the pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded.
• the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
• compositions can be included in a container, pack, or dispenser together with instructions for administration.
• a model of vascular injury that can be useful in testing potential therapeutic compositions is described by Simon et al. (J. Clin. Invest. 2000 105:293). Tang et al. (1997 J ExpMed 186:1853) describe CDl lb knockout mice that can be useful in various screening assays. An animal model of burn injury may also be useful (Plast Reconstr Surg 1995 96:1177).
• the present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant or unwanted integrin expression or activity.
• Treatment or “treating a patient”, as used herein, is defined as the application or administration of a therapeutic agent to a patient, or application or administration of a therapeutic agent to an isolated tissue or cell line from a patient, who has a disease, a symptom of disease or a predisposition toward a disease, with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, palliate, improve or affect the disease, the symptoms of disease or the predisposition toward disease.
• a therapeutic agent includes, but is not limited to, small molecules, peptides, antibodies, ribozymes and antisense oligonucleotides.
• 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 LD 5 0/ED 50 .
• Compounds that exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects can 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.

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