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Title:  Method of identifying modulators of nogo-functions
United States Patent: 
7,270,962
Issued: 
September 18, 2007

Inventors: 
Blackstock; Walter Philip (Stevenage, GB), Hale; Richard Stephen (Stevenage, GB), Prinjha; Rabinder (Harlow, GB), Rowley; Adele (Stevenage, GB)
Assignee:
Glaxo Group Limited (Greenford, GB), SmithKline Beecham plc (Brentford, GB)
Appl. No.: 
10/466,258
Filed: 
January 18, 2002
PCT Filed: 
January 18, 2002
PCT No.: 
PCT/GB02/00228
371(c)(1),(2),(4) Date: 
February 04, 2004
PCT Pub. No.: 
WO02/057483
PCT Pub. Date: 
July 25, 2002


 

Covidien Pharmaceuticals Outsourcing


Abstract

A method of identifying a modulator Nogo function, the method comprising: (i) providing (a) a BACE polypeptide; (b) a Nogo polypeptide; (c) a test agent under conditions that would permit binding of a BACE polypeptide (a) to a Nogo polypeptide (b) in the absence of the test agent (c) wherein said BACE polypeptide (a) is BACE or a variant thereof or a fragment of either thereof capable of binding Nogo; and polypeptide (b) is Nogo or a variant thereof or a fragment of either thereof capable of binding BACE; (ii) monitoring Nogo mediated activity; and (iii) determining thereby whether the test agent is a modulator of Nogo activity. Modulators identified by a method of the invention and use of such modulators in the manufacture of a medicament for the treatment of disorders responsive to the modulation of Nogo activity such as acute neuronal injury.

SUMMARY OF THE INVENTION

The present inventors have identified a novel interaction between Nogo and BACE. The interaction between Nogo and BACE provides a new therapeutic intervention point in disorders involving defective NOGO function and more specifically in acute neronal injury such as spinal injury, stroke, head injury and peripheral nerve damage, neoplastic disease, hyperproliferative disorders and dysproliferative disorders. In addition, BACE is now proposed as a target for identifying agents which may be useful in the treatment of acute neuronal injury, neoplastic disorders, hyperproliferative disorders and dysproliferative disorders.

Accordingly the invention provides a method of identifying a modulator NOGO function, the method comprising: (i) providing (a) a BACE polypeptide (b) a Nogo polypeptide (c) a test agent under conditions that would permit binding of a BACE polypeptide (a) to a Nogo polypeptide (b) in the absence of the test agent (c) and wherein said BACE polypeptide (a) is BACE or a variant thereof or a fragment of either thereof capable of binding Nogo and said Nogo polypeptide (b) is Nogo or a variant thereof or a fragment of either thereof capable of binding BACE. (ii) monitoring Nogo mediated activity; and (iii) determining thereby whether the test agent is a modulator of Nogo activity.

In a further aspect, the invention provides a method for identification of a modulator of BACE activity, which method comprises: (i) contacting BACE or a variant thereof or a fragment of either thereof which maintains a BACE function with a test agent; and (ii) monitoring for BACE activity thereby determining whether the test agent is a modulator of BACE activity. The invention also provides: a modulator identifiable by a method according to the invention; use of a modulator identifiable by a method according to the invention in the manufacture of a medicament for the treatment or prophylaxis of acute neuronal injury, neoplastic disorders, hyperproliferative disorders or dysproliferative disorders; use of a BACE polypeptide or a polynucleotide encoding a BACE polypeptide in the manufacture of a medicament for the treatment of acute neuronal injury, neoplasia, hyperproliferative disorders or dysproliferative disorders wherein said BACE polypeptide is BACE or a variant thereof or fragment of either thereof which is capable of binding Nogo; a method of treatment of acute neuronal injury, neoplasia, hyperproliferative disorders or dysproliferative disorders comprising administering an effective amount of a BACE polypeptide, a polynucleotide encoding a BACE polypeptide or a modulator of BACE function identified by a method of the invention to a human or animal in need of such treatment wherein said BACE polypeptide is BACE or a variant thereof or fragment of either thereof which variant or fragment is capable of binding Nogo; and a method of treatment of acute neuronal injury, neoplasia, hyperproliferative disorders or dysproliferative disorders comprising: (i) identifying a modulator of BACE activity; and (ii) administering a therapeutically effective amount of the said modulator to a patient in need thereof.

DETAILED DESCRIPTION OF THE INVENTION

Throughout the present specification and the accompanying claims the words "comprise" and "include" and variations such as "comprises", "comprising", "includes" and "including" are to be interpreted inclusively. That is, these words are intended to convey the possible inclusion of other elements or integers not specifically recited, where the context allows.

The invention provides a method for identifying a modulator of Nogo activity and a method for identifying a modulator of BACE activity. A modulator may modulate the interaction between Nogo and BACE.

A Nogo polypeptide for use in accordance with the invention is one which capable of binding BACE. The Nogo polypeptide may be NogoA, (accession number AJ251383), NogoB (accession number AB015639) or NogoC (accession number AF125103). The Nogo polypeptide comprises the amino acid sequence of SEQ ID No: 4, 9 or 11 or a functional variant or functional fragment thereof. The Nogo polypeptide preferably comprises the amino acid sequence of SEQ ID No: 4 or a functional variant or a functional fragment thereof. A variant may comprise a naturally occurring isoform or splice variant. A variant or fragment of SEQ ID No: 4, 9 or 11 for use in accordance with the invention is capable of binding to BACE. Particularly preferred variants of Nogo include other members of the reticulon protein family. Particularly preferred fragments and variants of SEQ ID No: 4 comprise the amino acid sequence shown in SEQ ID No: 5, 6 and/or 7.

A BACE polypeptide for use in accordance with the may comprise a naturally occurring BACE such as BACE (accession numbers AF190725, P56817) having the amino acid sequence of SEQ ID No: 1 or SEQ ID No: 2 or may comprise a variant or fragment of BACE which may be a naturally occurring BACE such as BACE2 (accession numbers AF204944, Q9Y5Z0) having the amino acid sequence of SEQ ID No: 12 or SEQ ID No: 13 or another unidentified isoform or splice variant which is homologous to or retains the desired function of a known BACE. Such a variant or fragment of BACE for use in the invention is one which is capable of binding to a Nogo polypeptide, in particular to a Nogo polypeptide having the sequence of SEQ ID No: 5, 6 or 7. Preferably a variant or fragment of BACE is capable of binding to full length NogoA, NogoB and/or NogoC. A preferred variant or a preferred fragment of BACE may also comprise an aspartyl protease active site. Such preferred variants and fragments retain the ability to cleave proteins and peptides comprising a .beta.-secretase cleavage site. Preferably such variants and fragments encompass amino acid residues 93 to 96 (DTGS) and/or residues 289-292 (DSGT) of SEQ ID No: 2 or residues 109-112 (DTGS) and/or 300-303 (DSGT) of SEQ ID No: 13.

To determine whether a variant or fragment of BACE is capable of binding to Nogo the variant or fragment can be contacted with Nogo under conditions suitable for the formation of a complex between BACE and Nogo. Similarly, to determine whether a variant or fragment of Nogo is capable of binding to BACE, the variant or fragment can be contacted with BACE under conditions suitable for the formation of a complex between Nogo and BACE. Any one of the assays described herein can be carried out in the absence of a test agent to determine the binding capabilities of these proteins.

Proteins with naturally occurring amino acid sequences are preferred for use in the assays. Preferred proteins are human proteins but homologues from other mammalian species, or other animal species may be used. Any allelic variant or species homologue of the defined proteins may be used. References to a variant or fragment of the protein as described below relates to a variant or fragment of both Nogo and BACE. For all the proteins described herein for use in an assay of the invention, the ability of the variant or fragment to bind BACE or Nogo as appropriate is preferably maintained.

Polypeptides that have been artificially mutated but retain BACE or Nogo binding activity or other Nogo or BACE activity may also be used in the invention. Such mutants may be generated by techniques well known in the art, including site directed mutagenesis, random mutagenesis and restriction enzyme digestion and ligation. A protein for use in the invention preferably has more than about 65% sequence identity to a natural protein, more preferably at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or at least 99% sequence identity thereto over a region of at least 20, preferably at least 30, for instance at least 40, at least 60 or at least 100 contiguous amino acids or over the full length of SEQ ID No: 2 or 13 or SEQ ID No: 4, 9 or 11. Amino acid substitutions may be made, for example from 1, 2 or 3 to 10, 20 or 30 substitutions. Conservative substitutions may be made, for example according to the following Table (see Original Patent). Amino acids in the same block in the second column and preferably in the same line in the third column may be substituted for each other.

The entire protein sequence of each of the proteins used in the assay may be present. Fragments of the proteins and variants described above that retain the ability to bind to the second component in the binding assay, i.e. BACE for Nogo polypeptides and Nogo for BACE polypeptides may also be used in the invention. Alternatively variants or fragments of BACE which retain a function of BACE may be used in assays to identify modulators of BACE activity. Preferred fragments of SEQ ID No: 2 will be at least 30, e.g. at least 100, at least 200, at least 300, at least 400 or at least 450 amino acids in length. Preferred fragments of SEQ ID No: 4 will be at least 30, e.g. at least 100, at least 200 or at least 250 amino acids in length. A fragment may comprise part of a polypeptide, for example a chimeric polypeptide. A chimeric protein may be used to facilitate the purification of a BACE or Nogo polypeptide. For example, the lumenal domain of BACE (amino acids 1 to 460 of SEQ ID No: 2) may be fused to human IgG at the carboxy-terminus.

As used herein, a Nogo polypeptide (a) is used to refer to Nogo having the sequence of SEQ ID No: 4, 9 or 11 or a variant thereof or a fragment of either thereof which variant or fragment is capable of binding to BACE, or to a variant or a fragment of BACE which is capable of binding to Nogo.

As used herein, a BACE polypeptide (a) is used to refer to BACE having the sequence of SEQ ID No: 2 or 13 or a variant thereof or a fragment of either thereof which variant or fragment is capable of binding to Nogo, or to a variant or a fragment of Nogo which is capable of binding to BACE.

The polypeptides for use in the invention may be chemically modified, e.g. post-translationally modified. For example, they may be glycosylated or comprise modified amino acid residues. The polypeptides may be tagged to aid detection or purification, for example using a HA, histidine, T7, myc or flag tag. The BACE polypeptide (a) and the Nogo polypeptide (b) may be tagged with different labels which may assist in identification of a BACE/Nogo complex.

Assays

Any suitable assay format may be used for identifying a modulator of a Nogo activity, for example a modulator of a BACE/Nogo interaction.

As the first step of the method for identifying a modulator of Nogo function, (a) a BACE polypeptide comprising the sequence of SEQ ID No: 2 or 13 or a variant thereof or a fragment of either sequence capable of binding to Nogo; (b) a Nogo polypeptide comprising the sequence of SEQ ID No: 4, 9 or 11 or a variant thereof or a fragment of either sequence capable of binding to BACE; and (c) a test agent are contacted under conditions that would permit binding of (a) to (b) in the absence of a test agent. An activity of Nogo is then monitored. For example, the interaction between the BACE polypeptide (a) and the Nogo polypeptide (b) may be analysed. The interaction between the BACE polypeptide (a) and the Nogo polypeptide (b) in the presence of a test agent may be compared with the interaction between the BACE polypeptide (a) and the Nogo polypeptide (b) in the absence of the test agent to determine whether the test agent modulates the binding of BACE polypeptide (a) and the Nogo polypeptide (b) and thereby whether the test agent enhances or inhibits the binding BACE to Nogo.

The test agent can be contacted with a cell harbouring a polynucleotide or expression vector encoding a BACE polypeptide (a) and a polynucleotide or expression vector encoding a Nogo polypeptide (b). Optionally, the cell may harbour a polynucleotide or expression vector encoding a test agent, wherein the test agent is a peptide or an antisense polynucleotide. The cell typically allows transcription and translation of the polynucleotides or vectors so that the polypeptides are expressed in the same cell.

The test agent may be provided in the extracellular medium used for washing, incubating or growing the cell. The test agent may modulate the interaction of the Nogo polypeptide (b) with the BACE polypeptide (a) indirectly from outside the cell, for example by interacting with an extracellular domain of BACE or Nogo or may be taken up into the cell from the extracellular medium. Where the BACE polypeptide (a) and the Nogo polypeptide (b) are coexpressed in a cell, the cell may express both proteins naturally, for example the cell may be a neuronal cell grown in a primary culture, or the cell may express both proteins recombinantly, or the cell may naturally express one protein and be transformed to express the other protein recombinantly.

The cell may be transiently or stably transfected or transformed. The BACE polypeptide (a) and the Nogo polypeptide (b) may both be transiently expressed, both stably expressed or one may be stably expressed and the other transiently expressed. Cells can be transfected by methods well known in the art, for example, by electroporation, calcium phosphate precipitation, lipofection or heat shock. The proteins may be expressed in mammalian cells such as human cells or non-mammalian cells such as yeast or bacteria. It is preferred that the cells are in culture. Preferred cell lines which may be used include HEK293, COS and PC12 cells.

A cell expressing a BACE polypeptide (a) or a cell homogenate, a cell lysate, a membrane preparation or a protein preparation derived from a cell expressing a BACE polypeptide (a) can be contacted with a cell expressing a Nogo polypeptide (b) or a cell homogenate, a cell lysate, a membrane preparation or a protein preparation derived from cells expressing a Nogo polypeptide (b).

The conditions which permit binding of a BACE polypeptide (a) to a Nogo polypeptide (b) in an extracellular environment can be determined by carrying out the assay in the absence of a test agent.

A control assay in which the agent to be tested is omitted and an assay in which a test agent is included can be carried out in parallel or subsequently. The results of the experiments using the test agent and the control experiments can be used to determine whether the test agent inhibits or enhances binding.

The agent tested may be tested with any other known interacting protein combinations to exclude the possibility that the test agent is a general inhibitor of protein/protein interactions.

Where the BACE polypeptide (a) used in the assay is a variant or fragment of SEQ ID No: 2 or 13, or the Nogo polypeptide (b) used in the assay is a variant or fragment of SEQ ID No: 4, 9 or 11, the assay is preferably run first in the absence of a test agent to ensure that the variant or fragment exhibits the activity being monitored, such as binding activity or protease activity.

A number of biochemical and molecular cell biology protocols known in the art can be used to analyse the interaction of a BACE polypeptide (a) and a Nogo polypeptide (b) (see for example Sambrook et al., 1989). Some specific examples are outlined below:

The BACE/Nogo interaction can be determined directly using a binding assay. For example, a radiolabelled BACE polypeptide (a) may be incubated with a Nogo polypeptide (b) in the presence and absence of the test agent and the effect of the test agent on the binding of the BACE polypeptide (a) to the Nogo polypeptide (b) is monitored. Typically, the radiolabelled BACE polypeptide (a) is incubated with cell membranes containing the Nogo polypeptide (b) until equilibrium is reached. The membranes can then be separated from non-bound radiolabelled BACE polypeptide (a) and dissolved in scintillation fluid to allow the radioactive content to be determined by scintillation counting. Non-specific binding of the agent may also be determined by repeating the experiment in the presence of a saturating concentration of a non-radioactive BACE polypeptide (a). Preferably a binding curve is constructed by repeating the experiment with various concentrations of the radiolabelled BACE polypeptide, both in the presence and absence of the test agent.

A yeast-2 hybrid assay system may be used to monitor the effect of a test agent on the BACE/Nogo interaction. For example, a polynucleotide encoding a BACE polypeptide (a) can be cloned into GAL4 binding domain vector (GAL4.sub.BD) and a Nogo polynucleotide (b) can be cloned into a GAL4 activation domain fusion vector (GAL4.sub.AD). The GAL4.sub.AD and GAL4.sub.BD vectors can then be expressed in yeast and the resulting .E-backward.-galactosidase activity in the presence and absence of the test agent can be assayed and quantified using the substrate o-nitrophenol .E-backward.-D-galactopyranoside (ONPG) using a liquid nitrogen freeze fracture regime as described by Harshman et al., 1998.

A "pull-down" assay system may also be used. Isolated BACE polypeptide (a) may be immobilised on a surface and binding of a Nogo polypeptide (b) to the surface may be monitored in the presence and absence of the test agent. The assay can also be carried out by immobilizing a Nogo polypeptide (b) and measuring the binding of a BACE polypeptide (a) to the immobilized protein.

Alternatively, of a BACE polypeptide (a) may be immunoprecipitated, immunopurified or affinity purified from a cell extract of cells co-expressing a BACE polypeptide (a) and a Nogo polypeptide (b). Coprecipitating/copurifying Nogo polypeptide (b) can then be detected, for example using Western blotting techniques or by radiolabelling recombinantly expressed proteins, and quantified using a phosphorimager or scintillation counter. The test agent is generally added to the cells or the cell growth medium prior to preparation of the cell lysate. Such assays may also be carried out by precipitating or purifying a Nogo polypeptide (b) and detecting coprecipitating or copurifying BACE polypeptide (a).

The assays may also be carried out monitoring other Nogo functions. For example, the neurite inhibitory activity of Nogo may be monitored. Neurite inhibitory activity may be monitored using any suitable assay format such as a dorsal root ganlion (DRG) neurite outgrowth assay, a DRG growth cone collapse assay, a neuronal cell line (for example, PC12 cell) neurite outgrowth assay or a fibroblast (such as NIH 3T3) cell spreading assay. For example, neurite outgrowth in the presence of a cell expressing BACE and Nogo may be monitored and the ability of a test agent to inhibit or promote neurite outgrowth may be assayed. To determine whether the effect of the test agent on neurite growth results from the effect of the test agent on BACE activity or on the BACE/Nogo interaction, a control assay may be carried out using cells expressing Nogo but not BACE. Typically, the cell will also express one or more neurotrophic factors.

An important aspect of the present invention is the use of a BACE polypeptide (a) in screening methods to identify agents that may act as modulators of BACE activity and in particular agents that may be useful in treating Nogo associated disease. Any suitable form may be used for the assay to identify a modulator of BACE activity. In general terms, such screening methods may involve contacting BACE polypeptide (a) with a test agent and then measuring activity. For example, the step of monitoring BACE activity may involve assessment of BACE protease activity, for example by cleaving a peptide comprising the .beta.-secretase cleavage site (SEVKM/DAEFR or SEVNL/DAEFR) or the effect of binding of BACE to other proteins. For example the assay may involve determination of APP processing as described in Vassar et al. (1999) Science 286, 735-741, Hussain et al. (1999) Molecular and Cellular Neuroscience 14, 419-427, Sinha et al. (1999) Nature 402, 537-540 or Yan et al. (1999) Nature 402, 533-537.

Modulator activity can be determined by contacting cells expressing a BACE polypeptide (a) of the invention with an agent under investigation and monitoring the effect of the agent on BACE activity. The cells expressing the polypeptide may be in vitro or in vivo. The polypeptide of the invention may be naturally or recombinantly expressed. Preferably, the assay is carried out in vitro using cells expressing recombinant polypeptide.

Candidate Modulators

A modulator of Nogo or BACE function may exert its effect by binding directly to Nogo or BACE or may have an upstream effect which prevents the BACE/Nogo interaction occurring or which inhibits Nogo or BACE mediated activity.

A modulator may directly inhibit the interaction of Nogo with BACE or inhibit interaction between BACE and a ligand. A test agent may comprise a fragment of a BACE which is capable of binding Nogo or a BACE ligand but which lacks any functional activity. Alternatively, a test agent may comprise a fragment of Nogo which is capable of binding BACE but which lacks any functional activity.

Antibodies, or antibody fragments that specifically bind to BACE or Nogo or chemical compounds capable of binding these proteins are also candidate compounds. An antibody, or other compound, "specifically binds" to a protein when it binds with high affinity to the protein for which it is specific but does not bind or binds with only low affinity to other proteins. A variety of protocols for competitive binding or immunoradiometric assays to determine the specific binding capability of an antibody are well known in the art (see for example Maddox et al. 1993). Such immunoassays typically involve the formation of complexes between the "specific protein" and its antibody and the measurement of complex formation.

Furthermore, combinatorial libraries, defined chemical identities, peptide and peptide mimetics, oligonucleotides and natural product libraries, such as display libraries (e.g. phage display libraries) may also be tested. The test agents may be chemical compounds. Batches of the test agents may be used in an initial screen of, for example, ten agents per reaction, and the agents of batches which show inhibition tested individually.

Modulators

A modulator of Nogo activity is an agent which produces a measurable reduction or increase in binding of a Nogo polypeptide (b) to BACE polypeptide (a) in the assays described above, or an effect on Nogo activity or BACE activity.

Preferred inhibitors are those which inhibit binding by at least 10%, at least 20%, at least 30%, at least 40% at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or at least 99% at a concentration of the inhibitor of 1 .mu.g ml.sup.-1, 10 .mu.g ml.sup.-1, 100 .mu.g ml.sup.-1, 500 .mu.g ml.sup.-1, 1 mg ml.sup.-1, 10 mg ml.sup.-1 or 100 mg ml.sup.-1.

Preferred activators are those which activate binding by at least 10%, at least 25%, at least 50%, at least 100%, at least, 200%, at least 500% or at least 1000% at a concentration of the activator 1 .mu.g ml.sup.-1, 10 .mu.g ml.sup.-1, 100 .mu.g ml.sup.-1, 500 .mu.g ml.sup.-1, 1 mg ml.sup.-1, 10 mg ml.sup.-1 or 100 mg ml.sup.-1.

The percentage inhibition or activation represents the percentage decrease or increase in expression/activity in a comparison of assays in the presence and absence of the test agent. Any combination of the above mentioned degrees of percentage inhibition or activation and concentration of inhibitor or activator may be used to define an inhibitor or activator of the invention, with greater inhibition or activation at lower concentrations being preferred.

Test agents which show activity in assays such as those described above can be tested in in vivo systems, an animal model. Candidate inhibitors could be tested for their ability to decrease Nogo mediated signalling, for example by monitoring the effect on axon growth.

Candidate activators could be tested for their ability to increase Nogo mediated signalling. Ultimately such agents would be tested in animal models of the target disease states.

Therapeutic Use

Modulators of the interaction between BACE and Nogo or of Nogo activity or of BACE activity identified by the methods of the invention may be used for the treatment or prophylaxis of a disorder that is responsive to modulation of Nogo activity or BACE activity.

In particular, neuronal disorders that are responsive to modulation of BACE and/or Nogo activity may be treated. A modulator of Nogo or BACE activity may be used to alleviate the symptoms or to improve the condition of a patient suffering from such a disorder.

Modulators of Nogo or BACE activity may be useful in axon regeneration. This may be useful in treating patients suffering injury to the nervous system, and in particular to the spinal cord, brain, for example following stroke, and peripheral nervous system. Such modulators will typically inhibit Nogo activity, for example by inhibiting the inhibitory effect of Nogo on axon regeneration.

Modulators of Nogo or BACE activity may be useful in treating or preventing neoplastic disorders, hyperproliferative disorders and dysproliferative disorders. In particular neoplastic disorders of the nervous system such as solid tumours, carcinomas, glioblastomas, oligodendrogliomas, neuroblastomas and retinoblastomas may be treated or prevented using modulators of Nogo or BACE activity. Hyperproliferative disorders and dysproliferative disorders that may be treated with a modulator of Nogo or BACE function include cirrhosis of the liver, psoraisis, benign tumours, keloid formation, fibrocystic conditions and tissue hypertrophy. Such modulators will typically enhance or promote Nogo activity, for example by promoting the inhibitory effect of Nogo on axon regeneration.

Modulators of Nogo or BACE activity may be useful in preventing metastasis or spreading of a cancer. For example, an agent which promotes the inhibitory activity of Nogo may be useful for preventing spreading of a CNS cancer to other organs of the body, such as lung, kidney, liver or muscle.

BACE polypeptides and polynucleotides encoding BACE polypeptides may also be used in the treatment or prophylaxis of such disorders.

The invention therefore provides a use of a polynucleotide which encodes BACE or a variant thereof which is capable of binding Nogo or a fragment of either thereof which is capable of binding Nogo, which polynucleotide comprises: (a) the sequence of SEQ ID No: 1 or 12; or (b) a sequence that hybridizes to the complement of SEQ ID No: 1 or 12; or (c) a sequence that is degenerate as a result of the genetic code with respect to a sequence defined in (a) or (b); or (d) a sequence that is complementary to a polynucleotide defined in (a), (b) or (c); in the manufacture of a medicament for use in a method of treatment of a disorder that is responsive to modulation of Nogo activity.

A polynucleotide comprising a sequence that hybridizes to the complement of the coding sequence of SEQ ID No: 1 or 12 can hydridize at a level significantly above background. Background hybridization may occur, for example, because of other cDNAs present in a cDNA library. The signal level generated by the interaction between a polynucleotide of the invention and the complement of the coding sequence of SEQ ID No: 1 or 12 is typically at least 10 fold, preferably at least 100 fold, as intense as interactions between other polynucleotides and the coding sequence of SEQ ID No: 1 or 12. The intensity of interaction may be measured, for example, by radiolabelling the probe, e.g. with .sup.32P. Selective hybridisation may typically be achieved using conditions of low stringency (0.3M sodium chloride and 0.03M sodium citrate at about 40.degree. C.), medium stringency (for example, 0.3M sodium chloride and 0.03M sodium citrate at about 50.degree. C.) or high stringency (for example, 0.03M sodium chloride and 0.003M sodium citrate at about 60.degree. C.). However, such hybridization may be carried out under any suitable conditions known in the art (see Sambrook et al., 1989). For example, if high stringency is required, suitable conditions include 0.2.times.SSC at 60.degree. C. If lower stringency is required, suitable conditions include 2.times.SSC at 60.degree. C.

A nucleotide sequence which is capable of selectively hybridizing to the complement of the DNA coding sequence of SEQ ID No: 1 or 12 will generally have at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% sequence identity to the coding sequence of SEQ ID No: 1 over a region of at least 20, preferably at least 30, for instance at least 40, at least 60, more preferably at least 100 contiguous nucleotides or most preferably over the full length of SEQ ID No: 1 or 12. Methods of measuring nucleic acid and protein homology are well known in the art. For example the UWGCG Package provides the BESTFIT program which can be used to calculate homology (Devereux et al., 1984). Similarly, the PILEUP and BLAST algorithms can be used to line up sequences (for example as described in Altschul, 1993 and Altschul et al., 1990.) Many different settings are possible for such programs. According to the invention, the default settings may be used.

Any combination of the above mentioned degrees of sequence identity and minimum sizes may be used to define polynucleotides encoding a BACE polypeptide, with the more stringent combinations (i.e. higher sequence identity over longer lengths) being preferred. Thus, for example a polynucleotide which has at least 90% sequence identity over 25, preferably over 30 nucleotides forms one aspect of the invention, as does a polynucleotide which has at least 95% sequence identity over 40 nucleotides.

The coding sequence of SEQ ID No: 1 or 12 may be modified by nucleotide substitutions, for example from 1, 2 or 3 to 10, 25, 50 or 100 substitutions. The polynucleotide of SEQ ID No: 2 or 13 may alternatively or additionally be modified by one or more insertions and/or deletions and/or by an extension at either or both ends. The modified polynucleotide generally encodes a protein that can bind Nogo. Typically the protein encoded by the modified polypeptide has aspartyl protease activity. Degenerate substitutions may be made and/or substitutions may be made which would result in a conservative amino acid substitution when the modified sequence is translated, for example as shown in the Table above (see Original Patent).

Polynucleotides may comprise DNA or RNA. They may also be polynucleotides which include within them synthetic or modified nucleotides. A number of different types of modification to polynucleotides are known in the art. These include methylphosphonate and phosphorothioate backbones, addition of acridine or polylysine chains at the 3' and/or 5' ends of the molecule. For the purposes of the present invention, it is to be understood that the polynucleotides described herein may be modified by any method available in the art. Such modifications may be carried out in order to enhance the in vivo activity or lifespan of polynucleotides of the invention.

Polynucleotides encoding a BACE polypeptide may be produced recombinantly, synthetically, or by any means available to those of skill in the art. They may also be cloned by standard techniques. The polynucleotides are typically provided in isolated and/or purified form.

Although in general the techniques mentioned herein are well known in the art, reference may be made in particular to Sambrook et al, 1989, Molecular Cloning: a laboratory manual.

A polynucleotide may also be an essential component in an assay of the invention, a probe (or template for designing a probe) for identifying proteins that may be used in the invention or a test agent. The nucleotides may be involved in recombinant protein synthesis as well as therapeutic agents in their own right, utilised in gene therapy techniques. Antisense sequences, may also be used in gene therapy, such as in strategies for down regulation of expression of BACE.

Polynucleotides for use in the invention can be inserted into expression vectors. Such expression vectors are routinely constructed in the art of molecular biology and may for example involve the use of plasmid DNA and appropriate initiators, promoters, enhancers and other elements, such as for example polyadenylation signals which may be necessary, and which are positioned in the correct orientation, in order to allow for protein expression. Other suitable vectors would be apparent to persons skilled in the art. By way of further example in this regard we refer to Sambrook et al.

Polynucleotides may also be inserted into the vectors described above in an antisense orientation in order to provide for the production of antisense RNA. Antisense RNA or other antisense polynucleotides may also be produced by synthetic means. Such antisense polynucleotides may be used as test compounds in the assays of the invention or may be useful in a method of treatment of a disorder responsive to modulation of Nogo activity, in particular for the treatment of injury to the spinal cord or peripheral nervous system.

Examples of suitable viral vectors include herpes simplex viral vectors and retroviruses, including lentiviruses, adenoviruses, adeno-associated viruses and HPV viruses (such as HPV-16 or HPV-18). Gene transfer techniques using these viruses are known to those skilled in the art. Retrovirus vectors for example may be used to stably integrate the polynucleotide giving rise to the antisense RNA into the host genome. Replication-defective adenovirus vectors by contrast remain episomal and therefore allow transient expression.

The formulation of an agent for use in preventing or treating any of the above mentioned conditions will depend upon factors such as the nature of the agent identified, whether a pharmaceutical or veterinary use is intended, etc. Typically a modulator is formulated for use with a pharmaceutically acceptable carrier or diluent. For example it may be formulated for topical, parenteral, intravenous, intramuscular, subcutaneous, intraocular, transdermal or oral administration. A physician will be able to determine the required route of administration for each particular patient. The pharmaceutical carrier or diluent may be, for example, an isotonic solution.

The dose of an agent may be determined according to various parameters, especially according to the agent used; the age, weight and condition of the patient to be treated; the route of administration; and the required regimen. Again, a physician will be able to determine the required route of administration and dosage for any particular patient.

Modulators may have to be administered to specific sites, or otherwise targeted to brain cells. For example, the modulator may be delivered to neurons. This may be achieved, for example, by delivery via a viral strain such as herpes simplex virus. Viral vectors comprising polynucleotides of the invention are described above. The viral vector delivery method may be used in the case of administration of, for example, polynucleotides of the invention. The vector may further comprise a promoter or other regulatory sequence that is specific to certain neurons.

The polynucleotides and vectors of the invention may be administered directly as a naked nucleic acid construct. Uptake of naked nucleic acid constructs by mammalian cells is enhanced by several known transfection techniques for example those including the use of transfection agents. Example of these agents include cationic agents (for example calcium phosphate and DEAE-dextran) and lipofectants (for example lipofectam.TM. and transfectam.TM.).

Typically, nucleic acid constructs are mixed with the transfection agent to produce a composition. Preferably the naked nucleic acid construct, viral vector comprising the polynucleotide or composition is combined with a pharmaceutically acceptable carrier or diluent to produce a pharmaceutical composition. Suitable carriers and diluents include isotonic saline solutions, for example phosphate-buffered saline. The composition may be formulated for parenteral, intramuscular, intravenous, subcutaneous, or transdermal administration.

The pharmaceutical composition is administered in such a way that the polynucleotide of the invention, viral vector for gene therapy, can be incorporated into cells at an appropriate area. When the polynucleotide of the invention is delivered to cells by a viral vector, the amount of virus administered is in the range of from 10.sup.6 to 10.sup.10 pfu, preferably from 10.sup.7 to 10.sup.9 pfu, more preferably about 10.sup.8 pfu for adenoviral vectors. When injected, typically 1-2 ml of virus in a pharmaceutically acceptable suitable carrier or diluent is administered. When the polynucleotide of the invention is administered as a naked nucleic acid, the amount of nucleic acid administered is typically in the range of from 1 .mu.g to 10 mg.

Where the polynucleotide giving rise to the product is under the control of an inducible promoter, it may only be necessary to induce gene expression for the duration of the treatment. Once the condition has been treated, the inducer is removed and expression of the polypeptide of the invention ceases. This will clearly have clinical advantages. Such a system may, for example, involve administering the antibiotic tetracycline, to activate gene expression via its effect on the tet repressor/VP16 fusion protein.

The use of tissue-specific promoters will be of assistance in the treatment of disease using the polypeptides, polynucleotide and vectors of the invention. It will be advantageous to be able express therapeutic genes in only the relevant affected cell types, especially where such genes are toxic when expressed in other cell types.

The routes of administration and dosages described above are intended only as a guide since a skilled physician will be able to determine readily the optimum route of administration and dosage for any particular patient and condition.
 

Claim 1 of 8 Claims

1. A method of identifying a modulator of Nogo function, the method comprising: (i) providing: (a) a BACE polypeptide having SEQ ID NO:2; (b) a Nogo polypeptide having a sequence selected from SEQ ID NOs:4-7, SEQ ID NO:9, SEQ ID NO:11; (c) a test agent under conditions that would permit binding of said BACE polypeptide to said Nogo polypeptide in the absence of said test agent; (ii) monitoring Nogo mediated activity; and (iii) wherein a change in BACE mediated activity in the presence of said test agent, compared to BACE mediated activity in the absence of said test agent, indicates said test agent is a modulator of Nogo activity.

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