AU2003261561B9 - Therapeutic agent - Google Patents

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AUSTRALIA

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Class Int. Class Application Number: Lodged: Complete Specification Lodged: Accepted: Published: Priority Related Art: Name of Applicant: The University of Bristol Actual Inventor(s): Alan George Simpson Robertson, Shelley Jane Allen, David Dawbarn Address for Service and Correspondence: PHILLIPS ORMONDE FITZPATRICK Patent and Trade Mark Attorneys 367 Collins Street Melbourne 3000 AUSTRALIA Invention Title: THERAPEUTIC AGENT Our Ref: 707295 POF Code: 247812/454326 The following statement is a full description of this invention, including the best method of performing it known to applicant(s): -1- GOOWq r i la THERAPEUTIC AGENT This application is a divisional application of Australian Patent Application 34336/99, the entire contents of which is herein incorporated by reference.

This invention relates to therapeutic agents and screening methods. In particular, the invention relates to the use of the Ig2 domain of the tyrosine kinase TrkA and fragments thereof in the treatment of disorders in which levels of neurotrophins, such as NGF, are elevated such as in pain disorders. It also relates to the use of the TrkAIg2 domain as a target for screening for compounds which act to antagonise or to mimic the actions of neurotrophins such as NGF. TrkAIg2 is defined here as including the TrkAIg-like sub-domain 2 together with the proline rich region (Fig. 1A).

Nerve Growth Factor (NGF) is a potent neurotrophic factor for forebrain cholinergic neurones and promotes the survival and differentiation of sympathetic and sensory neurones during development. In animal models it has been shown that administration of NGF is able to correct the effects of cholinergic atrophy in aged or lesioned animals. Purified mouse NGF has been used as a treatment for Alzheimer's disease. This treatment, however, requires invasive surgery and a long term solution would be the generation of small molecule agonists able to mimic the trophic actions of NGF. NGF usually exists as a dimer, however, for these purposes, the term NGF embraces monomeric dimeric, trimeric, or heterodimeric forms.

Evidence suggests that NGF may also act as a mediator of some persistent pain states (McMahon S.B. Series B-Biological Sciences, (1996), Vol.351, No.1338, 431-440) by interacting with receptors on nociceptive primary afferents. In a variety of experimental inflammatory conditions NGF levels are rapidly increased in the inflamed tissue. Similarly, the systematic or local application of exogenous NGF produces a rapid and prolonged behavioural hyperalgesia in both animals and humans. In a number of animal models, much of the hyperalgesia associated with experimental inflammation is blocked by molecules which are able to sequester NGF, including antibodies. Therefore W.AdakV*PDI of 3433&09.do f I 2 peripherally acting NGF sequestering agents or NGF antagonists may potentially be used in treating some chronic pain states.

Peripheral inflammation is usually characterised by heightened pain sensitivity or hyperalgesia, which- is the consequence of the release of inflammatory mediators, cytokines and growth factors. NGF seems to play a central role in pain mediation through its action on the TrkA receptors of a sub-group of the nociceptive sensory neurons of the dorsal root ganglion (DRG). In the adult this comprises some 40% of DRG cells. These neurons also express the peptides Substance P and calcitonin-gene related peptide (CGRP). By the action of NGF on TrkA receptors there results an increase in neuropeptide levels in these sensory neurons; in addition sodium and calcium channels are affected such that these neurons are increased in excitability. These actions may result in an increase in pain levels. Thus, NGF sequestering agents such as the TrkA extracellular domains may potentially be used to reduce these pain levels.

Under conditions of continual NGF up-regulation, chronic inflammation may:lead to a persistent pain state. There are various models of chronic inflammation which involve exogenous administration of NGF or its upregulation. One such model (Woolf, CJ. et al.

British Journal Of Pharmacology, (1997), Vol.121, No.3, 417- 424) is that induced by intraplantar injection of complete Freund's adjuvant in adult rats. This produces a localized inflammation of the hindpaw with elevation in the levels of TNF P, IL-1 P and NGF. TNF a injections have been reported to produce an increase in thermal and mechanical sensitivity which is attenuated by prior administration of anti-NGF antiserum. Carrageenan administration is known to cause a specific increase in NGF mRNA levels (of up to 500%) which is not seen for other neurotrophins such as NT-3 and BDNF.

In chronic inflammatory states the effects of consistently elevated levels of NGF may result in a long-term disabling pain state. Examples of this may be in some forms of bladder cystitis where raised levels of NGF have been found in biopsies (Lowe, E. M. et al British Journal Of Urology, (1997), Vol.79, No.4, 572-577 A rat model of human chronic cystitis, induced by administration of an irritant chemical can be treated, again by NGF sequestration, by administration of TrkA immunoadhesin (Dmitrieva, N. et al Neuroscience, (1997), Vol.78, No.2, 449-459 Systemic treatment with the

I,

3 NGF-sequestering molecule was able to partially and significantly reverse established inflammatory changes, by about 30-60%. The administration of exogenous NOF into the lumen of the urinary bladders of normal rats also has been shown to produce a rapid and marked bladder hyper-reflexia similar to that seen with experimental inflammation. It is also likely that chronically increased NGF levels may lead to both peripheral sensitization of nociceptors and central sensitization of dorsal horn neurons and perhaps even long-term sensory neuronal abnormalities (McMahon, S. B. Series B-Biological Sciences, "(1996), Vol.351, No. 1338, 431- 440).

In arthritic synovial fluid, high levels of NGF have been observed. Transgenic arthritic mice have also been shown to have raised levels of NGF and an increase in the number of mast cells (Aloe, L. et al International Journal Of Tissue Reactions-Experimental And Clinical Aspects, (1993), Vol.15, No.4, 139-143). Purified NGF antibodies injected into arthritic transgenic mice cause a reduction in the number of mast cells, as well as a decrease in histamine and substance P levels within the synovium (Aloe, L. et al.

Rheumatology International, (1995), Vol. 14, No.6, 249-252).

It seems likely also that the postherpetic neuralgia (PHN), associated with the disorder shingles, may involve upregulation of NGF protein. Varicella-zoster virus (VZV) is an a herpes virus responsible for two human diseases: chicken pox in childhood (varicella), and shingles. The virus remains latent in dorsal root ganglia and may re-emerge later in life, taking advantage of the decline in immune function that occurs with aging. Reactivation causes herpes zoster, commonly known as shingles. The incidence of herpes zoster increases with advancing age. Pain, allodynia, and sensory loss in the affected dermatome are the central manifestations of the disorder. Severe pain is the major cause of acute and chronic morbidity in patients with herpes zoster. The chronic and often debilitating pain, PHN, is the most common complication of herpes zoster. Up to 50% of elderly patients who have had shingles may develop PHN. Antiviral agents appropriately administered systemically greatly relieve the pain of acute shingles, also antidepressants maybe useful; conventional analgesics however are generally of little use, though in a few patients some relief has been obtained with opioids, particularly methadone. The difficulty with testing the effects of anti-NGF treatment is that the model for shingles is not possible in the rat, there is only a cat model. However, it may be possible to investigate such treatments in I i 4 human subjects, with the potential for reduction of NGF levels and alleviation of associated pain.

Chronic inflammatory conditions are widespread and current therapies are severely limited. For instance it is estimated that arthritis affects 37.9 million people and interstitial cystitis 450,00 people in the United States. In a study of rheumatoid arthritis, more than of the patients were in severe pain despite the fact that the majority were taking analgesics. Similarly, there is no effective therapy for interstitial cystitis, which is characterised by painful bladder symptoms.

NGF is one of a family of neurotrophins involved in the development and maintenance of the peripheral and central nervous system. NGF may be isolated from various sources, most particularly from male mice salivary glands. It may be isolated first as 75 NGP, named for its sedimentation coefficient, which is a complex of p-NGF and yNGF. NGF may be obtained from this. 2.5S NGF is known to be responsible for the neurotrophic biological activity of the complex. 2.5S NGF is 3NGF but often partially proteolysed at the amino and carboxy termini. The other members include for example BDNF, NT-3 and NT-4. All of the neurotrophins bind to a common receptor Each also binds to one of a homologous family of tyrosine kinase receptors: NGF binds to TrkA, BDNF and NT-4 bind to TrkB, and NT-3 binds to TrkC. NT-3 can also bind TrkA and TrkB with reduced affinity.

Although the three dimensional structure of the TrkA extracellular domain is unknown, distinct structural motifs in the sequence have been characterised (Figure IA). The Trk extracellular domain comprises three tandem leucine rich motifs (LRM), flanked by two cysteine cluster regions, followed by two immunoglobulin-like (Ig-like) domains. Based on sequence homology with the neural cell adhesion molecule and the platelet derived growth factor (PDGF) receptor, the Ig-like domains have previously been classified as belonging to the C2 class of the immunoglobulin superfamily (IgSF) (Williams, AF, and Barclay AN (1988) Ann Rev Immunol 6, 381-405). Numerous studies have defined neurotrophin residues which interact with p75NGFR and Trk receptors but little is known about the Trk residues which are involved in binding the neurotrophins.

i i Recently two groups have shown that the Ig-like domains of the Trk receptors play important roles in the binding of neurotrophin ligands and receptor activationi Perez P. et al (Molecular and Cellular Neuroscience 6: 97-105 (1995)) concluded that both of the Ig-like domains are important for the binding of NGF to TrkA. Urfer, R. et al (EMBO J.

14 p 27 9 5 2 8 0 5 (1995)) concluded that the second Ig-like sub-domain and proline rich region, Ig2 (Figure IA) provide the main contacts for NGF binding.

The extracellular domain of TrkA is 375 amino acids long. The inventors have recently shown that a protein comprising the two immunoglobulin-like domains and proline-rich region (amino acids 160-375) alone are able to bind NGF with a similar affinity to that of the complete extracellular domain (Holden P. H et al (1997) Nature Biotchnology 668-672). This region has been defined here as TrkAIgl,2. Surprisingly; the inventors have found that an even smaller domain of TrkA referred to as TrkAIg2 (amino acids 253-375) is able to bind NOF with a similar affinity to the complete extracellular domain or the TrkAIgl,2 region and is thus responsible primarily for its binding properties.

The inventors have demonstrated that the recombinant Ig-like domains are able to bind neurotrophins such as NGF with high affinity and inhibit the biological activity of NGF in vitro and in vivo. In particular, TrkAIg2 as defined by amino acids 253-375, (Figure 1A) is the major contributor to NGF binding. The inventors have used molecular modelling techniques to model the TrkAIgl and TrkAIg2 domains. Surprisingly, they find that TrkIg2 like sub-domain 2 is not of the C2 class but of the V set of Ig-like domains (Figure IB).

This gives rise to several uses for TrkAIg2 and polypeptides derived therefrom. Structural data from co-crystals of TrkAIg2-NGF will identify the residues in TrkA which are involved in binding NGF. This will enable rational design of neutrophin, particularly NGF, mimetics. Immobilised TrkAIg2 can be used as a target for phage display libraries as well as combinatorial chemical libraries and fungal extracts. This will allow for selection of molecules able to bind TrkA and thus either act as agonists or antagonists at the receptor. A third use of TrkAlg2 is as a therapeutic agent for a number of chronic pain states. NGF is particularly important for peripheral sensory neurones, evidence suggests that NGF may act as a mediator of some persistent pain states by interacting with receptors i i -6on nociceptive primary afferents and that peripherally acting NGF antagonists may be of use in treating some chronic pain states such as rheumatoid arthritis, interstitial cystitis and shingles.

Throughout this specification, discussion of prior publications and other prior knowledge does not constitute an admission that such material was published, known or part of the common general knowledge in Australia before the priority date of the claims.

A first aspect of the invention provides an isolated polypeptide comprising the amino acid sequence of residues 22 to 119 of Fig. 4(B) or a portion of the amino acid sequence of Figure the amino acid sequence being capable of binding a neurotrophin. Preferably, the polypeptide consists of the whole sequence of amino acids 22-144 of Figure The polypeptide may be TrkAlgl,2 or a portion thereof. Such a polypeptide may be produced by chemical or biological means.

We exclude the full coding sequence of natural TrkA.

The polypeptide may be derived from animal cells. More preferably, the polypeptide is selected from mammalian cells, and in particular, may be selected from human cells. Alternatively, the polypeptide may be selected from avian cells including chicken cells or reptile or amphibian or fish or insect.

Preferably, the neurotrophin is NGF, NT-3, or a neurotrophin which binds NGFR. Such a neurotrophin may exist in a monomeric, dimeric, trimeric or heterodimeric form, and may be from a mammalian, such as a human.

A second aspect of the invention provides a DNA sequence encoding a polypeptide according to a first aspect of the invention; or variants of such a DNA sequence due to the degeneracy of the genetic code, or insertion or deletion mutants thereof that encode a polypeptide according to a first aspect of the invention, and DNA sequences which hybridise at 65°C, 2 x SSC salt 6a concentration to such DNA sequences. This DNA sequence may be inserted into a plasmid or other vector such as pET15b. Accordingly, another aspect of the invention provides a plasmid or other vector comprising of DNA sequence according to the second aspect of the invention.

A .further aspect of the invention provides a complex comprising a polypeptide according to a first aspect of the invention in combination with at least one neurotrophin or neurotrophin subunit (such as NGF or NT-3), manomer or biologically active portion thereof.

A further aspect of the invention provides a method of producing a polypeptide according to a first aspect of the invention comprising introducing a DNA sequence according to a second aspect of the invention, or a plasmid containing the DNA sequence into a suitable host and cultivating that host whereby the DNA sequence is expressed. A suitable host may be selected from animal cells such as bacterial cells, insect cells and mammalian cells, particularly human cells.

Another aspect of the invention provides a method of producing a polypeptide according to the first aspect of the invention by chemical or biological means.

Further, the TrkAlg2 may be conveniently used as a. target for a high throughput screen for molecules which bind to the TrkA receptor using a polypeptide according to a first aspect of the invention. Such a method may involve the use of phage or peptide display libraries, combinatorial chemical libraries and fungal extracts, and ELISA techniques.

A further aspect of the invention comprises comparative binding of a putative ligand to at least a portion of TrkAlgl with its binding to at least a portion of TrkAlg2. Such methods may involve selecting molecules which bind to at least one solvent exposed loop of TrkAlg2, such as the E to F loop or C" to D loop as shown in Fig. The molecules selected may enhance the binding of a polypeptide according to a first aspect of the invention, or at least a portion of TrkA in its natural state, to a neurotrophin.

A further aspect of the invention provides a method of combinatorial chemistry comprising a compound generating step and a compound screening step which involves the binding of the generated compound with a polypeptide or a portion of a polypeptide according to a first aspect of the invention.

A further aspect of the invention comprises an antibody raised against a polypeptide according to a first aspect of the invention, particularly TrkAIg2.

7a A further aspect of the invention comprises a host cell containing a polypeptide according to a first aspect of the invention carried on a plasmid.

Such as host cell may be mammalian (including human), bacterial, insect, yeast, avian, amphibian, fish or reptilian. Another aspect of the invention comprises a host cell containing a DNA sequence, or plasmid or other vector containing said DNA sequence, according to a second aspect of the invention.

A further aspect of the invention comprises a diagnostic probe comprising a portion of a polypeptide according to a first aspect of the invention. The probe may be labelled with a fluorescent tag or radiolabel.

-8- A further aspect of the invention comprises diagnostic tests, assays, or monitoring methods using a polypeptide or fragment thereof according to a first aspect of the invention or an antibody derived therefrom, particularly in the detection of elevated neurotrophin levels. Alternatively, the invention comprises diagnostic tests, assays, or monitoring methods using a probe comprising at least a portion of a DNA sequence of the second aspect of the invention.

A further aspect of the invention comprises an organism engineered to express or overexpress a polypeptide according to a first aspect of the invention, or a DNA sequence according to a second aspect of the invention.

A further aspect of the invention comprises a method of treating a subject with pain associated with increased neurotrophin polypeptide levels, the method comprising supplying to the subject a pharmaceutical composition comprising a polypeptide according to a first aspect of the invention, or an NGF analogue isolated or identified by a screening procedure as described above.

The pain may be a symptom of ISU, interstitial cystitis, arthritis, shingles, peripheral inflammation, chronic inflammation, or postherpetic neuralgia.

A further aspect of the invention comprises a method of treating a subject with Alzheimer's disease comprising supplying to the subject a pharmaceutical composition comprising a polypeptide according to a first aspect of the invention, or a composition comprising a neurotrophin analogue isolated or identified by a screening procedure involving a polypeptide according to a first aspect of the invention.

A composition comprising a polypeptide according to a first aspect of the invention can be used for the control of pain associated with an increase in neurotrophin levels in a subject.

Another aspect of the invention provides a method of reducing free NGF levels in a subject, comprising supply to a subject a polypeptide according to 8a a first aspect of the invention. A polypeptide of a first aspect of the invention can also be supplied to a subject to reduce plasma extravasation.

All references above to neurotrophin embrace NGF and NT-3.

A further aspect of the invention includes a homology model having the coordinates shown in Fig. 21, and machine readable data storage medium on which such a homology model has been stored, and a computers programmed with, or arranged to provide such a homology model.

-9- A further aspect of the invention provides crystalline TrkAlg2.

A further aspect of the invention provides compounds obtained by a method as mentioned above, using a computer as mentioned above, or using a machine readable data storage medium as mentioned above.

A further aspect of the invention comprises a crystal comprising a polypeptide according to a first aspect of the invention, particularly a TrkAlg2 polypeptide.

The invention will now be described, by way of example only, with reference to the accompanying drawings Figures 1 to 20 in which Fig. 1(A) is a schematic representation of the TrkA structure (the filled circles represent consensus glycosylation sites); Fig. 1(B) shows a modelled structure for TrkAlgl and TrkAlg2; the most important binding determinates probably occur in the loop connecting strands E and F (the EF loop); Fig. 2(A) is a restriction map of the plasmid Fig. 2(B) shows the sequence of oligonucleotides used to amplify TrkAlgl,2; Fig. 3 shows the nucleotide sequence of the insert of pET15b-TrkAlg1,2 and its derived amino acid sequence; Fig. 4(A) shows the nucleotide sequence and derived amino acid sequence of his TrkAlgl; Fig. 4(B) shows the nucleotide sequence and derived amino acid sequence of his TrkAlg2; Fig. 4(C) shows the TrkAlg2 domain of a splice variant of TrkA including the six amino acid insert in the proline-rich region able to bind NT-3; -9a-.

Fig. 5 is a gel ilustrating expression of TrkAgl,2, TrkAIgl and TrkAIg2; Fig. 6(A) is a gel illustrating purification of TrkAlg2; Fig. 6(B) is a gel illustrating purification of TrkAIg 1; Fig. 7(A) shows an elution profile of TrkAIgl from Poros 20HQ after refolding; Fig. 7(B) shows an elution profile of TrkAIg2 from Poros 20HQ after refolding Fig. 8 shows a Circular Dichroism spectrum of TrkAIg2. The molecular ellipticity is shown as a function of wavelength.

Fig. 9 shows competitive binding Assay for TrkAIg 1,2 and TrkAIg2; The axis is given in logarithmic scale as I x 10" to I x 10' M.

Fig. 10 shows surface plasmon resonance (SPR) of NGF binding to Immobilised TrkAIg2; Fig. 11 illustrates the results of binding experiments where TrkAIg2 (2pM) and TrkAIgl (2iM) were incubated separately with a standard curve of ONGF (0-100pM); Fig. 12 illustrates the results of binding experiments where increasing concentrations of PNGF (1-200p.M) were incubated separately with 2pM TrkAlgl or 2pM TrkAIg2; Fig. 13 shows the effect of TrkAIg2 on NGF dependent neurite outgrowth on PC12 cells.

Fig. 14 A to F illustrates the effect of co-injected TrkAIgl,2 on NGF-induced plasma extravasation; Fig. 15 illustrates the effect of 5 minute pre-treatment with TrkAIgl,2 on NGF- induced plasma extravasation; Fig. 16 illustrates the effect of 40 minute pre-treatment with TrkAIgl,2 on NGF-induced plasma extravasation; Fig. 17 illustrates the effect of co-injected TrkAIgl on NGF-induced plasma extravasation; Fig. 18 illustrates the effect of co-injection of TrkAIg2 on NGF-induced plasma extravasation; 11 Fig. .19 illustrates the effect of 5 minute pre-treatment with TrkAIg2 on NGF-induced plasma extravasation; Fig. 20 illustrates the effect of 40 minute pre-treatment with TrkAlg2 on NGF-induced plasma extravasation.

Fig. 21 shows the coordinate data for the model of Fig. I Structure prediction of the extracellular domain of TrkA and modelling of the Ig-like domains: Secondary structure analysis of the Ig-like regions using PredictProtein (Rost B. and Sander C. (1993) PNAS 90: 7553-7562; Rost B. and Sander C. (1993) J. Mol. Biol. 232: 584-599; Rost B. and Sander C. (1994) Proteins 19: 55-72) showed defined stretches of P-strands. The first Ig-like sub-domain, TrkAIgl, consists of residues 160-252 (Fig. IA) in the mature extracellular domain of TrkA, while the second Ig-like sub-domain consists of residues 253-349 (Fig. IA). There is also a proline rich region at residues 349-375 (Fig.

1A).

For TrkAIgl, two known proteins (parents) were identified as homologues from which a model could be built. These are 2NCM (domain 1 of mouse NCAM) and 1VCA (domain 1 of human vascular cell adhesion molecule). Both domains are I-set Ig domains and have 32% and 29% sequence identity, respectively, with the target sequence: 2NCM was identified as the most suitable parent on which to base the model, apart from residues 38-50 connecting -strand C to D where the smallerloop found in 1VCA was used (Figure 1B).

For TrkAIg2, two parents were identified as homologues from which a model could be built. These are ITNM (titin module M5) and IHNG (CD2 domain The homologues are quite distantly related at 21% and 14% sequence identity and belong to the Ig-set I family and the V set family respectively. However, certain key features of the Ig fold can be identified including a disulphide bridge and a Trp in the C strand. This is surprising since both homologues lack a disulphide bond. These homologues show higher sequence identity in different regions, hence, a chimeric model was built using ITNM as the mnain 12 template and IHNG being used to model residues 39-59 (Figure IB) and the coordinate data is shown in Fig. 21.

Following slight manual interventions in the sequence alignment the inventors have elucidated a model containing 8 P-strands with strands (ABDE) in one sheet and (A'CFG) in the other sheet. Together they form the P-sandwich for TrkAIgl. For TrkAIg2, the A' strand is absent and two extra strands C' and C" are predicted with the P-sandwich formed by P-strands (ABDE) and For domain 1, the alignment mapped the disulphide between strands B and F across the P-sandwich to the same position as found in 2NCM.

This disulphide also superimposed onto the IVCA disulphide between residues 23-71.

Conversely for domain 2, a disulphide is predicted on the surface of the molecule bridging two adjacent P-strands, B and E, the second Cys aligns with a Ser in ITNM. This disulphide bond arrangement is similar to the model predicted by Urfer et al (Urfer, R., Tsoulfas, O'Connell, Hongo, Zhao, W. and Presta, L.G. (1998). J. Biol.Chem.

Urfer et at (supra) 273: 5829-5840) modelled on 1VCA domain I although our TrkAIg2 model predicts nine P-sheets, of the V-set, in contrast with the model with seven f-sheets in a I-set arrangement. The modelled structures are shown in Figure 1B and the co-ordinate data is shown in DATA. 1.

In terms of the structural model built here for TrkAIg2 the parents used in model construction, titin module M5 (ltnm) and CD2 domain I (Ihng) are clearly distant homologues, that can be identified by sensitive sequence search methods (Barton, G.J.

(1993) Comput. Appl. Biosci. 9: 729-734; Henikoff, S. and Henikoff, J.G. 1991. Nucleic Acids Research 19: 6565-6572). The VCAM domain I used to model build TrkAIg2 by Urfer et al. (Urfer, Tsoulfas, O'Connell, Hongo, Zhao, W. and Presta, L.G.

(1998) JBC 273: 5829-5840 is not significantly related by sequence, however, is homologous by virtue of being an Ig-fold. Relative to titin and VCAM (both I-set domains) the TrkAIg2 sequence has a significant insertion (-10 residues) between strands C and D. The region corresponding to positions 39-59 which includes this insert has more significant homology to CD2 domain 1 than other Ig domains. Furthermore, the predicted secondary structure (Rost B. and Sander C. (1993) PNAS 90: 7553-7562) of TrkAlg2 in this region corresponds to the existence of two extra strands and in accordance 13 with the CD2 structure. This results in a predicted V-set domain as opposed to the I-set domain proposed by Urfer et al. (Urfer, Tsoulfas, O'Connell, Hbngo, J.A., Zhao, W. and Presta, L.G. (1998). JBC 273: 5829-5840) The importance of key residues in binding NGF can be understood by reference to our model and the extensive mutational analysis of TrkAlg2 by Urfer et al. (Urfer, R., Tsoulfas, O'Connell, Hongo, Zhao, W. and Presta, L.G. 1998. J. Biol.Chem.

273: 5829-5840). The most important binding determinants in TrkAIg2 occur in the loop connecting strands E and F (the EF-loop) with single mutations T319A, H320A and N323A exhibiting greater than 100-fold reduction in binding. Reference to our structural model indicates that all three residues are in solvent exposed locations near the apex of the EF-loop. Minor contributors to loss in binding affinity also occur in the spatially adjacent AB-loop with mutations H258A, V261E, M263A and H264A. The first three residue locations are in solvent exposed locations on the surface of this loop. Only two other mutations exhibit greater than 50-fold reduction in binding affinity, these are P269E and H310A. These two residues are spatially adjacent to one another in our model and in close proximity to the disulphide bridge (C267-C312) connecting strands B and E. It is possible these residues play a direct role in binding NGF as suggested by Urfer et al. (Urfer, R., Tsoulfas, O'Connell, Hongo, Zhao, W. and Presta, L.G. 1998. J. Biol.Chem.

273: 5829-5840). However an alternative explanation may be their importance in maintaining the structural integrity of the disulphide bridge. Unlike the conserved core disulphide bond of canonical Ig domains the solvent exposed disulphide bridge may not be important in stabilising the structure of the domain, however, the covalent link between strands B and E may be important in maintaining the conformation of the AB and EF loops in binding. Indeed the loss of the disulphide with mutations C267A or C312A results in a 10 to 30-fold reduction in binding, underlining the importance of the disulphide bridge in the binding mechanism.

An alternatively spliced form of TrkA containing a six amino acid insert (at amino acid position 224-225 (Fig. in the proline rich domain, VSFSPV, shows a higher affinity for NT3 and therefore may be important for ligand binding (Clary, D. O Reichardt L. F.

(1994) PAISA 91: 11133-11137). This sequence is also found in the rat TrkA sequence and a similar sequence is found in the chicken TrkA. There is also a similar of polar residues in all of the TrkB sequences (Allen S. J. et al. (1994) Neuroscience 60: 825-834).

14 It is therefore possible that this region may contribute to the binding of the neurotrophins or to the receptor's specificity.

The TrkAlgl,2 region is generally considered as comprising amino acids 160-375 of the mature extracellular domain of TrkA (Fig. IA), TrkAIgl or TrkAlg like sub-domain 1, as comprising amino acids 160-252 and including TrkAIg like subdomain 2 as amino acids 253-349. TrkAIg2 here comprises amino acids 253-375 the proline rich region. In all cases the use of variants of TrkA and its sub domains such as those described above are embraced by the present invention.

Construction of TrkAlg2 with the Insert from the Alternatively Spliced Variant: TrkAIg2 with the insert from the alternatively spliced variant was created by PCR mutagenesis. The mutagenesis was done in two stages. First the 5' and 3' fragments were amplified such that there is an overlap encoding the sequence of the alternative spliced form of TrkA. In the second stage, the PCR products of the 5' and 3' fragments were spliced together using the overlapping sequence and the two flanking primers. The first round of PCR involved oligo66816 (ATCATATGCC GGCCAGTGTG CAGCT) and oligo49234 (CCACTGGCGA GAAGGAGACA GGGATGGGGT CCTCGGGG) to produce the 5'-fragment and oligo49233 (GTCTCCTTCT CGCCAGTGGA CACTAACAGC ACATCTGG) and the T7 terminator primer (GCTAGTTATTGCTCAGCGG) to produce the 3'-fragment. The products were then purified and used as target for a second round of PCR using oligo66816 and T7terminator primer. The PCR product from the second round of PCR was then cloned into pETISb and expressed in the same way as TrkAIg2.

Sub-cloning of TrkAgl,2: From the secondary structure prediction data, it was decided to subclone the DNA encoding amino acids 160 to 375 (Fig.lA)of the extracellular domain of TrkA.

Oligonucleotide primers (10692 and 10693) were designed that would provide appropriate restriction sites in order that the TrkAlgl,2 insert would be in-frame with the poly-histidine tag of the expression vector, pETl5b (Novagen) and two stop codons to terminate translation. A map of pETI 5b and the sequence of the oligonucleotide primers is shown in Figure 2.

Amplification by PCR was then carried out using the primers oligo 10692 and oligo10693 (Cruachem Ltd) and the full-length Human TrkA cDNA clone (a gift from David Kaplan, Montreal Neurological Institute, Canada) as target. The PCR product was then ligated into the plasmid pCRII (Invitrogen), to give pCRU-TrkAIgl,2. pCRII-TrkAIgl,2 was then digested with XhoI and the insert purified from a low-melting point agarose gel by phenol extraction and ligated into pET15b (Novagen) previously prepared by digesting with XhoI and dephosphorylating using Calf-Intestinal Alkaline Phosphatase (CIAP). After transformation into Escherichia coli XLIBlue (Stratagene), transformants were screened by PCR using the T7 promoter primer which anneals to pET15b and oligol0693. In this way, clones were identified which had the TrkAIgl,2 insert in the correct orientation for expression from the T7 promoter. The resulting clone, pETl5b-TrkAIgl,2 was sequenced from the T7 promoter primer and the T7 terminator primer to ensure that the insert had ligated to the pET15b at the Xhol site. The DNA sequence of the insert of pET15b-TrkAIgl,2 and the derived amino acid sequence are shown in bold in Fig. 3 (amino acids 24-239, nucleotides 71-718). Enzymes and enzyme buffers were..obtained from Boerhinger.

Sub-cloning of TrkAIgl: An oligonucleotide primer was designed which would allow amplification of the TrkAIgl domain using the left primer for TrkAIgl,2 such that the PCR product could be ligated into the XhoI site of pET15b in-frame with the poly-histidine tag.

oligo36770 Right Primer For TrkA Igl; cgg~gtag tta tca GAAGGAGACGTTGACC XhoI STOP STOP Amplification by PCR was then carried out using oligo1069 2 and oligo3 6 770 with pET15b-TrkAIgl,2 as target. The PCR product was then ligated into pCRII (Invitrogen) to give pCRII-TrkAIgl which was then digested with Xhol and subjected to low melting point agarose gel electrophoresis. The insert was then purified and ligated into previously digested with Xhol and treated with CIAP. After transformation into E. coli XLIBlue, transformants were screened by PCR using oligol0692 and the T7 terminator primer. The resulting clone pET15b-TrkAIgl, was then sequenced to ensure that the 16 reading frame of TrkAIgl was in-frame with the poly-histidine tag of pET15b. Figure 4a shows the nucleotide sequence (residues 71-349) and deduced amino acid sequence (residues 24-116) of TrkAIgl, in bold.

Sub-cloning of TrkAlg2: An oligonucleotide primer was designed which would allow amplification of the TrkAlg2 domain using the T7 terminator primer of pET 15b-TrkAIg 1,2; oligo66816 Left Primer For TrkA Ig2; atcatatCC GGCCAGTGTG CAGCT Ndel Amplification by PCR was then carried out using oligo66816 and the T7 terminator primer with pETlSb-TrkAIgl,2 as the template DNA. The PCR product was then digested with Ndel and BamHI and ligated into pET15b previously prepared by digestion with the same enzymes and treated with CIAP. Transformants were screened by PCR using the T7 promoter primer and oligo10693 and the positive clones were sequenced. Figure 4b shows, in bold, the nucleotide sequence (residues 65-433) and derived amino acid sequence (residues 22-144) of TrkAIg2.

Hybridisation to TrkA DNA sequence DNA encoding TrkAIgl,2 or TrkAIg2 (sequences according to Figures 3, and 4B) may be' used for a hybridization assay. A DNA sequence encoding TrkAIgl,2 or TrkAIg2 or portions of such a sequence may be obtained by reverse transcriptase PCR of genomic DNA or directly by PCR or restriction digest from the cDNA for TrkA. DNA or RNA which is complimentary to the DNA encoding TrkAgl,2 or TrkAIg2 or portions of such a sequence, or a sequence which is similar in composition but contains a degeneracy of sequence, may be hybridized to the DNA prepared above. Such a sequence is referred to herein as a probe. Usually, the complimentary DNA or RNA is tagged by radioactive or non-radioactive substances.

One example of this is the northern analysis of TrkAlg2 using a radioactively labelled cDNA probe. A cDNA probe is random primed (Stratagene, CA) with "P-dATP (6000Ci/mmol; Dupont NEN). The probe is then purified using a Nuctrap column (Stratagene), to a specific activity in the region of 2 x 106 cpm/ng. Chinese hamster ovary 17 cells (CHO) expressing TrkA are then homogenised in Ultraspec T M (Biotecx, Houston Texas) and total RNA extracted. The RNA is loaded onto a 1% denaturing agarkse gel and seperated by electrophoresis, before being blotted onto Hybond N (Amersham, Cardiff, UK) overnight and baked for 2 hours at 80C. These Hybond N filters are pre-hybridized for 4 hours at 65°C by revolving in hybridization buffer (6SSC, 5 x Denhardts, 0.5% SDS and 0.002% acid cleaved salmon sperm DNA), in a hybridization oven. The probe is then denatured for 5 minutes at 100°C, before being added to fresh hybridisation solution. Filters are then hybridized under these conditions of high stringency, overnight at 65°C. Stringency may be varied according to degeneracy of probe or homology of target. Lower temperatures such as 50C, and higher salt concentrations, such as 20x55C, will allow for lower stringency. The presence of formamide decreases the affinity of nucleic acid binding and allows for variance in stringency. Such strategies are well described Nucleic acid hybridisation, a practical approach edited by Hames and Higgins, IRL Press 1988). The next day, the filters are washed in 2 x SSC/ 0.5% SDS and washed twice for 30 minutes at in Hybaid with 2 x SSC/ 0.5% SDS. The filters are then dried and exposed to Hyperfilm (Hyperfilm MP, Amersham) overnight, at -70°C, and developed the following day. DNA probes which have bound to RNA encoding the TrkAIg2 sequence are visualised as exposed, black, areas of the autoradiographic film.

A further example of this is the detection of expression of TrkAIgl,2 or TrkAIg2, or a similar sequences in an expression library. A XGT10 human brain cDNA library (M Goedert, Cambridge) is used to infect E. coil c600 cells. These are plated onto 24cm x 24cm agar plates to give 10,00Opfu per plate. A plaque lift is then carried out by laying Nylon membrane Hybond N (Amersham, Cardiff, UK) onto the agar plate for 1 minute. The filter is then placed, DNA side up, on denaturing solution (1.5N NaCl, 0.5N NaOH) for sec, before being immersed for 2 minutes. The filter is then immersed into neutralising solution (1.5N NaCI, 0.5N Tris-HCI pH 8.0) for 5 min. Immersion is repeated in fresh neutralising solution. The filter is then rinsed briefly in 2 X SSC (0.3N NaCI, 0.03N Na 3 Citrate, pH 7.0) and placed on filter paper which is baked at 80°C for 2 hours.

Hybridization is carried out as described above. The position of DNA probes which have bound to plaques encoding the TrkA sequence is visualised as exposed, black, areas of the autoradiographic film. These exposed, black areas can be re-aligned to the plates to identify 18 positive clones expressing sequences similar to TrkAIgl.2 or TrkAIg2 or a portion of such a DNA sequence.

Hybridisation may also occur using homologous PCR techniques. Specific or degenerate oligonucleotides corresponding to a region in the sequence for TrkAIgl,2 may be used to amplify a portion of the sequence as described for example, in the section entitled 'sub-cloning of TrkAIg2'. Such hybridization assays may be used as tools to detect the presence of TrkAlgl,2 or TrkAIg2 sequences, or portions thereof, in diagnostic kits.

Expression of TrkAgl,2, TrkAIgl and TrkAIg2: Competent BL21(DE3) cells were transformed with the above vector and expression was carried out using a variation on the method described in the pET (Novagen) manual for difficult target proteins. Briefly, 2 ml of 2YT broth (containing 200mg/ml carbenecillin) was inoculated with a colony and grown at 37 0 C to mid log phase. Cells were not centrifuged and resuspended in 2YT (as in manual) but used directly to inoculate 50 ml of 2 YT broth (containing 500 mg/ml carbenecillin) and grown at 37 0 C to mid log phase. The cells were not harvested by centrifugation and resuspended but used directly to infect litres of 2 YT (containing 500 [lg/ml ampicillin). Once an ODra of 1 was reached the cell culture was induced by the addition of IPTG to a final concentration of I mM and the cells were grown for a further 2 hrs at 37°C. Figure 5 shows a 15% SDS PAGE gel of extracts of cultures of BL21(DE3) containing the various pETl5b-TrkAIg constructs. Further analysis of the cell extracts revealed that for all of the constructs, the expressed TrkAIg protein was insoluble. Several attempts were made to express the TrkAIg protein in the soluble fraction, but were unsuccessful. However, the fact that the TrkAIg proteins were insoluble faciliated in their purification.

Purification and Refolding of TrkAIgl,2: The harvested cells were resuspended in 10% glycerol, frozen at -70 0 C and the pellet was passed 3 times through an Xpress (BioX, 12 ton psi). The lysed cells were washed with mM Tris-HCI (pH 8.0) and centrifuged for 30 min at 10,000 rpm at 4,°C until all soluble matter was removed, leaving inclusion bodies containing insoluble protein. The purified t9 inclusion bodies were solubilised in 6M urea buffer (20 mM Tris-HCI pH 8.5, 1 mM P-mercaptoethanol) at approximately 0.1 mg/ml protein and incubated on ice with gentle shaking for 1 hour. Refolding was carried out by dialysis against 400x buffer (20 mM Tris-HCI, 100 mM NaCI, pH 8.5) for 24 hrs at 4°C, with one buffer change. The refolded TrkA-Igl,2 protein was loaded onto a Iml Resource Q (Pharmacia) column and eluted with a linear gradient of 0-1M NaCI in 20 mM Tris-HCl over 40mls at 2 mis per minute.

The main peak as detected at 280 nm (using a UV detector) was collected and affinity purified according to the Novagen His column purification protocol using a 2.5 ml disposable column of His-bind resin (Novagen). Finally, the eluted protein was re-applied to the Resource Q column to remove imidazole. This was eluted with a 10 ml salt gradient of 0-lm NaCI in 20 mM Tris buffer pH Purification of TrkAIgl and TrkAIg2: The harvested cells were resuspended in 10% glycerol, frozen at -70aC and the pellet was passed 3 times through an Xpress (BioX). The extract was then centrifuged at 10,000 rpm, 4°C for 30min to pellet the insoluble inclusion bodies. The inclusion bodies were then washed in 50 ml Triton X-100, 10 mMTrisHCl pH8.0, I mM EDTA followed by ml IM NaCI 1OmMTrisHCl pH8.0, 1 mM EDTA and finally 10 mM TrisHCl pH8.0, I mM EDTA. The inclusion bodies were then solubilised in 20 mM Na Phosphate, 30 mM Imidazole, 8 M Urea pH7.4. The solubilised inclusion bodies were then clarified by centrifugation before loading on a 5 ml HisTrap column (Pharmacia). The.column was washed with 50 ml 20 mM NaPhosphate, 30 mM Imidazole, 8 M Urea pH7:4 and the purified TrkAIgl and TrkAIg2 eluted with 25 ml 20 mM NaPhosphate, 300 mM Imidazole, 8 M Urea pH7.4 at 2 mis/minute (Figure 6(A) and Refolding of TrkAIgl and TrkAIg2: The purified TrkAIg proteins were adjusted to a concentration of 0.1 mg/ml in 20 mM NaPhosphate, 30 mM Imidazole, 8 M Urea pH7.4 with the addition of I mM P-mercaptoethanol and dialysed against 20 mM TrisHCI, 50 mM NaCl, pH8.5 for TrkAIg2 and 20 mM TrisHCl, 50 mM NaCI pH9.0 for TrkAIgl (2x100 volumes). The dialysed proteins were loaded onto a 1.6 ml Poros 20HQ column and eluted with a linear gradient of 0.05-1 M NaCI over 20 column volumes (Figure 7).

Three peaks were eluting from the Poros 20HQ column for TrkAIg2, all of which gave a band corresponding to TrkAIg2 (data not shown). Therefore the refolding prbcess must result in three species of TrkAIg2, all of which have a different conformation.

Displacement binding studies reveal that the first peak to elute binds NGF while the others do not. The first peak was therefore collected, glycerol added to a final concentration of and snap frozen in liquid nitrogen before storage at -70 0

C.

For TrkAIgl, only two peaks elute from the Poros 20HQ column with more protein in the flow through. Again SDS page of each peak and the flow through show that TrkAIgl is the only protein present. Displacement binding assays of the two peaks show that neither of these species of TrkAIgl bind to NGF (data not shown).

Circular Dichroism Studies on TrkAIg2 To determine the secondary structure content of the folded protein, far-UV circular dichroism (CD) measurements were made. The CD of proteins is primarily the CD of the amide chromophore, which begins absorbing far into the UV region with the first band at about 220 nm. Antiparallel P-sheet structures typically display a negative Cotton effect with a minimum near 218 nm and a positive effect with a maximum around 195 nm. The amplitude of the far-UV spectra of different immunoglobulins such as light chain variable and constant (CL) domains also show a minimum around 215-218 nm. Similar results were therefore expected with the TrkAIg proteins.

CD spectra were recorded at room temperature on a Jobin Yvon CD6 instrument using a cuvette of 0.5mm path length at a protein concentration of 40pM. Ten scans were accumulated with a scan speed of 0.5nm/s. Spectra were averaged and the small signal arising from the buffer was subtracted. The CD of the active TrkAlg2shows a minimum at 218nm and a maximum near 200nm (Figure This is typical of anti-parallel p-sheet, which display a negative Cotton effect with a minimum near 218nm and a positive Cotton effect with a maximum at around 195nm (Yang, Wu, C.S.C. and Martinez, H.M.

(1986). Methods Enzymol. 130: 208-269). Similar results have been reported for other immunoglobulin domains (Ikeda, Hamaguchi, K. and Migita, S. (1968) J. Biochem.

63: 654-660) and for TrkAIgl,2 (Holden, Asopa, Robertson, Clarke, Tyler, Bennett, Brain, Wilcock, Allen, Smith, S. and 21 Dawbarn, D. (1997) Nat. Biotechnol 15: 668-672). These results are consistent with the model of TrkAIg2 shown in Figure IB.

Thus the CD data indicates that TrkAIg2 eluting first from the Poros 20HQ column is folded into a compact structure and is likely to have a similar structure to the other immunoglobulin domains.

The binding of NGF to Immunoglobulin-like Domains of TrkA 1 Competitive Binding The binding affinity of '"I-NGF to the Ig-like domains of TrkA was determined by a competitive binding assay using the melanoma cell line A875 American Tissue Culture Collection (ATCC) which expresses the NGF receptor p 75 N0

G

l.

Purified recombinant human NGF was radioiodinated with 1125 using a lactoperoxidase method and equilibrium binding with was carried out (Treanor et al., 1991; Neuroscience Letters 121 p 7 3 7 6 Briefly A875 cells (106 per ml) were incubated with (0.14 nM) and serial dilutions of unlabeled human NGF (concentration range: 6 M to 1 x TrkAIgl,2 (concentration range: 4 x 10 6 M to 1 x 10-" M) or TrkAIg2 (concentration range 5 x 106 M to 1 x Tubes were shaken vigorously at room temperature for 1 hr. 100 pl aliquots were then layered over 200 pi sucrose (0.15 M in binding buffer) in Beckman tubes. After centrifugation (15 seconds at 20,000 g) bound and free were separated by freezing the tubes in liquid nitrogen and determining the bound of the cell pellet. Binding reactions were carried out in triplicate. Counts were corrected for background and specific binding was between 85-87% of total binding. The competitive binding assay (figure 9) allowed estimation of the binding affinity of ('"25I-NGF to the recombinant TrkAIg2 protein. A range of concentrations of Ig-like domains are incubated with '"I-NGF and A875 cells (Vale R. D.

Shooter E, M (1985) Methods in Enzymology 109: 21-39). This results in a competition 22 between the TrkAIg domains and the p 7 5

NG

FR for available '"I-NGF. Two competing equilibria are: Kdl Kd2 N+R N:R and N+T N:T where N represents. NGF; R the p 7 5 NGR cell receptor and T the TrkAIg2 domain.

The data represent the NGF bound to the cell at varying TrkAIg2 concentrations, as a fraction of that bound in the absence of TrkAlg2. Owing to the high affinity of NGF for the p75NGF cellular receptor, the analytical solution to the curve is complex thus data were fitted using numerical simulation (FACSIMILE, U.K.A.E.A).

The fitted value for the dissociation constant for the TrkAlgl,2/NGF interaction (Kd2) was 3.3 nM (Holden et al., 1997; Nature Biotechnology 15 p66 8 -67 2 This agrees well with a Ka of between 0.1 and 1.0 nM. for NGF binding to ectopically expressed TrkA in mammalian cells. The ICso (concentration of cold NGF required to inhibit '"I-NGF by for unlabelled (cold) NGF was 0.2nM (Holden, P. H et al. (1997) Nature Biotechnology 15: 668-672) (Figure 4B).

Results show that TrkAIg2 binds NGF with a similar affinity to TrkAIgl,2 (Fig. The SICso for TrkAIg2 is only three-fold higher than that of TrkAIgl,2, indicating a very similar affinity for NGF. This surprising result indicates that the major contribution to binding within TrkAIg 1,2 is found in the second Ig domain, TrkAIg2.

2 Surface Plasmon Resonance Studies: Kinetic data of the binding of NGF to TrkAIg2 was obtained using a BiaCore-X. Biacore technology allows real-time measurements of rate constants using very low amounts of protein. Briefly, varying concentrations of sample (analyte) are flowed across a sensor chip to which the protein of interest (the ligand) has been bound. As the analyte binds to the 23 ligand there is a change in the electron density on the surface of the sensor chip which affects the intensity and wavelength of light absorbed by the surface.

Since the data from competitive binding assays indicated that TrkAIg2 was the major contributor to NGF binding, this domain was further investigated.

TrkAIg2 was covalently attached to the surface of the sensor chip by coupling with amine groups on TrkAIg2 to carboxyl groups on the surface using BiaCore Amine Coupling kit and varying concentrations of NGF passed over at a constant flow rate of 20 pl/min for two minutes. Data were collected for a range of NGF concentrations of 1 pM to 1 nM. It was found that at the high concentrations and at the very low concentrations, the data became difficult to interpret possibly due to aggregation of the NGF at the high concentrations and to non-specific interactions with the surface at very low concentrations.

However, data collected for the range 40 nM to 500 nM could be successfully evaluated.

Using the fitting software, BiaEval 3.0, a Kd of 11.8 nM was obtained. The Kd value of 11.8 nM obtained is consistent with the fact that the ICso for TrkAIg2 is three fold higher than that of TrkAIgl,2 given that the Kd for TrkAlgl,2 binding to NGF is 3.3 nM as determined by competitive binding assay.

In addition, 20 pM BDNF was also passed over the TrkAIg2 with negligible observed binding. It is clear that as well as being the main contributor to the NGF binding capability of TrkA, TrkAIg2 is also specific for NGF.

3 Binding of TrkAIg-like domains using the ELISA Technique Method 1 Anti-PNGF (Sigma polyclonal rabbit anti mouse NGF, 1:1000) diluted in Coat I Buffer mM sodium carbonate pH 9.6, NaN3 is plated (50 pil per well) onto 96 well plates and left overnight at 4 0 C. Wells were emptied and 100 pl per well Coat II Buffer (Coat I plus 1% BSA) was added. After 2 hours at 4°C, the plate was washed 3 times using Wash Buffer (50 mM Tris HCI pH 7.2, 200 mM NaCI, 0.1% Triton X-100, 0.1% NaN 3 0.25% gelatin) and samples and standard curve of NGF (0-1000pg/ml) diluted in Sample Buffer (Wash buffer plus 1% BSA) were added (50 pl per well). Samples had-been 24 pre-incubated with varying concentrations of TrkAIg-like domains for ten minutes with shaking at room temperature before adding to the plate. The plate was left 6ne hour at room temperature before washing 3 times with Wash Buffer, anti PNGF galactosidase conjugate (Boerhinger: 2.5-20mU and 5-lOng antibody per assay) diluted (1:40) in wash buffer (50 pl per well was added). The plate was incubated for 2 hours at room temperature and then washed 3 times with Wash Buffer before adding 50 il of substrate (200 mM of 4-methyl umbelliferyl galactoside (4-MUG)) in Substrate Buffer (100 mM sodium phosphate pH 7.3, I mM MgC12). The production of a fluorescent product (4-methylubelliferone) from 4-MUG was then measured using a fluorimeter at excitation wavelength 364 nm, emission at 448 nm.

Method 2 The assay is similar to that of method 1 except that the TrkAIgl,2 domain was plated directly onto the 96 well plate in Coat I Buffer and left overnight at 4"C. The wells were then emptied and Coat II Buffer added for 2 hours at 4"C. A standard curve of pNGF (0-200 nM) was preincubated for 10 minutes at room temperature with 2 LM TrkAIgl or 2 pM TrkAIg2 and added to the plate. This was incubated at room temperature for one hour before washing and the addition of anti pNGF galactosidase conjugate. The plate was then incubated for 2 hours at room temperature and washed with Wash Buffer before adding substrate (200 mM of 4-MUG). The production of a fluorescent product was then measured using a fluorimeter at an excitation wavelength of 364 nm, emission at 448 nm..

The TrkAIgl had no effect on NGF binding to the anti-pNGF antibodies on the plate indicating that they were not sequestering NGF in the pre-incubation. By contrast the TrkAIg2 bound to 22% of the NGF at 0.5 nM and 38% at 1 nM NGF (Figure 11) TrkAIg2 was able to sequester NGF and thus less NGF was available for binding to the TrkAIgl,2. The binding was lowered by 40% at 200 nM NGF. TrkAIgl was not able to sequester NGF and therefore the binding to TrkAIgl,2 was unaffected (Figure 12).

These results show that TrkAIg2 will bind to NGF resulting in a lowering of NGF concentration available for binding to a 96 well plate. TrkAIgl is not able to do this. The preceding protocols describe a choice of methods whereby high throughput screening of non-peptide or peptide databases may be carried out on a 96 well plate format.

Competition by unknown ligands with NGF for binding to plated TrkAIg-like domains may be measured by diminution of fluorescence.

In Vitro Effects of TrkAIg-like Domains on NGF-Induced Neurite Outgrowth By PC12 Cells PCl2 (derived from a transplantable rat adrenal phaeochromocytoma, ECACC No.

88022401) cells grown in the presence of 4 ng NGF (Fig. 13A) differentiate and produce neurites after 72 hrs. This does not occur in the absence of NGF (Fig. 13B). TrkAIg2 added to PC12 cells in the presence of 4 ng NGF at 2.5 pM (Fig. 13C), 1.25 pM (Fig.

13D) and 0.625 pM (Fig. 13E) inhibits neurite outgrowth. Only when the TrkAIg2 concentration is reduced to 0.312 pM (Fig. 13F) does neurite outgrowth start to appear.

Results show that the TrkAIg2 domain is able to inhibit neurite outgrowth of PC12 cells by sequestration of NGF (Fig. 13) whereas TrkAIgl is not able to do this.

In Vivo Effects of TrkAIg-like domains: Inhibition of Plasma Extravasation Inhibition of NGF activity in vivo All in vivo experiments were carried out according to the Animals (Scientific Procedures) Act 1986 under terminal anaesthesia. Plasma protein extravasation in rat skin induced by intradermal NGF was measured by the extravascular accumulation of intravenous 1 25 I-human serum albumin (Brain, S A and Williams T. J. (1985) British Journal of Pharmacology 86: 855-860) Male Wistar rats (200-350 g) were anaesthetised with mg/kg intra peritoneal with maintenance doses (15 mg/ml) as necessary. The dorsal skin was shaved and marked out for injection of test substances according to a balanced, randomized plan with two sites per test agent. The rats received 25 I-human serum albumin (100 kBq) and Evans Blue dye (0.2-0.5 ml of 2.5 w/v in saline) i.v. via the tail vein at the start of the accumulation period. NGF and other test agents (in Tyrodes buffered salt 26 solution) were then injected i.d. and accumulation allowed over a 30 min period. A blood sample was taken by cardiac puncture (for plasma) and the rats killed by cervical dislocation. The dorsal skin was then removed and injection sites punched out (16 mm diameter). Plasma and skin sites were counted in a' gamma counter. The plasma protein extravasation at each site was expressed as volume of plasma extravasated.

For co-injection experiments, all skin sites received 100 pl of either NGF (8 pmol) or Tyrode (with or without TrkAIgl,2, TrkAIgl or TrkIg2). For pretreatment experiments, skin sites received 100 pl of either TrkAIgl,2 TrkAIgl or TrkIg2 (24 or 80 pmol) or vehicle (Tyrode solution) at -5 or -40 min. These sites then received 50 pl NGF (8 pmol) or Tyrode at start of accumulation period (0 min).

The effect of TrkAIgl,2 on NGF-induced plasma extravasation.

The effect of co-injection of TrkAIgl,2 on NGF-induced plasma extravasation is shown in Fig. 14. Results are expressed as plasma extravasated (pl/site) in response to intradermal test agent, mean s.e.mean, n 6. The response induced by 7S NGF(7S NGF is a complex of 2.55 (P-NGF) and y NGF), both alone and with co-injection of TrkAIgl,2, is shown (8 pmol, filled squares). For comparison, the response induced by Tyrode's solution (vehicle, open circles), alone and with co-injection of TrkAIgl,2 is also shown.

Plasma extravasation in sites receiving agent plus co-injected TrkAIgl,2 differing significantly from the sites receiving agent alone are shown as p 0.01, as assessed by ANOVA with Bonferroni's post-test.

The TrkAIgl,2 can antagonize the actions of NGF when used at a dose of 24 pmol, i.e.

threefold higher than the dose of NGF used. In contrast, injection of TrkAIg 1,2 in vehicle produced no significant plasma extravasation. Thus, TrkAIgl,2 can antagonize the action of NGF particularly when premixed and co-injected. This indicates that TrkAIgl2 is able to bind to, and thus sequester, NGF thus inhibiting its action of extravasation. To investigate the ability of TrkAIgl,2 to antagonize NGF in vivo, skin sites were pre-treated by intradermal injection of TrkAIgl,2, and NGF was given 5 min later. The results, shown in Fig. 15, show that 24 pmol TrkAIgl,2 can significantly inhibit the plasma extravasation induced by 8 pmol 7S NGF. Results are expressed as plasma extravasated (pl/site) in response to intradermal test agent, mean s.e.mean, n 4. The response induced by 7S. NGF (8 pmol) is shown in the filled squares, both alone and in sites pre-treated with increasing doses of TrkAIgl,2, shown. For comparison, the response induced 7S NGF (8 pmol) co-injected with TrkAIgl,2 (24 pmol) is shown in the filled bar.

Plasma extravasation induced by intradermal injection of GR 73632 (30 pmol) is shown in the filled triangles and Tyrode's solution (vehicle) in the open circles, with the pre-treatment dose of TrkAIg 1,2 shown. Plasma extravasation in sites receiving agent plus co-injected TrkAlgl,2 differing significantly from the sites receiving agent alone are shown as p 0.01, as assessed by ANOVA with Bonferroni's post-test.

The plasma extravasation seen with NGF in sites pre-treated with 24 pmol TrkAIgl,2 was similar to the plasma extravasation produced by NGF co-injected with 24 pmol TrkAlgl,2.

As with the co-injection experiments, pre-treatment with TrkAIgl,2 produced no significant plasma extravasation when injected alone. In an attempt to determine if the action of TrkAlgl,2 was specific to NGF-induced responses or a general anti-inflammatory effect, the NKl agonist GR73632 (30 pmol) was injected into TrkAIgl,2 pre-treated sites. The 5 min. pre-treatment failed to inhibit the plasma extravasation induced by GR73632, as also shown in Fig In order to evaluate the stability of the NGF sequestration, skin sites were pre-treated for a longer period (40 min) with TrkAIgl,2 and NGF given at the start of the accumulation period, as shown in Fig. 16. Results are expressed as plasma extravasated (pl/site) in response to intradermal test agent, mean s.e.mean, n 4. The response induced by 7S NGF (8 pmol) is shown in the filled squares, both alone and in sites pre-treated with increasing doses of TrkAIg1,2, is shown. For comparison, the response induced 7S NGF (8 pmol) co-injected with TrkAIgl,2 (24 pmol) is shown by the filled bar. Plasma extravasation induced by intradermal injection of GR73632 (30 pmol) is shown in the filled triangles and Tyrode's solution (vehicle) in the open circles, with the pre-treatment dose of TrkAIgl,2 shown on the y-axis. Plasma extravasation in sites receiving agent plus co-injected TrkAIgl,2 differing significantly from the sites receiving agent alone are shown as p 0.05, as assessed by ANOVA with Bonferroni's post-test.

In these experiments, NGF-induced plasma extravasation was significantly inhibited by pmol,.but not 24 pmol, TrkAIgl,2. The plasma extravasation induced by co-injection of 8 28 pmol NGF with 80 pmol TrkAIgl,2 is shown for comparison. In keeping with the results of the previous experiments, the doses of TrkAlgl,2 used failed to produce'significant plasma extravasation when injected alone and also failed to inhibit the plasma extravasation induced by GR73632 (as before).

The effect of TrkAIgl on NGF-induced plasma extravasation.

Following the previous series of experiments, using both immunoglobulin-like domains (TrkAIgl,2), we attempted to further characterize the binding of NGF to the immunoglobulin-like domains of TrkA. To do this, we used a sample of recombinant TrkAIgl, the first immunoglobulin-like domain. As can be seen in Fig. 17, co-injection experiments with TrkAIgl showed no significant inhibition of NGF-induced plasma extravasation at doses up to 80 pmol/site.

Results are expressed as plasma extravasated (pl/site) in response to intradermal test agent, mean s.e.mean, n 6. The response induced by 7S NGF (8 pmol) is shown in the filled squares, both alone and with co-injection of TrkAIgl, shown. For comparison, the response induced by Tyrode's solution (vehicle) is shown in the open circles, with the dose of TrkAIgl co-injected shown. Plasma extravasation' in sites receiving agent plus co-injected TrkAIgl differing significantly from the sites receiving agent alone are shown as ns, not significant, as assessed by ANOVA with Bonferroni's post-test.

The effect of TrkAIg2 on NGF-induced plasma extravasation.

The ability of TrkAIg2 to bind and sequester NGF was evaluated.

As can be seen in Fig. 18, co-injection of TrkAIg2 with NGF was able to produce significant inhibition of NGF-induced plasma extravasation, when given in a ten-fold excess. At all of the doses used, TrkAIg2 produced no inhibition of plasma extravasation induced by GR73632, and also produced no significant plasma extravasation when injected alone. Results are expressed as plasma extravasated (pl/site) in response to intradermal test agent, mean s.e.mean, n 4 8. The response induced by 7S NGF (8 pmol) is shown in the filled squares, both alone and with co-injection of TrkAIg2, shown.

For comparison, the response induced by GR73632 (30 pmol) is shown in the filled triangles and that induced by Tyrode's solution (vehicle) is shown in the open circles, with 29 the dose of TrkAIg2 co-injected shown. Plasma extravasation in sites receiving agent plus co-injected TrkAIg2 differing significantly from the sites receiving agent alond are shown as p 0.001, as assessed by ANOVA with Bonferroni's post-test.

Pre-treatment of skin sites with 80 pmol TrkAIg2 with NGF was also able to inhibit the plasma extravasation induced by 8 pmol NGF, given 5 min later Fig. 19. Results are expressed as plasma extravasated (pl/site) in response to intradermal test agent, mean s.e.mean, n 4. The response induced by 7S NGF (8 pmol) is shown in the filled squares, both alone and in sites pre-treated with increasing doses of TrkAIg2, shown. Plasma extravasation induced by intradermal injection of GR73632 (30 pmol) is shown in the filled triangles and Tyrode's solution (vehicle) in the open circles, with the pre-treatment dose of TrkAIg2 shown. Plasma extravasation in sites receiving agent plus co-injected TrkAIg2 differing significantly from the sites receiving agent alone are shown as 0.001, as assessed by ANOVA with Bonferroni's post-test. Again, this pre-treatment had no effect on GR73632-induced plasma extravasation, and produced no significant plasma extravasation when injected alone (Fig. 19).

Similar results were seen when TrkAIg2 was used as a 40 min pre-treatment, as shown in Fig. 20. Results are expressed as plasma extravasated (pl/site) in response to intradermal test agent, mean s.e.mean, n 3. The response induced by 7S NGF (8 pmol) is shown in the' filled squares, both alone and in sites pre-treated with increasing doses of TrkAIg2, shown. Plasma extravasation induced by intradermal injection of GR73632 (30 pmol) is shown in the filled triangles and Tyrode's solution (vehicle) in the open circles, with the pre-treatment dose of TrkAlg2 shown. Plasma extravasation in sites receiving agent plus co-injected TrkAIg2 differing significantly from the sites receiving agent alone are shown as p 0.001, as assessed by ANOVA with Student-Newman-Keuls post-test. The plasma extravasation induced by NGF was significantly inhibited by TrkAIg2 at 80 pmol.

For comparison, the plasma extravasation induced by 8 pmol 7S NGF co-injected with pmol TrkAIg2 is shown in the filled column. Pre-treatment with TrkAIg2 induced no plasma extravasation alone and did not affect the plasma extravasation induced by GR 73632.

The results clearly demonstrate that the TrkIg2 domain is able to bind to NGF in vivo and block its biological activity.

Crystallisation of TrkAIg2 Crystals of recombinant TrkA-Ig2 have been obtained under a variety of conditions between 14-20% MPD, pH5.0 (100mM Na-citrate), 300 to 500mM NaCI, pH 5.0 (100mM Na-citrate), most favourably at 500mM NaCI, pH 5.0. The crystals grow reproducibly to approximate dimensions of 0.2 x 0.2 x 0.2 mm. Crystals are then cryo-preserved. Using the home source (rotating anode, mirrors, imaging plate), and the synchrotron source at Hamburg, these crystals diffract to about 2.8 A. Assuming 50% solvent, it is estimated that there are 4 (or possibly 3) molecules in the asymmetric unit. Crystals of a selenoMet form of the protein have been prepared using a selenoMet auxotroph (there are 4 methionines in the construct) which has been used for MAD phasing and as a heavy atom derivative.

Recombinant forms of both the native and selenoMet TrkA-Ig2 were prepared, purified and refolded using the established procedures as defined elsewhere in the description.

Therapeutic Aspects of TrkAIg2 Since certain pain states are caused by overexpression of NGF, it is anticipated and evidence indicates, that application of NGF antagonists such as antibodies or recombinant TrkAIg2 binding domain may alleviate resulting pain states (McMahon, S. B.Series B-Biological Sciences, (1996), 351, No.1338, 431- 440; Woolf; C. J. et al. British Journal Of Pharmacology, (1997), 121, No.3, 417- 424; Lowe, E. M. et al. British Journal Of Urology, (1997), 79, No.4, 572-577; Dmitrieva, N. et al. Neuroscience, (1997), 78, No.2, 449-459; Aloe, L. et al. International Journal Of Tissue Reactions-Experimental And Clinical Aspects, (1993), 15, No.4, 139-143; Aloe, L. et al. Rheumatology International, (1995), 14, No.6, 249-252).

Therefore, in summary, the inventors have demonstrated the inability of the region referred to as TrkAIgl to bind NGF. The smallness of the TrkAIg2 molecule and the abundance with which this protein can be produced for example in E. coli, and purified and refolded into its correct formation confers certain advantages over the complete extracellular domain which, by necessity, must be made in mammalian or insect cells.

-31 There are known to be various pain states, often chronic inflammatory conditions which are associated with an increase in NGF protein levels.

These include idiopathic sensory urgency and interstitial cystitis, arthritis and shingles. It is also suggested that such chronic conditions may result in sensitization of peripheral neurons and perhaps even long-term sensory neuronal abnormalities. By sequestration of this increased NGF, by the use of TrkAlg2, it will be possible to alleviate pain in such conditions and in other conditions in which NGF is elevated.

Throughout the description and claims of the specification, the word "comprise" and variants of the word, such as "comprising" and "comprises", is not intended to exclude other additives, components, integers or steps.

Throughout the specification, the following abbreviations have been used: Abbreviations for amino acids Three-letter One-letter Amino acid abbreviation symbol Alanine Ala A Arginine Arg R Asparagine Asn N Aspartic acid Asp D Asparagine or aspartic acid Asx B Cysteine Cys C Glutamine Gin Q Glutamic acid Glu E Glutamine or glutamic acid Glx Z Glycine Gly G Histidine His H Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp W Tyrosine Tyr Y Valine Val V Abbreviations for nucleotides: Adenine Guanine Cytosine Thymine Uracil Abbreviations for mutations:

XINNNX

2

X

1 and X 2

NNN

an amino acid one letter symbol as defined above.

numerical digits indicating the position of the mutation within the amino acid sequence.

Claims (48)

1. An isolated polypeptide consisting of a portion of the amino acid sequence of residues 22 to 144 of Fig. 4B, the polypeptide being capable of binding a neurotrophin.

2. A polypeptide according to claim 1 which binds with high affinity to a neurotrophin.

3. A polypeptide according to claim 2 which binds to a neurotrophin with a disassociation constant of less than

4. A polypeptide according to claim 1, 2 or 3 wherein the polypeptide is isolated from animal cells. A polypeptide according to claim 4 wherein the animal cells are mammalian cells.

6. A polypeptide according to claim 5 wherein the mammalian cells are human cells.

7. A polypeptide according to claim 4 wherein the animal cells are insect cells reptilian cells, fish cells, avian cells or amphibian cells.

8. A polypeptide according to any preceding claim wherein the neurotrophin is NGF, NT-3 or a neurotrophin which binds

9. A polypeptide according to any preceding claim wherein the neurotrophin exists as a monomer, dimer, trimer, or a neurotrophin heterodimer. A polypeptide according to any preceding claim wherein the neurotrophin is from a mammal, insect, reptile, fish, bird or amphibian.

11. A polypeptide according to claim 10 wherein the mammalian neurotrophin is a human neurotrophin. 34

12. An isolated DNA sequence which encodes a polypeptide according to any of claims 1 to 11 or variants of such a DNA sequence due to the degeneracy of the genetic code, or insertion or deletion mutants thereof that encode a polypeptide according to any of claims 1 to 11.

13. A plasmid or other vector comprising a DNA sequence according to claim 12.

14. A plasmid according to claim 13 wherein the plasmid is an expression vector. A plasmid according to claim 13 or claim 14 wherein the plasmid is

16. A complex comprising at least one polypeptide according to any of claims 1 to 11 and at least one neurotrophin or neurotrophin subunit, manomer or biologically active portion thereof.

17. A method of producing a polypeptide according to any one of claims 1 to 11 comprising introducing a DNA sequence according to claim 12 or a plasmid according to any of claims 13 to 15 into a suitable host whereby the DNA sequence is expressed.

18. A method according to claim 17 wherein the host is an animal cell.

19. A method according to claim 18 wherein the host is a bacterial cell. A method according to claim 19 wherein the host is a mammalian cell.

21. A method according to claim 20 wherein the host is a human cell.

22. A method of screening for molecules which bind to the TrkA receptor using a polypeptide according to any of claims 1 to 11.

23. A method according to claim 22 comprising comparing the binding of a putative ligand to TrkAgl, or a portion thereof, with the binding of the same putative ligand to TrkAlg2 or a portion thereof.

24. A method according to claim 22 or claim 23 comprising selecting molecules which bind to at least one solvent-exposed loop of TrkAIg2. A method according to claim 24 wherein the solvent-exposed loop is loop E to F as shown in Fig. 1(3).

26. A method according to claim 24 or 25 wherein the solvent-exposed loop is loop C" to D as shown in Fig.1(B).

27. A method according to claim 25 or claim 26 wherein molecules with an affinity of at least 10nM are selected.

28. A method according to any claims 22 to 27 comprising selecting molecules which enhance binding of a polypeptide according to any one of claims I to 11 or TrkA or a portion thereof in its natural state to a neurotrophin.

29. A method of combinatorial chemistry comprising: 1. a compound generating step 2. a compound screening step which separates the compounds generated in step 1 on the basis of their binding affinities to a polypeptide or a portion of a polypeptide according to any one of claims 1 to .11. An antibody raised against a polypeptide according to any of claims 1 to 11.

31. An antibody according to claim 30 wherein the polypeptide is TrkAIg2. NO O 32. A host cell containing a DNA sequence according to claim 12 or a plasmid or other vector according to any of claims 13 to

33. A host cell according to claim 32 wherein the host cell is a mammalian, Sbacterial, insect, or yeast cell. O 34. A host cell according to claim 33 wherein the mammalian cell is a human cell.

35. A diagnostic probe wherein the probe comprises a polypeptide according to any S one of claims 1 to 11.

36. A diagnostic probe according to claim 35 wherein the probe is labelled.

37. A diagnostic probe according to claim 36 wherein the label comprises a fluorescent tag or a radiolabel.

38. Diagnostic tests, assays or monitoring methods using a polypeptide according to any of claims 1 to 11, or an antibody according to claim 30 or 31.

39. Diagnostic tests, assays or monitoring methods using a probe comprising a DNA sequence according to claim 12, or a probe according to any of claims to 37.

40. Diagnostic tests, assays or monitoring methods according to claim 37 or claim 38 wherein the tests, assays, or monitoring methods comprise microbiological, animal cell, or biodiagnostic tests, assays or monitoring methods.

41. Diagnostic tests, assays or monitoring methods according to any of claims 37 to 39 which detect elevated neurotrophin levels associated with peripheral inflammation, chronic inflammation, postherpetic neuralgia, interstitial cystitis, arthritis or shingles. P:\UseAalex\707295_dcms_4-.2.06 doc

42. A method of producing a polypeptide according to any of claims I to 11 by chemical or biological means.

43. An organism engineered to contain, express or overexpress a polypeptide according to any of claims 1 to 11 or a DNA sequence according to claim 14, wherein said organism is not human.

44. An organism according to claim 43 wherein the organism is an animal, bacteria, yeast, or insect. An organism according to claim 44 wherein the organism is a mammal, bacteria, yeast or insect.

46. A composition for the control of pain associated with an increase in neurotrophin levels comprising a polypeptide according to any of claims 1 to 11.

47. A method of treating a subject with pain associated with increased neurotrophin levels, the method comprising supplying to the subject a pharmaceutical composition comprising a polypeptide according to any of claims I to 11 or a neurotrophin analogue isolated or identified by a screening procedure involving a polypeptide according to any of claims I to 11.

48. A method according to claim 47 wherein the pain is a symptom of conditions selected from idiopathic sensory urgency (ISU), interstitial cystitis, arthritis, shingles, peripheral inflammation, chronic inflammation, or postherpetic neuralgia.

49. A method of treating a subject with Alzheimers disease, the method comprising supplying to the subject a pharmaceutical composition comprising a polypeptide according to any of claims 1 to 11. 38 N0 50. A method of treating a subject with Alzheimers disease, the method comprising Ssupplying to the subject a pharmaceutical composition comprising an Sneurotrophin analogue isolated or identified by a screening procedure involving Sa polypeptide according to any of claims 1 to 11.

51. A method of reducing free NGF levels in a subject, the method comprising supplying to a subject, a polypeptide according to any of claims 1 to 11. V)

52. A method of reducing plasma extravasation comprising supplying to a subject, a I 10 polypeptide according to any of claims 1 to 11.

53. A method according to any of claims 38 to 42 and 47 to 52 in which the neurotrophin is NGF.

54. A pharmaceutical composition comprising a polypeptide according to any of claims 1 to 11 together with a pharmaceutically acceptable carrier or diluent. A pharmaceutical composition according to claim 54 including at least one neurotrophin.

56. Compounds identified by a method according to any of claims 22 to 29 as binding to the TrkA receptor, when used to treat a subject with increased neurotrophin levels.

57. A crystal comprising a polypeptide according to any of claims 1 to 9.

58. A polypeptide according to claimi substantially as hereinbefore described with reference to any one of the figures or the examples.

59. A plasmid according to any one of claims 13 to 15, substantially as hereinbefore described with reference to the examples. A method of screening for molecules according to claim 22 substantially as hereinbefore described with reference to the examples. P:\Usefalex\707295_daims_4.12.-0.oc