WO2003001211A1

WO2003001211A1 - Method for testing the presence of prion proteins in tissue and culture samples

Info

Publication number: WO2003001211A1
Application number: PCT/EP2002/006789
Authority: WO
Inventors: Konstanze F. Winklhofer; Jörg TATZELT; Ulrich Hartl
Original assignee: MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V.
Priority date: 2001-06-22
Filing date: 2002-06-19
Publication date: 2003-01-03

Abstract

The present invention relates to a method for testing for the presence of prion proteins. Moreover, the present invention relates to a method for identifying and testing compounds useful in the prevention or reduction of sporadic, hereditary or transmissible spongiform encephalopathies. The invention further relates to methods of refining or modifying compounds identified in accordance with the method of the present invention. Furthermore, the present invention relates to the use of such compounds for the preparation of a pharmaceutical composition for the prevention or treatment of sporadic, hereditary or transmissible spongiform encephalopathies. Moreover, the present invention relates to methods for identifying agents specifically interacting with prion proteins and the use of the identified agents for the preparation of a diagnostic kit for the diagnosis of sporadic, hereditary or transmissible spongiform encephalopathies.

Description

Method for testing the presence of prion proteins in tissue and culture samples

Several documents are cited throughout the text of this specification. The disclosure content of the documents cited herein (including any manufacture's specifications, instructions, etc.) is herewith incorporated by reference.

The background of spongiform encephalopathies and prion proteins has been descπbed in detail in a review published in the internet on the homepage of the Prionics AG (http://www.prionics.com/review e.html). As described in said review, purified preparations of infectious agents (also denominated "Prion"; Prusiner, 1982) were found to contain a 27-30 kDa protease-resistant protein, termed PrP 27-30 (from Prion Protein), which accumulated in brain during the disease (Bolton et al., 1982; McKinley et al., 1983; Prusiner et al., 1984; Gabizon et al., 1988). The PrP 27- 30 turned out to be the protease-resistant core of an abnormal isoform of a host protein (Oesch et al., 1985; Basler et al., 1986; Borchelt et al., 1990). This abnormal isoform was denominated PrP^Sc (the scrapie-specific isoform of PrP) to distinguish it from its normal, protease-sensitive cellular isoform, PrP^c. When said isoforms are treated by proteinase, e.g. proteinase K, PrP^Sc is shortened to a 27-30 kDa fragment while PrP^c is digested (Bolton et ai., 1982; Oesch et al., 1985). It has been shown that PrP^c is attached to the cell surface by a glycosylphosphatidylinositol (GPl) anchor, while PrP^So accumulates intracellularly within cytoplasmatic vesicles (Stahl et al., 1987; Safar et al., 1990b; Taraboulos et al., 1990; Caughey et al., 1991 ; McKinley et al., 1991 ; Borchelt et al., 1992; Taraboulos et al., 1992). Experiments in cultured cells indicated that PrP^Sc is generated from PrP^c In a post-transitional process (Caughey et al., 1989; Borchert et al., 1990; Caughey and Raymond, 1991 ; Borchelt et al., 1992; Taraboulos et al., 1992). The conversion of PrP^c into PrP^Sc involves the reduction of α-helix structures and an increase in β-sheet structures in the protein (Pan et al., 1993). So far, no covalent modifications between the two isoforms have been observed (Turk et al., 1988; Pan et al., 1993; Stahl et a!., 1993).

Since prion proteins have been characterized in detail as described above, several tests for the diagnosis especially of BSE have been developed. For example, when BSE suspects are slaughtered, the primary test for diagnosis relies on histopathology. Said histopathological test is performed post mortem and requires brain material which firstly has to be preserved in formalin, and is then stained and examined under the microscope for the characteristic appearance of BSE-specific changes. The disadvantage of said proceeding is that any degree of decomposition before the brain is examined limits.the significance of said method.

Additionally, a number of diagnostic tests for BSE are based on their interaction of specific antibodies with the disease-specific protein PrP^Sc. The common principle of most of the available test-systems is the use of brain homogenates, which are incubated with proteinase K individually. Said step of individual treatment of the samples with proteinase K is a potential source of variability and false-positive test results, and the remaining PrP ^"protein is detected immunologically by ELISA or by laborious SDS-PAGE and Western blotting procedures.

Examples for commercially available diagnostic tests are:

1. A Western Blot test, which was developed by Prionics. Said test is used to detect PrP^So protein purified from treated brain material (obtained post mortem) by its molecular weight and reaction with specific antibodies. Said test is currently the standard test which is used for the diagnosis of BSE in several countries of the European Union.

2. Furthermore, BSE can be detected in animals by immunocytochemistry (ICC). Immunocytochemistry also relies on the detection of PrP^Sc using specific antibodies. Post mortem brain material is once again required, preserved. This test is performed directly on the tissue section and does not involve any protein purification steps. However, the sensitivity and specificity of said test is limited since the presence of the PrP^So protein can only be detected in a small slice of brain material in each sample.

3. A third method to detect the presence of prion protein, which appears to show also some promise for the use in live animals, is Immuno Capillary Electrophoresis, often referred to as ICE.

4. A further method which is used for the diagnosis of BSE is EL1SA (Enzyme Linked Immuno Sorbent Assay). One of said ELISAs has been developed by Enter Scientific (Ireland). The antibody used by this company was manufactured by a British company called Proteus. Another test which bases on the sandwich immuno assay technique, has been developed by CEA (France). Both tests are performed with brain tissue collected post mortem.

In a study of BSE tests carried out by the European Commission (EC) in 1999, the sensitivity and the specificity were studied (European Commission, 1999). All tests available on the market are either laborious or have inherent properties of diagnostic uncertainty, as described above. Further, from the present status of research, approaches to develop a medicament for treating or preventing sporadic, hereditary or transmissible spongiform encephalopathies appear remote.

Thus, the technical problem underlying the present invention was to provide a method which is easy to use and offers the opportunity to analyze a large number of samples for the presence of prion protein in one test, as well as to provide a method and means for the development of a prophylaxis or therapy of sporadic, hereditary or transmissible spongiform encephalopathies. The solution to this technical problem is achieved by providing the embodiments characterized in the claims.

Accordingly, the present invention relates to a method of testing for the presence of prion protein comprising the steps of:

(a) lysing cells or tissues in a solution comprising detergents in a concentration above the critical micelle concentration (CMC);

(ba) transferring the lysate onto a membrane and treating the proteins attached to the membrane with a protease added in a concentration and incubated in a time range conferring limited proteolysis; or

(bb) treating the lysate with a protease added in a concentration and incubated in a time range conferring limited proteolysis and transferring the not entirely degraded proteins of said lysate onto a membrane;

(c) contacting the proteins attached to the membrane with an agent specifically interacting with a prion protein; and

(d) detecting whether a specific interaction has occurred.

Between the various steps recited above washing steps using appropriate buffers may be carried out wherever appropriate.

In this context the term "prion protein" is defined in accordance with the present invention as the abnormal isoform PrP^Sc (the scrapie-specific isoform of PrP) of a cellular protein (PrP^c) as described supra.

The lysis of cells or tissues to be analyzed for the presence of prion protein of step (a) is carried out by the use of detergents under non-denaturing conditions. Examples for said detergents are known by a person skilled in the art, and comprise e.g. Triton-X-100, Sarkosyl, deoxycholate, NP 40 or Brij. Further examples are known by a person skilled in the art. Said detergents are used in a solution in a concentration above the critical micelle concentration (CMC). The term "critical micelle concentration (CMC)" is known by a person skilled in the art and also defined in context with the invention as the concentration of a detergent, at which the monomers of said detergent associate to form micelles (see also the Rehm ("Der Experimentator: Proteinbiochemie", 3^rd eddition, Gustav Fischer Verlag (2000), chapter 3). The CMC of a given detergent can be usually found in its instruction leaflet or a data sheet provided by the manufacturer. The CMC is dependent of the temperature, the ionic strength, the pH-conditions and the concentration of salt and non ionic substances in a solution.

The described transfer of the lysate obtained in step (a) onto a membrane to attach the proteins to said membrane in step (b) may be executed by different approaches, e.g. by dotbiot, centrifugation, gravity flow, or by the use a vacuum to draw the liquid of the lysates through the membrane while aggregated proteins contained in the lysate are retained on the membrane. An example for said transfer is described in Example 3.

Membranes suitable for the described methods are known to a person skilled in the art and may be cellulose membranes or derivatives thereof, e.g. nitrocellulose, cellulose acetate, regenerated cellulose, polyamide, polycarbonate, orpolytetrafluorethylene.

The protease in step (b) is used in a concentration and incubated in a time range conferring limited proteolysis. The term "limiting proteolysis" of the prion protein is characterized in accordance with the present invention by conditions which enable a digestion of the protein and the remainder of the protease-resistant core of the prion protein (PrP^So). An example for said procedure is described in Example 2. As described in a preferred embodiment said concentration for the protease proteinase K is in a range of 50 to 1000 μg/ml. A preferred time of incubation is in a range of 5 min to 20 h. The more preferred time range is 5 min to 4 h, even more preferred 10 min to 1 h and most preferred 10 to 20 min. The incubation is performed preferably at temperatures in a range between room temperature (RT) and 60°C. Corresponding concentrations and conditions for further proteases can be established by a person skilled in the art according to established protocols. If a detergent is combined with the protease, concentrations of the protease, which are required for limited proteolysis may be different for said protease as compared to the absence of detergent since the proteolytic activity of a protease is normally dependent on the concentration of detergents, such as SDS, sarcosyl, etc. as described herein above. The term "specifically interacting with a prion protein" defines the specific binding of a domain or the complete structure of said agents to prion protein. Said "specific interaction" of the agents is contrary to an unspecific interaction like cross-reaction with other proteins in the sample, the membrane or a buffer or a solvent. Specific interaction means that the interacting structure reacts in the system with the prion protein only, so that the desired signal can be measured. Example of a useful specific interaction is the binding of an antibody or a functional fragment or derivative thereof to its specific antigen or the specificity of a receptor to its specific ligand. A further example is the interaction of an enzyme with a non-processible substrate analogue. Additional examples of such specifically interacting structures are leucine zippers, calmodulin/M13 peptide, protein A/antibody constant regions, biotin/streptavidin. Said agents may be small molecules, peptides, plasminogen, receptors for the membrane bound or the cellular form of PrP^c or converted PrP^Sc, or derivatives thereof, antibodies comprising fragments and derivatives thereof, or aptamers. Concentrations and time ranges for incubation as well as the temperature of incubation may be different for every single agent.

The detection whether a specific interaction has occurred may comprise washing of the membrane to remove agent unspecifically bound to the membrane. Said detection may be performed by the use of agents which on the one hand are suitable for the detection of the presence of the specifically interacting agent. Furthermore said agents may comprises a domain or function which can be used for the generation of a detectable signal. The steps of contacting the proteins with said agents and detecting whether a specific interaction has occurred may be similar to the principle of im unodetectiσn of proteins by Western Blot known to the person skilled in the art.

In a preferred embodiment the tissues to be analyzed by said method are disrupted to yield isolated cells prior to the lysis with a low ionic detergent of step (a). In this context the term "disrupting tissue to yield isolated cells" includes mechanical, enzymatic and/or chemical disruption of said tissues. Examples for mechanical disruption of the tissues are shearing and/or pressure as used when pushing tissue through a sieve or through a needle of a syringe or by using a French press. Examples for enzymatic disruption of the tissues include the use of proteinase K or other proteinases suitable to dissolve the intercellular junctions in a tissue.

In a further preferred embodiment the cells or tissues are incubated prior to the lysis of step (a) with a protease in a final concentration and time range beiow the concentration and time range which disrupts the cell membrane. Said treatment of the cells or tissues and the subsequent washing of the cells/tissues reduces the amount of protein in the samples. The term "disrupting the cell membrane" is defined in the context of the present invention as the destruction of the cell membrane by the proteases resulting in the loss of the integrity of the plasma membrane. Conditions can be verified by testing the viability of the cells. Methods for said analysis of the viability include, e.g. use of Trypan Blue as a dye, the "Cell Proliferation Kit I (MTT)" (Boehringer Mannheim), or Annexin-V-FITC dye (Bender), or the use of propidium iodid (PI). By the use of said methods the amount/percentage of viable cell in a population can be assayed and only conditions for protease treatment ensuring a majority of viable cells are in line with the method described by the present invention.

In a more preferred embodiment said protease is trypsin in a final concentration in the range of 0.1 - 1.0% (w/v).

In a further preferred embodiment of the invention the cytosolic and the nucleic fraction of the lysates obtained in step (a) are separated prior to the transfer of the proteins onto the membrane in step (b). The nucleic fractions are discarded and only the cytosolic fractions are used in the further steps. As a consequence of said step, DNA will be removed from the samples. Said DNA might interfere with the agents used for the detection of the presence of prion proteins resulting in false positive results.

In a more preferred embodiment, said separation of cytosolic and nucleic fractions is carried out by centrifugation. The nucleic fraction which forms a pellet is discarded and only the supernatant containing the cytosolic fraction is used in the further steps.

in another preferred embodiment the proteins which were transferred onto a membrane in step (b)^'are denaturated prior to the contacting of the proteins attached to the membrane with an agent specifically interacting with a prion protein in step (c). The process of denaturation of proteins is generally known to the person skilled in the art and described in the literature, e.g. the textbook of Lehninger ("Principles of Biochemistry" (1982), page 140). Said step of denaturation may increase the specificity of the binding of an agent used for the detection of the presence of prion proteins in the samples.

In a more preferred embodiment said proteins are denaturated by the use of a chaotropic agent.

In a further more preferred embodiment said chaotropic agent is guanidine-HCI. To ensure denaturation of the proteins guanidine-HCI is used in a concentration in the range of 2 to 8 M. Said denaturation is also described herein in Example 3.

In another preferred embodiment of the invention the agent which specifically interacts with prion protein in step (c) is selected from the group comprising of polyclonal antisera, monoclonal antibodies, aptamers and plasminogen.

Moreover, in a preferred embodiment the samples analyzed by the use of the method of the present invention are samples which are derived from humans or animals.

In a more preferred embodiment said animals are mammals. In this context mammals are of special interest which are used in animal husbandry or which are used as hunted mammals, domestic mammals or mammals of zoos and sanctuaries.

More preferred, said mammals are selected from a group consisting of cattle, sheep, deer, elks, minks, hamsters, mice, canines or felines.

In another preferred embodiment said animals are fish or birds.

Furthermore, in a preferred embodiment said tissue samples are derived from neuronal or lymphatic tissue. Said neuronal tissues comprise tissues of the peripheral nervous system (PNS) as well as tissues of the different compartments of the central nervous system (CNS). Examples for lymphatic tissues are samples jerived from secondary lymphoid organs, e.g. spleen, lymph nodes and tonsils and from Mucosal Associated Lymphoid Tissues (MALT) such as Peyer's patches, etc.

In a more preferred embodiment said tissue samples are derived from brain.

In an alternative preferred embodiment said samples are derived from tissue cultures. Said tissue cultures may be cultures of isolated primary cells, as well as cultures of cell lines.

In a preferred embodiment of the present invention the prion proteins which are detected by the described method are indicative of sporadic, hereditary or transmissible spongiform encephalopathies. Examples for said spongiform encephalopathies in humans are Creutzfeldt-Jacob disease (CJD), the variant form of the Creutzfeldt-Jacob disease (vCJD), the Kuru disease, Gerstmann-Straussler- Scheinker syndrom (GSS), Fatal familial insomnia (FFI), Sporadic fatal insomnia. Examples for other neurodegenerative diseases in which protein aggregates occur are Alzheimer's disease, Parkinson's disease, Huntington's disease, Spinocerebellar ataxias, Amyotrophic lateral sclerosis (ALS) Frontotemporal dementia, Pick's disease, and progressive supranuclear palsy. Furthermore, for animals the following spongiform encephalopathies have been inter alia described: Scrapie, bovine spongiform encephalopathy (BSE), transmissible mink encephalopathy (TME), chronic wasting disease (CWD). In this context, the method of the present invention may be used for the diagnosis of said spongiform encephalopathies and the agents used for said method may be supplied in a diagnostic kit. An example for the diagnostic kit and the reagents, which may be needed for the use of said kit is given in example 5.

In an alternative embodiment, the invention relates to a method for the identification of compounds, which are capable of interfering with or preventing the development of prion proteins after inoculation of samples with infectious PrP^Sc comprising the following steps:

(a) lysing cells in a solution comprising a low ionic detergent in a concentration above the critical micelle concentration (CMC); (ba) transferring the lysate onto a membrane and treating the proteins attached to the membrane with a protease added in a concentration and incubated in a time range conferring limited proteolysis; or

(c) contacting the proteins attached to the membrane with an agent specifically interacting with the prion protein; and

(d) detecting whether a specific interaction has occurred.

An example for said method for the identification of a compound is described herein in Example 6.

The term "interfering with or preventing the development of prion proteins" is defined in the context of the present invention as a technical feature of said compounds describing a interaction, e.g. chemical or enzymatic, of the compounds with the cellular form of the prion protein (PrP^c) or the scrapie form of the prion protein (PrP^Sc). Said interaction may result in a prevention of the conversion of PrP^c into PrP^Sc or in a degradation of pre-existing PrP^Sc in the cell. A compound identified by the method of the invention is preferably a small molecule or a peptide which can be derived from an at least partially randomized peptide _.library. Said compounds may also comprise polypeptides such as proteins and fragments and derivatives thereof.

In a preferred embodiment the cells in step (a) of the method of the invention are isolated from tissue cultures, which were infected with infectious prions. A suitable procedure of infection has been described by the group of Butler (Butler et al., 1988). Said cells may be cultured in culture flasks or dishes, e. g. dishes with 6 or 24 wells.

In a more preferred embodiment said cells are cultured and/or infected in microtiter plates. Said microtiter plates may preferably be plates with 96 wells, or plates with 384 (or more) wells. ^' In a preferred embodiment said cells are incubated prior to the lysing of step (a) with a protease in a final concentration and time range below the concentration and time range which disrupts the cell membrane. Conditions suitable for the incubation of the cells with the protease can be established as defined supra.

In another preferred embodiment the cytosolic and the nucleic fractions of the lysates obtained in step (a) are separated from the nucleic fractions prior to step (b) and the nucleic fractions are discarded as described supra.

In a more preferred embodiment said separation of cytosolic and nucleic fractions is carried out by centrifugation.

In another preferred embodiment the protease of step (b) used for the degradation of the proteins is proteinase K in a final concentration in the range of 50 - 1 ,000 μg/ml. A preferred time of incubation is in a range of 5 min to 20 h. The more preferred time range is 5 min to 4 h, even more preferred is a time range of 10 to 20 min. The incubation is performed preferably at temperatures in a range between room temperature (RT) and 60°C. Corresponding concentrations and conditions for further proteases can be established by a person skilled in the art according to established protocols. If a detergent is combined with the._. . protease,., concentrations of the protease, which are required for limited proteolysis may be different for said protease as compared to the absence of detergent since the proteolytic activity of a protease is normally dependent on the concentration of detergents, such as SDS, sarcosyl, etc.

Furthermore, in another preferred embodiment the proteins which were transferred onto a membrane in step (b) are denaturated in a step (b') prior to step (c). As described supra the process of denaturation of proteins is known by a person skilled in the art and described in the literature, e.g. the textbook of Lehninger ("Principles of Biochemistry" (1982),^' page 140). Said step of denaturation may increase the specificity of the binding of the agent used for the detection of the presence of prion proteins in the samples.

In a more preferred embodiment said proteins are denaturated by the use of a chaotropic agent. Preferably, said chaotropic agent is guanidine-HCI. To ensure the denaturation of the proteins guanidine-HCI is used in a concentration in the range of 2 to 8 M (see also Example 3).

Moreover, in a preferred embodiment of the invention the agent which specifically interacts with prion proteins in step (c) is selected from the group consisting of polycional antisera, monoclonal antibodies, aptamers and plasminogen.

In another preferred embodiment all steps of the described method of the invention prior to the transfer of the proteins onto the membrane in step (b) are executed in microtiter plates. Said steps comprise the culture and infection of the cells as well as the following optional steps: incubation of the cells with a protease in a final concentration and time range below the concentration and time range which disrupts the cell membrane prior to step (a); lysing of the cells in step (a) in a solution comprising a low ionic detergent in a concentration above the CMC; separation of the nucleic and the cytosolic fractions of the lysates obtained in step (a) and discarding nucleic fractions prior to step (b); incubation of the lysates with said protease added in a concentration and incubated in a time range conferring limited proteolysis in step (b) prior to the transfer of the proteins onto the membrane.

Additionally, the invention relates to a method of refining a compound identified by the method as described herein above comprising the step of (1) identification of the binding sites of a compound for either the different forms of the prion protein or the DNA or mRNA responsible for the expression of said proteins by site directed mutagenesis or chimeric protein studies; (2) molecular modeling of the binding site of the compound; and (3) modification of the compound to improve its binding specificity for the different forms of the prion protein or the DNA or mRNA encoding the protein.

All techniques employed in the method of the invention are conventional or can be derived by the person skilled in the art from conventional techniques without further ado. Thus, biological assays based on the herein identified nature of polypeptides or other compounds as described supra may be employed to assess the specificity of binding or potency of the potential drug/compounds wherein the inhibition or prevention of a development of prion proteins or a reduction of already developed prion proteins may be used to monitor said specificity or potency, also of the modified compounds.

For example, identification of the binding site of a polypeptide identified as said drug by site-directed mutagenesis and chimerical protein studies can be achieved by modifications in the (poly)peptide primary sequence that affect the drug affinity; this usually allows to precisely map the binding pocket for the drug.

As regards step (2), the following protocols may be envisaged: Once the effector site for drugs has been mapped, the precise residues interacting with different parts of the drug can be identified by combination of the information obtained from mutagenesis studies (step (1)) and computer simulations of the structure of the binding site provided that the precise three-dimensional structure of the drug is known (if not, if can be predicted by computational simulation), if said drug is itself a peptide, it can be also mutated to determine which residues interact with other residues in the polypeptide of interest.

Finally, in step (3) the drug can be modified to improve its binding affinity or its potency and specificity. If, for instance, there are electrostatic interactions between a particular residue of the polypeptide of interest and some region of the drug molecule, the overall charge in that region can be modified to increase that particular interaction.

Identification of binding sites may be assisted by computer programs. Thus, appropriate computer programs can be used for the identification of interactive sites of a compounds and the polypeptide by computer-assisted searches for complementary structural motifs (Fassina, Immunomethods 5 (1994), 114-120). Further appropriate computer systems for the computer-aided design of proteins and peptides are described in the prior art, for example, in Berry, Biochem. Soc. Trans. 22 (1994), 1033-1036; Wodak, Ann. N. Y. Acad. Sci. 501 (1987), 1-13; Pabo, Biochemistry 25 (1986), 5987-5991. Modifications of the drug can be produced, for example, by peptidomimetics and other compounds can also be identified by the synthesis of peptidomimetic combinatorial libraries through successive chemical modification and testing the resulting compounds. Methods for the generation and use of peptidomimetic combinatorial libraries are described in the prior art, for example in Ostresh, Methods in Enzymology 267 (1996), 220-234 and Dorner, Bioorg. Med. Chem. 4 (1996), 709-715. Furthermore, the three-dimensional and/or crystallographic structure of such compounds can be used for the design of compounds with refined binding properties (Rose, Biochemistry 35 (1996), 12933- 12944; Rutenber, Bioorg. Med. Chem. 4 (1996), 545-1558).

In accordance with the above, in a preferred embodiment of the method of the invention said compound is further refined comprising modeling said compound by peptidomimetics and chemically synthesizing the modelled compound. A most suitable starting point for modeling by peptidomimetics is to test libraries of peptides of different lengths and sequences for interfering with or preventing the development of prion proteins in a cell.

The invention further relates to a method of modifying a compound identified by the method of the invention as a lead compound to achieve (i) modified site of action, spectrum of activity, organ specificity, and/or (ii) improved potency, and/or (iii) decreased toxicity (improved therapeutic index), and/or (iv) decreased side effects, and/or (v) modified onset of therapeutic action, duration of effect, and/or (vi) modified pharmacokinetic parameters (resorption, distribution, metabolism and excretion), and/or (vii) modified physico-chemical parameters (solubility, hygroscopicity, color, taste, odor, stability, state), and/or (viii) improved general specificity, organ/tissue specificity, and/or (ix) optimized application form and route by (i) esterification of carboxyl groups, or (ii) esterification of hydroxyl groups with carbon acids, or (iii) esterification of hydroxyl groups to, e.g. phosphates, pyrophosphates or sulfates or hemi succinates, or (iv) formation of pharmaceutically acceptable salts, or (v) formation of pharmaceutically acceptable complexes, or (vi) synthesis of pharmacologically active polymers, or (vii) introduction of hydrophilic moieties, or (viii) introduction/exchange of substituents on aromates or side chains, change of substituent pattern, or (ix) modification by introduction of isosteric or bioisosteric moieties, or (x) synthesis of homologous compounds, or (xi) introduction of branched side chains, or (xii) conversion of alkyl substituents to cyclic analogues, or (xiii) derivatisation of hydroxyl group to ketales, acetales, or (xiv) N-acetylation to amides, phenylcarbamates, or (xv) synthesis of Mannich bases, imines, or (xvi) transformation of ketones or aldehydes to Schiffs bases, oximes, acetales, ketales, enolesters, oxazoiidines, thiozolidines or combinations thereof.

The various steps recited above are generally known in the art. They include or rely on quantitative structure-action relationship (QSAR) analyses (Kubinyi, 1993), combinatorial biochemistry, classical chemistry and others (see, for example, Holzgrabe and Bechtold, 2000).

Moreover, the present invention relates to a method of producing a pharmaceutical composition comprising the step of formulating the compound identified by the screening method or refined according to the method as defined herein above with a pharmaceutically acceptable carrier and/or diluent.

The term "pharmaceutical composition", as used in accordance with the present invention, comprises at least the compound as identified herein above, such as a protein, an antigenic fragment said (refined) protein, a fusion protein, a nucleic acid molecule and/or an antibody or other (refined) compounds such as small molecules as described above and, optionally, further molecules, either alone or in combination, e.g., molecules which are capable of optimizing antigen processing, cytokines, immunoglobulins, or lymphokines, optionally, adjuvants.

The pharmaceutical composition of the present invention may further comprise, depending on the formulation desired, a pharmaceutically acceptable, usually sterile, non-toxic carrier and/or diluent which are defined as vehicles commonly used to formulate pharmaceutical compositions for animal or human administration. The diluent is selected so as not to affect the biological activity of the combination. Examples of such diluents are distilled water, physiological saline, Ringer's solutions, dextrose solution, and Hank's solution. In addition, the pharmaceutical composition or formulation may also include other carriers, adjuvants, or nontoxic, nontherapeutic, nonimmunogenic stabilizers and the like. Further examples of suitable pharmaceutical carriers are well known in the art and include phosphate buffered saline solutions, water, emulsions, such as oil/water emulsions, various types of wetting agents, sterile solutions etc. Compositions comprising such carriers can be formulated by well known conventional methods. These pharmaceutical compositions can be administered to the subject at a suitable dose. Administration of the suitable compositions may be effected by different ways, e.g., orally or parenterally by intravenous, intraperitoneal, subcutaneous, intramuscular, topical, intradermal, transdermal, transmucosal, e.g. intranasai or intrabronchial, or by surgery or implantation (e.g., with the compound being in the form of a solid or semi-solid biologically compatible and resorbable matrix).

A therapeutically effective dose refers to that amount of compound which ameliorate the symptoms or condition. Therapeutic efficacy and toxicity of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED₅₀ (the dose therapeutically effective in 50% of the population) and LD5₀ (the dose lethal to 50% of the population). The dose ratio between therapeutic and toxic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50.

The dosage regimen will be determined by the attending physician and clinical factors. As is well known in the medical arts, dosages for any one patient depends upon many factors, including the patient's size, body surface area, age, the particular compound to be administered, sex, time and route of administration, general health, the individual pharmacogenetic profile and other drugs being administered concurrently. A typical dose can be, for example, in the range of 0.001 to 1000 μg (or of nucleic acid for expression or for inhibition of expression in this range); however, doses below or above this exemplary range are envisioned, especially considering the aforementioned factors. Generally, the regimen as a regular administration of the pharmaceutical composition should be in the range of 1 μg to 10 mg units per day. If the regimen is a continuous infusion, it should also be in the range of 1 μg to 10 mg units per kilogram of body weight per minute, respectively. Progress can be monitored by periodic assessment. Dosages will vary but a preferred dosage for intravenous administration of DNA is from approximately 10⁶ to 10¹² copies of the DNA molecule. The compositions of the invention may be administered locally or systemically.

The compositions comprising, e.g., the compound which is a polynucleotide, polypeptide, antibody, compound drug, pro-drug or pharmaceutically acceptable salts thereof may conveniently be administered by any of the routes conventionally used for drug administration. Administration will generally be parenterally, e.g., intravenously; DNA may also be administered directly to the target site, e.g., by biolistic delivery to an internal or external target site or by catheter to a site in an artery. Preparations for parenteral administration include sterile aqueous or non- aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.

Acceptable salts comprise acetate, methylester, sulfate, chloride and the like. The drugs may be administered in conventional dosage forms prepared by combining the drugs with standard pharmaceutical carriers according to conventional procedures. The drugs and pro-drugs identified and obtained in accordance with the present invention may also be administered in conventional dosages in combination with a known, second therapeutically active compound. Such therapeutically active compounds comprise, for example, those mentioned above. These procedures may involve mixing, granulating and compressing or dissolving the ingredients as appropriate to the desired preparation. It will be appreciated that the form and character of the pharmaceutically acceptable character or diluent is dictated by the amount of active ingredient with which it is to be combined, the route of administration and other well-known variables. The carrier(s) must be "acceptable" in the sense of being compatible with the other ingredients of the formulation and not jeleterious to the recipient thereof. The pharmaceutical carrier employed may be, for example, either a solid or liquid. Exemplary of solid carriers are lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, stearic acid and the like. Exemplary of liquid carriers are phosphate buffered saline solution, syrup, oil such as peanut oil and olive oil, water, emulsions, various types of wetting agents, sterile solutions and the like. Similarly, the carrier or diluent may include time delay material well known to the art, such as glyceryl mono-stearate or giyceryl distearate alone or with a wax.

A wide variety of pharmaceutical forms can be employed. Thus, if a solid carrier is used, the preparation can be tableted, placed in a hard gelatin capsule in powder or pellet form or in the form of a troche or iozenge. The amount of solid carrier will vary widely but preferably will be from about 25 mg to about 1 g. When a liquid carrier is used, the preparation will be in the form of a syrup, emulsion, soft gelatin capsule, sterile injectable liquid such as an ampule or nonaqueaous liquid suspension.

in a further embodiment of the invention a method of treating a subject prophylactica!ly or treating a patient which suffers from sporadic, hereditary or transmissible spongiform encephalopathies comprising administering a suitable amount of said pharmaceutical composition or the compound identified by the method of the invention or the refined or modified compound as described above to a patient in the need thereof. Examples for spongiform encephalopathies are described supra. Said embodiment comprises the use of the identified compound or the refined or modified compound as described above for the preparation of a pharmaceutical composition for prophylaxis or treatment or sporadic, hereditary or transmissible spongiform encephalopathies.

Furthermore, the present invention relates to a method for identifying an agent which specifically interacts with native, non denaturated prion protein (PrP^Sc) without crossreacting with the physiological form of the protein (PrP^c) comprising the steps of:

(a) attaching proteins of a protein suspension containing PrP^Sc onto a membrane;

(b) contacting the proteins attached to the membrane with an agent specifically interacting with PrP^Sc; and (c) detecting whether a specific interaction has occurred.

Moreover, in another embodiment the present invention relates to a method for identifying an agent which specifically interacts with denaturated prion protein (PrP^Sc), comprising the steps of:

(b) denaturating the proteins attached to the membrane;

(c) contacting the denaturated proteins attached to the membrane with an agent specifically interacting with PrP^Sc; and

(d) detecting whether a specific interaction has occurred.

In a more preferred embodiment said method further comprises the step of:

(a*) attaching proteins of a protein suspension containing the physiological form of the protein onto said membrane or a different membrane; (b*)contacting the proteins which are attached to the membrane either after denaturation in a further step or directly in its native form with an agent specifically interacting with PrP^Sc; and (c*) detecting whether a specific interaction has occurred with either PrP^Sc, the physiological form of the protein (PrP^c) or with both..

Each of steps (a^*), (b*) and (c*) may be carried out simultaneously or separately with respect to steps (a), (b) and (c).

By the presence of PrP^c on the same or a different membane to which the prion proteins are attached to, the specific interaction of the tested agents can be characterized. It can be demonstrated whether an agent specifically binds to the native form of PrP^c or PrP^Sc, to the denaturated and/or protease treated form of PrP^c and PrP^Sc or to a combination of said forms of PrP^c and PrP^Sc. Therefore, the method of the present invention provides an agent which can distinguish between the different forms of the protein. The agent identified by the method of the invention is preferably a small molecule or a peptide which can be derived from an at least partially randomized peptide library. Said agents may also comprise polypeptides such as proteins and fragments and derivatives thereof.

In a further preferred embodiment the proteins denaturated in said methods are denaturated by the use of a chaotropic agent. Said chaotropic agent is defined in a more preferred embodiment as guanidine-HCI. To ensure the denaturation of the proteins guanidine-HCI is used in concentrations in the range of 2 to 8 M (see also Example 3).

In another preferred embodiment the proteins which are attached to the membrane in step (a) of the disclosed method are treated in a step (a') prior to step (b) with a protease added in a concentration and incubated in a time range conferring iimited proteolysis. The term "limited proteolysis" is used in the context of the present invention as defined supra.

In a preferred embodiment the agent identified by the method of the invention and specifically interacting with prion proteins is an aptamer.

In another preferred embodiment the agent identified by the method of the invention and specifically interacting with prion proteins is a monoclonal antibody or fragment thereof such as a Fab, a F(ab₂)' or Fv fragment or a derivative thereof such as an scFv fragment.

Furthermore, in another preferred embodiment the agent identified by the method of the invention and specifically interacting with prion proteins is a polyclonaf antiserum.

The present invention re⁾ates in another embodiment to a method for the preparation of a hybridoma cell line comprising the steps of identifying a animal that produces a polyclonal antiserum that specifically interacts with prion proteins identified by the above disclosed method, fusion of antibody producing cells from said animal with myeloma cells to hybridomas and selecting monoclonal hybridomas producing antibodies which specifically interact with prion proteins. The method of fusion of antibody producing cells from said animal with myeloma cells to hybridomas and selecting hybridomas producing monoclonal antibodies which specifically interact with an antigen has been described first by Kδhler and Mi/stein (1975) and is known in the art, e.g. described in the manual of Harfow and Lane (Antibodies, A laboratory manual; Cold Spring Harbor Laboratory; (1988); Chapter 6). Generally, the antibody producing cells are fused with myeloma cells which comprise a metabolic deficiency such as the deficiency of the gene of the enzyme hypoxanthine-guanine phosphoribosyl transferase (HPRT). The fused cells are cultured in selection media containing hypoxanthin, aminopterin and thymidine (HAT media). Said selection will result in the survival of fused cells only, because the non-fused antibody producing cells do not have the capacity to proliferate infinitely and the HAT media is toxic for non-fused myeloma cells. The surviving hybridomas are preferably cloned and screened again for the specificity of the produced antibodies for specific interaction with the prion protein.

In another embodiment the invention relates to a monoclonal antibody produced by the hybridoma cell line obtained by the method of the invention.

In another embodiment the invention relates to the use of an agent identified by any of the described methods or the monoclonal antibody of the invention for the preparation of a diagnostic kit for the diagnosis of sporadic, hereditary or transmissible spongiform encephalopathies. Finally, the invention relates to a kit comprising the above recited agents or antibody. The_ kit will contain one ore more containers comprising the agent etc.

The figures show

Figure 1 Flow chart of the filter retention assay describing alternative procedures for the detection of PrP^Sc in brain homogenates (see specification for details). In route B1 , treatment with PK is performed on the membranes (D), whereas in B2 incubation with PK occurs in the lysates. PNS, post-nuclear supernatant. The numbers in the figure indicate as follows: 1 : addition of trypsin, needle, trypsin inhibitor, centrifugation (800 rpm, 5 min); 2: in Triton X-100/DOC, 0,5%/0,5%; 3. in Triton X-100/DOC, 0,5%/0,5%, 1% Sarkosyl; 4: centrifugation (1 ,500 rpm, 10 min) 5: incubation with DNase (1h, 37°C); 6: incubation with PK (100μg/ml, 1h 37°C): 7. centrifugation (1,500 rpm, 20 min); 8: resuspension in 0,5% Sarkosyl; 9: incubation with PK (500μg/ml, 30 min, RT).

Figure 2 Selective filter retention of PrP^Sc from mouse brain homogenates. A. 10% brain homogenates were processed as described to obtain a post-nuclear supernatant or a high speed pellet fraction in Sarkosyl buffer (Fig. 1, B1). Serial dilutions were prepared in Sarkosyl buffer and applied onto cellulose acetate (CA) or nitrocellulose (NC) filters. Amounts of wet weight of brain tissue analyzed are indictaed in μg. B. Post-nuclear supernatant from scrapie-infected brain was diluted with nine volumes of post-nuclear supernatant from control brain. The amounts indicated refer to the wet weight of scrapie-infected brain tissue present in the sample. Immunodetection was carried out after PK digestion on the membrane (Fig. 1 , D) with the anti-PrP antibody A7 and the ECL detection system.

Figure 3 Detection of PrP^Sc in mouse brain by filter retention assay and by SDS- PAGE/ Western blotting. Brain homogenates were subjected to PK treatment (Fig. 1 , B2) and serial dilutions analyzed in parallel by the filter retention assay (A) and by SDS-PAGE and Western blotting (B). PrP was detected as in Figure 2. Results were quantified by phosphorimager analysis (right panels).

Figure 4 Detection of PrP^Sc in brain extracts of BSE-infected cattle. A. Serial dilutions of PNS were filtered onto nitrocellulose membranes (0.45 μm pore size) and membrane-bound proteins subjected to limited PK digestion. B. 10% brain homogenates were mock-treated (-PK) or incubated with PK (+PK), boiled in SDS sample buffer, separated by SDS-PAGE and electrotransferred onto nitrocellulose filters (0.45 μm). Immunodetection of membrane-bound PrP was carried out with anti- PrP antiserum A7.

Figure 5 A cell culture model for the screening of anti-prion compounds. A. Detection of PrP^Sc from scrapie-infected mouse neuroblastoma (ScN2a) cells. Protein lysates from ScN2a and non-infected N2a cells were prepared and PrP was analyzed by filter retention assay. 1. Total lysate with PK digestion; 2. total lysate without PK digestion; 3. PNS; 4. high speed pellet. B. DOSPA induces degradation of PrP^Sc. ScN2a cells cultivated for 4 days were incubated in DOSPA (5 or 10 nM) or mock-treated (DOSPA, 0 nM) for additional 16 h. PNS and high speed pellets were prepared and PrP analyzed by filter retention assay. Immunodetection was carried out as descibed in Figure 2.

The examples illustrate the invention:

Example 1 : Preparation of protein extracts

Mouse brain.

Whole brains derived from CD1 mice or from clinically ill CD1 mice infected with RML prions were homogenized at room temperature in 10 volumes of PBS (phosphate- buffered saline) containing 0.25% trypsin by successive passages through 16, 18 and 20 gauge needles as known by a person skilled in the art. Trypsin digestion was stopped by the addition of trypsin inhibitor. The homogenate was then centrifuged (800 rpm, 5 min) to remove debris and connective tissue (see Fig.1 , A). When PK digestion of membrane-bound PrP was performed (see example 2) the brain homogenate was diluted to 1% (w/v) with PBS-containing Triton X-100 and deoxycholate (DOC) (0.5% each), incubated on ice for 10 min and cleared by a low speed spin (1500 rpm, 10 min) to obtain a post-nuclear supernatant (PNS). The PNS was diluted with Sarkosyl buffer (0.5% in PBS) and analyzed by the filter retention assay (see example 3). Alternatively, the PNS was subjected to a high speed centrifugation (13,000 rpm, 20 min) and the pellet resuspended in Sarkosyl buffer prior to analysis by the filter retention assay (see Fig. 1 , B1 ).

Bovine brain.

Bovine brain stem tissue of a control and a BSE-diagnosed animal was homogenized in 10 volumes Triton-X 100/DOC buffer. PNS^" were prepared and filtered through nitrocellulose membranes as known by a person skilled in the art. Detection of PrP was carried out as described for the mouse brain extracts (see example 2). For Western blotting analysis the homogenates were digested with PK (100 μg/m!,1 h at 37°C) or mock-treated, the samples boiled in SDS sample buffer seperated by SDS- PAGE , followed by electrotransfer to nitrocellulose and Western blotting (Tatzelt et al., 1996).

Cultured cells.

N2a and ScN2a cells were grown in MEM Eagle's medium supplemented with antibiotics (1 U/ml penicillin G and 1 mg/ml streptomycin) and 10% fetal calf serum. N2a cells are an immortalized neuroblastoma cell line (ATCC No CCI 131). ScN2a cells were established by infecting N2a cells with an enriched preparation of prions solated from the brains of scrapie ill mice infected with RML prions (Butler et al., 1988). For treatment with DOSPA ScN2a cells cultivated for 4 days were incubated for 16 h in DOSPA as described (Winkihofer et al., 2000). Trypsin treatment of the cells (0.25% final) was carried out on the ceil culture dish maintained on ice. After complete detachment of the cells, digestion was terminated by the addition of a 10- fold excess of soybean trypsin inhibitor (Gibco BRL) in concentrations as known by a person skilled in the art. The cells were collected by a brief centrifugation, washed twice with PBS-containing trypsin inhibitor and then protein lysates were prepared as described for brain samples. An equivalent of 10⁶ cells was used for the filter retention assay (see example 3).

Example 2: Proteinase K treatment

In homogenates.

10% homogenates were first incubated with DNase I (Roche) (1 h, 37°C) to eliminate high molecular weight DNA. Subsequently, PK (Roche) (100 μg/ml) was added, the lysates incubated for 1 h at 37°C and proteolysis terminated by the addition of

Pefabloc (Roche). After a low speed spin the resultant supernatant was analyzed for

PrP^Sc (see Fig1 , B2).

On filter.

Membranes loaded with protein were submerged in PK buffer (500 μg/ml in PBS) for 30 min at room temperature. The reaction was stopped by extensive washing (three times in PBST buffer (PBS, 0.1 % Tween)) (see Fig..1 , D).

Example 3: Filter retention and immunodetection

A commercially available slot blot device (Amersham Pharmacia Biotec, PR 648 Slot Blot Manifold) was used for the filtration of protein homogenates through nitrocellulose (0.45 μm pore size) or cellulose acetate (0.2 μm pore size) membranes (Schleicher and Schuell, Dassel, Germany). All homogenates were applied in duplicate and in a stepwise 10-fold d^' ution with Sarkosyl buffer as the diluent. After the samples were filtered through the membrane each slot was washed with 500 μl Sarkosyl buffer (see Fig.1, C). For immunodetection the membranes were incubated with 3 M guanidiniu -HCL for 10 min, washed three times in PBST and PrP was detected by the anti-PrP antibody A7 using the ECL detection system (Amersham Pharmacia Biotech) (see Fig. 1 , E).

Example 4: Filter retention assay to detect PrP^Sc in brain homogenates

A filter retention assay, as described in example 3, was developed to monitor the presence of detergent-insoluble PrP^Sc aggregates in homogenates of scrapie- or BSE-infected brains and in lysates of scrapie-infected cultured cells. Alternative strategies were employed for the preparation of protein extracts from scrapie-infected mouse brains and the selective proteolysis of PrP^c. These variations of the procedure are outlined in the flow diagram of Figure 1. Whole mouse brains were homogenized in Triton X-100/deoxycholate (DOC) detergent buffer by successive passages through 16, 18 and 20 gauge needles (Fig. 1 , step A), as described in example 1. Addition of trypsin during homogenization facilitated tissue dissociation and degraded cell surface PrP^c. After addition of trypsin inhibitor, cell debris and connective tissue were removed by centrifugation. The resulting supernatant was processed either with or without proteinase K (PK) treatment. Homogenate B1 (no PK treatment) was subjected to low speed centrifugation to prepare a post-nuclear supernatant (PNS). After addition of Sarkosyl this PNS was used directly for analysis by filtration. Alternatively, PrP^Sc aggregates were first pelleted from the PNS and then resuspended in Sarkosyl buffer. Homogenate B2 (with PK treatment) was incubated with DNase to eliminate high molecular weight DNA prior to incubation with PK. Filtration through cellulose acetate or nitrocellulose membranes was performed with a commercially available slot biot device (step C). To minimize sample handling the possibility to degrade PrP^So directly on the filter membrane after filtration of the homogenates was also explored (step D). PrP^Sc was detected by immunostaining after a brief incubation of the membranes in 3 M guanidinium-HCI to expose PrP epitopes. Said step is known by a person skilled in the art and described by Taraboulos et al. (1992).

Figure 2A shows a comparison of the PrP^Sc retention properties of cellulose acetate (CA, 0.2 μ pore size) and nitrocellulose (NC, 0.45 μm pore size) membranes oaded with PNS or resuspended high speed pellets from scrapie-infected and control brains (see Fig. 1 , B1). PK digestion was performed after filtration directly on the membranes (see Fig. 1 , D). For both membranes the assay was highiy specific for PrP^Sc in scrapie-infected mice as no signal above background was detected with control homogenates from non-infected animals. Analysis of serial dilutions of the various preparations indicated that with both membranes a clear signal was obtained with an amount of homogenate corresponding to 50 μg of wet weight of brain tissue. Sensitivity and the signal to background ratio were better for the nitrocellulose membrane. To demonstrate that the sensitivity of the filter retention assay is unaffected by the total amount of tissue analyzed, homogenates of scrapie brain were serially diluted with control homogenate, leaving the total amount of protein constant. Again, the PrP^Sc present in 100 μg of scrapie brain homogenate, now analyzed in the presence of 900 μg of control homogenate, was clearly detected by the filter retention assay (Fig. 2B).

Homogenates treated with PK before filtration (see Fig. 1 , B2) were used to compare the sensitivity of the filter retention assay with the Western blotting procedure that is frequently used for the routine detection of PrP^Sc (Fig. 3A and B). After PK digestion equivalent amounts of homogenates were either filtered through a nitrocellulose membrane (Fig. 3A) or analyzed by SDS-PAGE and electrotransfer to the same type of nitrocellulose membrane (Fig. 3B). Immunodetection of PrP on both membranes was done in parallel. Similar to the results obtained with PK treatment after filtration, an amount of PrP^Sc derived from 150 μg brain tissue was clearly detected in the filter retention assay and PrP^Sc from 15 μg of tissue was still-weakly detectable (Figure 3A, left panel). The assay gave an essentially linear response between 15 μg and 15 mg of scrapie brain tissue. In contrast, the analysis of PrP^Sc by Western blotting was at least 10-times less sensitive (Figure 3B, right panel). in summary, the filter retention assay detects PrP^Sc in brain homogenates of mice with experimental scrapie specifically and with high sensitivity. The laborious steps of SDS-PAGE and immunoblotting can be omitted. PK treatment of individual samples is circumvented, thus further minimizing sample handling and avoiding a potential source of variability. Example 5: Detection of PrP^Sc in the brain of preclinical BSE-infected cattle

To test whether the filter retention assay for PrP^Sc can also be used to detect BSE- infected cattle. Bovine brain stem tissue from a diagnosed, preclinical animal was obtained from Dr. M. Groschup (Federal Research Center for Virus Diseases of Animals, Tubingen, Germany). The most rapid procedure for sample preparation outlined in Figure 1 was chosen for this analysis. Control and BSE-infected brain tissue was directly homogenized in Triton X-100/DOC buffer as known by a person skilled in the art. Post-nuclear supernatants were prepared and serial dilutions thereof filtered through a nitrocellulose membrane. Prior to immunodetection with the A7 anti-PrP antiserum, membrane-bound proteins were subjected to limited PK digestion. PrP^Sc was specifically detected in samples derived from 100 μg of BSE- brain tissue (Fig. 4A).

To compare the sensitivity of the filter retention assay with a Western blotting approach as known by a person skilled in the art, 10% brain homogenates were digested with PK (100 μg/ml, 1 h 37°C) separated with SDS-PAGE and transferred to nitrocellulose membranes. Immunodetection was done in parallel with the same type of nitrocellulose filter used in the filter assay approach. The BSE-infected sample was clearly identified, however, with an at least ten-fold reduced sensitivity compared to the filter retention assay (Fig. 4B). Thus, the filter retention assay is capable of conveniently detecting PrP^Sc in brain stem tissue of cattle with preclinical BSE.

Example 6: A screening method for antUprion. compounds

Scrapie-infected mouse neuroblastoma (ScN2a) cells offer the possibility to study the propagation of PrP^Sc in ceil culture (Butler et al., 1988; Caughey et al., 1991; Borchelt et al., 992). We succesfully used this cell culture model to identify compounds that interfere with the accumulation of PK resistant and infectious PrP^Sc (Tatzelt et al., 1996; Winkihofer et al., 2000; Gilch et al., 2001). Notably, the lipopolyamine DOSPA at nanomolar concentrations induced degradation of pre-existing PrP^Sc aggregates in live cells within 16 hours (Winkihofer et al., 2000). In order to explore the possible use of the filter retention assay as a screening method for anti-prion compounds, we adapted the sample preparation employed for brain tissue (see Fig. 1). Total cell lystates with and without PK digestion, post-nuclear supernatants and high speed >ellets were prepared from an equal number of cells (Fig. 5A). A positive signal for PrP was only obtained with lysates prepared from scrapie-infected cells (ScN2A), indicative of the presence of PrP^Sc.

Next, ScN2a cells that had accumulated substantial amounts of PrP^Sc were incubated for 16 h with increasing nanomolar concentrations of DOSPA (Fig. 5B). As for brain homogenates, low speed supernatants and resuspended high speed pellets of ceil lysates were analyzed by the filter retention assay. With both methods a concentration-dependent decrease in the amounts of detectable PrP^Sc was observed, demonstrating the suitability of the filter retention assay as a screening method for anti-prion compounds.

References

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Claims

A method of testing for the presence of prion proteins comprising the steps of: (a) lysing cells or tissues in a solution comprising a detergent in a concentration above the critical micelle concentration (CMC);

(d) detecting whether a specific interaction has occurred.

2. The method of claim 1 , wherein the tissues are disrupted to yield isolated ceils prior to the lysing of said tissues in step (a).

3. The method of claim 1 or 2, wherein the cells or tissues are incubated prior to the lysing of step (a) with a protease in a final concentration and time range below the concentration and time range which disrupts the cell membrane.

4. The method of claim 3, wherein said protease is trypsin in a final concentration in the range of 0.1 - 1.0% (w/v).

The method of claim 1 , wherein the cytosolic and the nucleic fraction of the lysate obtained in step (a) is separated prior to step (b) and the nucleic fraction is discarded.

6. The method of claim 5, wherein the separation of cytosolic and nucleic fractions is carried out by centrifugation.

7. The method of claim 1 , wherein the protease of step (b) is proteinase K in a final concentration in the range of 50 - 1 ,000 μg/ml.

8. The method of claim 1 , wherein the proteins which were transferred onto a membrane in step (b) are denaturated in a step (b') prior to step (c).

The method of claim 8, wherein said proteins are denaturated by the use of a chaotropic agent.

10. The method of claim 9, wherein said chaotropic agent is guanidine-HCI.

11. The method of any of claims 1 to 10, wherein said agent which specifically interacts with prion proteins in step (c) is selected from the group comprising of:

(a) polyclonal antisera;

(b) monoconal antibodies;

(c) aptamers; and

(d) plasminogen.

12. The method of any of claims 1 to 11 , wherein said samples are tissue samples derived from humans or animals.

13. The method of any of claims 1 to 12, wherein said animals are mammals.

14. The method of claim 13, wherein said mammals are cattle, sheep, deer, elks, minks, hamsters, mice, canine or feline.

15. The method of claim 12, wherein said animals are fish or birds.

16. The method of any of claims 1 to 15 wherein said tissue samples are derived from neuronal or lymphatic tissue.

17. The method of any of claim 16, wherein said tissue samples are derived from brain.

18. The method of any of claims 1 to 11 , wherein said samples are derived from tissue cultures.

19. The method of any one of claims 1 to 18 wherein said prion proteins are indicative of sporadic, hereditary or transmissible spongiform encephalopathies.

20. A method for the identification of compounds which are capable of interfering with or preventing the development of prion proteins after inoculation with infectious PrP^Sc comprising the following steps:

(a) lysing cells in a solution comprising a low ionic detergent in a concentration above the critical micelle concentration (CMC);

(ba) transferring the lysate onto a membrane and treating the proteins attached to the membrane with a protease added in a concentration and incubated in a time range conferring limited proteolysis; or (bb) treating the lysate with a protease added in a concentration and incubated in a time range conferring limited proteolysis and transferring the not entirely degraded proteins of said lysate onto a membrane;

(d) detecting whether a specific interaction has occurred.

21. The method of claim 20, wherein the cells of step (a) are isolated from tissue cultures, which were infected with the infectious prion.

22. The method of claim 21, wherein the said cells are cultured and/or infected in microtiter plates.

23. The method of claim 20 or 21, wherein the cells are incubated prior to the lysing of step (a) with a protease in a final concentration and time range below the concentration and time range which disrupts the cell membrane.

24. The method of claim 23, wherein said protease is trypsin in a final concentration in the range of 0.1 - 1.0% (w/v).

25. The method of claims 20 and 21 , wherein the cytosolic and the nucleic fractions of the lysate obtained in step (a) are separated prior to step (b) and the nucleic fraction is discarded.

26. The method of claim 25, wherein the separation of cytosolic and nucleic fractions is carried out by centrifugation.

27. The method of claims 20 and 21 , wherein the protease of step (b) is proteinase K in a final concentration in the range of 50 - 1 ,000 μtg/ml.

28. The method of claims 20 and 21 , wherein the proteins which were transferred onto a membrane in step (b) are denaturated in a step (b') prior to step (c).

29. The method of claim 28, wherein said proteins are denaturated by the use of a chaotropic agent.

30. The method of claim 29, wherein said chaotropic agent is guanidine-HCI.

31. The method of claims 20 and 21 , wherein said agent which specifically interacts with prion proteins in step (c) is selected from the group comprising of:

(a) polyclonal antisera;

(b) monoconal antibodies;

(c) aptamers; and

(d) plasminogen.

32. The method of any of claims 20 to 31 , wherein all steps prior to the transfer of the proteins onto the membrane in^' step (b) are executed in microtiter plates.

33. The method of any of claims 20 to 32 wherein said compound is a small molecule or a peptide derived from an at least partially randomized peptide library.

4. A method of refining a compound identified by the method of any of claim 20 to 33 comprising the steps of:

(1 ) identification of the binding site of a compound binding to either the different forms of the prion protein or the DNA or mRNA responsible for the expression of said proteins by site directed mutagenesis or chimeric protein studies

(2) molecular modeling of the binding site of the compound; and

(3) modification of the compound to improve its binding specificity for the different forms of the prion protein or the DNA or mRNA encoding the protein.

35. A method of refining a compound identified by any of the methods of claim 20 to 34 comprising:

(a) modeling said compound by peptidomimetics; and

(b) chemically synthesizing the modeled compound.

36. A method of modifying a compound identified by any of the methods of claims 20 to 32 or refined by the methods of claim 33 to 35 as a lead compound to achieve

(i) modified site of action, spectrum of activity, organ specificity; and/or (ii) improved potency; and/or

(iii) decreased toxicity (improved therapeutic index); and/or (iv) decreased side effects; and/or

(v) modified onset of therapeutic action, duration of effect; and/or (vi) modified pharmakinetic parameters (resorption, distribution, metabolism and excretion); and/or (vii) modified physico-chemical parameters (solubility, hygroscopicity, color, taste, odor, stability, state); and/or (viii) improved general specificity, organ/tissue specificity; and/or (ix) optimized application form and route by

(i) esterification of carboxyl groups; or (ii) esterification of hydroxyl groups with carbon acids; or

(iii) esterification of hydroxyl groups to, e.g. phosphates, pyrophosphates or sulfates or hemi succinates; or (iv) formation of pharmaceutically acceptable salts; or (v) formation of pharmaceutically acceptable complexes; or (vi) synthesis of pharmacologically active polymers; or (vii) introduction of hydrophilic moieties; or (viii) introduction/exchange of substituents on aromates or side chains, change of substituent pattern; or (ix) modification by introduction of isosteric or bioisosteric moieties; or (x) synthesis of homologous compounds; or (xi) introduction of branched side chains; or (xii) conversion of alkyl substituents to cyclic analogues; or (xiii) derivatisation of hydroxyl group to ketales, acetales; or (xiv) N-acetylation to amides, phenylcarbamates; or (xv) synthesis of Mannich bases, imines; or (xvi) transformation of ketones or aldehydes to Schiffs bases, oximes, acelales, ketales, enolesters, oxazolidines, thiozolidines; or combinations thereof.

37. A method of producing a pharmaceutical composition comprising the step of formulating the compound identified by the method of any one of claims 20 to 32 or refined by the methods of claim 33 to 35 with a pharmaceutically acceptable carrier or diluent.

38. A method of treating a subject prophylacfically or which suffers from sporadic, hereditary or transmissible spongiform encephalopathies comprising administering in a suitable amount, a compound identified by the method of any one of claims 20 to 32 or refined by the methods of claim 33 to 35 to a patient in the need thereof.

39. The use of a compound identified by the method of any of claims 20 to 32 or refined by the methods of claim 33 . to 35 for the preparation of a pharmaceutical composition for the prevention or treatment of sporadic, hereditary or transmissible spongiform encephalopathies.

40. A method for identifying an agent which specifically interacts with native, non denaturated prion protein without crossreacting with the physiological form of the protein comprising the steps of:

(b) contacting the proteins attached to the membrane with an agent specifically interacting with PrP^Sc; and

(c) detecting whether a specific interaction has occurred.

41. A method for identifying an agent which specifically interacts with denaturated prion proteins, comprising the steps of:

(b) denaturating the proteins attached to the membrane;

(d) detecting whether a specific interaction has occurred.

42. The method of claim 40 or 41 , further comprising:

(a*) attaching proteins of a protein suspension containing the physiological form of the protein onto said membrane or a different membrane; (b^*) contacting the proteins which are attached to the membrane either after denaturation in a further step or directly in its native form with an agent specifically interacting with prion proteins; and (c^*) detecting whether a specific interaction has occurred with either PrP^Sc, the physiological form of the protein (PrP^c) or with both.

43. The method of claim 41 or 42, wherein said proteins are denaturated by the use of a chaotropic agent.

44. The method of claim 43, wherein said chaotropic agent is guanidine-HCI.

45. The method of any of claims 41 to 44, wherein said proteins which are attached to the membrane in step (a) are treated in a step (a') prior to step (b) with a protease added in a concentration and incubated in a time range conferring limited proteolysis.

46. The method of any of claims 40 to 45, wherein the agent which specifically interacts with prion proteins is an aptamer.

47. The method of any of claims 40 to 45, wherein the agent which specifically interacts with prion proteins is a monoclonal antibody or a fragment or derivative thereof.

48. The method of any of claims 40 to 45, wherein the agent which specifically interacts with prion proteins is a polyclonal antiserum.

49. A method for the preparation of a hybridoma cell line comprising:

(a) identifying an animal that produces a polyclonal antiserum that specifically interacts with prion proteins identified by the method of claim 48;

(b) fusion of antibody producing cells from said animal with myeloma cells to hybridomas; and

(c) selecting hybridomas producing monoclonal antibodies which specifically interact with prion proteins.

50. A monoclonal antibody produced by the hybridoma cell line obtained by the method of claim 49.

51. The use of an agent identified by any of the methods of claims 40 to 48, or the monoclonal antibody of claim 50 for the preparation of a diagnostic kit for the diagnosis of sporadic, hereditary or transmissible spongiform encephalopathies.