Title of Invention

MODULAR ANTIGEN TRANSPORTER MOLECULES (MAT MOLECULES) FOR MODULATING IMMUNE REACTIONS, ASSOCIATED CONSTRUCTS

Abstract A modular antigen transport molecule (MAT molecule) at least consisting of at least one translocation module, at least one targeting module and at least one antigen molecule, where a) the translocation module is a molecular unit which brings about transport of the MAT molecule from the extracellular space into the interior of the cell., b) the targeting module is a molecular unit which brings about transport of the MAT molecule intracellularly to the organelles which are involved in the processing of antigens or the loading of MHC molecules with antigens, and c) the antigen module is a molecular unit which at least consists of one antigen and which determines the specificity of an immune response modulated by the MAT molecule in an individual.
Full Text FORM 2
THE PATENTS ACT,
1970 (39 of 1970)
As amended by the Patents (Amendment) Act, 2005
&
The Patents Rules, 2003
As amended by the Patents (Amendment) Rules, 2005
COMPLETE SPECIFICATION
(See section 10 and rule 13)
TITLE OF THE INVENTION
Modular antigen transporter molecules (MAT molecules) for modulating immune reactions, associated constructs
INVENTORS
1) Name : Lamping, Norbert
Nationality: German National
Address : Siegesstrasse 8, 30175, Hanover, Germany
2) Name : Crameri, Reto
Nationality : Swiss National
Address : Promenade 137A, CH-7260 Davos-Dorf, Switzerland
3) Name : Flueckiger, Sabine
Nationality: Swiss National
Address : Oberwiesstrasse 6, CH-7270 Davos-Platz, Switzerland
4)Name : Daigle, Isabelle
Nationality : Swiss Nationality GRANTED

17-1-2008

Address : Farbistrasse 1, CH-7270 Davos-Platz. Switzerland
APPLICANTS
Name : IMVISIONGMBH
Nationality : A Germany Company
Address : Feodor-Lynen-Strasse 5, 30625 Hannover, Germany
PREAMBLE TO THE DESCRIPTION
The following specification particularly describes the nature of this invention and the manner in which it is to be performed:
1 7 JAN 2008

Modular antigen transporter molecules (MAT molecules) for modulating immune reactions, associated constructs, methods and uses
Technical field of the invention
The invention is concerned with stimulation and inhibition of the immune system for prophylaxis, therapy or diagnosis of disorders associated with an immune system which is insufficiently stimulated or is excessively stimulated. These disorders include inter afia infectious diseases, neoplastic diseases, allergies, autoimmune diseases, transplant rejection reactions etc. The core of the invention is a novel method with which the immune system is influenced by giving a MAT molecule that consists at least of the three following constituents:
1. a translocation module which has the effect that the MAT{molecule\can

penetrate into cells from the outside,
2. an intracellular targeting module which has the effect that the MAT
molecule is processed within the cell in such a way that there is an altered immune response or an altered presentation of the antigen, and 3. an antigen module which determines the specificity of the modulated immune response.
Combination of these three elements to give a MAT molecule makes it possible for the imrmmesystem of the treated individual to be modulated in a targeted and specific manner, or makes it possible for the presentation of the antigen by the antigen-presenting cell to be altered.
Prior art
Processing of antigens by antigen-presenting cells
The processing of antigens by antigen-presenting cells (APC) takes place by two different routes. Antigens occurring inside the cell are presented by MHC I (major histocompatibility complex class I, MHC class I) molecules on the cell surface, whereas extracellular antigens are presented by MHC IT (major histocompatibility complex class II, MHC class II) molecules on the cell surface. Both mechanisms initiate an immune reaction by the host to the antigen. The route taken by the antigen
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from uptake into the cell until presentation on the cell surface in the form of an MHC H-antigen complex proceeds via various cell organelles, inter alia via the endoplasmic reticulum, the Golgi apparatus, the trans-Golgi network, lysosomes, endosomes and via MHC class II compartments (MIIC). The MIICs play an important part in the MHC Il-mediated antigen presentation. In these organelles of the cell, the MHC II molecules are loaded with low molecular weight antigens or with proteolytic fragments of proteins. In this process, the invariant chain (also called MHC II gamma chain or Ii) which is initially bound to the MHC II molecule undergoes proteolytic degradation, and the antigen is bound to the MHC II molecule under the regulation of various proteins which bind directly or indirectly to MHC II [1]. These regulatory molecules include inter alia HLA-DM, HLA-DO, LAMP-1, LAMP-2, CD63, CD83, etc. The exact function of these proteins is in part unexplained as yet, but many of them have signal sequences which promote their transport to the lysosomes, to the endosomes, to the trans-Golgi network, to the MIICs etc. [2-4]. A number of proteases are involved in the proteolytic reactions necessary so that the antigen can be presented on MHC II molecules. The proteases present in MIICs include inter alia various members of the cathepsin family such as, for example, cathepsin S and cathepsinL [1].
Targeting and targeting sequences
Amino acid sequences which have the property of accumulating inside or outside a
cell specifically at a particular site or in a particular cell organelle are frequently
referred to as targeting sequences. It should be emphasized in this connection that
various types of targeting can be distinguished. In particular there is a distinction
between intracellular and extracellular targeting. For extracellular targeting, for
example antibodies which bind from outside to directly accessible structures on the
cell surface, e.g. to the extracellular portion of membrane proteins, are used. An
antibody which binds a protein on the cell surface of tumor cells can be coupled for
example to a cytotoxin. This antibody then brings about an extracellular targeting of
the cytotoxin for the tumor cell, thus making targeted killing of the latter possible.
This type of targeting is fundamentally different from intracellular targeting, in which
it is often necessary to overcome intracellular membranes or in which the targeting
sequence is bound by intracellular receptors and thus penetrates for example into
particular cell organelles, or in which the targeting sequence can penetrate the specific
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channels, formed by specific proteins, into the cell organelle for which the targeting sequence is specific. If a targeting sequence or a targeting module is mentioned below in the present patent application, it is in principle always intracellular targeting and not extracellular targeting which is meant thereby, In addition, in the present patent application, targeting does not mean every type of intracellular targeting, but means only intracellular targeting which serves to transport molecules to organelles or intracellular regions involved in the processing, modification and/or binding of antigens to MHC molecules. Examples of such organelles or intracellular regions are the endoplasmic reticulum, the Golgi apparatus, the trans-Golgi network, endosomes, lysosomes and MIICs. Targeting sequences derived from various proteins are described in the literature [1-5].
Translocation and translocation sequences
In addition, numerous amino acid sequences, especially derived from viruses, e.g. HIV tat or the protein VP22 which is derived from herpes simplex virus, which promote the transport of proteins, peptides and other classes of substances, such as, for example, nucleic acids or pharmaceutically active substances, into the interior of cells are known from the literature. For this purpose, these so-called translocation sequences are linked to the molecules to be transported (also called cargo molecules) either via covalent or via noncovalent linkages. Extracellular addition of the resulting compounds of translocation sequence and cargo molecule to cells is then possible. The translocation sequence then brings about entry of the cargo molecule into the interior of the cell. This principle has likewise been described in numerous studies, especially for the HIV Tat sequence [6-8],
Although it was already possible and intended to use an antigen as cargo molecule, it has as yet not been possible with the aid of the known translocation means alone to generate an immune response in an individual in a sufficiently targeted and dosed manner as appears desirable for certain tasks - for example allergy desensitization. Hence there is a need for further methods for targeted immunomodulation.
Object of the invention
It is therefore the object of the invention to provide means for supplying any of a wide
variety of antigens in a sufficiently targeted manner to their processing site that even

better therapeutic and diagnostic use thereof is possible.
Achievement of the object
/The invention provides a method which makes it possible for antigens to be supplied
in a very targeted manner tocells in order to achieve an efficient, specific immune
reaction. The method makes it possible firstly to convey antigens efficiently from the lextracellular space to the intracellular space of the cell, and makes it possible secondly for the antigens, when they have arrived in the interior of the cell, to reach efficiently the cell organelles in which they are further processed for antigen presentation. This two-stage process can be utilized very generally for the targeted, efficient modulation of the immune reaction of an individual.
Special molecules have been developed as tool for achieving these effects and are referred to below in this patent application as "modular antigen transporter" molecules or MAT molecules. These MAT molecules, associated nucleic acids, vectors, cells, cell lines, vesicles, immunoglobulins, and uses and methods which belong to the invention and which relate to these constituents or operate with them are characterized in detail in the claims.
A previously undescribed combination of at least three modules to give a novel class of molecules, which are referred to as MAT molecules (modular antigen transport molecules), is provided to achieve the object. These three modules include at least one translocation module, at least one targeting module and at least one antigen module. The three different modules are coupled to one another via covalent or noncovalent linkages. The MAT molecule prepared in this way can be administered directly to an individual whose immune reaction to the antigens present in the MAT molecule is to be influenced. Alternatively, it is also possible for cells to be treated with MAT molecules in vitro, and for the cells thus treated subsequently to be administered to the individual. In this method, the translocation modules have the effect that the MAT molecule can penetrate into the cell, the targeting modules have the effect that the MAT molecule undergoes intracellular processing so that there is an immune response, and the identity of the antigens in the antigen modules determines the antigen against which the immune reaction is directed. A substantial advantage of this
novel method for modulating the immune response of an individual is in particular its
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universal applicability, i.e. it can operate with a wide variety of antigens, various translocation modules and various targeting modules. In addition, the use of a translocation module results in the method not being tissue- or cell-specific, but being suitable universally for immunomodulation of virtually all types of cells. A further advantage is the modular structure of the MAT molecule. The modular structure permits the MAT molecule to adapt quickly to the particular medical requirements. It is also possible to vary the exact arrangement of the three constituents of the MAT molecule and the nature of their connection together, as long as at least one module of all three types of modules is present in the MAT molecule. There are no restrictions relating to the antigens on the basis of the method. The method can be used for example for activating the immune system of an individual against pathogens such as, for example, against viruses, bacteria, parasites, etc., i.e. very generally as vaccine. In addition, the method can be used to activate the immune system against degenerate cells such as, for example, tumor cells, etc. However, it can also be used on the other hand for desensitization of the immune system of an individual against allergens such as, for example, pollen, animal hair, house dust mites, insect toxins, etc. or for targeted suppression of the immune system, e.g. if autoimmune reactions are present, such as, for example, arthritis, rheumatism, diabetes, SLE (systemic lupus erythematosus), etc., and for suppressing transplant rejection reactions. Further disorders which are not expressly mentioned and which are associated with an immune reaction which is too strong or too weak can likewise be treated with the MAT molecules of the invention.
It has to date in the prior art frequently been regarded as very disadvantageous that translocation sequences are not specific for particular types of cells, but are equally active in all types of cells [9]. However, in the present invention, the universal functionality of translocation modules is a great advantage which has not been realized in the prior art to date. It has often been attempted in the prior art to date to protect "cargo molecules", which are inserted into cells with the aid of translocation sequences, from proteolytic degradation in the cell [9]. In the present invention it is exactly the opposite which is expressly desired and advantageous for the mode of action of the invention. Proteolytic degradation of the antigen modules in the cell is advantageous for the effect of the invention, i.e. for efficient antigen presentation. The targeting modules therefore employed in the present invention specifically promote
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the transport of the antigen modules into cell compartments where they undergo proteolytic degradation.
The best-known amino acid sequences which can be used as translocation module for the purposes of the invention are the HIV Tat and the VP22 sequence. It is described for these sequences that they bring about both a translocation through the cell membrane and a transport into the cell nucleus [7], This transport into the cell nucleus is undesired in connection with the present invention, because no antigen processing takes place in the cell nucleus, and thus efficient antigen presentation does not occur. This previously unsolved problem is solved by the present invention through the use of a targeting module that has the effect that the MAT molecule is not transported intracellularly into the cell nucleus, but is transported specifically into those organelles in which antigen processing or the loading of MHC molecules with antigen take place. The intracellular translocation module of the MAT molecules of the invention therefore eliminates a substantial disadvantage shown by Tat antigen fusion proteins disclosed in the prior art to date.
Also known in the prior art to date are fusion proteins consisting of a targeting sequence, e.g. the invariant chain of the MHC II molecule, and of an antigen. However, these fusion proteins are incapable of efficient penetration into antigen-presenting cells. For this, when they are used for immunizing an individual, additionally an adjuvant that promotes uptake of the fusion protein into the cell is necessary. These adjuvants such as, for example, mineral oil, mycobacterial extracts or Freund"s adjuvant have, however, unwanted side effects such as, for example, local inflammatory reactions. The MAT molecules used in the present invention now have the advantage over conventional vaccines that they are coupled directly to a physiologically well-tolerated translocation module that very effectively promotes uptake into cells. It is thereby possible in some circumstances to dispense wholly or partly with additional adjuvants. The result of this is that distinctly fewer unwanted side effects will occur with immunizations using MAT molecules.
It has long been known that extra- or intracellular MHC I presented antigens lead to a cytotoxic immune response, but not to a strong protective humoral immune response. However, it is possible through the use of MAT molecules for the antigens present in
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the antigen module to be added extracellularly, but they act like intracellular antigens, because the translocation module transports the antigen into the intracellular space, and the targeting module influences intracellular transport of the antigen in such a way that there is a humoral immune response. It is possible through this novel method to achieve the strong induction, which has been desired for many years, of a humoral immune response with antigens added extracellularly (MAT molecules).
For this purpose, in contrast to the prior art to date, two mechanisms known per se are combined in a novel way in this invention, so that immunization with antigens is substantially improved. These mechanisms are in both cases targeted antigen transport mechanisms which overall lead to a very efficient immune response. Each of these two transport mechanisms is brought about by a defined module of the MAT molecule. Those concerned are:
1. transport of the antigen from the extracellular space into the intracellular space
(translocation module)
in combination with >
2. transport of the antigen within the cell specifically to the organelles
responsible for antigen processing
(targeting module)
This leads to the result: very efficient immunization, only IgG, no IgE
This novel combination of 2 known transport mechanisms leads to the possibility of immunization for example with much lower antigen concentrations, and additionally has the very great and surprising advantage that an immune response of the Thl type mainly occurs, i.e. an immune response in the form of IgG antibodies and not in the form of allergy-causing IgE antibodies.
Description of the invention in detail
Translocation sequences/translocation modules
The terms translocation sequence and translocation module are used side by side in
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the text of the present application as equivalent and having the same meaning. The term translocation module was introduced in order to make it clear that translocation modules are only one part of a MAT molecule for the purposes of the invention. In addition, translocation modules represent not only naturally occurring translocation peptide sequences such as, for example, HIV tat, but also, for example, peptidomimetics or other structures which are able to undertake the same function as the naturally occurring translocation peptide sequences.
The invention includes the use of various translocation modules for preparing MAT molecules which consist at least of one translocation module, at least one targeting module and at least one antigen module. In general, all translocation sequences which are currently known and will be known in future are suitable to be used for the purposes of the present invention. Numerous suitable translocation sequences are described in the literature. These translocation sequences include viral sequences, homeoprotein sequences, leucine zipper sequences, arginine- and lysine-rich sequences, and various other sequences of proteins which are secreted despite the absence of a secretion signal sequence, etc.
Viral peptide sequences suitable as translocation modules
The peptide sequences suitable as translocation modules for the purposes of this
invention include inter alia viral proteins or partial sequences of viral proteins such as,
for example, the protein HIV transcriptional activator protein (HIV tat). The suitable
Tat proteins include besides the Tat protein of the HIV-1 virus also the Tat proteins of
other lentiviruses [9]. Numerous modified Tat peptides have been described as
sequences able to bring about translocation. These include Tat peptides which
represent only partial sequences of the Tat protein [10], Tat peptides which comprise
point mutations [10], Tat peptides in which the sequence is reversed (inverted) [10],
or Tat peptides which comprise unusual amino acids such as, for example, D isomers
of amino acids [10], etc. All these variations of peptide sequences are therefore
generally suitable as translocation modules. Peptides also suitable for the purposes of
the present invention as translocation modules are those derived from other viruses
such as, for example, VP22 (herpes simplex virus-1 VP22 tegument protein) [9]. At
present, commercial expression vectors comprising a VP22 sequence suitable for
translocation are also available. These expression vectors therefore permit VP22
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fusion proteins to be prepared (Voyager VP22 system, Invitrogen, Breda, the Netherlands). However, no targeting module is present in the fusion protein on use of this expression system. Other viruses, e.g. Marek"s disease virus-1, a virus which causes lymphoma in chickens, also express a protein which is related to VP22 and which is likewise suitable as translocation module [11]. These proteins and partial sequences of these proteins are mentioned only as examples, and numerous further peptides are known at present, and will become known in future, which are suitable as translocation modules for the purposes of the invention.
Homeoproteins suitable as translocation modules
A further group of translocation modules suitable for the purposes of the present invention are peptides derived from the drosophila homeotic protein antennapedia (ANTp) [9]. Among others, ANTp peptides suitable as translocation module are those comprising an inverted sequence of ANTp [7], comprising D isomers of amino acids [7], or comprising point mutations in their sequence [7], It is additionally expected that numerous further ANTp sequence modifications are also possible and will presumably make translocation possible [7]. ANTp peptide variants are also referred to as transport peptides. Further homeoproteins such as, for example, engrailed 1 (Enl), engrailed 2 (En2), Hoxa-5, Hoxc-8, Hoxb-4 and KNOTTED-1 [7] likewise comprise sequences which can be used as translocation module for the purposes of the present invention. KNOTTED-1 is in fact a plant protein, but is likewise suitable as translocation module in animal cells. These peptides are mentioned only as examples, and numerous further homeoproteins which comprise peptide sequences which may be suitable as translocation module for the purposes of the invention are known [12]. Further previously undisclosed homeoproteins may also comprise sequences suitable as translocation module.
Leucine zipper proteins suitable as translocation module
A further group of sequences suitable as translocation module for the purposes of the
present invention are peptides comprising a leucine zipper domain. Examples of
proteins whose leucine zipper domains can be used as translocation sequence are, for
example, human cFos-(139-164), human cJun-(252-279), or the yeast transcription
factor yeast GCN4-(231-252) [8]. Further leucine zipper proteins already known or
which will become known in future are likewise suitable as translocation module for
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the purposes of the invention.
Arginine- or lysine-rich peptides suitable as translocation module
Arginine-rich peptides, frequently derived from RNA- and DNA-binding proteins, represent further peptide sequences which can be used as translocation modules for the purposes of the present invention. Examples of such sequences are HIV-1 rev-(34-50), flock house virus coat protein FHV coat-(35-49), BMV Gag-(7-25), HTLV-II Rex-(4-15), CCMV Gag-(7-25), P22 N-(14-30), lambda N-(l-22), phi 21 N-(12-29) and PRP6-(129-144) from yeast [8]. It is likewise possible to use for the purposes of the invention polyarginine peptides having 4 to 16 [8] or else having more than 16 arginine residues. In addition to polyarginine peptides, peptides which can also be used as translocation modules are those which, besides arginine, also comprise further amino acids, e.g. the W/R peptide (RRWRRWWRRWWRRWRR [9] or the R9-Tat peptide in which the 9 central amino acid residues of the total of 11 amino acids of a Tat peptide have been replaced by arginine residues (GRRRRRRRRRQ) [8]. It has additionally been possible to show that peptides which for example consist of nine lysine residues also have the ability to act as translocation module for the purposes of the invention [13], These peptides are mentioned only as examples and numerous further arginine- or lysine-rich peptides are suitable to be used as translocation module for the purposes of the invention [8, 13]. Further arginine- or lysine-rich peptides currently already known or to become known in future are presumably also suitable as translocation module. Sequences comprising guanidino or amidino groups are also suitable as translocation module for the purposes of the present invention [14].
Proteins without signal sequence which are suitable as translocation module A number of further proteins have the ability, without a secretion signal sequence being present, to penetrate the cell membrane from the inside to the outside, i.e. be secreted. These proteins are frequently also able conversely to penetrate into the interior of the cell from the outside. These proteins or partial sequences of these proteins can thus also be used as translocation modules for the purposes of the present invention. Some exemplary examples of such proteins are fibroblast growth factor 1 (FGF-1), fibroblast growth factor 2 (FGF-2), caveolin-1, lactoferrin, thioredoxin,
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interleukin 1 beta and ciliary neurotrophic factor (CNTF) [7], or interleukin 1 alpha, vas deferens protein, platelet-derived endothelial cell growth factor (PR-ECGF), thymosin, para-thymosin, 14.5 kDa lectin (L14), transglutaminase, thioredoxin-like protein (ADF), sciatic nerve growth-promoting activity, factor XHIa, mammary-derived growth inhibitor, galectin, rhodanase [15]. These peptides are mentioned only as examples, and numerous further peptides are known or will become known in future which are suitable as translocation module for the purposes of the invention.
Toxins suitable as translocation module
Many toxins or partial sequences of toxins have the property of acting as translocation module, such as, for example, following toxins: complete abrin, complete ricin, complete modeccin, complete pseudomonas exotoxin A, complete diphtheria toxin, complete pertussis toxin, complete Shiga toxin, the A chain of ricin, the A chain of abrin, the A chain of modeccin, the enzymatically active domain of pseudomonas exotoxin, the A chain of diphtheria toxin A, the enzymatically active domain of pertussis toxin, the enzymatically active domain of Shiga toxin, gelonin, pokeweed antiviral protein, saporin, tritin, barley toxin and snake venom peptides [16]. These toxins mentioned as examples, and many further other toxins not expressly mentioned or toxins to become known in future can be used as translocation module for the purposes of the present invention. Controlling the efficiency of translocation modules
The efficiency of translocation can be controlled by varying the length of, for example, a poly-arginine chain or by specific selection of, for example, only a partial sequence of the HIV Tat sequence, so that very efficient translocation of the corresponding MAT molecule, or a less efficient translocation takes place, depending on the particular requirements [8, 13], A very efficient translocation may have the advantage that the efficacy of the MAT molecule is increased and/or that the necessary dose of MAT molecule can be reduced, in turn saving vaccine costs. A reduced dose of MAT molecule in turn has the advantage that fewer side effects occur. On the other hand, a reduced efficiency of translocation makes it possible for the MAT molecules to be distributed widely in the treated individual, e.g. after intravenous injection, because they do not immediately penetrate locally and virtually quantitatively into all cells located in the vicinity.
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Examples of minimal sequences acting as translocation module It is not necessary for all the translocation sequences mentioned as examples to be in the form of the complete protein as constituent of the MAT molecule in order to be effective as translocation module for the MAT molecule for the purposes of the invention. On the contrary, a minimal sequence region which can be used as translocation sequence is known for many of said proteins. This sequence region includes for example for HIV Tat for example the following sequence: Tyr-Gly-Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg, for VP22 the following sequence: Asp-Ala-Ala-Thr-Ala-Thr-Arg-Gly-Arg-Ser-Ala-Ala-Ser-Arg-Pro-Thr-Glu-Arg-Pro-Arg-Ala-Pro-Ala-Arg-Ser-Ala-Ser-Arg-Pro-Arg-Arg-Pro-Val-Glu and for antennapedia the following sequence: Arg-GIn-Iso-Lys-Iso-Trp-Phe-Gln-Asn-Arg-Arg-Met-LysTrp-Lys-Lys [17]. It is additionally possible for the sequences also to be used in the form of fragments which do not correspond to the currently known minimal functional sequence segments, as long as the resulting sequence is still functional for the purpose of the translocation module.
Translocation modules need therefore not be in the form of the complete protein or the complete molecule as constituent of the MAT molecule in order to be effective as translocation module for the MAT molecule for the purposes of the invention. On the contrary, a sequence region which can be used as translocation module is known for example for some of the proteins mentioned. In addition, the protein sequences may also be used in the form of fragments which do not correspond to the previously disclosed functional sequence segments, as long as the resulting sequence is still functional as translocation module. Testing of the functionality of a translocation module can be ascertained for example by using fluorescence-labeled translocation modules or by using enzyme-labeled translocation modules or by using translocation modules labeled with metal particles. The translocation modules labeled in these ways are administered to an experimental animal or to cells cultivated in vitro, and the fate of the translocation modules is followed using methods such as FACS (fluorescence activated cell sorting), microscopy, confocal fluorescence microscopy, electron microscopy etc. These techniques for checking the functionality of translocation modules are described in the literature, and some of them have already been used to ascertain the functionality of sequences for translocation [8, 18].
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Targeting sequences/targeting modules
The terms targeting sequence and targeting module are used side by side in the text of the present application as equivalent and having the same meaning. Targeting in principle always means intracellular targeting in this patent application. The term targeting module was introduced in order to make it clear that translocation modules are only one part of a MAT molecule for the purposes of the invention.
The invention includes the use of various sequences as targeting modules for preparing MAT molecules which consist at least of one translocation module, at least one targeting module and at least one antigen module. In general, all amino acid sequences and molecules which are currently known and will become known in future and which are able to mediate targeting are suitable to be used as targeting modules for the purposes of the present invention. Numerous suitable sequences are described in the literature. Sequences included in these sequences suitable as targeting module are all those which have the effect that the MAT molecule is transported intracellularly to the sites or organelles within a cell at which processes involved in the presentation of the antigen modules present in the MAT molecule take place. These sites and organelles within the cell include, in particular, MHC class II compartments (MIICs), endosomes, lysosomes, the Golgi apparatus, the trans-Golgi network and the endoplasmic reticulum. These intracellular organelles are involved in processes such as, for example, the transport or processing of antigens, the preparation and loading of MHC II molecules with antigens or processed antigens, and the transport of the MHC II molecules loaded with antigens to the cell surface etc.
MHC molecules comprising sequences suitable as targeting module
A number of sequences are suitable in particular as targeting modules for the purposes
of the invention. The invariant chain of the MHC II molecule (Ii, invariant chain,
MHC II gamma chain) is the sequence described most often in the literature as being
able to mediate targeting. Various variants of the invariant chain in humans are
described and are also referred to as IiP33, IiP41, HP35 and IiP43 [1] and which are
suitable as targeting modules. Further sequences suitable as targeting module for the
purposes of the invention are the beta chain of the MHC II molecule [19]. Fragments
of said sequences are also suitable as targeting module.
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Lysosomal membrane proteins comprising sequences suitable as targeting module A number of membrane proteins which occur in lysosomes and are one of the major protein constituents there have sequence motifs which bring about targeting for the lysosome. This group of proteins includes inter alia Lamp 1 (lysosomal-associated membrane protein-1), Lamp 2, Lamp 3, Limp II (lysosomal integrated membrane protein II) and LAP (lysosomal acid phosphatase) [4]. These and other lysosomal proteins which are currently known or are to become known in future and which have targeting sequence motifs can be used as targeting modules for the purposes of the invention, it being possible to use the complete protein sequence or partial sequences thereof as targeting module.
Tetraspan proteins comprising sequences suitable as targeting module The members of a family of proteins which have four membrane-spanning domains (tetraspan proteins) are likewise suitable as targeting modules for the purposes of the invention, because these proteins enter MIIGs very efficiently. The mechanism by which "tetraspan" proteins enter MIICs is unclear because they comprise no known amino acid sequences which make targeting possible. Despite this, there are mechanisms which transport these proteins into the MIICs, meaning that they can be used as targeting modules for the purposes of the present invention. The family of "tetraspan" proteins includes CD37, CD53, CD63, CD81, CD82 and CD86 [20], It is known for CD63 and CD82 that they associate with MHCII, HLA-DO and HLA-DM molecules [20]. "Tetraspan" proteins are likewise present in the membranes of exosomes. Exosomes are vesicles which are formed after fusion of MIICs with the plasma membrane and thus are released by the antigen-presenting cell. Exosomes comprise MHC II molecules and are able to present antigens and thus stimulate T cells [20]. Further proteins which are very similar to the "tetraspan" protein family, and which are therefore likewise suitable as targeting module for the purposes of this invention, are the Schistosoma mansoni membrane protein SM23 and the tumor-associated antigen CO-029 [21]. Further tetraspan proteins, or partial sequences of tetraspan proteins, not expressly mentioned or currently as yet unknown may likewise comprise sequences which are suitable as targeting modules.
Further proteins having sequences suitable as targeting modules
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Numerous further proteins are to be found in the endosomal/lysosomal compartment of various cell types and therefore reach it via certain mechanisms which are currently known only in part. These proteins or partial sequences of these proteins are accordingly also suitable to be used as targeting modules for the purposes of the present invention. These proteins present in the endosomal/lysosomal compartment include inter alia the low density lipoprotein (LDL), insulin, epidermal growth factor (EGF), polymeric immunoglobulin, transferrin, the cation-dependent mannose 6-phosphate receptor, the cation-independent mannose 6-phosphate receptor, CD3, etc. [21], and CDlb [22], and many further proteins or protein sequences which are currently known or to become known in future and which permit targeting into the endosomal/lysosomal compartment. These sequences can be used as targeting module for the purposes of the invention. Various commercial suppliers supply expression vectors comprising nucleic acid sequences which code for sequences suitable for targeting. For example, both BD Bioscience Clontech (Palo Alto, CA, USA) and Stratagene (La Jolla, CA, USA) supply expression vectors with targeting modules which guide the resulting fusion protein to the Golgi apparatus or to the peroxisomes. However, these expression vectors do not allow fusion proteins comprising a translocation module to be prepared, so that they differ from the MAT molecules of the invention, hi the Clontech vectors for example a sequence of calreticulin (KDEL "retrieval sequence") is used for targeting the fusion protein to the Golgi apparatus. Further proteins which are not expressly mentioned or are currently as yet unknown may likewise comprise sequences suitable as targeting modules for the purposes of the invention.
Sequence motifs which occur in certain groups of targeting sequences Certain sequence motifs have been ascertained to be important for the function of various protein sequences as targeting module. For the beta chain of HLA-DM for example the sequence motif tyrosine-threonine-proline-leucine has been identified as targeting motif, with the tyrosine residue and the leucine residue apparently being of particular functional importance [2]. Tyrosine motifs important for intracellular targeting have been identified for various lysosomal membrane proteins such as LAP (lysosomal acid phosphatase), Lamp 1 (lysosomal associated membrane protein 1), Lamp 2 and Lamp 3 [3, 4] and for CDlb [22]. It was possible to identify a leucine motif important for intracellular targeting for a further lysosomal protein, Limp II
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(lysosomal integrated membrane protein II) [4], It was possible to show for Ii that two sequence regions are important independently of one another for the intracellular targeting (amino acid position 1 to 11 and position 12 to 29) [23]. Both targeting sequences are functional even on their own, land the sequence 1 to 11 comprises a functionally essential leucine-isoleucine motif at position 7 and 8 [23]. The beta chain of the MHC II molecule likewise comprises a sequence motif which comprises one or two functionally important leucine residues, and a conserved glycine residue is located N-terminally directly preceding this leucine motif [19]. In summary, accordingly, leucine and tyrosine residues in particular have an important function in targeting sequences and it is therefore possible to design specifically appropriate amino acid sequences as targeting modules. These can be used as targeting modules for the purposes of the invention.
"Non-amino acid structures" which can be used as targeting modules Molecules which do not correspond to an amino acid sequence or an amino acid can also be employed as targeting modules for MAT molecules for the purposes of the invention. An example which has long been known for a structure suitable for targeting in lysosomes is, for example, mannose 6-phosphate [24]. Proteins which comprise mannose 6-phosphate residues are transported by various mannose 6-phosphate receptors to the lysosomes. This mechanism can be used for the purposes of the invention to transport the MAT molecule into the lysosomes in order thus to achieve efficient presentation of the antigen. For this purpose, mannose 6-phosphate residues can be coupled covalently or noncovalently, alone or as constituent of more complex sugar structures, to the MAT molecule. It is generally possible to use all ligands of mannose 6-phosphate receptors as targeting modules for MAT molecules for the purposes of the present invention. Further currently known structures or structures to become known in future, which make it possible to target MIICs, endosomes, lysosomes, the Golgi apparatus, the trans-Golgi network or the endoplasmic reticulum, can be used as targeting module for the purposes of the invention.
All the targeting modules mentioned by way of example need not be in the form of
the complete protein or the complete molecule as constituent of the MAT molecule in
order to be effective as targeting module for the MAT molecule for the purposes of
17

the invention. On the contrary, a sequence region which can be used as targeting module is known for example for some of the proteins mentioned. In addition, the protein sequences mentioned by way of example may also be used in the form of fragments which do not correspond to the previously disclosed functional sequence segments, as long as the resulting sequence is still functional as targeting module. Testing of the functionality of a targeting module can be ascertained for example by using fluorescence-labeled targeting modules or by using enzyme-labeled targeting modules or by using targeting modules labeled with metal particles. The targeting modules labeled in these ways are administered to an experimental animal or to cells cultivated in vitro, and the fate of the targeting modules is followed using methods such as FACS (fluorescence activated cell sorting), microscopy, confocal fluorescence microscopy, electron microscopy etc.
Antigen modules
It is possible to employ as antigen modules for the purposes of the invention in
principle all types of antigens able to modulate an immune response. Both antigens
currently already known and antigens to be discovered in future are suitable. In some
circumstances, the antigens may also be those which do not lead to an immune
response with conventional immunization methods known in the art at present but
which lead on application of the novel method described in the present patent
application to an immune response by the individual. It is possible to use not only
proteins and peptides, but also sugar structures, lipids, e.g. lipopolysaccharides,
lipoteichoic acids and other constituents of bacterial membranes (CDlb binds, for
example, sugar structures and lipids), nucleic acids such as, for example, DNA
comprising CpG motifs, organic substances such as, for example, latex or
pharmaceutically active substances as antigen for the purposes of the invention. The
antigen may be derived from humans, animals, plants, fungi, parasites, unicellular or
multicellular microorganisms, viruses and other life forms. The antigens may have
been isolated from biological material, have been prepared as recombinant antigens or
have been prepared by synthesis, e.g. by peptide synthesis. Synthetically prepared
antigens may be substances which occur in nature or which do not occur in nature but
are obtainable by chemical synthesis. Examples of non-naturally occurring substances
which are, however, suitable as antigen in some circumstances are, for example,
synthetically prepared substances which are present in medicaments, or synthetic
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peptides having amino acid sequences which do not occur in nature, or peptidomimetics, etc. Naturally occurring or synthetic or recombinant antigens can be modified by molecular-biology, enzymatic, chemical and other methods in order to confer on them properties which are more advantageous for the particular application. These advantageous properties may be, inter alia, a higher or lower activity as antigen, a broader or a more specific action as antigen, a better solubility in hydrophilic or hydrophobic solvents, a greater permeability of the antigen modules for cell membranes, for membranes of organelles, for the blood-brain barrier, for the blood-CSF barrier etc., a higher or lower half-life in vivo or in vitro, a lower or higher toxicity, a better detectability of the antigen in vivo or in vitro after application of the antigen in the form of a MAT molecule etc. It is additionally possible for the purposes of the invention to combine a plurality of antigens in an antigen module [25]. For this it is possible for identical antigens to be present in more than one copy in the antigen module, or it is possible for example for different variants of the same antigen to be combined in an antigen module. Combination of antigens, e.g. of antigen 1, and other antigens, e.g. of antigen 2, in an antigen module is also possible, etc. Further combinations such as, for exampki antigen 1 in more than one copy and antigen 2 in a single copy may also be combined in an antigen module, etc. It is additionally possible also for one or more different and/or one or more identical antigen modules to be present in a MAT molecule. It is possible in principle for all possible combinations of singly and multiply present identical or altered copies of antigens derived from one or more different antigen to be combined for the purposes of the invention.
Antigens and allergens which can be used as antigen module
Numerous antigen, in particular allergens, have been described in the literature to
date. The allergens specifically known hereinafter can be used as antigen module for
the purposes of the invention. Further allergens and variants of allergens which can
likewise be used as antigen module for the purposes of the invention are known in the
art [26, 27], The allergens are arranged according to groups such as allergens from
plants and grasses, from trees, from mites, from fungi, from insects, from foods and
from other allergens such as, for example, latex allergens. The listing in the
enumerations is as follows: scientific name of the organism, a commonly used
abbreviation of the allergen directly followed by the GeneBank accession No. of the
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allergen (written in parentheses), where known.
Plant and grass allergens:
Ambrosia artemisiifolia, Amb a 1 and Amb a 2; Mercurialis annua, Mer a 1
(Y13271); Parietaria judaica, Par j 1 (X77414), Par j 2 (X95865; X95866); Cynodon
dactylon, Cyn d 1 (S83343); Dactylis glomerata, Dae g 3 (U25343); Holcus lanatus,
Hoi 11 (Z27084, Z68893); Lolium perenne, Lol p 1 (M57474), Lol p 2 (X73363) Lol
p 5 (M59163); Phalaris aquatica, Pha a 1 (S80654); Phleum pratense, Phi p 1
(X78813), Phi p 2 (X75925), Phi p 3, Phi p 5 (X74735)
Tree allergens:
Alnus glutinosa, Aln g 1 (S50892); Betula verrucosa, Bet v 1 (XI5877), Bet v 2, Bet v
Id; Carpinus betulus, Car b 1 (X66932, X66918); Corylus avellana, Cor a 1 (X70999,
X71000, X70997, X70998, Z72439, Z72440, AF136945, AF323973, AF323974,
AF323975); Ligustrum vulgare, Lig v 1 (X77787, X77788); Olea europea, Ole e 1
(S75766), Ole e 9 (AF249675); Syringa vulgaris, Syr v 1 (X76541); Cryptomeria
japonica, Cry j 1, Cry j 2 (D29772, D37765); Cupressus arizonica, Cup a 1
(AJ278498); Cupressus sempervirens, Cup s 1 (AF257491); Juniperus ashei, Jun a 2
(AJ404653)
Mite allergens:
Blomia tropicalis, B1o t 5 (U59102); Dermatophagoides farinae, Der f 1, Der f 2, Der
f 11; Dermatophagoides pteronyssinus, Der p 1, Der p 2, Der p 5, Der p 7;
Lepidoglyphus destructor, Lep d 2 (X81399); P. americana, Cra-A; T. putrescentiae,
Tyr p 2
Animal allergens:
Bos domesticus, Bos d 2 (L42867); Equus caballus, Equ c 1 (U70823); Felis
domesticus, Fel d 1 (M74952, M74953)
Fungal allergens:
Altemaria alternata, Alt a 1 (U82633), Alt a 2 (U62442); Aspergillus flavus, Asp fl 1
(AF137272); Aspergillus fumigatus, Asp f 1 (M83781, S39330), Asp fl/a, Asp f 2
(U56938), Asp f 3 (U20722, U58050), Asp f 4, Asp f 6, Asp f 8; Aspergillus niger,
Asp n 18; Aspergillus oryzae, Asp o 13 (X17561); C. comatus, Cop c 1; Penicillium
chrysogenum, Pen ch 13 (AF193420), Pen ch 20 (S77837); Penicillium oxalicum, Pen
o 18 (AAG44478); Malassezia sympodialis, Mai s 1 (X96486)
Insect allergens:
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Apis mellifera, Api m 1 (X16709), Api m 2 (L1 0710), Api m 4 (X02007); PLA2 (X16709); Blattella germanica, Bla g 1 (AF072219, L47595, AF072221, AF072220), Bla g 2 (U28863), Bla g 4 (U40767), Bla g 5 (U92412); Periplaneta americana, Per a
1 (AF072222), Per a 3 (L40819); Dolichovespula maculata, Dol m 1 (X66869), Dol m
2 (L34548), Dol m 5 (J03601); Dolichovespula arenaria, Dol a 5 (M98859), Polistes annularies, Pol a 5 (M98857); Vespula vulgaris, Ves v 1 (L43561), Ves v 2 (L43562), Ves v 5 (M98858); Myrmecia pilosula, Myr p 1 (X70256), Myr p 2 (581785)
Food allergens:
Salmo salar, Sal s 1 (X97824); Bos domesticus, Bos d 4 (Ml 8780), Bos d 5
(X14712); Gallus domesticus, Gal d 1 (J00902), Gal d 2 (J00992); Metapenaeus ensis,
Met s 1 (U08008); Hordeum vulgare, Hor v 15 (X63517); Oryza sativa, Ory s 1
(U31771); Apium graveolens, Api g 1 (Z48967); Daucus carota, Dau c 1 (U47087,
D88388); Malus domestica, Ma1 d 1 (X83672); Pyrus communis, Pyr c 1
(AF057030); Persea americana, Pers a 1 (Z78202); Prunus armeniaca, Pru ar 1
(U93165); Prunus avium, Pru av 1 (U66076); Arachis hypogaea, Ara h 1 (L34402),
Ara h 2 (L77197); Bertholletia excelsa, Ber e 1 (M17146); Juglans regia, Jug r 1
(U66866), Jug r 2 (AF066055); Ricinus communis, Ric c 1 (X54158); Sesamum
indicum, Ses i 1 (AF240005)
Further allergens (latex):
Hevea brasiliensis, Hev b 1 (X56535), Hev b 2, Hev b 3, Hev b 5 (U42640), Hev b 6
(M36986),Hevb7,Hev b 8
These known allergens are mentioned merely by way of example, and further
allergens which can likewise be used in antigen modules for the purposes of the
invention are known in the art.
Besides allergens, there are a number of known pathogens against which no effective
or lasting immunization is available at present. Since the method of the invention is
based on a novel immunization strategy, it is possible that shows an effect for
immunization against these disorders which cannot to date be satisfactorily treated
prophylactically by immunizations. These disorders include, in particular, infections
with HIV viruses, with hepatitis C viruses, with pathogens of tuberculosis
(Mycobacterium tuberculosis), leprosy (Mycobacterium leprae), plague (Yersinia
pestis) and with malaria pathogens (Plasmodium species, e.g. falciparum).
Further modules which may be present in MAT molecules
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Besides the three modules already described - translocation module, targeting module and antigen module - which must be present at least in the MAT molecule, it is also possible for further optional modules to be present in the MAT molecule. These optional modules include, for example, modules which make it possible to isolate or detect the MAT molecules. Such modules are often referred to in the art as "tags" and are therefore referred to as tag modules in this patent application below. Further modules optionally present in the MAT molecules may be spacer modules, i.e. modules which are arranged between the other modules and whose task is to couple these modules to one another. These modules are called spacer modules in this patent application below. It is also possible for certain modules simultaneously to undertake the function of two or more modules. For example, many tag modules can be used simultaneously for isolation and for detection of the MAT molecule, or an antigen module present in a MAT molecule might also be used for detection and/or isolation of the MAT molecule if, for example, an antibody against the antigen module is available, etc.
Tag modules which may be present in MAT molecules
For the purposes of the invention it is possible for one or more different and/or one or
more identical tag modules to be constituent of a MAT molecule. Tag modules may
be short peptides, frequently consisting of not more than 20 amino acid residues, but
may also correspond to complete protein sequences or certain domains of proteins.
Tag modules may also be functional groups which are not composed of amino acids,
such as, for example, biotin or digoxigenin. Almost all tag modules can be used in
two different ways. Firstly, they can be used to isolate the MAT molecule, and
secondly they can be used to detect the presence of the MAT molecule. In general, all
tag modules currently known and all those to become known in the future are suitable
for use for the purposes of the invention. Examples of suitable tag molecules which
can be used for the purposes of the present invention are: histidine sequences of 4 to
12 or more, preferably directly consecutive histidine residues, also called His tag,
His6 tag, HIS6 tag, penta His™, Tetra His™, RGS His™, etc. (Qiagen, Hilden,
Germany), Myc or c-Myc tag, PinPoint™ tag (a signal sequence which has the effect
that the corresponding protein is provided with a biotin group by bacteria in vivo),
HA tag, 6xHN tag (Promega Biosciences Inc., San Louis Obispo, CA, USA),
Xpress™ tag, myc tag, V5 tag (Invitrogen, Breda, the Netherlands), S tag, CBD tag,
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GST tag, HSV tag, T7 tag (Novagen Inc., Madison, WI, USA), FLAG tag, HA tag, c-myc tag., "calmodulin-binding peptide tag (CBP) tag (Stratagene, La Jolla, CA, USA), His tag, protein A tag, glutathione S-transferase (GST) tag (Amersham Biosciences, Uppsala, Sweden), Strep-tagll (IBA GmbH, Gottingen, Germany), His tag (Roche Applied Science, Rotkreuz, Switzerland), FLAG tag, GST tag, protein A tag (Sigma, St. Louis, MO, USA), maltose binding protein (MBP), chitin-binding tag (New England Biolabs, Beverly, MA, USA), His tag (BD Biosciences Clontech, Palo Alto, CA, USA). Applications in which more than one tag module are used in a molecule have also been described for some of these tag modules. For example, two tag modules can be coupled to the N terminus or to the C terminus of a protein, or one tag module can be coupled to each of the N terminus and C terminus (Qiagen, Hilden, Germany and Stratagene, La Jolla, CA, USA). Tag modules may also be introduced internally in the sequence of other proteins, e.g. between two domains of a protein (Strep-tagll, IBA, Gottingen, Germany).
Further tag modules are primarily used to detect the molecule to which they are coupled. However, these tag molecules may also be used in principle for isolating proteins, e.g. by use of affinity chromatography. It is possible to use for this purpose for example chromatography materials onto which antibodies against these tag modules are coupled. It is also possible to use for the purposes of the present invention tag modules such as, for example, the green fluorescent protein (GFP), the enhanced green fluorescent protein (EGFP), the enhanced cyan fluorescent protein (ECFP), the enhanced yellow fluorescent protein (EYFP), the red fluorescent protein (DsRed2) (BD Bioscience Clontech, Palo Alto, CA, USA), the renilla green fluorescent protein (hrGFP) (Stratagene, La Jolla, CA, USA). These tag modules may be located both at the N terminus and at the C terminus for example of a fusion protein. Besides fluorescent tag modules it is also possible to use enzymes as tag module. Examples of frequently used enzymes are luciferease, beta-galactosidase, alkaline phosphatase, horseradish peroxidase, etc. These enzymes can be detected via their respective enzymic activity, i.e. on the basis of the conversion of substrates of these enzymes. Various types of substrates are suitable for this purpose, such as, for example, substrates which absorb light in the visible region of the spectrum, fluorescent substrates, substrates whose conversion leads to the emission of light, or
substrates whose enzymatic conversion can be determined through the decrease in the
23

concentration of the substrate or the increase in the product by use of various detection methods, etc.
A further possible use of tag modules for the purposes of the present invention is the use of, for example, peptide sequences which are suitable as kinase substrates. These peptide sequences can then be radiolabeled by addition of radioactive phosphorus and addition of kinases. Examples of tag modules which can be used in this way for the present invention are: the kemptide tag (a peptide which can be phosphorylated by protein kinase A), the calmodulin-binding peptide tag (CBP), which can likewise be phosphorylated with protein kinase A (Stratagene, La Jolla, CA, USA), etc.
A further possible use of tag modules for the purposes of the present invention is the use of, for example, proteins, protein domains, or peptide sequences which specifically bind other proteins or other structures. Examples of such tag modules known from the literature are: protein A, protein G, protein A/G, protein L, all these proteins binding to antibody structures (Pierce, Rockford, IL, USA), glutathione S-transferase, which binds to glutathione, the maltose binding protein (MBP), that binds to amylose, streptavidin or avidin, both of which bind to biotin, the calmodulin-binding peptide, which binds to calmodulin, the chitin-binding tag, which binds to chitin, etc. It is possible in general to use all types of molecules which in each case bind specifically to other molecules as tag module for the purposes of the invention, i.e. receptor-ligand, antibody-antigen, lectin-sugar structure, protein-lipid, protein-nucleic acid, protein-protein, etc., and numerous further examples described in the literature [28].
Spacer modules
Spacer modules which can be used for the purposes of the invention are all types of
molecules suitable for coupling other modules, which are component of the MAT
molecule, to one another. The coupling can take place both by covalent and by
noncovalent linkages. The spacer modules have the task inter alia of separating the
various modules of the MAT molecule from one another in space so that they do not
have mutual adverse effects on their functionality. Modules of the MAT molecule for
the purposes of the invention can be coupled by spacer modules which can be cleaved
again at a later time by chemical or enzymatic reactions, e.g. by proteases. It is thus
24

possible to separate the modules of the MAT molecule, which are connected by the spacer modules, from one another again as required.
It is possible to use for this purpose in general all proteases currently known or to become known in future [29, 30]. Proteases frequently used at present are thrombin, factor Xa, enterokinase or the TAGZyme system (Qiagen, Hilden, Germany) etc. Various chemical reactions suitable for cleaving spacer modules are known to the skilled worker or can be found in the information from manufacturers of spacer molecules, e.g. from Pierce.
The spacer modules may be in particular peptide sequences or organic molecules. Numerous spacer molecules which can be used for the purposes of the invention are known in the art. In addition, it is also possible to use spacer molecules which will be developed or discovered in future for the purposes of the invention. Suitable spacer modules are, inter alia, peptide spacers, crosslinkers, natural or synthetic polymers such as, for example, nucleic acids, substituted or unsubstituted hydrocarbons, etc. It is additionally possible to use combinations of molecules as spacer modules which are able to form complexes with one another via noncovalent interactions, and thus able to join together two or more modules to give a MAT molecule. A known example of such a combination of molecules which bind to one another is biotin/streptavidin.
Peptide sequences as spacer modules
Many proteins consisting of a plurality of domains have in their amino acid sequence short sequence regions which are also referred to as spacers in the literature. These spacers have the task of separating the various domains of the protein spatially from one another in such a way that they do not have mutual adverse effects on their functionality. It is necessary for this purpose in particular to ensure that the spacer sequence is so flexible that the two domains do not impede one another sterically in their function.
Peptide sequences of this type can be used as spacer modules for the purposes of the present invention. A large number of different spacer peptide sequences are described in the literature. These spacers preferably have a length of between 2 and 60 amino
acids, but may also have longer sequences. Spacers may also consist of only one
25

amino acid. Many commercially available expression vectors already comprise sequence regions which code for peptide spacers which, for example, connect a tag sequence to the protein sequence to be introduced into the expression vector. Very short peptide spacers consisting of only two amino acids such as, for example, leucine-glycine, glycine-alanine or serine-alanine (IBA GmbH, Gottingen, Germany) are often used, or short amino acid sequences from 4 to 6 amino acids in length consisting of glycine and/or alanine (Qbiogene Inc., Carlsbad, CA, USA). Numerous further spacer sequences are described in the literature and can be used as spacer modules for the purposes of the present invention. It is possible in principle to employ all currently known spacer molecules and spacer molecules which will become known in future as spacer module in the MAT molecules of the invention. A method for identifying amino acid sequences suitable as spacer module is the use of databases which screen amino acid sequences for protein domains. Short amino acid sequences preferably with a length of from 2 to 60 amino acids, which are present between two protein domains identified in this way in an amino acid sequence, can be used as spacer module for the purposes of the invention. One of the currently available databases for identifying protein domains and thus also peptide sequences suitable as spacer module is the "SBASE protein domain library" [31].
Crosslinkers as spacer modules
Spacer modules also in the form of crosslinkers can be introduced into the MAT molecule for the purposes of the invention. For this purpose, the individual modules of the MAT molecule are prepared and then covalently coupled to one another by chemical reactions with crosslinkers. Numerous crosslinkers are commercially available for this purpose. For example, Pierce (Pierce Biotechnology, Inc., Rockford, IL, USA) supplies numerous different crosslinkers. It is possible at present to select for example from Pierce between crosslinkers which react with amino groups, sulfhydrol groups, sugar structures, carboxyl groups, hydroxyl groups or non-selectively with the modules which are to be combined to give a MAT molecule. Also currently available, e.g. from Pierce Biotechnology Inc. for preparing MAT molecules are crosslinkers which can be separated again by particular chemical reactions, e.g. by thiols, bases, periodate, hydroxylamine, by the action of light or by nonspecific reactions. It is additionally possible by targeted selection of crosslinkers to specifically fix the distance between the individual modules of the MAT molecule.
26

For example, Pierce currently supply crosslinkers which introduce a distance of 1.4 Angstrom (N-succinimidyl iodoacetate) to 34.7 Angstrom (bis(beta-(4-azido-salicylamido)ethyl) disulfide), depending on which crosslinker is used. A further possible variation in the use of crosslinkers for coupling various modules to give MAT molecules for the purposes of the present invention is the possibility of using the crosslinker sulfo-SBED from Pierce Biotechnology Inc. Sulfo-SBED couples on the one hand two modules by covalent reaction and additionally comprises a biotin group on the introduced spacer molecule. It is then possible to attach a further module of the MAT molecule by noncovalent linkages to this biotin group. For this purpose, the module to be introduced can be coupled for example to avidin or streptavidin. The streptavidin-coupled module produced in this way can then be coupled via the biotin group present in the crosslinker to the other modules. It is possible in principle to use all currently known crosslinkers and crosslinkers which will become known in future for linking modules to give a MAT molecule for the purposes of the invention.
Further spacer modules
Spacer modules for the purposes of the invention may consist for example of L isomers or of D isomers of amino acids, of unusual amino acids, of amino acids with postranslational modifications, of nucleic acids, of PNAs (peptide nucleic acids), of lipids, of sugar structures, or other natural or synthetic polymers such as, for example, substituted or unsubstituted hydrocarbons, polyacetate, polyethylene glycol, cyclodextrin, polymethacrylate, gelatin, oligourea etc., or of other substances or of combinations of the substances mentioned or others. It is possible in principle to use all currently known substances suitable for joining modules together to give a MAT molecule, and molecules which will become known in future and have corresponding properties, as spacer module for linking modules to give a MAT molecule for the purposes of the invention.
Spacer modules which are linked together by noncovalent interactions There is a large number of examples of this class of spacer molecules in the literature. Examples of such combinations of molecules which are linked together via noncovalent interactions and which are commercially available are: biotin/streptavidin or avidin or Strep-tagll (IBA GmbH, Gottingen, Germany) or PinPoint™ tag (Stratagene, La Jolla, CA, USA), glutathione S-transferase/glutathione and protein
A/constant portion of antibodies (FC part) (Pharmacia Amersham Biosciences,
27

Uppsala, Sweden, Sigma, St. Louis, MO, USA), maltose-binding protein (MBP)/amylose (New England Biolabs, Beverly, MA, USA), histidine tag/Ni chelate (Qiagen, Hilden, Germany, BD Bioscience Clontech, Palo Alto, Ca, USA, Invitrogen, Breda, the Netherlands, Novagen Inc., Madison, WI, USA, Roche Applied Science, Rotkreutz, Switzerland), chitin-binding tag/chitin (New England Biolabs, Beverly, MA, USA), calmodulin-binding protein/calmodulin (Stratagene, La Jolla, CA, USA). There is also in addition a number of further molecule combinations such as, for example, receptor/ligand combinations, antibody/antigen combinations, lectin/sugar structure combinations, etc. Numerous currently known protein-protein interactions are to be found in databases and can be used as spacer modules for the purposes of the invention [28]. All combinations which are currently known and will become known in future of molecules able to enter into noncovalent linkages with one another can in principle be used as spacer module for the purposes of the invention. A further method for introducing spacer modules into MAT molecules is the use of bispecific molecules which combine two different binding sites in one molecule. Examples of such molecules would be biotin-labeled lectins (Pierce Biotechnology, Inc., Rockford, IL, USA) which are able to link together for example a streptavidin-labeled module and a further module which has a sugar structure which is bound by the lectin. A further example of a possibility for coupling in this way are bispecific antibodies which recognize two different epitopes, etc.
A further variant for introducing spacer modules into MAT molecules is as follows: firstly, at least two modules are coupled to one another via a noncovalently linking spacer module, and then the complex is treated with chemical crosslinkers which introduce covalent bonds between modules which are in spatial proximity. This has the advantage that, in the first steps particular modules are coupled to one another in a targeted and defined manner and then the noncovalent coupling is converted into a more stable covalent coupling. If the modules are treated directly with crosslinkers which produce covalent bonds, the manner in which the modules are coupled to one another is usually random and not specific.
Structure of the MAT molecules
Any desired arrangement of the individual modules of the MAT molecule is possible
in general. Each module may be present one or more times in the MAT molecule. The
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minimum requirement is the need for the presence of at least one translocation module, at least one targeting module and at least one antigen module. Additional modules such as tag modules, spacer modules, etc. may optionally be present but need not be present. All modules may be present one or more times in the MAT molecule. If modules are present more than once, they may be present in the form of identical copies, or different versions of a module may be present in each case in a single copy or in more than one copy. It is also possible for entirely different modules of the same class of modules, e.g. a His tag module and a biotin tag module, to be present in a MAT molecule. Both modules undertake functionally the same task (tag module) in the MAT molecule, but need have nothing in common in terms of their molecular structure.
Two or more identical copies of an antigen module in a MAT molecule may serve for example to bring about an enhanced immune response to the relevant antigen. Two or more different antigen modules may for example be combined in one MAT molecule in order to modulate simultaneously the immune reaction to two or more different antigens. Two or more different translocation modules be used in a MAT molecule. For example, a Tat sequence and a VP22 sequence can serve to make translocation more efficient since the translocation of the MAT molecule then takes place efficiently in a broader spectrum of different cell types or tissue types. It is also possible for example to use two or more tag modules in a MAT molecule, e.g. a His tag and a FLAG tag, in which case for example the His tag is used to isolate the MAT molecule and for example the FLAG tag serves to detect the MAT molecule. It is possible to use two or more different targeting modules in a MAT molecule, e.g. a sequence from the invariant chain of the MHC II molecule and as further targeting module a mannose 6-phosphate group, of which for example the invariant chain acts as targeting module into the MIICs, and the mannose 6-phosphate group brings about a targeting into the lysosome, it thus being possible overall to increase the efficiency of antigen presentation or the number of different epitopes of the antigen presented by the antigen-presenting cells.
The position of the individual modules within the MAT molecule can also be varied
as desired as long as at least one translocation module, at least one targeting module
and at least one antigen module is present. It is also possible for all or some of the
29

modules of the MAT molecule for example to be present not in the form of a linear sequential arrangement of modules but as circular or as branched module structure or else in the form of dendrimers, or as a combination of linear and/or branched and/or circular and/or dendrimeric molecule portions. Circular module structures of the MAT molecule can be generated for example by reacting two cysteine residues with one another or by reacting one cysteine residue with a thiol ester group within a chain of modules which originally had a linear structure. There are commercial suppliers of expression vectors which supply specific vectors which make it possible to prepare circular fusion proteins by these mechanisms, such as, for example, the IMPACT™-TWIN system from New England Biolabs, Beverly, MA, USA. Branched modules might be prepared for example by synthesizing peptides in which, starting from poly L-lysine, a new lysine residue is attached to both free amino groups of each of the subsequent lysine residues. It is possible in this way to create a peptide structure with virtually any extent of branching. It is then possible for example for translocation modules and/or targeting modules subsequently to be synthesized onto the branched peptide basic structure [32]. Further modules can also be coupled onto a linear, circular or branched peptide basic structure by protein ligation [33, 34]. It is additionally possible to introduce for example biotin groups into the peptide basic structure during the peptide synthesis, and modules can then be attached to these biotin groups via, for example, streptavidin, the Strep tag system or via the PinPoint™ system (respectively IBA GmbH, Gottingen, Germany and Promega Biosciences Inc., San Louis Obispo, CA, USA) onto the peptide basic structure. Modules attached in this way are then coupled via noncovalent linkages to the peptide basic structure.
Figure 1 shows by way of example some examples of possible structures for MAT molecules in terms of their composition from various modules and in terms of the arrangement of the modules within the MAT molecule.
Structure of the modules of MAT molecules
Peptides, proteins, amino acids, unusual amino acids, postranslational modifications
etc.
The terms peptide and protein are used side by side as equivalent in the present patent
application. A peptide or a protein means for the purposes of the invention a covalent
30

connection of at least two amino acids via a peptide linkage. The term "amino acid" and the term "amino acid residue" are used as equivalent in the present application, i.e. the meaning of the two terms is identical. The terms amino acid/amino acid residue and peptide/protein are used in the present application in the form of the widest possible definition.
Amino acids mean for the purposes of the invention besides the 20 amino acids
determined by the genetic code also the amino acids which can be encoded by stop
codons, such as, for example, seleno-cysteine or pyrro-lysine. Additionally included
are all known amino acid and peptide derivatives such as, for example, glycosylated,
phosphorylated, sulfated amino acids/peptides, and L-isomeric and D-isomeric amino
acids, and amino acid and peptide derivatives which will be known in future. Amino
acid and peptide derivatives can arise, or be prepared specifically, by post-
translational modifications, by chemical modifications, by enzymatic modifications or
on the basis of other mechanisms. The resulting peptides may comprise modifications
which may occur in all regions of the peptide molecule. For example, modifications
may occur in the peptide backbone, in the amino acid side chains, at N-terminal ends
of the peptide or at C-terminal ends of the peptide. The modifications may be present
in single amino acids, in a plurality of amino acids or in all amino acids, and it is
possible for no, one or a plurality of types of modifications to be present in any
combinations in a peptide. The peptides may be branched, the peptides may be in
cyclic form, and any combinations of branched and cyclic peptides are possible.
Branched and/or cyclic peptides may arise through natural biological processes or be
prepared by synthesis. Examples of unusual amino acids which may be mentioned by
way of example are, inter alia: alpha-aminobutyric acid, beta-aminobutyric acid, beta-
aminoisobutyric acid, beta-alanine, gamma-aminobutyric acid, alpha-aminoadipic
acid, 4-aminobenzoic acid, aminoethylcysteine, alpha-aminopenicillanic acid,
allysine, 4-carboxyglutamic acid, cystathionine, carboxyglutamic acid,
carboxyamidomethylcysteine, carboxymethylcysteine, cysteic acid, citroline,
dehydroalanine, diaminobutyric acid, dehydroamino-2-butyric acid, ethionine,
glycine-proline dipeptide, 4-hydroxyproline, hydroxylysine, hydroxyproline,
homoserine, homocysteine, histamine, isovaline, lysinoalanine, lanthionine, norvaline,
norleucine, ornithine, 2-piperidinecarboxylic acid, pyroglutamic acid, pyrrolysine,
proline-hydroxyproline dipeptide, sarcosine, 4-selenocysteine, syndesines,
31

thioproline, etc. All said amino acids can be present in the form of their L isomers or in the form of their D isomers as long as this is permitted by their structure. In general, all currently known amino acids and amino acid derivatives which occur naturally or are formed or can be prepared enzymatically or chemically or in another way, and modifications of amino acids to become known in future, are included in the term "amino acid" and may be constituent of MAT molecules for the purposes of the invention.
Examples of postranslational or chemical modifications which may be present in one or more modules of the MAT molecule for the purposes of the invention and which are mentioned are, inter alia, modifications of the amino acid sequences by the following structures: binding of free cysteine to a cysteine in the peptide sequence, formation of disulfide linkages between two cysteine residues, methylations, acetylations, acylations, farnesylations, formylations, geranylgeranylations, biotinylations, stearoylations, palmitylations, lipoylations, C-mannosylations, myristoylations, phosphorylations, sulfatylations, N-glycosilations, O-glycosilations, amidations, deamidations, demethylations, cysteinylations, carboxylations, hydroxylations, iodinations, oxidations, pegylations, prenylations, ADP-ribosylations, 5"-adenosylations, 4"-phosphopan-theinations, glutathionylations, covalent bonding: of flavin, of heme groups (or other porphyrins), of nucleic acids or of nucleic acid derivatives, of lipids or of lipid derivatives, of phosphatidylmosistol, of glycosylphosphatidylinositol anchors (GPI anchors), of pyridoxal phosphate, of mannose 6-phosphate, modifications of cysteine to carboxyamidomethylcysteine or carboxymethylcysteine or pyridylethylcysteine, modification of lysine to lipoic acid, modification of glutamine to pyroglutamic acid, addition of amino acids onto peptides by tRNAs, ubiquitin labeling of peptides, branchings of peptides, e.g. in the form of poly-L-lysine, cyclizations of peptides, e.g. by forming disulfide linkages between 2 cystenine residues, etc., possible. Numerous further modifications of proteins which are, inter alia, also archived in databases are described in the literature [35]. In general, all currently known modifications of peptides which occur naturally or are formed or can be prepared enzymatically or chemically or in another way, and modifications of peptides which will be known in future, are included in the term "peptide" and may be constituent of MAT molecules for the purposes of the
invention.
32

Peptidomimetics
It is additionally possible for the purposes of the invention for one or more amino acids of modules or the complete module or all modules of the MAT molecule to be replaced by structures consisting of peptidomimetics. The term peptidomimetic is used in the present application in the form of the widest possible definition. A peptidomimetic is a substance which comprises non-peptide structural elements and is able to imitate or to antagonize the biological effect of the natural parent molecule. Numerous studies dealing in detail with possibilities for using peptidomimetics as replacement for conventional peptide structures are known in the art. It is generally possible for one or more modules of the MAT molecule to be composed entirely or partly of peptidomimetics [36-38], This may have various advantages. Translocation modules may possibly penetrate more efficiently into cells thereby, targeting modules may transport the MAT molecule more efficiently or less efficient and/or more specifically into the desired intracellular organelle, antigen modules may lead to an enhanced or reduced immune response relative to the immune response to the conventional antigen, or tag modules may have better physicochemical properties, improving their suitability for the isolation and/or detection of the MAT molecule, etc. It is additionally possible through the use of peptidomimetics in some circumstances to reduce or increase the in vivo stability of the MAT molecule, to reduce or increase its toxicity, to improve its solubility in hydrophilic or hydrophobic media, and to prolong its in vitro stability and possibly to reduce the costs for synthesizing the peptidomimetic relative to the cost for synthesizing the corresponding conventional peptide. One example of peptidomimetics are Spiegelmers® supplied by NOXXON Pharma AG, Berlin, Germany. This type of peptidomimetics has the advantage for example that they do not elicit an immune response and therefore could be employed in a worthwhile manner for example in translocation modules, targeting modules, tag modules, spacer modules, etc. of MAT molecules. Spiegelmers® would, however, not be suitable as antigen module.
Preparation and isolation of MAT molecules
A further embodiment of the invention is the isolation of MAT molecules using
recombinant expression systems, chromatography methods and chemical synthesis
protocols known to the skilled worker. The MAT molecules isolated in this way can
33

be used inter alia for producing medicaments and diagnostic aids and for producing antibodies in experimental animals and in in vitro systems.
Preparation of MAT molecules
Methods known to the skilled worker for preparing MAT molecules include
recombinant expression of peptides. It is possible to use for expression of the peptides
inter alia cell systems such as, for example, bacteria such as Escherichia coli, yeast
cells such as Saccharomyces cerevisiae, insect cells such as, for example, Spodoptera
frugiperda (Sf-9) cells, or mammalian cells such as Chinese hamster ovary (CHO)
cells. These cells are obtainable from the American Tissue Culture Collection
(ATCC). For recombinant expression of peptides, for example nucleic acid sequences
which code for entire MAT molecules or for individual molecules of MAT molecules
are introduced into an expression vector in combination with suitable regulatory
nucleic acid sequences such as, for example, selection markers, promoters, etc. using
methods of molecular biology. Suitable selection markers are, for example,
resistances to antibiotics such as ampicillin, kanamycin, neomycin, puromycin or
metabolic defects, e.g. yeast cells unable to produce alanine, leucine, tryptophan etc.,
or mammalian cells lacking the enzyme hypoxanthine-guanine
phosphoribosyltransferase and therefore unable to survive in HAT medium
(hypoxantines, aminopetrin, thymidine medium), etc. Suitable promoters are, for
example, the cytomegalovirus immediate early promoter (CMV promoter), the SP1
minimal promoter or the thymidine kinase promoter (TK promoter). In the selection
of the promoters it is necessary to select promoters suitable for the particular cell
system. For example, the T7 or the T7/lacO promoter is suitable for bacteria while,
for example, the nmt l promoter is suitable for yeast cells. If MAT molecules or
modules of MAT molecules are toxic it may be advantageous or necessary to use
expression vectors which make it possible to control the expression of these
molecules from outside, e.g. through the Tet-On™ and the Tet-Off™ expression
system (Promega Biosciences, San Louis, CA, USA). In this system, the activity of
the promoter of the expression vectors is regulated by addition of tetracycline to the
growth medium of the cells. Further examples of methods which can be used for
external regulation of the expression of MAT molecules or of modules of MAT
molecules is the induction of T7 polymerase by IPTG or the use of ecdysone-
inducible expression systems such as, for example, the Complete Control® Inducible
34

Mammalian Expression System (Stratagene, La Jolla, MO, USA). On use of vectors which comprise an IRES (internal ribosome entry site) sequence it is also possible for a plurality of molecules to be prepared simultaneously through the use of only one expression vector (e.g. pLP-IRESrieo vector, Promega Biosciences, San Louis; CA, USA). It is thus possible in this way for example for two or more modules of a MAT molecule which are intended to interact with one another by noncovalent linkages to be expressed in parallel with one another in appropriate stoichiometric ratios of amounts, and possibly also purified in parallel. Various companies supply commercially available expression vectors for various cell systems, e.g. Invitrogen, Qiagen, Stratagene, Clontech, Novagen, New England Biolabs, Pharmingen, Promega, Pharmacia, etc. The expression vectors isolated in this way can then be introduced into suitable cells, e.g. by electroporation, calcium phosphate coprecipitation, liposome-mediated transfection, etc., in a manner known to the skilled worker. Alternatively, it is also possible to use recombinant viruses produced by methods of molecular biology, which then in turn infect cells and bring about the expression of MAT molecules or modules of MAT molecules by the infected cells. Suitable viral expression systems are, for example, * the bacculovirus system, e.g. BacculoGold (BD Bioscience Pharmingen, Palo Alto, CA, USA), adenoviral expression systems such as, for example, ViraPort™ (Stratagene, La Jolla, CA, USA), retroviral expression systems such as, for example, AdEasy (Stratagene, La Jolla, CA, USA) etc.
It is also possible as alternative to transfection of expression vectors and to viral expression systems to use in vitro translation systems in which, for example, rabbit reticulocyte lysates or E. coli S30 extracts or wheatgerm extracts are used for the synthesis of MAT molecules or for the in vitro synthesis of modules of MAT molecules without living cells being necessary for the expression.
Cell systems for preparing MAT molecules
Cell lysates or cell culture supernatants can be used as starting material for preparing
MAT molecules or for preparing individual modules of MAT molecules. Cell systems
may be obtained for example from bacteria such as, for example, E. coli, bacillus,
caulobacter, pseudomonas or streptomycetes or yeasts such as, for example,
saccharomyces, pichia or hansenula, or insect cells such as, for example, Sf-9, Sf-21
35

or High Five, or mammalian cells such as, for example, CHO cells, COS cells, 3T3 cells, BHK cells, 293 cells, etc. It is possible through the use of signal sequences which bring about the export of proteins from the interior of the cell into the extracellular space for the protein to be expressed to accumulate specifically in the cell culture medium or in the periplasmic space of, for example, bacteria. A further source of starting material for preparing MAT molecules or modules of MAT molecules may be transgenic animals, transgenic plants, transgenic fungi or transgenic microorganisms into which nucleic acids which code for MAT molecules or modules of MAT molecules have been introduced stably or transiently. The corresponding nucleic acids may in this case both be integrated directly into the genome of the particular organism and be introduced for example in the form of plasmids or in the form of other DNA or RNA molecules into the organisms. The corresponding MAT molecules or modules of MAT molecules can then be isolated for example from the milk, the eggs, from serum, from urine, from tissue etc. of the transgenic animals, from, for example, storage tubers, seeds, leaves etc. of transgenic plants, from, for example, the mycelium, the fruiting body etc. of the transgenic fungi or from cells or other organisms cultivated in vitro, or from the corresponding cell culture media. All types of organisms are generally suitable for use as expression system for preparing MAT molecules or modules of MAT molecules.
Isolation of MAT molecules
The MAT molecules or modules of MAT molecules prepared in this way can be
isolated using techniques known to the skilled worker. Numerous methods known to
the skilled worker for isolating proteins can be used for this purpose, such as, for
example, precipitation methods, liquid phase separation methods, chromatographic
methods etc. Suitable precipitation methods include inter alia immunoprecipitation,
ammonium sulfate precipitation, polyethylene glycol precipitation, ethanol
precipitation, trichloroacetic acid precipitation (TCA precipitation), thermal
precipitation, etc. The liquid phase separation methods include for example extraction
with organic solvents such as, for example, alcohols, acetone, chloroform,
acetonitrile, etc., and the chromatographic methods include for example cation
exchanger chromatography, anion exchanger chromatography, isoelectric focussing,
reverse phase chromatography, gel filtration, immobilized metal ion affinity
chromatography (IMAC), it being possible to use various metal ions such as, for
36

example, nickel, zinc, cobalt etc., hydroxyapatite chromatography, numerous different affinity chromatography methods such as, for example, immunoaffinity chromatography, affinity chromatography using immobilized nucleic acids, or immobilized protease inhibitors, etc. The chromatographic media used may have structures based on an agarose matrix, based on magnetic particles, in the form of membranes, in the form of hollow fibers, based on various polymers such as, for example, polystyrene etc. Chromatographic methods can generally be carried out on a wide variety of scales starting from chromatography columns with a volume of a few ul up to large chromatography columns with a volume of several hundred liters. In addition, chromatographies can be carried out under normal atmospheric pressure, under medium pressures in the range from 1 to 50 bar (e.g. the FPLC system, Pharmacia Amersham Biosciences, Uppsala, Sweden) and under very high pressures in the range up to about 400 bar and possibly even greater pressures (HPLC systems). Chromatographies can be carried out under conditions which have native and denaturing effects on the MAT molecules. Various interactions between matrix material and a MAT molecule or module of a MAT molecule to be isolated can be used in affinity chromatography. These include numerous tag molecules which have already been mentioned elsewhere in the present patent application and which interact with certain functional groups or ligands and thus allow isolation of MAT molecules or modules of MAT molecules. However, it is possible in principle to use all types of interaction such as, for example, protein-protein interactions, nucleic acid-protein interactions, nucleic acid-nucleic acid interactions, sugar-lectin interactions, sugar-protein interactions, receptor-ligand interactions, antibody-antigen interactions (e.g. anti-FLAG, anti-HA, anti-myc tag antibodies), hapten-antibody interactions, Spiegelmer interactions (NOXXON Pharma AG, Berlin, Germany) etc.
Affinity chromatography
Methods which can be used for the affinity chromatography are in particular those based on selective binding of a tag module to a matrix. Suitable combinations of tag modules and relevant matrix for isolating a MAT molecule are, inter alia: histidine tag and nickel chelate matrix (Qiagen, Hilden, Germany), GST tag and glutathione-Sepharose (Amersham Biosciences, Uppsala, Sweden), maltose-binding protein tag and amylose matrix (New England Biolabs, Beverly, MA, USA), biotin tag and
streptavidin or avidin matrix (IBA GmbH, GSttingen, Germany), chitin-binding
37

protein tag and chitin matrix (New England Biolabs, Beverly, MA, USA), calmodulin-binding peptide tag and calmodulin matrix (Stratagene, La Jolla, CA, USA), protein A or protein G or protein A/G or protein L and particular regions, recognized by the respective proteins, of antibody molecules, such as, for example, the Fc portion of antibodies (Amersham Biosciences, Uppsala, Sweden), FLAG tag, HA tag, myc tag, histidine tag, etc. and a matrix to which an antibody against the particular tag is coupled (many different companies, including Promega Biosciences Inc., San Louis Obispo, CA, USA, Invitrogen, Breda, the Netherlands, Qiagen, Hilden, Germany) etc.
Protease recognition sequences
The MAT molecules or modules of MAT molecules isolated in this way can be separated where appropriate from their tag module and/or other modules. It is possible for this purpose to introduce for example a protease recognition sequence at suitable positions into the particular expression vector. Numerous suitable protease recognition sequences are known to the skilled worker, including the recognition sequences of proteases such as, for example, thrombin, factor Xa, enterokinase or the TAGZyme system (Qiagen, Hilden, Germany). The added proteases can be removed again for example through immobilized protease inhibitors such as, for example, EK-AWAY for enterokinase (Invitrogen, Breda, The Netherlands), Xa Removal Resin (Qiagen Hilden, Germany), benzamidine-Sepharose for removing thrombin, etc. A further possibility for isolating MAT molecules or modules of MAT molecules is the use of inteins, i.e. of proteases which are constituent of the MAT molecule and which then, under suitable experimental conditions, eliminate themselves proteolytically from the remainder of the MAT molecule or a module of a MAT molecule (Genease™, New England Biolabs, Beverly, MA, USA). In general, all protease recognition sequences currently known [29, 30] and to become known in future are suitable for removing constituents of MAT molecules for the purposes of the invention. The protease recognition sequences may moreover either be naturally occurring or have been designed specifically, and may be composed entirely or partly of natural amino acids, unusual amino acids, peptidomimetics etc.
Inclusion bodies
A further embodiment of the invention is the preparation of MAT molecules or of
, 38 .

modules of MAT molecules in the form of incorrectly folded protein aggregates, which are also referred to as inclusion bodies. Inclusion bodies can be prepared as molecules which comprise translocation modules which make transport possible from the extracellular space through the cell membrane into the interior of the cell. This translocation leads to the originally incorrectly folded molecules becoming correctly folded and then acting inside the cell like a MAT molecule correctly folded from the outset. This procedure has the advantage that unfolded proteins can be isolated under denaturing conditions, which is often associated with less technical complexity and thus financial cost. In addition, inclusion bodies are relatively stable structures. This has advantages in some circumstances for the storage and stability of MAT molecules which are kept for later medical use. It is also possible by this method to use unfolded or incorrectly folded MAT molecules or modules of MAT molecules for the purposes of the invention. Certain translocation modules bring about both translocation from the extracellular space into the cell and the reverse transport. Transformation of an as yet incorrectly folded MAT molecule can take place directly in vivo in the individual to be treated with the MAT molecule, or the folding of the MAT molecule can be carried out in a cell system in vitro. In addition, translocation of the unfolded MAT molecule into the interior of the cell, and the subsequent translocation of the then correctly folded MAT molecule into the extracellular space, can in some circumstances be brought about by the same translocation module. A mechanism of this type has been described for some sequences suitable as translocation module for the purposes of this invention, such as, for example, the VP22 sequence [39].
Modification of MAT molecules
MAT molecules or modules of MAT molecules can be modified enzymatically,
chemically or by other methods by numerous methods known to the skilled worker.
For example, peptides can be provided with phosphorus groups by using kinases,
phosphorus groups can be removed using phosphatases, sugar structures can be
removed using glycosidases, etc. Appropriate kinases, phosphatases and glycosidases
etc., and the appropriate protocols, are obtainable from various manufacturers such as,
for example, New England Biolabs, Beverly, MA, USA. Phosphorylation of MAT
molecules or of modules of MAT molecules can additionally be used to label MAT
molecules or modules of MAT molecules with radioactive phosphorus, thus making
them easily detectable in vitro and/or in vivo. It is also possible to modify MAT
39

molecules or modules of MAT molecules by chemical reactions. For example, disulfide bridges can be destroyed by reduction, thioester groups can react covalently with cysteine residues, or two cysteine residues can react to give a disulfide bridge, making it possible to prepare circular or branched MAT molecules or modules of MAT molecules (e.g. IMPACT™-TWTN Protein Fusion and Purification System, New England Biolabs, Beverly, MA, USA). It is also possible to have a specific influence on modifications of the MAT molecule or of modules of MAT molecules through the selection of the expression system. For example, no glycosylation takes place in bacteria, and insect cells synthesize only particular types of glycosylations, whereas mammalian cells produce complete glycosylations. It is also possible to use for the expression cell lines which have been modified in such a way, or have been selected in such a way, that they are able specifically to produce, or unable specifically to produce, particular postranslational modifications. These advantageous properties may be inter alia a better solubility in hydrophilic or hydrophobic solvents, a longer stability of the MAT molecule at, for example, at room temperature, at 37°C, at 4°C, at -20°C, at -70°C or at other temperatures, a longer molecular stability of the MAT molecules if they are present alone or mixed with other solid, liquid or gaseous substances, e.g. in the form of preparations as medicament or diagnostic aid, a higher penetrability of the MAT molecules for cell membranes, for membranes of organelles, for the blood-brain barrier, for the blood-CSF barrier and for other biological membranes and barriers, etc., a higher or lower in vivo or in vitro half-life, a lower or higher toxicity, a better in vivo or in vitro detectability of the MAT molecule etc.
Protein ligation
A further possibility for preparing MAT molecules or modules of MAT molecules is
protein ligation. By this is meant for example a chemical reaction in which two ends
of peptides are linked together covalently by one or more chemical reactions. One
example would be the reaction of a thiol ester with a cysteine side chain (e.g.
IMPACT™-TWIN Protein Fusion and Purification System, New England Biolabs,
Beverly, MA, USA). It is possible in this way to prepare for example cyclic peptides.
Branched MAT molecules can be prepared for example by chemical synthesis of
polylysine peptides in which two further lysine residues (one lysine on each amino
group of the lysine) are attached to each lysine, and thus a branched polylysine
peptide is formed. It is then possible subsequently to synthesize on each terminal
40

lysine a peptide chain, or to attach a peptide covalently by peptide ligation. Other branched polymers can also be used as carrier structure for MAT molecules or modules of MAT molecules for the purposes of the invention. One example thereof are, for example, PEG star molecules, which can be prepared by polymerizing ethylene oxide with crosslinked divinylbenzene.
Peptidomimetics
A further possibility for preparing MAT molecules or modules of MAT molecules is chemical synthesis of peptides or peptidomimetics [40] or of combinations of peptides and peptidomimetics. The preparation of MAT molecules or of modules of MAT molecules by chemical synthesis can take place for example by the Merrifield solid-phase synthesis protocol using automatic synthesizers and synthetic chemicals which are obtainable from various manufacturers. An example of a company which supplies syntheses of peptidomimetics is The Peptide Laboratory™, Benicia, CA, USA. Numerous synthons for conventional peptides and for peptidomimetics can be purchased, for example, from Sigma-Aldrich Co, St. Louis, MO, USA.
Composition of medicaments and diagnostic aids
The peptide portions, amino acid portions, amino acid derivative portions,
peptidomimetic portions etc., present in the medicaments and diagnostic aids, of the
MAT molecules may also be in the form of their salts as long as these salts are
pharmacologically acceptable salts. Medicaments or diagnostic aids intended for
injection may be for example sterile aqueous or oily solutions which are mixed
according to the prior art with suitable excipients such as, for example, dispersants,
humectants and agents which stabilize suspensions. The sterile solutions for injection
may be produced using pharmacologically acceptable diluents or solvents such as, for
example, 1,3-butanediol. Among the acceptable solvents and buffers which can be
used are, inter alia, water, Ringer"s solution, isotonic sodium chloride solutions etc. In
addition, sterile oils, including synthetic mono- or diglycerides, can be used. It is
possible in addition to employ fatty acids such as, for example, oleic acid to prepare
the solutions for injection. It is furthermore possible to use dimethylacetamide,
detergents, including ionic and nonionic detergents, polyethylene glycols, etc.
Mixtures of the abovementioned substances are likewise possible. It is additionally
41

possible for medicaments also to be produced in the form of mixtures with biodegradable polymers which release the medicaments continuously. One example of such a system is, for example, the Atrigel system (Atrix Labs, Fort Collins, CO, USA).
Preparations which can be used for rectal administrations are those consisting of mixtures consisting of MAT molecules and, where appropriate, further substances with a suitable, nonirritant ointment base or filler such as, for example, cocoa butter, synthetic mono-, di- or triglycerides, fatty acids or polyethylene glycol. It is additionally possible for colorants, preservatives and odorants to be present. These and further suitable substances are solid at room temperature and melt at body temperature, so that they release the contained substances.
It is possible to use for oral administration inter alia capsules, tablets, pills, powders, granules etc. In such dosage forms, the active substances of the medicaments and diagnostic aids are often combined with adjuvants suitable for the particular dosage form. The substances may be processed with lactose, sucrose, starch powder, cellulose esters, alkanoic acids, cellulose alkyl esters, stearic acid, magnesium stearate, magnesium oxide, sodium or calcium salts of phosphorous or sulfurous acid, gelatin, gum arabic, sodium alginate, polyvinylpyrrolidones, polyvinyl alcohol etc. to, for example, tablets, capsules etc. Such capsules, tablets etc. may additionally comprise substances which enable or promote controlled release of the active substances such as, for example, hydroxypropylmethylcellulose. It is additionally possible for buffer substances such as sodium citrate, magnesium or calcium carbonates or bicarbonates, etc. to be present. Further constituents may be colorants, fragrances, flavorings, preservatives and sweeteners. Tablets, pills, capsules etc. may additionally receive coatings which, on the one hand, make them resistant to gastric acid but, on the other hand, have the effect that they dissolve in the alkaline environment of the intestine.
It is also possible to use liquid, pharmaceutically acceptable emulsions, solutions,
syrups and gel-like preparations for oral administration. These preparations may
comprise solvents used in medicine, such as, for example, water, ethanol, etc. These
preparations may also comprise adjuvants, humectants, emulsifiers and suspending
42

agents, etc., and sweeteners, flavorings, colorants, preservatives and odorants.
Liquid preparations intended for injection purposes can be produced from sterile powders or from granules by dissolving in aqueous or nonaqueous solvents. The powders and granules on which these solutions are based may comprise one or more of the substances mentioned for medicaments which can be administered orally. Suitable solvents are, inter alia, water, polyethylene glycol, polypropylene glycol, ethanol, corn oil, cottonseed oil, coconut oil, benzyl alcohol, sodium chloride solutions or various other buffers. Further possible ingredients are colorants, preservatives etc.
The amount of MAT molecules and further ingredients of the medicaments depends on the dosage form, dosage frequency, the chosen administration route, the age, sex, weight and the state of health of the patient, etc. An additional factor to be taken into account is whether the treatment is carried out for diagnosis, therapy or for prophylaxis, and whether the aim of the treatment is to enhance the immune reaction or to depress the immune reaction. Numerous works on the formulation and dosage of medicaments are known to the skilled worker [41, 42].
Obtaining antibodies by use of MAT molecules
A further embodiment of the invention is the obtaining of monoclonal, oligoclonal or
polyclonal antibodies by use of MAT molecules. The antibodies are obtained in the
usual manner familiar to the skilled worker. Such antibodies obtained by use of MAT
molecules enable the specific immunological detection of the antigens present in the
antigen modules of the MAT molecules. The antibodies recognize exactly the
antigens present in the antigen modules, and/or antigens which are similar to the
antigens in the antigen modules, and/or one or more epitopes of the antigens in the
antigen modules, and/or one or more neo-epitopes of the antigens in the antigen
modules, and/or the corresponding complete antigens, although only parts of these
antigens were present in the antigen modules, etc. Polyclonal antibodies can be
produced by immunizations of suitable experimental animals such as, for example,
mice, rats, guinea pigs, hamsters, rabbits, goats, sheep, cats, dogs, monkeys, cattle,
horses, donkeys, chickens or other experimental animals. Monoclonal antibodies can
43

be produced for example by immunizations of experimental animals such as, for example, mice or rats and subsequent application of hybridoma techniques which are known to the skilled worker. Monoclonal antibodies may also be produced by recombinant experimental approaches in which, for example, nucleic acids which code for the particular monoclonal antibody are isolated from hybridoma cell lines which have been produced by immunization of experimental animals with MAT molecules. These nucleic acids can be used in recombinant expression systems or by use of in vitro translation systems to produce the corresponding antibodies. The antibodies produced in this way can be produced and used in the form of complete antibody molecules, as protein consisting of the complete antibody or parts of the antibody fused to other amino acid sequences, as F(ab) fragments, as F(ab)2 fragments, as single-chain variable fragments (ScFv) or as other antibody fragments.
Administration routes for medicaments and diagnostic aids of the invention
The medicaments and diagnostic aids of the invention can be administered to the
patient or to an experimental animal to be immunized by various routes. These
methods include inter alia oral and sublingual dosage, e.g. in the form of tablets,
coated tablets, capsules, granules, liquid solutions, powders to be dissolved in liquids,
etc., possible compositions for example of coated tablets, tablets, granules and
capsules where appropriate being such that, without being exposed to the acidic
environment of the stomach, the medicaments reach the intestine, and the ingredients
of the medicaments are released only there. It is additionally possible to administer
the medicaments by topical application to the skin or to mucous membranes for
example in the form of ointments, sprays, dusting powders, tinctures etc. or inhaled as
aerosol via the mucous membranes, e.g. of the respiratory tract. Rectal administration
in the form of suppositories, enemas, etc. is also possible. On transdermal
administration of the medicaments it is also possible to use aids such as, for example,
patches or iontoporesis appliances (transdermal administration with the assistance of
electric currents). Other forms which are suitable for the purposes of the invention for
administering the medicaments and diagnostic aids are injections, infusions or
administration via medicinal pump systems. Injections, infusions and administration
via pump systems may take place inter alia intravenously, intramuscularly,
subcutaneously, intracutaneously, intraarticularly, intrasternally, intrathecally,
intraperitoneally, etc. Direct injection of the MAT molecules into lymph nodes such
44

as, for example, inguinal lymph nodes is also possible. A further possible type of
administration of MAT molecules is the in vitro treatment of patients" cells, in
particular cells specialized for antigen presentation, such as, for example, dendritic
cells, B lymphocytes, macrophages, further macrophage-like cells, etc. As a further
example, cells of experimental animals, or cell lines can be treated with MAT
molecules. The treated cells can then subsequently be administered to the patient or
the experimental animal. The cells can be administered as living cells, as inactivated
cells no longer capable of division, or as killed cells to the patient or to the
experimental animal. Inactivated or killed cells can be obtained for example by
treatment with suitable substances or by irradiation, e.g. with radioactive or ultraviolet
radiation. A further possibility for administering the medicaments, in particular the
MAT molecules of the invention, is stable or transient transfection of animal, human
or plant cells with a vector which leads to expression of a MAT molecule. The cells
modified in this way can where appropriate be entrapped in a matrix which firstly
fixes them locally and secondly protects them from the patient"s or the experimental
animal"s immune system but which, on the other hand, allows the MAT molecules
released from the cells to escape into the patient"s or experimental animal"s body. In
some circumstances it is also possible for transfected cells to be administered directly
to the patient or experimental animal, in which case the cells are treated where
appropriate in such a way that they are no longer able to divide, e.g. by irradiation or
by treatment with suitable chemicals. The medicaments may additionally be
administered packaged in liposomes or other vesicles such as, for example, exosomes,
or deoxosomes, or the medicaments can be administered in the form of mixtures with
biodegradable polymers which release the medicaments continuously. One example
of such a system is, for example, the Atrigel system (Atrix Labs, Fort Collins, CO,
USA). It is additionally possible for further substances to be administered by the same
or by one or more other administration routes simultaneously or sequentially to the
dosage of the medicament or diagnostic aid of the invention. These further substances
may inter alia improve, via their immunostimulating properties, the effect of the
medicaments or diagnostic aids of the invention. Such substances given
simultaneously or sequentially may be inter alia adjuvants, mineral oil, Freund"s
adjuvant, immunostimulating proteins or mediators such as, for example, cytokines,
other vaccines etc. It is additionally worthwhile where appropriate for
immunosuppressant substances to be administered simultaneously or sequentially in
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order for example to reduce or suppress unwanted local immune reactions, while systemic immune reactions are retained. Simultaneous or sequential administration of immunosuppressant substances may, however, also conversely be used to prevent systemic immune reactions, while at the same time the local immune reaction are retained.
Possibilities for examining the efficacy of MAT molecules
Various in vitro and in vivo experiments can be carried out to examine the efficacy of
MAT molecules in relation to modulation of the immune response of an individual.
Suitable as in vitro model are, for example, peripheral blood mononuclear cells
(PBMCs), e.g. obtained from the blood of patients suffering from allergic disorders.
The advantage of such cells is that the exact antigen against which the particular
patient has an allergic response is often known. This knowledge makes it possible for
example to simulate a desensitization of the patient in vitro, before clinical studies are
carried out on the patient or in experimental animals. For this purpose, for example,
the PBMCs from allergic people can be treated with the particular antigen against
which the allergic person reacts, or with a MAT molecule which comprises the
particular allergen in the antigen module. Thus, the immunological reaction of the
primary patient"s cells to various dosage forms (complete MAT molecule, molecules
with/without translocation module, molecules with/without targeting module etc.) of
the allergen can be investigated. Suitable measurement parameters are inter alia
cytokine determinations in the cell culture supernatant. Various types of T cells are
involved in the immune response to an antigen, such as, for example, T-helper cells of
type 1 (Thl cells) or of type 2 (Th2 cells) or of type 0 (ThO cells). The type of T cells
involved in each case has a great effect on whether the immune response induced
against the antigen primarily consists of immunoglobulins of class E (IgE) or of
immunoglobulins of class G (IgG). It is known from the literature that, in particular,
IgE immune responses are responsible for allergic reactions and asthma, whereas IgG
immune responses are usually associated with a tolerance to the antigen. The
particular T cell type activated by the treatment of the PBMCs with an antigen can be
determined for example also by determining the expression of surface antigens on the
cell surface or by determining messengers such as, for example, cytokines which are
released by the PBMCs. Markers of a Thl immune response which can be determined
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are, for example, interferon gamma (INF-g) or interleukin-1 (IL-1) in the cell culture
medium, whereas IL-4, IL-5, IL-6, IL-10 and IL-13 indicate a Th2 immune response.
These cytokines can be detected by standard methods known to the skilled worker,
such as, for example, ELISA determinations from, for example, the cell culture
supernatants or FACS analyses of the messengers present on the surface or inside the
cells of the PBMCs, or by Western blots of cell culture supernatants or cell lysates
etc. Numerous other methods suitable for detecting these or other messengers are
disclosed in the literature [43, 44]. Besides the messengers released by the PBMCs, it
is also possible to use intracellular or membrane-associated messengers or further
proteins for immunological characterization of the T cells in PBMCs. Numerous
antibodies suitable for such investigations are supplied inter alia by Pharmingen, San
Diego, CA, USA, Beckmann Coulter Inc., Fullerton, CA, USA, Santa Cruz
Biotechnology Inc., Santa Cruz, CA, USA, etc. Corresponding investigations can,
however, be carried out not only with patients" primary cells but also with cells
obtained from appropriately treated experimental animals, e.g. mice, rats, guinea pigs,
etc. Experiments with experimental animals have the advantage that not only can the
cells of these animals be studied in vitro, but that the immune system can be
investigated in vivo in the context of an intact organism. It is thus also possible to
investigate the effect of the dosage, composition and administration form of the MAT
molecules and of corresponding controls such as, for example, molecules which
consist only of an antigen or which consist only of a translocation module and an
antigen module or which consist only of a targeting module and of an antigen module.
It is possible to investigate inter alia whether there are differences in the nature of the
immune response if MAT molecules or corresponding controls are injected
subcutaneously in a conventional way or if the injection takes place for example
directly into lymph nodes. It is also possible to investigate the effect of noninvasive
administrations such as, for example, orally or sublingual administration of the MAT
molecules and of corresponding controls. A further investigation which can be carried
out in experimental animals is administration of MAT molecules or corresponding
controls with and without simultaneous administration of adjuvants such as, for
example, mineral oil, mycobacterial extracts or Freund"s adjuvant. It is also possible
to ascertain the most effective or best-tolerated time schedule for the immunizations
to be carried out, and the dose and number of immunizations. Different antigen
modules can moreover be tested for their efficacy. It is possible in this way to
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ascertain the best immunization strategy for later studies on human patients.
Besides messengers, intracellular proteins and surface proteins, also suitable in particular for characterizing the immune reaction of cells cultivated in vitro or for characterizing the immune reaction of experimental animals or of human patients in clinical studies are immunoglobulins. It is possible for example by using ELISAs to investigate and quantify whether the antibodies released owing to the administration of the allergen or antigen are of the IgE type or of the IgG type. This information would indicate the type of immune reaction involved.
Since the messengers released by the T cells also inter alia have an effect on the proliferation of cells of the immune system which are present inter alia in PBMC preparations, it is also possible to characterize the immune response by determining the proliferation of cells such as, for example, PBMCs. It is possible for this purpose to carry out for example in vitro investigations such as, for example, DNA incorporation studies with tritium-labeled thymidine to detect cell growth. Numerous other methods known to the skilled worker for determining cell proliferation can likewise be used in these investigations. Proliferation of certain cells of the immune system can also be determined in vivo by for example carrying out FACS investigations with blood samples from experimental animals or human patients taking part in studies. It is possible by selecting suitable antibodies to quantify for example different subpopulations of cell types present in the blood. The effect of a treatment with MAT molecules or corresponding controls can be investigated in this way.
Exemplary embodiments
The following exemplary embodiments are intended to illustrate the invention by way of example but are by no means intended to restrict the range of protection of the invention.
Example 1:
Cloning of expression vectors for MAT molecules
All the molecular-biology methods described below were carried out in accordance
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with standard methods known to the skilled worker [43], The vector pQE-30 (Qiagen, Hilden, Germany) was used for cloning a vector for expression of MAT molecules (modular antigen transport molecules).
In a first step, a nucleic acid sequence which codes for a translocation module was
introduced into a bacterial expression vector. The DNA sequence which codes for the
amino acids GYGRKKRRQRRR of HIV Tat was introduced via synthetic
oligonucleotides into the vector pQE-30. The oligonucleotides comprised in addition
to the HIV Tat sequence at the 5" end a recognition sequence of the restriction
endonuclease Bgl II and at the 3" end recognition sequences for BamH I, Spe I, Pst I
and Hind III. The synthetically prepared HTV Tat sequence was subsequently cut with
Bgl II and Hind III and the vector pQE-30 was cut with the restriction endonucleases
Bam HI and Hind III. The Tat sequence and the vector pQE-30 were then isolated
using NucleoSpin extract 2 in 1 (Macherey-Nagel, Oensingen, Switzerland), joined
together using ligase, transformed into competent bacteria by electroporation, and
plated out on ampizilin-containing agar plates. Some of the resulting bacterial
colonies were selected, and vector DNA was isolated therefrom. The vectors obtained
in this way were sequenced using standard methods to confirm the nucleic acid
sequence. Bacterial clones which comprised vectors having the correct sequence were
used for further studies. In a second step, a targeting module was introduced into the
vector. For this purpose, mRNA from human peripheral mononuclear cells (PBMCs)
was isolated using standard methods known to the skilled worker and transcribed via
reverse transcriptase PCR into complementary DNA (cDNA). The nucleic acid
sequence of the human invariant chain of the MHC II molecule which codes for
amino acids 1 to 110 of the invariant chain of MHC II was obtained by using the
cDNA obtained in this way and by using various PCR primers which introduced a
Bgl II recognition sequence at the 5" end of the PCR product and introduced Spe I,
Bam HI, Pst I and Hind III recognition sequences at the 3" end of the PCR products.
This sequence region of the invariant chain of MHC II was introduced in accordance
with the first step behind the 3" end of the Tat sequence already introduced into the
pQE-30 vector. The sequence of the resulting vector was confirmed by sequencing.
Standard methods of site-directed mutagenesis known to the skilled worker were used
to replace cytosine by thymidine at position 292 and guanine by adenine at position
318. The two point mutations do not lead to changes in the amino acid sequence of
49

the corresponding protein, but merely remove unwanted recognition sequences of restriction endonucleases. In a third step, finally, an antigen module was introduced into the vector. Nucleic acid sequences of various antigens were obtained by using the pQE-30 vector into which the coding sequence of the particular antigen had previously been introduced and by using PCR primers which introduce an Spe I and/or BamH I recognition sequence at the 5" end of the PCR product and a stop codon and a Pst I or a Hind III recognition sequence at the 3" end of the PCR product. Inter alia, the nucleic acid sequence which codes for amino acids 1 to 222 of the antigen Der p 1 (based on the amino acid sequence of the mature Der p 1 protein) was obtained as antigen module. This sequence region of the antigen Der p 1 was introduced in accordance with the first two steps behind the 3" end of the sequence of the invariant chain of MHC II which had already been introduced into the pQE-30 vector. The correct sequences of the resulting vectors were confirmed by sequencings. For subsequent studies, the expression vectors were isolated using QIAfilter plasmid midi kits (Qiagen, Hilden, Germany) in accordance with the manufacturer"s protocol.
Example 2:
Obtaining the coding sequences of the antigens Bet v 1, Asp f 1, Asp f 6 and Der p 1 The coding sequences of the various antigens in the antigen modules were isolated by various methods known to the skilled worker [43]. The Bet v 1 sequence was obtained via synthetic oligonucleotides, the Asp fl and Asp f6 sequences were obtained in earlier studies and isolated from the vectors used in these studies [45, 46] and subsequently introduced into the pQE-30 vector, and the Derp 1 sequence was isolated by reverse transcriptase PCR using mRNA obtained from house dust mites (Dermatophagoides pteronyssinus).
Example 3:
Expression and isolation of MAT molecules in bacteria
The expression and isolation of MAT molecules was carried out in accordance with
the manufacturer"s information (Qiagen, Hilden, Germany). In detail, a preculture of
E. coli Ml5 bacteria transfected with the particular expression vector (pQE-30-MAT
molecule) was set up in 20 ml of medium (2x YT medium, 100 (xg/ml ampicillin,
25 (xg/ml kanamycin) in a bacterial shaker at 37°C overnight. The preculture was then
cultivated in 2000 ml of medium (2"x YT medium, 100 ug/ml ampicillin, 25 ug/ml
50

kanamycin) at 37°C in a bacterial shaker until it reached an optical density of 0.6 at a wavelength of 600 nm. After addition of IPTG in a final concentration of 1 mM and a renewed growth phase of from 4 to 15 h, the bacteria were separated from the culture medium by centrifugation at 2000 g for 20 minutes, and the bacterial pellet was stored at -20°C. Cell lysates were produced by thawing the bacterial pellet, resuspending in 8 M urea solution (5 ml of urea solution per gram wet weight of the bacterial pellets), cautiously stirring for 1 to 2 h and subsequently centrifuging at 48 000 g for 30 min. The clear supernatant was used for preparative nickel chelate chromatography of the MAT molecules. The MAT molecules were isolated by using 49 or 18 ml columns (Bio-Rad Laboratories Inc., Hercules, CA, USA), packed with 5 to 10 ml of Ni-NTA Superflow matrix (Qiagen) and a chromatography system from Bio-Rad (Econo pump and UV monitor). The chromatography column is initially washed with 5 column volumes of buffer A (100 mM NaH2P04, 10 mM Tris/HCl, 6 M guanidine HC1, pH adjusted to 8.0 with HC1) and then the bacterial lysate is loaded onto the column at a flow rate of 1.4 ml/min. Then 5 to 10 column volumes each of buffer A and buffer B (buffer B: 100 mM NaH2P04, 10 mM Tris/HCl, 8 M urea, pH 8.0) are pumped onto the column at a flow rate of 1.4 ml/min, and the absorption of the flow-through at a wavelength of 280 nm (A280) is observed. As soon as the flow-through has reached a stable A280 of less than about 0.01, the column is washed with 5 to 10 column volumes of buffer C (100 mM NaH2P04, 10 mM Tris/HCl, 8 M urea, pH adjusted to 6.3 with HC1) until finally a stable A280 of less than about 0.01 is reached. The MAT molecule is then eluted with buffer E (100 mM NaH2P04, 10 mM Tris/HCl, 8 M urea, pH adjusted to 4.5 with HC1) and collected.
Example 4:
Detection of MAT molecules with SDS polyacrylamide gels, Coomassie staining and with anti-His Western blotting SDS polyacrylamide gel electrophoresis:
Buffer, NuPAGE® gels and an Xcell SureLock™ electrophoresis chamber from Invitrogen (Invitrogen Life Technologies, Breda, The Netherlands) were used for the electrophoresis in accordance with the manufacturer"s information. 5 or 10 ug of the isolated MAT molecules per lane underwent electrophoretic separation in 12% NuPAGE® Novex bis-Tris gels (Invitrogen) at a constant voltage of 200 V using 1 * concentrated NuPAGE® SDS sample buffer under reducing conditions over the course
51

of 35 to 50 min. The running buffer used was MES or MOPS buffer (MES buffer: 50 mM MES (morpholinoethanesulfonic acid), 50 mM Tris/HCl, 3.5 mM SDS, 1 mM EDTA, pH 7.3, MOPS buffer: 50 mM MOPS (3-(N-morpholino)propanesulfonic acid), 50 mM Tris/HCl, 3.5 mM SDS, 1 mM EDTA, pH 7.7).
Coomassie blue staining:
The gels are stained by incubating them in staining solution (200 ml of methanol, 50 ml of acetic acid, 250 ml of water, 0.5 g of Coomassie blue R-250) for 1 h and then destaining with multiple changes of the destaining solution (200 ml of methanol, 50 ml of acetic acid, 250 ml of water) until the background of the gels is clear. The Xcell II™ blot module (Invitrogen) is used for electrotransfer of the proteins from the NuPAGE® gel onto a blotting membrane in accordance with the manufacturer"s information. The blotting apparatus is set up in accordance with the manufacturer"s information using lx NuPAGE® transfer buffer with 10 or 20% methanol. PVDF membranes were used as blotting membrane, and the electrotransfer took place at a constant voltage of 30 V for 1 h.
Immunological detection of MAT molecules:
Immunological detection of MAT molecules took place using anti-His antibodies in accordance with the manufacturer"s instructions (anti-RGS(His)4 antibodies, Qiagen, Hilden, Germany). All the experimental steps take place at room temperature. The PVDF membrane is initially dried and then incubated directly, without previous blocking of free protein-binding sites, with the anti-His antibody (Qiagen) in a dilution of from 1:1000 to 1:2000 in TBS (50 mM Tris/HCl, 150 mM NaCl, pH 7.5) with 3% BSA (bovine serum albumin) for 1 h. The membrane is then washed 3x with TBS, 0.05% Tween 20, 0.2% Triton X-100 for 10 min each time and subsequently washed once with TBS without further additions. The secondary antibody used is anti-mouse Ig-HRP conjugate (Amersham, Buckinghamshire, England) in a dilution of from 1:10 000 to 1:20 000 in TBS with 10% milk powder, incubating for 1 h. Finally, the blot is washed 4x with TBS, 0.05% Tween 20, 0.2% Triton X-100 for 10 min each time. The conjugate is detected using the ECL™ system (Amersham) in accordance with the manufacturer"s information. The chemilurninescence signal is detected using autoradiography films, which are developed in accordance with
standard protocols.
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Example 5:
Translocation of MAT molecules into cell lines and primary human cells PBMCs (peripheral blood mononuclear cells) were obtained from fresh, heparin-treated human blood from volunteer subjects by standard methods of density gradient centrifugation known to the skilled worker using Ficoll-Paque (Pharmacia, Uppsala, Sweden). The Jurkat cell line was obtained from the ATCC (American Type Culture Collection, Manassas, VA, USA). The cells were cultivated in RPMI-1640 medium containing the following additions: 10% fetal calf serum, 200 units/ml penicillin, 200 pg/ml streptomycin, MEM vitamins, MEM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine and 0.001% 2-mercaptoethanol. To determine the translocation, the cells were resuspended in a concentration of lx 10Exp6/ml RPMI medium with all additions. The cells were incubated in accordance with the respective information in the explanations for the figures with concentrations of from 0.01 to 5 mM of the recombinant molecules or MAT molecules over a period of 5 min at 4, 22 or 37°C. The cells were then centrifuged, and the cell pellet was incubated in 40 |j.l of lysis buffer (8 M urea, 100 mM sodium phosphate, l0 mM Tris/HCl, l00mM ammonium chloride) at room temperature for 5 min. Insoluble cell constituents were removed by centrifugation (15 000 g, 15 min) and the clear lysate was further investigated by Western blotting in accordance with example 4. An anti-His antibody was used to detect the proteins.
Example 6:
Stimulation of peripheral blood mononuclear cells (PBMC) from patients with
allergies
The methods described below for stimulating PBMCs and for determining the
proliferation of the stimulated PBMCs are described in the literature [44]. PBMCs
were isolated from fresh, heparin-treated blood from volunteer subjects by density
gradient centrifugation using Ficoll-Paque (Pharmacia, Uppsala, Sweden). The
volunteer subjects were patients with an allergy against an allergen known for the
individual patient. The patients were informed in accordance with Swiss laws about
the experiments carried out on their blood samples and gave their consent to take part
in this study. After the PBMCs had been obtained they were taken up in RPMI
medium with the additions according to example 5, and in each case from 0.01 to
53

100 nM of the recombinant antigen against which the particular patient shows an allergic reaction were added, In each case, the unmodified antigen and the antigen coupled to a translocation module and a targeting module (MAT molecule) were investigated. Experimental approaches in which no targeting module but only a translocation module and the antigen module were coupled were also carried out in some experiments (figure 7 A). The controls also used in some experiments were only the translocation module or a construct consisting of translocation module and targeting module but without antigen module. After an incubation time of 5 days, l0 pCi/ml tritium-labeled thymidine was added to the medium. The thymidine incorporation of the PBMCs wag ascertained as a measure of the efficiency of antigen presentation and the proliferation, associated therewith, of the treated cells. For this purpose, the radioactive cell culture medium was removed after 8 to 10 h, the cells were washed and the amount of incorporated radioactive thymidine was determined by measuring the radioactivity. A 1205 Betaplate liquid scintillation counter from Wallac ADL AG, Hiinenberg, Switzerland, was used for this. As control, cells not stimulated with antigen were likewise incubated with tritium-labeled thymidine and then analyzed in the same way. The result obtained is a measurement of the incorporation of radioactive thymidine as a measure of the proliferation and thus as a measure of the efficiency of Antigen presentation. A higher measured thymidine incorporation means a more efficient antigen presentation. Since antigen concentrations of from 0.01 nM to 100 nM were investigated in each experiment, it is additionally possible to determine the antigen concentration at which maximum antigen presentation takes place. A lower concentration means that the antigen is more effective as modulator of an immune response. As a further control, cells were treated with 0.5 ug/ml each of an anti-CD3 and of an anti-CD28 antibody, which treatment represents a very strong proliferation stimulus. It was thus possible to determine the maximum possible thymidine incorporation due to the proliferation of PBMCs for each experiment.
Example 7:
MAT molecule-stimulated cytokine release
PBMCs were isolated from the blood of allergic people as described in example 5 and diluted 10Exp6/ml of medium, 100 ul portions of this cell suspension were seeded in 96-well plates and treated with from 0.01 to 1000 nM of the isolated antigens for
54

5 days. The cell culture medium was not replaced in this time. After centrifugation of the 96-well plates, the supematants were removed and stored at -20°C until the cytokines were analyzed. The PBMCs were treated in each case with the antigen against which the patient from whom the PBMCs were isolated shows an allergic reaction. The following cytokines were investigated in the supematants obtained in this way: interferon gamma (INFg), interleukin-10 (IL-10) and interleukin-5 (IL-5). Figure 8A and 8B show results obtained with PBMCs from patients showing an allergic reaction to Bet v 1. The INFg, IL-10 and IL-5 immunoassays (ELISAs = enzyme-linked immunosorbent assays) were carried out by methods known to the skilled worker using DuoSet® ELISA Development Systems from R&D Systems Inc., Minneapolis, USA.
In parallel with the obtaining of the supematants for the cytokine determinations, stimulation experiments were also carried out with PBMCs from the same donors in accordance with example 6. The results of these cell proliferation assays are likewise depicted in figure 8A and 8B.
Example 8:
In vivo effect of unmodified antigens and antigens present in the antigen module of MAT molecules Immunization of mice
In order to test the efficacy of MAT molecules, CBA/2 mice were immunized 3 * at an interval of 2 weeks each time with recombinant MAT molecules together with aluminum hydroxide as adjuvant in a manner known to the skilled worker. The recombinant MAT molecules were produced as described in example 3. 3 different routes were used for the immunization. A series of experiments was carried out in each case with subcutaneous, intraperitoneal and intranodal injection of the antigens or of the controls. In the case of intranodal injection, the tissue was exposed surgically so that direct injection was possible. The MAT molecule used was a protein consisting of the HIV Tat sequence as translocation module, the human invariant chain as targeting module and the PLA2 (phospholipase A2 from bee venom) peptide as antigen module (designation: trans-target-PLA2). PLA2 (designation: PLA2) was used as control, and 0.9% strength saline solution (designation: control) was used as further control. The intranodal immunization took place with 0.1 (xg, the subcutaneous
55

and intraperitoneal immunization took place with 10 ug of MAT molecule or corresponding amounts of control protein or control buffer together with aluminum hydroxide as adjuvant. 3 animals were immunized in each experimental group, so that in each case 9 animals were used per experiment. 3 series of experiments were carried out, and a different immunization route (subcutaneous, intraperitoneal, intranodal) was tested in each series of experiments. Blood was taken from the tail vein of each experimental animal before the first immunization and subsequently after 2, 4 and 6 weeks. The blood coagulated at room temperature, and then the serum was obtained after centrifugation and stored at -20°C until analyzed. The sera produced in this way were used to determine the PLA2-specific IgG and IgE titers.
Determination of the PLA2-specific IgG2a titers in mouse sera
For determination of the PLA2-specific IgG2a titer, microtiter plates (96 cavities) were coated with 100 ul/cavity of a solution of 5 ug/ml PLA2 (Sigma-Aldrich, Buchs DG, Switzerland) in carbonate buffer at 4°C overnight. After washing 2x with phosphate-buffered sodium chloride solution (PBS), 0.05% Tween, free protein-binding sites were blocked by incubation with blocking buffer (PBS, 2.5% skim milk powder), 200 ul/cavity, at room temperature for 1 to 2 h. Washing 2x was repeated, and then serial 1:2 dilution series in blocking buffer (50 ul/cavity) of the serum samples to be tested (1:2 to 1:64 dilutions) were incubated at room temperature for 3 h or at 4°C overnight. Incubations without serum or with serum from untreated animals were carried out as negative controls. This was followed by washing 5X and incubating with a 1:500 dilution in blocking buffer of a biotin-labeled anti-mouse IgG2a (PharMingen GmbH, Hamburg, Germany) at room temperature (100 ul/cavity) for 2h, and again washing 5*. Finally, 100 ul/cavity of a horseradish peroxidase diluted 1:1000 in blocking buffer were incubated at room temperature for 1 h and then washed 6*. The color reaction was carried out with 100 ul/cavity of a solution of ABTS (2,2"-azinodi-(3-ethylbenzothiazolinesulfonic acid) in ABTS buffer in accordance with the manufacturer"s information with 0.1% (v/v) of a 30% strength hydrogen peroxide solution. After about 30 minutes, the absorption at a wavelength of 405 nm (reference filter: 595 run) was measured. The results of these tests are depicted in figure 9.
56

Determination of the PLA2-specific IgE titers in mouse sera
The PLA2 IgE ELISA is carried out in accordance with the protocol for the PLA2 IgG2a ELISA. The deviations occurring from the protocol described above are as follows: the microtiter plates are coated with 5 ug/ml of an anti-mouse IgE antibody. After the serum samples have been incubated and the plates have been washed, a 1:333 dilution of biotin-labeled PLA2 (Pierce Biotechnology Inc., Rockford, USA) is incubated. The development of color with ABTS takes about 1 h. The results of these tests are depicted in figure 9.
Explanations of the figures
Figure 1
Theoretical structure of MAT molecules
Figure 1 shows by way of example how the individual modules of a MAT molecule of the invention may be constructed diagrammatically. Therein "Trans" stands for a translocation module, "Target" stands for a targeting module, "AG" stands for an antigen module, "Tag" stands for a tag module and a dash (-) stands for a linker module. The linker module may connect the other modules together by covalent and/or noncovalent linkages. Figure 1 A depicts a number of examples of linear arrangements of the various modules. Figure 1 B depicts various examples of arrangements of branched MAT molecules, with dendrimeric structures also being included, and figure 1 C depicts some examples of arrangements of circular MAT molecules, it being possible to combine circular arrangements with linear and/or branched arrangements. In general, all the depicted arrangements are only examples intended to illustrate the fact that a wide variety of arrangements is possible. The diagrammatically depicted MAT molecule examples are by no means to be understood as limiting the scope of protection of the present invention.
57

Figure 2
Expression, purification and detection of fusion proteins
Various MAT molecules consisting of tag module (His6 tag), translocation module (Tat sequence), targeting module (human invariant chain of MHC II) and antigen module (Asp fl = Aspergillus fumigatus antigen 1) were expressed in E. coli and isolated under denaturing conditions using immobilized metal ion affinity chromatography. The steps were carried out in accordance with the information from the manufacturer of the expression system (Qiagen, Hilden, Germany) [47, 48]. 10 |xg or 5 \xg samples of the isolated proteins were fractionated by electrophoresis in SDS polyacrylamide gels and then either stained with Coomassie blue (fig. 2 A) or analyzed in a Western blot using antibodies which recognize the tag module (fig. 2 B). The positions of the expressed proteins are marked by arrows.
Figure 3
Temperature-independent translocation of proteins and MAT molecules
Primary human peripheral mononuclear cells (PBMCs) were incubated with the
particular proteins or MAT molecules in a concentration of 1 uM at 4, 22 or 37°C for
5 minutes, washed, taken up in urea-containing sample buffer and lyzed. The lysates
were then fractionated by electrophoresis in SDS polyacrylamide gels and
electrotransferred to PVDF membranes, and the proteins or MAT molecules were
detected using a specific antibody (anti-RGS(His)4 antibodies). The arrows show the
position of the proteins or MAT molecules. The fusion proteins were detectable in the
lysates of the cells at all temperatures, indicating successful translocation to the
interior of the cells.
Figure 4
Translocation of MAT molecules in cell lines and primary cells The result depicted in figure 4 was carried out with virtually the same methods as the experiment in figure 3, but with two deviations: figure 4 A shows that translocation of the MAT molecules was successful both in primary human cells (PBMCs) and in human tumor cell lines (Jurkat cells). The arrows show the position on the Western blot at which the protein or the MAT molecule was detected. Figure 4 A and 4 B additionally show that various antigen modules (Asp f 1 = Aspergillus fumigatus allergen, Der p 1 = house dust mite allergen, Bet vl= birch pollen allergen) can enter
58

primary human PBMC cells by translocation.
Figure 5
Dose kinetics of the translocation of MAT molecules
The result depicted in figure 5 was obtained with virtually the same methods as the
experiment in figure 3, but in this case three or four different concentrations of
proteins or MAT molecules were used (0.01 mM, 0.1 mM, 1 raM and 5 mM). It was
possible to show a clear dose dependency for the translocation reaction. Larger
amounts of the particular molecule were detected in the interior of the cells as the
concentration of added MAT molecules increased. The positions of the respective
molecules are marked with arrows.
Figure 6
Various functional structures of MAT molecules
The result depicted in figure 6 was obtained with virtually the same methods as the
experiment in figure 3, but in this case three different arrangements of translocation
module (Tat sequence) and antigen module (Asp f 1 = Aspergillus fumigatus allergen)
were investigated. The arrow in figure 6 A indicates the position at which the fusion
protein was detected in the Western blot. Figure 6 B depicts the structure of the three
different fusion proteins. Fusion proteins with N-terminal, inverted C-terminal and
with C-terminal translocation module were investigated. All three fusion proteins
were transported successfully by translocation into the interior of the cells.
Figure 7
Antigen/MAT molecule mediated in vitro cell proliferation of PBMCs of allergic people
Figure 7 depicts investigations on PBMCs (peripheral blood mononuclear cells) from allergic people which were put together with a MAT molecule in vitro. The MAT molecule comprised as antigen module the particular allergen against which the allergy patient shows an allergic reaction. An antigen presentation of the antigen-presenting cells of the allergic person which is more efficient owing to addition of the MAT molecule leads to stimulation of growth of the PBMCs. The cell proliferation resulting therefrom was quantified via the incorporation of radiolabeled DNA
building blocks (thymidine) (y axis). The x axis indicates the MAT molecule
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concentration used in the particular cell-stimulation test, or the antigen molecule concentration, in nM. On use of MAT molecules at relatively low concentrations there is a cell proliferation (= immunostimulation = increase in thymidine incorporation = increase in radioactivity) in all the patients investigated with all the antigen modules investigated (as part of the MAT molecule). As control, in each case the same PBMCs were treated only with water containing no MAT molecules or antigens (= control in the legend). In addition, the thymidine incorporation by cells treated with a strong growth stimulus (anti-CD3 and anti-CD28 antibodies, 0.5 ug/ml each) for 5 days was measured as positive control for each experiment. The growth obtained by this stimulus represents a check of the quality of the prepared PBMCs in relation to their ability to proliferate. The value resulting therefrom in the experiment in figure 7A was 77 864 ± 5347 cpm, the value resulting in the experiment in figure 7B was 100 374 ± 11 678 cpm and the value resulting in the experiments in figures 7C and D was 112 205 ±5958 cpm.
Figures 7 A to 7 G show that with all 7 tested antigens incorporation of the antigen into the antigen module of a MAT molecule leads to the onset of proliferation of the PBMCs of the allergic person even at relatively low concentrations. The antigens tested were Der p 1 (house dust mite allergen; fig. 7 A), Bet v 2 (birch pollen allergen, fig. 7 B), Asp f 1 (Aspergillus fumigatus allergen 1, fig. 7 C), Asp f 6 (Aspergillus fumigatus allergen 6, fig. 7 D), Asp f 3 (Aspergillus fumigatus allergen 3, fig. 7 E), PLA2 (phospholipase A2 allergen from bee venom, fig. 7F) and Fel d 1 (Felis domesticus, fig. 7G). Figure 7 H shows in addition for the antigen Bet v 1, on use of MAT molecules with Bet v 1 in the antigen module with 4 different patients (I. to IV.) with allergy to Bet v 1, that a proliferation of the PBMCs of the individual patients occurs in all 4 cases at lower concentrations than on use of Bet v 1 as antigen.
Figure 8
Antigen/MAT molecule mediated in vitro cytokine secretion by PBMCs from allergic
people
Figures 8A and 8B show for two independent patients showing an allergic reaction to
Betvl that PBMCs cultivated in vitro and stimulated with the Betvl antigen
(Bet v 1 alone or as module of a MAT molecule) display a defined cytokine secretion
pattern. I. shows in each case the result of a cell proliferation test (as in fig. 7), II.
60

shows the interferon gamma (INPg) levels, III. shows the interleukin-10 (IL-10) values and IV. shows the interleukin-5 (IL-5) levels in the cell culture supernatants. With a PBMC stimulation having the desensitizing effect, the PBMC proliferation and an increase in INFg release should take place even with lower antigen doses. In addition, the IL-5 production should be lower. This cytokine secretion pattern indicates a desensitization of the immune cells of the allergic people (Thl instead of Th2 immune response). The increase in the IL-10 concentration explains why the cell proliferation (fig. I.) falls at higher antigen doses. This cytokine secretion pattern occurs in both cases (fig. SA and fig. SB).
Figure 9
Antigen/MAT molecule mediated in vivo immune response in mice CBA/2 mice were immunized with isolated PLA2, with MAT molecules having PLA2 in the antigen module or with control buffer 3x at intervals of 2 weeks and then the PLA2-specific serum titers of IgG2a and IgE antibodies were measured. If there is desensitization, only PLA2-specific IgG, but not PLA2-specific IgE, antibodies should appear. IgE antibodies are responsible for allergic reactions. 3 different immunization routes were investigated, subcutaneous, intraperitoneal and intranodal injection of the antigens. It is found with all three immunization routes that immunization with PLA2 leads to a distinct IgE immune response (allergy) (fig. 9, left-hand column). On immunization with a MAT molecule which comprises PLA2 as antigen module, however, there is no IgE immune response (no allergy). By contrast, both immunization with PLA2 and with MAT molecules which comprise PLA2 in the antigen module lead to a desired IgG immune response which does not induce allergic reactions.
All the examples and enumerations in the present patent application are intended in principle to explain the subject matter but not to restrict the claims. In particular, the examples of translocation modules, targeting modules, antigen modules, spacer modules and tag modules are to be understood to be only examples, but not an exhaustive list of all possible constituents of the MAT molecule. The basic idea of the invention does not consist of a particular combination of particular translocation modules, particular targeting modules and particular antigen modules. The basic idea of the present invention is, on the contrary, to use a combination of at least these three
61

modules to give a MAT molecule for immunization. The specifically used example in each individual one of the modules is therefore immaterial for the concept of the invention, and it is consequently also possible to use other examples, including those not currently known, for the respective modules for the purposes of the invention.
If a term is not unambiguously defined in this patent, or is not known to the skilled worker in the particular art, or a term cannot be unambiguously defined from the context, then the definition mentioned for the respective term in the following standard works applies in each case. If a term is mentioned in more than one of the works cited below with different definitions, the definition which applies in each case is that mentioned in the first work mentioned in the following list. The following publications are cited for this purpose:
• The Merck Mannual [49]
• Molecular Cloning - A Laboratory Manual [43]
• Current Protocols in Immunology [44]
• Current Protocols in Protein Science [50]
• Current Protocols in Pharmacology [51]
• Current Protocols in Cell Biology [52]
62

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61

SEQUENCE LLSTim
a
D
BioVisioN AG
a
0
Modular antigen transporter molecules (MAT molecules)
for modulating immune reactions

D
MAT
0

EPO2O22774.0
0
2002-10-11
0
D
20
Patentlti version 3-3
X
68

870 DNA Human immunodeficiency virus + Homo sapiens + Aspergillus fumigstua
1
atgagaggat cgcatqacca tcaceaecae ggatctggtt acggtcgtaa aaagcgtcgc 60
cagcgtcgcc gtggatctat ggatgaccag cacgacctta tctccaacaa tgagcaactg 120
cccatgctgg gccggcgccc tggggccccg gagagcaagt gcagccgcgg agccctgtac 180
acaggctttt ccatcctggt gactctgctc ctcgctggcc aggccaccac cgcctacttc 240
ctgtaccagc agcagggccg gctggacaaa ctgacagtca cctcccagaa cttgeagctg 300
gagaacctgc goatgaaact tcccaagcct cccaagcctg tgagcaagat gcgcatggcc 360
accccgctgc tgatgcagge gctgcccatg ggagccctgc cccaggggac tagtggatcc 420
gcgacctgga catgcatcaa ccaacagctg aatcccaaga caaacaaatg ggaagaeaag 480
cggcttctat acagtcaagc caaagccgaa agcaactccc accacgcagc tctttccgac 540
ggcaagaccg gtagcagcta cccgcactgg ttcactaacg gctacgacgg gaatggcaag 600
ctcatcaagg gtcgcacgeo catcaaattc ggasaagccg actgtgaccg tcccccgaag 660
cgcagccaga acggcetggg caaggatgac cactacctgc sggagttccc gacttttcca 720
gatggecacg actataagtt tgactcgaag aaacccaagg aagacccggg cccagcgagg 780
gtcatctata cttatcccaa caaggtgttt tgcggcattg tggcccatca gcgggggaat 840
cagggagact tgagactgtg ttctcatteg 870
2 289
69

PRT
Human immunodeficiency virus + Homo sapiens + Aspergillus furcigatus
2
Met Arg Gly Ser His His Bis His flis His Gly Ser Gly Tyr Gly Arg
15 10 15
Lys Lys Arg Arg 20 25 30
leu He Ser Asn Asn GLu Gin Leu Pro Mat Leu Gly Arg Arg Pro Gly
35 40 45
Ala Pro Glu Ser lys Cys Ser Arg Gly Ala Leu Tyr Thr Gly Phe Ser
50 55 60
He Leu Val Thr Leu Leu Leu Ala Gly Gin Ala Thr Thr Ala Tyr Phe
65 70 75 80
Leu Tyr Gin Gin Gin Gly Arg Leo Asp Lys Leu Thr Val Thr Ser Gin
8 5 90 95
Asn Leu Gin Leu G,lu Asn Leu Arg Met Lys Leu Pro Lys Pro Pro Lys
100 105 110
pro val Ser Lys Met Arg Met Ala Thr Pro Leu Leu Met Gin Ala Leu
115 . 120 125
Pro Met Gly Ala Leu Pro Gin Gly Thr Ser Gly Ser Ala Thr Trp Thr
130 135 140
70

Cys lie Asn Gin Gin Leu Asn Pro Lys Thr Asn Lys Trp Glu Asp Lys
145 150 155 160
Arg Leu Leu Tyr Ser Gin Ala Lys Ala Glu Ser Asn Ser His Kis Ala
165 170 175
Pro Leu Ser Asp Gly Lys Thr Gly Ser Sez Tyr Pro His Trp Phe Thr
180 185 190
Asn Gly Tyr Asp Gly Asn Gly Lys Leu lie Lys Gly Arg Thr Pro lie
1S5 200 205
Lys Phe Gly Lys Ala Asp Cys Asp Atg ?ro Pro Lys Arg Ser Gin Asn
210 215 220
Gly Met Gly Lys Asp Asp His Tyr Leu Leu Glu Phe Pro Thr Phe Pro
225 230 235 240
Asp Gly His Asp Tyr Lys Phe Asp Ser Lys Lys Pro Lys Glu Asp Pro
245 250 255
Gly Pro Ala Arg Val lie Tyr Thr Tyr Pro Asn Lys Val Phe Cys Gly
260 265 270
He Val Ala His Gin Arg Gly Asn Gin Gly Asp Leu Arg Leu Cys Ser
275 280 2S5
His
3 1044
71

DMA
Human immunodeficiency virus + Homo sapiens + Aspergillus fumigatus
3
atgagaggat cgcatcaccs tcaccatcac ggatctggtfc aeggtcgtaa aaagcgtcgc 60
cagcgtcgcc gcggatctat ggatgaccag cacgacctta tctccaacaa tgagcaactg 120
cccatgctgg gccggcgccc tggggccccg gagagcaagt gcagccgcgg agccctgtac 180
aeaggctttt ccatcctggt gactctgcts ctcgctggcc aggceaccac cgcctacttc 240
ctgtaccagc agcagggecg gctggacaaa ctgacagtca cctcccagaa cttgcagctg 300
gagaacctgc gcatgaaact tcccaagcct cccaagcctg tgagcaagat gcgcatggec 360
acceegctgc tgatgcaggc gctgcccatg ggagccctgc cccaggggac tagtggatct 420
caatacacgc tcccacccct cccctaccce taegatgccc tecaacccta catctcccaa 480
cagatcatgg agctgcacca caaaaagcac cateaaacet acgtcaatgg cctgaatgcc 540
gcactcgagg cgcagaagaa agcggcggaa gccaccgacg tccccaagct cgtctccctg 600
cagcaagcga tcaaattcaa cggcgggggg cacatcaacc attccctctt ctggaagaat 660
ctggccccgg agaaatccgg gggtggcasg stcgateagg caecggtcct caaageagcc 720
atcgagcagc gttggggatc cttegataag ttcaaggatg ctttcaacac gaccctgctg 780
ggcattcagg gcagcggatg gggttggtta gtgacegaeg gacccaaggg aaagctagac 840
attaccacaa cccacgacca ggatccggtg accggggcgg cccccctett tggggtggat S00
atgtgggagc atgcttacta ccttcagtac ttgaacgaca aagcctcgta tgccaagggc 960
atctggaacg tgatcaactg ggctgaagcg gagaatcggt acatageggg tgaeaagggt 1020
ggacacccat tcatgaagct gtag 1044
72

4
317
PUT
Human immunodeficiency virus + Homo sapiens + Aspergillus fumigatus
Met Arg Gly Sar His His His His His His (Sly ser Gly Tyx Gly Arg
15 10 15
Lys Lys Arg Arg Gin Arg Arg Arg Gly Sec Met Asp Asp Gin His Asp
20 25 30
Leu He Ser Asn Asn Glu Gin Leu Pro Met Leu Qly Arg Arg ?ro Gly
35 40 45
Ala Pro Glu Ser Lys Cys Ser Arg Gly Ala Leu Tyr Thr Gly Phe Ser
50 55 60
He Lau Val Thr Leu Leu Leu Ala Gly Gin Ala Thr Thr Ala Tyr Fhe
65 70 75 SO
Leu Tyr Gin Glr. Glh Gly Arg Leu Asp Lys Leu Thr Vsl Thr Ser Gin
85 90 95
Asn Leu ein Leu Glu Asn Leu Arg Met Lys Leu Pro Lys Pro Pro Lys
100 105 110
Pro Val Ser Lys Met Arg Met Ala Thr Pro Leu Leu Met Gin Ala Leu
115 120 125
73

Pro Met Gly Ala Leu Pro Gin Gly Thr Ser Gly Ser Gin Tyr Thr Leu
130 135 140
Pro Pro Leu Pro Tyr Pro Tyr Asp Als teu Gin Pro Tyr lie Ser Gin
145 150 155 160
Gin lie Met Glu leu His His Lys Lys His His Gin Thr Tyr Val Asn
165 170 175
Gly Leu Asn Ala Ala Leu Glu Ala Gin Lys Lys Ala Ala Glu Ala Thr
180 185 190
Asp Val Pro Lys Leu Val Ser Val Gl.n Gin Ala lie Lys Phe Asn Gly
195 200 205
Gly Gly His lie Asn His Ser Lea Phe Trp Lys Asn Leu Ala Pro Glu
210 " 215 220
Lys Ser Gly Gly Gly Lys tie Asp Gin Ala Pro Val Leu Lys Ala Ala
225 230 235 240
lis Giu Gin Arg Trp Gly Ser Phe Asp Lys Phe Lys Asp Ala Phe Asn
245 250 255
Thr Thr Leu Leu Gly lie Gin Gly Ser Gly Trp Gly Trp Leu Val Thr
260 265 270
Asp Gly Pro Lys Gly Lys Leu Asp lie Thr Thr Thr His Asp Gin Asp
275 280 285
Pro Val Thr Gly Ala Ale Pro Val Phe Gly Val Asp Met Trp Glu His
290 295 300
74

Ala Tyr Tyr Leu Gin Tyr Leu Aan Asp Lys Ala Ser Tyr Ma Lys Gly
30S 310 315 320
lie Trp Asn Val He Asn Trp Ala Glu Ala Glu Asr. Arg Tyr lie Ala
325 330 335
Gly Asp Lys Gly Gly His Pro Phe Met, Lys Leu
340 345
5
903
DNA
5
atgagaggat cgcatcacca tcaceatcac ggatctggtt acggtcgtaa aaagcgtcgc 60
cagcgtcgcc gtggatctat ggatgaccag cacgacctta tctccaacaa tgagcaactg 120
cccatgctgg gccggcgccc tggggccccg gagagcaagt gcagccgcgg agccctgtac 180
acaggctttt costcctggt gsctctgetc ctcgctggcc aggccaccac cgcctacttc 240
ctgtaccagc agcegggccg getgggcaaa ctgacagtca cctcccsgaa cttgeagctg 300
gagaecctgc gcatgaaact tcccaagccfc cccaagcctg tgageaagat gcgcatggcc 360
accccgctgc tgatgcaggc gctgcccatg ggageectgc eccaggggac tagtggatcc 420
atgggtgttt teaactacga aaccgaaacc acctccgtta tcccggctgc tcgtctgctc 4 50
asggccttca tcctggacgg tgscaacctg ttccctaagg ttgctccgca ggctatctcc 54 0
tccgttgaaa acatcgaagg taacggtggc ccgggtacca tcaagaaaat ctccttcccg 60O
gaaggtctec catttsaata cgtaaaagac cgtgttgacg aagttgscca caccaacttc 660
75

aaasacaact actccgttat cgaaggtggt ccaattggtg acaqcctgga aaaaatctcc 720
aacgaaatca aaatcgtggc aaccecggac ggtggttcca tccttasgat ctccaacaaa 780
teceacacca aaggtgacca cgaagttaaa gctgaaeagg ttaaagcttc gagagaaatg 840
ggtgaaacec cgctgcgtgc tgttgaetcc tacctgctgg ctcactccga tgcatacaac 900
taa 903
&
6
Met Arg Giy S@r His His His His Kis His Cly Ser Gly Tyr Gly Arg
1 5 10 . 15
Lys iys Arg Arg Gin Arg Arg Arg Giy Ser Met Asp Asp Gin Kis Asp
20 25 30
Leu lie Ser Agn Asn Glu Gin L«U Pro Met Leu Gly Arg Arg Pro Gly
35 10 45
Ala Pro Glu Ser Lys Cys Ser Arg Gly Ala Leu Tyr Thr Gly Phe Ser
SO 55 €0
11© Leu Val Thr Leu Leu Leu Ala Gly Gin Ala Thr Thr Ala Tyr Phe
65 70 75 80
76

Leu Tyr Gln Gln Gln Gly Arg Leu Asp Lys Leu Thr Val Thr Ser Gin
85 90 95
Asn Leu Gin Leu Glu Asn Leu Arg Met Lys Leu Pro Lys Pro Pro Lys
100 105 110
Pro Val Ssr Lys Met Arg Met Ala Thr Pro Leu Leu Met Gin Ala Leu
115 120 125
Pro Met Gly Ala Leu Pro Gin Gly Thr Ser Gly Ser Met Gly Val Phe
130 135 140
Asn Tyr Glu Thr Glu Thr Thr Ser Val lie Pro Ala Ala Arg Leu Phe
145 150 155 160
Lys Ala Phe Tie LEIU Asp Gly Asp Asn Leu Phe Pro Lys Val Ala Pro
165 170 175
Gin Ala lie Ser Ser Val Glu Asn lie Glu Gly Asn Gly Gly Pro Gly
180 185 ISO
Thr He Lys Lys He Ser Phe Pro Glu Gly Phe Pro Phe Lys Tyr Val
195 200 205
Lys Asp Arg Val Asp Glu Val Asp His Thr Asn Phe Lys Tyr Asn Tyr
210 215 220
3er Val lie Qlu Gly Gly Pro lie Gly Asp Thr Leu Glu Lys lie Ser
225 230 235 240
^sn Glu lie Lys He Val Ala Thr Pro Asp Gly Gly Ser lie Leu Lys
245. 250 255
77

Ile Ser Asn Lys Tyr His Thr Lys Gly Asp His Glu Val Lys Ala Glu
260 265 270
Glu Val Lys Ma Ser Lys Glu Met Gly Glu Thr Leu Leu Arg Ala Val
275 280 285
Glu Ser Tyr Leu Leu Ala His Ser Asp Ala Tyr Asn
390 295 300
7 1089 DNA
Human iaununodsficiency virus + Homo sapiens + Dermatophagoides
pteronyssinus
atgagaggat cgcatcacca tcaccatcac ggatctggtt acggtcgtaa aaagcgtcgc 50
cagcgtcgcc gtggatctat ggatgaccag cacgacctta tctccaacaa tgagcaactg 120
cccatgctgg gccggcgccc tggggccccg gagagcaagt gcagccgcgg agccctgtac 180
acaggctttt ccatcctggt gactctgctc ctcgctggcc aggceaeeae cgcctaettc 240
ctgtaccagc agcagggccg gctggacaaa ctgacagtca cetcccagaa cttgcagctg 300
gagaacctgc gcatgaaact tcccaagcct cccaagcctg tgagcaagat gcgcatggcc 3§0
accccgotgc tgatgcaggc gctgcccatg ggagccctgc cccaggggac tagtggatcc 120
actaacgcat gtagtatcaa tggaaatgct ccagctgaaa tegatttgcg acaaatgcga 480
actgtcactc ccattcgtat gcaaggaggc tgtggttcat gttgggcttt ctctggtggt 540
gccgca^ictg aatcagctts tttggctcac cgtaatcaat cattggatct tgctgaacaa 60O
78

gesttagtcg attgtgcttc ccaacac«gt tgtcatggtg ataccattcc acgtgctett 660
gaatacatcc aacataatgg tgtcgtccaa gaaagctact atcgatacgt tgcacgagais 720
caatcatgcc gacgacc&aa tgcacaacgt, ttcggtatct caaactattg ccaaa^ttac 780
ceaccaaatg caaacaaaat tcgtgaagct ttggctcaaa cccacagcgc tsttgccgtc 84 0
attattggca tcaaagattt agacgcattc cgtcattatg atggccgaac aatcattcaa 900
cgcgataatg gttaccaacc aaactatcac gctgteaaca ttgttggtta cagtaacgea 560
caaggtgccg attattggat qgtacgaaac agttgggata ccaattgggg tgatastggt 1020
tacggttfltt ttgctgccaa catcgatttg atgatgattg aagaatatcc atatgttgtc 1080
attctctaa 1089
8
362
PRT
Human immunodeficiency virus + Homo sapiens + Dermacophagoides pteronyssinus
8
Met Arg Gly Ser His His His His His His Gly Ser Gly Tyr Gly Arg
15 10 15
Lys Lys Arg Arg Gin Arg Arg Arg Gly Ser Met Asp Asp Gin His Asp
20 25 30
Leu Ile Ser Asn Asn Giu Gin Leu Pro Met Leu Gly Arg Arg Pro Gly
35 40 45
79

Ala Pro Glu Ser Lys Cys Ser ftrg Gly Ala leu Tyr Thr Gly phe Ser
50 55 60
Ile Leu Yai Thr Leu Leu Leu Ala Gly Gin Ala Thr Thr Ala Tyr Phe
65 70 75 80
Leu Tyr Gin Gin Gin Gly Arg Leu Asp Lys Leu Thr val Thr Ser Gin
85 90 95
Asn Leu Gin Leu Glu Asn Leu Arg Met Lys Leu Pro Lys Pro Pro Lys
100 105 110
Pro Vai Ser Lys Met Arg Met Ala Thr Pro Leu Leu Met Gin Ala Leu
115 120 125
Pro Met Gly Ala Leu Pro Gin Gly Thr Ser Gly Ser Tnr Asn Ala Cys
130 135 140
Ser lie Asn Gly Asn Ala Pro Ala Glu He Asp Leu Arg Gin Met Arg
145 ISO 155 160
Thr Val Thr Pro Ile Arg Met Gin Gly Gly Cys Gly Ser Cys Trp Ala
165 170 175
Phe Ser Gly Gly Ala Ala Thr Glu Ser Ala Tyr Leu Ala His Arg Asn
180 185 190
Gin Ser leu Asp Leu Ala Glu Gin Glu Leu Val Asp Cys Ala Ser Gin
195 200 205
His Gly Cys His Gly Asp Thr Ile Pro Arg Gly Ile Glu Tyr Ile Gin
210 215 220
80

His Asn Gly Val Val Gin Glu Ser Tyr Tyr Arg Tyr Vaj Ala Arg Glu
225 230 235 240
Gin Ser Cys Arg Arg Pro Asn Ma Gin Arg Phe Gly He Ser Asn Tyr
245 250 255
Cys Gin Ile Tyr Pro Pro Asn Ala Asn Lys Ile Arg Glu Ala Leu Als
260 265 270
Gin Thr His Ser Ala Ile Als Val Ile He Gly Ile Lys Asp Leu Asp
275 280 285
Ala Phe Arg His Tyr Asp Gly Arg Thr He Tle Gin Arg Asp Asn Gly
290 295 300
Tyr Gin Pro Asn Tyr His Ala Val Asn lie Val Gly Tyr Ser Asn Ala
305 310 315 330
Gin Gly Val Asp Tyr l"rp He V^l Arg Asn Ser Trp Asp Thr Asn Trp
325 330 335
Gly Asp Asn Gly Tyr Gly Tyr Phe Ala Ala Asn lie Asp Leu Met Met
340 345 350
He Glu Glu Tyr Pro Tyr Val Val He Leu
355 360
9
39
DNA
Human immunodeficiency virus
81

S
ggttacggtc gtaaaaagcg tcgccagcgt cgccgtgga 39
10
13
PRT
Human immunodeficiency virus
10
Gly Tyr Gly Arg Lys Lys Arg Arg Gin Arg Arg Arg Gly
15 10
11
429
<:212> DNA
Komo sapiens
11
stgagaggat cgcatcacca tcaccatcac ggatctggct acggtcgtaa aaagcgtcgc 60
cagcgtcgcc gtggatctat ggatgaccag cacgacctta tcttcaacaa tgagcaactg 120
cccatgctgg gccggcgccc tggggccccg gagagcaagt gcagccgcgg agccctgtac ISO
aeaggctttt ccatcctggt gactctgctc ctcgctggcc aggccaccec cgcctacttc 2^0
ctgtaccagc agcagggecg gctggacaaa ctgacagtca cctcccagaa cttgcagctg 300
gagaacctge gcatgaaact tcccaagcct cccaagcetg tgagcaaget gcgcstggcc 360
82

aecccgctgc tgatgcaggc gctgcccatg ggagccctgc cccaggggac tagtctgcag 420
aagcttast 429
12 143
Homo sapiens
12
Met Arg Gly Ser His His His His His His Gly Ser Gly Tyr Gly Arg
15 10 15
Lys Lys Arg Arg Gin Arg Arg Arg Gly Ser Met Asp Asp Gin His Asp
20 25 30
Leu He Ser Aan hsn Glu Gin Leu Pro Met Leu Gly Arg Arg Pro Gly
33 40 45
Ala Pro Glu Ser Lye Cys Ser Arg Gly Ala Leu Tyr Thr Gly Phe Ser
50 55 60
lie Leu Val Thr Leu Leu Leu Ala Gly Gin Ala Thr Thr Ala Tyr Phe
65 70 75 80
Leu Tyr Gin Gin Gin Gly Arg Leu Asp Lys Leu Thr Val Thr Ser Gin
85 90 95
Asn Leu Gin Leu Glu Asn Leu Arg Met Lys Leu Pro Lys Pro Pro Lys
100 105 110
83

Pro Val ser Lys Met Arg Met Ala Thr Pro Leu Leu Met Gin Ala Lau
US 120 125
Pro Met Gly ala Leu Pro Gin Gly Thr Ser Leu Gin Lys Leu Asn
130 135 140
13
450
DNA
Aspergillus fumigatus
13
gcgaectgga catgcatcaa ccaacagctg satcccsaga caaacaaatg ggaagacaag 60
cggcttctat acagtcaagc ceaagccgaa agcaactccc aceacgeaec tctttccgac 120
ggcaagaccg gtagcagcta cccgcactgg ttcactaaqg gqtacgacgg gaatggcaag 180
ctcatcaagQ gtcgcacgcc catcaaattc ggaaaagccg actgtgaccg tcccccgaag 240
cacagccaga acggeatggg caaggatgac cactacctgc tggagttccc gacttttcca 300
gatggccacg actataagtt tgactcgaag aaacecaagg aagacccggg cccagcgagg 360
gtcatctata cttatcccaa caaggtgttt tgcggcattg tggcccatca gcgggggaat 420
cagggagact tgagacfcgtg ttctcattag 450
14 143 PRT
84

Aspergillus furaigatus
14
Ala Thr Trp Thr Cys Ile Asn Gin Gin Leu Asn Pro Lys Thr Asn Lys
15 10 15
Trp Glu Asp Lys Arg Leu Leu Tyr Ser Gin Ala Lys Ala Glu S&r Asn
20 25 30
Ser His His Ala Pro Leu Ser Asp Gly Lys Thr Gly Ser Ser Tyr Pro
35 40 45
His Trp Phe Thr Asn Gly Tyr Asp Gly asn Gly Lys Leu Ile Lys Gly
50 55 60
Arg Thr Pro ILe Lys Phe Gly Lys Ala Asp Cys Agp Arg Pro Pro Lys
65 70 75 80
His Ssr Gin Asn Gly Met Gly Lys Asp Asp His Tyr Leu Leu Glu Phe
05 90 95
Pro Thr Phe pro Asp Gly His Asp Tyr Lys Phe Asp Ser Lys Lys Pro
100 105 HO
Lys Glu Asp Pro Gly Pro Ala Arg Val He Tyr Thr Tyr Pro Asn Lys
115 3 20 125
Val Phe Cys Gly He Val Ala His Gin Arg Gly Asn Gin Gly Asp Leu
130 135 140
Arg Leu Cys Ser His
143
85

15
S33
DHA
Aspergillus fumigatus
15
atgtcacagc aatacacget cccaccccte ecctaeccct aggatgccct ccs^ccctac 60
atctcceaac agatcatgga gctgcaccac aaaaagcacc atcaaaccta cgtcaatggc 120
ctgaatgccg cactcgaggc geagaagaaa geggcggaag ccaccgaegt ccccaagctc 180
gtctccgtgc agcaagcg«t caaattcaac ggcggggggc acatcaacca ctccctcttc 240
tggaagaatc tggccccgg* gaastccggg ggtggcaaga cegstcaggc aecggtcctc 300
aaagcagcca tcgagcagcg ttggggatcc ttcgataagt tcaaggatgc tttcaacacg 360
aecctgctgg gcattcaggg cagcggatgg ggttggttag tgaccgacgg acccaaggga 420
aagctagaca ttaccacaac ccacgaccag gatccggtga ccggggcggc ccccgtcfctt 480
ggggtggata tgtgggagca tgcttactac cttcagtact tgaacgacaa agcctcgtat 540
gcca^gggca tctggaacgt gatcaactgg gctgaagcgg agaatcggta catagcgggt 600
gacaagggtg gacacccatt cstgaagctg tag 633
16
210
PKT
Aspergillus fumigates
86

16
Met Ser Gin Gin Tyr Thr Leu pro Pro Leu Pro Tyr Pro Tyr Asp Ala
15 10 15
Leu Gin Pro Tyr Ile Ser Gin sin Ile Met Glv Leu His Bis Lys lys
20 25 30
His His Gin Thr Tyr Val Asn Gly Leu Asn Ala Ale Leu Glu Ala Gin
35 40 -35
Lys Lys Ala Ala Glu Ala Thr Asp Val Pro Lys Leu Val Ser Val Gin
50 55 60
Gin Ala Ile Lys Phe Asn Gly Gly Gly His Ile Asn His Ser Leu phe
65 70 75 50
Trp Lys Aan Leu Ala Pro Glu Lys Ser Gly Gly Gly Lys Ile Asp Gin
85 90 95
Ala Pro Val Leu Lys Ala Ala lie Glu Gin Arg Trp Gly Ser Phe Asp
100 105 110
Lys Phe Lys Asp Ala Phe Asn Thr Thr Leu Leu Gly He Gin Gly Ser
115 120 125
Gly Trp Gly Trp Leu Val Thr Asp Gly Pro Lys Gly Lys Leu Asp He
130 135 140
Thr Thr Thr His Asp Gin Asp Pro Val Thr Gly Ala Ala Pro Val Phe
145 150 155 160
87

Gly Val Asp Met Trp Glu His Ala Tyr Tyr Leu Gin Tyr Leu Asn Asp
165 170 175
Lys Ala Sar Tyr Ala Lys Gly He Trp Asn Val He Asn Trp Ala Glu
180 185 190
Ala Glu Asn Arg Tyr He Ala Gly Asp Lys Gly Gly His Pro Phe Met
155 200 205
Lys Leu
210
17
519
DNA
Betula verrucosa
17
atgagaggat cgcatcacca tcaceatcae ggatccatgg gtgttttcaa ctacgaaacc 60
gaaaccacct ccgtcatccc ggctgctcgt ctgttcaagg ccttcatcct ggacggtgac 120
aacctgttcc ctaaggttgc tccgcaggct atctcctccg ttgaaaacat cgaaggtaac 180
ggtggcccgg gtaccatcaa gaaaatctec ttcccggaag gtttcccatt taaatacgta 240
aaagaccgtg ttgacgaagt tgaccacacc aactccaaat acaactagtc cgttatcgaa 300
ggtggtccaa ttggtgacac cctggaaaaa atctccaacg aaatcaaaat cgtggcaacc 360
ecggacggtg gttccatcct taagacctcc aacaaatacc acaccaaagg tgaccacgaa gttaaagctg aacaggttaa agctccgaaa gaaatgggtg aaaccctgct gcgtgctgtt 480
gsdtcccacc rgctggctca ctccgecgca tacaactaa 513
88

18
172
PRT
Betula verrucosa
18
Met Arg Gly Ser His His His His His His Gly Ser Met Gly Val Phe
15 10 15
Asn Tyr Glu Thr Glu Thr Thr Ser Val He Pro Ala Ala Arg Leu Phe
20 25 30
Lys Ala Phe He Leu Asp Gly Asp Asn Leu Phe Pro Lys Val Ala Pro
35 40 45
Gin Ala He Ser Ser Val Glu Asn Ile Glu Gly Asn Gly Gly Pro Gly
50 55 60
Thr Ile Lys Lys Ile Ser Phe Pro Glu Gly Phe Pro Phe Lys Tyr Val
65 70 75 80
Lys Asp Arg Val Asp Glu Val Asp His Thr Asn Phe Lys Tyr Asn Tyr
85 90 95
Ser Val He Glu Gly Gly Pro He Gly Asp Thr Leu Glu Lys He Ser
100 105 110
Asn Glu He Lys He Val Ala Thr Pro Asp Gly Gly Ser He Leu Lys
115 120 125
89

Ile 5er Asn Lys Tyr His Thr Lys Gly Asp His Glu val Lys Ala Glu
130 135 140
Gin Val Lys Ala Ser Lys Glu Met GLY Glu Thr Leu Leu Arg Ala val
145 150 15S 160
Glu Ser Tyr Leu Leu Ala His Ser Asp Ala Tyr Asn
165 170
19
1099
DNA
Dermatophagoides pteronyssinus
19
gaattccttt ttttttcttt ctctctctaa aatctaaaat ceatccaaca tgaaaattcgt 60
tttggccatc gcctcattgt tggcafctgag cgctgtttat gctcgtccat catcgatcaa 120
aacttttgaa gaatacaaaa aagecttcaa caaaagttat gctaccttcg aa^aegaaga 180
agctgcccgt aaaaactttt tggaatcagt aaaatatgtt caatcaaatg gaggtgccat 240
caaccatttg tcegstttgt cgttggatga attcaaaaac cgatttttga tgagtgcaga 300
agcttttgaa cacctcaaaa ctcaattcga tttgaatget gaaactaacg cctgcagtat 360
caatggaaat gctccagctg aaatcgattt gcgacaaatg cgaactgtca ctcccattcg 420
tatgcaagga ggctgtggtt catgttgggc tttctctggt gttgccgcaa etgaatcagc 4S0
ttatttggct taccgtaatc aaccattgga tcttgctgaa caagaattag tcgattgtgc 540
ttcccaacac ggttgtcatg gtgacaccat tccacgtggt attgasfcaca tccaacataa 600
90

tggtgtcgtc caagaaegct actatcgata cgttgcacga gaacaatcat gccgacgacc 660
aaatgcacaa cgtttcggta tctcaaacta ttgccsaatt tacccaccaa atgceaacaa 720
aattcgtgaa gctttggctc aaacccseag ggctattgcc gtcattattg goatcaaaga "?80
tttagacgca ttecgtcatt atgatggccg aacaatcatt caacgcgata atggttacca 840
accaasctat cacgctgtca acattgttgg ttacactaac gcacaaggtg tcgattattg 900
gatcgtacga aacagttggg ataccaattg gggtgataat ggttacggtt attttgctgc 960
caacatcgat ttgatgatga ttgaagaata tccatatgtt gtcattctct aaacaaaaag 1020
acaatttctt atatgattgt tactaattta tttaaaatca aaatttttag aaaatgaata 1080
aattcattca caaaaatta 1099
20
320
PRT
Dermatophagoides pfceronyssinus
20
Met Lys Ile val Leu Ala lie Ala Ser Leu Leu Ala Leu Ser Ala Val
1 5 10 15
Tyr Ala Arg Pro Ser Ser lie Lys ?hr Phs Glu Glu Tyr Lys Lys Ala
20 25 30
Ph© Asn Lys Ser Tyr Ala Thr Phe Glu Asp Glu Glu Ala Ala Arg Lys
35 90 45
91

Asn Phe Leu Glu Ser Val Lys Tyr Val Gln Ser Asn Gly Gly Ala lie
50 55 60
Asn His Leu Ser Asp Leu Ser Leu Asp Glu Phe Lys Asn Arg Phs Leu
63 70 75 SO
Met Ser Ala Glu Ala Phe Glu His Leu Lys Thr Gin Phe Asp Leu Asn
85 90 95
Ala Glu Thr Asn Ala Cys Ser He Asn Gly Asn Ala Pro Ala Glu Ile
100 105 110
Asp LEU Arg Gin Met Arg Thr Val Thr Pro He Arg Met Gin Gly Gly
115 120 125
Cys Gly Ser Cys Trp Ala Phe Ser Gly Vol Ala Ala Thr Glu Ser Ala
130 135 140
Tyr Leu Ala Tyr Arg Asn Gin Ser Leu Asp Leu Ala Glu Gin Glu Leu
145 150 155 160
Val Asp Cys Ala Ser Gin His Gly Cys His Gly Asp Thr Ile Pro Arg
165 170 175
Gly He Glu Tyr He Gin His Asn Giy Val Val Gin Glu Ser Tyr Tyr
180 185 190
Arg Tyr Val Ala Arg GZu Gin Ser Cys Arg Arg Pro Asn Ala Gin Asq
195 2CC 205
Phe Gly He Ser Asn Tyr Cys Gin II* Tyr Pro Pro Asn Val Asn Lys
210 215 220
92

lie Arg Glu Ala 225

Leu Ala Gin Thr 230

His Ser Ala He 235

Ala Val He He 240



Gly He Lys Asp

Leu Asp Ala Phe 245

Arg His Tyr Asp 250

Gly Arg Thr He 255



He Gin Arg Asp 260

Asn Gly Tyr Gin

Pro Asn Tyr His 265

Ala Val Asn He 270



Val Gly Tyr Ser 275

Asn Ala Gin Gly 280

Val Asp Tyr Trp

He Val Arg Asn 285



Ser Trp Asp Thr
290

Asn Trp Gly Asp 295

Asn Gly Tyr Gly 300

Tyr Phe Ala Ala



Asn He Asp Leu 305

Met Met He Glu 310

Glu Tyr Pro Tyr 315

Val Val He Leu 320

93




We claim:
1. A modular antigen-transport-molecule (MAT-molecule) containing at least one translocation module which brings about the transport of the MAT-molecule from the extracellular space into the interior of the cells, at least one targeting module which brings about the transport of the MAT-molecule intracellularly to the organelles which are involved in the processing of antigens or the loading of MHC molecules with antigens and at least one antigen module which determines the specificity of an immune response modulated by the MAT molecule in an individual, said modules being coupled to one another by covalent linkages, where
a) the translocation module is a molecule moiety of a peptide and is HIV-tat,
VP22 or Antennapedia, or a partial sequence thereof functional as a translocation module,
b) the targeting module is a molecule moiety having an amino acid sequence and is the MHC invariant chain (IiP33, IiP41, IiP35, IiP43) or a partial sequence thereof functional as a targeting module and
c) the antigen module is an allergen consisting of a protein or peptide.
The MAT molecule as claimed in claim 1, in which additionally at least one tag module is present, where the tag module is provided for the isolation and/or detection of the MAT molecule, and where the tag module is present N-terminally, C-terminally or internally in the MAT molecule.
The MAT molecule as claimed in claim 2, where at least one tag module is selected from the group of His tag with 4 to 6 consecutive histidine residues, Myc tag, FLAG tag, HA tag, Strep tag, Xpress tag, S tag, CBD tag, GST tag, HSV tag, T7 tag, protein A tag, V5 tag, chitin-binding tag, maltose-binding tag, calmodulin-
94

binding tag or a biotin group.
4. The MAT molecule as claimed in any one of claims 1to3 wherin the modules are covalently connected via spacer modules.
5. The MAT molecule as claimed in any of claims 1 to 4, which comprises at least one of the following building blocks:

a) D isomers of amino acids
b) modified D isomers of amino acids
c) L isomers of amino acids
d) modified L isomers of amino acids
e) building blocks having guanidino groups
f) building blocks having amidino groups
g) peptidomimetics
h) N-methyl amino acids i) unusual amino acids j) Spiegelmers.
6. A nucleic acid which codes for MAT molecule as claimed in any of claims 1 to 5,
the nucleic acid comprising nucleotide sequence selected from sequence ID Nos
1,3,5,7.
7. A vector which comprises at least one nucleic acid sequence as claimed in
claim 6, and preferably at least one of the following elements: a promoter which
is functionally coupled to the nucleic acid according to claim 6, a resistance gene
against an antibiotic, a resistance gene against an antimycotic.
8. A medicament, vaccine or diagnostic aid comprising MAT molecules as claimed in claims 1 to 5 and/or nucleic acids as claimed in claim 6.
9. The medicament, vaccine or diagnostic aid according to claim 8, which
95

additionally comprises at least one of the following constituents and/or other pharmaceutical acceptable excipients and additives:
a) a physiological sodium chloride solution
b) a pharmaceutically acceptable adjuvant
c) a pharmaceutically acceptable buffer substance
d) a pharmaceutically acceptable carrier protein
e) a pharmaceutically acceptable preservative
f) a pharmaceutically acceptable colorant.
10. The medicament, vaccine or diagnostic aid as claimed in claim 8 or 9, characterized in that the product is designed for subcutaneous injection, injection into a lymph node or for administration via the mucous membranes, in particular via the mucous membranes of the gastrointestinal tract or of the respiratory system.
Dated this 10th day of May 2005
(Jose M A)
of Khaitan & Co
Agent for the Applicants
96

Documents:

379-MUMNP-2005-CORRESPONDENCE(20-06-2008).pdf

397-mumnp-2005-abstract(granted)-(5-3-2008).pdf

397-mumnp-2005-cancelled pages(17-1-2008).pdf

397-mumnp-2005-claims(complete)-(10-5-2005).pdf

397-mumnp-2005-claims(granted)-(17-1-2008).doc

397-mumnp-2005-claims(granted)-(17-1-2008).pdf

397-mumnp-2005-claims(granted)-(5-3-2008).pdf

397-mumnp-2005-correspondence(17-1-2007).pdf

397-mumnp-2005-correspondence(4-10-2006).pdf

397-mumnp-2005-correspondence(ipo)-(18-1-2007).pdf

397-mumnp-2005-correspondence(ipo)-(28-3-2010).pdf

397-mumnp-2005-description(complete)-(10-5-2005).pdf

397-mumnp-2005-description(granted)-(5-3-2008).pdf

397-mumnp-2005-drawing(10-5-2005).pdf

397-mumnp-2005-drawing(granted)-(5-3-2008).pdf

397-MUMNP-2005-FORM 1(1-6-2005).pdf

397-mumnp-2005-form 1(10-5-2005).pdf

397-mumnp-2005-form 18(30-9-2005).pdf

397-mumnp-2005-form 2(complete)-(10-5-2005).pdf

397-mumnp-2005-form 2(granted)-(17-1-2008).doc

397-mumnp-2005-form 2(granted)-(17-1-2008).pdf

397-mumnp-2005-form 2(granted)-(5-3-2008).pdf

397-mumnp-2005-form 2(title page)-(complete)-(10-5-2005).pdf

397-mumnp-2005-form 2(title page)-(granted)-(5-3-2008).pdf

397-mumnp-2005-form 26(10-5-2005).pdf

397-mumnp-2005-form 3(10-5-2005).pdf

397-mumnp-2005-form 5(10-5-2005).pdf

397-mumnp-2005-form 8(17-1-2008).pdf

397-mumnp-2005-form-pct-isa-210(10-5-2005).pdf

397-mumnp-2005-specification(amended)-(17-1-2008).pdf


Patent Number 216022
Indian Patent Application Number 397/MUMNP/2005
PG Journal Number 13/2008
Publication Date 31-Mar-2008
Grant Date 05-Mar-2008
Date of Filing 10-May-2005
Name of Patentee IMVISION GMBH
Applicant Address FEODOR-LYNEN-STRASSE 5, 30625 HANNOVER. GERMANY
Inventors:
# Inventor's Name Inventor's Address
1 1) LAMPING NORBERT 2) CRAMERI RETO 3) FLUECKIGER SABINE 4) DAIGLE ISABELLE 1) SIEGESSTRASSE 8, 30175, HANOVER, GERMANY 2) PROMENADE 137A, CH-7260 DAVOS-DORF, SWITZERLAND 3) OBERWIESSTRASSE 6, CH- 7270 DAVOS-PLATZ, SWITZERLAND 4) FARBISTRASSE 1, CH-7270 DAVOS-PLATZ SWITZERLAND
PCT International Classification Number C12N15/62 A61K39/00
PCT International Application Number PCT/EP2003/011190
PCT International Filing date 2003-10-09
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 02022774.0 2002-10-11 EUROPEAN UNION