US20100048877A1

US20100048877A1 - Novel multivalent immunoglobulins

Info

Publication number: US20100048877A1
Application number: US12/307,578
Authority: US
Inventors: Florian Ruker; Gottfried Himmler; Gordana Wozniak-Knopp
Original assignee: F Star Biotechnologische Forschungs und Entwicklungsges mbH
Current assignee: F Star Biotechnologische Forschungs und Entwicklungsges mbH
Priority date: 2006-07-05
Filing date: 2007-06-26
Publication date: 2010-02-25
Also published as: ATE540056T1; JP2017163998A; CN101522712A; WO2008003103A2; US11827720B2; JP2013240338A; WO2008003103A3; EP2463302A1; ES2539593T3; AT503889B1; US20180051095A1; PL2463302T3; EP2046831A2; CN110041430A; JP6681855B2; HUE025035T2; EP2046831B1; AT503889A1; CN110078828A; PT2463302E

Abstract

The present invention provides a multivalent immunoglobulin or part thereof binding specifically to at least two cell surface molecules of a single cell with at least one modification in at least one structural loop region of said immunoglobulin determining binding to an epitope of said cell surface molecules wherein the unmodified immunoglobulin does not significantly bind to said epitope, its use and methods for producing it.

Description

The present invention provides a multivalent immunoglobulin or part thereof binding specifically to at least two cell surface molecules of a single cell, with at least one modification in at least one structural loop region of said immunoglobulin determining binding to an epitope of said cell surface molecules wherein the unmodified immunoglobulin does not significantly bind to said epitope.
Monoclonal antibodies have found use in many therapeutic, diagnostic and analytical applications.
The basic antibody structure will be explained here using as example an intact IgG1 immunoglobulin. Two identical heavy (H) and two identical light (L) chains combine to form the Y-shaped antibody molecule. The heavy chains each have four domains. The amino terminal variable domains (VH) are at the tips of the Y. These are followed by three constant domains: CH1, CH2, and the carboxy-terminal CH3, at the base of the Y's stem. A short stretch, the switch, connects the heavy chain variable and constant regions. The hinge connects CH2 and CH3 (the Fc fragment) to the remainder of the antibody (the Fab fragments). One Fc and two identical Fab fragments can be produced by proteolytic cleavage of the hinge in an intact antibody molecule. The light chains are constructed of two domains, variable (VL) and constant (CL), separated by a switch.
Disulfide bonds in the hinge region connect the two heavy chains. The light chains are coupled to the heavy chains by additional disulfide bonds. Asn-linked carbohydrate moieties are attached at different positions in constant domains depending on the class of immunoglobulin. For IgG1 two disulfide bonds in the hinge region, between Cys235 and Cys238 pairs, unite the two heavy chains. The light chains are coupled to the heavy chains by two additional disulfide bonds, between Cys229s in the CH1 domains and Cys214s in the CL domains. Carbohydrate moieties are attached to Asn306 of each CH2, generating a pronounced bulge in the stem of the Y.
These features have profound functional consequences. The variable regions of both the heavy and light chains (VH) and (VL) lie at the “tips” of the Y, where they are positioned to react with antigen. This tip of the molecule is the side on which the N-terminus of the amino acid sequence is located. The stem of the Y projects in a way to efficiently mediate effector functions such as the activation of complement and interaction with Fc receptors, or ADCC and ADCP. Its CH2 and CH3 domains bulge to facilitate interaction with effector proteins. The C-terminus of the amino acid sequence is located on the opposite side of the tip, which can be termed “bottom” of the Y.
Two types of light chain, termed lambda (λ) and kappa (κ), are found in antibodies. A given immunoglobulin either has κ chains or λ chains, never one of each. No functional difference has been found between antibodies having λ or κ light chains.
Each domain in an antibody molecule has a similar structure of two beta sheets packed tightly against each other in a compressed antiparallel beta barrel. This conserved structure is termed the immunoglobulin fold. The immunoglobulin fold of constant domains contains a 3-stranded sheet packed against a 4-stranded sheet. The fold is stabilized by hydrogen bonding between the beta strands of each sheet, by hydrophobic bonding between residues of opposite sheets in the interior, and by a disulfide bond between the sheets. The 3-stranded sheet comprises strands C, F, and G, and the 4-stranded sheet has strands A, B, E, and D. The letters A through G denote the sequential positions of the beta strands along the amino acid sequence of the immunoglobulin fold.
The fold of variable domains has 9 beta strands arranged in two sheets of 4 and 5 strands. The 5-stranded sheet is structurally homologous to the 3-stranded sheet of constant domains, but contains the extra strands C′ and C″. The remainder of the strands (A, B, C, D, E, F, G) have the same topology and similar structure as their counterparts in constant domain immunoglobulin folds. A disulfide bond links strands B and F in opposite sheets, as in constant domains.
The variable domains of both light and heavy immunoglobulin chains contain three hypervariable loops, or complementarity-determining regions (CDRs). The three CDRs of a V domain (CDR1, CDR2, CDR3) cluster at one end of the beta barrel. The CDRs are loops that connect beta strands B-C, C′-C″, and F-G of the immunoglobulin fold. The residues in the CDRs vary from one immunoglobulin molecule to the next, imparting antigen specificity to each antibody.
The VL and VH domains at the tips of antibody molecules are closely packed such that the 6 CDRs (3 on each domain) cooperate in constructing a surface (or cavity) for antigen-specific binding. The natural antigen binding site of an antibody thus is composed of the loops which connect strands B-C, C′-C″, and F-G of the light chain variable domain and strands B-C, C′-C″, and F-G of the heavy chain variable domain.
The loops which are not CDR-loops in a native immunoglobulin, or not part of the antigen-binding pocket as determined by the CDR loops, do not have antigen binding or epitope binding specificity, but contribute to the correct folding of the entire immunoglobulin molecule and/or its effector or other functions and are therefore called structural loops for the purpose of this invention. Prior art documents show that the immunoglobulin-like scaffold has been employed so far for the purpose of manipulating the existing antigen binding site, thereby introducing novel binding properties. So far, however, only the CDR regions have been engineered for antigen binding, in other words, in the case of the immunoglobulin fold, only the natural antigen binding site has been modified in order to change its binding affinity or specificity. A vast body of literature exists which describes different formats of such manipulated immunoglobulins, frequently expressed in the form of single-chain Fv fragments (scFv) or Fab fragments, either displayed on the surface of phage particles or solubly expressed in various prokaryotic or eukaryotic expression systems.
PCT/EP2006/050059 describes a method of engineering an immunoglobulin which comprises a modification in a structural loop region to obtain a new antigen binding sites. This method is broadly applicable to immunoglobulins and may be used to produce a series of immunoglobulins targeting a variety of antigens. Multivalent binders of cell-surface targets are not explicitly described.
US2005/266000A1 describes polypeptides comprising a variant heavy chain variable framework domain (VFR). A VFR is part of the antigen binding pocket or groove that may contact antigen. VFRs are part of the CDR loop region and located at a variable domain at the side of the CDR loops to support the antigen binding via the CDR loop region. Framework loops other than VFR have not been mutated for the purpose of engineering an antigen binding site.
Cell surface proteins associated with human cancers can be effective targets for monoclonal therapy. Antibodies can elicit antitumor responses by modulating cellular activation or through recruitment of the immune system.
Some mAbs exert part of their effect by cross-linking of the target, which may cluster the targets and result in activation, inhibition, or amplification of cell signalling, finally ending in cell arrest and/or apoptosis to the cellular target.
It has been demonstrated that some MAbs (anti-CD19, -CD20, -CD21, and -CD22) that have little or no inherent anti-growth activity on lymphoma cell lines can be converted into potent antitumor agents by using them as tetravalent homodimers. These activities might be enhanced in vivo by the recruitment of effector cells and/or complement.
Another strategy used for therapeutic mAbs is to couple a cytotoxic drug to the mAb. Such an immunotoxin may bind to the cell surface target followed by internalization, releasing the drug to kill the cell. Clustering of the target as a prerequisite to internalization may be necessary.
To enhance the potency of mAbs that exert their effect through the clustering of target molecules, various multivalent Ab formats have been designed. Covalently linked full-length IgGs that form tetravalent Abs and naturally occurring IgM and IgG Abs mimicking polymeric IgM and IgA via the use of their secretory tailpiece have been devised. Another tetravalent format was designed by adding Fab at the C terminus of each H chain of a full-length IgG.
To improve tumor penetration, smaller constructs using single-chain Fv (scFv)₂fragments (each Fv consisting of variable light and variable heavy domains connected by peptide linkers) have been joined together to form multivalent complexes. Such constructs may have relatively short half-lives (compared with those of full-length mAbs), consequently this has been addressed by joining these scFv multimers to IgG Fc fragments. With scfv and similar formats it is difficult to control formation of the exact multimerization degree, i.e., diners, trimers, tetramers, and larger complexes may form in varying ratios depending on the basic construct and expression method.
Any of the known formats to produce multivalent immunoglobulins have certain disadvantages, be it immunogenicity, in vivo-half life or production issues.
It is the object of the present invention to provide a modular system which allows designing a cell targeting multivalent immunoglobulin according to the respective need, to solve prior art problems.

BRIEF DESCRIPTION OF THE INVENTION

The present invention provides immunoglobulin domains which bind to cell surface proteins via modified structural loops to provide additional binding to a cell surface molecule thus enabling crosslinking of cell-surface receptors.
According to the present invention a multivalent immunoglobulin or binding part thereof is provided that specifically binds to at least two cell surface molecules of a single cell with at least one modification in at least one structural loop region of said immunoglobulin determining binding to an epitope of said cell surface molecules, including structures of antigenic properties, located on a single cell or available within a homogenous cell population, wherein the unmodified immunoglobulin does not significantly bind to said epitope.
According to the present invention, the inventive multivalent immunoglobulin can be further combined with one or more modified immunoglobulins or with unmodified immunoglobulins, or parts thereof, to obtain a combination immunoglobulin.
Preferably, the modification of the structural loop domain within the nucleotide or amino acid sequence is a deletion, a substitution, an insertion or a combination thereof.
The present invention also provides a nucleic acid encoding the inventive immunoglobulin or part thereof and a method for engineering a multivalent immunoglobulin according to the invention comprising the steps of:

- providing a nucleic acid encoding an immunoglobulin comprising at least one structural loop region,
- modifying at least one nucleotide residue of said structural loop region,
- transferring said modified nucleic acid in an expression system,
- expressing said multivalent immunoglobulin,
- contacting the expressed multivalent immunoglobulin with an epitope, and
- determining whether said multivalent immunoglobulin binds to said epitope.

Further, the use of the multivalent immunoglobulin according to the invention for the preparation of a medicament for therapeutic use, for example for tumor cell treatment and pathogen infected cells is provided.

DETAILED DESCRIPTION OF THE INVENTION

The modified immunoglobulin domains according to the invention can be used as such or incorporated into various known antibody formats such as complete antibodies, Fabs, single chain Fvs, Fab2, minibodies and the like to provide additional binding sites for cell surface epitopes or receptors.
In particular, the present invention relates to a method for engineering an immunoglobulin binding specifically to epitopes of antigens. Through the modification in the structural loop region the immunoglobulin may be engineered to bind to the epitope. In a preferred embodiment the immunoglobulin is binding specifically to at least two such epitopes that differ from each other, originating from or mimicking either the same antigen or different antigens.
For example, the method according to the invention refers to engineering an immunoglobulin binding specifically to at least one first epitope and comprising at least one modification in at least one structural loop region of said immunoglobulin and determining the specific binding of said at least one loop region to at least one second epitope, wherein
the unmodified structural loop region (non-CDR region) does not specifically bind to said at least one second epitope, comprising the steps of:

- providing a nucleic acid encoding an immunoglobulin binding specifically to at least one first epitope and comprising at least one structural loop region,
- modifying at least one nucleotide residue of at least one of said loop regions encoded by said nucleic acid,
- transferring said modified nucleic acid in an expression system,
- expressing said modified immunoglobulin,
- contacting the expressed modified immunoglobulin with said at least one second epitope, and
- determining whether said modified immunoglobulin binds specifically to the second epitope.

The method according to the invention preferably refers to at least one modification in at least one structural loop region of said immunoglobulin and determining the specific binding of said at least one loop region to at least one molecule selected from the group consisting of cell surface antigens, wherein the immunoglobulin containing an unmodified structural loop region does not specifically bind to said at least one molecule.
The term “immunoglobulin” as used herein is including immunoglobulins or parts or fragments or derivatives of immunoglobulins. Thus, it includes an “immunoglobulin domain peptide” to be modified according to the present invention (as used herein the terms immunoglobulin and antibody are interchangeable) as well as immunoglobulin domains or parts thereof that contain a structural loop, or a structural loop of such domains, such as a minidomain. The immunoglobulins can be used as isolated peptides or as combination molecules with other peptides. In some cases it is preferable to use a defined modified structural loop or a structural loop region, or parts thereof, as isolated molecules for binding or combination purposes. The “immunoglobulin domain” as defined herein contains such immunoglobulin domain peptides or polypeptides that may have specific binding characteristics upon modifying and engineering. The peptides are homologous to immunoglobulin domain sequences, and are preferably at least 5 amino acids long, more preferably at least 10 or even at least 50 or 100 amino acids long, and constitute at least partially a structural loop or the structural loop region, or the non-CDR loop region of the domain. Preferably the peptides exclude those insertions that are considered non-functional amino acids, hybrid or chimeric CDR-regions or CDR-like regions and/or canonical structures of CDR regions. The binding characteristics relate to specific epitope binding, affinity and avidity.
A derivative of an immunoglobulin according to the invention is any combination of one or more immunoglobulins of the invention and or a fusion protein in which any domain or minidomain of the immunoglobulin of the invention may be fused at any position of one or more other proteins (such as other immunoglobulins, ligands, scaffold proteins, enzymes, toxins and the like). A derivative of the immunoglobulin of the invention may also be obtained by recombination techniques or binding to other substances by various chemical techniques such as covalent coupling, electrostatic interaction, di-sulphide bonding etc.
The other substances bound to the immunoglobulins may be lipids, carbohydrates, nucleic acids, organic and anorganic molecules or any combination thereof (e.g. PEG, prodrugs or drugs). A derivative is also an immunoglobulin with the same amino acid sequence but made completely or partly from non-natural or chemically modified amino acids.
The engineered molecules according to the present invention will be useful as stand-alone proteins as well as fusion proteins or derivatives, most typically fused in such a way as to be part of larger antibody structures or complete antibody molecules, or parts thereof such as Fab fragments, Fc fragments, Fv fragments and others. It will be possible to use the engineered proteins to produce molecules which are bispecific, trispecific, and maybe even carry more specificities at the same time, and it will be possible at the same time to control and preselect the valency of binding at the same time according to the requirements of the planned use of such molecules.
Another aspect of the present invention relates to an immunoglobulin with at least one loop region, characterised in that said at least one loop region comprises at least one amino acid modification forming at least one modified loop region, wherein said at least one modified loop region binds specifically to at least one epitope of an antigen
It is preferred to molecularly combine at least one modified antibody domain, which is binding to the specific partner via the non-variable sequences or a structural loop) with at least one other binding molecule which can be an antibody, antibody fragment, a soluble receptor, a ligand or another modified antibody domain.
The molecule that functions as a part of a binding pair that is specifically recognized by the immunoglobulin according to the invention is preferably selected from the group consisting of proteinaceous molecules, nucleic acids and carbohydrates.
The loop regions of the modified immunoglobulins may specifically bind to any kind of binding molecules or structures, in particular to antigens, proteinaceous molecules, proteins, peptides, polypeptides, nucleic acids, glycans, carbohydrates, lipids, small organic molecules, anorganic molecules, or combinations or fusions thereof. Of course, the modified immunoglobulins may comprise at least two loops or loop regions whereby each of the loops or loop regions may specifically bind to different molecules or epitopes.
According to the present invention, binding regions to antigens or antigen binding sites of all kinds of cell surface antigens, may be introduced into a structural loop of a given antibody structure.
The term “antigen” according to the present invention shall mean molecules or structures known to interact or capable of interacting with the CDR-loop region of immunoglobulins. Structural loop regions of the prior art referring to native antibodies, do not interact with antigens but rather contribute to the overall structure and/or to the binding to effector molecules. Only upon engineering according to the invention structural loops may form antigen binding pockets without involvement of CDR loops or the CDR region.
The term “cell surface antigens” according to the present invention shall include all antigens on capable of being recognised by an antibody structure on the surface of a cell, and fragments of such molecules. Preferred “cell surface antigens” are those antigens, which have already been proven to be or which are capable of being immunologically or therapeutically relevant, especially those, for which a preclinical or clinical efficacy has been tested. Those cell surface molecules are specifically relevant for the purpose of the present invention, which mediate cell killing activity. Upon binding of the immunoglobulin according to the invention to at least two of those cell surface molecules the immune system provides for cytolysis or cell death, thus a potent means for attacking human cells may be provided.
Preferably the antigen is selected from cell surface antigens, including receptors, in particular from the group consisting of erbB receptor tyrosine kinases (such as EGFR, HER2, HER3 and HER4, but not limited to these), molecules of the TNF-receptor superfamily, such as Apo-1 receptor, TNFR1, TNFR2, nerve growth factor receptor NGFR, CD40, T-cell surface molecules, T-cell receptors, T-cell antigen OX40, TACI-receptor, BCMA, Apo-3, DR4, DR5, DR6, decoy receptors, such as DcR1, DcR2, CAR1, HVEM, GITR, ZTNFR-5, NTR-1, TNFL1 but not limited to these molecules, B-cell surface antigens, such as CD10, CD19, CD20, CD21, CD22, antigens or markers of solid tumors or hematologic cancer cells, cells of lymphoma or leukaemia, other blood cells including blood platelets, but not limited to these molecules.
According to a further preferred embodiment the antigen or the molecule binding to the modified structural loop region is selected from the group consisting of tumor associated antigens, in particular EpCAM, tumor-associated glycoprotein-72 (TAG-72), tumor-associated antigen CA 125, Prostate specific membrane antigen (PSMA), High molecular weight melanoma-associated antigen (HMW-MAA), tumor-associated antigen expressing Lewis Y related carbohydrate, Carcinoembryonic antigen (CEA), CEACAM5, HMFG PEM, mucin MUC1, MUC18 and cytokeratin tumor-associated antigen, bacterial antigens, viral antigens, allergens, allergy related molecules IgE, cKIT and Fc-epsilon-receptorI, IRp60, IL-5 receptor, CCR3, red blood cell receptor (CR1), human serum albumin, mouse serum albumin, rat serum albumin, neonatal Fc-gamma-receptor FcRn, Fc-gamma-receptors Fc-gamma RI, Fc-gamma-RII, Fc-gamma RIII, Fc-alpha-receptors, Fc-epsilon-receptors, fluorescein, lysozyme, toll-like receptor 9, erythropoietin, CD2, CD3, CD3E, CD4, CD11, CD11a, CD14, CD16, CD18, CD19, CD20, CD22, CD23, CD25, CD28, CD29, CD30, CD32, CD33 (p67 protein), CD38, CD40, CD40L, CD52, CD54, CD56, CD64, CD80, CD147, GD3, IL-1, IL-1R, IL-2, IL-2R, IL-4, IL-5, IL-6, IL-6R, IL-8, IL-12, IL-15, IL-17, IL-18, IL-23, LIF, OSM, interferon alpha, interferon beta, interferon gamma; TNF-alpha, TNFbeta2, TNFalpha, TNFalphabeta, TNF-R1, TNF-RII, FasL, CD27L, CD30L, 4-1BBL, TRAIL, RANKL, TWEAK, APRIL, BAFF, LIGHT, VEG1, OX40L, TRAIL Receptor-1, A1 Adenosine Receptor, Lymphotoxin Beta Receptor, TACI, BAFF-R, EPO; LFA-3, ICAM-1, ICAM-3, integrin beta1, integrin beta2, integrin alpha4/beta7, integrin alpha2, integrin alpha3, integrin alpha4, integrin alpha5, integrin alpha6, integrin alphav, alphaVbeta3 integrin, FGFR-3, Keratinocyte Growth Factor, GM-CSF, M-CSF, RANKL, VLA-1, VLA-4, L-selectin, anti-Id, E-selectin, HLA, HLA-DR, CTLA-4, T cell receptor, B7-1, B7-2, VNRintegrin, TGFbeta1, TGFbeta2, eotaxin1, BLyS (B-lymphocyte Stimulator), complement C5, IgE, IgA, IgD, IgM, IgG, factor VII, CBL, NCA 90, EGFR (ErbB-1), Her2/neu (ErbB-2), Her3 (ErbB-3), Her4 (ErbB4), Tissue Factor, VEGF, VEGFR, endothelin receptor, VLA-4, carbohydrates such as blood group antigens and related carbohydrates, Galili-Glycosylation, Gastrin, Gastrin receptors, tumor associated carbohydrates, Hapten NP-cap or NIP-cap, T cell receptor alpha/beta, E-selectin, P-glycoprotein, MRP3, MRP5, glutathione-S-transferase pi (multi drug resistance proteins), alpha-granule membrane protein (GMP) 140, digoxin, placental alkaline phosphatase (PLAP) and testicular PLAP-like alkaline phosphatase, transferrin receptor, Heparanase I, human cardiac myosin, Glycoprotein IIb/IIIa (GPIIb/IIIa), human cytomegalovirus (HCMV) gH envelope glycoprotein, HIV gp120, HCMV, respiratory syncital virus RSV F, RSVF Fgp, VNRintegrin, Hep B gp120, CMV, gpIIbIIIa, HIV IIIB gp120 V3 loop, respiratory syncytial virus (RSV) Fgp, Herpes simplex virus (HSV) gD glycoprotein, HSV gB glycoprotein, HCMV gB envelope glycoprotein, Clostridium perfringens toxin and fragments thereof.
Substructures of antigens are generally referred to as “epitopes” (e.g. B-cell epitopes, T-cell epitopes), as long as they are immunologically relevant, i.e. are also recognisable by natural or monoclonal antibodies. The term “epitope” according to the present invention shall mean a molecular structure which may completely make up a specific binding partner or be part of a specific binding partner to the binding domain or the immunoglobulin of the present invention.
Chemically, an epitope may either be composed of a carbohydrate, a peptide, a fatty acid, an anorganic substance or derivatives thereof and any combinations thereof. If an epitope is a peptide or polypeptide, there will usually be at least 3 amino acids, preferably 8 to 50 amino acids, and more preferably between about 10-20 amino acids included in the peptide. There is no critical upper limit to the length of the peptide, which could comprise nearly the full length of the polypeptide sequence. Epitopes can be either be linear or conformational epitopes. A linear epitope is comprised of a single segment of a primary sequence of a polypeptide chain. Linear epitopes can be contiguous or overlapping. Conformational epitopes are comprised of amino acids brought together by folding of the polypeptide to form a tertiary structure and the amino acids are not necessarily adjacent to one another in the linear sequence.
Specifically, epitopes are at least part of diagnostically relevant molecules, i.e. the absence or presence of an epitope in a sample is qualitatively or quantitatively correlated to either a disease or to the health status or to a process status in manufacturing or to environmental and food status. Epitopes may also be at least part of therapeutically relevant molecules, i.e. molecules which can be targeted by the specific binding domain which changes the course of the disease.
Preferably, the new antigen binding sites in the structural loops are introduced by substitution, deletion and/or insertion of one or more elements in the sequence of the immunoglobulin, in particular of the nucleotide sequence.
According to another preferred embodiment of the present invention the modification of at least one nucleotide results in a substitution, deletion and/or insertion of the amino acid sequence of the immunoglobulin encoded by said nucleic acid.
The modification of the at least one loop region may result in a substitution, deletion and/or insertion of 1 or more nucleotides or amino acids, preferably a point mutation, or even the exchange of whole loops, more preferred the change of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15, up to 30 amino acids. Thereby the modified sequence comprises amino acids not included in the conserved regions of the structural loops, the newly introduced amino acids being naturally occurring, but foreign to the site of modification, or substitutes of naturally occurring amino acids. When the foreign amino acid is selected from a specific group of amino acids, such as amino acids with specific polarity, or hydrophobicity, a library enriched in the specific group of amino acids at the randomized positions can be obtained according to the invention. Such libraries are also called “focused” libraries.
The randomly modified nucleic acid molecule may comprise the herein identified repeating units, which code for all known naturally occurring amino acids or a subset thereof. Those libraries that contain modified sequences wherein a specific subset of amino acids are used for modification purposes are called “focused” libraries. The member of such libraries have an increased probability of an amino acid of such a subset at the modified position, which is at least two times higher than usual, preferably at least 3 times or even at least 4 times higher. Such libraries have also a limited or lower number of library members, so that the number of actual library members reaches the number of theoretical library members. In some cases the number of library members of a focused library is not less than 10³times the theoretical number, preferably not less than 10²times, most preferably not less than 10 times.
A library according to the invention may be designed as a dedicated library that contains at least 50% specific formats, preferably at least 60%, more preferred at least 70%, more preferred at least 80%, more preferred at least 90%, or those that mainly consist of specific antibody formats. Specific antibody formats are preferred, such that the preferred library according to the invention it is selected from the group consisting of a VH library, VHH library, Vkappa library, Vlambda library, Fab library, a CH1/CL library and a CH3 library. Libraries characterized by the content of composite molecules containing more than one antibody domains, such as an IgG library or Fc library are specially preferred. Other preferred libraries are those containing T-cell receptors, forming T-cell receptor libraries. Further preferred libraries are epitope libraries, wherein the fusion protein comprises a molecule with a variant of an epitope, also enabling the selection of competitive molecules having similar binding function, but different functionality. Exemplary is a TNFalpha library, wherein trimers of the TNFalpha fusion protein are displayed by a single genetic package.
However, the maximum number of amino acids inserted into a loop region of an immunoglobulin preferably may not exceed the number of 30, preferably 25, more preferably 20 amino acids at a maximum. The substitution and the insertion of the amino acids occurs preferably randomly or semi-randomly using all possible amino acids or a selection of preferred amino acids for randomization purposes, by methods known in the art and as disclosed in the present patent application.
The site of modification may be at a specific single structural loop or a structural loop region. A loop regions usually is composed of at least two, preferably at least 3 or at least 4 loops that are adjacent to each other, and which may contribute to the binding of an antigen through forming an antigen binding site or antigen binding pocket. It is preferred that the one or more sites of modification are located within the area of 10 amino acids, more preferably within 20, 30, 40, 50, 60, 70, 80, 90 up to 100 amino acids, in particular within a structural region to form a surface or pocket where the antigen can sterically access the loop regions.
The at least one loop region is preferably mutated or modified to produce libraries, preferably by random, semi-random or, in particular, by site-directed random mutagenesis methods, in particular to delete, exchange or introduce randomly generated inserts into structural loops. Alternatively preferred is the use of combinatorial approaches. Any of the known mutagenesis methods may be employed, among them cassette mutagenesis. These methods may be used to make amino acid modifications at desired positions of the immunoglobulin of the present invention. In some cases positions are chosen randomly, e.g. with either any of the possible amino acids or a selection of preferred amino acids to randomize loop sequences, or amino acid changes are made using simplistic rules. For example all residues may be mutated preferably to specific amino acids, such as alanine, referred to as amino acid or alanine scanning. Such methods may be coupled with more sophisticated engineering approaches that employ selection methods to screen higher levels of sequence diversity.
A preferred method according to the invention refers to a randomly modified nucleic acid molecule coding for an immunoglobulin, immunoglobulin domain or a part thereof which comprises at least one nucleotide repeating unit within a structural loop coding region having the sequence 5′-NNS-3′, 5′-NNN-3′, 5′-NNB-3′ or 5′-NNK-3′. In some embodiments the modified nucleic acid comprises nucleotide codons selected from the group of TMT, WMT, BMT, RMC, RMG, MRT, SRC, KMT, RST, YMT, MKC, RSA, RRC, NNK, NNN, NNS or any combination thereof (the coding is according to IUPAC).
The modification of the nucleic acid molecule may be performed by introducing synthetic oligonucleotides into a larger segment of nucleic acid or by de novo synthesis of a complete nucleic acid molecule. Synthesis of nucleic acid may be performed with tri-nucleotide building blocks which would reduce the number of nonsense sequence combinations if a subset of amino acids is to be encoded (e.g. Yanez et al. Nucleic Acids Res. (2004) 32:e158; Virnekas et al. Nucleic Acids Res. (1994) 22:5600-5607).
The randomly modified nucleic acid molecule may comprise the above identified repeating units, which code for all known naturally occurring amino acids.
As is well-known in the art, there are a variety of selection technologies that may be used for the identification and isolation of proteins with certain binding characteristics and affinities, including, for example, display technologies such as phage display, ribosome display, cell surface display, and the like, as described below. Methods for production and screening of antibody variants are well-known in the art. General methods for antibody molecular biology, expression, purification, and screening are described in Antibody Engineering, edited by Duebel & Kontermann, Springer-Verlag, Heidelberg, 2001; and Hayhurst & Georgiou, 2001, Curr Opin Chem Biol 5:683-689; Maynard & Georgiou, 2000, Annu Rev Biomed Eng 2:339-76.
A “structural loop” or “non-CDR-loop” according to the present invention is to be understood in the following manner: immunoglobulins are made of domains with a so called immunoglobulin fold. In essence, antiparallel beta sheets are connected by loops to form a compressed antiparallel beta barrel. In the variable region, some of the loops of the domains contribute essentially to the specificity of the antibody, i.e. the binding to an antigen by the natural binding site of an antibody. These loops are called CDR-loops. The CDR loops are located within the CDR loop region, which may in some cases also the variable framework region (called “VFR”) adjacent to the CDR loops. It is known that VFRs may contribute to the antigen binding pocket of an antibody, which generally is mainly determined by the CDR loops. Thus, those VFRs are considered as part of the CDR loop region, and would not be appropriately used for the purpose of the invention. Contrary to those VFRs within the CDR loop region or located proximal to the CDR loops, other VFRs of variable domains would be particularly suitable to be used according to the invention. Those are the structural loops of the VFRs located opposite to the CDR loop region, or at the C-terminal side of a variable immunoglobulin domain.
All other loops of antibody domains are rather contributing to the structure of the molecule and/or the effector function. These loops are defined herein as “structural loops” or non-CDR-loops, which would also exclude any VFRs within the CDR loop region.
The nucleic acid molecules encoding the modified immunoglobulins (and always included throughout the whole specification below: immunoglobulin fragments or derivatives) may be cloned into host cells, expressed and assayed for their binding specificities. These practices are carried out using well-known procedures, and a variety of methods that may find use in the present invention are described in Molecular Cloning—A Laboratory Manual, 3.sup.rd Ed. (Maniatis, Cold Spring Harbor Laboratory Press, New York, 2001), and Current Protocols in Molecular Biology (John Wiley & Sons). The nucleic acids that encode the modified immunoglobulins of the present invention may be incorporated into an expression vector in order to express said immunoglobulins. Expression vectors typically comprise an immunoglobulin operably linked that is placed in a functional relationship, with control or regulatory sequences, selectable markers, any fusion partners, and/or additional elements. The modified immunoglobulins of the present invention may be produced by culturing a host cell transformed with nucleic acid, preferably an expression vector, containing nucleic acid encoding the modified immunoglobulins, under the appropriate conditions to induce or cause expression of the modified immunoglobulins. The methods of introducing exogenous nucleic acid molecules into a host are well known in the art, and will vary with the host used. Of course, also acellular or cell free expression systems for the expression of modified immunoglobulins may be employed.
The term “expression system” refers to nucleic acid molecules containing a desired coding sequence and control sequences in operable linkage, so that hosts transformed or transfected with these sequences are capable of producing the encoded proteins. In order to effect transformation, the expression system may be included on a vector; however, the relevant DNA may than also be integrated into the host chromosome.
According to a preferred embodiment of the present invention the expression system comprises a vector. Any expression vector known in the art may be used for this purpose as appropriate.
The modified immunoglobulin is preferably expressed in a host, preferably in a bacterial, a yeast, a plant cell, in an animal cell or in a plant or animal.
A wide variety of appropriate host cells may be used to express the modified immunoglobulin, including but not limited to mammalian cells (animal cells) or and plant cells), bacteria (e.g. Bacillus subtilis, Escherichia coli), insect cells, and yeast (e.g. Pichia pastoris, Saccharomyces cerevisiae). For example, a variety of cell lines that may find use in the present invention are described in the ATCC cell line catalog, available from the American Type Culture Collection. Furthermore, also plants and animals may be used as hosts for the expression of the immunoglobulin according to the present invention. The expression as well as the transfection vectors or cassettes may be selected according to the host used.
Of course also acellular or cell free protein expression systems may be used. In vitro transcription/translation protein expression platforms, that produce sufficient amounts of protein offer many advantages of a cell-free protein expression, eliminating the need for laborious up- and down-stream steps (e.g. host cell transformation, culturing, or lysis) typically associated with cell-based expression systems.
In a preferred embodiment of the present invention, the modified immunoglobulins are purified or isolated after expression. Modified immunoglobulins may be isolated or purified in a variety of ways known to those skilled in the art. Standard purification methods include chromatographic techniques, including affinity chromatography, ion exchange or hydrophobix chromatography, electrophoretic, immunological, precipitation, dialysis, filtration, concentration, and chromatofocusing techniques. Purification is often enabled by a particular fusion partner. For example, antibodies may be purified using glutathione resin if a GST fusion is employed, Ni+2 affinity chromatography if a His-tag is employed or immobilized anti-flag antibody if a flag-tag is used. For general guidance in suitable purification techniques, see Antibody Purification: Principles and Practice, 3.sup.rd Ed., Scopes, Springer-Verlag, NY, 1994. Of course, it is also possible to express the modified immunoglobulins according to the present invention on the surface of a host, in particular on the surface of a bacterial, insect or yeast cell or on the surface of phages or viruses.
Modified immunoglobulins may be screened using a variety of methods, including but not limited to those that use in vitro assays, in vivo and cell-based assays, and selection technologies. Automation and high-throughput screening technologies may be utilized in the screening procedures. Screening may employ the use of a fusion partner or label, for example an enzyme, an immune label, isotopic label, or small molecule label such as a fluorescent or calorimetric dye or a luminogenic molecule.
In a preferred embodiment, the functional and/or biophysical properties of the immunoglobulins are screened in an in vitro assay. In a preferred embodiment, the antibody is screened for functionality, for example its ability to catalyze a reaction or its binding affinity to its target.
Assays may employ a variety of detection methods including but not limited to chromogenic, fluorescent, luminescent, or isotopic labels.
As is known in the art, a subset of screening methods are those that select for favorable members of a library. The methods are herein referred to as “selection methods”, and these methods find use in the present invention for screening modified immunoglobulins. When immunoglobulins libraries are screened using a selection method, only those members of a library that are favorable, that is which meet some selection criteria, are propagated, isolated, and/or observed. As will be appreciated, because only the most fit variants are observed, such methods enable the screening of libraries that are larger than those screenable by methods that assay the fitness of library members individually. Selection is enabled by any method, technique, or fusion partner that links, covalently or noncovalently, the phenotype of immunoglobulins with its genotype, that is the function of a antibody with the nucleic acid that encodes it. For example the use of phage display as a selection method is enabled by the fusion of library members to the gene III protein. In this way, selection or isolation of modified immunoglobulins that meet some criteria, for example binding affinity to the immunoglobulin's target, also selects for or isolates the nucleic acid that encodes it. Once isolated, the gene or genes encoding modified immunoglobulins may then be amplified. This process of isolation and amplification, referred to as panning, may be repeated, allowing favorable antibody variants in the library to be enriched. Nucleic acid sequencing of the attached nucleic acid ultimately allows for gene identification.
A variety of selection methods are known in the art that may find use in the present invention for screening immunoglobulin libraries. These include but are not limited to phage display (Phage display of peptides and antibodies: a laboratory manual, Kay et al., 1996, Academic Press, San Diego, Calif., 1996; Low-man et al., 1991, Biochemistry 30:10832-10838; Smith, 1985, Science 228:1315-1317) and its derivatives such as selective phage infection (Malmborg et al., 1997, J Mol Biol 273:544-551), selectively infective phage (Krebber et al., 1997, J Mol Biol 268:619-630), and delayed infectivity panning (Benhar et al., 2000, J Mol Biol 301:893-904), cell surface display (Witrrup, 2001, Curr Opin Biotechnol, 12:395-399) such as display on bacteria (Georgiou et al., 1997, Nat Biotechnol 15:29-34; Georgiou et al., 1993, Trends Biotechnol 11:6-10; Lee et al., 2000, Nat Biotechnol 18:645-648; Jun et al., 1998, Nat Biotechnol 16:576-80), yeast (Boder & Wittrup, 2000, Methods Enzymol 328:430-44; Boder & Wittrup, 1997, Nat Biotechnol 15:553-557), and mammalian cells (Whitehorn et al., 1995, Bio/technology 13:1215-1219), as well as in vitro display technologies (Amstutz et al., 2001, Curr Opin Biotechnol 12:400-405) such as polysome display (Mattheakis et al., 1994, Proc Natl Acad Sci USA 91:9022-9026), ribosome display (Hanes et al., 1997, Proc Natl Acad Sci USA 94:4937-4942), mRNA display (Roberts & Szostak, 1997, Proc Natl Acad Sci USA 94:12297-12302; Nemoto et al., 1997, FEBS Lett 414:405-408), and ribosome-inactivation display system (Zhou et al., 2002, J Am Chem Soc 124, 538-543).
Other selection methods that may find use in the present invention include methods that do not rely on display, such as in vivo methods including but not limited to periplasmic expression and cytometric screening (Chen et al., 2001, Nat Biotechnol 19:537-542), the antibody fragment complementation assay (Johnsson & Varshavsky, 1994, Proc Natl Acad Sci USA 91:10340-10344; Pelletier et al., 1998, Proc Natl Acad Sci USA 95:12141-12146), and the yeast two hybrid screen (Fields & Song, 1989, Nature 340:245-246) used in selection mode (Visintin et al., 1999, Proc Natl Acad Sci USA 96:11723-11728). In an alternate embodiment, selection is enabled by a fusion partner that binds to a specific sequence on the expression vector, thus linking covalently or noncovalently the fusion partner and associated Fc variant library member with the nucleic acid that encodes them.
In an alternative embodiment, in vivo selection can occur if expression of the antibody imparts some growth, reproduction, or survival advantage to the cell.
A subset of selection methods referred to as “directed evolution” methods are those that include the mating or breeding of favourable sequences during selection, sometimes with the incorporation of new mutations. As will be appreciated by those skilled in the art, directed evolution methods can facilitate identification of the most favourable sequences in a library, and can increase the diversity of sequences that are screened. A variety of directed evolution methods are known in the art that may find use in the present invention for screening antibody variants, including but not limited to DNA shuffling (PCT WO 00/42561 A3; PCT WO 01/70947 A3), exon shuffling (U.S. Pat. No. 6,365,377; Kolkman & Stemmer, 2001, Nat Biotechnol 19:423-428), family shuffling (Crameri et al., 1998, Nature 391:288-291; U.S. Pat. No. 6,376,246), RACHITT™ (Coco et al., 2001, Nat Bio-technol 19:354-359; PCT WO 02/06469), STEP and random priming of in vitro recombination (Zhao et al., 1998, Nat Biotechnol 16:258-261; Shao et al., 1998, Nucleic Acids Res 26:681-683), exonuclease mediated gene assembly (U.S. Pat. No. 6,352,842; U.S. Pat. No. 6,361,974), Gene Site Saturation Mutagenesis™ (U.S. Pat. No. 6,358,709), Gene Reassembly™ (U.S. Pat. No. 6,358,709), SCRATCHY (Lutz et al., 2001, Proc Natl Acad Sci USA 98:11248-11253), DNA fragmentation methods (Kikuchi et al., Gene 236:159-167), single-stranded DNA shuffling (Kikuchi et al., 2000, Gene 243:133-137), and AMEsystem™ directed evolution antibody engineering technology (Applied Molecular Evolution) (U.S. Pat. No. 5,824,514; U.S. Pat. No. 5,817,483; U.S. Pat. No. 5,814,476; U.S. Pat. No. 5,763,192; U.S. Pat. No. 5,723,323).
According to a preferred embodiment of the present invention the specific binding of the modified immunoglobulin to the molecule is determined by a binding assay selected from the group consisting of immunological assays, preferably enzyme linked immunosorbent assays (ELISA), surface plasmon resonance assays, saturation transfer difference nuclear magnetic resonance spectroscopy, transfer NOE (trNOE) nuclear magnetic resonance spectroscopy, competitive assays, tissue binding assays, live cell binding assays and cellular extract assays.
Binding assays can be carried out using a variety of methods known in the art, including but not limited to FRET (Fluorescence Resonance Energy Transfer) and BRET (Bioluminescence Resonance Energy Transfer)-based assays, AlphaScreen™ (Amplified Luminescent Proximity Homogeneous Assay), Scintillation Proximity Assay, ELISA (Enzyme-Linked Immunosorbent Assay), SPR (Surface Plasmon Resonance, also known as BIACORE™), isothermal titration calorimetry, differential scanning calorimetry, gel electrophoresis, and chromatography including gel filtration. These and other methods may take advantage of some fusion partner or label.
The modified immunoglobulin is preferably conjugated to a label or reporter molecule, selected from the group consisting of organic molecules, enzyme labels, radioactive labels, colored labels, fluorescent labels, chromogenic labels, luminescent labels, haptens, digoxigenin, biotin, metal complexes, metals, colloidal gold and mixtures thereof. Modified immunoglobulins conjugated to labels or reporter molecules may be used, for instance, in diagnostic methods.
The modified immunoglobulin may be conjugated to other molecules which allow the simple detection of said conjugate in, for instance, binding assays (e.g. ELISA) and binding studies.
In a preferred embodiment, antibody variants are screened using one or more cell-based or in vivo assays. For such assays, purified or unpurified modified immunoglobulins are typically added exogenously such that cells are exposed to individual immunoglobulins or pools of immunoglobulins belonging to a library. These assays are typically, but not always, based on the function of the immunoglobulin; that is, the ability of the antibody to bind to its target and mediate some biochemical event, for example effector function, ligand/receptor binding inhibition, apoptosis, and the like. Such assays often involve monitoring the response of cells to the antibody, for example cell survival, cell death, change in cellular morphology, or transcriptional activation such as cellular expression of a natural gene or reporter gene. For example, such assays may measure the ability of antibody variants to elicit ADCC, ADCP, or CDC. For some assays additional cells or components, that is in addition to the target cells, may need to be added, for example serum complement, or effector cells such as peripheral blood monocytes (PBMCs), NK cells, macrophages, and the like. Such additional cells may be from any organism, preferably humans, mice, rat, rabbit, and monkey. Immunoglobulins may cause apoptosis of certain cell lines expressing the target, or they may mediate attack on target cells by immune cells which have been added to the assay. Methods for monitoring cell death or viability are known in the art, and include the use of dyes, immunochemical, cytochemical, and radioactive reagents. For example, caspase staining assays may enable apoptosis to be measured, and uptake or release of radioactive substrates or fluorescent dyes such as alamar blue may enable cell growth or activation to be monitored.
In a preferred embodiment, the DELFIART EuTDA-based cytotoxicity assay (Perkin Elmer, MA) may be used. Alternatively, dead or damaged target cells may be monitored by measuring the release of one or more natural intracellular components, for example lactate dehydrogenase. Transcriptional activation may also serve as a method for assaying function in cell-based assays. In this case, response may be monitored by assaying for natural genes or immunoglobulins which may be upregulated, for example the release of certain interleukins may be measured, or alternatively readout may be via a reporter construct. Cell-based assays may also involve the measure of morphological changes of cells as a response to the presence of modified immunoglobulins. Cell types for such assays may be prokaryotic or eukaryotic, and a variety of cell lines that are known in the art may be employed. Alternatively, cell-based screens are performed using cells that have been transformed or transfected with nucleic acids encoding the variants. That is, antibody variants are not added exogenously to the cells. For example, in one embodiment, the cell-based screen utilizes cell surface display. A fusion partner can be employed that enables display of modified immunoglobulins on the surface of cells (Witrrup, 2001, Curr Opin Biotechnol, 12:395-399).
In a preferred embodiment, the immunogenicity of the modified immunoglobulins may be determined experimentally using one or more cell-based assays. In a preferred embodiment, ex vivo T-cell activation assays are used to experimentally quantitate immunogenicity. In this method, antigen presenting cells and naive T cells from matched donors are challenged with a peptide or whole antibody of interest one or more times. Then, T cell activation can be detected using a number of methods, for example by monitoring production of cytokines or measuring uptake of tritiated thymidine. In the most preferred embodiment, interferon gamma production is monitored using Elispot assays (Schmittel et. al., 2000, J. Immunol. Meth., 24: 17-24).
The biological properties of the modified immunoglobulins of the present invention may be characterized ex vivo in cell, tissue, and whole organism experiments. As is known in the art, drugs are often tested in vivo in animals, including but not limited to mice, rats, rabbits, dogs, cats, pigs, and monkeys, in order to measure a drug's efficacy for treatment against a disease or disease model, or to measure a drug's pharmacokinetics, pharmacodynamics, toxicity, and other properties. The animals may be referred to as disease models. Therapeutics are often tested in mice, including but not limited to nude mice, SCID mice, xenograft mice, and transgenic mice (including knockins and knockouts). Such experimentation may provide meaningful data for determination of the potential of the antibody to be used as a therapeutic with the appropriate half-life, effector function, apoptotic activity, cytotoxic or cytolytic activity. Any organism, preferably mammals, may be used for testing. For example because of their genetic similarity to humans, primates, monkeys can be suitable therapeutic models, and thus may be used to test the efficacy, toxicity, pharmacokinetics, pharmacodynamics, half-life, or other property of the modified immunoglobulins of the present invention. Tests of the substances in humans are ultimately required for approval as drugs, and thus of course these experiments are contemplated. Thus the modified immunoglobulins of the present invention may be tested in humans to determine their therapeutic efficacy, toxicity, immunogenicity, pharmacokinetics, and/or other clinical properties. Especially those multivalent immunoglobulins according to the invention that bind to single cell through at least two surface antigens, preferably binding of at least three structures cross-linking target cells, would be considered preapoptotic and exert apoptotic activity upon cell targeting and cross-linking. Multivalent binding provides a relatively large association of binding partners, also called cross-linking, which is a prerequisite for apoptosis.
The modified immunoglobulins of the present invention may find use in a wide range of antibody products. In one embodiment the antibody variant of the present invention is used for therapy or prophylaxis, e.g. as an active or passive immunotherapy, for preparative, industrial or analytic use, as a diagnostic, an industrial compound or a research reagent, preferably a therapeutic. The modified immunoglobulin or antibody variant may find use in an antibody composition that is monoclonal or polyclonal. In a preferred embodiment, the modified immunoglobulins of the present invention are used to capture or kill target cells that bear the target antigen, for example cancer cells. In an alternate embodiment, the modified immunoglobulins of the present invention are used to block, antagonize, or agonize the target antigen, for example by antagonizing a cytokine or cytokine receptor.
In an alternately preferred embodiment, the modified immunoglobulins of the present invention are used to block, antagonize, or agonize growth factors or growth factor receptors and thereby mediate killing the target cells that bear or need the target antigen.
In an alternately preferred embodiment, the modified immunoglobulins of the present invention are used to block, antagonize, or agonize enzymes and substrate of enzymes.
The modified immunoglobulins of the present invention may be used for various therapeutic purposes, preferably for active or passive immunotherapy.
Specifically the immunoglobulin according to the present invention or obtainable by a method according to the present invention can be used for the preparation of a vaccine for active immunization. Hereby the immunoglobulin is either used as an antigenic drug substance to formulate a vaccine or used for fishing or capturing antigenic structures ex vivo or in vivo for use in a vaccine formulation.
In a preferred embodiment, an antibody comprising the modified immunoglobulins is ad-ministered to a patient to treat a specific disorder. A “patient” for the purposes of the present invention includes both humans and other animals, preferably mammals and most preferably humans. By “specific disorder” herein is meant a disorder that may be ameliorated by the administration of a pharmaceutical composition comprising a modified immunoglobulin of the present invention.
In one embodiment, a modified immunoglobulin according to the present invention is the only therapeutically active agent administered to a patient. Alternatively, the modified immunoglobulin according the present invention is administered in combination with one or more other therapeutic agents, including but not limited to cytotoxic agents, chemotherapeutic agents, cytokines, growth inhibitory agents, anti-hormonal agents, kinase inhibitors, anti-angiogenic agents, cardioprotectants, or other therapeutic agents. The modified immunoglobulins may be administered concomitantly with one or more other therapeutic regimens. For example, an antibody variant of the present invention may be administered to the patient along with chemotherapy, radiation therapy, or both chemotherapy and radiation therapy. In one embodiment, the modified immunoglobulins of the present invention may be administered in conjunction with one or more antibodies, which may or may not comprise a antibody variant of the present invention. In accordance with another embodiment of the invention, the modified immunoglobulins of the present invention and one or more other anti-cancer therapies are employed to treat cancer cells ex vivo. It is contemplated that such ex vivo treatment may be useful in bone marrow transplantation and particularly, autologous bone marrow transplantation. It is of course contemplated that the antibodies of the invention can be employed in combination with still other therapeutic techniques such as surgery.
A variety of other therapeutic agents may find use for administration with the modified immunoglobulins of the present invention. In one embodiment, the modified immunoglobulin is administered with an anti-angiogenic agent, which is a compound that blocks, or interferes to some degree, the development of blood vessels. The anti-angiogenic factor may, for instance, be a small molecule or a protein, for example an antibody, Fc fusion molecule, or cytokine, that binds to a growth factor or growth factor receptor involved in promoting angiogenesis. The preferred anti-angiogenic factor herein is an antibody that binds to Vascular Endothelial Growth Factor (VEGF). In an alternate embodiment, the modified immunoglobulin is administered with a therapeutic agent that induces or enhances adaptive immune response, for example an antibody that targets CTLA-4. In an alternate embodiment, the modified immunoglobulin is administered with a tyrosine kinase inhibitor, which is a molecule that inhibits to some extent tyrosine kinase activity of a tyrosine kinase. In an alternate embodiment, the modified immunoglobulins of the pre-sent invention are administered with a cytokine. By “cytokine” as used herein is meant a generic term for proteins released by one cell population that act on another cell as intercellular mediators including chemokines.
Pharmaceutical compositions are contemplated wherein modified immunoglobulins of the present invention and one or more therapeutically active agents are formulated. Stable formulations of the antibody variants of the present invention are prepared for storage by mixing said immunoglobulin having the desired degree of purity with optional pharmaceutically acceptable carriers, excipients or stabilizers (Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed., 1980), in the form of lyophilized formulations or aqueous solutions. The formulations to be used for in vivo administration are preferably sterile. This is readily accomplished by filtration through sterile filtration membranes or other methods. The modified immunoglobulins and other therapeutically active agents disclosed herein may also be formulated as immunoliposomes, and/or entrapped in microcapsules
Administration of the pharmaceutical composition comprising a modified immunoglobulin of the present invention, preferably in the form of a sterile aqueous solution, may be done in a variety of ways, including, but not limited to, orally, subcutaneously, intravenously, intranasally, intraotically, transdermally, mucosal, topically (e.g., gels, salves, lotions, creams, etc.), intraperitoneally, intramuscularly, intrapulmonary (e.g., AERx™ inhalable technology commercially available from Aradigm, or Inhance™ pulmonary delivery system commercially available from Inhale Therapeutics), vaginally, parenterally, rectally, or intraocularly.
As used herein, the term “specifically binds” refers to a binding reaction which is determinative of the cognate ligand of interest in a heterogeneous population of molecules. Thus, under designated conditions (e.g. immunoassay conditions in the case of an immunoglobulin), the specified antibody binds to its particular “target” and does not bind in a significant amount to other molecules present in a sample. Comparable to CDRs of antibodies the modified structural loop regions are antigen-, structure- or molecule-binding protein moieties and not antigens as such.
Another aspect of the present invention relates to a method for manufacturing an immunoglobulin or a pharmaceutical preparation thereof comprising at least one modification in a structural loop region of said immunoglobulin and determining the binding of said immunoglobulin to an epitope of an antigen, wherein the unmodified immunoglobulin does not significantly bind to said epitope, comprising the steps of:

- providing a nucleic acid encoding an immunoglobulin comprising at least one loop region,
- modifying at least one nucleotide residue of at least one of said loop regions,
- transferring said modified nucleic acid in an expression system,
- expressing said modified immunoglobulin,
- contacting the expressed modified immunoglobulin with an epitope,
- determining whether said modified immunoglobulin binds to said epitope, and
- providing the modified immunoglobulin binding to said epitope and optionally finishing it to a pharmaceutical preparation.

In a preferred embodiment the immunoglobulin according to the invention is a bispecific antibody or a bispecific single chain antibody. Further preferred is that the immunoglobulin comprises a bispecific domain or a part thereof including a minidomain.
In particular the present invention relates to a method for manufacturing a multi-specific immunoglobulin binding specifically to at least one first molecule or a pharmaceutical preparation thereof comprising at least one modification in at least one structural loop region of said immunoglobulin and determining the specific binding of said at least one loop region to at least one second molecule, which is an antigen such as selected from the group consisting of allergens, tumor associated antigens, self antigens, enzymes, bacterial antigens, fungal antigens, protozooal antigens and viral antigens, wherein the immunoglobulin containing an unmodified structural loop region does not specifically bind to said at least one second molecule, comprising the steps of:

- providing a nucleic acid encoding an immunoglobulin binding specifically to at least one first molecule comprising at least one structural loop region,
- modifying at least one nucleotide residue of at least one of said loop regions encoded by said nucleic acid,
- transferring said modified nucleic acid in an expression system,
- expressing said modified immunoglobulin,
- contacting the expressed modified immunoglobulin with said at least one second molecule, and
- determining whether said modified immunoglobulin binds specifically to the second molecule and
- providing the modified immunoglobulin binding specifically to said at least one second molecule and optionally finishing it to a pharmaceutical preparation.

The engineering of more than one specificity into a member of a specific binding pair is preferred (Kufer et al. (2004) Trends in Biotechnology vol. 22 pages 238-244).
Numerous attempts have been made to produce multi-specific, e.g. bispecific, monoclonal antibodies or antibody fragments. One problem in the production of bispecific antibodies made of two different polypeptide chains (heavy and light chain) is the necessity to express four different chains (two heavy and two light chains) in one cell resulting in a number of various combinations of molecules which have to be separated from the desired bispecific molecule in the mixture. Due to their similarity the separation of these molecules is difficult and expensive. A number of techniques have been employed to minimize the occurrence of such unwanted pairings (Carter (2001) Journal of Immunological Methods, vol 248, pages 7-15)
One solution to the problem is the production of one poly-peptide chain with two specificities, like e.g. two scFvs linked to each other or the production of so-called diabodies. Such molecules have been shown to be far away from the fold of a natural molecule and are notoriously difficult to produce (Le-Gall et al. (2004) Protein Engineering, Design & Selection vol 17 pages 357-366).
Another problem of the current design of bispecific antibodies is the fact that even if the parent antibodies are bivalently binding to their respective binding partner (e.g. IgG), the resulting bispecific antibody is monovalent for each of the respective binding partner.
The preferred multi-specific molecules of the present invention solve these problems: Expression of a bispecific molecule as one polypeptide chain is possible (a modified Ig domain with two binding specificities, see example section), which is easier to accomplish than the expression of two antibody polypeptide chains (Cabilly et al. Proc. Natl. Acad. Sci. USA 81:3273-3277 (1984)).
It can also be produced as an antibody like molecule (i.e. made of two polypeptide chains, either homodimeric or heterodimeric), due to the fact that the second specificity is located in the non-variable part of the molecule there is no need for two different heavy chains or different light chains. Thus, there is no possibility of wrong pairing of the two chains.
An antibody of the present invention may consist of a heavy chain and a light chain, which form together a variable region binding to a specific binding partner by a first specificity. The second specificity may be formed by a modified loop of any of the structural loops of either the heavy chain or the light chain. The binding site may also be formed by more than one non-CDR loops which may be structurally neighbored (either on the heavy chain or on the light chain or on both chains).
The modified antibody or derivative may be a complete antibody or an antibody fragment (e.g. Fab, CH1-CH2, CH2-CH3, Fc, with or without the hinge region).
It may bind mono- or multivalently to the same or different binding partners or even with different valency for the different binding partners, depending on the design.
As there are a number of various loops available for selection and design of a specific binding site in the non-CDR regions of heavy and light chains it is possible to design antibody derivatives with even more than two specificities without the problems mentioned above.
The specific binding domains within one polypeptide chain may be connected with or without a peptide linker.
The modified structural loop region of said inventive immunoglobulin can be within the constant and/or the variable domain of said immunoglobulin. In case the modified structural loop is within the constant domain, it is preferably within CH1, CH2, CH3, CH4, Igk-C, Igl-C, or a part thereof.
According to a preferred embodiment of the present invention the immunoglobulin is of human or murine origin.
Since the modified immunoglobulin may be employed for various purposes, in particular in pharmaceutical compositions, the immunoglobulin is preferably of human or murine origin. Of course, the modified immunoglobulin may also be a humanized or chimeric immunoglobulin.
According to another preferred embodiment of the present invention the human immunoglobulin is selected from the group consisting of IgA1, IgA2, IgD, IgE, IgG1, IgG2, IgG3, IgG4 and IgM.
The murine immunoglobulin is preferably selected from the group consisting of IgA, IgD, IgE, IgG1, IgG2A, IgG2B, IgG2C, IgG3 and IgM.
The modified immunoglobulin may be derived from one of the above identified immunoglobulin classes, and structurally changed thereafter.
The immunoglobulin comprises preferably a heavy and/or light chain of the immunoglobulin or a part thereof. Either a heterodimeric or a homodimeric molecule may be preferably provided for the purpose of the invention, as well as monomeric immunoglobulins.
The modified immunoglobulin may comprise a heavy and/or light chain, and at least one variable and/or constant domain.
The immunoglobulin according to the present invention comprises preferably at least one constant and/or at least one variable domain of the immunoglobulin or a part thereof including a minidomain.
A constant domain is an immunoglobulin fold unit of the constant part of an immunoglobulin molecule, also referred to as a domain of the constant region (e.g. CH1, CH2, CH3, CH4, Ck, Cl).
A variable domain is an immunoglobulin fold unit of the variable part of an immunoglobulin, also referred to as a domain of the variable region (e.g. Vh, Vk, Vl, Vd)
A preferred immunoglobulin according to the invention consists of a constant domain selected from the group consisting of CH1, CH2, CH3, CH4, Igk-C, Igl-C, or a part or combinations thereof, including a mini-domain, with at least one loop region, and is characterised in that said at least one loop region comprises at least one amino acid modification forming at least one modified loop region, wherein said at least one modified loop region binds specifically to at least one epitope of an antigen.
The modified immunoglobulin according to the present invention may comprise one or more constant domains (e.g. at least two, three, four, five, six, ten domains). If more than one do-main is present in the modified immunoglobulin these domains may be of the same type or of varying types (e.g. CH1-CH1-CH2, CH3-CH3, Fc region, (CH2)2-(CH3)2). Of course also the order of the single domains may be of any kind (e.g. CH1-CH3-CH2, CH4-CH1-CH3-CH2).
According to another preferred embodiment of the present invention the modified loop regions of CH1, CH2, CH3 and CH4 comprise amino acids 7 to 21, amino acids 25 to 39, amino acids 41 to 81, amino acids 83 to 85, amino acids 89 to 103 and amino acids 106 to 117.
According to another preferred embodiment of the present invention the amino acid residues of positions 15 to 17, 29 to 34, 85.4 to 85.3, 92 to 94, 97 to 98 and/or 108 to 110 of CH3 are modified.
The loop regions of Igk-C and Igl-C of human origin comprise preferably amino acids 8 to 18, amino acids 27 to 35, amino acids 42 to 78, amino acids 83 to 85, amino acids 92 to 100, amino acids 108 to 117 and amino acids 123 to 126.
The loop regions of Igk-C and Igl-C of murine origin comprise preferably amino acids 8 to 20, amino acids 26 to 36, amino acids 43 to 79, amino acids 83 to 85, amino acids 90 to 101, amino acids 108 to 116 and amino acids 122 to 125.
According to a specific embodiment the immunoglobulin according to the invention may contain a modification within the variable domain, which is selected from the group of VH, Vkappa, Vlambda, VHH and combinations thereof. More specifically, they comprise at least one modification within amino acids 7 to 21, amino acids 25 to 39, amino acids 41 to 81, amino acids 83 to 85, amino acids 89 to 103 or amino acids 106 to 117, where the numbering of the amino acid position of the domains is that of the IMGT.
Another preferred immunoglobulin according to the invention consists of a variable domain of a heavy or light chain, or a part thereof including a minidomain, with at least one loop region, preferably a structural loop region, and is characterised in that said at least one loop region comprises at least one amino acid modification forming at least one modified loop region, wherein said at least one modified loop region binds specifically to at least one epitope of an antigen.
In an alternative embodiment, the immunoglobulin according to the invention is characterised in that the loop regions of VH or Vkappa or Vlambda of human origin comprise at least one modification within amino acids 8 to 20, amino acids 44 to 50, amino acids 67 to 76 and amino acids 89 to 101, most preferably amino acid positions 12 to 17, amino acid positions 45 to 50, amino acid positions 69 to 75 and amino acid positions 93 to 98, where the numbering of the amino acid position of the domains is that of the IMGT.
The structural loop regions of the variable domain of the immunoglobulin of human origin, as possible selected for modification purposes according to the invention comprise preferably amino acids 8 to 20, amino acids 44 to 50, amino acids 67 to 76 and amino acids 89 to 101.
According to a preferred embodiment of the present invention the structural loop regions of the variable domain of the immunoglobulin of murine origin as possible selected for modification purposes according to the invention comprise amino acids 6 to 20, amino acids 44 to 52, amino acids 67 to 76 and amino acids 92 to 101.
The immunoglobulin according to the invention is preferably also of camel origin. Camel antibodies comprise only one heavy chain and have the same antigen affinity as normal antibodies consisting of light and heavy chains. Consequently camel antibodies are much smaller than, e.g., human antibodies, which allows them to penetrate dense tissues to reach the antigen, where larger proteins cannot. Moreover, the comparative simplicity, high affinity and specificity and the potential to reach and interact with active sites, camel's heavy chain antibodies present advantages over common antibodies in the design, production and application of clinically valuable compounds.
The immunoglobulin of camel or camelid origin comprises preferably at least one constant domain selected from the group consisting of CH1, CH2 and CH3. According to a preferred embodiment of the present invention the loop regions of CH1, CH2 and CH3 of the camel immunoglobulin comprise amino acids 8 to 20, amino acids 24 to 39, amino acids 42 to 78, amino acids 82 to 85, amino acids 91 to 103 and amino acids 108 to 117.
Even more specified, the immunoglobulin loop regions of VH of murine origin comprise at least one modification within amino acids 6 to 20, amino acids 44 to 52, amino acids 67 to 76 and amino acids 92 to 101, where the numbering of the amino acid position of the domains is that of the IMGT. The modified loop regions of a VHH of camelid origin preferably comprise at least one modification within amino acids 7 to 18, amino acids 43 to 55, amino acids 68 to 75 and amino acids 91 to 101, where the numbering of the amino acid position of the domains is that of the IMGT.
The above identified amino acid regions of the respective immunoglobulins are loop regions specified to be suitable for modification purposes according to the invention.
Yet another aspect of the present invention relates to a method for specifically binding and/or detecting a molecule comprising the steps of:

- (a) contacting a modified immunoglobulin according to the present invention or a modified immunoglobulin obtainable by a method according to the present invention with a test sample suspected to contain said molecule, and
- (b) detecting the potential formation of a specific immunoglobulin/molecule complex.

Another aspect of the present invention relates to a method for specifically isolating a molecule comprising the steps of:

- (a) contacting a modified immunoglobulin according to the present invention or a modified immunoglobulin obtainable by a method according to the present invention with a sample containing said molecule,
- (b) separating the specific immunoglobulin/molecule complex formed, and
- (c) optionally isolating the molecule from said complex.

The immunoglobulins according to the present invention may be used to isolate specifically molecules from a sample. If multi-specific immunoglobulins are used more than one molecules may be isolated from a sample. It is especially advantageous using modified immunoglobulins in such methods because it allows, e.g., to generate a matrix having a homogeneous surface with defined amounts of binding partners (i.e. Modified immunoglobulins) immobilised thereon which able to bind to the molecules to be isolated. In contrast thereto, if mono-specific binding partners are used no homogeneous matrix can be generated because the single binding partners do not bind with the same efficiency to the matrix.
Another aspect of the present invention relates to a method for targeting a compound to a target comprising the steps of:

- (a) contacting a modified immunoglobulin according to the present invention or a modified immunoglobulin obtainable by a method according to the present invention capable to specifically bind to said compound,
- (b) delivering the immunoglobulin/compound complex to the target.

Modified immunoglobulins according to the present invention may be used to deliver at least one compound bound to the CDRs and/or modified loop regions to a target. Such immunoglobulins may be used to target therapeutic substances to a preferred site of action in the course of the treatment of a disease.
Another aspect of the present invention relates to the use of an immunoglobulin according to the present invention or obtainable by a method according to the present invention for the preparation of a protein library of immunoglobulins. Further libraries according to the invention not just contain a variety of proteins or fusion proteins, genetic packages, but also precursors of proteins, nucleic acids, ribosomes, cells, virus, phages, and other display systems which express information encoding the proteins and/or the proteins as such.
Another aspect of the present invention relates to a protein library comprising an immunoglobulin according to the present invention or obtainable by the method according to the present invention.
Preferred methods for constructing said library can be found above and in the examples. The library according to the present invention may be used to identify immunoglobulins binding to a distinct molecule.
In particular the present invention relates to the use of a protein library comprising an immunoglobulin according to the present invention or obtainable by the method according to the present invention for the design of immunoglobulin derivatives.
An existing immunoglobulin can be changed to introduce antigen binding sites into any domain or minidomain by using a protein library of the respective domain of at least 10, preferably 100, more preferably 1000, more preferably 10000, more preferably 100000, most preferably more than 1000000 variant domains or minidomains with at least one modified loop, in particular one or more structural loops. The number of members of a library can even be higher, in most cases up to 10e12, with some display systems, such as ribosomal display the number can even be higher than that.
The library is then screened for binding to the specific antigen. After molecular characterization for the desired properties the selected domain or minidomain is cloned into the original immunoglobulin by genetic engineering techniques so that it replaces the wild type region. Alternatively, only the DNA coding for the loops or coding for the mutated amino acids may be exchanged to obtain an immunoglobulin with the additional binding site for the specific antigen.
The choice of the site for the mutated, antigen-specific structural loop is dependent on the structure of the original immunoglobulin and on the purpose of the additional binding site. If, for example, the original molecule is a complete immunoglobulin which needs to have inserted an additional antigen binding site without disturbance of the effector function, the loops to be modified would be selected from domains distant from CH2 and CH3 which are the natural binding partners to Fc-effector molecules. If the original immunoglobulin is a Fab fragment, modification of loops in constant domains of the light chains or the heavy chains or the respective variable domains is possible. To generate a library one may prepare libraries of mutant original molecules which have mutations in one or more structural loops of one or more domains. The selection with complete mutated original molecules may have some advantages as the selection for antigen binding with a modified structural loop will deliver the sterically advantageous modifications if tested also for the other properties the mutated immunoglobulin should show. In particular an Fc library is preferred, e.g. with binding sites in the C-terminal loop region.
The size requirement (i.e. the number of variant proteins) of a protein library of a mutated domain or a minidomain or a fusion molecule of a domain is dependent on the task. In general, a library to generate an antigen binding site de novo needs to be larger than a library used to further modify an already existing engineered antigen binding site made of a modified structural loop (e.g. for enhancing affinity or changing fine specificity to the antigen).
The present invention also relates to an immunoglobulin library or a nucleic acid library comprising a plurality of immunoglobulins, e.g. a constant or variable domain, a minidomain and/or at least one structural loop region contained in a mini-domain, or nucleic acid molecules encoding the same. The library contains members with different modifications, wherein the plurality is defined by the modifications in the at least one structural loop region. The nucleic acid library preferably includes at least 10 different members with a difference in the nucleotide sequence to obtain at least one different amino acid (resulting in one amino acid exchange) and more preferably includes at least 100, more preferably 1000 or 10000 different members (e.g. designed by randomization strategies or combinatory techniques). Even more diversified individual member numbers, such as at least 1000000 or at least 10000000 are also preferred.
A further aspect of the invention is the combination of two different immunoglobulins, domains or minidomains selected from at least two libraries according to the invention in order to generate multispecific immunoglobulins. These selected specific immunoglobulins may be combined with each other and with other molecules, similar to building blocks, to design the optimal arrangement of the domains or minidomains to get the desired properties. For example, a molecule based on Fc can be used as such, with antigen-binding properties, as a carrier for other binding motifs or as a building block to build an immunoglobulin with constant or variable domains, or else combined with constant domains only, such as multimeric Fc molecules, preferably with 2, 3, or 4 antigen binding sites.
Furthermore, one or more modified immunoglobulins according to the invention may be introduced at various or all the different sites of a protein possible without destruction of the structure of the protein. By such a “domain shuffling” technique new libraries are created which can again be selected for the desired properties.
Preferably, the immunoglobulin according to the present invention is composed of at least two immunoglobulin domains, or a part thereof including a minidomain, and each domain contains at least one antigen binding site.
Also preferred is an immunoglobulin according to the invention, which comprises at least one domain of the constant region and/or at least one domain of the variable region of the immunoglobulin, or a part thereof including a minidomain. Thus, a variable domain, which is for example modified in the C-terminal region, or the variable domain linked to a modified CH1 region, for instance a modified CH1 minidomain, is one of the preferred embodiments.
The preferred library contains immunoglobulins according to the invention, selected from the group consisting of domains of an immunoglobulin, minidomains or derivatives thereof.
A preferred embodiment of the present invention is a binding molecule for an antigen (antigen binding molecule) comprising at least one immunoglobulin domain and a structural loop region modified according to the present invention to bind to the antigen, wherein said binding molecule does not comprise variable domains of an antibody. It may comprise other parts useable for antibody activities (e.g. such as natural or modified effector regions (sequences); however, it lacks the “natural” binding region of antibodies, i.e. the variable domains or CDR loops, including VFR loops within the CDR region, in their naturally occurring position. These antigen binding molecules according to the present invention have the advantages described above for the present molecules, yet without the specific binding activity of antibodies mediated by CDR loops; however with a newly introduced specific binding activity in the structural loop region.
Preferably, these antigen binding molecules according to the present invention comprise CH1, CH2, CH3, CH4, Igk-C, Igl-C and combinations thereof; said combinations comprising at least two, preferably at least four, especially at least six constant domains and at least one structural loop or loop region modified according to the present invention. Preferably these structural loop regions are either connected via structural loop region modified according to the present invention or the structural loops being naturally present between such two constant domains. An embodiment of these antigen binding molecules according to the present invention consists of the Fc region of an antibody with at least one modification in a structural loop according to the present invention. Also for the antigen binding molecules according to the present invention it is preferred that the new antigen binding sites in the structural loops are introduced by randomizing technologies, i.e. by exchanging one or more amino acid residues of the loop by randomization techniques or by introducing randomly generated inserts into such structural loops. Alternatively preferred is the use of combinatorial approaches. Preferably the antigen binding sites in the modified structural loops are selected from suitable libraries.
According to another aspect, the present invention relates to a modified immunoglobulin having an antigen binding site to provide a specificity foreign to the unmodified immunoglobulin and incorporated in one or more structural loops. The term “foreign” means that the antigen is not recognized by the specific CDR binding region or other natural or intrinsic binding regions of the immunoglobulin. A foreign binding partner, but not the natural binding partner of an immunoglobulin, may thus be bound by the newly formed antigen binding site of a structural loop. This means that a natural binding partner, such as a an Fc-receptor or an effector of the immune system, is not considered to be bound by the antigen binding site foreign to the unmodified immunoglobulin.
Preferred immunoglobulins according to the present invention comprise at least two antigen binding sites, the first site binding to a first epitope, and the second site binding to a second epitope.
According to a preferred embodiment, the present immunoglobulin comprises at least two loop regions, the first loop region binding to a first epitope, and the second loop region binding to a second epitope. Either the at least first or at least second loop region or both may contain a structural loop. The immunoglobulins according to the present inventions include the fragments thereof known in the art to be functional which contain the essential elements according to the present invention: the structural loop or loop region modified according to the present invention.
The preferred immunoglobulin according to the invention comprises a domain that has at least 50% homology with the unmodified domain.
The term “homology” indicates that polypeptides have the same or conserved residues at a corresponding position in their primary, secondary or tertiary structure. The term also extends to two or more nucleotide sequences encoding the homologous polypeptides.
“Homologous immunoglobulin domain” means an immunoglobulin domain according to the invention having at least about 50% amino acid sequence identity with regard to a full-length native sequence immunoglobulin domain sequence or any other fragment of a full-length immunoglobulin domain sequence as disclosed herein. Preferably, a homologous immunoglobulin domain will have at least about 50% amino acid sequence identity, preferably at least about 55% amino acid sequence identity, more preferably at least about 60% amino acid sequence identity, more preferably at least about 65% amino acid sequence identity, more preferably at least about 70% amino acid sequence identity, more preferably at least about 75% amino acid sequence identity, more preferably at least about 80% amino acid sequence identity, more preferably at least about 85% amino acid sequence identity, more preferably at least about 90% amino acid sequence identity, more preferably at least about 95% amino acid sequence identity to a native immunoglobulin domain sequence, or any other specifically defined fragment of a full-length immunoglobulin domain sequence as disclosed herein.
“Percent (%) amino acid sequence identity” with respect to the immunoglobulin domain sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific immunoglobulin domain sequence, after aligning the sequence and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
Percent (%) amino acid sequence identity values may be obtained as de-scribed below by using the WU-BLAST-2 computer program (Altschul et al., Methods in Enzymology 266:460-480 (1996)). Most of the WU-BLAST-2 search parameters are set to the default values. Those not set to default values, i.e., the adjustable parameters, are set with the following values: overlap span=1, overlap fraction=0.125, word threshold (T)=11, and scoring matrix=BLOSUM62. When WU-BLAST-2 is employed, a % amino acid sequence identity value is determined by dividing (a) the number of matching identical amino acid residues between the amino acid sequence of the immunoglobulin domain of interest having a sequence derived from the native immunoglobulin domain and the comparison amino acid sequence of interest (i.e., the sequence against which the immunoglobulin domain of interest is being compared which may be the unmodified immunoglobulin domain) as determined by WU-BLAST-2 by (b) the total number of amino acid residues of the non-randomized parts of the immunoglobulin do-main of interest. For example, in the statement “a polypeptide comprising an amino acid sequence A which has or having at least 80% amino acid sequence identity to the amino acid sequence B”, the amino acid sequence A is the comparison amino acid sequence of interest and the amino acid sequence B is the amino acid sequence of the immunoglobulin domain of interest.
Another aspect of the present invention relates to a kit of binding partners containing
(a) a modified immunoglobulin having an antigen binding site foreign to the immunoglobulin incorporated in one or more structural loops, and
(b) a binding molecule containing an epitope of said antigen.
Such a binding molecule of this kit according to the present invention may be used as a capturing agent for identifying the binding specificity of the modified immunoglobulin according to the present invention. By using the binding molecule of this kit according to the pre-sent invention, the potency of the modified immunoglobulins according to the present invention may be determined.
Potency as defined here is the binding property of the modified molecule to its antigen. The binding can be determined quantitatively and/or qualitatively in terms of specificity and/or affinity and/or avidity as used for quality control purposes.
The binding properties of the molecules according to the invention obtained upon modification may further be tuned by standard techniques, such as affinity maturation. Thereby the nucleotide sequence within or surrounding the antigen binding site is further exchanged for modulating the binding properties.
Moreover, the binding molecule of a kit according to the present invention may be used for selecting the modified immunoglobulin with the appropriate potency according to the present invention from a library consisting of at least 10, preferably at least 100, more preferably at least 1000, more preferred at least 10000, especially at least 100000 immunoglobulins with different modifications in the structural loops.
Examples have shown that one of the key features is engineer those immunoglobulin domains or regions which are not normally involved in the desirable intrinsic functions of a antibody, such as antigen binding. Thus, modifying in regions other than the CDR region, including those loops adjacent to the CDR loops, of an antibody would preserve its antigen binding function. It was observed that the specific fold of immunoglobulin domains allows the introduction of random mutations in regions which are structurally analogous to the CDRs but different in position and sequence. The regions identified by the present invention are, like CDRs, loop regions connecting the beta strands of the immunoglobulin fold.
More specifically, it is described herein that by introducing mutations, e.g. random mutations in the loops connecting beta strands A-B and E-F of a human IgG1 CH3 domain, mutated CH3 domains were selected that bind specifically to either Toll like receptor 9-peptide (TLR-9) or to hen egg lysozyme, which are a peptide and a protein, respectively, that are not normally recognized and bound by human CH3 domains of IgG1. The mutations introduced by us include mutations in which selected amino acid residues in the wildtype sequence were replaced by randomly chosen residues, and they also include insertions of extra amino acid residues in the loops mentioned above.
By analogy the immunoglobulin domains from any class of immunoglobulins and from immunoglobulins from any species are amenable to this type of engineering. Furthermore not only the specific loops targeted in the present invention can be manipulated, but any loop connecting beta strands in immunoglobulin domains can be manipulated in the same way.
Engineered immunoglobulin domains from any organism and from any class of immunoglobulin can be produced according to the present invention either as such (as single domains), or as part of a larger molecule. For example, they can be part of an intact immunoglobulin, which accordingly would have its “normal” antigen binding region formed by the 6 CDRs and the new, engineered antigen binding region. Like this, a multi-specific, e.g. bispecific, immunoglobulin could be generated. The engineered immunoglobulin domains can also be part of any fusion protein. The use of these engineered immunoglobulin domains is in the general field of the use of immunoglobulins.
Except where indicated otherwise all numbering of the amino acid sequences of the immunoglobulins is according to the IMGT numbering scheme (IMGT, the international ImMunoGeneTics information system@imgt.cines.fr; http://imgt.cines.fr; Lefranc et al., 1999, Nucleic Acids Res. 27: 209-212; Ruiz et al., 2000 Nucleic Acids Res. 28: 219-221; Lefranc et al., 2001, Nucleic Acids Res. 29: 207-209; Lefranc et al., 2003, Nucleic Acids Res. 31: 307-310; Lefranc et al., 2005, Dev Comp Immunol 29:185-203).

SEQ ID No. 1

PREPQVYTLPPSRDELTKNQVSLTCLVKGF
YPSDIAVEWESNGQPENNYKTTPPVLDSDG
SFFLYSKLTVDKSRWQQGNVFSCSVMHEAL
HNHYTQKSLSLSPGKAAA

SEQ ID No. 2

ccatggcccc ccgagaacca caggtgtaca ccctgccccc atcccgtgac gagctcnnsn nsnnscaagt
cagcctgacc tgcctggtca aaggcttcta tcccagcgac atcgccgtgg agtgggagag caatgggcag
ccggagaaca actacaagac cacgcctccc gtgctggact ccgacggctc cttcttcctc tacagcaagc
ttaccgtgnn snnsnnsagg tggnnsnnsg ggaacgtctt ctcatgctcc gtgatgcatg aggctctgca
caaccactac acacagaaga gcctctccct gtctccgggt aaagcggccg ca
//

SEQ ID No. 3

MAPREPQVYTLPPSEDELXXXQVSLTCLVK
GFYPSDIAVEWESNGQPENNYKTTPPVLDS
DGSFFLYSKLTVXXXRWXXGNVFSCSVMHE
ALHNHYTQKSLSLSPGKAAA

SEQ ID No. 4

cttgccatgg ccccccgaga accacaggtg tac

SEQ ID No. 5

agtcgagctc gtcacgggat gggggcaggg

SEQ ID No. 6

gtacgagctc nnsnnsnnsc aagtcagcct gacctgcctg g

SEQ ID No. 7

tgccaagctt gctgtagagg aagaaggagc cg

SEQ ID No. 8

tgccaagctt accgtgnnsn nsnnsaggtg gnnsnnsggg aacgtcttct catgctccg

SEQ ID No. 9

agttgcggcc gctttacccg gagacaggga gag

SEQ ID No. 10

MAPREPQVYTLPPSRDELXXXQVSLTCLVK
GFYPSDIAVEWESNGQPENNYKTTPPVLDS
DGSFFLYSKLTVXXXXXXRWXXGNVFSCSV
MHEALHNHYTQKSLSLSPGKAAA

SEQ ID No. 11

ccatggcccc ccgagaacca caggtgtaca ccctgccccc atcccgtgac gagctcnnsn nsnnscaagt
cagcctgacc tgcctggtca aaggcttcta tcccagcgac atcgccgtgg agtgggagag caatgggcag
ccggagaaca actacaagac cacgcctccc gtgctggact ccgacggctc cttcttcctc tacagcaagc
ttaccgtgnn snnsnnsnns nnsnnsaggt ggnnsnnsgg gaacgtcttc tcatgctccg tgatgcatga
ggctctgcac aaccactaca cacagaagag cctctccctg tctccgggta aagcggccgc a

SEQ ID No. 12

tgccaagctt accgtgnnsn nsnnsnnsnn snnsaggtgg nnsnnsggga acgtcttctc
atgctccg

SEQ ID No. 13

MAPREPQVYTLPPSRDELXXXQVSLTCLVK
GFYPSDIAVEWESNGQPENNYKTTPPVLDS
DGSFFLYSKLTVXXXXXXXXRWXXGNVFSCSV
MHEALHNHYTQKSLSLSPGKAAA

SEQ ID No. 14

ccatggcccc ccgagaacca caggtgtaca ccctgccccc atcccgtgac gagctcnnsn nsnnscaagt
cagcctgacc tgcctggtca aaggcttcta tcccagcgac atcgccgtgg agtgggagag caatgggcag
ccggagaaca actacaagac cacgcctccc gtgctggact ccgacggctc cttcttcctc tacagcaagc
ttaccgtgnn snnsnnsnns nnsnnsnnsn nsaggtggnn snnsgggaac gtcttctcat gctccgtgat
gcatgaggct ctgcacaacc actacacaca gaagagcctc tccctgtctc cgggtaaagc ggccgca

SEQ ID No. 15

tgccaagctt accgtgnnsn nsnnsnnsnn snnsnnsnns aggtggnnsn nsgggaacgt
cttctcatgc tccg

Example 1

Construction of the CH3 Library and Phage Surface Display

The crystal structure of an IgG1 Fc fragment, which is published in the Brookhaven Database as entry 1OQO.pdb was used to aid in the design of the mutated CH3 domain.
The sequence which was used as the basis for construction of the CH3 library is given in SEQ ID No. 1. In this sequence, the first amino acid corresponds to Proline 343 of chain A of Brookhaven database entry 1oqo.pdb. The last residue contained in 1oqo.pdb is Serine 102 of SEQ ID No. 1. After detailed analysis of the structure of 1oqo.pdb and by visual inspection of the residues forming the loops which connect the beta strands, it was decided to randomize residues 17, 18 and 19, which are part of the loop connecting beta strand A-B as well as 71, 72, 73, 76, and 77, which are part of the loop connecting beta strand E-F of SEQ ID No. 1. The engineered gene was produced by a series of PCR reactions followed by ligation of the resulting PCR products. To facilitate ligation, some of the codons of the nucleotide sequence coding for SEQ ID No. 1 were modified to produce restriction sites without changing the amino acid sequences (silent mutations). For insertion into the cloning vector pHEN1 (Nucleic Acids Res. 1991 Aug. 11; 19(15):4133-7. Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. Hoogenboom H R, Griffiths A D, Johnson K S, Chiswell D J, Hudson P, Winter G.) in frame with the pelB secretion signal, extra nucleotide residues encoding Met-Ala were attached at the 5′ end of the sequence to create an NcoI restriction site. For the randomized residues, the codon NNS (IUPAC code, where S means C or G) was chosen which encodes all 20 naturally occurring amino acids, but avoids 2 out of 3 stop codons. The engineered sequence is given as a nucleotide sequence in SEQ ID No. 2 and as an amino acid sequence in SEQ ID No. 3. The Letter X in SEQ ID No. 3 denotes randomized amino acid residues. The sequences of the PCR primers used for assembly of the mutated CH3 domain are given in SEQ ID No. 4 through 9.
cDNA of the heavy chain of the human monoclonal antibody 3D6 (Felgenhauer M, Kohl J, Rüker F. Nucleotide sequences of the cDNAs encoding the V-regions of H- and L-chains of a human mono-lonal antibody specific to HIV-1-gp41. Nucleic Acids Res. 1990 Aug. 25; 18(16):4927.) were used as template for the PCR reactions. The 3 PCR products were digested with SacI and/or HindIII respectively and ligated together. The ligation product was further digested with NcoI and Not I and ligated into the surface display phagemid vector pHen1, which had previously been digested with NcoI and NotI. A number of selected clones were controlled by restriction analysis and by DNA sequencing and were found to contain the insert as planned, including the correctly inserted randomized sequences. For the following steps of phage preparation, standard protocols were followed. Briefly, the ligation mixture was transformed into E. coli TG1 cells by electroporation. Subsequently, phage particles were rescued from E. coli TG1 cells with helper phage M13-KO7. Phage particles were then precipitated from culture supernatant with PEG/NaCl in two steps, dissolved in water and used for selection by panning or, alternatively, they were stored at minus 80° C.

Example 2

Construction of the CH3+3 Library

This library was constructed and cloned in the same way as the CH3 library. The amino acid sequence of the construct is given in SEQ ID No. 10, the corresponding nucleotide sequence in SEQ ID No. 11, and the primers used for construction were SEQ ID No. 4-7, SEQ ID No. 9 and SEQ ID No. 12.

Example 3

Construction of the CH3+5 Library

This library was constructed and cloned in the same way as the CH3 library. The amino acid sequence of the construct is given in SEQ ID No. 13, the corresponding nucleotide sequence in SEQ ID No. 14, and the primers used for construction were SEQ ID No. 4-7, SEQ ID No. 9 and SEQ ID No. 15.

Example 4

Construction of a CH1 Library

In the human IgG1 CH1 library, Ser93, Ser94, Ser95, Gly98, Thr99 and Gln100 were randomized and 3 random residues additionally inserted using site directed random mutagenesis. Leu96 was not mutated. In another human IgG1 CH1 library, Pro92, Ser93, Ser94, Ser95 Leu96 Thr101, Gly98, Thr99 and Gln100 were randomized and 3 random residues additionally inserted using site directed random mutagenesis. The genes coding for the libraries were cloned in frame with the pelB leader at the N-terminus and in frame with protein III from fd phage at the C-terminus using the restriction sites NcoI and NotI of the phagemid vector pHEN1. Preparation of phage particles, panning and selection of specifically binding clones were performed using standard procedures.

Library Sequence:

Nucleotide sequence of the first CH1 library:

1	GCCTCCACCA AGGGCCCATC GGTCTTCCCC CTGGCACCCT CCTCCAAGAG CACCTCTGGG GGCACAGCGG CCCTGGGCTG CCTGGTCAAG GACTACTTCC
101	CCGAACCGGT GACGGTGTCG TGGAACTCAG GCGCCCTGAC CAGCGGCGTG CACACCTTCC CGGCTGTCCT ACAGTCCTCA GGACTCTACT CCCTCAGCAG
201	CGTGGTGACC GTGCCCNNSN NSNNSTTGNN SNNSNNSNNS NNSNNSACCT ACATCTGCAA CGTGAATCAC AAGCCCAGCA ACACCAAGGT GGACAAGAAA
301	GTTGAGCCCA AATCTGCGGC CGCA

Amino acid sequence of the first CH1 library:
MKYLLPTAAAGLLLLAAQPAMAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPXXXLXXXXX
XTYICNVNHKPSNTKVDKKVEPKSAAA

Nucleotide sequence of the second CH1 library:

1	GCCTCCACCA AGGGCCCATC GGTCTTCCCC CTGGCACCCT CCTCCAAGAG CACCTCTGGG GGCACAGGAG CCCTGGGCTG CCTGGTCAAG GACTACTTCC
101	CCGAACCGGT GACGGTGTCG TGGAACTCAG GCGCCCTGAC CAGCGGCGTG CACACCTTCC CGGCTGTCCT GCAGTCCTCA GGACTCTACT CCCTCAGCAG
201	CGTGGTGACC GTGNNSNNSN NSNNSNNSNN SNNSNNSNNS NNSNNSNNST ACATCTGCAA CGTGAATCAC AAGCCCAGCA ACACCAAGGT GGACAAGAAA
301	GTTGAGCCCA AATCTGCGGC CGCT

Amino acid sequence of the second CH1 library:
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVXXXXXXXXXXXXYICNVNHKPSNTKVDKKVEP
KSAAA

Example 4

Construction of a CL Library

In the human IgG1 CL library, Ser92, Lys93, Ala94, Asp95, Glu97, Lys98 and His99 were randomized and 3 random residues additionally inserted between Ser16 and Gly17 using site directed random mutagenesis. The genes coding for the libraries were cloned in frame with the pelB leader at the N-terminus and in frame with protein III from fd phage at the C-terminus using the restriction sites NcoI and NotI of the phagemid vector pHEN1. Preparation of phage particles, panning and selection of specifically binding clones were performed using standard procedures.

Nucleotide sequence of the CL Library:

1	GTGGCTGCAC CATCTGTCTT CATCTTCCCG CCATCTGATG AGCAGTTGAA ATCTNNSNNS NNSGGAACTG CCTCTGTTGT GTGCCTGCTG AATAACTTCT
101	ATCCCAGAGA GGCCAAAGTA CAGTGGAAGG TGGATAACGC CCTCCAATCG GGTAACTCCC AGGAGAGTGT CACAGAGCAG GACAGCAAGG ACAGCACCTA
201	CAGCCTCAGG TCGACCCTGA CGCTGNNSNN SNNSNNSTAC NNSNNSNNSA AAGTCTACGC CTGCGAAGTC ACCCATCAGG GCCTGAGCTC GCCCGTCACA
301	AAGAGCTTCA ACAGGGGAGA G

Amino acid sequence of the CL library:
VAAPSVFIFPPSDEQLKSXXXGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLRSTLTLXXXXYXXXKVYACEVTHQGLSSPVTKSF
NRGE

Example 5

Panning of the CH3-Phage Library on Rp10-L Peptide

3 panning rounds were performed. Maleimide activated plates (Pierce) were coated with a synthetic peptide Rp10-L, representing a mimotope of B-cell molecular marker CD20 (Perosa et al. Ann N Y Acad. Sci. (2005) 51:672-83). Its deduced amino acid sequence is as follows: ITPWPHWLERSS. 200 μl of the following solution were added per well: PBS, pH=7.2, with the following concentrations of dissolved peptide:

- 1^stpanning round: 100 μg/ml
- 2^ndpanning round: 100 μg/ml
- 3^rdpanning round: 50 μg/ml.

Incubation was overnight at 4° C., followed by blocking with 10 μg/ml cysteine-HCl in PBS, with 200 μl per well for 2 h at room temperature.
The surface display phage library, containing equal concentration of phage from libraries CH3, CH3+3, CH3+5, and CH3+7, was then allowed to react with the bound peptide by adding phage suspension and 2% BSA-PBS up to 200 μl, followed by incubation for 45 min with shaking and 90 min without shaking at room temperature.
Unbound phage particles were washed away as follows;

- after the 1^stpanning round: 15×200 μl T-PBS, 5×200 μl T-PBS
- after the 1^stpanning round: 15×200 μl T-PBS, 10×200 μl T-PBS
- after the 1^stpanning round: 20×200 μl T-PBS, 20×200 μl T-PBS.

Elution of bound particles was performed by adding 200 μl per well of 0.1 M glycine, pH=−2.2, and incubation with shaking for 30 min at room temperature. Subsequently, the phage suspension was neutralised by the addition of 60 μl 2M Tris-base, followed by the infection of E. coli TG1 cells by mixing 10 ml exponentially growing culture with 0.5 ml eluted phage and incubation for 30 min at 37°. Finally, infected bacteria were plated on TYE medium with 1% glucose and 100 μg/ml ampicillin, and incubated at 30° C. overnight.

Results of the Panning of the CH3-Phage Library on Rp10-L Peptide

Phage Titers


Panning	concentration
round	Rp10-L	input (phage/ml)	output (phage/ml)

1^st	100 μg/ml	2 × 10¹⁴	2 × 10¹⁰
2^nd	100 μg/ml	3 × 10¹⁷	3 × 10¹⁰
3^rd	50 μg/ml	6.02 × 10¹⁴	1.5 × 10¹⁰

Example 6

Cloning of Selected Clones for Soluble Expression

Altered CH3 domain-encoding sequences, contained within eluted phage particles, were batch amplified with PCR. After restriction with NcoI and NotI, they were inserted in pNOTBAD (Invitrogen vector pBAD with subsequently inserted NotI site). After transformation into E. coli E104, the cells were selected on TYE medium with 1% glucose and 100 μg/ml ampicillin at 30° C.

Soluble Expression of Selected Clones and Screening

4×96 ampicillin resistant colonies were cultured in 200 μl 2xYT medium with ampicillin in microtitre plates on a shaker overnight at 30° C. They were then induced with L-arabinose added to end concentration of 0.1%. After another overnight incubation, the cells were collected by centrifuging 15 min at 2000 rpm at room temperature and their periplasma proteins were released by resuspending in 100 μl Na-borate buffer (160 mM Na-borate, 200 mM NaCl, pH=8.0) and incubation for at least 6 hours.
For screening, 4 maleimide plates were coated with 100 μg/ml solution of 50 μg/ml peptide Rp10-L, dissolved in PBS, pH=7.2, overnight at 4° C. Plates were then blocked with 10 μg/ml cysteine-HCl in PBS, with 200 μl per well for 2 h at room temperature.
Released periplasmic protein was then allowed to react with the bound peptide by adding 50 μl lysate and 50 μl 2% BSA-PBS, followed by an overnight incubation at room temperature.
Binding of the his-tagged protein was revealed by 90-min-incubation with 100 μl per well solution of antibodies against tetra-his (QIAgen), diluted 1:1000 in 1% BSA-PBS, and a 90-min-incubation with 100 μl per well solution of goat anti-mouse antibodies, labelled with HRP (Sigma), diluted 1:1000 in 1% BSA-PBS. Signals were observed after the addition of substrate OPD (3 mg/ml) in Na-citrate/phosphate buffer, pH=4.5, and 0.4 μl/ml H₂O₂. The reaction was stopped with by adding 100 μl 1.25 M H₂SO₄.

Results of Screening for Binding of Rp10-L on a Single Well Per Clone


	Clone

A21

A57

B63

B78

C50

C55

D5

D37

D39

D80

D83

D91

A_492/620	0.395	0.039	0.063	0.075	0.190	0.045	0.644	0.071	0.448	0.077	0.426	0.142

Background Reaction

Plate A_492/620

A 0.027

B 0.035

C 0.037

D 0.035

Clones revealing a positive signal were cultured in 20 ml 2xYT with ampicillin, at 30° C. overnight. Then they were inoculated 1:20 into fresh medium, and after 3 h at 30° C. they were induced with end concentration of 0.1% L-arabinose, and allowed to express the recombinant CH3-domain overnight at 16° C. Periplasma of the expressing cells was then lysed in 1 ml of Na-borate buffer, pH=8.0, for a minimum of 6 h. Periplasmic extract was allowed to react with Rp10-L peptide and the binding was revealed exactly as described above.

Results of Screening for Binding of Rp10-L


Rp10-L	clone

μg/ml	A21	A57	B63	B78	C50	C55	D5	D37	D39	D80	D83	D91

—	0.265	0.006	0.006	0.005	0.803	0.006	0.035	0.006	0.469	0.004	0.088	0.009
0.81	0.362	0.005	0.007	0.006	1.202	0.008	0.052	0.008	0.660	0.007	0.106	0.009
1.63	0.383	0.006	0.007	0.006	1.308	0.014	0.050	0.014	0.719	0.008	0.129	0.005
3.13	0.352	0.008	0.010	0.005	1.453	0.006	0.060	0.006	0.719	0.008	0.210	0.006
6.25	0.343	0.005	0.008	0.006	1.516	0.007	0.057	0.007	0.694	0.006	0.114	0.008
12.5	0.315	0.007	0.009	0.006	1.495	0.007	0.064	0.007	0.770	0.007	0.130	0.009
25.0	0.335	0.008	0.010	0.008	1.603	0.009	0.063	0.009	0.868	0.008	0.120	0.007
50.0	0.398	0.009	0.011	0.009	1.632	0.009	0.070	0.009	0.765	0.008	0.125	0.008

Cloning of Selected Clones for Soluble Expression in pET27b

Altered CH3 domain-encoding sequences, contained within clones that produced a significant signal on binding to Rp10-L, were amplified with PCR. After restriction with NcoI and NotI, they were inserted in pET27b (Novagen). After transformation into E. coli BL21 (DE3), transformed cells were selected on TYE medium with 1% glucose and 50 μg/ml kanamycin at 30° C.
Clones revealing a positive signal were cultured in 20 ml M9ZB medium with 2% glucose and kanamycin, at 30° C. overnight. Then they were inoculated 1:20 into fresh medium, and after 3 h at 30° C. they were induced with medium containing 1% glycerin instead of glucose, kanamycin and 1 mM IPTG, and allowed to express the recombinant CH3-domain overnight at 16° C. Periplasma of the expressing cells was then lysed in 1 ml of Na-borate buffer, pH=8.0, for a minimum of 6 h. Periplasmic extract was analysed for the presence of recombinant protein with western blotting and detection with anti tetra-his antibodies (QIAgen).

Nucleotide Sequences and Inferred Protein Sequences of CD-20 Binding Clones


				source
clone	1^stgroup	2^ndgroup	3^rdgroup	library

A21	VDG	PWGPRD	WP	CH3 + 3

C50 *	LTH	ALCRWF	VQ	CH3 + 3

D5	ALR	FCGGVV	GL	CH3 + 3

D39	GWW	QQKPFA	TD	CH3 + 3

D83	APP	DLVHVA	MV	CH3 + 3

* an insertion of 2 nucleotides in the 2^ndgroup of mutated residues causes an insertion of G between otherwise constant residues R and W separating 2^ndand 3^rdgroup of mutated residues.

Protein Sequence of CD20 Specific CH3+3 Library Clone D83 (IMGT Numbering)

15-17
92-94
MAPREPQVYTLPPSRDELAPPQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTV
DLV

97-98
HVARWMVGNVFSCSVMHEALHNHYTQKSLSLSPGKAAA

Analysis of Binding of CD-20, Expressed on Cells, Using FACS

Approximately 10⁵Daudi cells were washed with PBS (800 rpm, 5 min, room temperature) and the recombinant CH3 domain in 1% BSA-PBS was allowed to bind for 2 h on ice. Cells were washed again with PBS and the allowed to react with 2 μg/ml anti penta His-Alexa fluor 488 antibody (QIAgen), diluted in 1% BSA-PBS, for 30 min on ice. After washing, the cells were analysed in FACS. Unlabelled cells, wild-type CH3 domain and cell line K562 were used as controls.

Example 7

Isolation of CH1-Mutant Proteins Binding CD20 Antigen

3 panning rounds were performed. Maleimide activated plates (Pierce) were coated with a synthetic peptide, representing a mimotope of B-cell molecular marker CD20. 200 μl of the following solution were added per well: PBS, pH=7.2, with the following concentrations of dissolved peptide:

Incubation was overnight at 4° C., followed by blocking with 10 μg/ml cysteine-HCl in PBS, with 200 μl per well for 2 h at room temperature.
The surface display phage library, displaying mutated CH1 domain, was then allowed to react with the bound peptide by adding phage suspension and 2% BSA-PBS up to 200 μl, followed by incubation for 45 min with shaking and 90 min without shaking at room temperature.
Unbound phage particles were washed away as follows;

- after the 1^stpanning round: 10×200 μl T-PBS, 5×200 μl T-PBS
- after the 1^stpanning round: 15×200 μl T-PBS, 10×200 μl T-PBS
- after the 1^stpanning round: 20×200 μl T-PBS, 20×200 μl T-PBS.

Elution of bound particles was performed by adding 200 μl per well of 0.1 M glycine, pH=2.2, and incubation with shaking for 30 min at room temperature. Subsequently, the phage suspension was neutralised by the addition of 60 μl 2M Tris-base, followed by the infection of E. coli TG1 cells by mixing 10 ml exponentially growing culture with 0.5 ml eluted phage and incubation for 30 min at 37°. Finally, infected bacteria were plated on TYE medium with 1% glucose and 100 μg/ml ampicillin, and incubated at 30° C. overnight.

Results of the Panning of the CH1-Phage Library on Rp10-L Peptide

Phage Titers


Panning	concentration
round	Rp10-L	input (phage/ml)	output (phage/ml)

1^st	100 μg/ml	5.6 × 10¹³	1.6 × 10¹⁰
2^nd	100 μg/ml	4.04 × 10¹⁴	8.55 × 10⁸
3^rd	50 μg/ml	3.53 × 10¹⁴	1.19 × 10¹²

Cloning of Selected Clones for Soluble Expression

Altered CH1 domain-encoding sequences, contained within eluted phage particles, were batch amplified with PCR. After restriction with NcoI and NotI, they were inserted in pNOTBAD (Invitrogen vector pBAD with subsequently inserted NotI site). After transformation into E. coli E104, the cells were selected on TYE medium with 1% glucose and 100 μg/ml ampicillin at 30° C.

Soluble Expression of Selected Clones and Screening

Results of Screening for Binding of Rp10-L on a Single Well Per Clone


	clone

	A13	A79	A96	B6	B17	B19	B21	B23

A492/620	0.027	0.353	0.023	0.038	0.036	0.037	0.032	0.035

clone

	C14	C45	C49	C68	C79	C81	D36	D82

A492/620	0.025	0.021	0.044	0.025	0.051	0.021	0.027	0.086

Background Reaction

Plate A_492/620

A 0.008

B 0.012

C 0.015

D 0.015

Clones revealing a positive signal were cultured in 20 ml 2xYT with ampicillin, at 30° C. overnight. Then they were inoculated 1:20 into fresh medium, and after 3 h at 30° C. they were induced with end concentration of 0.1% L-arabinose, and allowed to express the recombinant CH1-domain overnight at 16° C. Periplasma of the expressing cells was then lysed in 1 ml of Na-borate buffer, pH=8.0, for a minimum of 6 h. Periplasmic extract was allowed to react with Rp10-L peptide and the binding was revealed exactly as described above.

Results of Screening for Binding of Rp10-L


clone	+	−

A13	−0.002	−0.006
A79	0.004	0.001
A96	0.010	0.006
B6	0.004	0.001
B17	0.002	0.007
B19	−0.002	0.007
B21	0.002	0.001
B23	0.055	0.020
C14	0.015	0.017
C45	0.004	0.001
C49	0.005	−0.001
C68	0.003	0.001
C79	0.005	0.002
C81	0.004	0.002
D36	0.029	0.019
D62	0.137	0.126

Cloning of Selected Clones for Soluble Expression in pET27b

Altered CH1 domain-encoding sequences, contained within clones that produced a significant signal on binding to Rp10-L, were amplified with PCR. After restriction with NcoI and NotI, they were inserted in pET27b (Novagen). After transformation into E. coli BL21 (DE3), transformed cells were selected on TYE medium with 1% glucose and 50 μg/ml kanamycin at 30° C.
Clones revealing a positive signal were cultured in 20 ml M9ZB medium with 2% glucose and kanamycin, at 30° C. overnight. Then they were inoculated 1:20 into fresh medium, and after 3 h at 30° C. they were induced with medium containing 1% glycerin instead of glucose, kanamycin and 1 mM IPTG, and allowed to express the recombinant CH1-domain overnight at 16° C. Periplasma of the expressing cells was then lysed in 1 ml of Na-borate buffer, pH=8.0, for a minimum of 6 h. Periplasmic extract was analysed for the presence of recombinant protein with western blotting and detection with anti tetra-his antibodies (QIAgen).

Sequence of CD20 Specific CH1 SMID, Clone C45

LOCUS	C45 324 bp ds-DNA SYN 4-JUL-2006
1	gcctccacca agggcccatc ggtcttcccc ctggcaccct cctccaagag cacctctggg
61	ggcacagcag ccctgggctg cctggtcaag gactacttcc ccgaaccggt gacggtgtcg
121	tggaactcag gcgccctgac cagcggcgtg cacaccttcc cggctgtcct gcagtcctca
181	ggactctact ccctcagcag cgtggtgacc gtggcccctc tgggtgttgg tgggcatctc
241	gtcctgcact acatctgcaa cgtgaatcac aagcccagca acaccaaggt ggacaagaaa
301	gttgagccca aatctgcggc cgct
//

ENTRY	C45
	5 10 15 20 25 30
1	A S T K G P S V F P L A P S S K S T S G G T A A L G C L V K
31	D Y F P E P V T V S W N S G A L T S G V H T F P A V L Q S S
61	G L Y S L S S V V T V A P L G V G G H L V L H Y I C N V N H
91	K P S N T K V D K K V E P K S A A A

Analysis of Binding of CD-20, Expressed on Cells, Using FACS

Approximately 10⁵Daudi cells were washed with PBS (800 rpm, 5 min, room temperature) and the recombinant CH3 domain in 1% BSA-PBS was allowed to bind for 2 h on ice. Cells were washed again with PBS and the allowed to react with 2 μg/ml anti penta His-Alexa fluor 488 antibody (QIAgen), diluted in 1% BSA-PBS, for 30 min on ice. After washing, the cells were analysed in FACS. Unlabelled cells, wild-type CH1 domain and cell line K562 were used as controls.

Example 8

Isolation of CL-Mutant Proteins Binding CD20 Antigen

Incubation was overnight at 4° C., followed by blocking with 10 μg/ml cysteine-HCl in PBS, with 200 μl per well for 2 h at room temperature.
The surface display phage library, displaying mutated CL domain, was then allowed to react with the bound peptide by adding phage suspension and 2% BSA-PBS up to 200 μl, followed by incubation for 45 min with shaking and 90 min without shaking at room temperature.
Unbound phage particles were washed away as follows;

Results of the Panning of the CL-Phage Library on Rp10-L Peptide

Phage Titers


Panning	concentration
round	Rp10-L	input (phage/ml)	output (phage/ml)

1^st	100 μg/ml	2.8 × 10¹³	3.6 × 10⁷
2^nd	100 μg/ml	4.29 × 10¹⁴	6.88 × 10⁹
3^rd	50 μg/ml	1 × 10¹⁵	6.54 × 10¹¹

Cloning of Selected Clones for Soluble Expression

Altered CL domain-encoding sequences, contained within eluted phage particles, were batch amplified with PCR. After restriction with NcoI and NotI, they were inserted in pNOTBAD (Invitrogen vector pBAD with subsequently inserted NotI site). After transformation into E. coli E104, the cells were selected on TYE medium with 1% glucose and 100 μg/ml ampicillin at 30° C.

Soluble Expression of Selected Clones and Screening

Results of Screening for Binding of Rp10-L on a Single Well Per Clone


	clone

	A2	A51	A57	A64	B21	B23	B44	B92

A492/620	0.048	0.083	0.035	0.032	0.037	0.036	0.041	0.154

clone

	C18	C19	C28	C56	C76	D2	D51	D82

A492/620	0.153	0.033	0.042	0.062	0.030	0.016	0.033	0.046

Background Reaction

Plate A_492/620

A 0.016

B 0.016

C 0.012

D 0.014

Clones revealing a positive signal were cultured in 20 ml 2xYT with ampicillin, at 30° C. overnight. Then they were inoculated 1:20 into fresh medium, and after 3 h at 30° C. they were induced with end concentration of 0.1% L-arabinose, and allowed to express the recombinant CL-domain overnight at 16° C. Periplasma of the expressing cells was then lysed in 1 ml of Na-borate buffer, pH=8.0, for a minimum of 6 h. Periplasmic extract was allowed to react with Rp10-L peptide and the binding was revealed exactly as described above.

Results of Screening for Binding of Rp10-L


clone	+	−

A2	0.002	0.001
A57	0.006	0.004
A62	0.016	0.005
A64	0.006	0.006
B21	0.005	−0.002
B23	0.004	0.004
B44	0.007	0.002
B92	0.038	0.017
C18	0.025	0.041
C19	0.006	0.003
C28	0.010	0.003
C56	0.026	0.010
C76	0.075	0.034
D2	0.003	0.002
D82	0.007	−0.007

Cloning of Selected Clones for Soluble Expression in pET27b

Altered CL domain-encoding sequences, contained within clones that produced a significant signal on binding to Rp10-L, were amplified with PCR. After restriction with NcoI and NotI, they were inserted in pET27b (Novagen). After transformation into E. coli BL21 (DE3), transformed cells were selected on TYE medium with 1% glucose and 50 μg/ml kanamycin at 30° C.
Clones revealing a positive signal were cultured in 20 ml M9ZB medium with 2% glucose and kanamycin, at 30° C. overnight. Then they were inoculated 1:20 into fresh medium, and after 3 h at 30° C. they were induced with medium containing 1% glycerin instead of glucose, kanamycin and 1 mM IPTG, and allowed to express the recombinant CL-domain overnight at 16° C. Periplasma of the expressing cells was then lysed in 1 ml of Na-borate buffer, pH=8.0, for a minimum of 6 h. Periplasmic extract was analysed for the presence of recombinant protein with western blotting and detection with anti tetra-his antibodies (QIAgen).

Example 9

Cloning, Expression and Characterisation of an Integrin-Binding Fcab

The potentially cyclic peptide CRGDCL was originally isolated by Koivunen et al 1993 (J. Biol. Chem. 1993 Sep. 25; 268(27):20205-10) from a 6-amino acid peptide library expressed on filamentous phage and was shown to inhibit the binding of RGD-expressing phage to α_vβ₁integrin or the attachment of α_vβ₁-expressing cells to fibronectin. The peptide also inhibited cell attachment mediated by the α_vβ₁, α_vβ₃, and α_vβ₅integrins.
We have inserted the sequence GCRGDCL in the structural loop (the “EF” loop) of the CH3 domain of human IgG1. For that purpose, residues Asp92 and Lys 93 (IMGT numbering) were mutated to Gly and Leu respectively, and the 5 residues CRGDC were inserted between these mutated residues 92 and 93 to create the loop with the integrin-binding RGD motif, using standard cloning techniques. At the C-terminus of the insert, the sequence was fused in frame with the multiple cloning site of the vector so that the HSV-tag and the His-tag are attached C-terminally to the recombinant protein. The name of this recombinant protein Fcab-RGD4, or short RGD4. The DNA sequence coding for Fcab-RGD4 and the translation in amino acid sequence are shown below.
The sequences encoding Fcab-RGD4 and Fcab-wt, respectively, were introduced into the mammalian expression vector pCEP4 by conventional cloning techniques. HEK 293 cells were transiently transfected with these expression plasmids and the Fcab containing culture medium harvested after 3 days and after one week. The Fcabs were purified via a Protein A column and acidic elution from the column, followed by immediate neutralisation. The Fcabs were dialysed against PBS and tested in an ELISA for binding to human α_vβ₃integrin (Chemicon).
For the integrin ELISA, 1 μg/ml human α_vβ₃integrin in PBS was coated over night on Maxisorp plates and blocked for 1 h with BSA in PBS containing 1 mM Ca2+. Fcab-RGD4 and Fcab-wt, respectively, were allowed to bind for 1 h in various dilutions starting from 10 ug/ml purified protein. Bound Fcabs were detected by HRP labelled protein A and TMB as a substrate. Binding of RGD4 to integrin (red line) resulted in significant signals from 10 ug/ml protein down to 0.16 ug/ml. As negative controls, RGD4 did not bind to the plate in the absence of integrin (grey line), nor did Fcab-wt bind to the integrin coated plate (green line). The binding of the commercial mouse anti human α_vβ₃integrin mAb LM609 (Chemicon; blue line) served as a positive control.


protein			coating BLK	LM609 (anti
concentration	Fcab-RGD4	Fcab-wt	Fcab-RGD4	integrin mAb)
.□g/ml)	(OD 450)	(OD 450)	(OD 450)	(OD 450)

10	3.4513	0.0485	0.0152	0.6475
2.500	1.7446	0.0338	0.0127	0.6443
0.625	0.7068	0.0337	0.0125	0.6570
0.156	0.2384	0.0327	0.0123	0.6257
0.039	0.0829	0.0295	0.0127	0.3907
0.010	0.0388	0.0276	0.0103	0.1567
0.002	0.0303	0.0273	0.0112	0.0770

Table: ELISA data demonstrating the binding of RGD4 and LM609 to human α_vβ₃integrin. The various proteins were tested in concentrations as indicated in the first column resulting in the signals at 450 nm in the respective rows. Values for HEK produced and protein A purified Fcab-RGD4 binding to integrin are shown in the second column, Fcab-wt negative control in the third, and Fcab-RGD4 coating blank control in the fourth column. The values for binding of mouse anti α_vβ₃integrin mAb LM609 are shown in the last column.

Claims

1. A multivalent immunoglobulin or part thereof binding specifically to at least two cell surface molecules of a single cell with at least one modification in at least one structural loop region of said immunoglobulin determining binding to an epitope of said cell surface molecules wherein the unmodified immunoglobulin does not significantly bind to said epitope.

2. Immunoglobulin according to claim 1 wherein the modified structural loop region is within the constant domain of said immunoglobulin, preferably within CH1, CH2, CH3, CH4, Igk-C, Igl-C, or a part thereof.

3. Immunoglobulin according to claim 2, characterised in that said modified structural loop region comprises at least 6 amino acid modifications.

4. Immunoglobulin according to claim 2, characterised in that the modified structural loop region is within a constant domain selected from the group consisting of a CH1, a CH2, a CH3 and a CH4 domain of human or murine origin and comprises at least one modification within amino acids 7 to 21, amino acids 25 to 39, amino acids 41 to 81, amino acids 83 to 85, amino acids 89 to 103, or amino acids 106 to 117.

5. Immunoglobulin according to claim 2, characterised in that the immunoglobulin comprises Igk-C or Igl-C modified structural loop regions that are of human origin and comprise at least one modification within amino acids 8 to 18, amino acids 27 to 35, amino acids 42 to 78, amino acids 83 to 85, amino acids 92 to 100, amino acids 108 to 117, or amino acids 123 to 126.

6. Immunoglobulin according to claim 2, characterised in that the modified structural loop regions of Igk-C or Igl-C are of murine origin and comprise at least one modification within amino acids 8 to 20, amino acids 26 to 36, amino acids 43 to 79, amino acids 83 to 85, amino acids 90 to 101, amino acids 108 to 116, or amino acids 122 to 125.

7. Immunoglobulin according to claim 1, characterised in that the immunoglobulin comprises a constant domain of camelid origin.

8. Immunoglobulin according to claim 7, characterised in that the immunoglobulin comprises at least one modified constant domain selected from the group consisting of a CH1, CH2 and CH3 domain.

9. Immunoglobulin according to claim 8, characterised in that the modified constant domain comprises at least one modification within amino acids 8 to 20, amino acids 24 to 39, amino acids 42 to 78, amino acids 82 to 85, amino acids 91 to 103, or amino acids 108 to 117.

10. Immunoglobulin according to claim 1, characterised in that the immunoglobulin comprises a variable domain selected from the group consisting of VH, Vkappa, Vlambda, VHH, and combinations thereof.

11. Immunoglobulin according to claim 1, characterised in that the immunoglobulin comprises a modified structural loop region of a VH, a Vkappa, a Vlambda or a VHH domain comprising at least one modification within amino acids 7 to 21, amino acids 25 to 39, amino acids 41 to 81, amino acids 83 to 85, amino acids 89 to 103, or amino acids 106 to 117, where the numbering of the amino acid position of the domains is that of the IMGT.

12. Immunoglobulin according to claim 1, characterised in that the immunoglobulin comprises a modified structural loop region of a VH, Vkappa, or Vlambda domain of human origin and comprises at least one modification within amino acids 8 to 20, amino acids 44 to 50, amino acids 67 to 76 and amino acids 89 to 101, most preferably amino acid positions 12 to 17, amino acid positions 45 to 50, amino acid positions 69 to 75, and amino acid positions 93 to 98, where the numbering of the amino acid position of the domains is that of the IMGT.

13. Immunoglobulin according to claim 1, characterised in that the immunoglobulin comprises a modified structural loop region of a VH domain of murine origin and comprises at least one modification within amino acids 6 to 20, amino acids 44 to 52, amino acids 67 to 76, and amino acids 92 to 101, where the numbering of the amino acid position of the domains is that of the IMGT.

14. Immunoglobulin according to claim 1, characterised in that the immunoglobulin comprises a modified structural loop region of a VHH domain of camelid origin and comprises at least one modification within amino acids 7 to 18, amino acids 43 to 55, amino acids 68 to 75, and amino acids 91 to 101, where the numbering of the amino acid position of the domains is that of the IMGT.

15. Immunoglobulin according to claim 1, characterized in that the immunoglobulin is further combined with one or more additional modified immunoglobulins or with unmodified immunoglobulins, or parts thereof, to obtain a combination immunoglobulin.

16. Immunoglobulin according to claim 1, characterised in that the modification is a deletion, a substitution, an insertion or a combination thereof.

17. Nucleic acid encoding an immunoglobulin according to claim 1 or part thereof.

18. Method for engineering a multivalent immunoglobulin according to claim 1, comprising the steps of:

(a) providing a nucleic acid encoding an immunoglobulin comprising at least one structural loop region,

(b) modifying at least one nucleotide residue of said structural loop region,

(c) transferring said modified nucleic acid in an expression system,

(d) expressing said multivalent immunoglobulin,

(e) contacting the expressed multivalent immunoglobulin with an epitope, and

(f) determining whether said multivalent immunoglobulin binds to said epitope.

19. (canceled)