# Patent

## Title
Cytotoxic immunoglobulin

## Abstract

The invention relates to a cytotoxic modular antibody with a molecular weight of up to 60 kD, specifically binding to a cell surface target with a binding affinity of Kd<10−8 M, a method of producing such antibody and its use as a therapeutic.

## Background
This application is a continuation of U.S. application Ser. No. 14/470,425, filed Aug. 27, 2014, which is a continuation of U.S. application Ser. No. 12/990,119, filed Oct. 28, 2010, now U.S. Pat. No. 8,859,738, issued Oct. 14, 2014, which is a U.S. national phase entry of International Patent Application No. PCT/EP2009/052509, filed on Mar. 3, 2009, which claims the benefit of European Patent Application No. 08450068.5, filed May 2, 2008, the entirety of each of which is hereby incorporated by reference.


The invention relates to a cytotoxic immunoglobulin.
Monoclonal antibodies have been widely used as therapeutic binding agents. The basic antibody structure will be explained here using as example an intact IgGI 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 IgGI 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 (K), are found in antibodies. A given immunoglobulin either has K chains or λ chains, never one of each.
No functional difference has been found between antibodies having λ or K 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 and optionally adjacent loops within the CDR loop region, 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. In most cases 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.
WO06/072620A1 describes a method of engineering an immunoglobulin which comprises a modification in a structural loop region to obtain new antigen binding sites. This method is broadly applicable to immunoglobulins and may be used to produce a library of immunoglobulins targeting a variety of antigens. A CH3 library has been shown to be useful for selecting specific binders to an antigen.
WO08/003103A2 describes the panning of a CH3, CH1 or CL library on a synthetic peptide, representing a mimotope of the CD20 antigen.
Various immunoglobulin libraries have been proposed in the art to obtain specific immunoglobulin binders. The prior art refers to monomeric monovalent display of binding domains, in general. WO9209690A2 describes phagemid particles displaying a single copy of a fusion protein on the surface of the particle. Thereby it was described to obtain high affinity binders from a library of phagemid particles, also called bacteriophages. Replicable expression vectors comprising genes encoding a binding polypeptide and a phage coat protein are provided so to form a gene fusion encoding a fusion protein, which is a chimeric protein of a phagemid particle, the phage coat protein and the binding polypeptide.
U.S. Pat. No. 5,223,409 generally describes the method of fusing a gene encoding a protein of interest to the N-terminal domain of the gene III coat protein of the filamentous phage M13. The gene fusion is mutated to form a library of structurally related fusion proteins that are expressed in low quantity on the surface of a phagemid particle. Biological selection and screening is employed to identify novel ligands useful as drug candidates.
However, there are some limitations in using such “fusion phage” or monovalent phage display and respective single fusion proteins. Many biologicals naturally occur in oligomeric form. For the purpose of the present invention oligomeric means dimeric, trimeric or even higher polymeric forms, up to 24 monomers.
The fusion phages according to the prior art are described to display monomeric fusion proteins, mainly because it was believed that binders of highest affinity could only be selected from a library if single fusion proteins are displayed by the phagemid particles. Native proteins are however often assembled as a dimer or even at a higher degree of oligomerization. To obtain dimeric display with a single fusion protein, some techniques have been developed that involve conditional stop codons located between the coat protein and the binding polypeptide (Dall'Acqua et al. The Journal of Immunology, 2002, 169: 5171-5180). Thereby soluble monomers of the polypeptides in addition to those fused to the phage are expressed, thus enabling the formation of a dimer. However, such stop codons requires propagation in specific suppressor host cells that may translate a stop codon in an amino acid, to provide an appropriate amount of fusion proteins in addition to the soluble binding polypeptides.
Prior art fusion proteins involve in some cases linker sequences to display larger binding polypeptides. Linker sequences of up to 24 amino acids are usually employed for standard purposes of displaying variable domains of an antibody. See for example, the display vector pCOMB3× (Hybrid. Hybridomics. 2003 April; 22(2):97-108. Development of functional human monoclonal single-chain variable fragment antibody against HIV-1 from human cervical B cells. Berry J D, Rutherford J, Silverman G J, Kaul R, ENa M, Gobuty S, Fuller R, Plummer F A, Barbas C F.)
Immunoglobulins based on full length IgGI have been widely used for treating patients suffering from solid tumors, in particular those overexpressing a receptor of the erbB class. Among those receptors are EGFR (Her1), Her2, Her2neu, Her3 and Her4.
Herceptin (trastuzumab, humAb4D5) is a product based on a monoclonal antibody for use in breast cancer therapy. Herceptin antibody is specific for the 4D5 epitope of the HER2 extracellular domain of her2neu (also called c-erbB-2 or MAC117).
“HER2 extracellular domain” or “HER2 ECD” refers to a domain of HER2 that is outside of a cell, either anchored to a cell membrane, or in circulation, including fragments thereof. The extracellular domain of HER2 may comprise four domains: “Domain I” (amino acid residues from about 1-195, “Domain II” (amino acid residues from about 196-319), “Domain III” (amino acid residues from about 320-488), and “Domain IV” (amino acid residues from about 489-630) (residue numbering without signal peptide).
The “epitope 4D5” is the region in the extracellular domain of HER2 to which the antibody 4D5 (ATCC CRL 10463) and trastuzumab bind. This epitope is close to the transmembrane domain of HER2, and within Domain IV of HER2. The 4D5 epitope of HER2 encompasses any one or more residues in the region from about residue 529 to about residue 625, inclusive of the HER2 ECD, residue numbering including signal peptide.
The EGFR is a large (1,186 residues), monomeric glycoprotein with a single transmembrane region and a cytoplasmic tyrosine kinase domain flanked by noncatalytic regulatory regions. Sequence analyses have shown that the ectodomain (residues 1-621) contains four sub-domains, here termed L1, CR1, L2 and CR2, where L and CR are acronyms for large and Cys-rich respectively. The L1 and L2 domains have also been referred to as domains I and III, respectively. The CR domains have been previously referred to as domains II and IV, or as S1.1-S1.3 and S2.1-S2.3 where S is an abbreviation for small.
MAbs to the external domain of the EGFR have been developed that disrupt ligand binding to the receptor and subsequent signal transduction. Three EGFR-specific blocking antibodies have been characterized in greater detail in vitro and are presently used in clinical studies; these are mAbC225 (ERBITUX/cetuximab), mAb425 (EMD72000) and the human mAb ABX-EGF. C225 (Cetuximab/Erbitux) is FDA approved for metastatic colorectal cancer and mAb425 (EMD59000) whose humanized version (EMD72000) is currently in phase II clinical trials for various solid tumors expressing EGFr. C225 binds to distinct epitopes on the extracellular domain of EGFr. Independent binding of both antibodies to the wild type receptor and to the mutant receptor (EGFrVIII) which is prominently expressed in tumor cells, has been shown. Cetuximab interacts exclusively with domain III of the extracellular region of EGFR (sEGFR), particularly occluding the ligand binding region on this domain and sterically preventing the receptor from dimerization.
The spontaneously occurring mutant EGF receptor was first shown in glioblastoma. Known as EGFRvIII, this molecule represents a deletion of exons 2 through 7 in the extracellular domain of the EGF receptor. This removes 273 amino acids and creates a novel glycine at the fusion junction. The EGFRvIII (variously called de2-7 EGFR or deltaEGFR) has an in-frame deletion of the extracellular domain and is found in numerous types of human tumors.
WO9720858A1 relates to anti-Her2 antibodies which induce apoptosis in Her2 expressing cells. Therefore the monoclonal antibodies (mAbs), which bind to Her2, are generated by immunizing mice with purified soluble Her2.
WO06087637A2 relates to antibodies that recognise Her2/neu and exert an antiproliferative effect on Her2/neu expressing cells. This document describes an isolated antibody or a fragment, variant or derivative thereof, in particular the human Fab fragment, and the scFv fragment, capable of specifically binding to Her2neu, however, without cytotoxic activity.
Some prior art disclosures relate to antibody formats with a potential to inhibit tumor growth, in the absence of cytotoxic activities, such as ADCC.
Rovers et al (Cancer Immunol. Immunother. (2007) 56:303-317 describe anti-EGFR nanobodies with a potential to inhibit tumour cell growth.
WO03/075840A2 discloses antibodies that bind to KDR with an affinity comparable to or higher than human VEGF and that neutralizes activation of KDR, among them monovalent Fabs that neutralizes the activation of KDR, thus inhibiting angiogenesis and tumor growth. Other immunoglobulin fragments have been proposed for human therapy.
Patent application WO06036834A2 describes a biologically active peptide incorporated as an internal sequence into a loop region of an Fc domain; the specification concerns a molecule of which the internal peptide sequence may be added by insertion or replacement of amino acids in the previously existing Fc domain. An exemplary peptide is targeting p185HER2/neu.
Peptides targeting Her2/neu have been described by Park et al Nat. Biotechnol. (2000) 18(2):194-8. Though peptide binding affinities usually are in the lower range with a kD of greater than 10−6 M, the described exocyclic anti-HER2/neu peptide mimic exerted an unusually high affinity (KD=300 nM).
WO01/01748A2 describes peptide compounds that bind to human erbB2 gene product with low binding affinities. An exemplary peptide-Fc fusion protein directed to erbB2 was tested in a competition binding assays, with a low quantity of the same type of peptides used as competitors, resulting in a low IC50 value that would, however, not be indicative for a Kd or EC50 value, as determined in a saturation assay.
It is the object of present invention to provide improved immunoglobulin products binding to cell surfaces.
The object is solved by the subject matter as claimed.
SUMMARY OF THE INVENTION
According to the invention there is provided a cytotoxic modular antibody with a molecular weight of up to 60 kD, which is specifically binding to a cell surface target with a binding affinity of Kd<10−8 M, preferably in the nanomolar range or lower. The high affinity modular antibody according to the invention is thus small sized with the advantage of easy penetration through a cell layer or tumor, to effect cell lysis or cell death at the site where the target is overexpressed. Alternatively, the modular antibody according to the invention preferably has an IC50<10−8 M, as determined in a saturation binding assay.
The modular antibody according to the invention preferably exerts at least one of ADCC, ADCP, CDC or apoptotic activity.
The cytotoxic activity of the modular antibody according to the invention is preferably determined by its effector functions, as measured by at least one of ADCC, ADCP and CDC activity.
A preferred modular antibody according to the invention is an oligomer of modular antibody domains, in particular an oligomer of immunoglobulin domains, or a fragment of a full length immunoglobulin. The preferred antibody is a dimer selected from the group consisting of dimers of VHA/L, CH1/CL, CH2/CH2, CH3/CH3, Fc and Fab, or single chains thereof.
The modular antibody according to the invention preferably contains a binding site having a randomized antibody sequence and/or at least one binding site within a structural loop region, which is always understood to potentially include a terminal domain sequence that could be contributing to antigen binding. The site of the randomized antibody sequence may be within the CDR region or the structural loop region. Thus, binding to a target or a functional ligand, such as an effector molecule, which is in preferred cases also a scaffold ligand, is possible even through an immunoglobulin without CDR region, or at a site besides a CDR region.
According to a preferred embodiment, the cell surface target binding site is located within the CDR region, and the binding site with specificity to a functional ligand or a scaffold ligand is within the structural loop region.
According to an alternatively preferred embodiment, the binding site with specificity to a functional ligand or a scaffold ligand is within the CDR loop region and the cell surface target binding site located in a structural loop region.
The preferred modular antibody according to the invention has specific binding properties to bind a target, which is a receptor of the erbB class, such as selected from the group consisting of EGFR, Her2, Her2neu, HER3 and HER4. Preferred modular antibodies according to the invention are provided for treating patients suffering from a solid tumor, which tumor expresses a receptor of the erbB class.
Those anti-Her2 modular antibodies are particularly preferred that contain an amino acid sequence within the EF loop of a structural loop region, which sequence is selected from the group consisting of SEQ. ID. Numbers as listed in Table 4 and 5, which are optionally contained in an EF and/or AB and/or CD loop.
Though there was a long term need for highly effective, but small sized antibodies, it was the first time possible to obtain such modular antibody according to the invention, using a library of modular antibody domains, in particular a library of an oligomer of modular antibody domains binding to an effector ligand. Selected members of such a library have both properties, the target binding and the effector ligand binding, as a prerequisite for biological cytotoxicity or cytolysis. It is further preferred that the format of a modular antibody scaffold is not changed by producing variants and libraries of such scaffold, thus library members would still maintain the functional format as determined by binding to a scaffold ligand.
According to the invention there is further provided a method of producing a modular antibody according to claim 1, which comprises the steps of:

    
    
        a. providing a library of an oligomer of modular antibody domains,
        b. contacting said library with said target in the presence of an effector ligand,
        c. selecting a library member having both properties,
        
            (i) target binding affinity of Kd<10−8 M or IC50<10−8 M, and
            (ii) cytotoxic activity, and
        
        
        d. manufacturing a preparation of the modular antibody.
    
    


The preferred selection methods provide for the simultaneous binding of both, the target and the effector ligand, which is advantageous for the effective cytolysis. Simultaneous binding is preferably determined in a cell-based assay with two-dimensional differentiation, e.g. in a FACS system.
Preferably, the library members contain a randomized antibody sequence, wherein the site of mutagenesis optionally is within the CDR region or aside from the CDR region, preferably within the structural loop region, potentially including a terminal sequence.
The library as used in the method according to the invention is preferably produced according to a design that provides for mutagenesis aside from binding sites interacting with the effector ligand. Thus, a high quality library is preferably used, as determined by quality control measures employing assays of effector molecule binding or scaffold ligand binding.
The preferred method according to the invention further comprises the step of affinity maturation to increase the binding affinity to the cell surface target. This affinity maturation is preferably performed through mutagenesis of a selected immunoglobulin that has a determined binding specificity to bind the target, not cross-reacting with control proteins, however, having still a medium or low affinity. Preferably a library member that has a binding affinity with an IC50 or Kd<10−6 M is further mutagenized to provide an affinity matured binder or a pool of such binders, i.e. a library of affinity matured binders with higher affinity with an IC50 or Kd<10−7 M, preferably with an IC50 or Kd<10−8 M, or even in the nanomolar or lower range. In this case, it is preferred the modular antibody according to the invention is still functional with regard to its cytotoxic effect.
According to a preferred embodiment there is provided a method of preparing a modular antibody according to the invention, for treating a patient suffering from a solid tumor, which tumor expresses a receptor of the erbB class.
The modular antibody according to the invention is preferably used for treating a patient suffering from a solid tumor, which tumor expresses a receptor of the erbB class.



FIGURES
FIG. 1:
Schematic presentation of the PCRs used for production of the fragments used for assembly of the library Fcab01. PCR primers are indicated by arrows with their respective 5′-3′ orientation, and vertical lines indicate the approximate positions of the introduced restriction sites which were used for assembly of the mutated gene. The restriction sites are contained on the primers for ligations of the PCR fragments.
FIG. 2:
Amino acid sequence and secondary structure of a CH3 domain (IMGT numbering) where SEQ ID NO:440 reflects the linear sequence of the residues identified in the folded sequence. The randomization scheme is provided for the libraries Fcab01 to Fcab06. Randomized positions in the AB and EF loop are marked with a circle. X stands for all 20 amino acids, z only for Ala, Asp, Ser, Tyr.
FIG. 3:
crystal structure of an IgGI Fc fragment (amino acid sequence)
FIG. 4:
human IgG including randomized amino acid modifications (amino acid sequence)
FIG. 5:
amino acid sequence of FcabRGD4L (amino acid sequence)
FIGS. 6A and 6B:
vector pHENFcabRGD4 (nucleotide sequence)
FIGS. 7A and 7B:
vector pHENFcabRGD4L (nucleotide sequence)
FIGS. 8A and 8B (SEQ ID No.15):
vector pYDIdX (nucleotide sequence)
FIGS. 9A and 9B and 9C (SEQ ID No.16):
vector pYDIdXFc (nucleotide sequence)
FIGS. 10A and 10B and 10C (SEQ ID No.17):
pYD1 CH12 (nucleotide sequence)
FIG. 11 (SEQ ID No.18):
Fcab01 (nucleotide sequence)
FIG. 12 (SEQ ID No.19):
Fcab02 (nucleotide sequence)
FIG. 13 (SEQ ID No.20):
Fcab03 (nucleotide sequence)
FIG. 14 (SEQ ID No.21):
Fcab04 (nucleotide sequence)
FIG. 15 (SEQ ID No.22):
Fcab05 (nucleotide sequence)
FIG. 16 (SEQ ID No.23):
Fcab06 (nucleotide sequence)
FIGS. 17A and 17B and 17C (SEQ ID No.72):
vector pYD 1 (nucleotide sequence)
FIGS. 18A and 18B (SEQ ID No.73):
modified vector pYD1Nhe (nucleotide sequence)
FIGS. 19A and 19B (SEQ ID No.74):
vector pYD1Ink (nucleotide sequence)
FIGS. 20A and 20B (SEQ ID No.75):
vector pYDI mata (nucleotide sequence)
FIGS. 21A and 21B (SEQ ID No.76):
vector pYDIgal (nucleotide sequence)
FIG. 22 (SEQ ID No.77):
4D5H (nucleotide sequence)
FIG. 23 (SEQ ID No.78):
4D5L (nucleotide sequence)
FIGS. 24A and 24B and 24C (SEQ ID No.79):
vector pYD4D5hc (nucleotide sequence)
FIG. 25 (SEQ ID No.80):
4D5hp (amino acid sequence)
FIGS. 26A and 26B and 26C (SEQ ID No.81):
vector pYD4D5h1 (nucleotide sequence)
FIG. 27 (SEQ ID No.82):
4D5lp (amino acid sequence)
FIGS. 28A and 28B and 28C (SEQ ID No.427):
plasmid pYD1dX_dCH1dCH3_Fcab_wt (nucleotide sequence)
FIGS. 29A and 29B (SEQ ID No.428):
pYD1_dX_dCH1_Fcab_wt (nucleotide sequence)



DETAILED DESCRIPTION OF THE INVENTION
Definitions
Specific terms as used throughout the specification have the following meaning.
The term “immunoglobulin” as used according to the present invention is defined as polypeptides or proteins that may exhibit mono- or bi- or multi-specific, or mono-, bi- or multivalent binding properties, preferably at least two, more preferred at least three specific binding sites for epitopes of e.g. antigens, effector molecules or proteins either of pathogen origin or of human structure, like self-antigens including cell-associated or serum proteins. The term immunoglobulin as used according to the invention also includes functional fragments of an antibody, such as Fc, Fab, scFv, single chain dimers of CH1/CL domains, Fv, dimers like VH/VL, CH1/CL, CH2/CH2, CH3/CH3, or other derivatives or combinations of the immunoglobulins, like single chains of pairs of immunoglobulin domains. The definition further includes domains of the heavy and light chains of the variable region (such as dAb, Fd, V1, Vk, Vh, VHH) and the constant region or individual domains of an intact antibody such as CH1, CH2, CH3, CH4, Cl and Ck, as well as mini-domains consisting of at least two beta-strands of an immunoglobulin domain connected by a structural loop.
“Modular antibodies” as used according to the invention are defined as antigen-binding molecules, like human antibodies, composed of at least one polypeptide module or protein domain, preferably in the natural form. The term “modular antibodies” includes antigen-binding molecules that are either immunoglobulins, immunoglobulin-like proteins, or other proteins exhibiting modular formats and antigen-binding properties similar to immunoglobulins or antibodies, which can be used as antigen-binding scaffolds, preferably based on human proteins.
The term “immunoglobulin-like molecule” as used according to the invention refers to any antigen-binding protein, in particular to a human protein, which has a domain structure that can be built in a modular way. Immunoglobulin-like molecules as preferably used for the present invention are T-cell receptors (TCR) or soluble parts thereof, fibronectin, transferrin, CTLA-4, single-chain antigen receptors, e.g. those related to T-cell receptors and antibodies, antibody mimetics, adnectins, anticalins, phylomers, repeat proteins such as ankyrin repeats, avimers, VersabodiesTM, scorpio toxin based molecules, and other non-antibody protein scaffolds with antigen binding properties.
Ankyrin repeat (AR), armadillo repeat (ARM), leucine-rich repeat (LRR) and tetrathcopeptide repeat (TPR) proteins are the most prominent members of the protein class of repeat proteins. Repeat proteins are composed of homologous structural units (repeats) that stack to form elongated domains. The binding interaction is usually mediated by several adjacent repeats, leading to large target interaction surfaces.
Avimers contain A-domains as strings of multiple domains in several cell-surface receptors. Domains of this family bind naturally over 100 different known targets, including small molecules, proteins and viruses. Truncation analysis has shown that a target is typically contacted by multiple A-domains with each domain binding independently to a unique epitope. The avidity generated by combining multiple binding domains is a powerful approach to increase affinity and specificity, which these receptors have exploited during evolution.
Anticalins are engineered human proteins derived from the lipocalin scaffold with prescribed binding properties typical for humanized antibodies. Lipocalins comprise 160-180 amino acids and form conical beta-barrel proteins with a ligand-binding pocket surrounded by four loops. Small hydrophobic compounds are the natural ligands of lipocalins, and different lipocalin variants with new compound specificities (also termed ‘anticalins’) could be isolated after randomizing residues in this binding pocket.
Single chain antigen receptors contain a single variable domain and are 20% smaller than camelid single domain antibodies. Phylomers are peptides derived from biodiverse natural protein fragments.
It is understood that the term “modular antibody”, “immunoglobulin”, “immunoglobulin-like proteins” includes a derivative thereof as well. A derivative is any combination of one or more modular antibodies of the invention and or a fusion protein in which any domain or minidomain of the modular antibody of the invention may be fused at any position of one or more other proteins (such as other modular antibodies, immunoglobulins, ligands, scaffold proteins, enzymes, toxins and the like). A derivative of the modular antibody of the invention may also be obtained by association 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 inorganic molecules or any combination thereof (e.g. PEG, prodrugs or drugs). A derivative would also comprise an antibody with the same amino acid sequence but made completely or partly from non-natural or chemically modified amino acids. The term derivative also includes fragments and functional equivalents. The preferred derivatives still are functional with regard to both, target binding and cytotoxic activity.
A “structural loop” or “non-CDR-loop” according to the present invention is to be understood in the following manner: modular antibodies, immunoglobulins or immunoglobulin-like substances 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 include part of the variable framework region (called “VFR”), which is adjacent to the CDR loops. It is known that some loops of the VFR may contribute to the antigen binding pocket of an antibody, which generally is mainly determined by the CDR loops. Thus, those VFR loops are considered as part of the CDR loop region, and would not be appropriately used for engineering new antigen binding sites. Loops aside from the antigen-binding pocket or CDR loop region are usually called structural loops or non-CDR-loops. Contrary to the VFR within the CDR loop region or located proximal to the CDR loops, other loops of the VFR of variable domains would be considered structural loops and particularly suitable for use according to the invention. Those are preferably the structural loops of the VFR located opposite to the CDR loop region, or at the C-terminal side of a variable immunoglobulin domain. Constant domains have structural loops within a structural loop region, e.g. either at the C-terminal side of an antibody domain or at an N-terminal side, even within a side chain of an antibody domain. Constant domains are also called part of the framework region.
The term “antigen” or “target” as used according to the present invention shall in particular include all antigens and target molecules capable of being recognised by a binding site of a modular antibody. Specifically preferred antigens as targeted by the molecule according to the invention are those antigens or molecules, which have already been proven to be or are capable of being immunologically or therapeutically relevant, especially those, for which a clinical efficacy has been tested.
The term “target” or “antigen” as used herein shall in particular comprise molecules selected from the group consisting of allergens, tumor associated antigens, self antigens including cell surface receptors, enzymes, Fc-receptors, FcRn, HSA, IgG, interleukins or cytokines, proteins of the complement system, transport proteins, serum molecules, bacterial antigens, fungal antigens, protozoan antigen and viral antigens, also molecules responsible for transmissible spongiform encephalitis (TSE), such as prions, infective or not, and markers or molecules that relate to inflammatory conditions, such as pro-inflammatory factors, multiple sclerosis or alzheimer disease, or else haptens.
The term “cell surface antigens” shall include all antigens 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 preferably 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.
The antigen is either recognized as a whole target molecule or as a fragment of such molecule, especially substructures of targets, generally referred to as epitopes. 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” as used herein according to the present invention shall in particular refer to a molecular structure which may completely make up a specific binding partner or be part of a specific binding partner to a binding site of modular antibody or an immunoglobulin of the present invention. The term epitope may also refer to haptens. Chemically, an epitope may either be composed of a carbohydrate, a peptide, a fatty acid, an organic, biochemical or inorganic substance or derivatives thereof and any combinations thereof. If an epitope is a polypeptide, it will usually include at least 3 amino acids, preferably 8 to 50 amino acids, and more preferably between about 10-20 amino acids in the peptide. There is no critical upper limit to the length of the peptide, which could comprise nearly the full length of a polypeptide sequence of a protein. Epitopes can be either 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 of a patient 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.
As used herein, the term “specifically binds” or “specific binding” 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), the modular antibody binds to its particular target and does not bind in a significant amount to other molecules present in a sample. The specific binding means that binding is selective in terms of target identity, high, medium or low binding affinity or avidity, as selected. Selective binding is usually achieved if the binding constant or binding dynamics is at least 10 fold different, preferably the difference is at least 100 fold, and more preferred a least 1000 fold.
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 then also be integrated into the host chromosome. Alternatively, an expression system can be used for in vitro transcription/translation.
All numbering of the amino acid sequences of the immunoglobulins is according to the IMGT numbering scheme (IMGT, the international ImMunoGeneTics, Lefranc et al., 1999, Nucleic Acids Res. 27: 209-212).
For the purposes of this invention, the term “binding agent” or “ligand” refers to a member of a binding pair, in particular binding polypeptides having the potential of serving as a binding domain for a binding partner. Examples of binding partners include pairs of binding agents with functional interactions, such as receptor binding to ligands, antibody binding to antigen or receptors, a drug binding to a target, and enzyme binding to a substrate
The term “fusion protein” or “chimeric fusion protein” as used for the purpose of the invention shall mean the molecule composed of a genetic package, at least part of an outer surface structure, such as a coat protein, optionally a linker sequence, and a binding agent. The fusion protein is encoded by a vector with the gene of the binding agent and information to display a copy of the binding agent at the surface of the genetic package.
The term “cytotoxic” or “cytotoxic activity” as used for the purpose of the invention shall refer to any specific molecule directed against cellular antigens that, when bound to the antigen, activates the complement pathway or activates killer cells, resulting in cell lysis or triggers apoptosis. In particular it is referred to the activity on effector cells resulting in activation of cytotoxic T-cells or cells which mediate antibody-dependent cell cytotoxicity (ADCC), complement dependent cytotoxicity (CDC) and/or cellular phagocytosis (ADCP). It is further referred to an apoptotic effect, thus triggering programmed cell death (PCD). Modular antibodies according to the invention thus kill antibody-coated target cells, optionally either by binding to Fc receptors of effector cells or by inducing programmed cell death.
“Scaffold” shall mean a temporary framework either natural or artificial used to support the molecular structure of a polypeptide in the construction of variants or a repertoire of the polypeptide. It is usually a modular system of polypeptide domains that maintains the tertiary structure or the function of the parent molecule. Exemplary scaffolds are modular antibodies, which may be mutagenized to produce variants within said scaffold, to obtain a library.
The term “scaffold ligand” as used for the purpose of the invention shall mean a ligand that binds to a scaffold or the backbone of modular antibodies, thus determining the molecular structure or primary function and specificity of said modular antibody. In preferred cases the scaffold ligand is a functional ligand, mediating a biological function upon binding, like an effector ligand. In an alternative embodiment the scaffold ligand is a functional ligand, which is a specific target bound by the CDR region or structural loop region. The same scaffold ligand can bind many variants of a modular antibody regardless of their target specificities. In general, the presence of scaffold ligand binding site indicates that the variant is expressed and folded correctly. Thus, binding of the scaffold ligand to its binding site provides a method for preselecting, coselecting, characterization and screening of functional polypeptides functional polypeptides from a repertoire of polypeptides. Designing variants of modular antibodies that keep the binding property to a scaffold ligand avoids the preparation of variants that are non-functional, for example as a result of the introduction of mutations, folding mutants or expression mutants which would be or are incapable of binding to substantially any target or effector ligand. Such non-functional mutants sometimes are generated by the normal randomisation and variation procedures employed in the construction of polypeptide repertoires. Providing functional mutants that bind to a scaffold ligand permits the person skilled in the art to prepare a library of modular antibodies which is enriched in functional, well folded and highly expressed library members. For example, the scaffold can be a parent Fab and at least 20%, preferably at least 30%, more preferred at least 40% of the parent Fab variants are binding to the CDR-target of said parent Fab.
The term “effector ligand” as used for the purpose of the invention shall mean a ligand mediating effector functions, like an effector molecule. Exemplary effector ligands are Fc receptors or Fc receptor-like molecules interfering with immunoglobulins. An Fc receptor is a protein found on the surface of certain cells—including natural killer cells, macrophages, neutrophils, and mast cells—that contribute to the protective functions of the immune system. Its name is derived from its binding specificity for a part of an antibody known as the Fc (Fragment, crystallizable) region. Fc receptors bind to antibodies that are attached to infected cells or invading pathogens. Their activity stimulates phagocytic or cytotoxic cells to destroy microbes, or infected cells by antibody-mediated cellular phagocytosis (ADCP) or antibody-dependent cell-mediated cytotoxicity (ADCC). There are several different types of Fc receptors, which are classified based on the type of antibody that they recognize; for example those that bind the most common class of antibody, IgG, are called Fc-gamma receptors (FcγR), those that bind IgA are called Fc-alpha receptors (FcαR) and those that bind IgE are called Fc-epsilon receptors (FcεR). Equivalent to an effector ligand and thus incorporated into the definition is any surrogate ligand that recognizes the same or similar binding site within the modular antibody, such as Protein A.
All FcγRs belong to the immunoglobulin superfamily and are the most important Fc receptors for inducing phagocytosis of opsonized (coated) microbes. This family includes several members; for example FcγRI (CD64), FcγRIIA (CD32a), FcγRIIB (CD32b), FcγRIIIA (CD16a), FcγRIIIB (CD16b); that differ in their antibody affinities due to their different molecular structure. For instance, FcγRI binds to IgG more strongly than FcγRII and FcγRIII, and has an extracellular portion composed of three immunoglobulin (Ig)-like domains, one more domain than FcγRII and FcγRIII. These properties allow activation of FcγRI by a sole IgG molecule (or monomer), while the latter two Fcγ receptors must bind multiple IgG molecules within an immune complex to be activated.
Another FcR is expressed on multiple cell types and is similar in structure to MHC class I. This receptor also binds IgG and is involved in preservation of this antibody. However, since this Fc receptor is also involved in transferring IgG from a mother either via the placenta to her fetus or in milk to her suckling infant, it is called the neonatal Fc receptor (FcRn). Recently this receptor has been implicated in being involved in homeostasis of IgG serum levels.
Antibody-Dependent Cell-Mediated Cytotoxicity (ADCC) is a mechanism of cell-mediated immunity whereby an effector cell of the immune system actively lyses a target cell that has been bound by specific antibodies. It is one of the mechanisms through which antibodies, as part of the humoral immune response, can act to limit and contain infection. Classical ADCC is mediated by natural killer (NK) cells; monocytes and eosinophils can also mediate ADCC. For example Eosinophils can kill certain parasitic worms known as helminths through ADCC. ADCC is part of the adaptive immune response due to its dependence on a prior antibody response.
The term “foreign” in the context of amino acids shall mean the newly introduced amino acids being naturally occurring, but foreign to the site of modification, or substitutes of naturally occurring amino acids. “Foreign” with reference to an antigen binding sites means that the antigen binding site is not naturally formed by the specific binding region of the agent, and a foreign binding partner, but not the natural binding partner of the agent, is bound by the newly engineered binding site.
The term “variable binding region” sometimes called “CDR region” as used herein refers to molecules with varying structures capable of binding interactions with antigens. Those molecules can be used as such or integrated within a larger protein, thus forming a specific region of such protein with binding function. The varying structures can be derived from natural repertoires of binding proteins such as immunoglobulins or phylomers or synthetic diversity, including repeat-proteins, avimers and anticalins. The varying structures can as well be produced by randomization techniques, in particular those described herein. These include mutagenized CDR or non-CDR regions, loop regions of immunoglobulin variable domains or constant domains.
Modified binding agents with different modifications at specific sites are referred to as “variants”. Variants of a scaffold are preferably grouped to form libraries of binding agents, which can be used for selecting members of the library with predetermined functions. In accordance therewith, an antibody sequence is preferably randomized, e.g. through mutagenesis methods. According to a preferred embodiment a loop region of a binding agent, such as the parent antibody sequence comprising positions within one or more loops or at a terminal site, potentially contributing to a binding site, 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 loops or a loop region, preferably into the CDR loop region or structural loop region, which may include terminal sequences, that are located at one of the termini of an antibody domain or substructure.
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.
The cytotoxic modular antibody according to the invention with a molecular weight of less than 60 kD or up to 60 kD has a small size as compared to full length antibodies. The preferred size is up to 55 kD. Modular antibody single domains usually have a molecular size of 10-15 kD, thus a molecule based on, or consisting of 4 modular antibody domains would have a molecular size of 40-60 kD, depending on the glycosylation or any additional conjugation of pharmacologically active substances, like toxins or peptides.
The preferred format is an oligomer, composed of modular antibody domains, preferably up to 4 domains, more preferred 3 domains, and even more preferred based on 2 domains, which oligomer preferably comprises a heterodimer, such as Fab, or a homodimer, such as Fc. Formats based on the combination of 5 modular antibody domains or more are commonly thought not to exert the specific advantages of small sized antibody fragments, which are ease of expression in various expression systems and tissue penetration.
It is feasible to provide the preferred modular antibody of the invention as a single domain antibody. However, antibody domains tend to dimerize upon expression, either as a homodimer, like an Fc, or a heterodimer, like an Fab. The dimeric structure is thus considered advantageous to provide a stable molecule. The preferred dimers of immunoglobulin domains are selected from the group consisting of single domain dimers, like VHA/L, CH1/CL (kappa or lambda), CH2/CH2 and CH3/CH3. Dimers or oligomers of modular antibody domains can also be provided as single chain or two chain molecules, in particular those linking the C-terminus of one domain to the N-terminus of another.
Binding partners are agents that specifically bind to one another, usually through non-covalent interactions. Examples of binding partners include pairs of binding agents with functional interactions, such as receptor binding to ligands, antibody binding to antigen, a drug binding to a target, and enzyme binding to a substrate. Binding partners have found use in many therapeutic, diagnostic, analytical and industrial applications. Most prominent binding pairs are antibodies or immunoglobulins, fragments or derivatives thereof. In most cases the binding of such binding agents is required to mediate a biological effect or a function, a “functional interaction”.
According to a specific embodiment of the present invention the cytotoxic modular antibody is a binding agent, which is an immunoglobulin of human or murine origin, and may be employed for various purposes, in particular in pharmaceutical compositions. Of course, the modified immunoglobulin may also be a humanized or chimeric immunoglobulin. The binding agent, which is a human immunoglobulin, is preferably selected or derived from the group consisting of IgA1, IgA2, IgD, IgE, IgG1, lgG2, lgG3, lgG4 and IgM. The murine immunoglobulin binding agent is preferably selected or derived from the group consisting of IgA, IgD, IgE, IgGI, lgG2A, lgG2B, lgG2C, lgG3 and IgM.
Such a binding agent comprises preferably a heavy and/or light chain or a part thereof. A modified immunoglobulin according to the invention may comprise a heavy and/or light chain, at least one variable and/or constant domain, 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)
An exemplary modular antibody according to the invention consists of a constant domain selected from the group consisting of CH1, CH2, CH3, CH4, Igk-C, Igl-C, combinations, derivatives or a part 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.
Another modular antibody according to the invention can consist of a variable domain of a heavy or light chain, combinations, derivatives or a part thereof including a minidomain, 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 modular antibody according to the present invention may comprise one or more domains (e.g. at least two, three, four, five, six, ten domains). If more than one domain is present in the modular antibody these domains may be of the same type or of varying types (e.g. CH1-CH1-CH2, CH3-CH3, (CH2)2-(CH3)2, with or without the hinge region). Of course also the order of the single domains may be of any kind (e.g. CH1-CH3-CH2, CH4-CH1-CH3-CH2).
The invention preferably refers to part of antibodies, such as parts of IgG, IgA, IgM, IgD, IgE and the like. The modular antibodies of the invention may also be a functional antibody fragment such as Fab, Fab2, scFv, Fv, Fc, FcabTM, an antigen-binding Fc, or parts thereof, or other derivatives or combinations of the immunoglobulins such as minibodies, domains of the heavy and light chains of the variable region (such as dAb, Fd, VL, including Vlambda and Vkappa, VH, VHH) as well as mini-domains consisting of two beta-strands of an immunoglobulin domain connected by at least two structural loops, as isolated domains or in the context of naturally associated molecules. A particular embodiment of the present invention refers to the Fc fragment of an antibody molecule, either as antigen-binding Fc fragment (FcabTM) through modifications of the amino acid sequence or as conjugates or fusions to receptors, peptides or other antigen-binding modules, such as scFv.
The modular antibodies can be used as isolated polypeptides or as combination molecules, e.g. through recombination, fusion or conjugation techniques, with other peptides or polypeptides. The peptides are preferably 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 the loop region of the immunoglobulin domain. The preferred binding characteristics relate to predefined epitope binding, affinity and avidity.
The modular antibody according to the invention is possibly further combined with one or more modified modular antibodies or with unmodified modular antibodies, or parts thereof, to obtain a combination modular antibody. Combinations are preferably obtained by recombination techniques, but also by binding through adsorption, electrostatic interactions or the like, or else through conjugation or chemical binding with or without a linker. The preferred linker sequence is either a natural linker sequence or functionally suitable artificial sequence.
In general the modular antibody according to the invention may be used as a building block to molecularly combine other modular antibodies or biologically active substances or molecules. It is preferred to molecularly combine at least one antibody binding to the specific partner via the variable or non-variable sequences, like structural loops, with at least one other binding molecule which can be an antibody, antibody fragment, a soluble receptor, a ligand or another antibody domain, or a binding moiety thereof. Other combinations refer to proteinaceous molecules, nucleic acids, lipids, organic molecules and carbohydrates.
The engineered molecules according to the present invention will be useful as stand-alone molecules, as well as fusion proteins or derivatives, most typically fused before or after modification in such a way as to be part of larger structures, e.g. of complete antibody molecules, or parts thereof. Immunoglobulins or fusion proteins as produced according to the invention thus also comprise Fc fragments, Fab fragments, Fv fragments, single chain antibodies, in particular single-chain Fv fragments, bi- or multispecific scFv, diabodies, unibodies, multibodies, multivalent or multimers of immunoglobulin domains and others. It will be possible to use the engineered proteins to produce molecules which are monospecific, bispecific, trispecific, and may even carry more specificities. By the invention it is be possible to control and preselect the valency of binding at the same time according to the requirements of the planned use of such molecules.
According to the present invention, the modular antibody optionally exerts one or more binding regions to antigens, including the binding site binding specifically to the cell surface target and the binding sites mediating effector function. Antigen binding sites to one or more antigens may be presented by the CDR-region or any other natural receptor binding structure, or be introduced into a structural loop region of an antibody domain, either of a variable or constant domain structure. The antigens as used for testing the binding properties of the binding sites may be naturally occurring molecules or chemically synthesized molecules or recombinant molecules, either in solution or in suspension, e.g. located on or in particles such as solid phases, on or in cells or on viral surfaces. It is preferred that the binding of an immunoglobulin to an antigen is determined when the antigen is still adhered or bound to molecules and structures in the natural context. Thereby it is possible to identify and obtain those modified immunoglobulins that are best suitable for the purpose of diagnostic or therapeutic use.
Modular antibody or immunoglobulin domains may be modified according to the present invention (as used herein the terms immunoglobulin and antibody are interchangeable) which modifications are preferably effected in immunoglobulin domains or parts thereof that are either terminal sequences, preferably a C-terminal sequence, and/or part of a loop region, which contains a loop, either a CDR-loop or a non-CDR loop, structural loops being the preferred sites of modifications or mutagenesis. According to a specific embodiment the structural loop region also includes a terminal sequence, which contributes to antigen binding. 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.
It is particularly preferred that the modular antibody according to the invention is binding to said cell surface target through at least part of a structural loop and/or CDR loop.
In an alternate embodiment it is preferred that the modular antibody according to the invention is binding to said effector ligand, or a surrogate ligand for such an effector ligand, like protein A, through at least part of a structural loop and/or CDR loop, thus mediating the effector function.
In a preferred embodiment the binding agent is binding with its native or modified binding structure or newly formed binding site, specifically to at least two such epitopes that are identical or differ from each other, either of the same antigen or of different antigens.
In a preferred domain structure of a binding agent it is preferred to modify or randomize the modular antibody within at least one loop region or terminal region, resulting in a substitution, deletion and/or insertion of one 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 loops, the newly introduced amino acids being naturally occurring, but foreign to the site of modification, or substitutes of naturally occurring amino acids.
However, the maximum number of amino acids inserted into a loop region of a binding agent 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 loop or a loop region, in particular a structural loop or a structural loop region. A loop region 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.
In this regard the preferred modifications are engineered in the loop regions of CH1, CH2, CH3 and CH4, in particular in the range of 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, or within the terminal sequences, preferably within 6 amino acids from the C- or N-terminus of the antibody domain.
In another preferred embodiment a modification in the structural loop region comprising amino acids 92 to 98 is combined with a modification in the structural loop region comprising amino acids 8 to 20.
The above identified amino acid regions of the respective immunoglobulins comprise loop regions to be modified. Preferably, a modification in the structural loop region comprising amino acids 92 to 98 is combined with a modification in one or more of the other structural loops.
In a preferred embodiment a modification in the structural loop region comprising amino acids 92 to 98 is combined with a modification in the structural loop region comprising amino acids 41 to 45.2.
Most preferably each of the structural loops comprising amino acids 92 to 98, amino acids 41 to 45.2 and amino acids 8 to 20 contain at least one amino acid modification.
In another preferred embodiment each of the structural loops comprising amino acids 92 to 98, amino acids 41 to 45.2, and amino acids 8 to 20 contain at least one amino acid modification.
According to another preferred embodiment the amino acid residues in the area of positions 15 to 17, 29 to 34, 41 to 45.2, 84 to 85, 92 to 100, and/or 108 to 115 of CH3 are modified.
The preferred modifications of Igk-C and IgI-C of human origin are engineered in the loop regions in the area of amino acids 8 to 20, amino acids 26 to 36, amino acids 41 to 82, amino acids 83 to 88, amino acids 92 to 100, amino acids 107 to 124 and amino acids 123 to 126, or within the terminal sequences, preferably within 6 amino acids from the C- or N-terminus of the antibody domain.
The preferred modifications of loop regions of Igk-C and IgI-C of murine origin are engineered at sites in the area of 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 126.
Another preferred immunoglobulin preferably used as a therapeutic 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 forms a relevant binding site as described above.
According to a specific embodiment the immunoglobulin preferably used 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 22, amino acids 39 to 55, amino acids 66 to 79, amino acids 77 to 89 or amino acids 89 to 104, where the numbering of the amino acid position of the domains is that of the IMGT, or within the terminal sequences, preferably within 6 amino acids from the C- or N-terminus of the antibody domain.
In a specific embodiment, the immunoglobulin preferably used 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 7 to 22, amino acids 43 to 51, amino acids 67 to 77, amino acids 77 to 88, and amino acids 89 to 104, most preferably amino acid positions 12 to 17, amino acid positions 45 to 50, amino acid positions 68 to 77, amino acids 79 to 88, and amino acid positions 92 to 99, 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 are preferably located in the area of amino acids 8 to 20, amino acids 44 to 50, amino acids 67 to 76, amino acids 78 to 87, and amino acids 89 to 101, or within the terminal sequences, preferably within 6 amino acids from the C- or N-terminus of the antibody domain.
According to a preferred embodiment the structural loop regions of the variable domain of the immunoglobulin of murine origin as possible selected for modification purposes are preferably located in the area of amino acids 6 to 20, amino acids 43 to 52, amino acids 67 to 79, amino acids 79 to 87, and amino acids 91 to 100, or within the terminal sequences, preferably within 6 amino acids from the C- or N-terminus of the antibody domain.
The immunoglobulin preferably used as a therapeutic according to the invention may also be of camelid 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.
According to another preferred embodiment of the present invention the structural loop regions of a modular antibody or an immunoglobulins of camelid origin are modified, e.g. within a VHH, in the region of amino acids 7 to 19, amino acids 43 to 55, amino acids 68 to 76, amino acids 80 to 87 and amino acids 91 to 101, or within the terminal sequences, preferably within 6 amino acids from the C- or N-terminus of the antibody domain.
The preferred method of producing the modular antibody according to the invention refers to engineering a modular antibody that is binding specifically to at least one first epitope, which comprises modifications in each of at least two sites or loops within a structural loop region, and determining the specific binding of said structural 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. Thus, an antibody or antigen-binding structure specific for a first antigen may be improved by adding another valency or specificity against a second antigen, which specificity may be identical, either targeting different epitopes or the same epitope, to increase valency or to obtain bi-, oligo- or multispecific molecules.
On the other hand it is preferred to make use of those modular antibodies that contain native structures interacting with effector molecules or immune cells, preferably to bind an effector ligand. Those native structures either remain unchanged or are modulated for an increased effector function. Binding sites for e.g. Fc receptors are described to be located in a CH2 and/or CH3 domain region, and may be mutagenized by well known techniques.
ADCC, antibody-dependent cell-mediated cytotoxicity, is the killing of antibody-coated target cells by cells with Fc receptors that recognize the constant region of the bound antibody. Most ADCC is mediated by NK cells that have the Fc receptor FcgammaRIII or CD16 on their surface. Typical assays employ target cells, like Ramos cells, incubated with serially diluted antibody prior to the addition of freshly isolated effector cells. The ADCC assay is then further incubated for several hours and % cytotoxicity detected. Usually the Target: Effector ratio is about 1:16, but may be 1:1 up to 1:50.
Complement-dependent cytotoxicity (CDC) is a mechanism of killing cells, in which antibody bound to the target cell surface fixes complement, which results in assembly of the membrane attack complex that punches holes in the target cell membrane resulting in subsequent cell lysis. The commonly used CDC assay follows the same procedure as for ADCC determination, however, with complement containing serum instead of effector cells.
The cytotoxic activity as determined by either of ADCC and CDC assay is proven for a modular antibody according to the invention, if there is a significant increase in the percentage of cytolysis as compared to a control. The cytotoxic activity related to ADCC or CDC is preferably measured as the absolute percentage increase, which is preferably higher than 5%, more preferably higher than 10%, even more preferred higher than 20%.
The antibody-dependent cellular phagocytosis, ADCP sometimes called ADPC, is usually investigated side by side with cytolysis of cultured human cells. Phagocytosis by phagocytes, usually human monocytes or monocyte-derived macrophages, as mediated by an antibody can be determined as follows. Purified monocytes may be cultured with cytokines to enhance expression of FcγRs or to induce differentiation into macrophages. ADCP and ADCC assays are then performed with target cells. Phagocytosis is determined as the percentage of positive cells measured by flow cytometry. The positive ADCP activity is proven with a significant uptake of the antibody-antigen complex by the phagocytes. The cytotoxic activity related to ADCP is preferably measured as the absolute percentage uptake of the antibody-antigen complex by the phagocytes, which is preferably higher than 5%, more preferably higher than 10%, even more preferred higher than 20%.
In a typical assay PBMC or monoycytes or monocyte derived macrophages are resuspended in RF2 medium (RPMI 1640 supplemented with 2% FCS) in 96-well plates at a concentration of 1×105 viable cells in 100 ml/well. Appropriate target cells, expressing the target antigen, e.g. Her2/neu antigen and SKBR3 cells, are stained with PKH2 green fluorescence dye. Subsequently 1×104 PKH2-labeled target cells and an Her2 specific (IgGI) antibody (or modular antibody) or mouse IgGI isotype control (or modular antibody control) are added to the well of PBMCs in different concentrations (e.g. 1-100 μg/ml) and incubated in a final volume of 200 ml at 37° C. for 24 h. Following the incubation, PBMCs or monoycytes or monocyte derived macrophages and target cells are harvested with EDTA-PBS and transferred to 96-well V-bottomed plates. The plates are centrifuged and the supernatant is aspirated. Cells are counterstained with a 100-ml mixture of RPE-conjugated anti-CD11 b, anti-CD14, and human IgG, mixed and incubated for 60 min on ice. The cells are washed and fixed with 2% formaldehyde-PBS. Two-color flow cytometric analysis is performed with e.g. a FACS Calibur under optimal gating. PKH2-labeled target cells (green) are detected in the FL-1 channel (emission wavelength, 530 nm) and RPE-labeled PBMC or monoycytes or monocyte derived macrophages (red) are detected in the FL-2 channel (emission wavelength, 575 nm). Residual target cells are defined as cells that are PKH2+/RPE− Dual-labeled cells (PKH2+/RPE−) are considered to represent phagocytosis of targets by PBMC or monoycytes or monocyte derived macrophages. Phagocytosis of target cells is calculated with the following equation: percent phagocytosis=100×[(percent dual positive)/(percent dual positive+percent residual targets)]. All tests are usually performed in duplicate or triplicate and the results are expressed as mean 6 SD.
The apoptotic activity is preferably measured using standard methods of determinating dying or dead cells. In order to measure necrosis and apoptosis, cytotoxicity assays can be employed. These assays are can be radioactive and nonradioactive assays that measure increases in plasma membrane permeability, since dying cells become leaky or colorimetric assays that measure reduction in the metabolic activity of mitochondria; mitochondria in dead cells cannot metabolize dyes, while mitochondria in live cells can.
One can also measure early indicators for apoptosis such as fragmentation of DNA in populations of cells or in individual cells, in which apoptotic DNA breaks into different length pieces, alterations in membrane asymmetry (Phosphatidylserine based and Annexin V based assays), measurement of activation of apoptotic caspases or measurement of release of cytochrome C and AIF into cytoplasm by mitochondria.
The preferred cytotoxic activity of the modular antibody according to the invention amounts to at least 20% of cytolysis as measured in a respective ex vivo cell lysis assay.
Preferably the cytotoxic activity of the modular antibody according to the invention is mediating cell lysis or cell killing in a cell-based assay with an EC50<10−8 M, preferably in the nanomolar range or below.
The effector function of the modular antibody according to the invention preferably is a biological cytotoxic activity, which usually differs from any synthetic cytotoxic activity, e.g. as provided through a toxin that may be conjugated to an immunoglobulin structure. Toxins usually do not activate effector molecules and the biological defence mechanism. Thus, the preferred cytotoxic activity of the modular antibodies according to the invention is a biological cytotoxic activity, which usually is immunostimulatory, leading to effective cytolysis.
The cytotoxic activity further is differentiated from the simple cell inhibition effect, where a substance is inhibiting cell growth, e.g. by binding to the receptor of a growth factor, thus blocking the growth factor function, or by inhibiting angiogenesis. Cytotoxicity is essentially considered as an active attack to kill cells, thus leading to cell death or lysis, and thus considered as a highly efficient way to immediately reduce the number of malignant or infected cells. As compared to cytotoxicic compounds, cell growth inhibors do not immediately kill cells, but only reduce the cell growth and proliferation, thus are considered to be less active for therapeutic purposes.
The modular antibody according to the invention 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, organic molecules, in particular small organic molecules, anorganic molecules, or combinations or fusions thereof, including PEG, prodrugs or drugs. The preferred modular antibody according to the invention 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.
Preferably the target 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, in particular those epitopes of the extracellular domains of such receptors, e.g. the 4D5 epitope), 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 target antigen is selected from those antigens presented by cells, like epithelial cells, cells of solid tumors, infected cells, blood cells, antigen-presenting cells and mononuclear cells. Those target antigens expressed or overexpressed by cells are preferably targeted, which are 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-receptorl, IRp60, IL-5 receptor, CCR3, red blood cell receptor (CR1), human serum albumin, mouse serum albumin, rat serum albumin, Fc receptors, like neonatal Fc-gamma-receptor FcRn, Fc-gamma-receptors Fc-gamma R1, 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, 4-1 BBL, 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 alphaδ, integrin alphaθ, 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 llb/llla (GPIIb/llla), human cytomegalovirus (HCMV) gH envelope glycoprotein, HIV gp120, HCMV, respiratory syncytial virus RSV F, RSVF Fgp, VNRintegrin, Hep B gp120, CMV, gpllbllla, HIV IMB 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.
Preferred modular antibodies according to the invention are binding said target antigen with a high affinity, in particular with a high on and/or a low off rate, or a high avidity of binding. Usually a binder is considered a high affinity binder with a Kd<10−9 M. Medium affinity binders with a Kd of less than 10−6 up to 10−9 M may be provided according to the invention as well, preferably in conjunction with an affinity maturation process.
Affinity maturation is the process by which antibodies with increased affinity for antigen are produced. With structural changes of an antibody, including amino acid mutagenesis or as a consequence of somatic mutation in immunoglobulin gene segments, variants of a binding site to an antigen are produced and selected for greater affinities. Affinity matured modular antibodies may exhibit a several logfold greater affinity than a parent antibody. Single parent antibodies may be subject to affinity maturation. Alternatively pools of modular antibodies with similar binding affinity to the target antigen may be considered as parent structures that are varied to obtain affinity matured single antibodies or affinity matured pools of such antibodies.
The preferred affinity maturated variant of a modular antibody according to the invention exhibits at least a 10 fold increase in affinity of binding, preferably at least a 100 fold increase. The affinity maturation may be employed in the course of the selection campaigns employing respective libraries of parent molecules, either with modular antibodies having medium binding affinity to obtain the modular antibody of the invention having the specific target binding property of a binding affinity Kd<10−8 M and/or a potency of IC50<10−8 M. Alternatively, the binding potency or affinity may be even more increased by affinity maturation of the modular antibody according to the invention to obtain the high values corresponding to a Kd or IC50 of less than 10−9 M, preferably less than 10−10 M or even less than 10−11 M, most preferred in the picomolar range.
The IC50, also called EC50 or 50% saturation concentration, is a measure for the binding potency of a modular antibody. It is the molar concentration of a binder, which produces 50% of the maximum possible binding at equilibrium or under saturation. The potency of a binder is usually defined by its IC50 (hereby understood as an EC50 value). This can be calculated for a given binder by determining the concentration of binder needed to elicit half saturation of the maximum binding. Elucidating an IC50 or EC50 value is useful for comparing the potency of antibodies or antibody variants with similar efficacies, in particular when determined in saturation binding assays, not in competition assays. In this case it is considered as the concentration, which determines the plasma concentration to obtain a half-maximal (50%) effect in vivo. The lower the IC50 or EC50, the greater the potency of the modular antibody, and the lower the concentration of the antibody that is required to inhibit the maximum biological response, like effector function or cytotoxic activity. Lower concentrations of antibodies may also be associated with fewer side effects.
The binding affinity of an antibody is usually characterized in terms of the concentration of the antibody, at which half of the antigen binding sites are occupied, known as the dissociation constant (Kd, or K0).
Usually the affinity of an antibody correlates well with the IC50, when determined in a saturation binding assay. The affinity of an antagonist for its binding site (K1) is understood as its ability to bind to a receptor, which determines the duration of binding and respective agonist activity. Measures to increase the affinity by affinity maturation usually also increase the potency of binding, resulting in the respective reduction of IC50 values in the same range of the Kd values.
The IC50 and Kd values may be determined using the saturation binding assays well-known in the art. Contrary to competition assays, the saturation binding assays provide a value independent on the concentration of a competitor, thus a comparable value, which may be indicative for the binding affinity in vivo.
The modular antibody according to the invention 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 assay systems or diagnostic methods.
The modular antibody according to the invention 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, CDC or apoptotic activity. For some assays additional cells or components, that is in addition to the target cells, may need to be added, for example 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. Modular antibodies 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 modular antibodies. 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 modular antibodies 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.
The biological properties of the modular antibody according to the 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 modular antibody according to the invention. Tests of the substances in humans are ultimately required for approval as drugs, and thus of course these experiments are contemplated. Thus the modular antibodies of the present invention may be tested in humans to determine their therapeutic efficacy, toxicity, immunogenicity, pharmacokinetics, and/or other clinical properties. Especially those modular antibodies according to the invention that bind to single cell or a cellular complex through at least two binding motifs, preferably binding of at least three structures cross-linking target cells, would be considered effective in effector activity or preapoptotic or 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 and cell death.
The modular antibody of the present invention may find use in a wide range of antibody products. In one embodiment the modular antibody 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 modular antibody may find use in an antibody composition that is monoclonal or polyclonal. In a preferred embodiment, the modular antibodies 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 modular antibodies 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 modular antibodies 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 modular antibodies of the present invention are used to block, antagonize, or agonize enzymes and substrate of enzymes.
In a preferred embodiment, a modular antibody is administered 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 modular antibody according to the present invention is the only therapeutically active agent administered to a patient. Alternatively, the modular antibody 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 modular antibody may be administered concomitantly with one or more other therapeutic regimens. For example, a modular antibody 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 modular antibody of the present invention may be administered in conjunction with one or more antibodies, which may or may not comprise a modular antibody of the present invention. In accordance with another embodiment of the invention, the modular antibody of the present invention and one or more other anti-cancer therapies is 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 modular antibody of the present invention. In one embodiment, the modular antibody 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 modular antibody 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 modular antibody of the present invention is 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 modular antibodies of the present invention and one or more therapeutically active agents are formulated. Stable formulations of the modular antibodies 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, 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 modular antibody and other therapeutically active agents disclosed herein may also be formulated as immuno liposomes, and/or entrapped in microcapsules.
Administration of the pharmaceutical composition comprising a modular antibody 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.), intraperitonear, intramuscularly, intrapulmonary (e.g., AERxTM inhalable technology commercially available from Aradigm, or InhanceTM pulmonary delivery system commercially available from Inhale Therapeutics), vaginally, parenterally, rectally, or intraocularly. A preferred method according to the invention refers to modular antibodies that are modified by a mutagenesis method to obtain a new binding site. The preferred mutagenesis refers to randomization techniques, where the amino acid sequence of a peptide or polypeptide is mutated in at least one position, thus a randomized sequence is obtained, which mediates antigen binding. For instance, specific antibody sequences are randomly modified to obtain a nucleic acid molecule coding for an immunoglobulin, immunoglobulin domain or a part thereof which comprises at least one nucleotide repeating unit, preferably within a structural loop coding region or within a terminal 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 oligonuleotides 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).
Another important aspect of the invention is that each potential binding domain remains physically associated with the particular DNA or RNA molecule which encodes it, and in addition, the fusion proteins oligomerize at the surface of a genetic package to present the binding polypeptide in the native and functional oligomeric structure. Once successful binding domains are identified, one may readily obtain the gene for expression, recombination or further engineering purposes. The form that this association takes is a “replicable genetic package”, such as a virus, cell or spore which replicates and expresses the binding domain-encoding gene, and transports the binding domain to its outer surface. Another form is an in-vitro replicable genetic package such as ribosomes that link coding RNA with the translated protein. In ribosome display the genetic material is replicated by enzymatic amplification with polymerases.
Those cells or viruses or nucleic acid bearing the binding agents which recognize the target molecule are isolated and, if necessary, amplified. The genetic package preferably is M13 phage, and the protein includes the outer surface transport signal of the M13 gene III protein.
The preferred expression system for the fusion proteins is a non-suppressor host cell, which would be sensitive to a stop codon, such as an amber stop codon, and would thus stop translation thereafter. In the absence of such a stop codon such non-suppressor host cells, preferably E. coli, are preferably used. In the presence of such a stop codon supressor host cells would be used.
Preferably in the method of this invention the vector or plasmid of the genetic package is under tight control of the transcription regulatory element, and the culturing conditions are adjusted so that the amount or number of vector or phagemid particles displaying less than two copies of the fusion protein on the surface of the particle is less than about 20%. More preferably, the amount of vector or phagemid particles displaying less than two copies of the fusion protein is less than 10% the amount of particles displaying one or more copies of the fusion protein. Most preferably the amount is less than 1%.
The expression vector preferably used according to the invention is capable of expressing a binding polypeptide, and may be produced as follows: First a binding polypeptide gene library is synthesized by introducing a plurality of polynucleotides encoding different binding sequences. The plurality of polynucleotides may be synthesized in an appropriate amount to be joined in operable combination into a vector that can be propagated to express a fusion protein of said binding polypeptide. Alternatively the plurality of olynucleotides can also be amplified by polymerase chain reaction to obtain enough material for expression. However, this would only be advantageous if the binding polypeptide would be encoded by a large polynucleotide sequence, e.g. longer than 200 base pairs or sometimes longer than 300 base pairs. Thus, a diverse synthetic library is preferably formed, ready for selecting from said diverse library at least one expression vector capable of producing binding polypeptides having the desired preselected function and binding property, such as specificity.
The randomly modified nucleic acid molecule may comprise the above 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 103 times the theoretical number, preferably not less than 102 times, most preferably not less than 10 times.
Usually libraries according to the invention comprise at least 10 fusion proteins or potential binding agents or variants of scaffold proteins, preferably at least 100, more preferred at least 1000, more preferred at least 104, more preferred at least 105, more preferred at least 106, more preferred at least 107, more preferred at least 108, more preferred at least 109, more preferred at least 1010, more preferred at least 1011, up to 1012, in cases of in vitro display methods, such as ribosomal display, even higher number are feasible.
Various alternatives are available for the manufacture of the gene encoding the randomized library. It is possible to produce the DNA by a completely synthetic approach, in which the sequence is divided into overlapping fragments which are subsequently prepared as synthetic oligonucleotides. These oligonucleotides are mixed together, and annealed to each other by first heating to ca. 100° C. and then slowly cooling down to ambient temperature. After this annealing step, the synthetically assembled gene can be either cloned directly, or it can be amplified by PCR prior to cloning. Alternatively, other methods for site directed mutagenesis can be employed for generation of the library insert, such as the Kunkel method (Kunkel T A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci USA. 1985 January; 82(2):488-92) or the Dpnl method (Weiner M P, Costa G L, Schoettlin W, Cline J, Mathur E, Bauer J C. Site-directed mutagenesis of double-stranded DNA by the polymerase chain reaction. Gene. 1994 Dec. 30; 151 (1-2):119-23.).
For various purposes, it may be advantageous to introduce silent mutations into the sequence encoding the library insert. For example, restriction sites can be introduced which facilitate cloning or modular exchange of parts of the sequence. Another example for the introduction of silent mutations is the ability to “mark” libraries, that means to give them a specific codon at a selected position, allowing them (or selected clones derived from them) e.g. to be recognized during subsequent steps, in which for example different libraries with different characteristics can be mixed together and used as a mixture in the panning procedure.
The invention also provides a method of producing an oligomer of modular antibody domains binding to a target comprising the steps of:

    
    
        providing a library of oligomers of modular antibody domains produced according to the inventive method as described
        contacting said library with said target in the presence of a scaffold ligand,
        selecting a library member binding to said target in the presence of a scaffold ligand, and
        manufacturing a preparation of the functional oligomer.
    
    


The scaffold ligand can be selected from the group consisting of an effector molecule, FcRn, Protein A, Protein G, Protein L and CDR target. As an example, the effector molecule can be selected from the group consisting of CD64, CD32, CD16, Fc receptors.
The oligomers can be dimers selected from the group of VHA/VL, CH1/CL, CH2/CH2, CH3/CH3, Fc and Fab, or single chains thereof.
The method according to the invention can provide a library containing at least 102 independent clones expressing functional oligomers of modular antibody domains or variants thereof. According to the invention it is also provided a pool of preselected independent clones, which is e.g. affinity maturated, which pool comprises preferably at least 10, more preferably at least 100, more preferably at least 1000, more preferably at least 10000, even more than 100000 independent clones. Those libraries, which contain the preselected pools, are preferred sources to select the high affinity modular antibodies according to the invention.
Libraries as used according to the invention preferably comprise at least 102 library members, more preferred at least 103, more preferred at least 104, more preferred at least 105, more preferred at least 106 library members, more preferred at least 107, more preferred at least 108, more preferred at least 109, more preferred at least 1010, more preferred at least 1011, up to 1012 members of a library, preferably derived from a parent molecule, which is a functional modular antibody as a scaffold containing at least one specific function or binding moiety, and derivatives thereof to engineer a new binding site apart from the original, functional binding region of said parent moiety.
Usually the libraries according to the invention further contain variants of the modular antibody, resulting from mutagenesis or randomization techniques. These variants include inactive or non-functional antibodies. Thus, it is preferred that any such libraries be screened with the appropriate assay for determining the functional effect. Preferred libraries, according to the invention, comprise at least 102 variants of modular antibodies, more preferred at least 103, more preferred at least 104, more preferred at least 105, more preferred at least 106, more preferred at least 107, more preferred at least 108, more preferred at least 109, more preferred at least 1010, more preferred at least 1011, up to 1012 variants or higher to provide a highly diverse repertoire of antibodies for selecting the best suitable binders. Any such synthetic libraries may be generated using mutagenesis methods as disclosed herein.
Preferably the library is a yeast library and the yeast host cell exhibits at the surface of the cell the oligomers with the biological activity. The yeast host cell is preferably selected from the genera Saccharomyces, Pichia, Hansenula, Schizisaccharomyces, Kluyveromyces, Yarrowia and Candida. Most preferred, the host cell is Saccharomyces cerevisiae. 
The invention further provides a high quality library containing at least 102 independent clones of functional dimers of modular antibody domains or variants thereof, or the pools of optimized or preselected clones, e.g. the affinity matured clones, which pools are containing at least 10 independent clones that are binding to a target and to a scaffold ligand. The target can be a ligand binding to a parent molecule subject to amino acid variation. The parent molecule can be a functional oligomer, in particular a functional Fc or a functional Fab, or part thereof.
The library can contain functional dimers of modular antibody domains that are binding to a target and to a scaffold ligand, and at least 20%, preferably at least 30%, more preferred at least 40% of the functional dimers are binding to CD64. This is particularly preferred with a modular antibody that contains CH2 domains, such as an Fc scaffold.
Alternatively, the library can contain functional dimers of modular antibody domains that are binding to a target and to a scaffold ligand, and at least 20%, preferably at least 30%, more preferred at least 40% of the functional dimers are binding to protein A. This is particularly preferred with a modular antibody that contains CH2 and CH3 domains, such as an Fc scaffold.
Alternatively, the library can contain functional dimers of modular antibody domains that are binding to a target and to a scaffold ligand, and at least 20%, preferably at least 30%, more preferred at least 40% of the functional dimers are binding to the same CDR target. This is particularly preferred with modular antibodies containing a variable region, such as an Fab scaffold with specificity to a single CDR target.
As is well-known in the art, there is a variety of display and 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 cellular and non-cellular, in particular mobilized display systems. Among the cellular systems the phage display, virus display, yeast or other eukaryotic cell display, such as mammalian or insect cell display, may be used. Mobilized systems are relating to display systems in the soluble form, such as in vitro display systems, among them ribosome display, mRNA display or nucleic acid display.
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 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, an Fc 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.
The foregoing description will be more fully understood with reference to the following examples. Such examples are, however, merely representative of methods of practicing one or more embodiments of the present invention and should not be read as limiting the scope of invention.
EXAMPLES
Example 1
Construction of the Non-Focussed Fcab Library (Fcab0D and Phage Surface Display
The crystal structure of an IgGI Fc fragment, which is published in the Brookhaven Database as entry 1 OQO.pdb was used to aid in the design of the Fcab library.
The sequence which was used as the basis for construction of the Fcab library is given in SEQ ID No.1 (FIG. 3). In this sequence, the first amino acid corresponds to GIu 216 of human IgGI (EU numbering; according to the IMGT database
(imgt.cines.fr/textes/IMGTrepertoire/Proteins/protein/human/IGH/IGHC/Hu_IGHC allgenes.html; lookup 2007 06 25), it is the first residue of the human IgGI hinge region, which is given as: (E)PKSCDKTHTCPPCP) (SEQ ID NO:441) of the heavy constant chain hinge region of human IgGI.) The second-last residue of SEQ ID No.1 (FIG. 3) corresponds to GIy 446 of human IgGI (EU numbering; IMGT: residue number 129 of the CH3 domain of human IgG1).
After detailed analysis of the structure of loqo.pdb and by visual inspection of the residues forming the loops which connect the beta strands, it was decided to randomize residues 144, 145 and 146, which are part of the loop connecting beta strand A-B as well as 198,199, 200, 203 and 204, which are part of the loop connecting beta strand E-F of SEQ ID No.1 (FIG. 3). In addition to the mutated residues, 5 residues were inserted at residue number 198 of SEQ ID No.1 (FIG. 3). In SEQ ID No.2 (FIG. 4), the sequence of the library insert of library Fcab0I is given in which all randomized residue positions as well as the 5 inserted residues are designated with the letter X.
The engineered gene was produced by a series of PCR reactions using degenerate primers 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 (FIG. 3) 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, the Ncol restriction site close to the 3′ end of the pelB secretion signal was used. For the randomized residues, the codon NNS (IUPAC code, where S means nucleotides C and G) was chosen which encodes all 20 naturally occurring amino acids, but avoids 2 out of 3 stop codons. Other codons such as for example the NNB (B meaning nucleotides T, C and G) can also be used. The engineered sequence is given as a nucleotide sequence in SEQ ID No.3 (FIG. 5). This sequence also includes the restriction sites used for cloning into the phagmid display vector pHEN1, namely an Ncol site at the 5′ end and a Notl site at the 3′ end.
The sequences of the PCR primers used for assembly of the mutated CH3 domain are given in SEQ ID No.4 through SEQ ID No.9.







(PCR primer EPKSNCO)


SEQ ID No. 4


ccatggccgagcccaaatcttgtgacaaaactc


 


(PCR primer CH3LSAC)


SEQ ID No. 5


agtcgagctcgtcacgggatgggggcaggg


 


(PCR primer CH3CSAC)


SEQ ID No. 6


gtacgagctcnnsnnsnnscaagtcagcctgacctgcctgg


 


(PCR primer CH3CHIN)


SEQ ID No. 7


tgccaagcttgctgtagaggaagaaggagccg


 


(PCR primer CH3RHIN)


SEQ ID No. 8


tgccaagcttaccgtgnnsnnsnnsaggtggnnsnnsgggaacgtcttct


catgctccg


 


(PCR primer CH3RNOT)


SEQ ID No. 9


agttgcggccgctttacccggagacagggagag






FIG. 1 shows a schematic presentation of the PCR fragments generated for assembly of the mutated gene, and the primers used therefore.
cDNA of the heavy chain of the human monoclonal antibody 3D6 (Felgenhauer M, Kohl J, R{umlaut over (υ)}ker F. Nucleotide sequences of the cDNAs encoding the V-regions of H- and L-chains of a human mono-clonal antibody specific to HIV-1-gp41. Nucleic Acids Res. 1990 Aug. 25; 18(16):4927.) was used as template for the PCR reactions. The 3 PCR products were digested with Sacl and/or Hindlll respectively and ligated together. The ligation product was further digested with Ncol and Notl and ligated into the surface display phagmid vector pHEN1, which had previously been digested with Ncol and Notl. The ligation product was then transformed into E. coli by electroporation. 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/NaCI 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 Focused Fcab Library (Fcab02) and Phage Surface Display
As described in example 1, an Fcab library was prepared in which the randomized library positions are fully randomized, i.e. they are encoded by a codon such as NNS, NNB, NNK, NNN or others are used.
For clarity, the meaning of the letters such as N, B, S or K is defined by the IUPAC nucleotide ambiguity code, which is given in the following table:







TABLE 1







IUPAC nucleotide ambiguity code









Symbol
Meaning
Nucleic Acid





A
A
Adenine


C
C
Cytosine


G
G
Guanine


T
T
Thymine


U
U
Uracil


M
A or C



R
A or G



W
A or T



S
C or G



Y
C or T



K
G or T



V
A or C or G



H
A or C or T



D
A or G or T



B
C or G or T



X
G or A or T or C



N
G or A or T or C





Source: Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. A Cornish-Bowden, Nucleic Acids Res. 1985 May 10; 13(9): 3021-3030.






These codons given above are designed such that all 20 amino acids are encoded by them. It may be preferable to choose subsets out of the possible amino acids. Examples can be found in the literature (Fellouse F A, Li B, Compaan D M, Peden A A, Hymowitz S G, Sidhu S S. Molecular recognition by a binary code. J MoI Biol. 2005 May 20; 348(5):1153-62. Epub 2005 Apr. 1; Fellouse F A, Wiesmann C, Sidhu S S. Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. Proc Natl Acad Sci USA. 2004 Aug. 24; 101 (34):12467-72. Epub 2004 Aug. 11). Focused libraries which for example allow for only 4 different amino acid types can be constructed e.g. by employing the codon KMT, which codes for the amino acids Ser, Tyr, Ala and Asp.
A focused Fcab library, designated Fcab02, has been constructed in the same way as described in example 1, except that the NNS codons were replaced by KMT codons.
Therefore, the letter “X” in SEQ ID No.2 (FIG. 4) now means “S, Y, A and D” (Ser, Tyr, Ala and Asp) in order to describe the focused library Fcab02
Example 3
Construction of a Phage Surface Display Library with Additional Amino Acid Residues Between the Library Insert (Binding Partner) and p3
In order to investigate accessibility of the potential binding site of the displayed protein a binding assay is performed: the phage suspension is reacted with anti-myc mAb 9E10-coated microplates (or immunotubes). After washing, the bound phages are detected with anti-M13-enzyme conjugate. As a control, helper phage—which does not display the protein fusion and the myc-tag is reacted with the plates. Other controls are reaction of phages with non-coated plates and reaction of phages with antiserum recognizing the p3-fusion partner of the phages.
Ideally, the anti-myc-reactivity of phages displaying the p3-fusion protein should give very clear ELISA readouts whereas helper phage reactions to anti-myc-mAb should not be above background (non-coated plates).—The structure of a CH3 dinner displayed at the surface of an M13 phage through binding to protein III as an anchor is such, that each CH3 is anchored to protein III using various linker length and compositions. Thus, the CH3 dinner is preferably displayed by two anchors.
Linker Optimization:
The linker between the protein to be displayed and the anchor protein of the genetic package (in case of filamentous phage e.g. p3, p8, pX, plX, pVII) is especially important if the potential binding site of the displayed molecule is in spatial vicinity of the phage particle. In antibody libraries utilizing variable domains and antigen binding sites formed by CDR-loops and display of the library members as amino-terminal fusion to p3 the potential antigen binding site is directed away from the phage particle. Therefore, the linker structure between library members and the phage coat protein is not important. Engineering the bottom loops of immunoglobulin domains and performing phage display may however be an inefficient process and decreases yields of antigen binding clones or even preclude it. Varying the linker between a library member protein and its fusion partner on the surface can solve or may at least reduce this problem.
In order to select for optimal linker sequences (in terms of length and flexibility as well as stability) a library of linkers can be prepared in which the anchor protein at the surface of the genetic replicable package is fused to a known binding protein which is for sterical reasons notoriously difficult to select for.
This library of sequences can be varied in length and amino acid content.
Selection methods of the linker library for optimal linkers depend on the application but basically it should be for selecting all properties one wishes to have in a certain methodology. Enrichment against a difficult to select for antigen may yield linker sequences which allow library members a good access to the antigen. Incubation in protease solutions or under other harsh conditions or frequent passaging through host cells under proteolytic conditions (e.g. old microbial cultures) may be an appropriate selection for stable display linkers.
A library of linkers may be produced by any well known library technology. Synthetic linker sequence lengths may vary between 10-500 amino acids. Alternatively, linker can be complete proteins known to be of flexible nature.
Linker optimization Fcab0I:
As an example, library Fcab0I (as described in example 1) can be used. Originally, this library is cloned in the phagmid display vecor pHEN1, using Ncol and Notl restriction sites. When cloned in this manner, 18 amino acid residues are in between the C-terminal amino acid residue of the Fcab0I library insert and the N-terminal amino acid residue of phage M13 p3. The sequence of this junction region is given in SEQ ID No.10 SPGKAAAEQKLISEEDLNGAATVES—and is explained as follows: the first 4 residues, SPGK, (SEQ ID NO:442) are the 4 C-terminal residues of the Fcab0I library insert, followed by the amino acid sequence AAA, which is the amino acid residues encoded by the Notl restriction site, followed by the sequence EQKLISEEDL, (SEQ ID NO:443) which is the myc epitope, followed by NGAA, (SEQ ID NO:445) after which there is an amber stop codon, which is translated to Glutamine (Q) in amber suppressor strains of E. coli such as TG1. The C-terminal 4 residues of SEQ ID No.10, TVES, (SEQ ID NO:444) are the N-terminal 4 residues of phage M13 p3 as present in the vector pHEN1.
In order to construct a phage which displays an Fcab insert with an increased distance between the Fcab (the binding partner) and the body of the phage (the genetic package), 5 additional residues were inserted at the C-terminus of the Fcab insert FcabRGD4, directly upstream of the Notl cloning site, resulting in the clone FcabRGD4L. FcabRGD4 is an Fcab that has an integrin-binding RGD motif inserted in the EF-loop of the CH3 domain and which binds to ccvβ3-integπn in ELISA. As an increased-length linker sequence, the amino acid sequence EGGGS, which appears 8 times in the phage M13 p3 sequence was used. The resulting amino acid sequence of FcabRGD4L as expressed after cloning in pHEN1 is given in SEQ ID No.11 (FIG. 5). In SEQ ID No.11 (FIG. 5), amino acid residues 198-204 represent the RGD motif, amino acid residue 237 is the C-terminal residue of the Fcab insert, residues 238-242 represent the inserted linker sequence (which is the difference to unmodified pHEN1), which is followed by myc tag, amber stop codon and the p3 sequence.
For cloning of the construct, the FcabRGD4 sequence was amplified from pHENFcabRGD4 (SEQ ID No.12) using PCR primers EPKSNCO (SEQ ID No.4) and CH3rlink actagcggccgcagagccaccaccctccttacccggagacagggagag (SEQ ID No.13) and cloned via Ncol and Notl restriction sites into the vector pHEN1. The resulting vector, pHENFcabRGD4L (SEQ ID No.14/FIGS. 7A and 7B), has the additional linker sequence at nucleotide positions 3057-3071.
The two phagemid vectors, pHENFcabRGD4 and pHENFcabRGD4L were transformed into E. coli TG1. Subsequently, phage particles were rescued from E. coli TG1 cells with helper phage
M13-K07. Phage particles were then precipitated from culture supernatant with PEG/NaCI in 2 steps, dissolved in water and used for ELISA. Phage ELISA was performed as follows:
The phage suspension is reacted with αvβ3-integrin-coated microplates (or immunotubes). After washing, the bound phages are detected with anti-M13-enzyme conjugate. As controls, helper phage—which does not display the protein fusion and the myc-tag is reacted with the plates as well as phage particles carrying wtFcab on their surface. Other controls are reaction of phages with non-coated plates and reaction of phages with antiserum recognizing the Fcab-fusion partner of the phages. Phage particles with the increased-length linker resulting from pHENFcabRGD4L react more readily with αvβ3-integhn than phage particles with the original linker as contained in pHENFcabRGD4, and therefore give a stronger signal in ELISA.
Phage selections can be performed in which phage particles with wtFcab are mixed with small amounts of phage particles carrying either FcabRGD4 or FcabRGD4L. After several (typically 3-5) rounds of panning, preferentially phages displaying FcabRGD4L are selected.
Example 4
FcabTM Library Design
Design of Fcab Libraries (illustrated in FIG. 2): amino acid positions in nonCDR-loops of CH3 constant domains of antibodies are considered for randomization. Especially loops A-B, C-D and E-F are considered as they are on one side of the domain. Some of the design criteria for randomization at a certain position are described herein.
Amino acids frequently involved in antigen antibody interactions are described herein to be included in a focused library.
Libraries with restricted amino acid utilization have been shown to be sufficient to generate binders against virtually any antigen (Sidhu & Fellhouse, NATURE CHEMICAL BIOLOGY VOLUME 2 page 682ff.; Koide et al PNAS, volume 104 p 6632-6637). The advantage of such restricted (or focused) libraries is that they can be covered completely by current technologies. Ideally, the amino acid utilization reflects a natural amino acid utilization of ligand receptor binding. However, even libraries utilizing only 2 amino acids (Tyrosine and Serine) have been reported to yield good selection results (in terms of frequency of binders against different binders and in terms of affinity).
Loop Flexibility:
Certain loop structures may be required by the scaffold protein in order to keep the overall natural structure. Randomizing many amino acid positions in loops and even elongation of loops may be facilitated by building certain sequences either on one or on both sides of the randomized positions. These sequences may be flexible sequences in order to allow compensating for any tensions with certain library sequences in such a position.







TABLE 2







Exemplary Fcab TM libraries, focused and non-focused











# of
Theorectical
Number of



randomized 
diversty on 
independent 



positions
amino acid level
bacterial clones













Fcab01
13
8.2 × 1018
0.6 × 109


Fcab02
13, focused
6.7 × 107 
0.6 × 109


Fcab03
13
8.2 × 1018
1.0 × 109


Fcab04
13, focused
6.7 × 107 
0.8 × 109


Fcab05
15
1.3 × 1018
0.8 × 109


Fcab06
15, focused
1.3 × 109 
1.0 × 109









Fcab0I library is described in the examples above. The sequence space of the focused library designs Fcab02, Fcab04 and Fcab06 are covered by the actual bacterial library sizes of approximately 10e9. In contrast, the completely randomized libraries Fcab0I, Fcab03 and Fcab06 are actually grossly underrepresented.
Design of Loop Randomization in Yeast.
Similar to the examples mentioned above for Fcab library design and generation of the library in bacteria, yeast libraries were generated. As shown in Table 3, various combinations of modified AB loops, CD loops and EF loops were generated. The AB loop modified in this example is ranging from amino acid 358 to 362 (wt sequence “LTKNQ”), the CD loop from amino acid 384 to 388 (wt sequence “NGQPE”), and the EF loop from 413 to 419 (wt sequence “DKSRWQQ”).
As mentioned before, “X” stands for a complete randomization, and “Z” for a focused design. Amino acids, that were inserted and are not present on the wt Fc scaffold, are written between brackets in Table 3. For those libraries, where the loops were not modified, the one letter amino acid code of the respective wt sequence is mentioned in the table. As the number of theoretical combinations exceeds in most of these libraries the experimental number of clones, the number of independent yeast clones generated is shown in the last column.







TABLE 3 







Exemplary Fcab TM libraries, focused and non-focused, with AB loop, CD loop


and EF loop mutations and insertions.












Library
theoretical



Independent


name
size
AB loop
CD loop
EF loop
clones





Fcab05
2.0 × 1022
ZXXXZ
NGQPE
(XXXXX)X
2.2 × 104





(SEQ ID
XXRWXX






NO: 447)




 


Fcab05sABCD
7.5 × 1031
XXXXX
XXXXX
(XXXXX)X
1.1 × 106





(XXXXX)
XXRWXX



 


Fcab05sCD
6.8 × 1029
ZXXXZ
XXXXX
(XXXXX)X
8.6 × 106






XXRWXX



 


Fcab05sAB
1.3 × 1024
XXXXX
NGQPE
(XXXXX)X
5.3 × 107





(SEQ ID
XXRWXX






NO: 447)




 


Fcab07
3.4 × 1010
LTKNQ
NGQPE
XXXXXXX
5.3 × 107




(SEQ ID
(SEQ ID






NO: 446)
NO: 447)




 


Fcab07AB
1.2 × 1018
XXXXX
NGQPE
XXXXXXX
4.8 × 106





(SEQ ID







NO: 447)




 


Fcab07ABb
1.2 × 1018
XXXXX
NGQPE
XXXXXXX
1.3 × 107





(SEQ ID







NO: 447)




 


Fcab07b
3.4 × 1010
LTKNQ
NGQPE
XXXXXXX
3.7 × 107




(SEQ ID
(SEQ ID






NO: 446)
NO: 447)




 


Fcab07CD
1.2 × 1018
LTKNQ
XXXPE
XXXXXXX
1.9 × 107




(SEQ ID







NO: 446)





 


Fcab07CDAB
3.9 × 1025
XXXXX
XXXPE
XXXXXXX
1.7 × 107


Fcab08
3.4 × 107
XXXXX
NGQPE
DKSRWQQ
8.5 × 106





(SEQ ID
(SEQ ID






NO: 447)
NO: 448)



 


Fcab08EF
1.2 × 1018
XXXXX
NGQPE
XXXXXXX
2.2 × 107





(SEQ ID







NO: 447)









Example 5
Cloning of Yeast Display Libraries by Homologous Recombination Vector
pYD1 (Invitrogen) is used as the basic vector. The vector is modified as follows, in order to remove an Xhol site: pYD1 is cleaved with Xhol, treated with Klenow fragment of DNA polymerase and religated. The resulting sequence is given in pYDIdX (SEQ ID No.15/FIGS. 8A and 8B). pYDIdX contains a unique BamHI restriction site at position 921/925 and a unique Notl restriction site at position 963/967. It is opened with these two restriction enzymes. An insert encoding CH1-hinge-CH2-CH3 from human IgGI is prepared by PCR from cDNA encoding the heavy chain of a human IgGI monoclonal antibody. In this insert, a point mutation is introduced using standard procedures to mutate the C-terminal Cystein residue of the CH1 domain to a Serine. The insert is amplified using PCR primers that attached a BamHI and a Not restriction site to both ends respectively. These restriction sites are then used for cloning the insert into pYDIdX to yield the display vector pYDIdXFc (SEQ ID No.16/FIGS. 9A and 9B and 9C). The mutated codon at the C-terminus of the CH1 domain (Cys to Ser) is at positions 1233-1235 in the sequence pYDI DxFc. The stop codon of the insert is at position 1917/1919.
This vector is used as a positive control for the display of human CH1-hinge-CH2-CH3 on the surface of yeast and as a starting point for the construction of the vector pYD1 CH12 (see below).
Cloning of Libraries
Cloning of libraries in which mutations are introduced into structural loops of CH3 domains is performed in yeast by homologous recombination (gap repair). For this purpose, a recipient vector is prepared that lacks the CH3 domain: pYDIdXFc is cleaved with Xhol (position 1603/1607) and Notl (position 1921/1925), the large fragment is prepared by preparative gel electrophoresis, treated with Klenow fragment of DNA polymerase and re-ligated. This procedure reconstitutes a unique Xhol site (position 1603/1607) and yielded vector pYD1 CH12 (SEQ ID No.17/FIGS. 10A and 10B and 10C). pYD1 CH12 is subsequently cleaved with Xhol and is used as recipient vector for gap repair in yeast.
Alternatively, for the libraries listed in Table 3, a different recipient vector was constructed, which comprised only the hinge region, the CH1 and the CH2 domains, but was lacking the CH1 domain. In this vector, the CH1 domain was removed by cutting BamH1 (position:921/926) and Xhol (position: 1603/1608). Instead, we introduced a fragment produced by PCR that comprises the hinge region, the CH2 domain and the corresponding restriction enzyme sites. The resulting plasmid is pYD1_dX_dCH1_Fcab_wt (SEQ ID No.428/FIGS. 29A and 29B). In a further step we removed the CH3 domain of the latter plasmid digesting with Xhol (1309/1314) and Notl (1626/1633) and replaced it instead by two sequential tags: the V5 tag followed with the His6 tag, This sequence was obtained by PCR amplification from the pYD1 vector and cloned using Xhol and Notl restriction enzyme sites. The final plasmid, pYD1dX_dCH1dCH3_Fcab_wt (SEQ ID No.427/FIGS. 28A and 28B and 28C), was used as the library recipient vector. The pYD1dX_dCH1dCH3_Fcab_wt is coding for a human IgGI fragment starting from the hinge region and finishing at the beginning of CH3 domain. It contains a unique BamHI (921/926), Xhol (1309/1314) and Notl restriction site (1422/1429). The latter 2 are used for introducing the CH3 libraries by homologies recombination. The vector pYD1_dX_dCH1_Fcab_wt is used as a positive control for the display of human hinge-CH2-CH3 on the surface of yeast and pYD1dX_dCH1dCH3_Fcab_wt as a starting point for the construction of the libraries listed in Table 3.
As a source of insert for pYDIdXFc, Fcab libraries Fcab0I (SEQ ID No.18), Fcab02 (SEQ ID No.19), Fcab03 (SEQ ID No.20), Fcab04 (SEQ ID No.21), Fcab0δ (SEQ ID No.22) and Fcab06 (SEQ ID No.23) are used. These libraries are prepared by Standard DNA synthesis, and contain randomized residues as well as inserted residues in the AB loop (between residues 359 and 361 (EU numbering)) as well as in the EF loop (between residues 413 and 419 (EU numbering)) of the CH3 domain of human IgGI. From this synthetic DNA, the insert for gap repair in yeast is amplified by PCR using PCR primer pair







gapch35


(SEQ ID No. 24)


caacaaggccctgcctgcccccatcgagaagaccatctccaaggccaagg


gccagcctcgagaaccacaggtgtacaccctgccc


and


 


gapfcs3


(SEQ ID No. 25)


gagaccgaggagagggttagggataggcttaccttcgaagggccctctag


actcgatcgagcggccgctcatttacccggagacagggagagctc ttc.






100 μg of Xhol cleaved vector pYD1CH12 and 100 μg of insert are mixed and transformed in Saccharomyces strain EBY100 (Invitrogen) using the Lithium acetate procedure according to the following protocol, which is upscaled by a factor 100 to transform the required amount of cells and of DNA. Briefly, for a single transformation of 1 μg vector DNA and 1 μg insert DNA, 10 ml of YPD (2% peptone, 2% dextrose (D-glucose)) are inoculated with a yeast colony and shaken overnight at 30° C. The OD600 of the overnight culture is determined and the culture diluted to an OD600 of 0.4 in 50 ml of YPD and grown for an additional 2-4 hours. Cells are pelleted at 2500 rpm and resuspended in 40 ml 1× TE (10 mM Tris, pH 7.5, 1 mM EDTA). Cells are pelleted again at 2500 rpm and resuspended in 2 ml of 1 M LiAc/0.5× TE, followed by incubation at room temperature for 10 minutes. 1 μg vector DNA, 1 μg insert and 100 μg denatured sheared salmon sperm DNA (2 mg/ml) are mixed with 100 μl of the yeast suspension. 700 μl of 1 M LiAc/40% PEG-3350/1× TE are added and mixed with the yeast/DNA suspension, followed by incubation at 30° C. for 30 minutes. 88 μl DMSO are added, mixed and the mixture is incubated at 42° C. for 7 minutes, followed by centrifugation in a microcentrifuge for 10 seconds. The supernatant is then removed, the cell pellet is resuspended in 1 ml 1× TE and re-pelleted. The pellet is then resuspended in 50-100 μl TE and plated on minimal dextrose plates containing leucine (10 g/l yeast nitrogen base, 20 g/l dextrose, 0.1 g/l leucine, 15 g/l agar). After incubation of the plates at 30° C. for 2 to 4 days single colonies appeared that are subsequently harvested.
As a source of insert for the vector pYD1dX_dCH1dCH3, Fcab libraries listed in Table 3 are used. These libraries are prepared by standard DNA synthesis, and contain randomized residues as well as inserted residues in the AB loop, and the CD loop, as well as in the EF loop of the CH3 domain of human IgGI (see Table 3). From this synthetic DNA, the insert for gap repair in yeast is amplified by PCR using the oligos YCH3.25rec.back and YCH3.25rec.opt.for (primers used listed below). The basic transformation mix comprises 2 μg of Xhol-cleaved pYD1dX_dCH1dCH3_Fcab_wt and 1 μg of insert DNA, which are mixed and transformed in Saccharomyces strain EBY100 (Invitrogen) using the Lithium acetate procedure, which is upscaled by a factor 100 to get the required amount of transformants. Briefly, for a single transformation of 2 μg vector DNA and 1 μg insert DNA, 10 ml of YPD (2% peptone, 2% dextrose (D-glucose)) are inoculated with a yeast colony and shaken overnight at 30° C. The OD600 of the overnight culture is determined and the culture diluted to an OD600 of 0.3 in 50 ml of YPD and grown for an additional 6 hours or OD600 of 2.5. Cells are pelleted at 2500 rpm, washed twice: first, with 25 ml distilled water and then with 100 mM LiAc; and finally resuspended in 50 OuL 10 OmM LiAc. 2 μg vector DNA, 1 μg insert and 100 μg denatured sheared salmon sperm DNA (2 mg/ml) are mixed with 50 μl of the yeast in a solution containing PEG3500 (33% w/v) and 10 OmM LiAc in a final volume of 360 μL. After a good homogenization the yeasts are kept at 30° C. for 30 minutes and then at 42° C. for 45 minutes. The supernatant is then removed and the cell pellet is resuspended in YPD and the cells are allowed to recover for another 60-90 minutes at 30° C. The pellet is then incubated in selective media (plates and/or liquid, see below) at 30° C. for 2 days. The diversity of the library is determined by the number of single cells grown up to colonies on plates which have been prepared and inoculated immediately after the recovery period.








List of Primers:



a) CH3seqs/2 (SEQ ID No. 429): 5′-AAGGAGTACAAGTGCAAGG-3′


 


b) reverse primers:


CDmut_back (SEQ ID No. 430): 5′-GCT CTC CCA CTC CAC G-3′


EFmut_back (SEQ ID No. 431): 5′-CAC GGT GAG CTT GCT GTA GAG-3′


ABMUT5/2_back (SEQ ID No. 432): 5′-CTCATCCCGGGATGGG-3′


 


c) Forward primers (X = trinucleotide − synthesis for randomized


aminoacids)


CDmut5cod_for (SEQ ID No. 433):


5′-GTG GAG TGG GAG AGC X X X X X AAC AAC TAC AAG ACC ACG-3′


EFMUT7cod_for (SEQ ID No. 434):


5′-AGC AAG CTC ACC GTG X X X X X X X GGG AAC GTC TTC TCA TGC-3′


EFMUT3+2_for (SEQ ID No. 435):


5′-AGC AAG CTC ACC GTG X X X AGG TGG X X GGG AAC GTC TTC TCA TGC-3′


ABMUT5 (wt)_for (SEQ ID No. 436):


5′-CCA TCC CGG GAT GAG X X X X X GTC AGC CTG ACC TGC CTG G-3′


 


d) CH3seqAS (SEQ ID No. 437):


5′-TAGAATCGAGACCGAGG-3′


e)YCH3.25rec.opt.for (SEQ ID No. 438):


5′-A CCA TCT CCA AGG CCA AGG-3′


 


f)Ych3.25rec.back (SEQ ID No. 439):


5′-AAG GGC CCT CTA GAC TCG-3′






Cultivation—Induction
The harvested yeast libraries (yFcab libaries) are inoculated in 10 ml SD-CAA medium (10 g/l yeast nitrogen base, 10 g/l casamino acids, and 20 g/l dextrose, 0.1 g/l leucine, 9.67 g/l NaH2PO4-2H2O and 10.19 g/l Na2HPO4-7H2O) and grown on a shaker at 250 rpm at 28° C. for 6-8 hours. The OD600 of the culture is determined, and the culture is diluted to an OD600 of 0.2, and grown under the same conditions until an OD600 of 1-2 is reached. Cells are harvested by centrifugation (3000 rpm/5 min/4° C.) and resuspended in induction medium SG/R-CAA (10 g/l yeast nitrogen base, 10 g/l casamino acids, and 20 g/l galactose, 10 g/l raffinose, 0.1 g/l leucine, 9.67 g/l NaH2PO4-2H2O and 10.19 g/l Na2HPO4-7H2O). Cultures are induced by incubation for 2 days on a shaker at 250 rpm at 20° C. and subsequently analysed and sorted. Alternatively, cultures were induced by incubation for 1 day on a shaker at 250 rpm at 37° C. and subsequently analysed and sorted.
Quality Control of yFcab Libraries
yFcab libraries are tested for their expression level and quality of expressed Fcab's two days after induction with SD-CAA medium. The expression level is tested using a polyclonal anti human IgG-Fc antiserum (Sigma). For this purpose 0.5×10e6 library cells are diluted in 1 ml staining buffer (SB), which comprises of PBS with 2% BSA. Cells are pelleted and stained with 100 μl SB containing 1/2000 diluted anti human IgG-Fc-PE antiserum (Sigma) for 30 min on ice, washed twice with SB and subsequently analyzed in the FACS. In general 70%-80% of all cells in each library express Fcabs on their cell surface. To test correct folding of Fcabs, staining with Protein A is performed. Again 0.5×10e6 library cells are diluted in 1 ml staining buffer SB, cells are pelleted and stained with 100 μl SB containing 1 μg/ml Prot-A-FITC (Fluka) for 30′ on ice, washed twice with SB and subsequently analyzed in the FACS. In general, the yFcab libraries as described above show >40% Prot A positive cells.
In order to test whether the Fcabs are expressed as dimers on the surface of the cells a staining with human CD64 is performed. 5×10e5 cells are pelleted and stained 30 min on ice with 50 μl SB containing 1 μg/ml CD64 (R&D Systemns). After a washing step, cells are resuspended in 50 μl SB containing 1 μg/ml Penta His Alexa Fluor 488 (QIAgen) and incubated another 30′ on ice. The cells are washed and resuspended in 200 μl ice cold SB for FACS analysis. As control the cells are incubated with equivalent of the Penta His Alexa Fluor 488, without pre-incubation with CD64. After incubation the cells are washed once with ice cold SB and analysed in the FACS. In general, >50% of all cells in each library express dimeric Fcabs on their cell surface.
Biotinylation of Antigen (Her2)
Recombinant antigen e.g. Her2 (Bendermedsystems) was done with he EZ link system of Pierce according to the manufacturers instruction. In short, the antigen is dialyzed against PBS, diluted to 1 mg/ml in PBS and mixed with 10 mM sulfo-LC-LC-biotin (EZ link, Pierce), which was predisolved in water. The final ratio between antigen and biotin is 1:3 and the mixture is incubated at room temperature from 30′. Afterwards the mixture is “dialyzed” against PBS using Vivaspin MWCO3000 (Sartorius) columns (5×8′, 4000 rpm). Finally the concentration of the biotinylated antigen (Her2) is tested by HPLC and aliquots are stored at −20° C.
The quality of the biotinylated antigen is tested by ELISA. First the plates are coated with an anti-Her2 antibody (e.g. Herceptin) at 10 μg/ml in PBS, 100 μl/well overnight at 4° C., after this the plate is washed 3× with washing buffer (WB)(PBS+0.05% Tween20) and blocked by blocking buffer (BB) (PBS+2% BSA) 1 h at room temperature. After 3× washing with WB, different concentrations of Her2-biotin are added in 100 μl/well BB for 1 h at room temperature, followed by 3× washing with WB. Finally the plate is incubated with 1:25000 streptavidin-HRP (GE healthcare) in BB for 1 h at room temperature and washed 3× with WB. Colour is developed by adding 100 μl/well of the substrate TMB (Sigma) after −10 minutes the reaction is stopped by adding 100 μl/well of 30% H2SO4. The results is analysed with an ELISA reader at 450-630 nm.
Example 6
Production of Antigen Specific (Her2) Fcabs
Selection of Antigen Specific (Her2) Fcabs using FACS
First Selection Round:
Two days before FACSorting a yeast library containing 2.5×10e 8 individual Fcab clones is induced with SG/R-CAA medium to express the Fcabs on their cell surface as described above. After two days, the amount of cells covering e.g. 10 times the library (=2.5×10e9) is incubated for 30′ on ice with 500 nM biotinylated antigen (Her2) in 2 ml SB. Then the cells are washed once with cold SB and subsequently incubated for 30′ on ice with streptavidin-PE (from R&D systems) diluted 1:100 in SB. The cells are washed twice with ice cold SB and diluted to an end concentration of 1×10e9 cells/ml. Control stainings with 5×10e6 cell/ml in 100 μl are made with streptavidin-PE only, in the absence of antigen. Both the complete library and the control stainings are analysed in e.g. a FACS ARIA from BD. To set the gates for sorting the control cells are used. First a FSC/SSC gate (G1) is set to identify healthy yeast cells, from G1 a FSC-width versus FSC-area plot is made and only non-aggregating cells are selected in a new gate (G2). Cells in G2 are subsequently analysed for reactivity with streptavidin-PE using FSC versus FL-2 (PE channel). G3 is set to include 0.1% of (false) positive cells. Subsequently, at least 5×10e8 stained cells (twice the library size ideally more) are analysed with the settings as indicated above and the cells in G3 are sorted into a tube containing 2-3 ml SD-CAA medium. Roughly 5×10e5 cells (Pool1) are harvested in the first round of selection and propagated for 1 to 2 days, after which the cells can be stored at −80° C. and aliquots can be induced to express the Fcabs as described above. After two more days the next selection round can take place.
Second Selection Round:
Pool1 selected in round 1 are induced to express the Fcab on their surface as described above. At least 5×10e6 cells (comprising multiple copies of Pool1) are incubated for 30′ on ice with 500 nM biotinylated antigen (Her2) in 1 ml SB. Then the cells are washed once with cold SB and subsequently incubated for 30 min on ice with streptavidin-PE (from R&D systems) diluted 1 in 100 in SB together with 2 μg/ml Protein A-FITC (Fluka). Next the cells are washed twice with ice cold SB and diluted to an end concentration of about 2×10e6 cells/ml. In addition, control stainings are made in which 5×10e6 cells/ml of PooM in 100 μl cells are incubated with a mixture of Prot A and streptavidin-PE as indicated above, but without the incubation with the antigen (Her2). In addition, 5×10e5 cell in 100 μl of a yeast clone expressing Fcab wt non randomized Fc fragment) is stained with Prot A—FITC as described above in the absence of streptavidin-PE. Fcab-wt expressing cells are analysed in e.g. a FACS ARIA from BD to set gates for sorting. First a FSC/SSC gate (G1) is set to identify healthy yeast cells, from G1 a FSC-width versus FSC-area plot is made and only non aggregating cells are selected in new gate (G2). Cells in G2 are subsequently analysed for Protein A expression using FSC versus FL-1 (FITC). G3 is set to cover strong Prot A positive cells (50-60% of parent gate) and G4 is set to cover weak Prot A positive cells (20-30% of parent cells). G3+G4 will include roughly 70-80% of all cells in G2. Now the Pool cells stained for streptavidin-PE in the presence of Prot A-FITC are used to set the rest of the sorting gates. First G1 and G2 are checked with the Pool cells and if necessary adjusted. Pool cells will have lesser events in G3 and maybe also in G4 indicating that not all cells in PooM express Fcabs that are folded as the Fcab-wt. Using the control stained Pool cells a new gate is prepared both for G3 and G4. The new gates are set in a plot FSC and FL-2 (PE). Gate (G5) is prepared that includes 0.1% (false) streptavidin positive cells in G3 and the same is done for cells in G4 resulting in G6. In the next step at least 5×10e6 cells stained for Her2-biotin+streptavidin-PE and Prot A-FITC are sorted by the FACS-ARIA. Cells are collected from G5 (Pool2.1 and G6 (Pool2.2) in separate tubes containing 2-3 ml yeast culture medium. Between 10 and 1000 clones can be expected from both gates. Both new pools are propagated for 1 or 2 days and stored at −80° C. Cells from 2.1 and 2.2 may be either used for direct further sorting in a third round or they may be subjected, (preferably after mixing the two clone together again) to a round of additional randomization of the AB loop (affinity maturation) before they are further sorted in FACS.
Affinity Maturation for Selected Clones/Pools
For affinity maturation, diversity is introduced in selected clones or in pools of selected clones preferably in one loop only, here the AB loop. For this purpose, a PCR was made with a primer that contained degenerate codons at positions 359, 360 and 361 (EU numbering) (primer Abmut, gaaccacaggtgtacaccctgcccccatcccgggatgagctgnnbnnbnnbcaggtcagcctgacctgcc tggtcaaag, SEQ ID No.26), or alternatively with a primer that contained degenerate codons at positions 358, 359, 360,361 and 362 (EU numbering) (primer Abmut2LR, gaaccacaggtgtacaccctgcccccatcccgggatgagnnbnnbnnbnnbnnbgtcagcctgacctgcctggtca aag, SEQ ID No.27).
The second primer used in these PCRs is gapfcs3 in both cases. In order to create flanking sequences for efficient gap repair in yeast, the resulting PCR products were further amplified with the primer pair gapch35 and gapfsc3 and subsequently transformed in Saccharomyces cerevisiae strain EBY100 by Lithiumacetate transformation together with Xhol cleaved pYD1 CH12 as described above. As alternative primers for randomization of the described residues in the AB loop, primers such as Abmuti L (gaaccacaggtgtacaccctgcccccatcccgggatgagnnbnnbnnbnnbcaggtcagcctgacctgcctggtca aag, SEQ ID No.28) or Abmuti R (gaaccacaggtgtacaccctgcccccatcccgggatgagctgnnbnnbnnbnnbgtcagcctgacctgcctggtca aag, SEQ ID No.29) were also used used. In an analogous manner, residues in the EF loop were randomized by total randomization.
Alternatively randomization was performed using spiked oligonucleotides as primers on the individual clone y-Her.C2.P4.2-9. In this case the oligos were designed similar to the before mentioned for complete randomization of the respective loops, however the randomized part contained 70% of the original base in the first and second position of the codon and 10% of each of the other 3 nucleotides. The third position was containing 70% of the original base and 30% of the base according to the NNK or NNS codon.
The Abmut primer resulted in 8000 new variants (Pool2.3) of each clone and the Abmut2LR primer lead to 3×10e6 new variants (Pool2.4) upon complete randomization. Therefore Pools 2.3 and 2.4 both resulted in new libraries of approximately 10e8 individual since the starting material (Pool2.1+2.2) already contained approximately 10-1000 clones.
Third Selection Round
Affinity matured pools 2.3 and 2.4 and if necessary Pool2.1 (only the Prot A positive cells are preferred) were induced to express Fcabs on their cell surface as described above and subsequently sorted as described for “Second selection round”, with exception that the Pools 2.3 and 2.4 are much bigger and therefore staining volumes for the pools are equal to those of the library staining described in “First selection round”. In the third selection round, only Her2 positive/Prot A positive cells were sorted. Pools derived from these selections contained typically >20% Her2/Prot A positive cells. If not then a fourth and fifth (or even more) round(s) of selection for Her2 together with or also without protein A were performed. For example, affinity maturation of the H242-9Q clone yielded an increase in the binding affinity from EC50=155 nM to 18.9 nM (H10-03-6 clone).
Clone Analyses:
Individual clones from pools containing Her2/Prot A cells (>20% is preferred) were prepared either by plating the pools on agar plates with SD-CAA medium or by spotting the singles cells (=clones) directly from the FACS ARIA onto the plates without generating a pool. Clones are allowed to grow and are transferred to liquid cultures and stored in −80° C. Aliquots of the clones were subsequently induced to express Fcabs on their cell surface as described above and screened for a number of parameters in the FACS. These parameters were: a dose response range of the antigen used for selection (Her2) with and without the presence of Prot A-FITC, CD64 staining as described above. In addition using similar staining protocols a number of irrelevant biotinylated antigen was screened to identify non-cross reacting Fcabs.
It was observed that, after several rounds of selecting antigen (Her2)+Prot A positive cells, a large percentage of clones show >25% antigen (Her2) positivity when stained with 500 nM antigen (Her2) and >70% Prot A positivity when stained with 2 μg/ml Prot A-FITC. In most of the cases these clones also showed >50% CD64 binding. Thus this reflects the Prot A and CD64 staining levels of non-randomized Fc fragments (Fcab wt) expressed on yeast.
Clones selected as described above with characteristics as described above were produced as soluble molecules. This was done mainly by transient transfection but also by stable transfection of the Fcab DNA into new host cells. For this purpose the DNA from individual yeast clones was isolated using standard procedures. The relevant DNA coding for the complete CH3 domain or only the part of the CH3 domain that is randomized in the library was amplified by PCR and transferred into a new expression vector containing the missing part of the Fcab and a suitable promoter and one of more selection markers such as G418, that allows selection of transfected cells out of a pool of non transfected cells. The new vector was then transiently transfected into a new host cell such as HEK293 or CHO. The host cells were allowed to recover and were subsequently cultured for up to 10 days. The supernatant of the cultures which contain the soluble Fcab was used for further testing after purification over Prot A. Stable cell lines can also be made by standard procedures.







TABLE 4







Sequences of selected Her2 binding yeast clones from initial


libraries, after pool expansion and after affinity maturation:


with reference to numbering of SEQ ID No. 1 (FIG. 3)


(CD loop: AA169ffNGQPE)










AB loop
EF Loop


Clone name
AA143ff
AA198ff





Fcab wt
LTKNQ (SEQ ID No. 30)
---DKSRWQQ


 


y-Her.C2-P3.1-1
LDNSQ (SEQ ID No. 31)
IRSSVGSRRWWS (SEQ ID No. 51)


 


y-Her.C2-P3.1-3
YEGSS (SEQ ID No. 32)
ARYSPRMLRWAH (SEQ ID No. 52)


 


y-Her.C2-P3.1-5
YMSAD (SEQ ID No. 33)
SRRDSSLLRWAH (SEQ ID No. 53)


 


y-Her.C2-P3.1-6
YRRGD (SEQ ID No. 34)
APGSKGYRRWAL (SEQ ID No. 54)


 


y-Her.C2-P3.1-8
LMSRQ (SEQ ID No. 35)
DKPFWGTSRWSE (SEQ ID No. 55)


 


y-Her.C2-P3.1-16
LHLAQ (SEQ ID No. 36)
SINDLINHRWPY (SEQ ID No. 56)


 


y-Her.C2-P3.1-18
YLSKD (SEQ ID No. 37)
MWGSRDYWRWSH (SEQ ID No. 57)


 


y-Her.C2-P3.2-3
YRSGS (SEQ ID No. 38)
NSGSAMMVRWAH (SEQ ID No. 58)


 


y-Her.C2-P3.2-9
LRDGQ (SEQ ID No. 39)
QRSRLSRQRWWR (SEQ ID No. 59)


 


y-Her.C2-P4.2-3
YSANT (SEQ ID No. 40)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-4
YASNT (SEQ ID No. 41)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-5
YSGGS (SEQ ID No. 42)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-6
YGRDS (SEQ ID No. 43)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-8
YAGGT (SEQ ID No. 44)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-10
YSSDS (SEQ ID No. 45)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-12
YHSGS (SEQ ID No. 46)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-15
YLTNS (SEQ ID No. 47)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-18
YGSEE (SEQ ID No. 48)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-19
YRSGE (SEQ ID No. 49)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-20
YGTDD (SEQ ID No. 50)
ARYSPRMLRWAH (SEQ ID No. 60)


 


y-Her.C2-P4.2-9
YLHGD (SEQ ID No. 161)
ARYSPRMLRWAH (SEQ ID No. 60)


 


HAF1311A1
YLHGD (SEQ ID No. 161)
VSRYSMTMWRWAH (SEQ ID No. 61)


 


HAF1311A10
YLHGD (SEQ ID No. 161)
VSRYSRSMMRWAH (SEQ ID No. 62)


 


HAF1311A11
YLHGD (SEQ ID No. 161)
VPRYSQMMWRWAH (SEQ ID No. 63)


 


HAF1311A12
YLHGD (SEQ ID No. 161)
ITRYSRQMLRWAH (SEQ ID No. 64)


 


HAF1311A2
YLHGD (SEQ ID No. 161)
VPRYSALMWRWAH (SEQ ID No. 65)


 


HAF1311A3
YLHGD (SEQ ID No. 161)
VARHSEAMWKWGH (SEQ ID No. 66)


 


HAF1311A4
YLHGD (SEQ ID No. 161)
VGRYSQRMWRWAH (SEQ ID No. 67)


 


HAF1311A5
YLHGD (SEQ ID No. 161)
VARYSPTMWRWAH (SEQ ID No. 68)


 


HAF1311A6
YLHGD (SEQ ID No. 161)
VGRHSPTMWRWAH (SEQ ID No. 69)


 


HAF1311A7
YLHGD (SEQ ID No. 161)
LGRWSPKMWRWAH (SEQ ID No. 70)


 


HAF1311A8
YLHGD (SEQ ID No. 161)
VARWSPSMWRWAH (SEQ ID No. 71)


 


HAF1311A9
YLHGD (SEQ ID No. 161)
VARNSPSMWRWAH (SEQ ID No. 83)


 


HAF1311B1
YLHGD (SEQ ID No. 161)
VARWSPSMVRWAH (SEQ ID No. 84)


 


HAF1311B10
YLHGD (SEQ ID No. 161)
VARKNMRKWRRTH (SEQ ID No. 85)


 


HAF1311B12
YLHGD (SEQ ID No. 161)
VSRYSPTMWQWAH (SEQ ID No. 68)


 


HAF1311B2
YLHGD (SEQ ID No. 161)
VARYSQTNWRWAH (SEQ ID No. 87)


 


HAF1311B3
YLHGD (SEQ ID No. 161)
MPRFSPSMWRWAH (SEQ ID No. 88)


 


HAF1311B4
YLHGD (SEQ ID No. 161)
VTRYSQSMWRWAH (SEQ ID No. 89)


 


HAF1311B5
YLHGD (SEQ ID No. 161)
IERYSTRMWSWAH (SEQ ID No. 90)


 


HAF1311B6
YLHGD (SEQ ID No. 161)
VARHSPEMWHWAH (SEQ ID No. 91)


 


HAF1311B7
YLHGD (SEQ ID No. 161)
VARGSPSMWSWGH (SEQ ID No. 92)


 


HAF1311B8
YLHGD (SEQ ID No. 161)
VARHSQTMWRWAH (SEQ ID No. 93)


 


HAF1311B9
YLHGD (SEQ ID No. 161)
LARYSPGMWRWAH (SEQ ID No. 94)


 


HAF1311B1
YLHGD (SEQ ID No. 161)
VPRFSPTMWKWAH (SEQ ID No. 95)


 


HAF1311C1
YLHGD (SEQ ID No. 161)
VPRWSRTMLRWAH (SEQ ID No. 96)


 


HAF1311C10
YLHGD (SEQ ID No. 161)
VPRWSRTMLRWAH (SEQ ID No. 97)


 


HAF1311C11
YLHGD (SEQ ID No. 161)
VPRYSPRMWRWAH (SEQ ID No. 98)


 


HAF1311C2
YLHGD (SEQ ID No. 161)
IARHSKSMWSWAH (SEQ ID No. 99)


 


HAF13112C3
YLHGD (SEQ ID No. 161)
MPRWSKSLSGWAH (SEQ ID No. 100)


 


HAF1311C5
YLHGD (SEQ ID No. 161)
VARYTPSMWRWAH (SEQ ID No. 101)


 


HAF1311C7
YLHGD (SEQ ID No. 161)
VARNSLTMWRWAH (SEQ ID No. 102)


 


HAF1311C8
YLHGD (SEQ ID No. 161)
VARYSPSMWKWAH (SEQ ID No. 103)


 


HAF1311C9
YLHGD (SEQ ID No. 161)
VARFSPSMWRWAH (SEQ ID No. 104)


 


HAF1311D2
YLHGD (SEQ ID No. 161)
LARWSPSLSRWAH (SEQ ID No. 105)


 


HAF1311D3
YLHGD (SEQ ID No. 161)
VARYSPSMWRWAH (SEQ ID No. 106)


 


HAF1311D4
YLHGD (SEQ ID No. 161)
VPRSSLTMWKWAH (SEQ ID No. 107)


 


HAF1311D5
YLHGD (SEQ ID No. 161)
VPRHSTRMWKWAH (SEQ ID No. 108)


 


HAF1311D6
YLHGD (SEQ ID No. 161)
VPRHSRRMWRWAH (SEQ ID No. 109)


 


HAF1311D7
YLHGD (SEQ ID No. 161)
VTRYSPSMWRWAH (SEQ ID No. 110)


 


HAF1311E10
YLHGD (SEQ ID No. 161)
VPRHSRRMWRWAH (SEQ ID No. 109)


 


HAF1311E2
YLHGD (SEQ ID No. 161)
MPRWSKSLSGWAH (SEQ ID No. 100)


 


HAF1311E3
YLHGD (SEQ ID No. 161)
VTRHSSSMWRWAH (SEQ ID No. 111)


 


HAF1311E4
YLHGD (SEQ ID No. 161)
VARYSRSMKKWAH (SEQ ID No. 112)


 


HAF1311E5
YLHGD (SEQ ID No. 161)
VARGSTTMWRWAH (SEQ ID No. 113)


 


HAF1311E6
YLHGD (SEQ ID No. 161)
VARSSPEMWRWAH (SEQ ID No. 114)


 


HAF1311E7
YLHGD (SEQ ID No. 161)
VARYSTGMWNWAH (SEQ ID No. 115)


 


HAF1311E8
YLHGD (SEQ ID No. 161)
VPRYSQRMWRWAH (SEQ ID No. 116)


 


HAF1311E9
YLHGD (SEQ ID No. 161)
VPRNSPRMWRWAH (SEQ ID No. 117)


 


HAF1312F1
YLHGD (SEQ ID No. 161)
LARWSPSMSRWAH (SEQ ID No. 118)


 


HAF1312G12
YLHGD (SEQ ID No. 161)
LARWSPSMKSWAH (SEQ ID No. 119)


 


HAF1312F11
YLHGD (SEQ ID No. 161)
LPRYSTKMKRWAH (SEQ ID No. 120)


 


HAF1312F7
YLHGD (SEQ ID No. 161)
IPRWSQQMSRWAH (SEQ ID No. 121)


 


HAF1312F3
YLHGD (SEQ ID No. 161)
VGRWTPSMWRWAH (SEQ ID No. 122)


 


HAF1312F5
YLHGD (SEQ ID No. 161)
VGRWTPSMWRWAH (SEQ ID No. 123)


 


HAF1312G10
YLHGD (SEQ ID No. 161)
VKRSSPSMWRWAH (SEQ ID No. 124)


 


HAF1312G2
YLHGD (SEQ ID No. 161)
VARFSPSMWRWAH (SEQ ID No. 104)


 


HAF1312G1
YLHGD (SEQ ID No. 161)
LARYSPGMWNWAH (SEQ ID No. 125)


 


HAF1312G9
YLHGD (SEQ ID No. 161)
IARYSPNMWNWAH (SEQ ID No. 126)


 


HAF1312G8
YLHGD (SEQ ID No. 161)
IARYSPSMWRWAH (SEQ ID No. 127)


 


HAF1312F12
YLHGD (SEQ ID No. 161)
VARFSPSMLKWAH (SEQ ID No. 128)


 


HAF1312F2
YLHGD (SEQ ID No. 161)
VARYSKSMLKWAH (SEQ ID No. 129)


 


HAF1312F10
YLHGD (SEQ ID No. 161)
VARHSRTMWRWGH (SEQ ID No. 130)


 


HAF1312G7
YLHGD (SEQ ID No. 161)
IARHSREMLRWAH (SEQ ID No. 131)


 


HAF1312F8
YLHGD (SEQ ID No. 161)
VARYSSTMSRWAH (SEQ ID No. 132)


 


HAF1321A1
YLHGD (SEQ ID No. 161)
VPRYSQRMWRWAH (SEQ ID No. 116)


 


HAF1321B11
YLHGD (SEQ ID No. 161)
VPRYSQMMWRWAH (SEQ ID No. 63)


 


HAF1321A2
YLHGD (SEQ ID No. 161)
VPRYSPRMWRWAH (SEQ ID No. 98)


 


HAF1321A10
YLHGD (SEQ ID No. 161)
IPRWSQQMSRWAH (SEQ ID No. 122)


 


HAF1321A4
YLHGD (SEQ ID No. 161)
VPRHSLKKLQRKH (SEQ ID No. 133)


 


HAF1321B10
YLHGD (SEQ ID No. 161)
VARHSLSMWRWAH (SEQ ID No. 87)


 


HAF1321A5
YLHGD (SEQ ID No. 161)
VARYSPSMWNWAH (SEQ ID No. 134)


 


HAF1321B1
YLHGD (SEQ ID No. 161)
VARYSPTMWKWAH (SEQ ID No. 148)


 


HAF1321A11
YLHGD (SEQ ID No. 161)
VARFSPSMWRWAH (SEQ ID No. 104)


 


HAF1321B5
YLHGD (SEQ ID No. 161)
VSRFSPSMWRWAH (SEQ ID No. 149)


 


HAF1321B2
YLHGD (SEQ ID No. 161)
VGRWTPSMWRWAH (SEQ ID No. 123)


 


HAF1321B6
YLHGD (SEQ ID No. 161)
IARYSPSMWRWAH (SEQ ID No. 127)


 


HAF1321B7
YLHGD (SEQ ID No. 161)
IARYSPSMWRWAH (SEQ ID No. 127)


 


HAF1321B9
YLHGD (SEQ ID No. 161)
IPRYTPSMWRWAH (SEQ ID No. 150)


 


HAF1322C10
YLHGD (SEQ ID No. 161)
IPRWSQQMSRWAH (SEQ ID No. 122)


 


HAF1322C11
YLHGD (SEQ ID No. 161)
VPRHSRRMWRWAH (SEQ ID No. 151)


 


HAF1322C7
YLHGD (SEQ ID No. 161)
LPRHSRRMWRWAH (SEQ ID No. 152)


 


HAF1322C6
YLHGD (SEQ ID No. 161)
LARWSPSMLRWAH (SEQ ID No. 153)


 


HAF1322C3
YLHGD (SEQ ID No. 161)
VARHSLSMWRWAH (SEQ ID No. 87)


 


HAF1322C4
YLHGD (SEQ ID No. 161)
VARHSPAMWRWAH (SEQ ID No. 154)


 


HAF1322C8
YLHGD (SEQ ID No. 161)
VARSSPSMWRWAH (SEQ ID No. 147)


 


H10-03-6
YLHGD (SEQ ID No. 161)
VPRHSARMWRWAH (SEQ ID No. 155)


 


H10-03-6R
YLYGD (SEQ ID No. 161)
VPRHSARMWRWAH (SEQ ID No. 155)


 


H10-03-6Y
YLYGD (SEQ ID No. 161)
VPRYSARMWRWAH (SEQ ID No. 156)


 


ABEFs0101
YLYGD (SEQ ID No. 161)
VARYSPSMWRWGH (SEQ ID No. 135)


 


ABS0101G
YLSAD (SEQ ID No. 161)
VARYSPSMWRWAH (SEQ ID No. 106)


 


ABS0101P
YLSAD (SEQ ID No. 161)
VPRYSASMWRWGH (SEQ ID No. 136)


 


ABS0101PG
YLSAD (SEQ ID No. 161)
VPRYSASMWRWAH (SEQ ID No. 137)


 


EF3-1
YLHGD (SEQ ID No. 161)
LPRYSPGMWRWAH (SEQ ID No. 138)


 


EF3-2
YLHGD (SEQ ID No. 161)
VARYSPSMWNWAH (SEQ ID No. 134)


 


EF3-3
YLHGD (SEQ ID No. 161)
VARYSPSMWRWGH (SEQ ID No. 135)


 


EF3-4
YLHGD (SEQ ID No. 161)
IPRWSQQMSRWAH (SEQ ID No. 122)


 


EF3-6
YLHGD (SEQ ID No. 161)
VARYSQTMSRWAH (SEQ ID No. 139)


 


EF3-7
YLHGD (SEQ ID No. 161)
IARYSPSMWRWAH (SEQ ID No. 127)


 


EF3-8
YLHGD (SEQ ID No. 161)
VAGYRPRRSGSSH (SEQ ID No. 140)


 


EF3-9
YLHGD (SEQ ID No. 161)
LARHSANMKRWAH (SEQ ID No. 141)


 


EF3-13
YLHGD (SEQ ID No. 161)
VARHSPSMWSWAH (SEQ ID No. 124)


 


EF3-14
YLHGD (SEQ ID No. 161)
VARYTPSMWRWAH (SEQ ID No. 101)


 


EF3-15
YLHGD (SEQ ID No. 161)
VARWSPSMFRWAH (SEQ ID No. 143)


 


EF3-16
YLHGD (SEQ ID No. 161)
LARWSPSMFRWAH (SEQ ID No. 119)


 


EF3-17
YLHGD (SEQ ID No. 161)
VARHSRTMWRWGH (SEQ ID No. 130)


 


EF3-18
YLHGD (SEQ ID No. 161)
LARWSPSMSRWAH (SEQ ID No. 118)


 


EF3-20
YLHGD (SEQ ID No. 161)
VARWSPSMLRWAH (SEQ ID No. 144)


 


EF10-01
YLHGD (SEQ ID No. 161)
VARSSPTMWRWAH (SEQ ID No. 145)


 


EF10-02
YLHGD (SEQ ID No. 161)
VARYSPSMWRWAH (SEQ ID No. 106)


 


EF10-03
YLHGD (SEQ ID No. 161)
VARWSPSMMRWAH (SEQ ID No. 71)


 


EF10-04
YLHGD (SEQ ID No. 161)
VTRWSPTMMRWAM (SEQ ID No. 146)


 


EF10-07
YLHGD (SEQ ID No. 161)
VARNSPSMWRWAH (SEQ ID No. 83)


 


EF10-08
YLHGD (SEQ ID No. 161)
LARWSPSLSRWAH (SEQ ID No. 105)


 


EF10-09
YLHGD (SEQ ID No. 161)
VARSSPSMWRWAH (SEQ ID No. 147)


 


EF10-10
YLHGD (SEQ ID No. 161)
VARYSPRMWRWAH (SEQ ID No. 157)


 


EF10-13
YLHGD (SEQ ID No. 161)
VARYSRKMSSWGH (SEQ ID No. 158)


 


EF10-14
YLHGD (SEQ ID No. 161)
LASYSPSMWRWGH (SEQ ID No. 159)


 


EF10-15
YLHGD (SEQ ID No. 161)
VARYSPTMKRWAH (SEQ ID No. 160)
















TABLE 5







Sequences of selected Her2 binding yeast clones from initial 


libraries, after pool expansion and after affinity maturation: 


with reference to numbering of SEQ ID No. 1 (FIG. 3)











AB loop
CD loop
EFLoop


Clone name
AA143ff
AA169ff
AA198ff





H542-M3C8
LSLPC
ISGPE
PQTPPSQ



(SEQ ID No. 164)
(SEQ ID No. 240)
(SEQ ID No. 340)


 


H541-M2D7
REGGR
NGQPE
DKPFWGTSRWSR



(SEQ ID No. 165)
(SEQ ID No. 241)
(SEQ ID No. 55)


 


H541-M2E11
LTKNQ
DGRPE
DKPFWGTSRWSR



(SEQ ID No. 166)
(SEQ ID No. 242)
(SEQ ID No. 55)


 


H541-M2D12
TKSFY
NGQPE
PPSPPRT



(SEQ ID No. 167)
(SEQ ID No. 241)
(SEQ ID No. 341)


 


H541-M2H10
TKGL_
NGQPE
PPSPPRT



(SEQ ID No. 172)
(SEQ ID No. 241)
(SEQ ID No. 341)


 


H541-M2H8
TLAFY
NGQPE
PPSPPRT



(SEQ ID No. 167)
(SEQ ID No. 241)
(SEQ ID No. 341)


 


H542-M3A10
WWLFG
NGQPE
PWVRWMQ



(SEQ ID No. 168)
(SEQ ID No. 241)
(SEQ ID No. 342)


 


H542-M3F10
IKKKK
NGQPE
SRARWRH



(SEQ ID No. 169)
(SEQ ID No. 241)
(SEQ ID No. 343)


 


H542-M3D5
KWNKK
NGQPE
SRSRWRG



(SEQ ID No. 170)
(SEQ ID No. 241)
(SEQ ID No. 344)


 


H542-M4A4
KKKKK
NGQPE
PRWKM



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 345)


 


H542-M3G11
YKTKD
NGQPE
KRYNPRMVRWAH



(SEQ ID No. 173)
(SEQ ID No. 241)
(SEQ ID No. 346)


 


H542-M3D9
KKKKK
NGQPE
PQSRWYN



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 347)


 


H542-M3F7
KKKKK
NGQPE
PWSRWRL



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 348)


 


H542-M4B12
RKEKK
NGQPE
PQKRWRS



(SEQ ID No. 174)
(SEQ ID No. 241)
(SEQ ID No. 349)


 


H542-M3D11
WWVGG
DAGPE
PWVRWMQ



(SEQ ID No. 176)
(SEQ ID No. 243)
(SEQ ID No. 342)


 


H542-M3A4
WWRGG
NGQPE
PWVRWLQ



(SEQ ID No. 176)
(SEQ ID No. 241)
(SEQ ID No. 350)


 


H542-M3B8
WWRGG
NGQPE
PWVRWMQ



(SEQ ID No. 177)
(SEQ ID No. 241)
(SEQ ID No. 342)


 


H542-M3C4
YGHKY
NKQNH
PQKRWRS



(SEQ ID No. 178)
(SEQ ID No. 244)
(SEQ ID No. 349)


 


H542-M4D4
TKKET
NGQPE
ELEGEEQ



(SEQ ID No. 179)
(SEQ ID No. 241)
(SEQ ID No. 351)


 


H542-M3A7
TGGNK
NMGPE
NRSRWQQ



(SEQ ID No. 166)
(SEQ ID No. 245)
(SEQ ID No. 352)


 


H542-M3C12
LTKNQ
NGQPE
KKKKLKQ



(SEQ ID No. 166)
(SEQ ID No. 241)
(SEQ ID No. 353)


 


H542-MCE10
LTKNQ
NGQPE
KKKQLKK



(SEQ ID No. 180)
(SEQ ID No. 241)
(SEQ ID No. 354)


 


H542-M3E6
LDGDQ
NGQPE
QQKKRKKKK



(SEQ ID No. 181)
(SEQ ID No. 241)
(SEQ ID No. 355)


 


H542-M4E9
FIPHN
DCGPE
PPPLCAP



(SEQ ID No. 182)
(SEQ ID No. 246)
(SEQ ID No. 356)


 


H542-M4D8
KKKGK
NGQPE
SLNRWKR



(SEQ ID No. 166)
(SEQ ID No. 241)
(SEQ ID No. 357)


 


H542-M4H8
KKKGK
NGQPE
SLNRWKR



(SEQ ID No. 182)
(SEQ ID No. 241)
(SEQ ID No. 357)


 


H542-M4B11
LTKNQ
NGQPE
KNKKKRK



(SEQ ID No. 166)
(SEQ ID No. 241)
(SEQ ID No. 358)


 


H542-M4C10
LTKNQ
MDGPE
KKKKIKK



(SEQ ID No. 166)
(SEQ ID No. 247)
(SEQ ID No. 359)


 


H542-M4F11
LTKNQ
NGQPE
KKKKMKK



(SEQ ID No. 166)
(SEQ ID No. 241)
(SEQ ID No. 360)


 


H542-M4C8
LTKNQ
NGQPE
KRKKLKK



(SEQ ID No. 166)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H542-M4G2
KNKKK
NGQPE
REREWRK



(SEQ ID No. 183)
(SEQ ID No. 241)
(SEQ ID No. 362)


 


H542-M4C7
TKKET
NGQPE
ELEGEEQ



(SEQ ID No. 178)
(SEQ ID No. 241)
(SEQ ID No. 351)


 


H561G3M1B8
KKKNN
YPEKH
DKSRWQQ



(SEQ ID No. 184)
(SEQ ID No. 248)
(SEQ ID No. 363)


 


H542-M4D10
TKKET
NGQPE
ELEGEEQ



(SEQ ID No. 178)
(SEQ ID No. 241)
(SEQ ID No. 351)


 


H542-M4B3
KKKKR
NGQPE
PLRLPPM



(SEQ ID No. 185)
(SEQ ID No. 241)
(SEQ ID No. 364)


 


H542-M4A6
YGHKY
NKQBH
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 244)
(SEQ ID No. 349)


 


H561G3M1C6
LKKKT
NGQPE
PRSNWYGNRWRR



(SEQ ID No. 186)
(SEQ ID No. 241)
(SEQ ID No. 365)


 


H542-M4C1
KKKKK
NGQPE
PQSRWYN



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 347)


 


H542-M4F4
KKKKK
NGQPE
PWSRWRL



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 348)


 


H561G3M1E1
TKGRW
NGAPQ
SRARWRH



(SEQ ID No. 187)
(SEQ ID No. 249)
(SEQ ID No. 343)


 


H542-M4F6
LSLPC
ISGPE
PQTPPSQ



(SEQ ID No. 164)
(SEQ ID No. 240)
(SEQ ID No. 340)


 


H561G3M1A1
KKKKK
NGQPE
TPGNLAL



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 366)


 


H561G3M1A10
KKKKN
NGQPE
SREDFRA



(SEQ ID No. 188)
(SEQ ID No. 241)
(SEQ ID No. 367)


 


H561G3M1A9
KHAET
NGQPE
LVSISVG



(SEQ ID No. 189)
(SEQ ID No. 241)
(SEQ ID No. 368)


 


H561G3M1B10
-KKKK
DYGPM
PSRRWRE



(SEQ ID No. 190)
(SEQ ID No. 250)
(SEQ ID No. 369)


 


H561G3M1G4
FFTYW
NGQPE
DRRRWTA



(SEQ ID No. 191)
(SEQ ID No. 241)
(SEQ ID No. 370)


 


H561G3M1B9
EGKRK
NGQPE
SRARWRH



(SEQ ID No. 192)
(SEQ ID No. 241)
(SEQ ID No. 343)


 


H561G3M1C1
RHGGW
NGQPE
DLQDKKY



(SEQ ID No. 193)
(SEQ ID No. 241)
(SEQ ID No. 371)


 


H561G3M1C2
KKKKK
NGQPE
ISVPPDE



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 372)


 


H561G3M1H8
-KSGY
RKKKW
SRARWRH



(SEQ ID No. 194)
(SEQ ID No. 251)
(SEQ ID No. 343)


 


H561G3M1C8
AKEGG
NGQPE
TGPDITV



(SEQ ID No. 195)
(SEQ ID No. 241)
(SEQ ID No. 373)


 


H561G3M1D1
KYWMA
NGQPE
IVLSGFR



(SEQ ID No. 196)
(SEQ ID No. 241)
(SEQ ID No. 374)


 


H561G3M1D5
KKKNK
DAGPE
MGIHNIN



(SEQ ID No. 188)
(SEQ ID No. 243)
(SEQ ID No. 375)


 


H564G11M2F4
LTKNQ
NGQPE
MKQDEMA



(SEQ ID No. 166)
(SEQ ID No. 241)
(SEQ ID No. 376)


 


H561G3M1E2
FFTYW
NGQPE
DRRRWTA



(SEQ ID No. 191)
(SEQ ID No. 241)
(SEQ ID No. 370)


 


H561G3M1E6
KKKKK
NGQPE
PQWRLQW



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 377)


 


H561G3M1E7
KKKNK
NGQPE
HRRLVAR



(SEQ ID No. 188)
(SEQ ID No. 241)
(SEQ ID No. 378)


 


H561G3M1F10
QLRNK
NGQPE
KQNLRRK



(SEQ ID No. 197)
(SEQ ID No. 241)
(SEQ ID No. 379)


 


H561G3M1F2
QRGRM
KGGRE
SRARWRH



(SEQ ID No. 198)
(SEQ ID No. 252)
(SEQ ID No. 343)


 


H561G3M1G1
QRGRM
KGGRE
SRARWRH



(SEQ ID No. 198)
(SEQ ID No. 252)
(SEQ ID No. 343)


 


H564G11M2F12
KNHNT
NGQPE
SRSRLHGNRWRR



(SEQ ID No. 199)
(SEQ ID No. 241)
(SEQ ID No. 380)


 


H561G3M1H3
KKKKK
GNWQP
NRERWRR



(SEQ ID No. 171)
(SEQ ID No. 253)
(SEQ ID No. 381)


 


H561G3M1H7
MSENE
NGQPE
TWVRWMQ



(SEQ ID No. 200)
(SEQ ID No. 241)
(SEQ ID No. 382)


 


H564G11M2G2
KKKNK
TTGPY
PWSRWRL



(SEQ ID No. 188)
(SEQ ID No. 254)
(SEQ ID No. 348)


 


H564G11M2A10
KKKNK
NGQPE
PHWQWKW



(SEQ ID No. 188)
(SEQ ID No. 241)
(SEQ ID No. 383)


 


H564G11M2A4
YGHKY
DMNQP
SKKKLRK



(SEQ ID No. 177)
(SEQ ID No. 255)
(SEQ ID No. 384)


 


H564G11M2A5
YGHKY
KWPMF
PWKELEK



(SEQ ID No. 177)
(SEQ ID No. 256)
(SEQ ID No. 385)


 


H564G11M22A9
WWMDY
NGQPE
KEKKLKK



(SEQ ID No. 201)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H564G11M2B1
YGHKY
HDQRH
TQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 257)
(SEQ ID No. 386)


 


H564G11M2B12
MKKNK
LGMYM
PQKRWRS



(SEQ ID No. 202)
(SEQ ID No. 258)
(SEQ ID No. 349)


 


H564G11M2B3
YGHKY
NKMFT
NRKHLRA



(SEQ ID No. 177)
(SEQ ID No. 259)
(SEQ ID No. 387)


 


H564G11M2B4
EYFRH
NGQPE
TRRRWTR



(SEQ ID No. 203)
(SEQ ID No. 241)
(SEQ ID No. 388)


 


H564G11M2B5
KKKNK
NGQPE
DHRRINR



(SEQ ID No. 188)
(SEQ ID No. 241)
(SEQ ID No. 389)


 


H564G11M2B7
FDMRD
NGQPE
KRKKLKK



(SEQ ID No. 204)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H564G11M2C1
MKKPY
LGYPE
KKKKYHK



(SEQ ID No. 205)
(SEQ ID No. 260)
(SEQ ID No. 390)


 


H564G11M2C11
KKKNN
HGYQL
PWVRWMQ



(SEQ ID No. 184)
(SEQ ID No. 261)
(SEQ ID No. 345)


 


H564G11M2C3
YGHKY
NVFIE
QKKKLKK



(SEQ ID No. 177)
(SEQ ID No. 262)
(SEQ ID No. 391)


 


H564G11M2C7
FEMPY
NGQPE
KRKKLKK



(SEQ ID No. 206)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H564G11M2C9
YGHKY
NRGWH
PQKKLRK



(SEQ ID No. 177)
(SEQ ID No. 263)
(SEQ ID No. 392)


 


H564G11M2D1
KKKNH
PFTLK
DKRGIRK



(SEQ ID No. 207)
(SEQ ID No. 264)
(SEQ ID No. 393)


 


H564G11M2D10
FFTYW
NGQPE
DRRRWTA



(SEQ ID No. 191)
(SEQ ID No. 241)
(SEQ ID No. 370)


 


H564G11M2D4
-KKKK
DYGPM
PSRRWRE



(SEQ ID No. 190)
(SEQ ID No. 250)
(SEQ ID No. 369)


 


H564G11M2D9
YGHKY
STTRV
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 265)
(SEQ ID No. 349)


 


H564G11M2E10
KKKNH
WDQHQ
EKKRWKE



(SEQ ID No. 207)
(SEQ ID No. 266)
(SEQ ID No. 394)


 


H564G11M2E11
-KKKK
DYGPM
TSRRWRE



(SEQ ID No. 190)
(SEQ ID No. 250)
(SEQ ID No. 395)


 


H564G11M2E3
YGHKY
SGWMM
KKEKLRK



(SEQ ID No. 177)
(SEQ ID No. 267)
(SEQ ID No. 396)


 


H564G11M2E8
YGHKY
WRKMT
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 268)
(SEQ ID No. 349)


 


H564G11M2H10
YGHKY
FPKKY
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 269)
(SEQ ID No. 349)


 


H564G11M2F2
MWEPS
NGQPE
KKKKLKK



(SEQ ID No. 208)
(SEQ ID No. 241)
(SEQ ID No. 397)


 


H564G11M2F5
LRGST
SYYFV
KKKKIMK



(SEQ ID No. 209)
(SEQ ID No. 270)
(SEQ ID No. 398)


 


H564G11M2F6
KKKKK
IRGTS
DQTRWRR



(SEQ ID No. 171)
(SEQ ID No. 271)
(SEQ ID No. 399)


 


H564G11M2F7
DSYMI
NGQPE
TWVRWMQ



(SEQ ID No. 210)
(SEQ ID No. 241)
(SEQ ID No. 382)


 


H564G11M2F9
YGHKY
QVPGW
KKKEIKK



(SEQ ID No. 177)
(SEQ ID No. 272)
(SEQ ID No. 400)


 


H564G11M2G4
YGHKY
DLPYQ
KKNKLKK



(SEQ ID No. 177)
(SEQ ID No. 273)
(SEQ ID No. 401)


 


H564G11M2G6
YGHKY
PRSHW
PQKRWRS



(SEQ ID No. 188)
(SEQ ID No. 274)
(SEQ ID No. 349)


 


H564G11M2G7
KKKNK
LYGHA
NRERWRR



(SEQ ID No. 188)
(SEQ ID No. 275)
(SEQ ID No. 381)


 


H564G11M2G9
KKKNK
NGQPE
PWWQFRQ



(SEQ ID No. 188)
(SEQ ID No. 241)
(SEQ ID No. 402)


 


H564G11M2H2
YGHKY
APYVH
KKKEIKK



(SEQ ID No. 177)
(SEQ ID No. 279)
(SEQ ID No. 400)


 


H564G11M2H3
MEQHS
NGQPE
KRKKLKK



(SEQ ID No. 211)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H564G11M2H4
YGHKY
RTGQK
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 277)
(SEQ ID No. 349)


 


H564G11M2h8
YGHKY
PTYWY
NRKHLRA



(SEQ ID No. 177)
(SEQ ID No. 278)
(SEQ ID No. 387)


 


H564G11M2h9
KKKKH
EGMEI
PSRRWRE



(SEQ ID No. 212)
(SEQ ID No. 279)
(SEQ ID No. 369)


 


H565_G12C1
LKKKT
NGQPE
PRSNWYGNRWRR



(SEQ ID No. 186)
(SEQ ID No. 241)
(SEQ ID No. 365)


 


H565_G12D5
KKKKK
PVVGA
DQSKLSSLRWKK



(SEQ ID No. 171)
(SEQ ID No. 280)
(SEQ ID No. 403)


 


H565_G12E4
KKKKK
PLMVD
DQSKLSSLRWKK



(SEQ ID No. 171)
(SEQ ID No. 281)
(SEQ ID No. 403)


 


H565_G12A1
KKKNH
KYGSQ
PQKRWRS



(SEQ ID No. 207)
(SEQ ID No. 282)
(SEQ ID No. 349)


 


H565_G12C4
KKKNH
RWNNQ
PQKRWRS



(SEQ ID No. 207)
(SEQ ID No. 283)
(SEQ ID No. 349)


 


H565_G12F1
KKKNH
VYKQD
PQKRWRS



(SEQ ID No. 207)
(SEQ ID No. 284)
(SEQ ID No. 349)


 


H565_G12A10
KKKNH
NQMKF
PQKRWRS



(SEQ ID No. 207)
(SEQ ID No. 285)
(SEQ ID No. 349)


 


H565_G12A8
KKKNH
NHQHT
PQKRWRS



(SEQ ID No. 207)
(SEQ ID No. 286)
(SEQ ID No. 349)


 


H565_G12A4
KKKNH
KRFVD
PNEKLKK



(SEQ ID No. 207)
(SEQ ID No. 287)
(SEQ ID No. 404)


 


H565_G12B2
KKKNH
HHEPL
PLSRWKR



(SEQ ID No. 207)
(SEQ ID No. 288)
(SEQ ID No. 405)


 


H565_G12F4
KKKNH
PKMPY
NRKHLRA



(SEQ ID No. 207)
(SEQ ID No. 289)
(SEQ ID No. 387)


 


H565_G12H5
KKKNH
PKDHE
ARSRWRK



(SEQ ID No. 207)
(SEQ ID No. 290)
(SEQ ID No. 408)


 


H565_G12G6
LTKNQ
AKGSI
PKKRLRR



(SEQ ID No. 166)
(SEQ ID No. 291)
(SEQ ID No. 409)


 


H565_G12A5
YGHKY
EDPEM
KNKKRKK



(SEQ ID No. 177)
(SEQ ID No. 292)
(SEQ ID No. 410)


 


H565_G12E9
YGHKY
EFDHQ
KNKKRKK



(SEQ ID No. 177)
(SEQ ID No. 293)
(SEQ ID No. 410)


 


H565_G12F8
YGHKY
NEKQD
NTKKLKK



(SEQ ID No. 177)
(SEQ ID No. 294)
(SEQ ID No. 411)


 


H565_G12D2
YGHKY
APHYY
NRKRIRK



(SEQ ID No. 177)
(SEQ ID No. 295)
(SEQ ID No. 412)


 


H565_G12F7
YGHKY
PQLHL
SRKRFRS



(SEQ ID No. 177)
(SEQ ID No. 296)
(SEQ ID No. 413)


 


H565_G12G2
YGHKY
NWRAE
ARSRWRK



(SEQ ID No. 177)
(SEQ ID No. 297)
(SEQ ID No. 408)


 


H565_G12H11
YGHKY
NNQYK
PFRRWVK



(SEQ ID No. 177)
(SEQ ID No. 298)
(SEQ ID No. 414)


 


H565_G12A7
YGHKY
-RSIH
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 299)
(SEQ ID No. 349)


 


H565_G12A9
YGHKY
RDRIM
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 300)
(SEQ ID No. 349)


 


H565_G12B3
YGHKY
YGKGH
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 301)
(SEQ ID No. 349)


 


H565_G12B5
YGHKY
GKGGK
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 302)
(SEQ ID No. 349)


 


H565_G12E3
YGHKY
RHIGK
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 303)
(SEQ ID No. 349)


 


H565_G12E12
YGHKY
QYTYH
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 304)
(SEQ ID No. 349)


 


H565_G12B1
YGHKY
LHSHV
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 305)
(SEQ ID No. 349)


 


H565_G12B11
YGHKY
STTRV
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 265)
(SEQ ID No. 349)


 


H565_G12D1
YGHKY
ARDKR
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 306)
(SEQ ID No. 349)


 


H565_G12E2
YGHKY
EHKKT
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 307)
(SEQ ID No. 349)


 


H565_G12C5
YGHKY
MDEVP
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 308)
(SEQ ID No. 349)


 


H565_G12C7
-KKKK
QDWQR
PQKRWRS



(SEQ ID No. 190)
(SEQ ID No. 309)
(SEQ ID No. 349)


 


H565_G12G1
-KKKK
PSDRE
PQKRWRS



(SEQ ID No. 190)
(SEQ ID No. 310)
(SEQ ID No. 349)


 


H565_G12G8
NKKKK
QNTRW
PQKRWRS



(SEQ ID No. 213)
(SEQ ID No. 311)
(SEQ ID No. 349)


 


H565_G12C9
-KKKK
DEGLH
PQKRWRS



(SEQ ID No. 190)
(SEQ ID No. 312)
(SEQ ID No. 349)


 


H565_G12A11
IMNDW
NGQPE
KRKKLKK



(SEQ ID No. 214)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12D10
WTNGD
NGQPE
KRKKLKK



(SEQ ID No. 215)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12F6
WWHDM
NGQPE
KRKKLKK



(SEQ ID No. 216)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12B4
WENPH
NGQPE
KRKKLKK



(SEQ ID No. 217)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12H2
LYHEH
NGQPE
KRKKLKK



(SEQ ID No. 218)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12H8
GGDQH
NGQPE
KRKKLKK



(SEQ ID No. 219)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12C12
IYVPY
NGQPE
KRKKLKK



(SEQ ID No. 220)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12G10
FEMPY
NGQPE
KRKKLKK



(SEQ ID No. 206)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12C2
VVTSQ
NGQPE
KRKKLKK



(SEQ ID No. 221)
(SEQ ID No. 241)
(SEQ ID No. 361)


 


H565_G12B6
WWNSK
NGQPE
KKKQLKK



(SEQ ID No. 222)
(SEQ ID No. 241)
(SEQ ID No. 354)


 


H565_G12A12
MTGPG
NGQPE
KKKKIKK



(SEQ ID No. 223)
(SEQ ID No. 241)
(SEQ ID No. 359)


 


H565_G12D7
MWEPS
NGQPE
KKKKLKK



(SEQ ID No. 208)
(SEQ ID No. 241)
(SEQ ID No. 397)


 


H565_G12F3
DTYHD
NGQPE
KKKKLKK



(SEQ ID No. 224)
(SEQ ID No. 241)
(SEQ ID No. 397)


 


H565_G12F5
QDEKT
NGQPE
KKKKIKK



(SEQ ID No. 225)
(SEQ ID No. 241)
(SEQ ID No. 359)


 


H565_G12B12
GDHRI
NGQPE
KKKKLKQ



(SEQ ID No. 226)
(SEQ ID No. 241)
(SEQ ID No. 353)


 


H565_G12D8
RNSNS
NGQPE
KKKKLKQ



(SEQ ID No. 227)
(SEQ ID No. 241)
(SEQ ID No. 353)


 


H565_G12D9
RENTM
NGQPE
NKKKKKK



(SEQ ID No. 228)
(SEQ ID No. 241)
(SEQ ID No. 415)


 


H565_G12
VNDKM
NGQPW
SKKKLRK



(SEQ ID No. 229)
(SEQ ID No. 241)
(SEQ ID No. 364)


 


H565_G12
RKKDE
WPNME
KKKKLKK



(SEQ ID No. 230)
(SEQ ID No. 313)
(SEQ ID No. 397)


 


H565_G12
SNSGY
MDGPE
KKKKIKK



(SEQ ID No. 231)
(SEQ ID No. 247)
(SEQ ID No. 359)


 


H565_G12
FEYRH
NGQPW
PKKRLRR



(SEQ ID No. 232)
(SEQ ID No. 241)
(SEQ ID No. 409)


 


H565_G12
QRGRM
KGGRE
SRARWRH



(SEQ ID No. 198)
(SEQ ID No. 252)
(SEQ ID No. 343)


 


H565_G12
KKKKK
NGQPW
NGKRLHS



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 416)


 


H565_G12
KKKKK
NGQPW
PKWLWHQ



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 417)


 


H565_G12
KKKKK
NGQPW
PWWKHHV



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 418)


 


H565_G12
KKKKK
NGQPW
PNWKYQW



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 419)


 


H565_G12
KKKKK
NGQPW
PQRKVAP



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 420)


 


H565_G12
RKKKK
NGQPW
PWYKVLM



(SEQ ID No. 223)
(SEQ ID No. 241)
(SEQ ID No. 421)


 


H565_G12
KKKKK
NGQPW
DRKWWTF



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 422)


 


H565_G12
KKKKK
MTGRV
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 314)
(SEQ ID No. 407)


 


H565_G12
KKKKK
GKYNI
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 315)
(SEQ ID No. 407)


 


H565_G12
KKKKK
NAYLL
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 316)
(SEQ ID No. 407)


 


H565_G12
KKKKK
NGQPW
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 241)
(SEQ ID No. 407)


 


H565_G12
KKKKK
AQYNV
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 317)
(SEQ ID No. 407)


 


H565_G12
KKKKK
LYGHA
NRERWRR



(SEQ ID No. 171)
(SEQ ID No. 275)
(SEQ ID No. 381)


 


H565_G12G58
KKKKK
LYGHA
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 275)
(SEQ ID No. 407)


 


H565_G12A6
KKKKK
NQVMT
PSRRWRE



(SEQ ID No. 171)
(SEQ ID No. 318)
(SEQ ID No. 368)


 


H565_G12E6
KKKKK
VVHDT
PRHEWVM



(SEQ ID No. 171)
(SEQ ID No. 319)
(SEQ ID No. 423)


 


H565_G12B10
KKKKK
NIWHQ
DKSRWQQ



(SEQ ID No. 171)
(SEQ ID No. 320)
(SEQ ID No. 363)


 


H565_G12H6
KKKKK
QWGNM
DKSRWQQ



(SEQ ID No. 171)
(SEQ ID No. 321)
(SEQ ID No. 363)


 


H565_G12D12
KKKKK
MHVKS
PWSRWMQ



(SEQ ID No. 171)
(SEQ ID No. 322)
(SEQ ID No. 424)


 


H565_G12B9
-KKKK
EYTVV
PLSRWKR



(SEQ ID No. 190)
(SEQ ID No. 323)
(SEQ ID No. 405)


 


H565_G12E11
-KKKK
GPYQD
PLSRWKR



(SEQ ID No. 190)
(SEQ ID No. 324)
(SEQ ID No. 405)


 


H565_G12F9
KKKKK
QGVLE
TQNQIKK



(SEQ ID No. 171)
(SEQ ID No. 325)
(SEQ ID No. 406)


 


H571A1
KKKKK
LYGHA
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 275)
(SEQ ID No. 407)


 


H571C10
KKKKK
QQPGV
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 326)
(SEQ ID No. 407)


 


H571E6
KKKKK
NQVRG
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 327)
(SEQ ID No. 407)


 


H571D10
KKKKK
VPHVL
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 328)
(SEQ ID No. 407)


 


H571D4
KKKKK
DGRKQ
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 329)
(SEQ ID No. 407)


 


H571C3
KKKKK
NASFE
DRERWRR



(SEQ ID No. 171)
(SEQ ID No. 330)
(SEQ ID No. 407)


 


H571A3
LTKNQ
KKRVV
SRARWLH



(SEQ ID No. 166)
(SEQ ID No. 331)
(SEQ ID No. 425)


 


H571D7
YGHKY
KGIKK
SRARWLH



(SEQ ID No. 177)
(SEQ ID No. 332)
(SEQ ID No. 425)


 


H571B1
QRGRM
KGGRE
SRARWLH



(SEQ ID No. 198)
(SEQ ID No. 252)
(SEQ ID No. 425)


 


H571B9
TKGRW
NGAPQ
SRARWLH



(SEQ ID No. 187)
(SEQ ID No. 249)
(SEQ ID No. 425)


 


H571E5
EGKRK
NGQPE
SRARWLH



(SEQ ID No. 192)
(SEQ ID No. 241)
(SEQ ID No. 425)


 


H571A5
YGHKY
PMGMG
PKKRLRR



(SEQ ID No. 177)
(SEQ ID No. 333)
(SEQ ID No. 409)


 


H571A9
YGHKY
PMGKY
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 334)
(SEQ ID No. 349)


 


H571C9
YGHKY
FPKKY
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 269)
(SEQ ID No. 349)


 


H571B3
YGHKY
RHIGK
PQKRWRS



(SEQ ID No. 177)
(SEQ ID No. 303)
(SEQ ID No. 349)


 


H571D9
YGNSY
RGIAK
PQKRWRS



(SEQ ID No. 234)
(SEQ ID No. 335)
(SEQ ID No. 349)


 


H571C2
KKKNK
LWGGM
PQKRWRS



(SEQ ID No. 188)
(SEQ ID No. 336)
(SEQ ID No. 349)


 


H571C5
KKKNH
NAHYI
PQKRWRS



(SEQ ID No. 207)
(SEQ ID No. 337)
(SEQ ID No. 349)


 


H571B11
RNRKK
SGTRL
PSRRWRE



(SEQ ID No. 235)
(SEQ ID No. 338)
(SEQ ID No. 369)


 


H571A6
WDHGS
NGQPE
KKKKIKK



(SEQ ID No. 236)
(SEQ ID No. 241)
(SEQ ID No. 359)


 


H571F3
FAKRT
NGQPE
KKKKLKQ



(SEQ ID No. 237)
(SEQ ID No. 241)
(SEQ ID No. 353)


 


H571E12
SMDKV
NLGPE
DKSRWQQ



(SEQ ID No. 238)
(SEQ ID No. 339)
(SEQ ID No. 363)


 


H571A7
FFTYW
NGQPE
DRRRWTA



(SEQ ID No. 191)
(SEQ ID No. 241)
(SEQ ID No. 370)


 


H571D12
EYFRH
NGQPE
TRRRWTR



(SEQ ID No. 203)
(SEQ ID No. 241)
(SEQ ID No. 388)


 


H571D6
RHQDR
NGQPE
NRSRLHGNRWRR



(SEQ ID No. 239)
(SEQ ID No. 241)
(SEQ ID No. 426)


 


H571A2
LKKKT
NGQPE
PRSNWTGNRWRR



(SEQ ID No. 186)
(SEQ ID No. 241)
(SEQ ID No. 365)









Expression and Purification of Antigen Specific Clones in Mammalian Cells:
Clones selected as described above with characteristics as described above are cloned into a mammalian expression vector such as pCEP4 (Invitrogen). Highly purified plasmid DNA (Qiagen) is used to transiently transfect HEK293 freestyle cells with FreestyleTM MAX Reagent as recommended by the manufacturer (Invitrogen). On day 5 post transfection, cell supernatants are cleared from cell debris by centrifugation and filtration through a 0.2 μM Stericup filter (Millipore). Alternatively, HEK293 freestyle cells or CHO cells are transfected with expression plasmids containing genes for antibiotics resistance such as neomycin or puromycin. The transfected cells are cultivated in the presence of the antibiotics resulting in specific survival of cell clones which stably express the antibiotics resistance gene together with the antigen specific Fc fragment. Such stable transfectants consistently secrete the protein of interest over long time periods. The antigen specific Fcabs are purified from cell supernatants by Protein A immuno-affinity chromatography. Bound Fcabs are eluted from Protein A by washing the column with glycine buffer (pH=2.9-4.0), followed by dialysis against PBS (pH=6.8). The purity of the Fcabs is determined by non-reducing SDS-PAGE analysis and potential aggregates are detected by size-exclusion HPLC using a Zorbax GF250 column and PBS as running buffer.
Structural Characterization of Fcabs:
Binding to Fc receptors and Protein A was used to estimate the overall structural integrity of the purified Fcabs. Association with the neonatal Fc receptor (FcRn) was measured by adding 10 μg/ml Fcab to a Biacore CM5 chip coupled to 5000 response units (RU) of recombinant human FcRn at pH=6.0. The dissociation of Fcab from FcRn was tested at pH=7.4. These experiments demonstrated a pH dependent interaction of the Her-2 specific Fcabs with FcRn with binding characteristics very similar to wild type Fcab. Binding of Fcabs to the high affinity Fc receptor CD64 was measured using a Biacore CM5 chip coated with 3000 RU Protein A, followed by adding a 10 μg/ml Fcab solution. Finally, human soluble CD64 at 5 μg/ml was added. The resulting binding curves were indistinguishable from those obtained with wild type Fcab. Interaction of recombinant Fcabs (10 m/ml) with Protein A was also measured by SPR using a Protein A coated Biacore CM5 chip (3000 RU). Again, the affinities were comparable wild the ones obtained with wild type Fcab.
Antigen Specific Binding of Fcabs:
The potency and specificity of Her-2 specific Fcabs to bind to Her-2 was assessed by ELISA. Human soluble Her-2 (Bender Med Systems, Austria) was coated to plastic at 2 μg/ml. After washing and blocking unspecific binding sites, increasing concentrations of Fcabs were added. To detect Her-2 bound Fcabs, anti-Fc CH2 domain specific monoclonal antibodies which were conjugated to horse radish peroxidase (Serotec) were added. The results demonstrated that some Her-2 specific Fcabs could interact with its target in the low nanomolar range (Table 6). This interaction was specific since binding to other Her family members (HeM, Her3 and Her4) was >100 fold weaker as judged by ELISA. No binding to Her-2 unrelated antigens was detected.







TABLE 6







Binding affinities of Her-2 specific Fcabs in ELISA:










Her-2 ELISA EC50
SKBR3 cell


Fcab clone
[nM]
binding EC50 [nM]












y-Her.C2.P4.2-3
463
nd


y-Her.C2.P4.2-4
370
nd


H561G3M1G4
263
nd


y-Her.C2.P4.2-19
93
nd


ABEFs0101
16.1
5.2


H10-03-6
4.8
10.3


EF3-17
4.7
1.3


y-Her.C2.P4.2-9
4.3
nd


H10-03-6R
2.6
11.1





nd = not done.






Antigen binding was also determined by SPR. Biacore CM5 chips were coated with different amounts of human soluble Her-2 followed by addition of increasing concentrations of Fcabs. The affinity (K0) of the Fcabs was calculated from the resulting binding curves after fitting using the software BiaEval. In these experimental conditions, the Her-2 specific Fcabs H561 G3M1 G4 and H10-03-6 bound to Her-2 with K0 values of 7.5 nM and 8.6 nM, respectively. Antigen binding was also assessed by FACS using the Her-2 over-expressing human breast cancer cell lines SKBR3 and Calu-3. 1×105 cells were incubated with increasing concentrations of Fcabs for 60 minutes on ice. Then, unbound antibodies were removed by centrifugation and washing. Cell bound Fcabs were detected by incubation with anti-human Fc specific antibodies conjugated to phycoerythrin (Sigma) for 60 minutes on ice. After washing the cells, the intensity of fluorescence on the cell surface was measured in a FACS Calibur instrument (Beckton Dickinson). All tested Her-2 specific Fcabs bound to SKBR3 and Calu-3 cells but only minimally to MDA-MB468 cells which do not express Her-2 confirming the weak antigen cross-reactivity seen in ELISA. The apparent affinities (EC5O) Of Her-2 specific Fcabs on SKBR3 cells are listed in Table 6.
Effector Function of Antigen Specific Fcabs (ADCC):
In order to determine if Her-2 specific Fcabs mediate Fc effector functions, ADCC assays are performed. In these types of assays, antibodies are bound to target cells and mark them for apoptosis by virtue of binding to Fc receptors on effector cells, such as natural killer (NK) cells. SKBR3 cells (target cells) which are labelled with the fluorescent dye carboxy-fluorescein succinimidyl ester (CFSE) are incubated with increasing concentrations of Her-2 specific Fcabs for 20 minutes at 37° C. Untouched NK cells are isolated from human blood of healthy donors by negative depletion in a AutoMACS device using MACS magnetic beads according to the manufacturers instructions (Miltenyi Biotech). Purified NK cells are mixed with opsonized SKBR3 cells in a ratio of 5:1 and incubated for 4 hours at 37° C. Afterwards, the fluorescence dye 7-amino actinomycin (7-AAD) is added which specifically stains apoptotic cells. Apoptotic SKBR3 cells are enumerated in the FACS as 7-AAD/CSFE double positive cells. Her-2 specific Fcabs H10-03-6 and ABEFs0101 proved to be potent mediators of SKBR3 cell killing with EC5O values of 1.1 nM and 1.0 nM, respectively. The mechanism of apoptosis induction is dependent on the presence of NK-cells which demonstrates that Her-2 specific Fcabs possess ADCC functionality.
Example 7
Yeast Display of 4D5 Fab
For the display of a Fab fragment on yeast, the yeast display vector pYD1 (Invitrogen) (SEQ ID No.72/FIGS. 17A and 17B and 17C) is modified as follows:
A Nhel restriction site is introduced by site directed mutagenesis at position 581/586 to yield the modified vector pYDI Nhe (SEQ ID No.73/FIGS. 18A and 18B). This vector is restricted with Nhel and Pmel, to yield 3 fragments. The largest fragment is the remaining vector backbone, in which a synthetic oligonucleotide linker is inserted to yield the vector pYDI Ink (SEQ ID No. 74/FIGS. 19A and 19B). A cassette which includes the MATa transcription termination region is then amplified by PCR from the vector pYD1 and is cloned into pYDI Ink via BamHI and Pstl restriction and ligation. The resulting vector is pYDI mata (SEQ ID No.75/FIGS. 20A and 20B). A cassette that contains the GAL1 promotor, the gene coding for Aga2 and a synthetic linker with Notl and Sfil cloning sites is amplified by PCR from pYD1 and cloned in pYDI mata via EcoRI and Pad restriction to yield the vector pYDIgal (SEQ. ID No.76/FIGS. 21A and 21B).
As an example for a Fab to be displayed on yeast, the genes coding for VH-CH1 and VL-CL respectively of the antibody 4D5 (Herceptin) are made synthetically (sequences 4D5H (SEQ ID No.77/FIG. 22) and 4D5L (SEQ ID No.78/FIG. 23)).
4D5H is flanked by Sfil and Notl restriction sites, and cloned into the vector pYDIgal to yield the vector pYD4D5hc (SEQ ID No.79/FIGS. 24A and 24B and 24C). In this vector, the N-terminus of 4D5H is fused to the C-terminus of Aga2, and at the C-terminus of 4D5H, a hexahistidine tag is attached, followed by the stop codon. The amino acid sequence of VH-CH1 of 4D5 is given in 4D5hp (SEQ ID No.80/FIG. 25).
4D5L is flanked by Ncol and Ascl restriction sites, and cloned into the vector pYD4D5hc to yield the vector pYD4D5h1 (SEQ ID No.81/FIGS. 26A and 26B and 26C). 4D5L is preceded by an Aga2 secretion signal, and carries a stop codon after the C-terminal Cysteine residue of the CL domain. The amino acid sequence of VL-CL of 4D5 is given in 4D5lp (SEQ ID No.82/FIG. 27).
For display of the 4D5 Fab, the vector pYD4D5h1 is transformed into the yeast strain EBY100 (Invitrogen), transformants are selected on minimal medium without tryptophan, and expression of the recombinant protein is induced by growth on galactose containing medium according to standard protocols (Invitrogen).
Example 8
Construction of a Library with Randomized Residues in Structural Loops of the CL Domain of 4D5 Fab 
As first step in the yeast display library construction, the wildt e CL (C kappa) domain is cut out from the display vector pYD4D5h1 (SEQ ID No.81) with restriction enzymes BsiWI and Ascl. A synthetic gene encoding human C kappa domain flanked by BsiWI and Ascl sites (in the context according to pYD4D5hl) is prepared in which random mutations and insertions respectively are introduced in the AB and EF loops. In this particular example, insertions of 3, 4 or 5 NNB codons are made between amino acid positions 16 and 17 of the human C kappa domain, and residue positions 92, 93, 94, 95, 97, 98 and 99 are replaced by NNB codons. (IMGT numbering, see FIG. 2). An NNB codon contains all 4 nucleotides at positions 1 and 2, and C, G and T at position 3. NNB therefore encodes all 20 naturally encoded amino acids.
The library is prepared and selected following standard procedures.
As a scaffold ligand the CDR target Her2neu and 4D5 epitope is used. Those members of the library are selected for production of a cytotoxic modular antibody according to the invention, that have a binding site engineered into the CL domain, which is specifically binding to an effector molecule, such as an Fcgamma receptor. The resulting Fab is tested for (i) Her2neu binding with a Kd<10−8 M and an IC50<10−8 M, and (ii) effector function using a CDC and/or ADCC assay.

## Claims

1. An isolated protein that binds specifically to human Her2, wherein the isolated protein comprises two polypeptides, wherein each polypeptide comprises a human IgG1 heavy chain fragment comprising a CH2 domain and a CH3 domain, wherein the CH3 domain comprises an AB loop comprising the amino acid sequence of SEQ ID NO: 191, a CD loop comprising the amino acid sequence of SEQ ID NO: 241 and an EF loop comprising the amino acid sequence of SEQ ID NO: 370.

2. The isolated protein of claim 1, wherein the CH3 domain comprises the amino acid sequence of the CH3 domain in SEQ ID NO: 1 or SEQ ID NO: 440 exclusive of that of loops AB and EF.

3. The isolated protein of claim 1, wherein the CH2 domain comprises the amino acid sequence of the CH2 domain in SEQ ID NO: 1.

4. The isolated protein of claim 2, wherein the CH2 domain comprises the amino acid sequence of the CH2 domain in SEQ ID NO: 1.

5. The isolated protein of claim 1, wherein the human IgG1 heavy chain fragment comprises a hinge.

6. The isolated protein of claim 1, wherein the human IgG1 heavy chain fragment comprises the amino acid sequence SEQ ID NO: 1 exclusive of that of loops AB and EF.

7. The isolated protein of claim 1, wherein the two polypeptides are connected by a disulfide bond.

8. The isolated protein of claim 7, wherein the two polypeptides are connected by 2 disulfide bonds.

9. The isolated protein of claim 1, which binds to human Her2 with a binding affinity of Kd<10−8 M.

10. The isolated protein of claim 1, which is cytotoxic.

11. The isolated protein of claim 10, which triggers at least one of antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), complement dependent cytotoxicity (CDC), or apoptotic activity.

12. The isolated protein of claim 1, having a molecular weight of up to 60 kD.

13. An isolated protein that specifically binds to human Her2, wherein the isolated protein comprises two polypeptides, wherein each polypeptide comprises a human IgG1 heavy chain fragment comprising a CH2 domain and a CH3 domain, wherein the CH3 domain comprises an AB loop comprising the amino acid sequence of SEQ ID NO: 191, a CD loop comprising the amino acid sequence of SEQ ID NO: 241 and an EF loop comprising the amino acid sequence of SEQ ID NO: 370; and wherein the isolated protein has a molecular weight of up to 60 kD, a binding affinity of Kd<10−8 M and is cytotoxic.

14. A pharmaceutical composition comprising the isolated protein of claim 1 and a pharmaceutically acceptable carrier.

15. The isolated protein of claim 10, which triggers apoptotic activity.

16. The isolated protein of claim 13, wherein the CH3 domain comprises the amino acid sequence of the CH3 domain in SEQ ID NO: 1 or SEQ ID NO: 440, exclusive of that of loops AB and EF.

17. The isolated protein of claim 13, wherein the CH2 domain comprises the amino acid sequence of the CH2 domain in SEQ ID NO: 1.

18. The isolated protein of claim 16, wherein the CH2 domain comprises the amino acid sequence of the CH2 domain in SEQ ID NO: 1.

19. The isolated protein of claim 13, wherein the human IgG1 heavy chain fragment comprises a hinge.

20. The isolated protein of claim 13, wherein the two polypeptides are connected by a disulfide bond.

21. The isolated protein of claim 20, wherein the two polypeptides are connected by 2 disulfide bonds.

22. The isolated protein of claim 13, which triggers apoptotic activity.

23. The isolated protein of claim 13, wherein the polypeptides are connected by a disulfide bond, and wherein the CH2 domain comprises the amino acid sequence of the CH2 domain of SEQ ID NO: 1 and the CH3 domain comprises the amino acid sequence of the CH3 domain of SEQ ID NO: 1 or SEQ ID NO: 440 exclusive of that of loops AB and EF.

24. The isolated protein of claim 23, which triggers apoptotic activity.

25. The isolated protein of claim 23, wherein the AB loop consists of the amino acid sequence of SEQ ID NO: 191, the CD loop consists of the amino acid sequence of SEQ ID NO: 241 and the EF loop consists of the amino acid sequence of SEQ ID NO: 370.

26. The isolated protein of claim 25, which triggers apoptotic activity.

27. The isolated protein of claim 13, wherein the polypeptides are connected by 2 disulfide bonds, and wherein the CH2 domain comprises the amino acid sequence of the CH2 domain of SEQ ID NO: 1 and the CH3 domain comprises the amino acid sequence of the CH3 domain of SEQ ID NO: 1 or SEQ ID NO: 440 exclusive of that of loops AB and EF.

28. The isolated protein of claim 27, which triggers apoptotic activity.

29. The isolated protein of claim 27, wherein the AB loop consists of the amino acid sequence of SEQ ID NO: 191, the CD loop consists of the amino acid sequence of SEQ ID NO: 241 and the EF loop consists of the amino acid sequence of SEQ ID NO: 370.

30. The isolated protein of claim 29, which triggers apoptotic activity.