US20060194950A1

US20060194950A1 - Mutant protein

Info

Publication number: US20060194950A1
Application number: US11/374,532
Authority: US
Inventors: Sophia Hober; Hans Johansson
Original assignee: GE Healthcare Bio Sciences AB
Current assignee: Cytiva Sweden AB
Priority date: 2002-03-25
Filing date: 2006-03-13
Publication date: 2006-08-31
Also published as: US10918971B2; CN102558318A; EP1972689A3; CN102516372A; US20100022760A1; US9156892B2; US8354510B2; US20170080358A1; KR20110004456A; CN102516371A; ES2634145T3; ES2325362T3; CN102558317A; EP3249047A2; EP3249047B1; US20110112276A1; DK3249047T3; KR20120125674A; CN102532284B; EP1972689A2

Abstract

The present invention relates to an immunoglobulin-binding protein, wherein at least one asparagine residue has been mutated to an amino acid other than glutamine or aspartic acid, which mutation confers an increased chemical stability at pH-values of up to about 13-14 compared to the parental molecule. The protein can for example be derived from a protein capable of binding to other regions of the immunoglobulin molecule than the complementarity determining regions (CDR), such as protein A, and preferably the B-domain of Staphylococcal protein A. The invention also relates to a matrix for affinity separation, which comprises an immunoglobulin-binding protein as ligand coupled to a solid support, in which protein ligand at least one asparagine residue has been mutated to an amino acid other than glutamine.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. patent application Ser. No. 10/508,625 filed Sep. 20, 2004, which is a filing under 37 U.S.C. § 371 and claims priority to international patent application number PCT/SE03/00475 filed Mar. 20, 2003, published on Oct. 2, 2003 as WO03/080655 and also claims priority to patent application number 0200943-9 filed in Sweden on Mar. 25, 2002; the disclosures of which are incorporated herein by reference in their entireties.

TECHNICAL FIELD

The present invention relates to the field of mutant proteins, and more specifically to a mutant protein that exhibits improved stability compared to the parental molecule as well as to a method of producing a mutant protein according to the invention. The invention also relates to an affinity separation matrix, wherein a mutant protein according to the invention is used as an affinity ligand.

BACKGROUND OF THE INVENTION

A great number of applications in the biotechnological and pharmaceutical industry require comprehensive attention to definite removal of contaminants. Such contaminants can for example be non-eluted molecules adsorbed to the stationary phase or matrix in a chromatographic procedure, such as non-desired biomolecules or microorganisms, including for example proteins, carbohydrates, lipids, bacteria and viruses. The removal of such contaminants from the matrix is usually performed after a first elution of the desired product in order to regenerate the matrix before subsequent use. Such removal usually involves a procedure known as cleaning-in-place (CIP), wherein agents capable of eluting contaminants from the stationary phase are used. One such class of agents often used is alkaline solutions that are passed over said stationary phase. At present the most extensively used cleaning and sanitising agent is NaOH, and the concentration thereof can range from 0.1 up to e.g. 1 M, depending on the degree and nature of contamination. NaOH is known to be an effective CIP agent achieving multilog reduction of contaminants, such as microbes, proteins, lipids and nucleic acids. Another advantage of NaOH is that it can easily be disposed of without any further treatment. However, this strategy is associated with exposing the matrix for pH-values above 13. For many affinity chromatography matrices containing proteinaceous affinity ligands such alkaline environment is a very harsh condition and consequently results in decreased capacities owing to instability of the ligand to the high pH involved.
An extensive research has therefore been focussed on the development of engineered protein ligands that exhibit an improved capacity to withstand alkaline pH-values. For example, Gülich et al (Susanne Gülich, Martin Linhult, Per-Åke Nygren, Mathias Uhlèn, Sophia Hober, Journal of Biotechnology 80 (2000), 169-178: Stability towards alkaline conditions can be engineered into a protein ligand) suggested protein engineering to improve the stability properties of a Streptococcal albumin-binding domain (ABD) in alkaline environments. Previously, it was shown that structural modification, such as deamidation and cleavage of the peptide backbone, of asparagine and glutamine residues in alkaline conditions is the main reason for loss of activity upon treatment in alkaline solutions, and that asparagine is the most sensitive of the two (Geiger, T., and S. Clarke. 1987. Deamidation, Isomerization, and Racemization at Asparaginyl and Aspartyl Residues in Peptides. J. Biol. Chem. 262:785-794). It is also known that the deamidation rate is highly specific and conformation dependent (Kosky, A. A., U. O. Razzaq, M. J. Treuheit, and D. N. Brems. 1999. The effects of alpha-helix on the stability of Asn residues: deamidation rates in peptides of varying helicity. Protein Sci. 8:2519-2523; Kossiakoff, A. A. 1988. Tertiary structure is a principal determinant to protein deamidation. Science. 240:191-194; and Lura, R., and V. Schirch. 1988. Role of peptide conformation in the rate and mechanism of deamidation of asparaginyl residues. Biochemistry. 27:7671-7677), and the shortest deamidation half times have been associated with the sequences—asparagine-glycine- and—asparagine-serine. Accordingly, Gülich et al created a mutant of ABD, wherein all the four aspargine residues of native ABD have been replaced by leucine (one residue), asparte (two residues) and lysine (one residue). Further, Gülich et al report that their mutant exhibits a target protein binding behaviour similar to that of the native protein, and that affinity columns containing the engineered ligand show higher binding capacities after repeated exposure to alkaline conditions than columns prepared using the parental non-engineered ligand. Thus, it is concluded therein that all four asparagine residues can be replaced without any significant effect on structure and function.
Thus, the studies performed by Gülich et al were performed on a Streptococcal albumin-binding domain. However, affinity chromatography is also used in protocols for purification of other molecules, such as immunoglobulins, e.g. for pharmaceutical applications. A particularly interesting class of affinity reagents is proteins capable of specific binding to invariable parts of an antibody molecule, such interaction being independent on the antigen-binding specificity of the antibody. Such reagents can be widely used for affinity chromatography recovery of immunoglobulins from different samples such as but not limited to serum or plasma preparations or cell culture derived feed stocks. An example of such a protein is staphylococcal protein A, containing domains capable of binding to the Fc and Fab portions of IgG immunoglobulins from different species.
Staphylococcal protein A (SpA) based reagents have due to their high affinity and selectivity found a widespread use in the field of biotechnology, e.g. in affinity chromatography for capture and purification of antibodies as well as for detection. At present, SpA-based affinity medium probably is the most widely used affinity medium for isolation of monoclonal antibodies and their fragments from different samples including industrial feed stocks from cell cultures. Accordingly, various matrices comprising protein A-ligands are commercially available, for example, in the form of native protein A (e.g. Protein A Sepharose™, Amersham Biosciences, Uppsala, Sweden) and also comprised of recombinant protein A (e.g. Protein A Sepharose™, Amersham Biosciences, Uppsala, Sweden). More specifically, the genetic manipulation performed in said commercial recombinant protein A product is aimed at facilitating the attachment thereof to a support.
Accordingly, there is a need in this field to obtain protein ligands capable of binding immunoglobulins, especially via the Fc-fragments thereof, which are also tolerant to one or more cleaning procedures using alkaline agents.

BRIEF SUMMARY OF THE INVENTION

One object of the present invention is to provide a mutated immunoglobulin-binding protein ligand that exhibits an improved stability at increased pH-values, and accordingly an improved tolerance to cleaning under alkaline conditions, as compared to the parental molecule.
Another object of the invention is to provide such a protein ligand, which binds specifically to the Fc-fragment of immunoglobulins, such as IgG, IgA and/or IgM.
Yet another object of the invention is to provide a protein ligand as described above, which also exhibits an affinity which is retained for a longer period of time in alkaline conditions than that of the parental molecule.
A further object of the present invention is to provide an affinity separation matrix, which comprises mutant protein ligands capable of binding immunoglobulins, such as IgG, IgA and/or IgM, preferably via their Fc-fragments, which ligands exhibit an improved tolerance to cleaning under alkaline conditions, as compared to the parental molecule ligand.
One or more of the above-defined objects can be achieved as described in the appended claims.

DETAILED DESCRIPTION OF THE DRAWINGS

FIG. 1 (SEQ ID NOs: 5-9, 1 & 10-11, respectively, in order of appearance) shows amino acid alignments of the five homologous domains (E,D,A,B and C) of SpA. Horizontal lines indicate amino acid identity. The three boxes show the α-helices of Z_wtas determined by Tashiro and co-workers (Tashiro et al., 1997). The asparagine residues, and also one glycine residue in the B domain, which were replaced, are underlined in the figure. Also, amino acid alignments for Zwt and Z(N23T) are shown.
FIG. 2 illustrates the results obtained after alkaline treatment (cleaning-in-place) of mutant proteins according to the invention as compared to the destabilised protein Z. A comparison of the capacity after repeated CIP-treatment following an ordinary affinity chromatography scheme. 0.5 M NaOH was used as cleaning agent. The protocol was run 16 times and the duration for the alkaline sanitisation was 30 minutes in each round. FIG. 2(a) shows the inactivation pattern for Z(F30A) and variants thereof, whereas FIG. 2(b) shows the inactivation pattern for Zwt and Z(N23T).
FIG. 3 (SEQ ID NOs: 12-13) shows the gene encoding the Z(N23T/N3A/N6D)-Cys after insertion into vector as described in example 4(a). The mutations are marked with *.
FIG. 4 shows a plasmid map of the plasmid pAY91, which contains the gene encoding Z(N23T/N3A/N6D)-Cys as described in example 4(a).
FIG. 5 (SEQ ID NOs: 14-15) shows the gene encoding the Z(N23T/N3A/N6D) after insertion into vector as described in example 4(b). The mutations are marked with *.
FIG. 6 shows an example of plasmid map for the plasmid pAY100 expressing the tetramer of Z(N23T/N3A/N6D)-Cys as described in example 5.
FIG. 7 (SEQ ID NOs: 16, 17 & 16, respectively, in order of appearance) shows the adapter for introducing a KpnI-site into a vector with SPA promoter and signal sequence according to example 6.
FIG. 8 shows the plasmid pAY104, which contains SPA promoter and signal sequence to be used for introduction of an adapter containing a KpnI-site, as described in example 6.
FIG. 9 shows the resulting plasmid, pAY128, after insertion of the adapter according to example 6.
FIG. 10 (SEQ ID NO: 18) shows the constructed cloning cassette of example 6, where the original adapter is underlined.
FIG. 11 shows plasmid pAY114 after insertion of the Z(N23T/N3A/N6D)-Cys-tetramer as described in Example 6.
FIG. 12 (SEQ ID NOs: 19-21, respectively, in order of appearance) shows the constructed cloning cassette of example 7, where the original adapter is underlined.
FIG. 13 shows the resulting plasmid, pAY129, after insertion of the adapter according to example 7.
FIG. 14 shows plasmid pAY125 after insertion of the Z(N23T/N3A/N6D)tetramer-Cys as described in example 7.
FIG. 15 is a chromatogram obtained from a run as described in example 8, where the first peak corresponds to the flow-through material and the second peak corresponds to eluted hIgG.
FIG. 16 shows graphs that represent the remaining dynamic binding capacity of the matrices in accordance with example 8. From top to bottom they represent Z(N23T/N3A/N6D)dimer-Cys, Z(N23T/N3A)dimer-Cys, Z(N23T)dimer-Cys and Z(N23T/K4G)dimer-Cys respectively. Due to software problems the last two measure points for Z(N23T/N3A)dimer-Cys are lacking.
FIG. 17 shows the results of Experiment 1 as described in Example 9 below, wherein Herceptin, a monoclonal antibody which comprises VH3, is separated on 4 different matrices as described in the Experimental part below.
FIG. 18 shows the results of Experiment 1 as described in Example 9 below, wherein Enbrel, a recombinant protein, is separated on the same 4 matrices.
FIG. 19 shows the results of Experiment 1 as described in Example 9 below, wherein the monoclaonal antibody Synagis is separated on 4 different matrices.
FIG. 20 shows the results of Experiment 2 as described in Example 9 below, wherein Herceptin is separated on 4 different matrices as described in the Experimental part below.
FIG. 21 shows the results of Experiment 2 as described in Example 9 below, wherein Enbrel is separated on 4 separation matrices.
FIG. 22 shows the results of Experiment 2 as described in Example 9 below, wherein Synagis is separated on 4 different separation matrices.

DEFINITIONS

The term “protein” is used herein to describe proteins as well as fragments thereof. Thus, any chain of amino acids that exhibits a three dimensional structure is included in the term “protein”, and protein fragments are accordingly embraced.
The term “functional variant” of a protein means herein a variant protein, wherein the function, in relation to the invention defined as affinity and stability, are essentially retained. Thus, one or more amino acids that are not relevant for said function may have been exchanged.
The term “parental molecule” is used herein for the corresponding protein in the form before a mutation according to the invention has been introduced.
The term “structural stability” refers to the integrity of three-dimensional form of a molecule, while “chemical stability” refers to the ability to withstand chemical degradation.
The term “Fc fragment-binding” protein means that the protein is capable of binding to the Fc fragment of an immunoglobulin. However, it is not excluded that an Fc fragment-binding protein also can bind other regions, such as Fab regions of immunoglobulins.
In the present specification, if not referred to by their full names, amino acids are denoted with the conventional one-letter symbols.
Mutations are defined herein by the number of the position exchanged, preceded by the wild type or non-mutated amino acid and followed by the mutated amino acid. Thus, for example, the mutation of an asparagine in position 23 to a threonine is denoted N23T.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to the preparation and use of protein-based ligands, often denoted affinity ligands. The present invention relates to a method of preparing a chromatography matrix comprising at least one ligand with affinity for the Fc part of an antibody, which method comprises

(a) providing a nucleic acid sequence encoding at least one alkali-stable domain B of staphylococcal Protein A (SpA);
(b) mutating said nucleic acid sequence to encode for a recombinant protein wherein at least one glycine has been replaced by alanine;
(c) expressing the protein encoded by the nucleic acid sequence resulting from (b) in a host cell; and
(d) coupling the expressed protein to a support,
the improvement being that the ligand(s) so prepared lack affinity for the Fab part of an antibody. In one embodiment, the ligand(s) so prepared lack any substantial affinity for the Fab part of an antibody.

In one embodiment of the present method, in the alkali-stable domain B, the alkali-stability has been achieved by mutating at least one asparagine residue to an amino acid other than glutamine. In an advantageous embodiment, the alkali-stability of domain B has been achieved by mutating at least one asparagine residue to an amino acid other than glutamine; and (b) is a mutation of the amino acid residue at position 29 of the alkali-stable domain B. Thus, in the last embodiment, the mutation is a G29A mutation. The numbering used herein of the amino acids is the conventionally used in this field, and the skilled person in this field can easily recognize the position to be mutated.
In another embodiment, the recombinant protein expressed in (c) is Protein Z in which the alkali-stability has been achieved by mutating at least one asparagine residue to an amino acid other than glutamine. In an advantageous embodiment, the recombinant protein expressed in (c) is Protein Z in which the alkali-stability has been achieved by mutating at least the asparagine residue at position 23 to an amino acid other than glutamine. In another embodiment, the alkali-stable protein is a native protein which is substantially stable at alkaline conditions.
As the skilled person in this field will easily understand, the mutations to provide alkaline-stability and the G to A mutation of (b) may be carried out in any order of sequence. Consequently, the method according to the invention embraces a method wherein an alkali-stable protein is mutated from G to A; as well as the equivalent method comprising to first provide a nucleic acid encoding a G to A mutated protein which sequence is subsequently mutated to provide alkali-stability.
Thus, in one embodiment, the present invention is a method of preparing a separation matrix comprising at least one ligand with affinity for the Fc part of an antibody, which method comprises

(a) providing a nucleic acid sequence encoding a recombinant domain B of staphylococcal Protein A (SpA), such as Protein Z;
(b) mutating said nucleic acid sequence to encode for a recombinant protein wherein at least one asparagine has been replaced by an amino acid other than glutamine;
(c) expressing the protein encoded by the nucleic acid sequence resulting from (b) in a host cell; and
(d) coupling the expressed protein to a support,
the improvement being that the ligand(s) so prepared lack affinity for the Fab part of an antibody. In one embodiment, the ligand(s) so prepared lack any substantial affinity for the Fab part of an antibody.

Further, as the skilled person will understand, a protein having the advantageous properties disclosed herein, such allowing elution of antibodies at relatively high pH values when used in chromatography, may be prepared by other methods than expression in host cells. Thus, one aspect of the invention is a method of preparing a separation matrix comprising at least one ligand with affinity for the Fc part of an antibody, which method comprises

(a) providing a protein ligand having the amino acid sequence of an alkali-stable protein as discussed above, wherein at least one asparagine has been replaced by an amino acid other than glutamine; and
(b) coupling the expressed protein to a support,
the improvement being that the ligand(s) so prepared lack affinity for the Fab part of an antibody. In one embodiment, the ligand(s) so prepared lack any substantial affinity for the Fab part of an antibody. In an advantageous embodiment, the protein is provided according to (a) by protein synthesis. Methods for synthesizing peptides and proteins of predetermined sequences are well known and commonly available in this field.

Thus, in the present invention, the term “alkali-stable domain B of Staphylococcal Protein A” means an alkali-stabilized protein based on Domain B of SpA, such as the mutant protein described in the present patent application; as well as other alkali-stable proteins of other origin but having a functionally equivalent amino acid sequence.
Methods of providing mutations such as disclosed herein are well known in this field and easily carried out by the skilled person following standard procedures. As the skilled person will understand, the expressed protein should be purified to an appropriate extent before being immobilized to a support. Such purification methods are well known in the field, and the immobilization of protein-based ligands to supports is easily carried out using standard methods. Suitable methods and supports will be discussed below in more detail.
In an advantageous embodiment of the present method, the nucleic acid provided encodes a multimer of two or more domains wherein at least one is Protein Z in which the alkali-stability has been achieved by mutating at least one asparagine residue to an amino acid other than glutamine. In an especially advantageous embodiment, the nucleic acid encodes a recombinant protein comprising two, three, four or five such domains, preferably combined by suitable linker elements.
In another aspect, the present invention relates to a method of separating antibodies, preferably monoclonal antibodies, from a liquid. Such separation is preferably a process of purifying antibodies by chromatography. Thus, in one embodiment of this aspect, the method is a method of separating one or more antibodies from a liquid, which method comprises

(a) contacting the liquid with a separation matrix comprising ligands immobilised to a support;
(b) allowing antibodies to adsorb to the matrix by interaction with the ligands;
(c) an optional step of washing the adsorbed antibodies;
(d) recovering antibodies by contacting the matrix with an eluent which releases the antibodies;
the improvement being that ligands comprise one or more alkali-stable domain B of staphylococcal Protein A (SpA) which have been mutated to encode for a recombinant protein wherein at least one glycine has been replaced by an alanine. In this context, it is understood that the term “antibodies” embraces fusions comprising an antibody portion as well as antibody fragments and mutated antibodies, as long as they have substantially maintained the binding properties of an antibody.

The conditions for the adsorption step may be any conventionally used, appropriately adapted depending on the properties of the target antibody such as the pI thereof. The elution may be performed by using any commonly used buffer. In an advantageous embodiment, the recovery of antibodies is achieved by adding an eluent having a pH in the range of 3.6-4.0, preferably 3.7-3.9. In one embodiment, the elution pH is 3.7±0.1. Thus, an advantage of this embodiment is that the target antibody is exposed to pH values during elution which are as a rule higher than conventionally used with protein A-based ligands, which for most antibodies will result in less degradation caused by reduced pH.
The present method is useful to capture target antibodies, such as a first step in a purification protocol of antibodies which are e.g. for therapeutic or diagnostic use. In one embodiment, at least 75% of the antibodies are recovered. In an advantageous embodiment, at least 80%, such as at least 90%, and preferably at least 95% of the antibodies are recovered using an eluent having a pH in the range of 3.8-3.9. The present method may be followed by one or more additional steps, such as other chromatography steps. Thus, in a specific embodiment, more than about 98% of the antibodies are recovered.
Further details and embodiments of the separation matrix provided in (a) may be as discussed above. In a specific embodiment, the separation matrix used in the present method is MabSelect™ SuRe (GE Healthcare, Uppsala, Sweden). Thus, the invention also relates to the use of MabSelect™ SuRe in chromatography wherein the elution pH is increased as compared to what is conventionally used for Protein A-based ligands.
In one aspect, the present invention relates to an immunoglobulin-binding protein capable of binding to other regions of the immunoglobulin molecule than the complementarity determining regions (CDR), wherein at least one asparagine residue of a parental immunoglobulin-binding protein has been mutated to an amino acid other than glutamine, which mutation confers an increased chemical stability at alkaline pH-values compared to the parental molecule. The increased stability means that the mutated protein's initial affinity for immunoglobulin is essentially retained for a prolonged period of time, as will be discussed below.
The retained affinity for the target protein achieved according to the invention is in part due to a retained spatial conformation of the mutant protein. The affinity of mutated proteins to immunoglobulins can for example be tested by the skilled person using biosensor technology using for example a Biacore™ 2000 standard set-up (Biacore AB, Uppsala, Sweden), as will be illustrated in the experimental part below. In this context, it is understood from the term “essentially” retained that the mutated protein exhibits an affinity for immunoglobulin which is of the same order of magnitude as that of the parental molecule. Accordingly, in an initial phase, the binding capacity of the mutated protein is comparable with that of the parental molecule. However, due to the below-discussed chemical stability of the mutated protein, which is retained in time, its binding capacity will decrease more slowly than that of the parental molecule in an alkaline environment. The environment can be defined as alkaline, meaning of an increased pH-value, for example above about 10, such as up to about 13 or 14, i.e. from 10-13 or 10-14, in general denoted alkaline conditions. Alternatively, the conditions can be defined by the concentration of NaOH, which can be up to about 1.0 M, such as 0.7 M or specifically about 0.5 M, accordingly within a range of 7-1.0 M.
The increased chemical stability of the mutated protein according to the invention can easily be confirmed by the skilled person in this field e.g. by routine treatment with NaOH at a concentration of 0.5 M, as will be described in the experimental part below. In this context, it is to be understood that similar to what is said above, an “increased” stability means that the initial stability is retained during a longer period of time than what is achieved by the parental molecule. Even though similar mutations have been reported for a Streptococcal albumin-binding domain (Gülich et al, see above), it is well known that the rate of the deamidation involved in protein susceptibility to degradation in alkaline environments is highly sequence and conformation dependent. Since the amino acid sequence of ABD comprises no amino acid sequence similarity to immunoglobulin-binding proteins such as the individual domains staphylococcal protein A, it would not appear as though the teachings of Gülich et al could be applied also to immunoglobulin-binding proteins. However, the present invention shows for the first time that mutation of one or more asparagine residues of an immunoglobulin-binding protein surprisingly provides an improved chemical stability and hence a decreased degradation rate in environments wherein the pH is above about 10, such as up to about 13 or 14.
Thus, the present invention provides a mutated protein, which is useful e.g. as a protein ligand in affinity chromatography for selective adsorption of immunoglobulins, such as IgG, IgA and/or IgM, preferably IgG, from a mammalian species, such as a human. The purpose of the adsorption can be either to produce a purified product, such as a pure immunoglobulin fraction or a liquid from which the immunoglobulin has been removed, or to detect the presence of immunoglobulin in a sample. The ligand according to the invention exhibits a chemical stability sufficient to withstand conventional alkaline cleaning for a prolonged period of time, which renders the ligand an attractive candidate for cost-effective large-scale operation where regeneration of the columns is a necessity.
Accordingly, in the protein according to the invention, one or more asparagine (N) residues have been mutated to amino acids selected from the group that consists of glycine (G), alanine (A), valine (V), leucine (L), isoleucine (I), serine (S), threonine (T), cysteine (C), methionine (M), phenylalanine (F), tyrosine (Y), tryptophan (W), glutamic acid (E), arginine (R), histidine (H), lysine (K) or proline (P), or any modified amino acid that is not susceptible to the undesired deamidation and isomerisation. Alternatively, one or more asparagine (N) residues have been mutated to glutamine (Q).
The immunoglobulin-binding protein can be any protein with a native immunoglobulin-binding capability, such as Staphylococcal protein A (SpA) or Streptococcal protein G (SpG). For a review of other such proteins, see e.g. Kronvall, G., Jonsson, K. Receptins: a novel term for an expanding spectrum of natural and engineered microbial proteins with binding properties for mammalian proteins, J. Mol. Recognit. 1999 January-February; 12(1):38-44. Review.
In one embodiment, the present invention is a mutated protein, which comprises at least the binding region of an immunoglobulin-binding protein and wherein at least one such asparagine mutation is present within said region. Accordingly, in this embodiment, a mutated protein according to the invention comprises at least about 75%, such as at least about 80% or preferably at least about 95%, of the sequence as defined in SEQ ID NOs: 1 or 2, with the proviso that the asparagine mutation is not in position 21.
In the present specification, SEQ ID NO: 1 defines the amino acid sequence of the B-domain of SpA and SEQ ID NO: 2 defines a protein known as protein Z. Protein Z is synthetic construct derived from the B-domain of SpA, wherein the glycine in position 29 has been exchanged for alanine, and it has been disclosed in the literature, see e.g. Stahl et al, 1999: Affinity fusions in biotechnology: focus on protein A and protein G, in The Encyclopedia of Bioprocess Technology: Fermentation, Biocatalysis and Bioseparation. M. C. Fleckinger and S. W. Drew, editors. John Wiley and Sons Inc., New York, 8-22. Further, protein Z has been used both as a ligand in affinity chromatography. However, even though protein Z exhibits an improved chemical stability to certain chemicals other than NaOH as compared to the SpA B-domain, it is still not as stable in conditions of increased pH-values as required to withstand the many CIP regeneration steps desired in an economic industrial plant.
In one embodiment, the above described mutant protein is comprised of the amino acid sequence defined in SEQ ID NOs: 1 or 2, or is a functional variant thereof. The term “functional variant” as used in this context includes any similar sequence, which comprises one or more further variations in amino acid positions that have no influence on the mutant protein's affinity to immunoglobulins or its improved chemical stability in environments of increased pH-values.
In an advantageous embodiment, the present mutation(s) are selected from the group that consists of N23T; N23T and N43E; N28A; N6A; N11S; N11S and N23T; and N6A and N23T; and wherein the parental molecule comprises the sequence defined by SEQ ID NO: 2. As mentioned above, in order to achieve a mutant protein useful as a ligand with high binding capacity for a prolonged period of time in alkaline conditions, mutation of the asparagine residue in position 21 is avoided. In one embodiment, the asparagine residue in position 3 is not mutated.
In the most advantageous embodiment, in the present protein, an asparagine residue located between a leucine residue and a glutamine residue has been mutated, for example to a threonine residue. Thus, in one embodiment, the asparagine residue in position 23 of the sequence defined in SEQ ID NO: 2 has been mutated, for example to a threonine residue. In a specific embodiment, the asparagine residue in position 43 of the sequence defined in SEQ ID NO: 2 has also been mutated, for example to a glutamic acid. In the embodiments where amino acid number 43 has been mutated, it appears to most advantageously be combined with at least one further mutation, such as N23T.
The finding according to the invention that the various asparagine residues of the B-domain of SpA and protein Z can be ascribed different contributions to affinity and stability properties of the mutated protein was quite unexpected, especially in view of the above discussed teachings of Gülich et al wherein it was concluded that all the asparagine residues of ABD could be mutated without any internal discrimination.
Thus, the invention encompasses the above-discussed monomeric mutant proteins. However, such protein monomers can be combined into multimeric proteins, such as dimers, trimers, tetramers, pentamers etc. Accordingly, another aspect of the present invention is a multimer comprised of at least one of the mutated proteins according to the invention together with one or more further units, preferably also mutant proteins according to the invention. Thus, the present invention is e.g. a dimer comprised of two repetitive units.
In one embodiment, the multimer according to the invention comprises monomer units linked by a stretch of amino acids preferably ranging from 0 to 15 amino acids, such as 5-10. The nature of such a link should preferably not destabilise the spatial conformation of the protein units. Furthermore, said link should preferably also be sufficiently stable in alkaline environments not to impair the properties of the mutated protein units.
In the best embodiment at present, the multimer is a tetramer of protein Z comprising the mutation N23T, wherein the length of the linking units are 5-10 amino acids. In one embodiment, the present multimer comprises the sequence VDAKFN-Z(N23T)-QAPKVDAKFN-Z(N23T)QAPKC (SEQ ID NO: 22). In another embodiment, the multimer comprises the sequence VDAKFD-Z(N23T)-QAPKVDAKFD-Z(N23T)-ZQAPKC (SEQ ID NO: 23).
In a specific embodiment, the present multimer also comprises one or more of the E, D, A, B, and C domains of Staphylococcal protein A. In this embodiment, it is preferred that asparagine residues located in loop regions have been mutated to more hydrolysis-stable amino acids. In an embodiment advantageous for structural stability reasons, the glycine residue in position 29 of SEQ ID NO: 1 has also been mutated, preferably to an alanine residue. Also, it is advantageous for the structural stability to avoid mutation of the asparagine residue in position 52, since it has been found to contribute to the α-helical secondary structure content of the protein A molecule.
In a further aspect, the present invention relates to a nucleic acid encoding a mutant protein or multimer as described above. Accordingly, the invention embraces a DNA sequence that can be used in the production of mutant protein by expression thereof in a recombinant host according to well-established biotechnological methods. Consequently, another aspect of the present invention is an expression system, which enables production of a mutant protein as described above. Bacterial hosts can conveniently be used, e.g. as described in the experimental part below. In an alternative embodiment, the present invention is a cell line that has been genetically manipulated to express a mutant protein according to the invention. For methods to this end, see e.g. Sambrook et al., Molecular Cloning: A Laboratory Manual (2^nded), vols. 1-3, Cold Spring Harbor Laboratory, (1989).
Naturally, once the desired sequence has been established, the mutant protein according to the invention can alternatively be produced by synthetic methods.
Accordingly, the present invention also includes a biotechnological or synthetic method of producing a mutant protein or a multimer according to the invention.
In another aspect, the present invention relates to a matrix for affinity separation, which matrix comprises ligands that comprise immunoglobulin-binding protein coupled to a solid support, in which protein at least one asparagine residue has been mutated to an amino acid other than glutamine. The present matrix, when compared to a matrix comprised of the parental molecule as ligand, exhibits an increased binding capacity during two or more separations with intermittent alkaline cleaning. The mutated protein ligand is preferably an Fc-fragment-binding protein, and can be used for selective binding of IgG, IgA and/or IgM, preferably IgG.
The matrix according to the invention can comprise the mutant protein as described above in any embodiment thereof as ligand. In the most preferred embodiment, the ligands present on the solid support comprise a multimer as described above.
The solid support of the matrix according to the invention can be of any suitable well-known kind. A conventional affinity separation matrix is often of organic nature and based on polymers that expose a hydrophilic surface to the aqueous media used, i.e. expose hydroxy (—OH), carboxy (—COOH), carboxamido (—CONH₂, possibly in N-substituted forms), amino (—NH₂, possibly in substituted form), oligo- or polyethylenoxy groups on their external and, if present, also on internal surfaces. In one embodiment, the polymers may, for instance, be based on polysaccharides, such as dextran, starch, cellulose, pullulan, agarose etc, which advantageously have been cross-linked, for instance with bisepoxides, epihalohydrins, 1,2,3-trihalo substituted lower hydrocarbons, to provide a suitable porosity and rigidity. In the most preferred embodiment, the solid support is porous agarose beads. The supports used in the present invention can easily be prepared according to standard methods, such as inverse suspension gelation (S Hjertèn: Biochim Biophys Acta 79(2), 393-398 (1964). Alternatively, the base matrices are commercially available products, such as Sepharose™ FF (Amersham Biosciences, Uppsala, Sweden). In an embodiment, which is especially advantageous for large-scale separations, the support has been adapted to increase its rigidity, and hence renders the matrix more suitable for high flow rates.
Alternatively, the solid support is based on synthetic polymers, such as polyvinyl alcohol, polyhydroxyalkyl acrylates, polyhydroxyalkyl methacrylates, polyacrylamides, polymethacrylamides etc. In case of hydrophobic polymers, such as matrices based on divinyl and monovinyl-substituted benzenes, the surface of the matrix is often hydrophilised to expose hydrophilic groups as defined above to a surrounding aqueous liquid. Such polymers are easily produced according to standard methods, see e.g. “Styrene based polymer supports developed by suspension polymerization” (R Arshady: Chimica e L'Industria 70(9), 70-75 (1988)). Alternatively, a commercially available product, such as Source™ (Amersham Biosciences, Uppsala, Sweden) is used.
In another alternative, the solid support according to the invention comprises a support of inorganic nature, e.g. silica, zirconium oxide etc.
In yet another embodiment, the solid support is in another form such as a surface, a chip, capillaries, a or filter.
As regards the shape of the matrix according to the invention, in one embodiment the matrix is in the form of a porous monolith. In an alternative embodiment, the matrix is in beaded or particle form that can be porous or non-porous. Matrices in beaded or particle form can be used as a packed bed or in a suspended form. Suspended forms include those known as expanded beds and pure suspensions, in which the particles or beads are free to move. In case of monoliths, packed bed and expanded beds, the separation procedure commonly follows conventional chromatography with a concentration gradient. In case of pure suspension, batch-wise mode will be used.
The ligand may be attached to the support via conventional coupling techniques utilising, e.g. amino and/or carboxy groups present in the ligand. Bisepoxides, epichlorohydrin, CNBr, N-hydroxysuccinimide (NHS) etc are well-known coupling reagents. Between the support and the ligand, a molecule known as a spacer can be introduced, which will improve the availability of the ligand and facilitate the chemical coupling of the ligand to the support. Alternatively, the ligand may be attached to the support by non-covalent bonding, such as physical adsorption or biospecific adsorption.
In an advantageous embodiment, the present ligand has been coupled to the support by thioether bonds. Methods for performing such coupling are well-known in this field and easily performed by the skilled person in this field using standard techniques and equipment. In an advantageous embodiment, the ligand is firstly provided with a terminal cysteine residue for subsequent use in the coupling. The skilled person in this field also easily performs appropriate steps of purification.
As mentioned above, the affinity to immunoglobulin i.e. the binding properties of the present ligand, and hence the capacity of the matrix, is not essentially changed in time by treatment with an alkaline agent. Conventionally, for a cleaning in place treatment of an affinity separation matrix, the alkaline agent used is NaOH and the concentration thereof is up to 0.75 M, such as 0.5 M.
Thus, another way of characterising the matrix according to the invention is that due to the above discussed mutations, its binding capacity will decrease to less than about 70%, preferably less than about 50% and more preferably less than about 30%, such as about 28%, after treatment with 0.5 M NaOH for 7.5 h.
In a further aspect, the present invention relates to a method of isolating an immunoglobulin, such as IgG, IgA and/or IgM, wherein a mutant protein, a multimer or a matrix according to the invention is used. Thus, the invention encompasses a process of chromatography, wherein at least one target compound is separated from a liquid by adsorption to a mutant protein or a multimer or matrix described above. The desired product can be the separated compound or the liquid. Thus, this aspect of the invention relates to affinity chromatography, which is a widely used and well-known separation technique. In brief, in a first step, a solution comprising the target compounds, preferably antibodies as mentioned above, is passed over a separation matrix under conditions allowing adsorption of the target compound to ligands present on said matrix. Such conditions are controlled e.g. by pH and/or salt concentration i.e. ionic strength in the solution. Care should be taken not to exceed the capacity of the matrix, i.e. the flow should be sufficiently slow to allow a satisfactory adsorption. In this step, other components of the solution will pass through in principle unimpeded. Optionally, the matrix is then washed, e.g. with an aqueous solution, in order to remove retained and/or loosely bound substances. The present matrix is most advantageously used with a washing step utilising an alkaline agent, as discussed above. In a next step, a second solution denoted an eluent is passed over the matrix under conditions that provide desorption i.e. release of the target compound. Such conditions are commonly provided by a change of the pH, the salt concentration i.e. ionic strength, hydrophobicity etc. Various elution schemes are known, such as gradient elution and step-wise elution. Elution can also be provided by a second solution comprising a competitive substance, which will replace the desired antibody on the matrix. For a general review of the principles of affinity chromatography, see e.g. Wilchek, M., and Chaiken, I. 2000. An overview of affinity chromatography. Methods Mol. Biol. 147: 1-6.
In an alternative embodiment, a mutant protein according to the invention is used as a lead compound in a process wherein an organic compound is modelled to resemble its three dimensional structure. The so modelled compound is known as a mimetic. Mimetic design, synthesis and testing can be used to avoid randomly screening large number of molecules. In brief, such a method can involve determining the particular parts of the protein that are critical and/or important for a property such as immunoglobulin-binding. Once these parts have been identified, its structure is modelled according to its physical properties, e.g. stereochemistry, bonding, size, charge etc using data from a range of sources, such as spectroscopic techniques, X-ray diffraction data and NMR. Computational analysis, similarity mapping and other techniques can be used in this process. Important considerations in this kind of process are the ease to synthesise a compound, pharmacological acceptance, degradation pattern in vivo etc.
Finally, the present invention also comprises other uses of the mutant protein described above, such as in analytical methods, for medical purposes, e.g. for diagnosis, in arrays etc.

EXAMPLES

Below, the present invention will be described by way of examples, which are provided for illustrative purposes only and accordingly are not to be construed as limiting the scope of the present invention as defined by the appended claims. All references given below and elsewhere in this application are hereby included herein by reference.
In this part, since Z in its original form already has a significant but non-sufficient stability towards alkaline treatment, it was assumed that small changes in stability due to the mutations would be difficult to assess in laboratory testings. Therefore, a suppressor mutation method (Kotsuka, T., S. Akanuma, M. Tomuro, A. Yamagishi, and T. Oshima. 1996. Further stabilisation of 3-isopropylmalate dehydrogenase of an extreme thermophile, Thermus thermophilus, by a suppressor mutation method. J. Bacteriol. 178:723-727; and Sieber, V., A. Plückthun, and F. X. Schmidt. 1998. Selecting proteins with improved stability by a phage-based method. Nature Biotechnology. 16:955-960) was used to provide a variant of the Z domain with a decreased structural stability. According to this strategy the destabilised variant of protein Z, herein denoted Z(F30A) (Cedergren et al., 1993, supra) was used as scaffold for subsequent introduction of additional mutations related to investigations of alkaline stability. The binding properties of this variant are similar to native protein Z, since F30 is not involved in the Fc-binding.
Further, Zwt denotes the wild type Z domain, not containing the F30A substitution.
Experimental Strategy
To analyze which asparagines in the Z domain that are responsible for its instability in alkaline conditions, a mutational analysis was performed. In order to enable detection of improvements regarding the alkaline stability of the Z domain, it was decided to use a mutated variant, Z(F30A), since the Z-domain already possesses a significant but non-sufficient stability towards alkaline conditions. Z(F30A) has earlier been shown to possess an affinity to IgG that is similar to the wild type, but also a remarkably decreased structural stability due to the mutation of an amino acid that normally takes part in the hydrophobic core (Cedergren et al., 1993, supra; Jendeberg, L., B. Persson, R. Andersson, R. Karlsson, M. Uhlen, and B. Nilsson. 1995. Kinetic analysis of the interaction between protein A domain variants and human Fc using plasmon resonance detection. Journal of Molecular Recognition. 8:270-278). The Z-domain is a three-helix bundle consisting of 58 amino acids, including eight asparagines (N3, N6, N11, N21, N23, N28, N43 and N52) (FIG. 1) (Nilsson, B., T. Moks, B. Jansson, L. Abrahmsen, A. Elmblad, E. Holmgren, C. Henrichson, T. A. Jones, and M. Uhlen. 1987. A synthetic IgG-binding domain based on staphylococcal protein A. Protein Eng. 1:107-113). To evaluate the effect of the different asparagines on the deactivation rate in alkaline conditions, seven of these residues were exchanged for other amino acids. Since N3 is located in the flexible amino-terminal of the domain, it was excluded from the study. It was assumed that a degradation of this amino acid would not affect the activity of a monomeric ligand and would therefore not be detectable in the present assay, which measures the retained activity. Moreover, since the amino acid is located outside the structured part of the domain it will presumably be easily replaceable during a multimerisation of the domain to achieve a protein A-like molecule. To facilitate the protein design, a comparison with the homologous sequences from the other domains of protein A was made (FIG. 1) (Gülich et al., 2000a). From the comparison, it was decided to exchange asparagine 11 for a serine and 23 for threonine and finally 43 for a glutamic acid. Asparagine 6 was exchanged for alanine since the alternative when looking on the homologous sequences was aspartic acid, which also has been reported to be sensitive in alkaline conditions. All five domains of protein A have asparagines in the other positions (21, 28, 52). Hence, they were exchanged for alanines.

Example 1

Mutagenesis, Expression and Purification of Mutant Protein Z Materials and Methods

Site-directed mutagenesis was performed using a two-step PCR-technique (Higuchi et al., 1988). Plasmid pDHZF30A (Cedergren et al., 1993) was used as template. Oligonucleotides coding for the different asparagine replacements and the A29G replacement were synthesised by Interactiva (Interactiva Biotechnologie GmbH, Ulm, Germany). The restriction enzymes XbaI and HindIII (MBI Fermentas Inc., Amhurst, NY) were used for cloning into the vector pDHZ (Jansson et al., 1996) that was performed according to Sambrook (Sambrook et al., 1987). To create pTrpZ, the Z domain was amplified by PCR, using plasmid pKN1 as template (Nord et al., 1995). The fragment was restricted with XbaI and PstI and ligated into the vector pTrpABDTIT2 (Kraulis et al., 1996) that had been restricted with same enzymes. A MegaBACE 1000 DNA Sequencing System (Amersham Biosciences, Uppsala, Sweden) was used to verify correct sequence of inserted fragments. MegaBACE terminator chemistry (Amersham Biosciences, Uppsala, Sweden) was utilised according to the supplier's recommendations in a cycle sequencing protocol based on the dideoxy method (Sanger et al., 1977). During cloning procedures, Escherichia coli strain RRIAM15 (American Type Culture Collection, Rockville, Mass.) was used, whereas for expression of the different gene products 017 (Olsson, M. O., and L. A. Isaksson. 1979. Analysis of rpsD Mutations in Escherichia coli. I: Comparison of Mutants with Various Alterations in Ribosomal Protein S4. Molec. gen. Genet. 169:251-257) was used.
Production and purification of Z(F30A) and the different constructs thereof were performed according to the protocol outlined by Gülich (Gülich et al., 2000b, see above). The production of Z and pZ(N23T) were performed as described in Kraulis et al (Kraulis, P. J., P. Jonasson, P.-Å. Nygren, M. Uhlèn, L. Jendeberg, B. Nilsson, and J. Kördel. 1996. The serum albumin-binding domain of streptococcal proteinG is a three-helix bundel: a heteronuclear NMR study. FEBS lett. 378:190-194). Relevant fractions were lyophilised. The amount of protein was estimated by absorbance measurements at 280 nm using the specific absorbance coefficient, a (1 g⁻¹cm⁻¹), Z 0.156; Z(N23T), 0.169; Z(F30A), Z(F30A,N43E), Z(F30A,N23T,N43E) 0.157; Z(F30A,N6A), Z(F30A,N11S), Z(F30A,N21A), Z(F30A,N23T), Z(F30A,N28A), Z(F30A,N52A), Z(F30A,N6A,N23T), Z(F30A,N11S,N23T) 0.158. The concentration was confirmed by amino acid analysis (BMC, Uppsala, Sweden). The homogeneity was analysed by Sodium Dodecyl Sulfate PolyAcrylamide Gel Electrophoresis (SDS-PAGE) (Laemmli, U.K. 1970. Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4. Nature. 227:680-685) using the Phast system. Lyophilised proteins were loaded on high-density gels (Amersham Biosciences, Uppsala, Sweden) under reducing conditions and stained with Coomassie Brilliant Blue according to the supplier's recommendations. The homogeneity and the molecular weights were further confirmed by mass spectrometry.
For CD spectroscopy, protein samples were prepared in a phosphate buffer (8.1 mM K₂HPO₄, 1.9 mM KH₂PO₄, pH 7.5) to a concentration of 10 μM. Spectra were recorded using a J-720 spectropolarimeter (JASCO, Tokyo, Japan) in the far UV region from 250 to 200 nm at RT in a quartz cell of path length 0.1 cm and with a scan speed of 10 nm min⁻¹. Each spectrum was the mean of five accumulated scans and the final spectra were converted into mean residue ellipticity (MRE) (deg cm²dmol⁻¹).
Results (Example 1)
All Z variants were successfully produced intracellular in E. coli at 37° C. and show the same expression levels, approximately 50 mg/l as estimated from SDS-PAGE. The proteins were all purified by IgG affinity chromatography. After the purification, samples were analysed with SDS-PAGE (data not shown), lyophilised and stored for further analyses. The molecular mass for protein Z and the different mutants thereof were also confirmed by mass spectrometry. The data confirmed correct amino acid content for all mutants (data not shown). Also, structural analyses were performed on a Circular Dichroism (CD) equipment, since it previously has been proven to be suitable for detecting structural changes in α-helical proteins (Johnson, C. W., Jr. 1990. Protein secondary structure and circular dichroism: a practical guide. Proteins. 7:205-214; and Nord, K., J. Nilsson, B. Nilsson, M. Uhlèn, and P.-Å. Nygren. 1995. A combinatorial library of an a-helical bacterial receptor domain. Prot. eng. 8:601-608). All spectra show a minimum at 208 nm and at 222 nm in combination with a maximum around 195 nm, indicating a similar structure for the mutants and the parental molecule. However, Z(F30A,N52A) seems to have a somewhat lower α-helicity than the wild type Z and the other mutants thereof (data not shown).

Example 2

Biospecific Interaction Analysis

Materials and Methods
Differences in affinity and kinetic constants of the association and dissociation states were detected on a Biacore™ 2000 instrument (Biacore, Uppsala, Sweden). Human polyclonal IgG and HSA (negative reference) were immobilised by amine coupling on the carboxylated dextran layer of a CM5 sensor chip (Biacore) according to the supplier's recommendations. The immobilisation of IgG resulted in approximately 2000 RU. Z, ZF30A, and the different mutants were prepared in HBS (10 mM HEPES, 0.15 M NaCl, 3.4 mM EDTA, 0.005% surfactant P20, pH 7.4) at 10 different concentrations (100-550 nM). The samples were injected over the surfaces as duplicates in random order at a flow rate of 30 μl min⁻¹. 10 mM HCl was used to regenerate the surface. The data was analysed using the BIA evaluation 3.0.2b software (Biacore AB). The signals from a control surface immobilized with HSA were subtracted from the IgG surface. A 1:1 Langmuir model was assumed and apparent kinetic constants and also affinity constants were calculated. Also, the change in free binding energy (AAG=−RTln K_{aff, mutant}/K_{aff, native}) in relation to the native molecule was calculated.
Results (Example 2)

To determine the differences in affinity for the Z variants towards IgG, surface plasmon resonance (SPR) using a Biacore was carried out. The aim was to compare the affinity for the different mutated Z variants according to the invention with the parental molecule. As mentioned above, due to the high alkaline stability of the parental Z domain it was decided to use a structurally destabilised variant of Z including the F30A mutation (Cedergren, L., R. Andersson, B. Jansson, M. Uhlèn, and B. Nilsson. 1993. Mutational analysis of the interaction between staphylococcal protein A and human IgG₁ . Protein eng. 6:441-448). Therefore, it was of importance to first confirm that the affinity between the mutated molecule and IgG was retained despite the mutation. As can be seen in table 1 below, the affinity of Z(F30A) is not significantly affected. The very small change in affinity gives a slightly higher stability to the complex of Z(F30A) and IgG compared to the parental molecule Z and IgG. This is in accordance with results earlier reported by Jendeberg et al. (Cedergren et al., 1993, supra; Jendeberg et al., 1995, supra). All mutants constructed with Z(F30A) as scaffold were analysed and compared with their parental molecule (Z(F30A)). The results show that the overall affinity is not significantly affected by the mutations, indicating that none of the asparagine mutations according to the invention are very important for the binding to IgG (see table 1 below). In all Z variants including the N21A or the N43E mutation, only a slightly lower affinity constant was observed. For mutants with the N23T mutation, surprisingly, the affinity even seems to be slightly higher. Also, in the case of the N28A-mutation, the decrease in affinity is very small, and cannot be expected to have any essential influence if the mutant protein is used e.g. as a protein ligand. Furthermore, all constructs including the N28A-mutation have a remarkably increased off-rate. For the mutants including the N23T mutation the somewhat increased affinity seems to be due to a slightly increased on-rate. Also, the N6A-mutation gives a higher on-rate, but the affinity constant is not affected because of the increased off-rate that also follows the mutation.

TABLE 1


An overview of the kinetic study on the different
Z domains carried out using the Biacore.

	kon	koff	Kaff	ΔΔG (vs	ΔΔG (vs
	[10⁵M⁻¹	[10⁻³	[110⁷	Zwt)	Z(F30A))
Mutant	s⁻¹]	s⁻¹]	M⁻¹]	[kcal/mol]	[kcal/mol]

Zwt	1.5	3.7	4.0	0
Z(N23T)	2.7	3.9	7	−0.3
Z(F30A)	1.9	4.17	4.5	−0.1	0.0
Z(F30A, N6A)	7	21	3.3	0.1	0.2
Z(F30A, N11S)	1.6	4.9	3.2	0.1	0.2
Z(F30A, N21A)	1	3.8	2.6	0.3	0.4
Z(F30A, N23T)	2.1	3.75	5.6	−0.2	−0.1
Z(F30A, N28A)	3.1	9.87	3.2	0.1	0.2
Z(F30A, N43E)	1.3	5.1	2.6	0.3	0.4
Z(F30A, N52A)	1.5	4.9	3	0.2	0.3
Z(F30A, N23T, N43E)	0.8	3.8	2	0.4	0.5

Z_wtwas used as an internal standard during the different measurements. The differences in free binding energy are calculated relative to Zwt and Z(F30A) respectively.

Example 3

Stability Towards Alkaline Conditions

Materials and Methods
The behaviour of the variants of domain Z as affinity ligands was analysed by immobilisation to a standard affinity matrix. Z, Z(F30A), and mutated variants were covalently coupled to HiTrap™ affinity columns (Amersham Biosciences, Uppsala, Sweden) using the N-hydroxysuccinimide chemistry according to the manufacturer's recommendations. The columns were pulsed with TST and 0.2 M HAc, pH 3.1. Human polyclonal IgG in TST was prepared and injected onto the columns in excess. A standard affinity chromatography protocol was followed for 16 cycles on the AKTA™Explorer 10 (Amersham Biosciences, Uppsala, Sweden). Between each cycle a CIP-step was integrated. The cleaning agent was 0.5 M NaOH and the contact time for each pulse was 30 minutes, resulting in a total exposure time of 7.5 hours. Eluted material was detected at 280 nm.
Results (Example 3)
Z, Z(F30A), and mutants thereof were covalently attached to HiTrap™ columns using NHS-chemistry. IgG in excess was loaded and the amount of eluted IgG was measured after each cycle to determine the total capacity of the column. Between each cycle the columns were exposed to CIP treatment consisting of 0.5 M NaOH. After 16 pulses, giving a total exposure time of 7.5 hours, the column with the Z(F30A)-matrix shows a 70% decrease of the capacity. The degradation data in FIG. 2 a suggest that four of the exchanged asparagines (N6, N11, N43 and N52) are less sensitive to the alkaline conditions the mutants are exposed for in this experiment. In contrast, N23 seems to be very important for the stability of Z(F30A). Z(F30A,N23T) shows only a 28% decrease of capacity despite the destabilising F30A-mutation. Hence, the Z(F30A,N23T) is almost as stable as Zwt and thereby the most stabilised variant with Z(F30A) as scaffold. Also the Z(F30A)-domain with two additional mutations Z(F30A,N23T,N43E) shows the same pattern of degradation as Z(F30A,N23T). An exchange of N28 to an alanine also improves the stability of Z(F30A) towards alkaline conditions. Surprisingly, the column with Z(F30A,N21A) as affinity ligand reveals a dramatic loss of capacity when exposed to NaOH compared to the parental molecule. These data make Z(N23T) to a very advantageous candidate as ligand in affinity purification of IgG.
To finally prove the reliability of the strategy using a structurally destabilised variant of a molecule in order to make small changes in stability detectable, the N23T-mutation was grafted into the parental Z-domain. Both the parental Z-domain and Z(N23T) were coupled to HiTrap-columns and exposed to alkaline conditions in the same way as for the already mentioned mutants. As can be seen in FIG. 2 b, the Z(N23T)-mutant shows higher stability than Zwt when exposed to high pH.

Example 4

Construction of Monomers of Z-Mutants with and without a C-Terminal Cysteine

Three different mutations were introduced in a gene encoding Z(N23T): K4G, N3A and the double-mutation N3A/N6D.
The mutations were originally introduced into two different vectors: one with a cysteine in the C-terminus and one without the cysteine. This was done to later facilitate the construction of multimers with one single C-terminal cysteine.

Example 4(a)

Cysteine-Containing Monomer Construction

As template for the construction, a plasmid denoted “pGEM ZN23T”, was used. This already contained the N23T-mutation in the Z-gene.
A PCR-reaction was performed with this plasmid as template and the two oligonucleotides

AFFI-63:

TTT TTT GTA GAC AAC GGA TTC AAC AAA GAA C

GRTO-40:

GAT CTG CTG CAG TTA GCA TTT CGG CGC CTG AGC ATC

ATT TAG
for the K4G-mutation (SEQ ID NOs: 24-25),

AFFI-64:

TTT TTT GTA GAC GCC AAA TTC AAC AAA GAA C

GRTO-40:

GAT CTG CTG CAG TTA GCA TTT CGG CGC CTG AGC ATC

ATT TAG
for the N3A-mutation and (SEQ ID NOs: 26-27),

AFFI-65:

TTT TTT GTA GAC GCC AAA TTC GAC AAA GAA C

GRTO-40:

GAT CTG CTG CAG TTA GCA TTT CGG CGC CTG AGC ATC

ATT TAG

for the N3A/N6D-mutation (SEQ ID NOs: 28-29).
PCR reaction tubes containing: 0.5 μl template pGEM ZN23T [500 ng/μl], 5 pmol of each primer (Interactiva, Thermo Hybaid GmbH, Ulm, Germany), 5 μl of dNTP-mix ([10 mM], Applied Biosystems, CA, USA), 5 μl of PCR-buffer 10× (Applied Biosystems, CA, USA), 0.1 μl of AmpliTaq ([5 U/μl], Applied Biosystems, CA, USA) and sterile water to a final volume of 50 μl. The PCR-program consisted of 2 min at 94° C. followed by 30 cycles of 15 sec at 96° C., 15 sec at 50° C., 1 min at 72° C. and concluded with an additional min at 72° C. The PCR reactions were performed on GeneAmp® PCR System 9700 (Applied Biosystems, CA, USA).
The PCR-product was analysed on 1% agarose gel and, after confirming an obtained product of correct size, purified with QIAquick® PCR purification kit (QIAGEN GmbH, Hilden, Germany).
The PCR-products were cleaved according to Sambrook (Sambrook et al.) with the restriction enzymes AccI and PstI (New England Biolabs, NEB, MA, USA). The cleavage products were analysed on agarose gel and purified from the agarose with QIAquick® Gel Extraction Kit (QIAGEN GmbH, Hilden, Germany) prior to ligation. The fragments were ligated into a vector denoted “pTrp-protA-stab-(multi9)”, already cleaved with the enzymes AccI and PstI and purified, by adding T4 DNA ligase and ligation buffer (MBI Fermentas, Lithuania), and subsequently transformed into RRIΔM15-cells (ATCC, MA, USA). The constructs were given the names pAY87 (Z(N23T/K4G)-Cys), pAY89 (Z(N23T/N3A)-Cys) and pAY91 (Z(N23T/N3A/N6D)-Cys), respectively.
A MegaBACE™ 1000 DNA Sequencing System (Amersham Biosciences, Uppsala, Sweden) was used to verify correct sequences of inserted fragments. MegaBACE™ terminator chemistry (Amersham Biosciences, Uppsala, Sweden) was utilised according to the supplier's recommendations in a cycle sequencing protocol based on the dideoxy method (Sanger et al., 1977).

Example 4(b)

Non-Cysteine-Containing Monomer Construction

As template for the construction, a plasmid denoted “pTrp(-N)ZN23T-Cys”, was used. This plasmid already contained the gene with the N23T-mutation.
A PCR-reaction was performed with this plasmid as template and the two oligonucleotides

AFFI-63:

TTT TTT GTA GAC AAC GGA TTC AAC AAA GAA C

GRTO-41:

GAT CTC GTC TAC TTT CGG CGC CTG AGC ATC ATT TAG
for the K4G-mutation (SEQ ID NOs: 30-31),

AFFI-64:

TTT TTT GTA GAC GCC AAA TTC AAC AAA GAA C

GRTO-41:

GAT CTC GTC TAC TTT CGG CGC CTG AGC ATC ATT TAG
for the N3A-mutation (SEQ ID NOs: 32-33),

AFFI-65:

TTT TTT GTA GAC AAC GGA TTC AAC AAA GAA C

GRTO-41:

GAT CTC GTC TAC TTT CGG CGC CTG AGC ATC ATT TAG

and for the N3A/N6D-mutation (SEQ ID NOs: 34-35).
PCR-reaction tubes containing: 0.5 μl template pTrp(-N)ZN23T-Cys [500 ng/μl], 5 pmol of each primer (Interactiva, Thermo Hybaid GmbH, Ulm, Germany), 5 μl of dNTP-mix (10 mM, Applied Biosystems, CA, USA), 5 μl of PCR-buffer 10× (Applied Biosystems, CA, USA), 0.1 μl of AmpliTaq ([5 U/μl], Applied Biosystems, CA, USA) and sterile water to a final volume of 50 μl. The PCR-program consisted of 2 min at 94° C. followed by 30 cycles of 15 sec at 96° C., 15 sec at 50° C., 1 min at 72° C. and concluded with an additional min at 72° C. The PCR reactions were performed on GeneAmp® PCR System 9700 (Applied Biosystems, CA, USA).
The PCR-products were directly TA-cloned into the vector pGEM according to the manufacturer's instructions (Promega, WI, USA) and subsequently transformed into RRIΔM15-cells (ATCC, MA, USA). The constructs were given the names pAY86 (Z(N23T/K4G), pAY88 (Z(N23T/N3A) and pAY90 (Z(N23T/N3A/N6D) respectively.
A MegaBACE™ 1000 DNA Sequencing System (Amersham Biosciences, Uppsala, Sweden) was used to verify correct sequences of inserted fragments. MegaBACE™ terminator chemistry (Amersham Biosciences, Uppsala, Sweden) was utilised according to the supplier's recommendations in a cycle sequencing protocol based on the dideoxy method (Sanger et al., 1977).

Example 5

Construction of the Gene Encoding Monomers and Oligomers with a C-Terminal Cysteine in pTrp-Vector

All of the above described plasmids pAY 86 to pAY91 (a total of six plasmids) were cleaved with the restriction enzyme AccI. This resulted in releasing the Z-mutants completely from the pAY86-, pAY88- and pAY90-vectors and a single opening at the 3′-end of the gene in the pAY87-, pAY89- and pAY91-vectors.
The cleaved vectors were treated with Calf Intestine Alkaline Phosphatase (CIAP, MBI Fermentas, Lithuania) according to the manufacturer's recommendations. This step was performed to dephosphorylate the 5′-ends to avoid self-ligation of the vectors.
The released Z-mutant-fragments were analysed on agarose gel and subsequently purified from the agarose before the fragments was ligated into the opened vectors according to the following:
fragment from pAY86 to pAY87
fragment from pAY88 to pAY89
fragment from pAY90 to pAY91
For the ligation reactions, different proportions of fragment versus vector were mixed and the result was that a range of different multimers, as expected, ranging from dimers to pentamers was obtained.

The different multimers were transformed into RRIΔM15-cells (ATCC, MA, USA) and the correct sequences were verified by analysis on a sequencing equipment at the Royal Institute of Technology as described above. The newly constructed plasmids were denoted as shown in the table below:

TABLE 2


Summary of constructed plasmids

Plasmid no.
pAY	Expressed protein from construct

86	Z(N23T/K4G)
87	Z(N23T/K4G)-Cys
88	Z(N23T/N3A)
89	Z(N23T/N3A)-Cys
90	Z(N23T/N3A/N6D)
91	Z(N23T/N3A/N6D)-Cys
92	Z(N23T/K4G)dimer-Cys
93	Z(N23T/N3A)dimer-Cys
94	Z(N23T/N3A/N6D)dimer-Cys
95	Z(N23T/K4G)trimer-Cys
96	Z(N23T/N3A)trimer-Cys
97	Z(N23T/N3A/N6D)trimer-Cys
98	Z(N23T/K4G)tetramer-Cys
99	Z(N23T/N3A)tetramer-Cys
100	Z(N23T/N3A/N6D)tetramer-Cys
101	Z(N23T/K4G)pentamer-Cys
102	Z(N23T/N3A)pentamer-Cys
103	Z(N23T/N3A/N6D)pentamer-Cys

The above described plasmid vectors, except pAY86, pAY88 and pAY90 have Trp promoter, Trp leader sequence and a gene for kanamycin (Km) resistance. pAY86, pAY88 and pAY90 have a gene for ampicillin resistance instead.

Example 6

Construction of Genes Encoding Monomers and Oligomers with a C-Terminal Cysteine in pK4-Vector

The genes encoding the proteins as summarised in Table 2 were to be transferred to a vector containing SPA promoter and signal sequence. To enable this procedure, an adapter containing the cleavage site for the restriction enzyme KpnI (New England Biolabs, NEB, MA, USA) was to be constructed. The adapter was constructed by the two oligonucleotides (Interactiva, Thermo Hybaid GmbH, Ulm, Germany)
The plasmid pAY104 (pK4-cys-ABDstabdimer) was cleaved with FspI and PstI (New England Biolabs, NEB, MA, USA). The vector was purified on agarose gel and the released fragment was removed and the remaining vector was purified from the agarose with QIAquick® Gel Extraction Kit (QIAGEN GmbH, Hilden, Germany).
The two oligomers AFFI-88 and AFFI-89 were mixed in ligation buffer (MBI Fermentas, Lithuania) and heated to 50° C. and the mixture was allowed to cool to room temperature where after the cleaved plasmid vector was added together with T4 DNA ligase (MBI Fermentas, Lithuania). After the ligation reaction, the product was transformed into RRIΔM15-cells and the correct sequence was verified as described above. The resulting plasmid was denoted pAY128.

The plasmid pAY128 was then cleaved with the restriction enzymes KpnI and PstI and the cleaved vector was analysed on agarose gel and subsequently purified from the agarose with QIAquick® Gel Extraction Kit (QIAGEN GmbH, Hilden, Germany). The fragments expressing the two mutated Z-genes Z(N23T/N3A) and Z(N23T/N3A/N6A) from pAY86 to pAY 103 were cleaved with KpnI and PstI (New England Biolabs, NEB, MA, USA), separated and purified after agarose gel separation. The different fragments were ligated into the cleaved vector originating from pAY128 and the resulting plasmids were, after verifying correct sequences, denoted pAY107 to pAY116 as summarised in Table 3.

TABLE 3


Summary of constructed plasmids with
SPA promoter and signal sequence.

Plasmid no.
pAY	Expressed protein from construct

107	Z(N23T/N3A)-Cys
108	Z(N23T/N3A/N6D)-Cys
109	Z(N23T/N3A)dimer-Cys
110	Z(N23T/N3A/N6D)dimer-Cys
111	Z(N23T/N3A)trimer-Cys
112	Z(N23T/N3A/N6D)trimer-Cys
113	Z(N23T/N3A)tetramer-Cys
114	Z(N23T/N3A/N6D)tetramer-Cys
115	Z(N23T/N3A)pentamer-Cys
116	Z(N23T/N3A/N6D)pentamer-Cys

Example 7

Construction of Genes Encoding a Part of the E-Gene (E′) from Protein A N-Terminally Fused to Monomers and Oligomers with a C-Terminal Cysteine in pK4-Vector

The genes encoding the proteins, as summarised in Table 2, were transferred to a vectors containing the SPA promoter and signal sequence and a part of the gene encoding the E-region of protein A (E′). It has earlier been shown that an addition of the N-terminal IgG-binding part of the mature protein A (region E), or parts thereof, may increase correct processing and also facilitate secretion of the gene product to the surrounding culture medium (Abrahmsèn et al., 1985). An adapter containing the cleavage site for the restriction enzyme KpnI and a part of region E from protein A (E′) was constructed by the two oligonucleotides (Interactiva, Thermo Hybaid GmbH, Ulm, Germany)
The plasmid pAY 104 (pK4-cys-ABDstabdimer) was cleaved with FspI and PstI (New England Biolabs, NEB, MA, USA). The vector was purified on agarose gel and the released fragment was removed and the remaining vector was purified from the agarose with QIAquick® Gel Extraction Kit (QIAGEN GmbH, Hilden, Germany). The two oligonucleotides were mixed in ligation buffer and heated to 75° C. and the mixture was allowed to cool to room temperature where after the cleaved plasmid vector was added, together with T4 DNA ligase (MBI Fermentas, Lithuania). After the ligation reaction the product was transformed into RRIΔM15-cells and the correct sequence was verified as described above. The resulting plasmid was denoted pAY129.

The plasmid pAY129 was then cleaved with the restriction enzymes KpnI and PstI and the cleaved vector was analysed on agarose gel and subsequently purified from the agarose with QIAquick® Gel Extraction Kit (QIAGEN GmbH, Hilden, Germany). The fragments expressing the two mutated Z-genes Z(N23T/N3A) and Z(N23T/N3A/N6A) from pAY86 to pAY103 were cleaved with KpnI and PstI, separated and purified after agarose gel separation. The different fragments were ligated into the cleaved vector originating from pAY129 and the resulting plasmids were, after verifying correct sequences, denoted pAY118 to pAY127 as summarised in Table 4.

TABLE 4


Summary of constructed plasmids with SPA promoter and
signal sequence and a part of region E from protein A - E′.

Plasmid no.
pAY	Expressed protein from construct

118	E′-Z(N23T/N3A)-Cys
119	E′-Z(N23T/N3A/N6D)-Cys
120	E′-Z(N23T/N3A)dimer-Cys
121	E′-Z(N23T/N3A/N6D)dimer-Cys
122	E′-Z(N23T/N3A)trimer-Cys
123	E′-Z(N23T/N3A/N6D)trimer-Cys
124	E′-Z(N23T/N3A)tetramer-Cys
125	E′-Z(N23T/N3A/N6D)tetramer-Cys
126	E′-Z(N23T/N3A)pentamer-Cys
127	E′-Z(N23T/N3A/N6D)pentamer-Cys

Example 8

Stability Towards Alkaline Conditions

To evaluate the stability of the proteins towards alkaline conditions, four different proteins were tested in an environment of high pH. The different proteins were Z(N23T)dimer-Cys, Z(N23T/K4G)dimer-Cys, Z(N23T/N3A)dimer-Cys and Z(N23T/N3A/N6D)dimer-Cys.
(Z(N23T)dimer-Cys), (Z(N23T/N3A)dimer-Cys), (Z(N23T/N3A/N6D)dimer-Cys) and (Z(N23T/K4G)dimer-Cys) were cultivated in fermenters. The harvested media were purified and coupled to HF Agarose (Amersham Biosciences, Uppsala, Sweden) using standard methods before the alkaline tests. The HF agarose-coupled proteins were denoted as follows

Z(N23T)dimer-Cys U631049

Z(N23T/K4G)dimer-Cys U631079

Z(N23T/N3A)dimer-Cys U631064

Z(N23T/N3A/N6D)dimer-Cys U631063
The matrices were packed in columns (HR 5/2, Amersham Biosciences, Uppsala, Sweden) to a final volume ranging from 0.1 to 0.3 ml. The purification equipment used was an ÄKTA™ Explorer 10 (Amersham Biosciences, Uppsala, Sweden) with a UV sample flow cell with a path length of 2 mm (Amersham Biosciences, Uppsala, Sweden).
The buffers used contained

- Running buffer: 25 mM Tris-HCl, 1 mM EDTA, 200 mM NaCl, 0.05%
- Tween 20, 5 mM ammonium acetate, pH 8.0
- Elution buffer: 0.2 M acetic acid (HAc), pH 3.1
- Cleaning-In-Place (CIP) buffer: 0.5 M NaOH

A typical chromatographic run cycle consisted of

- Equilibrium of the column with running buffer
- Sample application of 10 mg polyclonal human IgG (hIgG) at 0,2 ml/min
- Extensive washing-out of unbound proteins
- Elution at 1.0 ml/min with elution buffer
- Re-equilibration with running buffer
- Cleaning-In-Place (CIP) with CIP-buffer with a contact time between column matrix and 0.5 M NaOH of 1 hour
- Re-equilibration with running buffer

The amount of hIgG loaded at each run was well above the total dynamic binding capacity of the column since the breakthrough of unbound protein was considerable when loading the sample onto the columns in all cases.
After one cycle, including the steps above, a new cycle was started which again included one hour of exposure of 0.5 M sodium hydroxide. To measure the decrease of the dynamic binding capacity of the column the peak area of the eluted peak was compared with the original peak area of the eluted peak when the matrix had not been exposed to the sodium hydroxide. Setting the original peak area as 100% of binding capacity the decrease of the binding capacity of hIgG was observed. The peak area was calculated with the UNICORN™ software accompanying the purification system.
Each cycle was repeated 21 times resulting in a total exposure time between the matrix and the sodium hydroxide of 20 hours for each different matrix. The normalised peak areas were visualised in a graph as can be seen below (FIG. 16). All 21 cycles were repeated for each mutant.
Both Z(N23T/N3A/N6D)dimer-Cys and Z(N23T/N3A)dimer-Cys showed improved stability against alkaline conditions compared to the originally produced Z(N23T)dimer-Cys.

Example 9

Preparation of an Fc-Binding Affinity Ligand

Materials
Samples
Herceptin:

- Herceptin® 150 mg
- powder to concentrate to
- infusion liquid, solution
- Trastuzumab
- Roche
- Lot B 1171
- EU/1/00/145/001
- Roche Registration Limited
- 40 Broadwater Road
- Welwyn Garden City
- Hertfordshire, AL7 3AY
- UK
  Enbrel:
- Enbrel 25 mg
- powder to injection liquid, solution
- etanercept
- Wyeth®
- Lot 18028
- EU/1/99/126/003
- Wyeth Europe Ltd.,
- Huntercombe Lane South,
- Taplow, Maidenhead,
- Berkshire,
- SL6 0PH,
- UK
  Synagis:
- Synagis® 100 mg
- Palivizumab
- powder and liquid to
- injection liquid, solution
- Abbott
- Lot 28423TFX
- EU/1/99/117/H002
- Abbott Laboratories Ltd.
- Queenborough
- Kent ME11 5EL
- UK
  Columns

The columns used in this example were as presented in Table 5 below:

TABLE 5


Name in
report	Ligand	Column	Batch

Zwt	(Zwt)4	Column 2	1555047B
MabSelect ™	MabSelect	Column	2	U1555045A
Bwt	(Bwt)4	Column 1	U1555051B
SuRe	Alkali-	Column 6	U669082
	stabilized
	Domain B
SuRe	Alkali-	Column 2	U669082
	stabilized
	Domain B

Zwt refers to Protein Z, which is a mutated Domain B. It is denoted Zwt for ‘wild type’ herein, to clarify that the only mutation it comprises is that from Domain B to Protein Z. Protein Z has been described e.g. in U.S. Pat. No. 5,143,844.
MabSelect™ refers to the commercially available product (GE Healthcare, Uppsala, Sweden), wherein the ligands are comprised of recombinantly produced Protein A, which has not been mutated to improve the stability under alkaline conditions. Bwt refers to the true wild type of Domain B of SpA.
SuRe refers to the alkali-stable Domain B of SpA (SuRe) prepared according to the present invention, as described in the preceding examples.
Each column was packed with 2 ml matrix.
SuRe Column 6 was used for both Herceptin runs in Experiment 1 and one of the Enbrel runs in Experiment 1 (see Method description below).
SuRe Column 2 was used in the rest of the runs.
Reagents and Chemicals

Citric acid: Citric Acid Monohydrate, Merck, 1.00244.0500, lot K91294344538
NaCl: NaCl, Scharlau, SO 0227, lot 75078
NaOH: Sodium hydroxide solution 50%, Merck, 1.58793.1000, lot B612893517
Water: MilliQ
Sterile water: Autoclaved MilliQ
pH 7 standard: Buffer solution pH=7.00 (20° C.), yellow-coloured, Scharlau SO2007, Batch 73997
pH 2 standard: Buffer solution pH=2 (Citric acid/Sodium hydroxide/Hydrochloric acid), Scharlau S01022, Batch 72053
Buffers and Solutions
Buffer A: 50 mM Citric acid, 0.15 M NaCl, pH 6.0
Buffer B: 50 mM Citric acid, 0.15 M NaCl, pH 2.5
Instruments
Chromatography system: ÄKTA™explorer 10 controlled by the software UNICORN™ 5.01, GE Healthcare
Column hardware: Tricorn™ 5/100 GL, GE Healthcare nSample application device: Superloop™ (50 ml), GE Healthcare
pH meter: Laboratory pH Meter CG 842, SCHOTT
Filter for buffer: 75 mm Bottle Top Filter—500 ml, 0.2 μm pore size, Nalgene
Filter for sample: Minisart® Single use syringe filter, 0.2 μm pore size, Sartorius
Methods
Buffer Preparation

Citric acid and NaCl were dissolved in water. A pH meter was calibrated using pH 7 and pH 2 standard buffers. The pH was monitored while adding NaOH to the buffers until pH reached 6 and 2.5 for Buffer A and Buffer B respectively. The buffers were degassed and filtered prior use.
Sample Preparation
Preparation of Herceptin
Herceptin was dissolved to 21 mg/ml according to the manufacturers instructions by adding 7.2 ml sterile water into a vial containing lyophilized Trastuzumab (Herceptin).
For Experiment 1 a 1 mg/ml solution of Herceptin was prepared by diluting the 21 mg/ml solution with Buffer A.
For Experiment 2 a 5 mg/ml solution of Herceptin was prepared by diluting the 21 mg/ml solution with Buffer A.
Preparation of Enbrel
Enbrel was dissolved to 25 mg/ml according to the manufacturers instructions by adding 1 ml water for injection (provided by the manufacturer) into a vial containing lyophilized etanercept (Enbrel).
For Experiment 1 a 1 mg/ml solution of Enbrel was prepared by diluting the 25 mg/ml solution with Buffer A.
For Experiment 2 a 2.5 mg/ml solution of Enbrel was prepared by diluting the 25 mg/ml solution with Buffer A.
Preparation of Synagis
Synagis was dissolved to 100 mg/ml according to the manufacturers instructions by adding 1 ml water for injection (provided by the manufacturer) into a vial containing lyophilized Palivizumab (Synagis).
For Experiment 1 a 1 mg/ml solution of Synagis was prepared by diluting the 100 mg/ml solution with Buffer A. The 1 mg/ml solution was filtered prior sample application due to low levels of precipitation formed upon dilution.
For Experiment 2 a 5 mg/ml solution of Synagis was prepared by diluting the 100 mg/ml solution with Buffer A. The 5 mg/ml solution was filtered prior sample application due to low levels of precipitation formed upon dilution.
Method Description
This report describes two experiments—Experiment 1 and Experiment 2.
In Experiment 1 three biopharmaceuticals (Herceptin, Enbrel and Synagis) were loaded on and eluted from four different columns (packed with Zwt, MabSelect, Bwt and SuRe).
In Experiment 2 a higher load of the three biopharmaceuticals was applied onto two columns packed with MabSelect and SuRe.
Experiment 1
Each “run” in Experiment 1 was a scouting in which one type of sample was run on four different columns. Two such runs were performed on each sample and three different samples were used. This makes 4×2×3=24 individual runs i.e. chromatograms.
The following text describes a typical run. Four different columns were attached to ÄKTAexplorer 10. A 1 mg/ml solution of one type of sample (Herceptin, Enbrel or Synagis) was injected into a Superloop. Four collection tubes were connected to four positions of the outlet valve. Buffer tubing from the A pump was placed in Buffer A and buffer tubing from the B pump was placed in Buffer B. The ÄKTAexplorer pH electrode was calibrated with pH 7 and pH 2 standard buffers. A 1 cm UV cell was used.
ÄKTAexplorer 10 was controlled by UNICORN and schematically the program, or method, for Experiment 1 consisted of following parts:

Equilibration: 3 column volumes (CV) equilibration of the column with Buffer A.
Sample loading: 2 ml 1 mg/ml sample loaded onto the column (1 mg sample per ml matrix).
Wash: 4 CV wash of the column with Buffer A.
Elution: 20 CV gradient from 0% Buffer B to 100% Buffer B. After the gradient the column was washed with 5 additional column volumes of 100% Buffer B.
Reequilibration: 3 CV reequilibration with Buffer A.

In the elution step a watch function was included in the method: when the absorbance at 280 nm reached 50 mAu this watch was activated and made the outlet valve to switch to a specified position, enabling the collection of an eluted peak in a collection tube. When the absorbance at 280 nm dropped below 50 mAu the outlet valve switched back to its default waste position. Since a scouting run included four different columns the eluted peaks were collected in four individual tubes. Collecting peaks this way made it possible to measure pH of the peak i.e. the pH at which the sample was eluted. pH values of the eluates were measured with a laboratory pH meter calibrated with pH 7 and pH 2 standard buffers. pH was also monitored during the run with the ÄKTA pH meter.
Experiment 2
In Experiment 2 a higher amount of sample was applied to the columns. This was done to achieve conditions similar to those used in Protein A chromatography processes. Experiment 1 and Experiment 2 were performed essentially in the same way. The differences are listed below:

Columns: Two columns were used in this experiment—MabSelect and SuRe
Number of runs: Single runs were performed (i.e. two columns, one run per sample and three different samples makes six individual runs, or chromatograms).
Sample:
- 8 ml 5 mg/ml Herceptin (20 mg sample per ml matrix)
- 7 ml 2.5 mg/ml Enbrel (8.75 mg sample per ml matrix)
- 8 ml 5 mg/ml Synagis (20 mg sample per ml matrix)
UV cell: A 0.2 cm UV cell was used. This cell is less sensitive and more appropriate for larger amounts of sample.
Watch: The peak collection watch in the gradient was set to 100 mAU.
Evaluation of Chromatographic Results

pH of the eluted peaks was measured with an external pH meter after each scouting run. These pH values are called “External pH on eluate” in 3.1. pH measurements with the ÄKTA pH electrode could not be used in the evaluation of the results in the most desired way due to a drift of the pH curve over time. However, one pH curve—the curve that best matched the pH of the buffers (pH 6 and 2.5)—was used for all chromatograms when measuring the pH at which the eluted peak had its maximum absorbance at 280 nm (called “ÄKTA pH at max UV” in 3.1).
UV₂₈₀curves from the chromatographic runs were overlaid and grouped by sample. Thus, in Experiment 1 there are three figures for three samples (Herceptin, Enbrel and Synagis). Each figure displays two curves from four columns (Zwt, MabSelect, Bwt and SuRe). In Experiment 2 there are three figures for three samples (Herceptin, Enbrel and Synagis). Each figure displays one curve from two columns (MabSelect and SuRe).
Results

Experiment 1

TABLE 6


		ÄKTA pH	External pH
Sample	Ligand	at max UV	on eluate

Herceptin	Zwt	3.60	3.60
Herceptin	Zwt	3.61	3.63
Herceptin	MabSelect	3.14	3.17
Herceptin	MabSelect	3.13	3.15
Herceptin	Bwt	3.14	3.18
Herceptin	Bwt	3.14	3.18
Herceptin	SuRe	3.65	3.68
Herceptin	SuRe	3.64	3.67

TABLE 7


		ÄKTA pH	External pH
Sample	Ligand	at max UV	on eluate

Enbrel	Zwt	3.76	3.82
Enbrel	Zwt	3.76	3.84
Enbrel	MabSelect	3.84	3.88
Enbrel	MabSelect	3.84	3.88
Enbrel	Bwt	3.79	3.83
Enbrel	Bwt	3.79	3.85
Enbrel	SuRe	3.75	3.81
Enbrel	SuRe	3.76	3.77

TABLE 8


		ÄKTA pH	External pH
Sample	Ligand	at max UV	on eluate

Synagis	Zwt	3.76	3.81
Synagis	Zwt	3.76	3.79
Synagis	MabSelect	3.79	3.81
Synagis	MabSelect	3.79	3.78
Synagis	Bwt	3.77	3.83
Synagis	Bwt	3.76	3.79
Synagis	SuRe	3.76	3.77
Synagis	SuRe	3.76	3.78

Experiment 2

TABLE 9

ÄKTA pH External pH

Sample Ligand at max UV on eluate

Herceptin MabSelect 3.27 3.36

Herceptin SuRe 3.72 3.81

TABLE 10


		ÄKTA pH	External pH
Sample	Ligand	at max UV	on eluate

Enbrel	MabSelect	3.92	4.14
Enbrel	SuRe	3.84	4.05

TABLE 11


		ÄKTA pH	External pH
Sample	Ligand	at max UV	on eluate

Synagis	MabSelect	3.96	4.21
Synagis	SuRe	3.90	4.12

The above examples illustrate specific aspects of the present invention and are not intended to limit the scope thereof in any respect and should not be so construed. Those skilled in the art having the benefit of the teachings of the present invention as set forth above, can effect numerous modifications thereto. These modifications are to be construed as being encompassed within the scope of the present invention as set forth in the appended claims.

Claims

1. In a method of preparing a separation matrix comprising at least one ligand with affinity for the Fc part of an antibody, which method comprises

(a) providing a nucleic acid sequence encoding at least one alkali-stable domain B of staphylococcal Protein A (SpA);

(b) mutating said nucleic acid sequence to encode for a recombinant protein wherein at least one glycine has been replaced by an alanine;

(c) expressing the protein encoded by the nucleic acid sequence resulting from (b) in a host cell; and

(d) coupling the expressed protein to a support, the improvement being that the ligand(s) so prepared lack affinity for the Fab part of an antibody.

2. The method of claim 1, wherein in the alkali-stable domain B, the alkali-stability has been achieved by mutating at least one asparagine residue to an amino acid other than glutamine.

3. The method of claim 1, wherein in the alkali-stable domain B, the alkali-stability has been achieved by mutating at least one asparagine residue to an amino acid other than glutamine; and wherein glycine at position 29 of the alkali-stable domain B has been replaced by an alanine.

4. The method of claim 1, wherein the recombinant protein expressed in (c) is Protein Z in which the alkali-stability has been achieved by mutating at least one asparagine residue to an amino acid other than glutamine.

5. The method of claim 1, wherein the recombinant protein expressed in (c) is Protein Z in which the alkali-stability has been achieved by mutating at least the asparagine residue at position 23 to an amino acid other than glutamine.

6. The method of claim 1, wherein the nucleic acid provided encodes a multimer of two or more domains wherein at least one is Protein Z in which the alkali-stability has been achieved by mutating at least one asparagine residue to an amino acid other than glutamine.

7. In a method of separating one or more antibodies from a liquid, which method comprises

(a) contacting liquid with a separation matrix comprising ligands immobilised to a support;

(b) allowing antibodies to adsorb to said matrix by interaction with said ligands;

(c) optionally washing the adsorbed antibodies; and

(d) recovering antibodies by contacting said matrix with an eluent which releases the antibodies;

the improvement being that said ligands comprise one or more alkali-stable domain B of staphylococcal Protein A (SpA) wherein at least one glycine has been replaced by an alanine.

8. The method of claim 7, wherein the recovery of antibodies is achieved by adding an eluent having a pH in the range of 3.8-3.9.

9. The method of claim 7, wherein at least 80% of the antibodies are recovered using an eluent having a pH in the range of 3.7-3.9.

10. The method of claim 7, wherein at least 90% of the antibodies are recovered using an eluent having a pH in the range of 3.7-3.9.

11. The method of claim 7, wherein at least 95% of the antibodies are recovered using an eluent having a pH in the range of 3.7-3.9.