Patent Application
20210199653
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 2, 2020 is named P33225-US_1_Sequence_Listing.txt and is 75,296 bytes in size.
Herein is reported a fast and easy method for determining affinity constants of human IgG1s binding di- or multimeric antigens using surface plasmon resonance. The method is based on a highly specific and quantitative digestion with lysine-gingipain of Porphyromonas gingivalis generating a homogenous pool of intact Fab and Fc-fragments without any over-digestion of the fragments typically associated with other proteolytic enzymes.
The quality of a biopharmaceutical product is of decisive importance in addition to its action. Therefore in addition to a detailed investigation of the modes of action, it is absolutely essential to determine the identity, purity and activity of protein-based drugs in order to use them safely as therapeutic agents.
Although mAbs can be successfully analyzed by means of various separation and testing techniques, it has for a long time been difficult to apply and optimize RP-HPLC methods (RP-HPLC, Reversed Phase-High Performance Liquid Chromatography) to separate antibody species. However, various modifications of the antibody are often present simultaneously during the course of a degradation process, which makes it more difficult to analyze the diverse chromatographic and electrophoretic bands. Analysis by means of liquid chromatographic separation methods coupled with high resolution mass spectrometers (LC/MS, liquid chromatography/mass spectrometry) yields information about the exact mass of the various species and thus facilitates the identification of the antibody variants (Dillon, T. M., et al., J. Chromatogr. A, 1053 (2004) 299-305).
Papain, a cysteine protease, cleaves peptide bonds relatively non-specifically after arginine (R), lysine (K), glutamic acid (E), histidine (H), glycine (G) and tyrosine (Y). If the incubation period is sufficiently long, the papain digestion leads to a total hydrolysis. However, antibodies can be cleaved relatively selectively in their hinge region by a limited proteolysis (Lottspeich, F., and Engels, J. W., “Bioanalytik Spektrum Akademischer Verlag” Munich 2nd Edition (2006) 201-214). The cleavage occurs on the N-terminal side of the disulfide bridges which connect the two heavy chains together. The disulfide bridges are retained in this process so that three fragments (2 Fab fragments, 1 Fc fragment) are obtained after the digestion. The two N-terminal fragments are referred to as antigen-binding fragments (Fab, antigen-binding fragment), the C-terminal fragment is referred to as the crystalline fragment (Fc, crystallizing fragment). Each Fab fragment is composed of a complete light chain and the amino-terminal half of the heavy chain. The Fc fragment is composed of the two carboxy-terminal halves of the heavy chains which are still linked together by the disulfide bridge.
In recent years different IgG specific proteases have been identified.
In WO 2015/40125 streptococcal erythrogenic toxin B (SpeB) is reported. It is described as a cysteine protease from Streptococcus pyogenes, shown to cleave IgG in the hinge region into two stable monomeric Fab fragments and one Fc fragment. It is further reported that SpeB cleaves the hinge region of IgG between positions 238 and 239 according to the Kabat numbering system (positions 225 and 226 according to EU numbering system).
The cysteine endoprotease IdeS (Immunoglobulin degrading enzyme S) from the human pathogen Streptococcus pyogenes which is also referred to as Mac-1 or sib-38, is a cysteine protease that specifically cleaves the heavy chain of antibodies of the immunoglobulin G type (IgG). IgG is hitherto the only known substrate of IdeS (Vincents, B., et al., Biochem. 43 (2004) 15540-15549). IdeS consists of 339 amino acids including a signal peptide comprising 29 amino acids (von Pawel-Rammingen, U., et al., EMBO J. 21 (2002) 1607-1615) where an RGD motif is formed by the amino acids 214 to 216. IdeS cleaves human IgG (class G immunoglobulin) in the hinge region between positions 249 and 250 according to the Kabat numbering system (positions 236 and 237 according to EU numbering system) (Gly-Gly) which are contained in the recognition sequence LLGGP. Human IgG2 is cleaved between the amino acids alanine and glycine in the recognition motif PVAGP. Murine antibodies of the IgG2a and IgG3 type are also cleaved (Vincents, B., et al., Biochem. 43 (2004) 15540-15549).
Porphyromonas gingivalis is a major pathogenic factor of the progressive periodontal disease (see e.g. Kadowaki, T., et al., J. Biol. Chem. 269 (1994) 21371-21378). Therefrom different enzymes have been isolated, amongst them gingipains, trypsin-like cysteine proteases.
Kikuchi, Y., et al. reported the determination of concentration and binding affinity of antibody fragments by use of surface plasmon resonance (J. Biosci. Bioeng. 100, (2005) 311-317).
In WO 95/11298 a substantially pure Lys-gingipain complex preparation is provided, wherein Lys-gingipain being characterized as having an apparent molecular mass of 105 kDa as estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis, where sample is prepared without boiling, said Lys-gingipain having amidolytic and proteolytic activity for cleavage after lysine residues and having no amidolytic and/or proteolytic activity for cleavage after arginine residues, wherein the amidolytic and/or proteolytic activity is inhibited by TLCK, cysteine protease group-specific inhibitors including iodoacetamide and iodoacetic acid, wherein the amidolytic and/or proteolytic activity of said Lys-gingipain is not sensitive to inhibition by leupeptin, antipain, trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane, serine protease group-specific inhibitors including diisopropylfluorophosphate and phenylmethyl sulfonylfluoride, and antibodies specific for the Lys-gingipain protein complex and its catalytic component, methods for preparation.
Herein is reported a method for the determination of the binding affinity of a full length antibody of the human IgG1 subclass to its antigen using the fragment antigen binding (Fab) generated thereof in a surface plasmon resonance method whereby the Fabs are generated enzymatically by incubation with lysine-gingipain of Porphyromonas gingivalis and the reaction mixture is directly used for affinity determination without intermediate purification.
One aspect as reported herein is a method for determining the binding affinity of the binding sites of a bivalent full length antibody of the human IgG1 subclass to its homo-multimeric antigen comprising the following steps:
One aspect as reported herein is a method for determining the binding affinity of the binding sites of a bivalent full length antibody of the human IgG1 subclass to a homo-multimeric antigen comprising the following steps:
In one embodiment the method comprises the following steps:
In one embodiment the polypeptide that is derived from lysine-gingipain of Porphyromonas gingivalis is the lysine-gingipain of Porphyromonas gingivalis. In one embodiment the polypeptide that is derived from lysine-gingipain of Porphyromonas gingivalis comprises the amino acid sequence of SEQ ID NO: 02 or SEQ ID NO: 03 or SEQ ID NO: 04 or a functional variant thereof. In one embodiment the lysine-gingipain of Porphyromonas gingivalis has the amino acid sequence of SEQ ID NO: 02 or SEQ ID NO: 03 or SEQ ID NO: 04 or is a functional variant thereof. In one embodiment the polypeptide that is derived from lysine-gingipain of Porphyromonas gingivalis has an amino acid sequence that comprises at least residues 230 to 739 of SEQ ID NO: 01.
In one embodiment the reducing agent is selected from the group consisting of 2-mercaptoethanol, cysteine, and dithiothreitol. In one embodiment the reducing agent is cysteine. In one embodiment the reducing agent is cysteine at a concentration of (from) 0.5 mM to 10 mM. In one embodiment the reducing agent is cysteine at a concentration of about 2 mM.
In one embodiment the pH value is about pH 8.
In one embodiment the temperature is of (from) 35° C. to 38° C. In one embodiment the temperature is about 37° C.
In one embodiment the incubating is for a time of (from) 30 min. to 120 min. In one embodiment the incubating is for a time of about 60 min.
In one embodiment the antibody comprises in the Fc-region the mutations P329G, L234A and L235A in both heavy chain polypeptides.
One aspect as reported herein is a method for selecting an antibody (specifically binding to a homo-multimeric antigen) comprising the following steps:
As used herein, the amino acid positions of all constant regions and domains of the heavy and light chain are numbered according to the Kabat numbering system described in Kabat, et al., Sequences of Proteins of Immunological Interest, 5th ed., Public Health Service, National Institutes of Health, Bethesda, Md. (1991) and is referred to as “numbering according to Kabat” herein. Specifically, the Kabat numbering system (see pages 647-660) of Kabat, et al., Sequences of Proteins of Immunological Interest, 5th ed., Public Health Service, National Institutes of Health, Bethesda, Md. (1991) is used for the light chain constant domain CL of kappa and lambda isotype, and the Kabat EU index numbering system (see pages 661-723) is used for the constant heavy chain domains (CH1, Hinge, CH2 and CH3, which is herein further clarified by referring to “numbering according to Kabat EU index” in this case).
It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to “a cell” includes a plurality of such cells and equivalents thereof known to those skilled in the art, and so forth. As well, the terms “a” (or “an”), “one or more” and “at least one” can be used interchangeably herein. It is also to be noted that the terms “comprising”, “including”, and “having” can be used interchangeably.
The term “about” denotes a range of +/−20% of the thereafter following numerical value. In one embodiment the term about denotes a range of +/−10% of the thereafter following numerical value. In one embodiment the term about denotes a range of +/−5% of the thereafter following numerical value.
The term “lysine-gingipain of Porphyromonas gingivalis” denotes a polypeptide that specifically cleaves human IgG1 and IgG3 subclass heavy chains between positions 238 and 239 according to the Kabat numbering system (positions 225 and 226 according to EU numbering system), i.e. the hinge region amino acid sequence DKTHTCPPCPAPELLGGPSVF (SEQ ID NO: 05) is cleaved after the second amino acid residue resulting in the fragments DK (SEQ ID NO: 06) and THTCPPCPAPELLGGPSVF (SEQ ID NO: 07). In one embodiment the polypeptide, i.e. the lysine-gingipain of Porphyromonas gingivalis, comprises the amino acid sequence of SEQ ID NO: 02 or SEQ ID NO: 03 or SEQ ID NO: 04 or a functional variant thereof. In one embodiment the polypeptide, i.e. the lysine-gingipain of Porphyromonas gingivalis, has an amino acid sequence that comprises at least residues 230 to 739 of SEQ ID NO: 01. The “lysine-gingipain of Porphyromonas gingivalis” has the EC number 3.4.22.47 and is also denoted as gingipain K, KGP, Lys-gingipain, PrtP proteinase, lysine-specific cysteine protease, lysine-specific gingipain, lysine-specific gingipain K, or lysine-specific gingipain proteinase. The full length amino acid sequence of an exemplary lysine-gingipain of Porphyromonas gingivalis is denoted in SEQ ID NO: 01. This polypeptide is an endopeptidase with strict specificity for lysyl bonds. The enzymatic activity of the polypeptide is activated by the addition of about 30 2-mercaptoethanol, about 50 mM cysteine, about 30 mM dithiothreitol, about 2 mM EDTA, about 2 mM EGTA or glutathione. It is active in the pH range from pH 6.5 to pH 9.5, with a pH of from about pH 7.5 to about pH 8.5 (preferably about pH 8.0) being suitable for the hydrolysis of immunoglobulins. In an exemplary IgG degradation method the following conditions are used: IgG (final concentration 15 μM), KGP (final concentration 10 nM active protease), Tris buffer (0.1 mol/L, pH 8.0), EDTA (final concentration 1 mM), L-cysteine (final concentration 2 mM), 37° C. Human IgGs are cleaved once but if the glycostructures are removed a second cleavage might occur. The enzymatic cleavage can be negatively affected if chaotropic reagents and/or detergents are present. Thus, in one embodiment the method is performed in the absence of chaotropic reagents and/or detergents from all solutions used in the method.
The term “full-length antibody” denotes an antibody which comprises two so called light immunoglobulin chain polypeptides (light chain) and two so called heavy immunoglobulin chain polypeptides (heavy chain). Each of the heavy and light immunoglobulin chain polypeptides of a full-length antibody contains a variable domain (variable region) (generally the amino terminal portion of the polypeptide chain) comprising binding regions that are able to interact with an antigen. Each of the heavy and light immunoglobulin chain polypeptides of full-length antibody comprises a constant region (generally the carboxyl terminal portion). The constant region of the heavy chain mediates the binding of the antibody i) to cells bearing a Fc gamma receptor (FcγR), such as phagocytic cells, or ii) to cells bearing the neonatal Fc receptor (FcRn) also known as Brambell receptor. It also mediates the binding to some factors including factors of the classical complement system such as component (Clq). The variable domain of an antibody's light or heavy chain in turn comprises different segments, i.e. four framework regions (FR) and three hypervariable regions (CDR).
The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e. the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations, which include different antibodies directed against different antigenic sites (determinants or epitopes), each monoclonal antibody is directed against a single antigenic site on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies. The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies and is not to be construed as requiring production of the antibody by any particular method.
The “Fc-region” of an antibody is not involved directly in binding to the antibody's antigen, but exhibits various effector functions. Depending on the amino acid sequence of the constant region of the heavy chains, antibodies (immunoglobulins) are divided in the classes: IgA, IgD, IgE, IgG, and IgM. Some of these classes are further divided into subclasses (isotypes), i.e. IgG in IgG1, IgG2, IgG3, and IgG4, or IgA in IgA1 and IgA2. According to the immunoglobulin class to which an antibody belongs are the heavy chain constant regions of immunoglobulins are called □□□IgA), □(IgD), □ (IgE)□□□(IgG), and □ (IgM), respectively. The antibodies according to the invention belong preferably to the IgG class. An “Fc-region of an antibody” is a term well known to the skilled artisan and defined on basis of the papain cleavage of antibodies.
Normally antibodies, such as full length antibodies of the IgG class, are bivalent. Thus, when determining the affinity it should be a “true” affinity avoiding the avidity effect of the bivalent binder. To determine the affinity and binding kinetics of antibodies binding bi- or multivalent targets it is therefore necessary to turn the bivalent antibodies into monovalent binding entities like fragment antigen-binding (Fab) units.
Currently methods for the determination of the affinity of bivalent antibodies are two step methods:
Alternatively it is possible to re-clone and express the Fab fragment for which even more time and labor are required as for the approach outlined above.
Often, Fab fragments are generated by partial proteolytic digestions of IgGs with unspecific proteases like papain or pepsin, which cleave above or below the hinge region, respectively. The fragments contain the disulphide bonds that join the heavy chains, but the cleavage is below the site of the disulphide bond between the light chain and heavy chain (Porter, 1959; Nisonoff et al., 1960; Akita and Nakai, 1993, Andrew and Titus, 2003; Mage, 1987; Zhao et al., 2009; Andrew, S. M. and J. A. Titus. 2003).
IgGs digested with pepsin results in F(ab′)2 fragments that are subsequently mildly reduced to give Fab′ fragments. Most likely the hinge region is more susceptible to the attack of proteases as it is exposed and flexible. Subsequently, the fragments are then purified from the digestion mix.
However, lack of reproducibility, uncut IgG and over-digestion is often a problem.
With papain digestion, e.g., it is difficult to obtain homogeneous Fabs (Parham, 1983; 1986; Mage, 1987). Immobilized papain products (e.g. papain agarose resins; see e.g. Tischer, W., and V. Kasche, 1999; Luo, Q., et al. 2002) allow better control of the digestion reaction and efficient removal of the Fab and Fc fragments from the crude protease digest; nevertheless purification is still required.
Another approach to obtain monomeric antigen-binding fragments include the generation of F(ab′)2 fragments by digestion with Immunoglobulin G-degrading enzyme of S. pyogenes (IdeS) and mild reduction with 2-mercaptoethylamine (2-MEA) to generate Fab′ fragments (von Pawel-Rammingen, U., et al. 2002+2003; Ishikawa, E. and S. Yoshitake, 1980; DeSilva, B. S., et al., 1995).
The two antigen-binding domains of an antibody of the IgG class can also be obtained by reducing the IgG to two half-IgGs (rIgG; see e.g. Billah, M. M., et al., 2010). It is the product of selectively reducing just the hinge-region disulphide bonds which are the most accessible and easiest to reduce, especially with a mild reducing agents like 2-MEA.
Finally, a Fab can also be obtained by recombinant expression of the light chain and the heavy chain Fd-fragment (VH-CH1) (Zhao et al., 2009). This is however time consuming and laborious if several different Fabs are needed for e.g. a comparison.
A limited digestion using the endoproteinase Lys-C in a 40 min digestion of hIgG1's to analyze the chain assembly by mass spectrometry has been reported in PCT/EP2015/057164. Using this procedure Lys-C exclusively cuts once above the hinge region generating Fab and Fc-fragments.
A protease that cleaves selectively in the upper hinge region of antibodies of the IgGs class is streptococcal erythrogenic toxin B (SpeB) from S. pyogenes (von Pawel-Rammingen, U., et al. 2002). This protease requires reducing agent like DTT or TCEP in the range of 1-5 mM for activity (Persson, H., et al., 2013; www.genovis.com/fabulous) resulting in the concomitant reduction of the interchain thiols of the digested antibody.
IgG-specific proteases and their cleavage sites are shown in the following Table (see also Brerski, R. J. and Jordan, R. E., mAbs 2 (2010) 212-220).
porphyromonas
gingivalis
S. pyogenes
S. aureus,
S. pyogenes
The P. gingivalis proteases have been studied since more than 30 years. They have been identified as cysteine-proteinases requiring the presence of reducing agents for activity. One of them is the cysteine protease gingipain K (EC. 3.4.22.47).
Scott et al. purified lysine-gingipain of Porphyromonas gingivalis (KGP) back in 1993 (Scott, C. F., et al., J. Biol. Chem. 268 (1993) 7935-7942).
Scott et al. identified cysteine, dithiothreitol, glutathione and 2-mercaptoethanol to be suitable reducing agents for the activation of KGP.
KGP cleaves peptides with Lys in the P1 position, and the residue at P2 appears to be less important. However, if P2 is occupied by Lys or Arg, hydrolysis appears to be blocked. KGP is capable of hydrolyzing protein substrates such as BSA, casein, hemoglobin, acid-soluble human placental type I collagen, human IgG, and IgA (Curtis, M. A., et al., Crit. Rev. Oral Biol. Med. 12 (2001) 192-216).
The amino acid sequence of lysine-gingipain of Porphyromonas gingivalis including an identification of the respective domains was reported by Okamoto, K., et al. (J. Biochem. 120 (1996) 398-406). The kgp gene was reported and deposited by Slakeski, N., et al. under accession number U75366 and AAB60809.1 (Oral Microbiol. Immunol. 14 (1999) 92-97). Several C-terminally truncated but active forms have been identified. It has been found that for the C-terminally truncated proteins KGP(Δ1292-1732), KGP(Δ1157-1732), KGP(Δ738-1732), KGP(Δ681-1732) and KGP(Δ602-1732) enzymatic activity was only barely measurable for the last two mutants (see e.g. Sztukowska, M., et al., Mol. Microbiol. 54 (2004) 1393-1408).
KGP has a narrow specificity for synthetic substrates, limited to peptide bonds containing arginine and lysine residues, respectively, but they can nevertheless degrade immunoglobulins G and A in a limited degradation manner (Yamamoto, K., et al., In: Proteases: new Perspectives (1999), V. Turk (ed.), Birkhäauser Verlag Basel (CH), 175-184; Yamamoto, K., et al., In: N Katunuma, H Kido, H Fritz, J Travis (Eds): Medical Aspects of Proteases and Protease Inhibitors. 105 Press, Amsterdam, 139-149; Kadowaki, T., et al., J. Biol. Chem. 269 (1994) 21371-21378; Abe, N., et al., J. Biochem. 123 (1998) 305-312).
Comparative properties of envelope-associated arginine-gingipains (RGP) and lysine-gingipain (KGP) of Porphyromonas gingivalis have been reported in 1998 by Fujimura et al. (Microbiol. Lett. 163 (1998) 173-179). The enzymes were commonly activated by reducing reagents such as mercaptoethanol, dithiothreitol and cysteine. RGP-B was activated markedly by glycyl-glycine and KGP was activated significantly by EDTA and EGTA. The hydrolytic activities of RGPs and KGP to chromogenic synthetic substrates were limited to the compounds with arginine and lysine in the P-1 positions, respectively. When IgG was treated with the three enzymes separately, it was demonstrated that two new fragments of 34 kDa and 15 kDa (SDS under reducing conditions) were generated in each reaction product. The optimum pH for the activity of KGP was found to be 7.5. Thiol reagents activated both RGPs and KGP, whereas dithiothreitol was the best activator of KGP (at 20-30 mM), followed by mercaptoethanol (at 20-30 mM) and cysteine (at more than 1.5 mM but less than 10 mM). KGP split only X-Y-Lys-pNA.
Vincents, B., et al. reported that gingipain K of Porphyromonas gingivalis can hydrolyze subclass 1 and 3 of human IgG, whereby the heavy chain of IgG1 was cleaved at a single site within the hinge region, generating Fab and Fc fragments and that IgG3 was also cleaved within the heavy chain, but at several sites around the CH2 region (FASEB J., 25 (2011) 3741-3750). Cleavage of IgG2 is not mediated by KGP (Guentsch, A., et al., J. Periodont. res. 48 (2013) 458-465).
An high-resolution crystal structure of KGP active site was reported by de Diego, I., et al. suggesting that catalysis may require a catalytic triad, Cys477-His444-Asp388, rather than the cysteine-histidine dyad normally found in cysteine peptidases (J. Biol. Chem. 289 (2014) 32291-32302).
Different antibody fragments are described in the following:
Different from antibodies binding monomeric antigens, it is not feasible to determine the affinity without the influence of avidity of antibodies binding di- or multimeric antigens, for example by surface plasmon resonance (SPR).
Affinity describes the strength of a single interaction between antibody and its antigen. A bivalent antibody of the IgG class has two antigen-binding sites, and the avidity is commonly applied to antibody interactions in which multiple antigen-binding sites simultaneously interact with the target antigen, often in multimeric structures. The avidity of an antibody refers to the accumulated strength of multiple affinities. Avidity is commonly obtained regarding interactions in which multiple antigen-binding sites, often in multimeric structures, are involved. To determine the affinity of antibodies it is necessary to convert the bivalent antibodies into monovalent binding entities like antigen-binding fragments (Fab).
The determination of affinity constants of antibodies targeting di- or multimeric antigens by SPR therefore necessitates the generation of monomeric antigen-binding fragments, such as e.g. Fabs. The generation of Fabs is however laborious. Often, Fabs are generated by partial proteolytic digestions with papain.
Herein is reported a fast and easy method for the generation of Fabs from full length antibodies of the IgG1 subclass. It has been found that the lysine-gingipain of Porphyromonas gingivalis can be used for the generation of Fabs from full length antibodies of the IgG1 subclass as with this enzyme a highly specific and quantitative protease digestion generating a homogenous pool of intact Fab and Fc-fragments without any over-digestion typically associated with other proteolytic enzymes can be achieved and the reaction mixture can directly, i.e. without any intermediate purification, be applied to a surface plasmon resonance chip.
In more detail this is done by in solution digestion and direct kinetic affinity determination of the Fab fragment by SPR without any prior purification or cleaning step. The complete digestion by the lysine-gingipain of Porphyromonas gingivalis of human IgG1s was verified by ESI-QTOF-MS.
The method as reported herein can be used for the determination of kinetic rate constants of human or humanized antibodies, e.g. of the subclass IgG1 or comprising an Fc-region derived from the human subclass IgG1, specifically binding to di- or multimeric antigens using a surface plasmon resonance method. The method comprises in one embodiment the following steps: 1) incubating the antibody with the lysine-gingipain of Porphyromonas gingivalis to cleave it completely generating a homogenous pool of Fabs and Fc-fragments, and 2) determining the binding affinity of the Fab in the digestion mixture by surface plasmon resonance (SPR). Direct SPR on the digestion mixture allows precise kinetic characterization of the Fab fragment without any prior purification.
It has been found that the affinity constants determined by SPR of Fabs of antibodies of the IgG1 subclass obtained by digesting with the lysine-gingipain of Porphyromonas gingivalis without subsequent purification correspond to affinity constants of Fabs obtained by recombinant expression, or by digesting with papain and subsequent purification prior to SPR measurement.
One aspect as reported herein is a method for determining the binding affinity of the binding sites of a bivalent full length antibody of the human IgG1 subclass to its antigen comprising the following steps:
In one embodiment the method comprises the following steps:
In one embodiment the polypeptide that is derived from lysine-gingipain of Porphyromonas gingivalis is the lysine-gingipain of Porphyromonas gingivalis. In one embodiment the polypeptide that is derived from lysine-gingipain of Porphyromonas gingivalis comprises the amino acid sequence of SEQ ID NO: 02 or SEQ ID NO: 03 or SEQ ID NO: 04 or a functional variant thereof. In one embodiment the polypeptide that is derived from lysine-gingipain of Porphyromonas gingivalis has an amino acid sequence that comprises at least residues 230 to 739 of SEQ ID NO: 01.
In one embodiment the reducing agent is selected from the group consisting of 2-mercaptoethanol, cysteine, and dithiothreitol. In one embodiment the reducing agent is cysteine. In one embodiment the reducing agent is cysteine at a concentration of from 0.5 mM to 10 mM. In one embodiment the reducing agent is cysteine at a concentration of about 2 mM.
In one embodiment the pH value is about pH 8.
In one embodiment the temperature is of from 35° C. to 38° C. In one embodiment the temperature is about 37° C.
In one embodiment the incubating is for a time of from 30 min. to 120 min. In one embodiment the incubating is for a time of about 60 min.
In one embodiment the antibody comprises in the Fc-region the mutations P329G, L234A and L235A in both heavy chain polypeptides.
In one embodiment the antigen is multimeric antigen. In one embodiment the antigen is a homo-multimeric antigen. In one embodiment the antigen is selected from the group consisting of vascular endothelial growth factor A (VEGF-A), carcinoembryonic antigen (CEA), angiopoietin-2 (ANG2), and fibroblast activation protein (FAP).
One aspect as reported herein is a method for selecting an antibody comprising the following steps:
The method as reported herein allows for a fast determination of the affinity of a bivalent full length antibody for its antigen without the requirements to recombinantly produce a single binding site version of the antibody. With the method as reported herein the determination of the biding affinity of the bivalent full length antibody for its antigen is possible without the need for an intermediate purification of the reaction mixture that has been used for the generation of the Fabs of the bivalent full length antibody.
The method as reported herein has been exemplified in the following with the antibody bevacizumab. Bevacizumab is a humanized anti-VEGF antibody of the human IgG1 subclass. The therapeutic antibody bevacizumab binds a dimeric antigen, i.e. VEGF-A (dimeric is a form of homo-multimeric).
The quality of the bevacizumab Fabs and digests was analyzed by UHR ESI-QTOF mass spectrometry. The deconvoluted mass spectra of the purified Fab following a papain digest, and a purified recombinant Fab provided proof for the high quality of both materials as only the masses of the Fab fragments could be detected.
In more detail, complete digestion of bevacizumab by the lysine-gingipain of Porphyromonas gingivalis was verified by electrospray ionization mass spectrometry after desalting of the reaction mixture using a size exclusion chromatography. No fragmentation or side products could be identified in the MS spectra.
For comparison bevacizumab has been digested using the enzyme papain. Form the MS spectra it can be seen that papain is not suitable for functional assessment due to unspecific fragmentation of the antibody and loss of function.
The respective MS-spectra are shown in
In more detail, the quality of the recombinant bevacizumab Fab and papain and lysine-gingipain of Porphyromonas gingivalis digests were analyzed by UHR ESI-QTOF mass spectrometry. The deconvoluted mass spectra of the purified Fab following a papain digest, and a purified recombinant Fab revealed the high quality of both materials as only the masses of the intact Fab 48208 Da (theoretical average mass: 48208 Da) and 47726 Da (theoretical average mass: 47726), respectively, could be detected. The evaluation of the mass spectrum of bevacizumab digested with papain revealed not only the presence of the 48207 Da Fab (theoretical average mass: 48208 Da) and the Fc-fragments (multiple masses present due to heterogeneity of the Fc N-glycan's). In addition, unassignable fragments corresponding to the masses x:23422 Da and 23453 Da, y:34587 Da, and z:47607 Da were detected in the papain digest. In contrast the deconvoluted mass spectrum of bevacizumab digested with the lysine-gingipain of Porphyromonas gingivalis demonstrated only the presence of the 47969 Da Fab (theoretical average mass: 47970 Da) and the Fc-fragment (multiple masses present due to the Fc N-glycan's). The digestion with the lysine-gingipain of Porphyromonas gingivalis was complete without any undigested or single cut IgG (IgG without one Fab) detectable by mass spectrometry. Nor could any unspecific digestion, over-digestion, or further degradation of the fragments be detected in the crude digestion mixture of the lysine-gingipain of Porphyromonas gingivalis digest.
The method as reported herein was performed with different bevacizumab-derived samples:
In order to compare the affinities of the different produced Fabs of bevacizumab the binding affinities of bevacizumab digested with the lysine-gingipain of Porphyromonas gingivalis without purification of the Fab and the binding affinities of a recombinant transiently expressed bevacizumab Fab, a purified Fab following a papain digest were determined.
For determining the affinities a murine anti-His-tag antibody was immobilized and the dimeric VEGF-A conjugated to a His-tag was captured on the sensor chip surface. Afterwards, the analytes binding to VEGF-A were injected and flew over the surface. The derived sensorgrams were fitted to a 1:1 Langmuir binding model and used to determine the association rate constants ka, the dissociation rate constants kd, and the binding constants KD. Generally, the rate and binding constants for the Fab fragments were all very similar (see Table below). The binding constant of the Fab in the lysine-gingipain of Porphyromonas gingivalis digestion mixture was found to be 1.1 nM, and those of the recombinant Fab and the purified Fab after digestion with papain were determined to 0.8 and 1.0 nM, respectively. The KD of the full length bivalent antibody was determined to be 0.18 nM demonstrating the avid binding to the dimeric VEGF-A. But when the papain digestion mixture was applied to the immobilized chip surface, we did not observe binding to the captured dimeric VEGF-A. Consequently, no binding constant could be determined for the papain digestion mixture. It has been found that the VEGF-A surface was damaged after applying the papain containing samples as it could not be used anymore.
The results are presented in the following Table.
It can be seen that as the lysine-gingipain of Porphyromonas gingivalis is specific for human IgG1, it does not destroy the immobilized chip surface. In contrast thereto no binding was observed after the not purified papain digestion reaction mixture was applied to the immobilized chip surface. The VEGF surface could not be used any more after applying the papain containing sample as it has been damaged by the presence of papain.
The respective SPR diagrams are shown in
Storage of the lysine-gingipain of Porphyromonas gingivalis-digested bevacizumab and repeated affinity determinations by SPR allowed to conclude the digests to be stable at 4° C. for at least 24 and 48 hours, respectively, i.e. no further digestion or fragmentation occurred.
Beside the use of lysine-gingipain of Porphyromonas gingivalis for the determination of affinities of human IgG1 s binding di- or multimeric antigens, the protease can also be used in cases where IgG1s binding monomeric antigens are difficult to immobilize on the SPR metal surface.
In addition, the lysine-gingipain of Porphyromonas gingivalis will be very beneficial for the structural analysis of the Fab fragments and structure-function relationships of human IgG1-antigen binding at atomic resolution, e.g., by X-ray crystallography. Compared with IgGs, Fab fragments are more amenable to crystallization.
Antibodies may be produced using recombinant methods and compositions, e.g., as described in U.S. Pat. No. 4,816,567. In one embodiment, isolated nucleic acid encoding an antibody as described herein is provided. Such nucleic acid may encode an amino acid sequence comprising the VL and/or an amino acid sequence comprising the VH of the antibody (e.g., the light and/or heavy chains of the antibody). In a further embodiment, one or more vectors (e.g., expression vectors) comprising such nucleic acid are provided. In a further embodiment, a host cell comprising such nucleic acid is provided. In one such embodiment, a host cell comprises (e.g., has been transformed with): (1) a vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and an amino acid sequence comprising the VH of the antibody, or (2) a first vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and a second vector comprising a nucleic acid that encodes an amino acid sequence comprising the VH of the antibody. In one embodiment, the host cell is eukaryotic, e.g. a Chinese Hamster Ovary (CHO) cell or lymphoid cell (e.g., Y0, NS0, Sp20 cell). In one embodiment, a method of producing an antibody as reported herein is provided, wherein the method comprises culturing a host cell comprising a nucleic acid encoding the antibody, as provided above, under conditions suitable for expression of the antibody, and optionally recovering the antibody from the host cell (or host cell culture medium).
For recombinant production of an antibody, nucleic acid encoding an antibody, e.g., as described above, is isolated and inserted into one or more vectors for further cloning and/or expression in a host cell. Such nucleic acid may be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody).
Suitable host cells for cloning or expression of antibody-encoding vectors include prokaryotic or eukaryotic cells described herein. For example, antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed. For expression of antibody fragments and polypeptides in bacteria, see, e.g., U.S. Pat. Nos. 5,648,237, 5,789,199, and 5,840,523. (See also Charlton, K. A., In: Methods in Molecular Biology, Vol. 248, Lo, B. K. C. (ed.), Humana Press, Totowa, N.J. (2003), pp. 245-254, describing expression of antibody fragments in E. coli.) After expression, the antibody may be isolated from the bacterial cell paste in a soluble fraction and can be further purified.
In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for antibody-encoding vectors, including fungi and yeast strains whose glycosylation pathways have been “humanized,” resulting in the production of an antibody with a partially or fully human glycosylation pattern. See Gerngross, T. U., Nat. Biotech. 22 (2004) 1409-1414; and Li, H. et al., Nat. Biotech. 24 (2006) 210-215.
Suitable host cells for the expression of glycosylated antibody are also derived from multicellular organisms (invertebrates and vertebrates). Examples of invertebrate cells include plant and insect cells. Numerous baculoviral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells.
Plant cell cultures can also be utilized as hosts. See, e.g., U.S. Pat. Nos. 5,959,177, 6,040,498, 6,420,548, 7,125,978, and 6,417,429 (describing PLANTIBODIES™ technology for producing antibodies in transgenic plants).
Vertebrate cells may also be used as hosts. For example, mammalian cell lines that are adapted to grow in suspension may be useful. Other examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293 cells as described, e.g., in Graham, F. L. et al., J. Gen Virol. 36 (1977) 59-74); baby hamster kidney cells (BHK); mouse sertoli cells (TM4 cells as described, e.g., in Mather, J. P., Biol. Reprod. 23 (1980) 243-252); monkey kidney cells (CV1); African green monkey kidney cells (VERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); human lung cells (W138); human liver cells (Hep G2); mouse mammary tumor (MMT 060562); TRI cells, as described, e.g., in Mather, J. P. et al., Annals N.Y. Acad. Sci. 383 (1982) 44-68; MRC 5 cells; and FS4 cells. Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including DHFR-CHO cells (Urlaub, G. et al., Proc. Natl. Acad. Sci. USA 77 (1980) 4216-4220); and myeloma cell lines such as Y0, NS0 and Sp2/0. For a review of certain mammalian host cell lines suitable for antibody production, see, e.g., Yazaki, P. and Wu, A M., Methods in Molecular Biology, Vol. 248, Lo, B. K. C. (ed.), Humana Press, Totowa, N.J. (2004), pp. 255-268.
General chromatographic methods are known to a person skilled in the art e.g. Chromatography, 5th edition, Part A: Fundamentals and Techniques, Heftmann, E. (ed.); Elsevier Science Publishing Company, New York, (1992); Advanced Chromatographic and Electromigration Methods in Biosciences, Deyl, Z. (ed.), Elsevier Science BV, Amsterdam, The Netherlands, (1998); Chromatography Today, Poole, D. F., and Poole, S. K., Elsevier Science Publishing Company, New York, (1991); Scopes, Protein Purification: Principles and Practice (1982); Sambrook, J., et al. (ed.), Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; or Current Protocols in Molecular Biology, Ausubel, F. M., et al. (eds.), John Wiley & Sons, Inc., New York.
The following examples and figures are provided to aid the understanding of the present invention, the true scope of which is set forth in the appended claims. It is understood that modifications can be made in the procedures set forth without departing from the spirit of the invention.
Bevacizumab was obtained from Roche Diagnostics GmbH (Mannheim, Germany). Papain was obtained as suspension with a concentration of 10 mg/mL from Sigma-Aldrich/Roche Diagnostics GmbH. Lysine-gingipain of Porphyromonas gingivalis was obtained under the trade name GingisKHAN from Genovis (Lund, Sweden). GingisKHAN was reconstituted in 200 μL double distilled water (ddH2O) resulting in 2000 U/200 μL, and the 10× reducing agent was freshly prepared in 50 μL ddH2O (final concentration: 20 mM cysteine) prior to each digestion.
The antibody light chain and heavy chain Fd-fragments were ordered as gene syntheses and cloned via unique restriction sites using standard cloning procedures into separate expression vectors for each chain enabling secretory expression in HEK cells growing in suspension. Transfection (1:1 plasmid ratios) into HEK293-F cells (Invitrogen, Cat. No. 510029) was performed according to the cell supplier's instructions using Maxiprep (Qiagen, Cat. No. 12163) preparations of the antibody vectors, Opti-MEM I medium (Invitrogen, Cat. No. 31985) 293fectin (Invitrogen, Cat. No. 31985070), and an initial cell density of 1-2×10E+06 viable cells/mL in serum-free FreeStyle 293 expression medium (Invitrogen, Cat. No. 12338018). Antibody containing cell culture supernatants were harvested after 7 days of cultivation in shake flasks by centrifugation at 14,000×g for 30 min. and filtered through a 0.22 μm sterile filter (Thermo Scientific, Cat. No. 566-0020). The antibodies were purified directly from the supernatant, or the supernatant was stored at −80° C. until purification. The quality of the purified Fab was analyzed by SEC and BioAnalyzer.
Enzymatic Cleavage of Bevacizumab with Papain
The antibody was diluted in 20 mM Histidine, 140 mM NaCl, pH 6.0 to a final concentration of 1 mg/mL, added 2 μL 250 mM L-cysteine (Sigma-Aldrich, Schnelldorf, Germany) and 10.9 μL diluted papain (7.34 U/mL in 20 mM Histidine, 140 mM NaCl, pH 6.0), and incubated 1 h at 37° C.
The antibody was incubated with Papain (0.8 U/mg mAb; Sigma-Aldrich/Roche) in presence of 5 mM Cystein for 170 minutes at 37° C. To isolate the Fab from non-cleaved antibodies, Fc-fragments and Papain, the mixture was applied to a CaptureSelect IgG-CH1 and MabSelectSuRe affinity chromatography (GE Healthcare) according to manufacturer protocol. Finally, a size exclusion chromatography using a Superdex 75 10/300 GL column (GE Healthcare) was performed using 140 mM NaCl, 20 mM histidine (pH 6.0) as running buffer. Protein concentration of the Fab was determined by measuring the optical density (OD) at 280 nm, using the molar extinction coefficient calculated on the basis of the amino acid sequence. The purity was analyzed by SDS-PAGE in the presence and absence of a reducing agent (5 mM 1,4-dithiotreitol) and staining with Coomassie brilliant blue.
Enzymatic Cleavage of Bevacizumab with Lysine-Gingipain of Porphyromonas Gingivalis
GingisKHAN was reconstituted in 200 μL ddH2O resulting in 2000 U/200 μL, and the 10× reducing agent was freshly prepared in 50 μL ddH2O (final concentration: 20 mM Cysteine) prior to each digestion. 100 μg antibody was diluted to a final concentration of 1 mg/mL in 100 mM Tris, pH 8.0 and subsequently digested with 10 μL GingisKHAN and 11 μL of freshly prepared 10× reducing agent at 37° C. for 1 hour.
Samples were desalted by HPLC on a Sephadex G25 column (Kronlab, 5×250 mm, TAC05/250G0-SR) using 40% acetonitrile with 2% formic acid (v/v). The total mass was determined via ESI-QTOF MS on a maXis 4G UHR-QTOF MS system (Bruker Daltonik) equipped with a TriVersa NanoMate source (Advion). Calibration was performed with sodium iodide (Waters ToF G2-Sample Kit 2 Part: 700008892-1). For the recombinant and purified Fabs, data acquisition was done at 900-2600 m/z (ISCID: 0.0 eV), for the hIgG1s or digested hIgG1s, data acquisition was done at 900-4000 m/z (ISCID: 0.0 eV). The raw mass spectra were evaluated and transformed into individual relative molar masses using an in-house developed Roche software tool. For visualization of the results, the same in-house developed software was used to generate deconvoluted mass spectra.
Binding affinities and kinetics were investigated by surface plasmon resonance using a BIAcore T200 instrument (GE Healthcare). All experiments were performed at 25° C. using PBS-T (10 mM Na2HPO4, 140 mM NaCl, 0.05% Tween 20, pH 7.4) as running and dilution buffer. An anti-His-tag (GE Healthcare, #28995056) or an anti-human Fab antibody (GE Healthcare, #28958325) was immobilized on a Series S CMS Sensor Chip (GE Healthcare, #29104988) using standard amine coupling chemistry. Histidine-tagged human VEGF or full length IgG/Fabs were captured on the surface leading to a response between 10 and 50 RU. The analytes were injected for 180 s at concentrations from 2.2 nM up to 1800 nM onto the surface (association phase) at a flow rate of 30 μL/min. The dissociation phase was monitored for up to 3600 sec. by washing with running buffer. The surface was regenerated by injecting 10 mM Glycine pH 1.5 for 60 sec. at a flow rate of 5 μL/min. Bulk refractive index differences were corrected by subtracting the response obtained from a mock surface and by subtracting blank injections (double referencing). The derived curves were fitted to a 1:1 Langmuir binding model using the BIAevaluation software.
| Number | Date | Country | Kind |
|---|---|---|---|
| 15198556.1 | Dec 2015 | EP | regional |
This application is a continuation of U.S. application Ser. No. 16/003,450, filed on Jun. 8, 2018, which is a continuation of International Patent Application No. PCT/EP2016/079756, having an international filing date of Dec. 5, 2016, the entire contents of which are incorporated herein by reference, and which claims benefit under 35 U.S.C. § 119 to European Patent Application No. 15198556.1, filed on Dec. 9, 2015.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16003450 | Jun 2018 | US |
| Child | 17062279 | US | |
| Parent | PCT/EP2016/079756 | Dec 2016 | US |
| Child | 16003450 | US |
