Patent Application
20150274807
The invention relates to a method for preparing a mixture of homodimer proteins, in particular to a method for preparing a mixture of homodimer proteins by using repulsive interaction of charges. The invention further relates to a homodimer protein mixture obtained by the method and uses of the method for preparing the homodimer protein mixture.
Monoclonal antibody drugs have made significant progress in recent 15 years and have become driving force in pharmaceutical industry. Since 1996, about 30 monoclonal antibody drugs in total have been approved, wherein the annual sales for nine drugs reached over 1 billion US dollars. In 2010, the overall sales of monoclonal antibody drugs were over 30 billion US dollars and the annual rate of growth was over 10%. The monoclonal antibody only inhibits a single target due to the high specificity against the target thereof. However, it may be necessary to inhibit multiple targets/signal pathways to avoid a compensatory effect for tumors, autoimmune diseases, and other diseases. For viral infection, due to the high mutation rate of viruses, in general, it is necessary to inhibit multiple antigenic sites in order to prevent escape. There are several alternative solutions. One is to use polyclonal antibodies, or to obtain a heterodimer, e.g. a bispecific antibody, by modifying Fc fragments of antibodies. Another solution is to use an antibody mixture for treatment, wherein the antibody mixture comprises two or more antibodies against different epitopes on the same target, or against different targets.
U.S. Pat. No. 7,262,028 discloses a method for producing a bivalent antibody or a mixture of bivalent antibodies from a single host cell clone by expression of one light chain and different heavy chains, and also provides a method for producing a combination of antibodies which can be screened for the usefulness in various applications.
WO/2010/084197 describes a method for producing a mixture comprising two or more different antibodies from a single host cell clone. In one embodiment, a mixture of different monovalent antibodies is produced. In another embodiment, a mixture of monovalent and bivalent antibodies is produced. In the method, homodimers are stabilized by virtue of the natural exchange phenomenon between two Fab arms of IgG4, wherein some residues of the hinge region and CH3 domain which caused the phenomenon are changed. However, the patent does not mention whether the problem of existence of heterodimers is completely solved.
U.S. Pat. No. 5,789,208 and U.S. Pat. No. 6,335,163 described a method for expressing a library of polyclonal antibodies, wherein a library of polyclonal Fab fragments was expressed on a phage display vector, and then screened for the reactivity to antigens. The selected combinations of variable region genes of heavy chains and light chains are transferred in a linked pairing way into an eukaryotic expression vector comprising constant region genes so as to obtain a sub-library of complete polyclonal antibodies. After the sub-library is transfected into myeloma cells, stable clones would produce antibodies which can be mixed to obtain a mixture of monoclonal antibodies. By using the method, although it is theoretically possible to directly obtain polyclonal antibodies from one recombination production process by culturing a group of mixed transfected cells, there may be potential problems in terms of the stability of group of the mixed cells and thus the consistency of the produced polyclonal antibodies. In a pharmaceutically acceptable large-scale (industrial) production method, it is an arduous task to control different cells in a whole group. For example, the properties such as the growth rate of cells and the production rate of antibodies should be kept stable for all single clones in the non-clonal group, so that the ratio of the antibodies in the mixture of polyclonal antibodies can be kept constant. Therefore, although the production for mixed antibodies may have been realized in the art, there are still no ameanable solutions which are economically and practically sounding for large scale manufacturing.
Recently, Merck and Symphogen A/S company from Denmark signed an exclusive worldwide license agreement for Sym004. Sym004 is a novel antibody mixture which is now being developed and targets the epithelial growth factor receptor (EGFR).
Sym004 consists of two antibodies, can block ligand binding, receptor activation and downstream signaling, and is also considered to elicit removal of the EGFR receptors from the cancer cell surface by inducing EGFR internalization and degradation. Sym004 is currently being evaluated in a Phase I/II trial for the treatment of patients with advanced wild-type KRAS metastatic colorectal cancer (mCRC) who have previously progressed on treatment with standard chemotherapy and a commercially available anti-EGFR monoclonal antibody. In addition, a Phase II trial in patients with squamous cell carcinoma of the head and neck (SCCHN) who have failed anti-EGFR-based therapy is currently ongoing.
The antibody mixture technology of Symphogen A/S company involves the following: firstly obtaining a plurality of antibodies against the same target by an antibody screening platform, then performing molecular construction for each antibody, culturing cells in shake-flask, and mixing the cells, and culturing the cell mixture in a way of gradual amplification culture, then performing a optimized purification to obtain the final product. However, the method still involves the problems caused by unstable cell growth rate and antibody production rate, since recombinant host cells are used in the method for producing a mixture of various homodimers. Because a single antibody is expressed in a single cell in the method, the method does not involve the problem of heterodimers.
In all means, it would be a more ideal for producing a protein or antibody mixture, If two or more proteins or antibodies can be produced in single recombinant cell clone,
Based on a large body of experiments, the inventors developed a method for simultaneously preparing two or more proteins or antibodies from a single recombinant cell clone. The invention specifically comprises the following aspects:
The first aspect of the invention relates to a method for obtaining a mixture containing two or more proteins by using single recombinant cell clone, wherein the protein is in the form of a dimer which is formed by polymerization between monomer chains, and the two or more proteins contain the same domain, wherein the method comprises the step of replacing part of residues of the two monomer chains in the same domain of one or more proteins with the opposite-charged amino acid(s), so that the monomer chains from different proteins are unfavorable to forming heterodimers due to the repulsive interaction between like charges, while the monomer chain from the same protein is more favorable to forming homodimers due to the attractive interaction between opposite charges.
In an embodiment of the invention, the protein is an antibody or a fusion protein comprising a part of the antibodies.
The method according to any one embodiment of the first aspect of the invention, the residues of at most one protein are not replaced. In an embodiment of the invention, the residues of one protein are not replaced while the residues of the other protein are replaced. In another embodiment of the invention, the residues of the two proteins are both replaced.
When the residues of multiple (two or more) proteins are replaced, at least one position of the replaced residues among different proteins are different, preferably, all the positions of the replaced residues among different proteins are different.
The method according to any one embodiment of the first aspect of the invention, the same domain refers to CH3 domain of an antibody.
The method according to any one embodiment of the first aspect of the invention, the same domain refers to Fc region of an antibody.
The method according to any one embodiment of the first aspect of the invention, the antibodies are derived from mammals, such as human, mice or rats.
The method according to any one embodiment of the first aspect of the invention, the antibodies are selected from the group consisting of IgG (such as IgG1, IgG2, IgG3), IgA (such as IgA1, IgA2), IgE, IgD and IgM (such as IgM1, IgM2).
The method according to any one embodiment of the first aspect of the invention, replacing part of residues in the same domains with the opposite-charged residues comprises the following steps:
(1) obtaining the interface residues between the same domains of the two monomer chains of the protein;
(2) selecting paired residues with paired positive and negative charges from the interface residues obtained in step (1); and
(3) selecting one or more pairs (such as two pairs, three pairs or four pairs) of residues from the paired residues with the paired positive and negative charges obtained in step (2), and replacing residues of the selected pairs with the opposite-charged residues.
In an embodiment of the invention, the charged amino acid is selected from the group consisting of lysine (lys), arginine (Arg), histidine (His), aspartic acid (Asp) and glutamic acid (Glu).
In an embodiment of the invention, the same domain refers to the Fc region or the CH3 domain of the antibody, and the paired charged residues with the paired positive and negative charges are selected from the group consisting of the following paired residues as shown in a)-h):
a) Glu (E) at position 356 of the first chain and Lys (K) at position 439 of the second chain;
b) Glu (E) at position 357 of the first chain and Lys (K) at position 370 of the second chain;
c) Lys (K) at position 370 of the first chain and Glu (E) at position 357 of the second chain;
d) Lys (K) at position 392 of the first chain and Asp (D) at position 399 of the second chain;
e) Asp (D) at position 399 of the first chain and Lys (K) at position 392 of the second chain;
f) Asp (D) at position 399 of the first chain and Lys (K) at position 409 of the second chain;
g) Lys (K) at position 409 of the first chain and Asp (D) at position 399 of the second chain; and
h) Lys (K) at position 439 of the first chain and Glu (E) at position 356 of the second chain;
the positions of the above 8 pairs of residues are determined according to the EU numbering index of KABAT system for antibody.
In an embodiment of the invention, replacing the part of residues of the two monomer chains in the same domains of one or more proteins with the opposite-charged residues refers to one or any combination of the following situations:
(1) replacing Lys at position 392 with Asp, replacing Lys at position 409 with Asp and replacing Asp at position 399 with Lys for one protein;
(2) replacing Glu at position 356 with Lys and replacing Lys at position 439 with Glu for one protein;
(3) replacing Glu at position 357 with Lys and replacing Lys at position 370 with Glu for one protein;
(4) replacing Glu at position 357 with Lys, replacing Lys at position 370 with Glu, replacing Lys at position 392 with Asp, replacing Lys at position 409 with Asp and replacing Asp at position 399 with Lys for one protein;
(5) replacing Lys at position 392 with Asp and replacing Asp at position 399 with Lys for one protein;
(6) replacing Asp at position 399 with Lys and replacing Lys at position 409 with Asp for one protein;
(7) replacing Lys at position 392 with Asp, replacing Lys at position 409 with Asp and replacing Asp at position 399 with Lys for one protein; and simultaneously, replacing Glu at position 357 with Lys and replacing Lys at position 370 with Glu for the other protein; and
(8) replacing Lys at position 392 with Asp, replacing Lys at position 409 with Asp and replacing Asp at position 399 with Lys for one protein; and simultaneously, replacing Glu at position 356 with Lys and replacing Lys at position 439 with Glu for the other protein.
In an embodiment of the invention, the paired charged residues with the paired positive and negative charges in sequence as shown in SEQ ID NO: 2 are 8 pairs of residues as shown in a1)-h1):
a1) Glu (E) at position 161 of the first chain and Lys (K) at position 244 of the second chain;
b1) Glu (E) at position 162 of the first chain and Lys (K) at position 175 of the second chain;
c1) Lys (K) at position 175 of the first chain and Glu (E) at position 163 of the second chain;
d1) Lys (K) at position 197 of the first chain and Asp (D) at position 204 of the second chain;
e1) Asp (D) at position 204 of the first chain and Lys (K) at position 197 of the second chain;
f1) Asp (D) at position 204 of the first chain and Lys (K) at position 214 of the second chain;
g1) Lys (K) at position 214 of the first chain and Asp (D) at position 204 of the second chain;
h1) Lys (K) at position 244 of the first chain and Glu (E) at position 161 of the second chain.
In an embodiment of the invention, the paired charged residues with the paired positive and negative charges in the sequence as shown in SEQ ID NO: 4 are 8 pairs of residues as shown in a2)-h2):
a2) Glu (E) at position 399 of the first chain and Lys (K) at position 482 of the second chain;
b2) Glu (E) at position 400 of the first chain and Lys (K) at position 413 of the second chain;
c2) Lys (K) at position 413 of the first chain and Glu (E) at position 400 of the second chain;
d2) Lys (K) at position 435 of the first chain and Asp (D) at position 442 of the second chain;
e2) Asp (D) at position 442 of the first chain and Lys (K) at position 435 of the second chain;
f2) Asp (D) at position 442 of the first chain and Lys (K) at position 452 of the second chain;
g2) Lys (K) at position 452 of the first chain and Asp (D) at position 442 of the second chain;
h2) Lys (K) at position 482 of the first chain and Glu (E) at position 399 of the second chain.
The method according to any one embodiment of the first aspect of the invention, the process of replacing part of residues in the same domains with the opposite-charged residues comprises the steps of obtaining a nucleotide sequence encoding the protein resulted from replacement of the residues, and expressing the nucleotide sequence with the recombinant host cell to obtain the protein resulted from replacement of the residues.
In the invention, the protein mixture can be obtained by separately cloning the different proteins into expression vectors, co-transfecting the different expression vectors into a host cell, and culturing the recombinant host cell to express the proteins; or by operably connecting and cloning the different proteins into one expression vector, and further transferring the expression vector into the host cell for culture.
In the invention, the process for obtaining the encoding nucleotide sequence based on the amino acid sequence resulted from replacement is well known in the art.
The second aspect of the invention relates to a mixture containing two or more proteins, wherein the proteins is in the form of a dimer which is formed by polymerization between monomer chains, and the two or more proteins contain the same domain, wherein part of residues of the two monomer chains in the same domain of one or more proteins are replaced with the opposite-charged amino acid(s), so that the monomer chains from the different proteins are unfavorable to forming a heterodimer due to the repulsive interaction between like charges, while the monomer chain from the same protein is more favorable to forming a homodimer due to the attractive interaction between opposite charges.
In an embodiment of the invention, the proteins are antibodies or fusion proteins comprising a part of the antibodies.
The mixture according to any one embodiment of the second aspect of the invention, the residues of at most one protein or antibody are not replaced. In an embodiment of the invention, the residues of one protein are not replaced and the residues of the other protein are replaced. In another embodiment of the invention, the residues of the two proteins are both replaced.
When the residues of multiple (two or more) proteins are replaced, at least one position of the replaced residues among different proteins are different, preferably, all the positions of the replaced residues among different proteins are different.
The mixture according to of any one embodiment of the second aspect of the invention, the same domain refers to CH3 domain of an antibody.
The mixture according to any one embodiment of the second aspect of the invention, the same domain refers to Fc region of an antibody.
The mixture according to any one embodiment of the second aspect of the invention, the antibodies are derived from mammals, such as human, mice or rats.
The mixture according to any one embodiment of the second aspect of the invention, the antibodies are selected from the group consisting of IgG (such as IgG1, IgG2, IgG3), IgA (such as IgA1, IgA2), IgE, IgD and IgM (such as IgM1, IgM2).
The mixture according to any one embodiment of the second aspect of the invention, wherein the part of the residues are interface residues between the same domains of the two monomer chains of the protein, preferably, the interface residues are the charged residues with paired positive and negative charges; and more preferably, one or more pairs (such as two pairs, three pairs or four pairs) of paired residues are replaced with the opposite-charged residues.
In an embodiment of the invention, the charged amino acid is selected from the group consisting of lysine (lys), arginine (Arg), histidine (His), aspartic acid (Asp) and glutamic acid (Glu).
In an embodiment of the invention, the same domain refers to Fc region or CH3 domain of the antibody, and the paired charged residues with paired positive and negative charges are selected from the group consisting of the following paired residues as shown in a)-h):
a) Glu (E) at position 356 of the first chain and Lys (K) at position 439 of the second chain;
b) Glu (E) at position 357 of the first chain and Lys (K) at position 370 of the second chain;
c) Lys (K) at position 370 of the first chain and Glu (E) at position 357 of the second chain;
d) Lys (K) at position 392 of the first chain and Asp (D) at position 399 of the second chain;
e) Asp (D) at position 399 of the first chain and Lys (K) at position 392 of the second chain;
f) Asp (D) at position 399 of the first chain and Lys (K) at position 409 of the second chain;
g) Lys (K) at position 409 of the first chain and Asp (D) at position 399 of the second chain; and
h) Lys (K) at position 439 of the first chain and Glu (E) at position 356 of the second chain;
the positions of the above 8 pairs of residues are determined according to the EU numbering index of KABAT system for antibody.
In an embodiment of the invention, replacing the part of residues of the two monomer chains in the same domains of one or more proteins with the opposite-charged residues refers to one or any combination of the following situations:
(1) replacing Lys at position 392 with Asp, replacing Lys at position 409 with Asp and replacing Asp at position 399 with Lys for one protein;
(2) replacing Glu at position 356 with Lys and replacing Lys at position 439 with Glu for one protein;
(3) replacing Glu at position 357 with Lys and replacing Lys at position 370 with Glu for one protein;
(4) replacing Glu at position 357 with Lys, replacing Lys at position 370 with Glu, replacing Lys at position 392 with Asp, replacing Lys at position 409 with Asp and replacing Asp at position 399 with Lys for one protein;
(5) replacing Lys at position 392 with Asp and replacing Asp at position 399 with Lys for one protein;
(6) replacing Asp at position 399 with Lys and replacing Lys at position 409 with Asp for one protein;
(7) replacing Lys at position 392 with Asp, replacing Lys at position 409 with Asp and replacing Asp at position 399 with Lys for one protein; and simultaneously, replacing Glu at position 357 with Lys and replacing Lys at position 370 with Glu for the other protein; and
(8) replacing Lys at position 392 with Asp, replacing Lys at position 409 with Asp and replacing Asp at position 399 with Lys for one protein; and simultaneously, replacing Glu at position 356 with Lys and replacing Lys at position 439 with Glu for the other protein.
In an embodiment of the invention, the paired charged residues with the paired positive and negative charges in a sequence as shown in SEQ ID NO: 2 are 8 pairs of residues as shown in a1)-h1):
a1) Glu (E) at position 161 of the first chain and Lys (K) at position 244 of the second chain;
b1) Glu (E) at position 162 of the first chain and Lys (K) at position 175 of the second chain;
c1) Lys (K) at position 175 of the first chain and Glu (E) at position 163 of the second chain;
d1) Lys (K) at position 197 of the first chain and Asp (D) at position 204 of the second chain;
e1) Asp (D) at position 204 of the first chain and Lys (K) at position 197 of the second chain;
f1) Asp (D) at position 204 of the first chain and Lys (K) at position 214 of the second chain;
g1) Lys (K) at position 214 of the first chain and Asp (D) at position 204 of the second chain;
h1) Lys (K) at position 244 of the first chain and Glu (E) at position 161 of the second chain.
In an embodiment of the invention, the paired charged residues with the paired positive and negative charges in the sequence as shown in SEQ ID NO: 4 are 8 pairs of residues as shown in a2)-h2):
a2) Glu (E) at position 399 of the first chain and Lys (K) at position 482 of the second chain;
b2) Glu (E) at position 400 of the first chain and Lys (K) at position 413 of the second chain;
c2) Lys (K) at position 413 of the first chain and Glu (E) at position 400 of the second chain;
d2) Lys (K) at position 435 of the first chain and Asp (D) at position 442 of the second chain;
e2) Asp (D) at position 442 of the first chain and Lys (K) at position 435 of the second chain;
f2) Asp (D) at position 442 of the first chain and Lys (K) at position 452 of the second chain;
g2) Lys (K) at position 452 of the first chain and Asp (D) at position 442 of the second chain;
h2) Lys (K) at position 482 of the first chain and Glu (E) at position 399 of the second chain.
The third aspect of the invention relates to the protein mixture obtained according to the method of any one embodiment of the first aspect of the invention.
Polypeptides containing CH3 domains form interaction interfaces due to interaction between residues and thus form dimers, therefore, in an embodiment of the invention, a method for obtaining a homodimer mixture is described, wherein the attractive interaction between two CH3 domains in a heterodimer can be reduced by modifying the residues on the interaction interfaces of CH3 domains through the repulsive effect of the charges, resulting in a mixture of homodimer. Generally speaking, on heterodimer's CH3-CH3 interface, the repulsive effect of the charges can be formed by modifying the related residues as charged residues. In some cases, when a certain amino acid with positive charges (lysine, arginine, histidine) on the interface is mutated to one with negative charges (aspartic acid, glutamic acid), the repulsive effect can be formed, and vise versa.
In an embodiment of the invention, upon interaction of the residues on CH3-CH3 interface, the interaction between the charged residues in the pairs is determined, any one or more of the residues are selected, and the effect of the selected residues on the formation of homodimers and heterodimers is analyzed, then the selected residues are mutated to charged residues, and the effect of mutated residues on the formation of homodimers and heterodimers after mutation is investigated, then the effects after and before the mutations are compared, and an appropriate mutation would result in the effect of strengthening the formation of homodimers and weakening the formation of heterodimers. Finally, reasonable mutations of the residues are selected to maximize the effect of strengthening the formation of homodimers and weakening the formation of heterodimers.
In a specific embodiment, the method described above is defined as follows: the paired charged residues in the CH3 domains of the homodimer proteins are mutated to the opposite-charged residues, so that homodimers can be formed between Fc of the two monomer chains, due to the interaction resulted from the attractive interaction of the paired opposite-charged residues, while heterodimers cannot be formed due to the repulsive interaction of like charges resulted from the interchange of the electric properties of the charges of the paired amino acids on one chain, and thus obtaining the Fc antibody or Fc-fusion protein mixture which only comprises the homodimers.
In the invention, the protein, also called polypeptide, contains more than 10 residues, preferably more than 50 residues and more preferably more than 100 residues. In an embodiment of the invention, the protein is an antibody or comprise a part of an antibody. In the specific embodiment of the invention, the protein is Fc fragment of IgG1. In another embodiment of the invention, the protein is a fusion protein of single-chain variable-fragment (ScFv) and Fc fragment of IgG1.
In the invention, the host cell is a cell suitable for expressing proteins or antibodies, such as a prokaryotic cell or a eukaryotic cell. One example for a prokaryotic cell is E. coli; the examples for a eukaryotic cell are a yeast cell or a mammalian cell; and the examples for a mammalian cell are a human epithelial cell (such as 293H), a Chinese hamster ovary cell (CHO) or a myeloma cell.
In the invention, the different protein contains the same domain. In an embodiment of the invention, the same domains refer to CH3 domains of antibodies or Fc regions of antibodies.
In the invention, the monomer chain, also called the single polypeptide, refers to one monomer or one subunit to form the dimer protein. In an embodiment of the invention, the two monomer chains forming the dimer are symmetric, namely the sequences of the two monomer chains are the same.
In the invention, replacing the residues refers to replacing the residues in the corresponding positions of the two monomer chains forming the dimer protein.
In the invention, the dimer refers to a combination formed by two subunits or two monomers during the formation of protein or nucleic acid, and the subunits or monomers can be combined by covalent bonds or non-covalent bonds; the homodimer means that the sequence of two subunits forming the dimer are the same; and the heterodimer means that the two subunits of the dimer are different.
In the invention, the domain refers to the region with specific structure and independent function in bio-macromolecules, particularly in proteins. In an embodiment of the invention, the domain refers to CH3 domain of an antibody or Fc region of an antibody.
In the invention, the interface residues refer to the residues which form contact interfaces between the domains. The interface residues consist of two or more residues.
In the invention, the one protein or the same protein refers to the protein expressed from of one nucleotide sequence, namely the protein formed as homodimer.
The protein or antibody mixture obtained using the method of the invention can be a mixture of two or more protein or antibody homodimers, preferably a mixture of two protein or antibody homodimers.
In an embodiment of the invention, the domain containing CH3 can be only CH3 domain, or human immunoglobulin Fc region containing CH3 domain. In general, the polypeptides of CH3 domains of human immunoglobulin Fc region are derived from wild-type human immunoglobulin Fc region. The wild-type human immunoglobulin Fc refers to an amino acid sequence that occurs within human population. Of course, Fc sequence may vary slightly among individuals. The human immunoglobulin Fc in the invention also contains fragments with several residue alterations as compared with the wild-type human immunoglobulin Fc sequence, such as alterations of some residues in Fc region, comprising some residues mutated at glycosylation sites or other mutations. The sequence of CH3 domain can be for example the sequence as shown in positions 148-252 of SEQ ID NO: 2. The sequence of Fc region can be for example the sequence as shown in positions 26-252 of SEQ ID NO: 2.
In the invention, the term “human immunoglobulin Fc” refers to human immunoglobulin fragment crystallizable, is the C-terminal part of a human immunoglobulin chain constant region, in particular the immunoglobulin heavy chain constant region. For example, the immunoglobulin Fc region may comprise the combination of two or more domains of CH2, CH3 and CH4 of heavy chains with an immunoglobulin hinge region. Herein, Fc region of IgG corresponds to the lower hinge region —CH2-CH3 domain (for IgG, CH2 and CH3 are also called Cγ2 and Cγ3 domains). In the background of human IgG1, according to EU indexes in Kabat system, the lower hinge region refers to positions 226-236, CH2 domain refers to positions 237-340, and CH3 domain refers to positions 341-447. According to the amino acid sequence of heavy chain constant region, immunoglobulins can be divided into different types. There are mainly five types of immunoglobulins: IgA, IgD, IgE, IgG and IgM, wherein some of the immunoglobulins can be further divided into sub-types (isotypes): such as IgG-I, IgG-2, IgG-3, IgG-4, IgA-I and IgA-2. The similar domains of other IgG sub-types can be determined by comparing heavy chains or heavy chain fragments of the IgG sub-types with the amino acid sequence of heavy chain or heavy chain fragments of human IgG1. Selecting specific immunoglobulin Fc regions from specific immunoglobulin types and sub-types is within the scope of those skilled in the art. Because the residues interactive interface of immunoglobulin monomers are highly conserved between human and murine, the method of preparing a homodimer protein or antibody mixture by using the repulsive interaction of charges is also suitable for both human and murine IgA, IgD, IgE, IgG and IgM. The related method is also suitable for mutating the non-charged residues of CH3domains to the charged residues.
In the invention, the residues in Fc region are numbered according to the EU indexes for the immunoglobulin heavy chain (Kabat, et al., Sequences of Proteins of Immunological Interest, 5th Ed, Public Health Service, National Institutes of Health, Bethesda, Md. (1991), which is cited here for reference). The EU indexes of Kabat system refer to the EU residue numbering for human IgG1 antibody. The positions in the amino acid sequence of antibody Fc region are indicated with the EU indexes mentioned in Kabat, et al.
In the invention, the antibody prototypes for producing homodimer protein mixture can be antibodies, immunoglobulins, Fc fusion polypeptides, Fc conjugates (see
In the invention, the homodimer proteins may be a homodimer protein of a polypeptide containing Fc regions, which include but are not limited to antibodies, Fc fusion proteins, Fc conjugates, Fc-derived polypeptides, isolated Fc and fragments thereof. Therefore, the homodimer protein may be a natural polypeptide, variants of the natural polypeptide, engineered forms of the natural polypeptides, synthetic polypeptides or polypeptides containing non-protein fragments. The engineered forms of the natural polypeptides are polypeptides which are not encoded by natural genes. For example, the engineered polypeptides can be chimeric antibodies or humanized antibodies.
In the invention, the homodimer mixture may be purified from the recombinant cells with a standard experimental technique. For example, when the homodimer protein comprises an Fc region, the protein may be purified using protein A. The purification methods include but are not limited to chromatographic methods such as size exclusion, ion exchange, affinity-based chromatography and ultrafiltration. The separation and purification methods of the homodimer mixture of the invention also include any appropriate combination of the above methods.
The invention further relates to an engineered monomer chain or an engineered single polypeptide for constituting the homodimer protein or antibody.
The invention further relates to a nucleic acid sequence encoding the engineered homodimer protein or antibody (or the monomer chain or the single polypeptide).
The invention further relates to a pharmaceutical composition comprising the engineered homodimer protein or antibody (or the monomer chain or the single polypeptide).
Due to the interaction between the same domains of different proteins (such as Fcs of antibodies), the formation of the homodimers and heterodimers is a dynamic and complex process, which involves the formation of stable homodimers due to the interaction of the interface residues of the homodimers, and the formation of stable heterodimers due to the interaction of the interface residues of the heterodimers, as well as the dynamic changes in the content of the heterodimers due to the existence of homodimers, and the dynamic changes in the content of the homodimers due to the existence of heterodimers. The invention provides a method for preparing a mixture of two or more proteins or antibodies with a single recombinant cell clone, which can increase the content of the homodimers of the proteins or antibodies and can reduce the content of other undesired products, such as the heterodimers. The experimental results show that the protein or antibody mixture obtained by the invention has pure components and desired stability. The protein or antibody mixture prepared by the invention can simultaneously act on different epitopes of the same target, or simultaneously inhibit the functions of different antigens, thereby providing a new method and routine for treatment of tumors and other diseases.
The embodiments of the invention are illustrated in detail by referring to the examples, but those skilled in the art would understand that the following examples are merely for illustrating the invention and should not be deemed as restriction of the invention. The examples in which specific conditions are not given are performed according to conventional conditions or conditions suggested by manufacturers. The reagents or instruments for which manufacturers are not given are all conventional products commercially available.
Unless otherwise specified, the experimental methods used in the following examples are conventional methods.
Unless otherwise specified, materials, reagents and the like used in the following examples are commercially available.
1. Obtaining of Sequences and Structures
Crystal structures of 48 human IgG1 antibody containing Fc regions are obtained from a protein database (PDB, www.pdb.orq) and Fc fragments of the 48 antibodies were derived from 1DN2 (PDB number) upon a structure similarity searching algorithm (Reference: Yuzhen Ye and Adam Godzik. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res., 2004, 32(Web Server issue): W582-585.).
2. Determination of Interface Residues
Interface amino acid prediction software CMA (URL: http://ligin.weizmann.acil/cma/) was used for screening and recognizing contact residues between CH3-CH3 in the antibodies (PDB number: 1 DN2) based on the distances of residues interaction. According to the contact rules of amino acid residues, the interface residues refer to those with the distances (from the heavy atoms of a side chain to the heavy atoms of any of residues of another chain) smaller than a limit. In this example, the distance limit was set as either 4.5 Å or 5.5 Å (See B. Erman, I. Bahar and R. L. Jernigan. Equilibrium states of rigid bodies with multiple interaction sites. Application to protein helices. J. Chem. Phys. 1997, 107:2046-2059.). The conservation of contact interfaces of residues of human and murine IgG subtype could be determined by multiple alignments of sequences in
3. Searching for Paired Charged Residues
On the basis of the CH3-CH3 interface residues listed in Table 1, the paired charged residues were selected according to the charges of the residues, the results were shown in Table 2 and there were 8 pairs of charged residues.
4. Mutation of Charged Residues
According to the results of Table 2, the two Fc chains of antibody 1DN2 are two symmetrical chains. Thus, for the paired residues of any chain, if the residue at a certain position of one chain is mutated to the residue with opposite charge, then the residue at the same position of the two chains of the antibody are both mutated, and for example, for the paired residues Glu356A-Lys439B, the two types of mutation are as follows:
1) the Glu356A is mutated to Lys356A or Arg356A, and/or the Lys439A is mutated to Glu439A or Asp439A; and
2) the Glu356B is mutated to Lys356B or Arg356B, and/or the Lys439B is mutated to Glu439B or Asp439B.
In this case, the opposite charges mean that the positive-charged residues (lysine (Lys, K) or arginine (Arg, R) or histidine (His, H)) are mutated to the negative-charged residues (aspartic acid (Asp, D) or glutamic acid (Glu, E)) or the negative-charged residues (aspartic acid or glutamic acid) are mutated to the positive-charged residues (lysine or arginine). The specific mutation positions are as shown in Table 3 and Table 4.
In addition, in more complicated cases, the operation can also be based on the method as above or the combinations of mutations of the paired residues described above. The method for modifying Fc (for preparation of Fc mixture) and preparing an antibody mixture according to the solution of the invention was not limited by double mutations of paired residues of the single-chain as mentioned above or any combination of the mutations.
1. Construction of a recombinant vector pcMVβ-SP-Fc for expressing a Fc fragment of human IgG1
According to the gene sequence of Fc fragment (hing-CH2-CH3) of human IgG1 in a gene database, a human Fc gene as shown in SEQ ID NO: 1, which contained at two terminals Hind III and EcoRI as recognition sequence and protective bases respectively (780 bp in length and named as SP-Fc), was obtained by artificial synthesis. The Fc gene was double digested with EcoRI and Hind III, and the resulted fragment was connected with the vector backbone of expression vector pcMVβ for mammalian cells (Invitrogen) which had been double digested with EcoRI and Hind III, and the recombinant vector pcMVβ-SP-Fc (the schematic diagram of its structure is as shown in
The amino acid sequence of Fc protein encoded by the nucleotide sequence of the positions 16 to 771 in SEQ ID NO: 1 is as follows (as shown in SEQ ID NO: 2):
PPKPKDTLMISRTPEVTCVVVDVSHENPEVKFNWYVDGVEVHNAKTKP
REEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKA
KGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQP
ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK.
2. Construction of a Recombinant Vector pcDNA3.1-zeo-ScFv-Fc for Expressing aScFv-Fc Fusion Protein
The gene encoding ScFv-Fc fusion protein as shown in SEQ ID NO: 3 which contained Hind III and EcoRI at both terminals as recognition sequence and protective bases respectively was obtained by gene synthesis. The ORF encoding ScFv-Fc fusion protein was double digested with EcoRI and Hind III, and the resulted fragment was connected with the backbone of expression vector pcDNA3.1-zeo for mammalian cells (Invitrogen) which had been double digested with EcoRI and Hind III, and the recombinant vector pcDNA3.1-zeo-ScFv-Fc (the schematic diagram of the structure is as shown in
The amino acid sequence of ScFv-Fc fusion protein encoded by the nucleotide sequence of the positions 16 to 1488 in SEQ ID NO: 3 is as follows (as shown in SEQ ID NO: 4):
PKDTLMISRTPEVTCVVVDVSHENPEVKFNWYVDGVEVHNAKTKPREE
QYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQ
PREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN
YKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQ
KSLSLSPGK.
The amino acid sequence of underlined parts in SEQ ID NO: 2 and SEQ ID NO: 4 are the same.
3. Preparation of a Engineered Recombinant Vector by Selecting Amino Acid Positions for Mutagenesis
According to the residues to be mutated in Table 3 and Table 4 of Example 1, an overlapping PCR method was used for mutation and combined mutation of nucleotide sequences (SEQ ID NO: 1 and SEQ ID NO: 3) encoding scFV-Fc and Fc. As shown in the mutation combinations 1-8 in Table 5, 8 recombinant vectors pcDNA3.1-zeo-ScFv-Fc and pcMVβ-SP-Fc were obtained after engineering.
4. Detection of Transfected Cells and the Antibody Mixture
The expression vectors harbor 8 mutation combinations in step 3 were separately transfected with PEI into suspension adapted 293H cells (ATCC CRL-1573), the co-transfection ratio of plasmids pcDNA3.1-zeo-ScFv-Fc to pcMVβ-SP-Fc was 1:1, and after 3-4 days, cell culture supernatant was collected. Immuno precipitation was performed with protein A agarose resin, and the content of the homodimer proteins or antibodies (ScFv-Fc/ScFv-Fc and Fc/Fc) and the heterodimer protein or antibody (ScFv-Fc/Fc) was detected by SDS-PAGE under non-reducing conditions. Gel-Pro professional image analysis software (Media Cybernetics company) was used for analyzing the proportion of the homodimer proteins or antibodies (ScFv-Fc/ScFv-Fc and Fc/Fc) and the heterodimer protein or antibody (ScFv-Fc/Fc). The results were as shown in
The method used for analyzing the composition of protein or antibody mixture is as follows: fusion protein ScFv-Fc has a greater molecular weight than Fc, therefore upon combination of ScFv-Fc and Fc, the homodimers (ScFv-Fc/ScFv-Fc and Fc/Fc) and the heterodimer (ScFv-Fc/Fc) would show different bands at positions in SDS-PAGE, the proportion of the homodimers and the heterodimer can be detected. The expression vectors of ScFv-Fc and Fc are co-transfected, and the homodimers (ScFv-Fc/ScFv-Fc and Fc/Fc) and the heterodimer (ScFv-Fc/Fc) can be visualized simultaneously.
In order to investigate the influence of the co-transfection ratio of plasmids pcDNA3.1-zeo-ScFv-Fc to pcMVβ-SP-Fc on the ratios of the homodimers to the heterodimer, the plasmids pcDNA3.1-zeo-ScFv-Fc and pcMVβ-SP-Fc with the mutation combination 1 were co-transfected with PEI into 293H cells (ATCC CRL-1573) in suspension culture in the ratios of 4:1, 1:1 and 1:4, and after culturing for 3-4 days, the cell culture supernatant was collected. Immuno precipitation was performed with protein A agarose resin, and the content of the homodimer proteins or antibodies (ScFv-Fc/ScFv-Fc and Fc/Fc) and the heterodimer protein or antibody (ScFv-Fc/Fc) were detected by SDS-PAGE under non-reducing conditions. The results are shown in Table 7. It can be seen from the results that, by changing the co-transfection ratio of ScFV-Fc to Fc, the proportion of the different homodimers change, but the proportion of the heterodimer is always lower than 5%, suggesting that the mutation combination 1 can stably exclude the heterodimer.
According to the invention, by changing the co-transfection ratio of two plasmids comprising different Fc chains, the ratio of different homodimers can be adjusted to a certain extent, but the overall proportion of the homodimer as well as the proportion of the heterodimers cannot be significantly changed, indicating that the overall proportion of the homodimers keep stable while the co-transfection ratio of the plasmids is changed.
5. Accelerated Stability Study of the Antibody Mixtures
Based on the results from the various mutation combinations on SDS-PAGE in step 4, we selected the antibody mixtures of mutation combination 1, 4, 6 and 0 (wild type, only the scFV-Fc wild type is transfected) to perform accelerated stability study over 31 days under 45° C., and the SDS-PAGE analysis is performed on the day 0, 4, 8, 16, 21 and 31. Similarly, we selected antibody mixtures of the mutation combination 1 (mix 1), combination 6 (mix 2) and combination 0 (wild type, control) to perform CE-SDS (capillary electrophoresis) analysis on the day 0, 8, 21 and 31.
The 31-day accelerated stability SDS-PAGE results indicated that the mutation combination 1 and 6 showed very high stability, as the wild type (scFV/scFV homodimer, control) antibody mixtures. From Day 16, the ScFV-Fc/ScFV-Fc homodimers were partially degraded, while the Fc/Fc homodimers showed excellent stability till Day 31. Considering the instability of ScFV, it is considered that the antibody mixtures of mutation combination 1 and 6 had no differences in stability compared with wild-type Fc. It should be noticed that the antibody mixture produced by the mutation combination 4 showed relatively significant degradation with precipitation observed. It is speculated that with five mutations on single Fc chain (that is 10 mutations on Fc dimer), the structure was affected that causes the instability. The related results are as shown in
In contrast to traditional SDS-PAGE, CE-SDS has advantages such as small loading amount of samples, capable of obtaining accurate molecular weight markers, in line detection with ultraviolet and the like, and quantitative analysis, etc. Thus this method can be used for measuring the degradation of the homodimer mixtures more accurately. It could be seen from
Although the specific models for carrying out the invention have been described in detail, those skilled in the art will understand these details can be modified and changed according to all teachings in the art, and these changes are within the protection scope of the invention. The whole scope of the invention is given by the attached claims and any equivalents thereof.
| Number | Date | Country | Kind |
|---|---|---|---|
| 201210258592.8 | Jul 2012 | CN | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2013/080060 | 7/25/2013 | WO | 00 |
