Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/46—Hybrid immunoglobulins
  • C07K16/461—Igs containing Ig-regions, -domains or -residues form different species
  • C07K16/464—Igs containing CDR-residues from one specie grafted between FR-residues from another
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/24—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
  • C07K16/244—Interleukins [IL]
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/2866—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for cytokines, lymphokines, interferons
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/46—Hybrid immunoglobulins
  • C07K16/461—Igs containing Ig-regions, -domains or -residues form different species
  • C07K16/464—Igs containing CDR-residues from one specie grafted between FR-residues from another
  • C07K16/465—Igs containing CDR-residues from one specie grafted between FR-residues from another with additional modified FR-residues
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
  • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
  • C07K2317/565—Complementarity determining region [CDR]

Definitions

• VH variable antibody heavy chain domain
• VL variable antibody light chain domain
• SDRs specificity determining regions
• FR residues spaced between the CDRs can also participate in antigen recognition, but to a lesser extent (the surface of such regions may account for up to 15% of the antigen and antibody contact surface) (see, e.g., Altshuler, E.P., Chemie 50 (2010) 203-258; Bujotzek, A., et al, mAbs 8 (2016) 288-305).
• the secondary and tertiary antibody structure is disclosed, e.g., in EP 0 239 400.
• the four framework regions largely adopt a ⁇ -sheet conformation and the CDRs form loops connecting, and in some cases forming part of, the ⁇ -sheet structure.
• the CDRs are held in close proximity by the framework regions and, with the
• CDRs from the other variable domain contribute to the formation of the antigen binding site (see, e.g., Poljak, R.J., et al, Proc. Natl. Acad. Sci. USA, 70 (1973) 3305-3310; Segal, D.M., et al, Proc. Natl. Acad. Sci. USA, 71 (1974) 4298-4302, Marquart, M., et al, J. Mol. Biol, 141, (1980) 369-391).
• variable domains are solvent accessible (see, e.g., Amit, A.G., et al, Science, 233 (1986) 747-753).
• the packing together and orientation of the two disulphide bonded ⁇ -sheets are relatively conserved, although, small shifts in packing and orientation of these ⁇ -sheets do occur (see, e.g., Lesk, A.M. and Chothia, C, J. Mol. Biol, 160, 325-342, 1982; Chothia, C, et al, J. Mol. Biol, 186 (1985) 651-653, 1985).
• the variable regions of the two parts of an antigen binding site are held in the correct orientation by inter-chain non-covalent interactions. These may involve amino-acid residues within the CDRs.
• immunoglobulin molecule The function of an immunoglobulin molecule is dependent on its three dimensional structure, which in turn is dependent on its primary amino acid sequence.
• WO 2005/061540 discloses a method for the humanization of antibodies and humanized antibodies obtained thereby. Humanizing antibodies by CDR grafting is disclosed by Williams et al. (in “Antibody Engineering”, Springer (Berlin), 2010, pages 319-339).
• WO 2014/100542 discloses high-throughput antibody humanization. Prediction of VH-VL domain orientation for antibody variable domain modeling is disclosed by Bujotzek et al. (Prot. Struct. Funct. Bioinf. 83 (2015) 681-695).
• WO 2016/062734 discloses VH-VL-interdomain angle based antibody humanization. STJMMARY
• humanized antibodies obtained with a method according to the invention have more humaneness (human character) compared to humanized antibodies obtained with conventional humanization methods not using an additional topological characterization.
• the method according to the current invention comprises as essential step the quantification of the effect on topology, i.e. three dimensional structure and orientation, of each amino acid difference between the selected acceptor sequence for the transfer of the complementarity determining regions (CDRs) of the non- human antibody and the parental non-human antibody.
• CDRs complementarity determining regions
• the (topological) quantification is done by providing a score for each change/difference individually or for all changes/differences together. This score is based on the one hand on the structural difference between the changed amino acid residues and on the other hand on the topology of the position of said change.
• the score is in one embodiment assigned base on/using a three- dimensional homology model. The score reflects the impact of the amino acid difference on the framework stability or CDR conformation and is as follows: 0: no influence; 1 : slight influence; 2: moderate influence; 3: may affect framework stability; 4: will break framework stability or CDR conformation.
• the invention is based at least in part on the finding that by a quantitative analysis of the three-dimensional structure of an antibody, more precisely of the structural difference between the parent non-human antibody structure and the structure of the humanization candidate, suitable (and required) amino acid change(s) can be identified, which result(s) in a different, preferably lower or even none, influence on/deformation of the framework/CDR conformation and thereby, amongst other things, an increased binding of the humanized antibody to its antigen.
• the current invention provides for an improved humanization method.
• One aspect of the invention is a method for providing (or synthesizing or identifying or producing) a nucleic acid sequence encoding an (humanized) immunoglobulin variable domain comprising the following steps a) aligning the amino acid sequence of a non-human heavy chain or light chain variable domain with a first humanized variant of said non-human heavy chain or light chain variable domain obtained by grafting the CDRs or hypervariable regions or specificity determining residues of the respective non-human antibody heavy chain or light chain variable domain on i) a human germline amino acid sequence with the highest sequence homology to the non-human variable domain, or two or more human germline amino acid sequence fragments that when aligned form a complete variable domain and have a homology higher than a single human germline amino acid sequence, or iii) a human germline amino acid sequence that allows maintaining VH/VL angle, or iv) a humanized antibody variable domain,
• step b) further comprises generating a three-dimensional model of the non-human variable domains or the non-human antibody using homology modeling.
• step b) further comprises assigning to the respective positions one of the topology classifiers I, E, C, A, L, S, or N.
• step b) further comprises assigning a score to each difference of O, 1, 2, 3, or 4.
• step b) further comprises assigning a score of 0, 1, 2, 3, or 4 to each difference whereby a score of 0 is assigned to a change of an amino acid residue with the topology E to any amino acid residue except proline, a change to proline is assigned a score of 3 or 4 if the proline replacement changes the phi and psi angles around this residue, if a change to proline is not changing the conformation of the amino acid stretch around the residue it is assigned a score of 0 or 1 , a score of 0 is assigned to a change of an amino acid residue with the topology I to an amino acid residue with a smaller side chain, the replacement with an amino acid residue with a side chain that has one carbon atom more will be assigned a score of 1, the replacement with an amino acid residue with a side chain that has two carbon atoms more will be assigned a score of 2, the replacement with an amino acid residue with a side chain that has three carbon atoms more will be assigned a score of 3, and all other changes will be assigned a score of 0, 1,
• the antigen binding site of an antibody is formed by the heavy chain variable domain (VH) and the light chain variable domain (VL). These domains interact via the five-stranded beta-sheets to form a nine-stranded beta-barrel of about 8.4 A radius, with the strands at the domain interface inclined at approximately 50° to one another.
• the HVRs i.e. the amino acid loops formed by the HVR amino acid residues are brought in close proximity to each other. This can be seen when viewed from the top of the structure. Also the HVR contribute to 25 % or more of the VH/VL interface.
• the revised Chothia numbering approach is based on the Chothia numbering scheme and includes also the framework residues with positional corrected FR indels (see, e.g., Abhinandan, K.R. and Martin, A.C., Mol. Immunol. 45 (2008) 3832-3839).
• a further method is the AbM definition used by Oxford Molecular's AbM antibody modeling software (see, e.g., Protein Sequence and Structure Analysis of Antibody Variable Domains. In: Antibody Engineering Lab Manual (Ed.: Duebel, S. and Kontermann, R., Springer- Verlag, Heidelberg)).
• hypervariable region refers to each of the regions of an antibody variable domain comprising the amino acid residue stretches which are hypervariable in sequence ("complementarity determining regions” or “CDRs") and/or form structurally defined loops ("hypervariable loops"), and/or contain the antigen-contacting residues ("antigen contacts").
• CDRs complementarity determining regions
• hypervariable loops form structurally defined loops
• antigen contacts Generally, antibodies comprise six HVRs; three in the VH (HI, H2, H3), and three in the VL (LI, L2, L3).
• HVRs include (a) hypervariable loops occurring at amino acid residues 26-32 (LI), 50-52
• HVR residues and other residues in the variable domain are numbered herein according to Kabat et al, supra.
• Lefranc and colleagues developed the IMGT numbering scheme.
• the AHo numbering scheme (Honegger, A. and Plueckthun, A., J. Mol. Biol. 309 (2001) 657-670) is based on spatially aligned 3D structures.
• the WolfGuy numbering defines CDR regions as the set union of the Kabat and Chothia definition. Furthermore, the numbering scheme annotates CDR loop tips based on CDR length (and partly based on sequence) so that the index of a CDR position indicates if a CDR residue is part of the ascending or the descending loop. A comparison with established numbering schemes is shown in the following
• WolfGuy is designed such that structurally equivalent residues (i.e. residues that are very similar in terms of conserved spatial localization in the Fv structure) are numbered with equivalent indices (as far as possible).
• Chimeric antibodies are obtained by grafting the complete variable domains of the light and heavy chains of a non-human antibody onto a human constant region (CHl-hinge-CH2-CH3 for the heavy chain variable domain and CL for the light chain variable domain). These chimeric antibodies have a reduced immunogenicity but nevertheless induce an immune response of the recipient (see, e.g., WO 86/01533; US 4,816,567; Morrison, S.L., et al. Proc. Natl. Acad. Sci.
• thermodynamic computational analysis can be used for evaluating structural compatibility of a tester sequence with a target structural template.
• the structural evaluation was based on an empirical and parameterized function and was intended to reduce the number of subsequent in vitro screenings necessary.
• the function consists of three energy terms: nonpolar salvation, side-chain entropy, and electrostatic energy.
• 592 106 disclosed a method of producing an antibody or fragment thereof which comprises humanized heavy and light chains of a rodent antibody variable region comprising generating sequence alignments, in framework positions only, from relative accessibility distributions from x-ray crystallographic structures of a pool of antibody variable region heavy and light chains to give a set of heavy and light chain surface exposed framework positions.
• homology For grafting human germline, mature or consensus antibody variable regions that have the greatest "homology” are chosen in the art as acceptors.
• the term "homology”, “homolog” or “homologous” denotes a sequence or structural or functional identity (equivalence). Homology can be determined using methods known to a person skilled in the art, such as e.g. FASTA, BLAST (Mount, D.M., (2004) in Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY. ISBN 0-87969-608-7), EMBOSS, MPsrch or Scanps.
• a "sequence alignment” can be performed with any method or computer program known to a person skilled in the art. The alignment can be based on sequence and/or structural homology (see, e.g., WO 2012/006490).
• Pair-wise alignment methods can be employed in order to identify the best- matching local (fragment sequence) or global (total sequence) alignment of two sequences.
• the pair-wise alignment can be performed once or multiple times. Pair- wise alignments can be made using different methods known to a person skilled in the art, such as dot-matrix methods, dynamic programming, BLAST2SEQ and word methods.
• a multiple sequence alignment is an extension of a pair-wise alignment performed on more than two sequences simultaneously. In a multiple alignment all query sequences are aligned to each other and conserved sequence residues and/or regions are identified.
• Local alignments can be made using e.g. the Smith- Waterman algorithm (Smith, T.F. and Waterman, M.S., J. Mol. Biol. 147 (1981) 195-197).
• Global alignments can be made using e.g. the Needleman-Wunsch algorithm (Needleman, S.B. and Wunsch, CD., J. Mol. Biol. 48 (1970) 443-453).
• sequence identity of two sequences in question can be done as follows: The sequences in question are arranged to result in the best alignment, i.e. with the fewest number of mismatches and gaps (gaps can be introduced in one or both sequences). Generally, the part of a reference sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%>, least 60%, at least 70%, at least 80%, at least 90%, or 100% of the total length of the reference sequence. Thereafter the amino acid residues at corresponding positions are compared.
• amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”).
• sequence identity (normally given as percentage value) between two sequences depends on the number of identical positions shared by the two sequences, whereby the number of gaps, and the length of each gap, which had been added to the sequence in order to obtain the best alignment of the two sequences, are taken into account.
• sequence alignments can be made e.g. using the DALI method (Holm, L. and Sander, C, Science 273 (1996) 595-603), the SSAP method (sequential structure alignment program; Taylor, W.R., et al, Prot. Sci. 3 (1994) 1858-1870), or the combinatorial extension method.
• gaps can be inserted in one, multiple or all aligned sequences at the same or different positions in order to obtain an alignment with increased stretches of sequence identity.
• the non-human variable domain in question is aligned with human variable domains.
• the human sequence that resembles the non-human sequences best is chosen as acceptor (Sims, M.J., et al, J. Immunol. 151 (1993) 2296-2308; Chothia et al, J. Mol. Biol. 196 (1987) 901-917).
• a particular framework sequence is derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains.
• the consensus sequence can be derived from the most abundant human subclasses, VL6 subgroup I (VL6I) and VH subgroup III (VHIII) (Carter, P., et al, Proc. Natl. Acad. Sci. USA 89 (1992) 4285-4289; Presta, L., et al, J. Immunol. 151 (1993) 2623-2632).
• human framework sequences are chosen from the set of human germline genes based on the structural similarity of the human CDRs to those of the mouse antibody to be humanized.
• the structural similarity is evaluated by scoring residue-to-residue homology of the mouse CDRs to human candidates with the same Chothia canonical structures. No mutations of the human framework are introduced whatsoever (see e.g. Hwang, W.Y.K., et al. Methods 36 (2005) 35- 42).
• variable domains were selected as acceptor sequences that had a sequence identity (excluding the CDRs) above a threshold value.
• This threshold could be as low as 65 % but also up to 80 % or more. But it turned out that it was in most cases not possible to transfer the binding characteristics of the non-human antibody to the humanized antibody by simple grafting of the CDRs. Frequently backmutations of additional residues in the CDRs or the framework of the non-human antibody were necessary to restore the binding characteristics at least in part. The additional residues were required to preserve the CDR three- dimensional conformation. As the additionally transferred residues are mutations within the chosen acceptor antibody they are termed "back mutations" (see e.g. Kabat, E.A.
• backmutation or “back to [non-human species] mutation” denotes an amino acid residue that is reverted back from the human residue to the non-human species residue in order to improve the properties of the humanized antibody. This could also be a somatically mutated amino acid, which is replaced with the corresponding germline residue.
• To identify candidate residues for backmutation the amino acid sequence of a primary humanized antibody is aligned with the respective germline sequence, e.g. obtained from the VBASE database (VBASE is a comprehensive directory of all human germline variable region). Each amino acid residue identified as a candidate residue for backmutation has to be examined for a direct or indirect involvement in antigen binding. Amino acid residues identified (e.g. after mutation) to be able to modify a characteristic of the humanized antibody should be reverted back to the non-human residue.
• WO 90/07861 disclosed four rules for designing humanized antibodies: 1) homology between human acceptor and non-human donor sequences; 2) use donor rather than acceptor amino acids where the acceptor amino acid is unusual at that position; 3) use donor framework amino acids at positions adjacent to the CDR; 4) use donor amino acids at framework positions where the side chain atom is within 3 Angstroms of the CDR in a 3-D model.
• SDR grafting Another humanization approach in the art is "SDR grafting". This approach is based on the finding that a lower number of amino acid residues than those forming the CDRs actually make contact with the antigen and, thus, determine the binding specificity of an antibody. These residues were termed “specificity determining residues (SDRs)". They account for about one third of the total CDR residues. Only those residues are transferred in the grafting process (see e.g. Padlan et al, FASEB J. 9 (1995) 133-139; Kashmiri et al, Methods 36 (2005) 25-34).
• a surface residue has generally a relative solvent accessibility that is 30% or more (see e.g. Pedersen, J., et al, Mol. Biol. 235 (1994) 959-973). It was disclosed that specific surface positions have a preference for a specific limited number of residues (see e.g. Padlan, et al, Mol. Immunol. 28 (1991) 489-498; Pedersen, et al, J. Mol. Biol. 235 (1994) 959-973; Roguska et al, Prot. Eng. 9 (1996) 895-904).
• canonical CDR structure types i.e., a second set of canonical CDR structure types
• CDRs for each sequence within the library of human variable region sequences are identified.
• the method uses these candidate human variable region sequences as a basis for constructing a chimeric molecule that includes at least two of the CDR sequences from the non-human variable region (e.g., of the mouse CDRs) combined with the framework regions from candidate human variable region sequences.
• the chimeric antibody contains each of the non-human CDR sequences substituted for each of the human CDR sequences at corresponding locations in the variable regions so that the framework sequences in the chimeric antibody differs from the candidate human framework sequences by no more than 10 amino acid residues (see WO 2004/006955; Tan, P., et al, J. Immunol. 169 (2002) 1119-1125).
• HSC Human String Content
• MSDs minimum specificity determinants
• a D segment or a CDR3, or a CDR3-FR4, or any other CDR3-FR4 fragment that comprises the minimal essential binding specificity determinant. It was assumed that with this method the binding epitope is retained and antibodies that are 91-96 % homologous to human germline gene antibodies can be isolated (see e.g. WO 2005/069970).
• humanized antibody denotes an antibody comprising the minimal number of amino acid residues from a non-human antibody, but having a comparable antigen specificity and affinity as the non-human antibody and at the same time the humanized antibody has no or only a very low immunogenicity when applied to a human being.
• Another approach in the art is based on the analysis and comparison of three- dimensional models of the non-human antibody and different humanized antibody variants, to identify the likely role of residues with respect to antigen binding. Thereby donor residues might be identified relating to the binding characteristics of the non-human antibody.
• variable domains and thereby the three dimensional conformation of the CDRs is made up of amino acid-amino acid interactions, such as ionic interactions, hydrogen bonds or hydrophobic interactions.
• the different amino acid residues have due to their structure different properties and, thus, changes from one amino acid residue to a different amino acid reside can affect the three dimensional structure/stability of the variable domain and thereby the characteristics of the humanized antibody.
• the replacement of the amino acid residue glycine with the amino acid residue alanine introduces a new CH3 group and thereby reduces the possible orientations of this amino acid residue due to the increased spatial demand, thereby reduces the conformational flexibility and increases the entropy of unfolding resulting in an improved conformational stability of the variable domain (Manning, M.C., et al, Pharm. Res. 6 (1989) 903-917).
• Protein folding is initiated by the formation of hydrophobic interactions.
• the three dimensional orientation of amino acid residues can be assumed to be a "standard geometry" based on bond lengths and angles from small molecule structures (see e.g. Weiner, S.J., et. al, J. Amer. Chem. Soc, 106 (1984) 765-784).
• a computational three-dimensional approximation or model of an antibody is generated based on the known three- dimensional structure of a reference antibody.
• the reference antibody and the antibody in question have a related three-dimensional structure an alignment between the reference antibody and the antibody in question can be generated.
• the amino acid sequences of these two antibodies are aligned and the three-dimensional coordinates of identical sequence stretches are directly transferred from the reference antibody to the antibody in question.
• the three-dimensional coordinates are determined based on generic structural templates with energy refinement.
• Homology modeling can be used to identify residues of the non-human antibody that potentially are involved in supporting the structure of the binding site formed by the CDRs (see, e.g., Kolinski et al, Proteins. 37 (1999) 592-610; Rost et al, Protein Sci. 5 (1996) 1704-1718; US 7,212,924; US 6,256,647; US 6,125,331; Xiang, et al, Curr. Prot. Pept. Sci. 7 (2006) 217-227).
• the alignment of different three-dimensional structures can be made by superimposing one on the other.
• one is three dimensionally fixed and the other is rotated and translated in space, in order to orientate the secondary structural elements of alpha-helices and beta-sheets to have them as congruent (similar/close in spatial position and orientation) to one another as possible.
• the distance between the alike primary carbon atoms is calculated for each amino acid residue. Based on these distances it can be evaluated which of the amino acid residues have the same position and which have different positions. Generally, if the Ca - Ca distance for an amino acid residue is 1.0 A or below, that position can be deemed three dimensional similar or even identical, and if the Ca - Ca distance for an amino acid residue is more than 1.0 A that position can be deemed three dimensional different.
• the likelihood that an identified framework amino acid residue influences the binding characteristics of the humanized antibody is dependent on the spatial distance. Based on the structural model the residues identified to potentially interfere with antigen binding are ranked based on the spatial distance from residues in the CDRs. Generally, residues that are within 4.5 A of any CDR atom are considered potentially interacting residues.
• three-dimensional immunoglobulin models are commonly available and are familiar to persons skilled in the art. The three-dimensional configurations of the different classes of immunoglobulins are known (see, e.g., Abbas et al. Cellular and Mol. Immunology, 4th ed., W.B. Saunders, Co., (2000)). With the aid of specified computer programs, it is possible to display calculated three-dimensional conformational structures of antibody variable domains (see e.g. US 5,821,337).
• Crystal structure databanks e.g. Protein Data Bank, pdb
• Crystal structure databanks can be used as source of the structures (see e.g. Bernstein, F.C., et al, J. Mol. Biol, 112 (1977) 535-542).
• WO 2006/096653 disclosed a method of humanizing an immunoglobulin (Ig) variable region which comprises a) variable region framework (FR) amino acid residues from an acceptor immunoglobulin variable region and b) complementarity determining regions (CDRs) from a non-human donor immunoglobulin variable region, the method comprising, i) providing data which allows prediction of a 3-D conformation of at least one CDR; ii) identifying which FR amino acid residues are predicted to affect the 3-D conformation of the at least one CDR; iii) identifying at least one candidate donor CDR amino acid residue for substitution with an elected amino acid residue, wherein the elected amino acid residue conformationally accommodates a FR amino acid residue difference between the donor immunoglobulin variable region and the acceptor immunoglobulin variable region without affecting the CDR conformation: and iv) substituting the at least one candidate donor CDR amino acid residue with the elected amino acid residue to form a humanized immunoglobulin variable region.
• Ig immunoglobul
• a method of designing a humanized immunoglobulin variable region which comprises a) variable framework regions (FRs) from an acceptor immunoglobulin variable region and b) complementarity determining regions (CDRs) from a non- human donor immunoglobulin variable region, the method comprising, (a) identifying framework region (FR) amino acids which differ between the acceptor immunoglobulin variable region and the donor immunoglobulin variable region; (b) identifying amino acids adjacent to the FR amino acid(s) identified in step (a); (c) identifying at least one candidate amino acid from the amino acids identified in step (b) for substitution with an elected amino acid residue which conformationally accommodates the FR amino acid(s) identified in step (a).
• FR variable framework regions
• CDRs complementarity determining regions
• US 2006/0258852 disclosed an exemplary approach to redesigning the variable region sequences (e.g. CDR sequences, and optionally FR sequences) by using structure-based computational design methods.
• the identity of the residues in the flexible zone is fixed to acceptor residues, but their 3-dimensional positions are allowed to change during the calculation.
• the residues in the mutation zone are allowed to change both their amino acid identity and conformation. All residues in the CDRs outside of the mutation zone are donor, and all residues in the FR outside of the mutation zone are acceptor.
• the candidate residues e.g. CDR residues, and optionally FR residues
• side chains that are geometrically close e.g.
• step 2 is simultaneously mutated computationally to all possible 3-dimensional conformations (rotamers) of any of the 20 naturally occurring amino acids and the resulting mutants are evaluated computationally.
• One such method is known as side chain repacking method.
• the candidate amino acid residues can be modified computationally, and the stability of the resulting polypeptide mutants evaluated computationally.
• the side chain repacking calculation generates a ranked list of the variants that have altered stability (i.e., altered intramolecular energy).
• Mutants which result in low free energy, and which are confirmed as conformationally accommodating by visual inspection of a 3- dimensional model, can then be selected for experimental expression.
• the list of computationally generated mutants can be sorted by calculated stability of the mutant in order to generate a list of variants that will be expressed experimentally.
• the protein backbone is allowed very little or no flexibility, which ensures that the designed mutants are predicted to be stable with the given CDR conformations.
• the computational analysis allows one to predict structurally compatible sequences, in particular CDR sequences, with given FR domains within a variable region.
• WO 2007/109742 disclosed a method of designing a humanized immunoglobulin comprising the steps of a) determining the three dimensional structure of a parent antibody variable domain or a parent antibody variable domain bound to hapten; b) identifying the specificity determining residues (SDR) of said parent structure; c) dividing said structure into sections comprising the six complementarity determining region (CDR) loops and the framework region (FR) comprising both heavy and light chains; d) superimposing the three dimensional structures of said sections onto a defined database of corresponding three dimensional CDR loop and framework structures of human acceptor antibodies; e) grafting parental SDR into a selected acceptor structure to determine a model of the amino acid sequence of said humanized immunoglobulins; f) calculating the energy value for amino acid residue substitutions; g) optimizing the amino acid sequence of said humanized immunoglobulins by choosing residues with negative energy values; and h) designating the amino acid sequences of humanized immunoglobulin variable region segments.
• Different humanization variants are produced and evaluated by suitable screening methods.
• antibody screening There are different known methods for antibody screening, such as e.g. in vitro assays, in vivo and cell-based assays, and selection methods.
• an assay is a binding assay in which the antibody binds to its target and either the binding is determined or an effect initiated by the binding is determined.
• the determination of the binding in a binding assay can be performed using different methods, such as e.g. FRET (Fluorescence Resonance Energy Transfer),
• BRET Bioluminescence Resonance Energy Transfer
• SPR surface plasmon resonance
• phage display Phage display of peptides and proteins: a laboratory manual, Kay et al, Academic Press, San Diego, Calif, (1996); Lowman et al, Biochemistry 30 (1991) 10832-10838; Smith, Science 228 (1985) 1315-1317
• selective phage infection Malmborg et al, J. Mol. Biol. 273 (1997) 544-551
• selectively infective phage Krebber et al, J. Mol. Biol. 268 (1997) 619-630
• delayed infectivity panning Benhar et al, J. Mol. Biol.
• BiotechnoL 15 (1997) 553- 557), and mammalian cells (Whitehorn et al., BiotechnoL 13 (1995) 1215-1219), in vitro display (Amstutz et al., Curr. Opin. BiotechnoL 12 (2001) 400-405), polysomic display (Mattheakis et al., Proc. Natl. Acad. Sci. USA 91 (1994) 9022- 9026), ribosome display (Hanes et al., Proc. Natl. Acad. Sci. USA 94 (1997) 4937- 4942), mRNA display (Roberts & Szostak, Proc. Natl. Acad. Sci.
• yeast two hybrid screen (Fields & Song, Nature 340 (1989) 245-246; Visintin et al, Proc. Natl. Acad. Sci. USA, 96 (1999) 11723-11728).
• Solubility and overall structural integrity of an antibody for example can be quantitatively or qualitatively determined by methods such as, e.g., gel electrophoresis, isoelectric focusing, capillary electrophoresis, chromatography such as size exclusion chromatography, ion-exchange chromatography, and reversed-phase high performance liquid chromatography, peptide mapping, oligosaccharide mapping, mass spectrometry, ultraviolet absorbance spectroscopy, fluorescence spectroscopy, circular dichroism spectroscopy, isothermal titration calorimetry, differential scanning calorimetry, analytical ultra-centrifugation, dynamic light scattering, proteolysis, and cross-linking, turbidity measurement, filter retardation assays, immunological assays, fluorescent dye binding assays, protein-staining assays, microscopy, and detection of aggregates via ELISA or other binding assay, X-ray crystallography, and NMR spectroscopy.
• methods such as, e.
• a humanization is carried out in general as follows:
• the method comprises the following central or core steps: alignment and ranking of the amino acid sequence to be humanized with all potential acceptor sequences; ranking can be done on similarity or at the end on scores / score on acceptor sequences / score on final sequences, i.e.
• a bunch of humanization (suggestion) candidates can be ranked; optionally assigning the canonical loop structure to further identify more important structural influencing residues; optionally search in protein data bank (PDB) to get a starting point for building a model; build a model; this is required to attribute (final) scores; this includes a search to identify substructures with the same topology that lead to the model with high accuracy; thus, a three-dimensional search is performed to have a three- dimensional environment dependent model built; check alignment for insertions, for deletions and, if present, for particular segments with lower homology; if the HVR differs in the built model from the HVR in the found structure a search is done in the structure database for each HVR loop separately or even only for ascending and descending loop parts of each HVR;
• PDB protein data bank
• VH/VL-orientation adjustment has been demonstrated as important to arrange the HVR residues with the right distance between HVR- Hs and HVR-Ls; the relative orientation is triggered mainly by residues at the interface between VH and VL; these can be framework residues as well as HVR residues; energy minimization of the model; recommended to relax the system but not essential assign scores for each change/difference based on the topology sorting of proposed sequences based on individual or overall scores select germline of choice; if similar overall scores, then frequently used germline should be chosen/preferred decide on V and J combination based on the scoring decide on required backmutations to eliminate most or all of 4 or 4 and 3 scores; this can lead to several variants with some 3 scores instead of none or all of them; considering changes for which the score is 1 or 2 and considering forward mutations for which the score is also low.
• humanized antibodies obtained with the method as reported herein have more humaneness (human character) compared to humanized antibodies obtained with conventional methods, which are not using the topological effect considerations according to the method of the current invention. Without being bound by this theory it is assumed that this is due to the fact that in the art longer, non-interrupted stretches are taken from the human germline sequence. By using smaller sub-structures as in the method according to the current invention an improved model can be build and improved humanized antibodies can be obtained.
• the inventive method comprises the step of quantifying (by obtaining a score for) each/any amino acid difference between an acceptor sequence (e.g. a human germline sequence), which has been selected for the transfer of the hypervariable regions of the non-human antibody, and the non-human antibody itself, which is based on the three-dimensional structure, the topology and the interactions of the respective residue with its environment.
• an acceptor sequence e.g. a human germline sequence
• the topology identifiers have the following gradation: A first, then L, then S or C (depending on the topological influence; e.g. a contact position C can be more influencing than salt bridge far away from an A residue), then I, then E. The structural difference is reflected in a score.
• the magnitude of the score is influenced/determined by the impact of the amino acid difference on framework stability or HVR conformation: wherein 0 denotes no influence, 1 denotes slight influence, 2 denotes moderate influence, 3 denotes a potentially affected framework stability and 4 denotes that framework stability or HVR conformation will severely be disturbed/influenced.
• the structural difference can be determined for each amino acid of the 20 naturally occurring amino acid residue, to be more precise for the 19 different amino acid residues, if assumed to be present at the respective position. It can also be linked to the (more limited number of different) amino acid residues that are present at said position in the human germline sequence. Thereby a (scoring) matrix reflecting the resulting (overall) structural differences is obtained.
• the invention is based at least in part on the finding that based on the identified structural difference a suitable amino acid change can be identified, if required.
• This difference/change results in a different, preferably lower, structural distortion (e.g. a reduced influence on/deformation of the framework/HVR conformation) and thereby an increased binding of the humanized antibody to its target.
• a humanized antibody with improved properties can be provided when a method according to the current invention is used. For example, the reduction of the binding affinity of the humanized antibody can be minimized.
• One aspect as reported herein is a method for producing an antibody comprising the following steps: a) sequencing (the amino acid sequence of or the nucleic acid sequence encoding) the variable domains of a non-human antibody and thereby obtaining the amino acid sequence of the variable domains of the non-human antibody, b) optionally generating a three-dimensional homology model of said non-human antibody, c) identifying and selecting as variable domain acceptor sequence for each variable domain (independently of each other for i) and ii) and depending on each other for iii) and iv)) i) a human germline sequence with the highest sequence homology to the respective non-human antibody variable domain, or ii) two or more human germline sequence fragments forming together a complete variable domain that, when aligned, have a sequence homology higher than a single human germline sequence to the respective non- human antibody variable domain, or iii) human germline amino acid sequences that allow maintaining heavy chain variable domain to light chain variable domain angle (VH/
• this method is further performed only for a non-human antibody light chain variable domain or a non-human antibody heavy chain variable domain.
• One aspect as reported herein is a method for synthesizing or producing or providing a nucleic acid sequence encoding an immunoglobulin variable domain comprising the following steps a) aligning the amino acid sequence of a non-human antibody heavy chain or light chain variable domain with a first humanized variant of said non-human antibody heavy chain or light chain variable domain obtained by grafting the CDRs or hypervariable regions (HVRs) or specificity determining residues (SDRs) of a non-human antibody heavy chain or light chain variable domain on i) a human germline amino acid sequence with the highest sequence homology to the respective non-human antibody heavy chain or light chain variable domain, or ii) two or more human germline amino acid sequence fragments forming a complete variable domain that, when aligned, have a homology higher than a single human germline amino acid sequence to the respective non-human antibody variable domain, or iii) a human germline amino acid sequence that allows maintaining VH/VL angle of the non-human antibody variable domain, or iv
• step b) mutating the first humanized variant of said non-human heavy chain or light chain variable domain amino acid sequence by replacing one or more amino acid residue determined in step b) with amino acid residue(s) that influences antigen binding and/or three dimensional structure to a lesser extent than the replaced amino acid residue(s) (, i.e.
• step c) to obtain a new humanized variant of said non-human heavy chain or light chain variable domain with reduced three-dimensional difference, d) optionally repeating steps b) and c) with the new humanized variant obtained in step c) as first humanized variant until the three-dimensional difference is no longer changing/can no longer be reduced/is less than 10 % as determined by RMSD analysis, e) synthesizing or producing or providing a nucleic acid sequence encoding the modified variable domain obtained in step c) or d).
• One aspect as reported herein is a method for producing an immunoglobulin comprising the following steps a) individually for the heavy chain variable domain and light chain variable domain aligning the amino acid sequence of a non-human heavy chain or light chain variable domain with a first humanized variant of said non-human heavy chain or light chain variable domain obtained by grafting the CDRs or hypervariable regions or specificity determining residues of a non-human antibody heavy chain or light chain variable domain on i) a human germline amino acid sequence with the highest sequence homology to the non-human variable domain, or ii) two or more human germline amino acid sequence fragments that when aligned have a homology higher than a single human germline amino acid sequence, or iii) a human germline amino acid sequence that allows maintaining VH/VL angle, or iv) a human or humanized antibody heavy chain or light chain variable domain,
• all amino acid residues are characterized based on their position in the three- dimensional structure, e.g. obtained from a homology model.
• amino acid residues are classified as follows based on their topology:
• topology identifiers As shown above can be assigned. Generally, the more important is chosen.
• the topology identifiers according to the current invention have the following gradation: A first, then L, then S or C (depending on the topological influence; e.g. a contact position C can be more influencing than salt bridge far away from an A residue), then I, then E.
• the quantifying the effect of the different amino acid residue in aligned framework positions is done by using the three-dimensional structure of the VH and/or VL.
• the three-dimensional structure is obtained by X-ray crystallography or by homology modeling.
• the generation of a three-dimensional model of the non-human variable domains or the non-human antibody is by homology modeling.
• the homology modelling is done using a model generated based on substructures of the entire sequence.
• the substructure comprises at most complete regions of the variable domain.
• the substructure comprises at most 20 amino acid residues.
• the substructure comprises at most 15 amino acid residues.
• the substructure comprises at most 10 amino acid residues.
• the homology model used in the method as reported herein is built in one embodiment for each framework region, HVR and conjunction of framework and HVR separately.
• Strall structure all
• Buried solvent exposure below 20% in model vs in GXG
• Strltd particular residues making hydrophobic, electrostatic, or ionic, interactions with CDR or at the interface.
• the topology identifiers according to the current invention have the following gradation: A first, then L, then S or C (depending on the topological influence; e.g. a contact position C can be more influencing than salt bridge far away from an A residue), then I, then E.
• a residue in the HVR is of topology A
• a change is assigned a score of 4, i.e. it is highly influencing the structure and therefore it is highly risky to change it
• a residue of the topology L has also the topology S
• a change is assigned a score of 4 rather than a 3 for some changes because it accumulates topological importance
• - if a residue of the topology C (contact between VH and VL) or A
• a higher score due their potential effect on VH-VL destabilization or on the orientation/conformation of the A residue is assigned to a change; in other words, for the 3 categories A, C, and L, a forward mutation in HVRs gets a high score as well as a back mutation in framework avoids getting a high score; if a residue of the topology C, has a short side chain not making contact with the neighbored variable domain its replacement by a smaller amino acid will get a score of 1 or 2 compared to other replacements with bigger amino acid side chain which can be scored a 2 or 3 depending on the size of the side chain and of the nature of the contact with the neighbored variable domain; if a residue of the topology C, has a short side chain not making contact with the neighbored variable domain and the replacement takes place with a side chain that is so huge that the accommodation for such side chain can only be achieved by a change of
• the difference can be quantified, i.e. by assigning a score.
• the replacement by a similar (physically, volumetric) amino acid normally results in a lower score, i.e. is usually tolerated, while completely changing the side chain characteristics results in a higher score.
• the score for a change is also depending on the topography of the position (e.g. changing an I- nternal side chain is/could be more dramatic/damageable for the entire structure than changing an E-xternal side chain) due to the different spatial constrains.
• any method according to the current invention further comprises in the step of quantifying the difference of aligned framework positions in which the non-human heavy chain or light chain variable domain and the (first) humanized variant of said non-human heavy chain or light chain variable domain have different amino acid residues, which, due to the difference, influence antigen binding and/or three dimensional structure, by assigning a score to each difference of 0 (no influence on the conformation), 1 (slightly local influence), 2 (influence on the local conformation), 3 (strongly influence the local conformation and the neighboring strand or loop conformation), or 4 (will break the local conformation so severely that the antigen recognition will be disrupted).
• a score of 0 is assigned to changes of surface located amino acid residues (in beta sheets or loops) as the side chains of 19 amino acid residues (all except proline) can be accommodated due to the free space present.
• An exception is proline: when the three-dimensional structure does not change the change is assigned a score of 0 otherwise, depending on the influence on antigen binding, the change is assigned a score of 3 or 4.
• a score of 0 is assigned to a change of an amino acid residue with the topology E to any amino acid residue except proline (for which constrains as a cyclic residue are more important).
• Introduction of a proline has to be considered with regard to compatible Phi and Psi angles around this residue. For example, assuming that a polar residue in close proximity to CDR/HVR residues is replaced by a proline from the chosen germline, this replacement can be scored i) as 1 due to the change from a polar to hydrophobic residue, ii) as 2 or 3 depending on the angle compatibility, and iii) as 4 when angles and conformational changes for CDR/HVR residue(s) is(are) expected.
• a score of 0 is assigned to a change of an amino acid residue with the topology I to an amino acid residue with a smaller side chain (i.e. for a conservative replacement), a score of 1 will be assigned to a change to an amino acid residue with a side chain that has one carbon atom more, a score of 2 will be assigned to a change to an amino acid residue with a side chain that has two carbon atoms more, a score of 3 will be assigned to a change an amino acid residue with a side chain that has three carbon atoms more, and a score of 4 will be assigned to all other changes.
• a score of 4 is assigned to a change of an amino acid residue with the topology A to any other amino acid residue.
• Amino acids that are not directly in contact with the antigen but are extremely close to amino acids designated as A are designated as L. Changes thereof lead sometimes to conformational changes that will be assigned a score of 3 or 4. If an amino acid residue that is part of a pi-pi-/hydrophobic interaction is replaced by a non-hydrophobic amino acid residue the hydrophobic interaction is broken. Such a replacement will be assigned a score of 3.
• a score of 3 is assigned to the change of an amino acid residue with the topology C to a non-hydrophobic amino acid residue if thereby the interaction with an amino acid residue in the same domain or the corresponding variable domain is changed (reduced or eliminated).
• a score of 3 is assigned to a change of an amino acid residue with the topology S to an oppositely charged or not-charged amino acid residue in cases in which the salt bridge is solvent exposed and a score of 4 is assigned in cases in which the salt bridge is internal.
• topology change score Some exemplary changes and the resulting score are shown in the following table.
• V->F 3 The method as reported herein is in certain embodiments as follows:
• the method as reported herein combines a three-dimensional assessment of the effect of changes with sequence information.
• the non-human antibody is aligned with suitable human germline sequences.
• the differences/required changes are quantified based on the topology in combination with the kind of change for each residue.
• the results are collected in a matrix.
• the inventive method in general comprises the following steps:
• the binding specificity of the non-human antibody is transferred onto a human or humanized acceptor framework to eliminate or at least reduce potential immunogenicity issues arising from non-human sequence stretches that the human body may recognize as foreign.
• This is done by engrafting the hypervariable regions (HVRs) of the non-human (donor) antibody onto a human/humanized (acceptor) antibody framework.
• HVRs hypervariable regions
• a suitable human (acceptor) antibody framework is identified in one case by aligning the non-human variable domain amino acid sequence to a collection of human germline antibody V-genes (germlines), and sorting them according to sequence identity and homology.
• the acceptor sequence is selected based on high overall sequence homology and optionally also the presence of the right canonical residues already in the acceptor sequence (see Poul, M-A. and Lefranc, M-P., in "Ingenierie des anticorps banques combinatores” ed. by Lefranc, M-P. and Lefranc, G., Les Editions INSERM, 1997).
• the conservation of the VH/VL angle can be taken into account.
• the germline V-gene encodes only the region up to the beginning of CDR3 for the heavy chain, and till the middle of CDR3 of the light chain. Therefore, the genes of the germline V-genes are not aligned over the whole V-domain.
• the humanized construct comprises the human frameworks 1 to 3 and the non-human HVRs.
• the human framework 4 sequence is derived from a human JK-element or a human JH- element for light and heavy chain, respectively.
• the so-called canonical loop structures of the donor antibody can be determined (see, e.g., Morea, V., et al, Methods, 20 (2000) 267-279). These canonical loop structures are determined by the type of residues present at so-called canonical positions. These positions lie (partially) outside of the HVRs and should be kept functionally equivalent in the final construct in order to retain the HVR conformation of the parental (donor) antibody.
• VH 122 amino acid residues
• VL (107 amino acid residues) (SEQ ID NO: 05):
• the PDB is searched for a homolog to check if a very close homolog is present in the structure database for both framework regions and HVRs.
• the alignment is checked to identify if there is some insertion or deletion and if there is a particular framework where the homology is particularly poor (in such cases it is possible to search for specific framework 1, 2, or 3 separately).
• HVR-H1 is different in the model build on the structure found by blending the HVRs with regard to the X-ray structure. Now, then searching is done for every HVR loop separately. In this case, gaps are not allowed; if the short segment has a different length, it has then a different conformation.
• HVR-H1 TGFSITTSGYYWTW Structpro: 3B2UF IMC-11F8 FAB LIGHT CHAIN; CHAI : L, Dl
• HVR-H2 WMGYIGYNSKTYYNP
• HVR-H3 YCARSLYGGYKDAFDSWG
• the modeling can use the WolfGuy antibody numbering scheme that assigns a unique index to every position in the Fv, identifies CDR loop tips and discriminates between ascending and descending loop segments.
• the initial WolfGuy numbering of the input sequences forms the basis for template selection, VH- VL orientation adjustment and model refinement.
• framework templates are not selected per VH and VL or per Fv, but for every framework segment separately to minimize the number of necessary amino acid exchanges.
• each residue is examined with regard to its (altered) chemical neighborhood formed by certain types of sidechains in its vicinity. Based on a conserved neighborhood definition for each position in the Fv, the sidechain (and to a certain extent also backbone) conformation of a given residue are adopted from matching known chemical neighborhood constellations. Finally, the VH-VL orientation is adjusted based on first predicting the absolute parameters of VH-VL orientation from the amino acid types of certain key residues at the domain interface, followed by a coordinate transformation that applies the predicted orientation parameters to the model. The same procedure is performed for the light chain variable domain.
• RMSD root-mean-square deviation
• the ABangle concept is a method which fully characterizes VH-VL orientation in a consistent and absolute sense using five angles (HL, HC1, LCI, HC2 and LC2) and a distance (dc).
• the pair of variable domains of an antibody, VH and VL, is denoted collectively as an antibody Fv fragment.
• VH and VL core-sets The most structurally conserved residue positions in the heavy and light domains are used to define domain location. These positions are denoted as the VH and VL core-sets. These positions are predominantly located on the ⁇ -strands of the framework and form the core of each domain.
• the core-set positions are given in the following Table: light chain heavy chain
• the core-set positions were used to register frames of reference onto the antibody Fv region domains.
• the two reference frame planes are mapped onto any Fv structure. Therefore, the measuring of the VH-VL orientation can be made equivalent to measuring the orientation between the two planes. To do this fully and in an absolute sense requires at least six parameters: a distance, a torsion angle and four bend angles. These parameters must be measured about a consistently defined vector that connects the planes. This vector is denoted C in the following. To identify C, the reference frame planes were registered onto each of the structures in the non- redundant set as described above and a mesh placed on each plane. Each structure therefore had equivalent mesh points and thus equivalent VH-VL mesh point pairs. The Euclidean distance is measured for each pair of mesh points in each structure. The pair of points with the minimum variance in their separation distance is identified.
• the vector which joins these points is defined as C.
• the coordinate system is fully defined using vectors, which lie in each plane and are centered on the points corresponding to C.
• HI is the vector running parallel to the first principal component of the VH plane, while H2 runs parallel to the second principal component.
• LI and L2 are similarly defined on the VL domain.
• the HL angle is a torsion angle between the two domains.
• the HC1 and LCI bend angles are equivalent to tilting-like variations of one domain with respect to the other.
• the HC2 and LC2 bend angles describe twisting-like variations of one domain to the other.
• VH-VL orientation is used in accordance with its common meaning in the art as it would be understood by a person skilled in the art (see, e.g., Dunbar et al, Prot. Eng. Des. Sel. 26 (2013) 611-620; and Bujotzek, A., et al, Proteins,
• VH-VL orientation is defined by
• the complex VH-VL is then energy minimized, e.g. using the module "discover" of Insight.
• the minimization process e.g., follow the VA09A gradient for 600 cycles with a threshold derivative of 1 kcal/A; the partial charges are considered.
• the quantification is done for each position and each replacement.
• a topological description is assigned for each position based on the structure:
• amino acid with external side chain on beta sheets or exposed loops for a change in such a position, the assigned score is normally "0" because most of the 20 naturally occurring amino acid residues can be accommodated due to the free space present; proline or big residues like tryptophan have to be assigned on a case by case basis.
• amino acid with internal side chain the assigned score is depending on the free space available; replacement of linear trough branched amino acids must be checked with effective replacement and eventually minimization (strong deviations are leading to high scores).
• amino acid with antigen contacting side chain when an amino acid is supposed to directly interact with the antigen, any replacement thereof is assigned a score of "4".
• linker amino acid those amino acids that are not directly in contact with the antigen but are extremely close to amino acids designated as "A”; strong differences for such amino acids can lead to conformational changes resulting in high scores of "3" or "4".
• amino acid with contact side chain such amino acids are located at the interface between light and heavy chains; are important for the stability of the complex; if a salt bridge is present, any replacement should allow this closed interaction to take place after replacement; similarly, hydrogen bonds are directional interactions; replacement of side chain leads usually to disruption of the directionality and have to be scored high ("3" or "4").
• Salt bridges that are not (much) exposed to solvent are bringing a lot of interaction energy between the positive and the negative charges; breaking salt bridges may lead to a significant loss of stability within a domain or at the interface between the light and the heavy chain. structure comment
• a protein structure has also internally some available space around an amino acid side chain; not all atoms of an internal amino acid side chain are in contact with neighboring amino acids; replacement is assigned a score based on the available free space.
• a "A” will be chosen for all side chains oriented toward a putative
• aromatic, linear or branched are describing the amino acid side chains.
• polar, negative or positive are describing the functionality at the end of the side-chain. structure amino acid (one letter code "
• acids are disulfide hydrophobic amino acids bigger than bridges is residue are bigger alanine assigned a is assigned a than high score score glycine
• hydrophobic aromatic with a normally scored with a polar function at the end "4"
• E has the phenyl ring
• the assigned scores for each putative replacement at each position of the variable domain based on the available human germline sequences can be collected in a matrix.
• amino acid replacements with scores up to 2 are accepted and amino acid changes with scores of 3 or 4 are not accepted (these amino acid residues are not changed and kept as original); within HVRs all amino acids enclosed between 2 residues with a score of 4 are kept as original (not changed to human).
• HVRs are not fixed as defined by Chothia or Kabat: in some cases, the HVRs may be smaller than the above definition; on the other hand, HVRs can include some amino acids of the previous or subsequent framework. For a less conservative humanization only amino acid changes with score of 4 are rejected and backmutated in the framework regions; within HVRs all amino acids enclosed between 2 residues with a score of 4 are kept as original (not changed to human).
• Example 1 humanization of murine anti-IL-17 antibody
• HC-2a-h murine germline fragment: SEQ ID NO: 10
• HC-2a-HC-2h SEQ ID NO: 1 1 to 18
• Example 2 anti-CCR5 antibody
• a humanized antibody comprising amino acid sequence of a non-human antibody and a human germline sequence, utilizing the steps of: a) obtaining the amino acid sequences of a non-human antibody variable domain and of i) a human germline sequence with the highest sequence homology to the non-human variable domain, or ii) two or more human germline sequence fragments that when aligned have a homology higher than a single human germline sequence, or iii) based on the VH/VL angle; b) identifying hypervariable region amino acid sequences in the non-human antibody variable domain and the human germline sequences: c) substituting a non-human antibody hypervariable region amino acid sequence for the corresponding human germline hypervariable region amino acid sequence; d) aligning the amino acid sequences of a framework region (FR) of the non- human antibody and the corresponding FR of the human germline sequence; e) identifying non-human antibody FR residues in the aligned
• the method further comprises aligning non-human antibody and the human germline FR sequences, identifying non-human antibody FR residues which are non-identical with the aligned human germline FR sequence, and for each such non-identical non-human antibody FR residue, determining if the corresponding human germline residue represents a residue which is highly conserved across all species at that site, and if it is so conserved, preparing a humanized antibody which comprises the human germline amino acid residue at that site.
• the root mean square difference (RMSD) of the main chain conformations of the non-human antibody sequence and the template sequence is less than 4 A, less than 3 A, and preferably less than 2 A.
• a method for the production of a humanized antibody comprising at least one light chain and one heavy chain, the method comprising the steps of: a) selecting a non-human antibody having at least one HVR; b) selecting a human antibody heavy chain or germline sequence; c) selecting a human antibody light chain or germline sequence d) introducing at least one HVR from the non-human antibody heavy chain into the human antibody heavy chain, to form a recombinant heavy chain; and e) introducing at least one HVR from the non-human antibody light chain into the human antibody light chain, to form a recombinant light chain; f) changing amino acid residues in both variable domain amino acid sequences based on the method as reported herein, wherein the selection of each of the human antibody heavy and light chains is determined solely by sequence homology with the non-human antibody heavy and light chains, respectively.
• a method of producing a humanized antibody comprising: comparing the variable (V) region framework (FR) sequences of a non- human antibody to the variable (V) region framework (FR) sequences of human antibodies or human antibody germline sequences to determine the degree of sequence homology between the non-human antibody FRs and the human antibody or human germline FRs; and replacing FRs in the non-human antibody with the human antibody or human germline FRs determined with the method as reported herein.
• the assigning of a score comprises all changes as outlined herein.
• the assigning of a score further comprises assigning a score of 0, 1, 2, 3, or 4 to each difference whereby a change of a residue in the HVR of topology A is assigned a score of 4, a change of a residue of the topology L, which has also the topology S, is assigned a score of 3 or 4 (with 4 being preferred), a change of a residue of the topology C, which has a short side chain, to an amino acid residue with a smaller amino acid (based on volume) is assigned a score of at most 2, a change of a residue of the topology C, which has a short side chain, to an amino acid residue with a bigger (volumetric) side chain is assigned a score of 2 or 3 depending on the size of the side chain and of the nature of the contact with the neighbored variable domain, a change of a residue of the topology C, which has a short side chain, to an amino acid residue with a side chain that results in a change of the VH-VL orientation is assigned a score of 4, a score of
• NUNC® MaxiSorp plates (96-well) were coated with recombinant human IL-17 (Peprotech # 200-17, www.peprotech.com) at a concentration of 0.5 ⁇ g/ml in PBS (100 ml/well). Plates were incubated at 37 °C on an orbital shaker with agitation for 2 hours. Thereafter coating solution was removed and 100 ⁇ /well PBSTC
• PBST phosphate buffered saline, 0.05 % Tween®-20
• 100 ⁇ /well ABTS® Roche Diagnostics GmbH, Mannheim, Germany
• Plasmid p6454 was the expression plasmid for the expression of an anti-IL-17- antibody (genomically organized expression cassette with retained exon-intron organization) in eukaryotic cells. It comprises the following functional elements:
• an expression cassette for the expression of the gamma 1 -heavy chain comprising the following elements:
• hCMV IE1 promoter the major immediate-early promoter and enhancer from the human cytomegalovirus (hCMV IE1 promoter), - a synthetic 5 'UTR including a Kozak sequence,
• VH heavy chain variable region
• IGHG1 human immunoglobulin heavy chain gamma 1-gene including exons CHI, Hinge, CH2 and CH3, intervening introns and the 3 'UTR bearing the polyadenylation signal sequence
• an expression cassette for the expression of the kappa- light chain comprising the following elements:
• IGK human immunoglobulin kappa gene
• DHFR murine dihydrofolate reductase
• P6454 was transfected into CHO-Kl cells and stable cell lines were isolated after selection with methotrexate (MTX) and were screened for production of humanized antibody by ELISA for human IgG.
• MTX methotrexate
• NHDF Normal human dermal fibroblasts
• NHDF cells were cultured in Fibroblast Growth Medium-2 (Cambrex, #CC 3132) at a density of 4xl0 5 cells/ml in a volume of 0.5 ml per well in a 48-well plate. NHDF cells were incubated overnight at 37 °C and 5 % CO2 to adhere. After overnight incubation, the media was aspirated off and replaced with 300 ⁇ fresh media, cells were then treated with the antibody for 30 minutes across a range of antibody concentrations (3000, 1000, 300, 100, 30, 10, 3, 1, 0 ng/ml). The antibody dilution series was made with medium using 100 ⁇ /well (5x concentrated). After 30 min.
• the cells were stimulated with 10 ng/ml hIL-17 (100 ⁇ of 50 ng/ml 5x concentration, R&D Systems #317-IL) and incubated overnight (18 h) at 37 °C and 5 % CO2.
• 10 ng/ml hIL-17 100 ⁇ of 50 ng/ml 5x concentration, R&D Systems #317-IL
• 100 ⁇ of media was used (with and without antibodies present).
• supernatants were transferred into fresh tubes and either analyzed immediately or stored at -80 °C until analysis by ELISA.
• Human IL6 ELISA hIL-6 ELISA (BD Biosciences #555220) was used according to the manufacturer's instructions to measure hIL-6 levels in the culture supernatants to assess the potency of antibodies at inhibiting IL-17 induced hIL-6.
• BIAcore 3000 instrument All measurements were performed using the BIAcore 3000 instrument at 25 °C.
• the system and sample buffer was HBS-EP (10 mM HEPES, 150 mM NaCl, 3.4 mM EDTA, 0.005 % Polysorbate 20 (v/v)).
• a BIAcore CM5 sensor chip was subjected to a preconditioning procedure. Sequentially 0.1 % SDS, 50 mM NaOH, 10 mM HC1 and 100 mM H3PO4 was injected for 30 sec. over the flow cells.
• the amine coupling procedure was done according to the manufacturer's instructions using the BIAcore 3000 wizard v. 4.1.
• a polyclonal goat anti-human IgG antibody (Jackson) was immobilized on all sensor flow cells (FCs).
• 30 ⁇ g/ml polyclonal goat anti-human IgG antibody in 10 mM NaAc pH 5.0 was used at 10 ⁇ /min for 7 min. to immobilize about 10,000 RU of the antibody capturing system.
• the surface was deactivated by saturation with ethanolamine.
• the human capture system sensor was conditioned with 5 cycles of binding of hulgG analyte (Bayer) at 10 ⁇ /min for 2 min and regeneration with 10 mM glycine pH 1.7 at 30 ⁇ /min for 3 min.
• the antibody was injected to form the capture system.
• the antigen was injected within a defined concentration range.
• the binding responses (resonance units, RU) obtained after injection of the antigen correlate with the amount of antigen bound to the antibody and were plotted against the antigen concentration range used.
• the resulting linear plot was analyzed by appropriate computer software (e.g. XLfit4, IDBS Software), which fits a 2- parametric line and hence allows determination of the y-axis intercept as the biological activity readout.

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• 2018
  • 2018-07-27 CN CN202310957514.5A patent/CN117050176A/zh active Pending
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• 2021
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