),
`
`·. · U1 715272 · .
`JPRESS MAIL LABEL NO. 859937585
`DATE MAILED: June 14, 1991
`GENENTECH, INC.
`
`
`
`460 Point San Bruno Boulevard, South San Francisco, CA 94080
`(415) 266-1000
`
`Docket No. 709
`
`
`
`NEW APPLICATION TRANSMITTAL
`
`r·
`
`SIR:
`
`
`
`
`
`Transmitted herewith for filing is the patent application of lnvantor(sl:
`PAUL J. CARTER ET AL.
`
`
`
`
`
`
`
`Title: IMMUNOGLOBULIN VARIANTS
`
`
`
`CERTIFICATION UNDER 37 CFR §1.10
`
`I hereby certify that this New Application and the docunents referred to es enclosed herein ere being deposited with the United
`
`
`
`
`
`
`
`Mell Ing Lebel Mell Post Office To Addressee" States Postal Service on this date June 14, 1991, In en envelope bearing "Express
`
`
`
`
`
`
`
`Nurt>er 859937585 addressed to: Patent Application, Honorable Comnlssloner of etents nd T ad ks, ashlngton, D.C. 20231.
`
`Carolyn R, Adler
`
`(Name of person malling paper)
`
`Enclosed are:
`
`1.· The papers required for filing date under CFR § 1.53(b):
`
`
`
`
`
`.1filL Pages of specification (Including claims); _L Sheets of drawings Lformal / .lL informal)
`
`.2L Declaration/Oath/Power of Attorney
`
`
`_ Assignment of the invention to GENENTECH, INC.
`4. Fee Calculation
`
`3.
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`CLAIMS AS FILED
`
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`X $20.00
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`I-
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`*
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`Total Claims
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`16 -20"
`
`. \ndep. Claims
`
`8 -3 ..
`
`I Basic Fee
`I
`x S60.00
`·s200.ooI
`
`$630
`
`630.
`
`300.
`
`tNll!ber F !led INuroer Extra
`-
`I
`* 5
`depe ndent c:lalm.<s>, If any
`Hllltlple
`011•
`11
`Recordlng Assignment [$8.001 Total Fees Enclosed
`
`
`*If less than zero, enter
`8. Payment of Fees
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`SU tbi§ tran.s,mjttl,ll l§ attached.
`..lL Charge Account No. 07-0630 In the amount of $_. A mtQllcate
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`Fees 9. -2L Authorization to Charge Additional
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`The Commissioner is hereby authorized to charge any additional fees (or credit any overpayment) associated
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`
`with this communication and which may be required under 37 CFR § 1.16 or § 1. 17 to Account No. 07-0630.
`8 sfypljcate sheet is
`attached.
`
`
`1'0. Information Disclosure Statement
`
`11. .2L . Return Receipt Postcard
`
`7.
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`$
`
`
`
`. . . . . . $930.00
`
`14, 1991
`Dated _June
`
`�,�/(,�
`Name: CarotvnRAd1er
`
`Registration No. 32,324
`
`. .
`
`·Pfizer v. Genentech
`IPR20I 7-01489
`
`
`
`I
`
`
`
`
`
`Genentech Exhibit 2032
`
`

`

`o 2
`rroune ia: v, owsrn
`=
`
`s7522°70
`
`10
`
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`
`4D5
`
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`
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`
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`prgltnasrS$hsaSveoRvritcRASQDVNTAVANYGQKPGRAPKLLTYSASFLES
`p0M7QSPSSLSASVGDRVIITCRASQDVSSYLAWYQQKPGKAPKLLTYAASSLES
`V,_-CDR1.
`V,-CDR2
`
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`
`30
`
`40
`
`50
`
`an the ten fente Sen cee me se RAENGem in Sh
`
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`
`4D5
`
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`
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`
`60
`70
`80. 90
`100
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`evebarbchascrprniarsstorEpraryveqgiymnrprecacnkvErKt
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`
`ea ete ce ne a ere Ue HN sea
`
`
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`
`

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`oe.
`FIGURE 1B: Vy DOMAIN
`
`e
`
`|
`
`I 715272
`
`4D5
`
`HU4D5
`
`HUV,III
`
`A
`50
`40
`30
`-20 |
`10 -
`EVQLQQSGPELVKPGASLKLSCTASGENIKDTYIHWVKQRPEQGLEWIGRIYPTN
`|
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`poyiid
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`— a ee oe
`
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`
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`70
`80
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`
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`
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`
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`
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`
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`
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`
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`
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`. GOGTLVTVSS
`
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`
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`
`
`
`

`

`Figure 2
`Anneal huV,_ or huV, oligomers to pAKI template
`
`715272
`
`
`
`1. Ligate
`2. Isolate assembled oligomers
`3. Anneal to pAK1 template (Xhol-, Stul*)
`4. Extend and ligate
`
`| Xhol ~
`
`
`
`1. Transform E.coli
`2. Isolate phagemid pool
`3. Enrich for huV, and huVy(Xho II+, Stul-)
`4. Sequence verify
`
`\
`
`,
`
`

`

`muMAb4D5
`
`715272
`
`416
`
`~ buMAD4D5-8
`
`4 8 12
`[MAb4D5variant] pg/ml
`
`pl
`
`Percentofcontrolcell
`proliferation
`
`
`
`

`

`Wl 718272
`
`
`
`

`

` eo
`
`pense
`
`DOCKET 709 |
`.
`EXPRESS MAIL NO. B59937585
`
`MAILED 14 JUNE 1991
`
`4
`
`A6/
`
`IMMUNOGLOBULIN VARIANTS
`
`Field of the Invention
`
`This invention relates to methods for the preparation and useof
`variant antibodies and finds application particularly in the fields of
`
`Immunology and cancer diagnosis and therapy.
`
`Backoround of the Invention
`
`Naturally occurring antibodies (immunoglobulins) comprise two
`heavy chains linked together by disulfide bonds and twolight chains, one
`light chain being linked to each of the heavy chainsby disulfide bonds. Each
`heavy chain has at one end a variable domain (V,) followed by a numberof
`constant domains. Each light chain has a variable domain (V,) at one end
`and a constant domainat its other end; the constant domain of the light
`chain is aligned withthe first constant domain of the heavy chain, and the
`
`light chain variable domain is aligned with the variable domain of the heavy
`chain. Particular amino acid residues are believed to forman interface
`betweenthe light and heavy chain variable domains, see e.g. Chothia etal.,
`J. Mol. Biol. 186:651-663 (1985); Novotny and Haber, Proc. Natl. Acad. Sci.
`
`10
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`15
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` ©@
`
`e
`USA 82:4592-4596 (1985).
`involved directly in binding the
`The constant domains are not
`antibody to an antigen, but are involved in various effector functions, such
`as participation of the antibody in antibody-dependentcellular cytotoxicity.
`The variable domains of each pairof light and heavy chains are involved
`directly in binding the antibody to the antigen. The domains of natural light
`and heavy chains have the same genera! structure, and each domain
`
`comprises four framework (FR) regions, whose sequences are somewhat
`conserved,
`connected
`by three hyper-variable
`or
`complementarity
`determining regions (CDRs) (see Kabat, E. A. et af., Sequences of Proteins
`of Immunological Interest, National Institutes of Health, Bethesda, MD,
`(1987)). The four framework regions largely adopt a B-sheet conformation
`and the CDRs form loops connecting, and in somecasesforming part of, the
`B-sheet structure. The CDRs in each chain are held in close proximity by the .
`framework regions and, with the CDRs from the other chain, contribute to
`the formation of the antigen binding site.
`Widespread use has been made of monoclonal antibodies,
`particularly those derived from rodents including mice, however they are
`frequently antigenic in human clinical use. For example, a major limitation in
`the clinical use of rodent monoclonal antibodies is an anti-globulin response
`during therapy (Miller, R. A. et a/., Blood 62:988-995 (1983); Schroff, R. W.
`et al., Cancer Res. 45:879-885 (1985)).
`
`|
`
`The art has attempted to overcome this problem by constructing
`
`“chimeric” antibodies in which an animal antigen-binding variable domain is
`coupled to a human constant domain (Cabilly et a/., U.S. patent No.
`4,816,567; Morrison, S.L. et al., Proc. Natl. Acad. Sci. USA 81:6851-6855
`(1984); Boulianne, G. L. et a/., Nature 312:643-646 (1984); Neuberger, M.
`
`S. et al., Nature 314:268-270 (1985))..The term"chimeric" antibody is used
`herein to describe a polypeptide comprising at least the antigen binding
`portion of an antibody molecule linked to at least part of another protein |
`
`(typically an immunoglobulin constant domain).
`The isotype of the human constant domain maybeselected totailor
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`the chimeric antibody for participation in antibody-dependent cellular
`cytotoxicity (ADCC) and complement-dependent cytotoxicity (see e.g.
`Briiggemann,M.et a/., J. Exp. Med. 166:1351-1361 (1987); Riechmann,L.
`et al., Nature 332:323-327 (1988); Love et a/., Methods in Enzymology
`“178:515-527 (1989); Bindon et a/., J. Exp. Med. 168:127-142 (1988).
`In the typical embodiment, such chimeric antibodies contain about
`
`one third rodent (or other non-human species) sequence and thus are capable
`of eliciting a significant anti-globulin response in humans. For example,in the
`-case of
`the murine anti-CD3 antibody, OKT3, much of
`the resulting
`anti-globulin responseis directed against the variable region rather than the
`constant region (Jaffers, G. J. et al, Transplantation 41:572-578 (1986)).
`in a further effort
`to resolve the antigen binding functions of
`antibodies and to minimize the use of heterologous sequences-in human
`antibodies, Winter and colleagues (Jones, P. T. et al., Nature 321:522-525
`(1986); Riechmann, L. et al., Nature 332:323-327 (1988); Verhoeyen, M. et
`al., Science 239:1534-1536 (1988)).have substituted rodent CDRs or CDR
`sequences for the corresponding segments of a humanantibody. As used
`herein,
`the term "humanized" antibody is an embodiment of chimeric
`‘antibodies wherein substantially less than an intact human variable domain
`has been substituted by the corresponding sequence from a non-human
`species.
`In practice, humanized antibodies are typically human antibodies in
`which some CDRresidues and possibly some FR residues are substituted by
`residues from analogous sites in rodent antibodies.
`,
`The therapeutic promise of this approachis supported by the clinical
`efficacy of a humanized antibody specific for the CAMPATH-1 antigen with
`two non-Hodgkin lymphomapatients, one of whom had previously developed
`an anti-globulin response to the parentalrat antibody (Riechmann, L. et a/.,
`Nature 332:323-327 (1988); Hale, G. et a/., Lancet ist 394-1399 (1988)).
`A murine antibody to the interleukin 2 receptor has also recently been
`humanized (Queen, C. et a/., Proc. Natl, Acad. Sci. USA 86:10029-10033
`(1989)) as a potential immunosuppressive reagent. Additional references
`related to humanization of antibodies include Co et a/., Proc. Natl, Acad. Sci.
`4uv
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`
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`

`USA 88:2869-2873 (1991); Gorman et al., Proc. Natl. Acad. Sci. USA
`88:4181-4185 (1991); Daugherty etal., NucleicAcids Research 19(9):2471-
`2476 (1991); Brown et al., Proc. Nath Acad. Sci, USA 88:2663-2667
`(1991); Junghanset a/., Cancer Research 50:1495-1502 (1 990).
`In some cases, substituting CDRs from rodent antibodies for the
`human CDRs in human frameworks is sufficient to transfer high antigen
`binding affinity (Jones, P. T. et a/., Nature 321:522-525 (1986); Verhoeyen,
`M. et al., Science 239:1534-1536 (1988)), whereas in-other casesit has
`been necessary to additionally replace one (Riechmann,L. et a/., Nature |
`332:323-327 (1988)) or several (Queen, C. et al., Proc. Natl. Acad. Sci. USA
`86:10029-10033 {1989)) framework region (FR) residues. See also Co ef.
`
`a/., supra.
`.
`.
`For a given antibody a small number of FR residues are anticipated
`to be important for antigen binding. Firstly for example, certain antibodies
`have been shown to contain a few FR residues which directly contact antigen
`in crystal structures of antibody-antigen complexes (e.g., reviewed in Davies,
`D. R. et a/., Ann. Rev. Biochem. 59:439-473 (1990)). Secondly, a number
`of FR residues have beenproposed by Chothia, Lesk and colleagues (Chothia,
`. & Lesk, A. M., J. Mol, Biol. 196:901-917. (1987); Chothia, C. e¢ a/.,
`Nature 342:877-883 (1989); Tramontano, A. et al.,
`J. Mol. Biol.
`215:175-182 (1990)) as critically affecting the conformation of particular
`CDRsand thustheir contribution to antigen binding. See also Margolies et
`‘al., Proc. Natl. Acad. Sci. USA 72:2180-2184 (1975).
`It is also known that, in a few instances, an antibody variable
`‘domain (either V,, or V,) may contain glycosylation sites, and that this
`glycosylation may improve
`or
`abolish antigen binding, Pluckthun,
`Biotechnology 9:545-51 (1991); Spiegelberget a/., Biochemistry 9:4217-
`4223 (1 970); Wallic et a/., J. Exp. Med. 168:1099-1109 (1988); Sox etal,
`Proc. Natl. Acad. Sci. USA 66:975-982 (1970); Margni et a/., Ann. Rev.
`Immunol. 6:535-554 (1988). Ordinarily, however, glycosylation has no
`_ influence on the antigen-binding properties of an antibody, Pluckthun, supra,
`
`(1991).
`
`10
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`
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`

`

`' The three-dimensional structure of immunoglobulin chains has been
`studied, and crystal structures for intact ifnmunoglobulins, for a variety of
`
`immunoglobulin fragments, and for antibody-antigen complexes have been
`
`published (see e.g., Saul et a/., Journal of Biological Chemistry 25:585-97
`re 978); Sheriff et a/., Proc. Natl. Acad. Sci. USA 84:8075-79 (1987); Segal
`et al., Proc. Natl. Acad. Sci. USA 71:4298-4302 (1974): Eppet al.,
`Biochemistry 14(22):4943-4952 (1975); Marquart
`et a/., J. Mol. Biol.
`141:369-391 (1980); Furey et a/., J. Mol.Biol. 1 67:661-692 (1983); Snow
`and Amzel, Protein: Structure, Function, and Genetics 1:267-279, Alan R.
`Liss, Inc. pubs. (1986); Chothia and Lesk,J. Mo/. Biol. 196:901-917 (1 987):.
`Chothia eta/., Nature 342:877-883 (1989); Chothia eta/., Science 233:755-
`58 (1986); Huber et a/., Nature 264:415-420 (1976); Bruccoleri et a/.,
`Nature 335:564-568 (1988) and Nature 336:266 (1988); Sherman et a/.;
`Journal of Biological Chemistry 263:4064-4074 (1988); Amzel and Poljak,
`‘Ann. Rev. Biochem. 48:961-67 (1979); Silverton et al, Proc. Natl. Acad.
`Sci. USA 74:5140-5144 (1977); and Gregory et a/., Molecular Immunology
`24:821-829 (1987).
`It
`is known that the function of an antibody is
`dependent on its
`three dimensional
`structure, and that amino acid
`substitutions can change the three-dimensional structure of an antibody,
`Snow and Amzel, supra.
`It has previously been shown that the antigen
`binding affinity of a humanized antibody can.be increased by mutagenesis
`based upon molecular modelling (Riechmann,L. et a/., Nature 332:323-327
`(1988); Queen, C. et a/., Proc. Natl Acad. Sci. USA 86:10029-10033
`
`(1989)).
`
`.
`Humanizing an antibody with retention of high affinity for antigen
`‘and other desired biological activities is at present difficult to achieve using
`currently available procedures. Methods are needed for rationalizing the
`selection of sites for substitution in preparing such antibodies and thereby
`increasing the efficiency of antibody humanization.
`The proto-oncogene HER2
`(human epidermal growth factor.
`receptor 2) encodes a protéin tyrosine kinase (p1g5HER2) that is relatedto
`and. somewhat homologous to the human epidermal growth factor receptor
`
`5
`
`au
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`

`“
`
`
`
`15
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`20
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`30
`
`eo ®
`(see Coussens,L. et a/., Science 230:1132-1139 (1985); Yamamoto,T. et
`al., Nature 319:230-234 (1986); King, C. R. et al., Science 229:974-976 |
`Q 985). HER2is also knownin thefield as c-erbB-2, and sometimes by the
`name of the rathomolog, neu. Amplification and/or overexpression of HER2.
`is associated with multiple human malignancies and appears to be integrally
`involved in progression of 25-30% of human breast and ovarian cancers
`(Slamon, D. J. et al., Science 235:17.7-182 (1987), Slamon, D. J. et a/.,
`Science 244:707-712 (1989)). Furthermore, the extent of amplification is
`inverselycorrelated with the observed median patient survival time (Slamon,
`supra, Science 1989).
`—_ Ce .
`.
`The murine monoclonal antibody known as muMAb4D5 (Fendly, B.
`M. et af, Cancer Res. 50:1550-1558- (1990)), directed against
`the
`extracellular domain (ECD) of p18S4ER2, specifically inhibits the growth of
`tumor cell lines overexpressing p1 g5HER2 in monolayer culture or in soft agar
`(Hudziak, R. M. et al., Molec. Cell, Biol. '9:1165-1172 (1989); Lupu,R. et af,
`Science 249:1552-1555 (1990)). MuMAb4D5also has the potential of
`enhancing tumor cell sensitivity to tumor necrosis factor, an important
`effector molecule in macrophage-mediated tumorcell cytotoxicity (Hudziak,
`supra, 1989; Shepard, H. M. ‘and Lewis, G. D. J. Clinical Immunology-
`8:333-395 (1988)). Thus muMAb4D5 has potential for clinical intervention
`in and imaging of carcinomas in which pi gsHeR2 is overexpressed. The
`muMAb4D5 and its uses are described in copending U.S. patent applications
`07/143,912 and 07/147,461, and in corresponding PCT application WO
`89/06692 published 27 July 1989. This murine antibody was deposited
`with the ATCC and designated ATCC CRL 10463. However,this antibody
`may be immunogenic in humans.
`.
`it is therefore an object of this invention to provide methodsfor the
`preparation of antibodies whichare less antigenic in humans than non-human
`antibodies but have desired antigen binding and other characteristics and
`activities.
`.
`It is a further object of this invention to provide methods for the
`efficient humanization of antibodies, i.e. selecting non-human amino acid
`
`6
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`

`

` — e
`eo
`residues for importation into. a human antibody background sequence in such
`a fashion as to retain or
`improve the affinity of the non-human donor
`antibody for a given antigen.
`,
`It
`is another object of
`this invention to provide humanized
`antibodies capable of binding pig5hER2
`Other objects, features, and characteristics of the present invention
`will become apparent upon consideration of the following description and the
`appended claims.
`
`.
`
`Summary
`
`of
`
`the Invention
`
`b.
`
`c.
`
`d.
`
`The objects of this invention are accomplished. by a method for
`making a humanized antibody comprising amino acid sequence of an import,
`non-human antibody anda human antibody, comprising the steps of:
`a.
`obtaining the amino acid sequencesof at least a portion
`of animport antibody variable domain and of a consensus
`human variable domain;
`.
`identifying Complementarity Determining Region (CDR)
`amino acid sequences in ‘the import and the human
`variable domain sequences;
`|
`;
`.
`substituting an import CDR amino acid sequencefor the
`corresponding human CDR amino acid sequence;
`aligning the amino acid sequences of a Framework Region
`(FR) of the import antibody and the corresponding FR of
`the consensus antibody:
`identifying import antibody FR residues in the aligned FR
`sequencesthat are non-homologous to thecorresponding
`consensus antibody residues;
`-determining if the non-homologous import amino acid
`residue Is reasonably expected to have at least one of the
`following effects:
`1.
`non-covalently binds antigen directly,
`
`e.
`
`f.
`
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`

`g.
`
`interacts with a CDR; or
`2.
`participates in the V, - V,, interface; and
`3.
`for. any non--homologous import antibody amino acid
`residue whichis reasonably expected to have at least one-
`of
`these effects,
`substituting that
`residue for
`the
`corresponding amino acid residue in the consensus
`antibody FR sequence.
`|
`Optionally, the method of this invention comprises the additional
`stepsof determining if any non-homologous residues identified in step (e)are
`exposedon the surface of the domain or buried within it, and if the residue
`is exposed but has none of the effects identified in step (f), retaining the
`consensusresidue.
`|
`‘Additionally, in certain embodirnents the method of this invention
`comprises the feature wherein the corresponding consensus antibody -
`residues identified in step (e) above are selected from the group consisting
`of 4L, 35L, 36L, 38L, 43L, 44L, 46L, 58L, 62L, 63L, 64L, 65L, 66L, 67L,
`68L, 69L, 7OL, 71L, 73L, 85L; 87L, 98L, 2H, 4H, 24H, 36H, 37H, 39H,
`43H, 45H, 49H, 58H, 60H, 68H, 69H, 70H, 73H, 74H, 75H, 76H, 78H,
`91 H, 92H, 93H, and 103H(utilizing the numbering system set forthin Kabat,
`E. A. et al, Sequences of ‘Proteins of Immunological interest (National
`Institutes of Health, Bethesda, MD, 1987).
`In certain embodiments, the method ofthis invention comprises the
`additional steps of searching either or both of the import, non-human and the
`consensus variable domain sequences for glycosylation|sites,determining if
`reneeSate eenmwenre9ARO
`. RCA Beh
`ate
`the glycosylation is reasonablyexexpected to be important for the desired
`antigenbindingand biological activity oftheantibody(i.e.é.,,_determiningi ifthe.
`glycosylation site binds to antigen or changes a side chain of an amino acid
`residue that binds to antigen, or if the glycosylation enhances or weakens
`antigen binding, or is important for maintainingantibody affinity).
`If the
`importsequence bearstheglycosylation site, itis preferred to substitutethat
`site for the corresponding residues in the consensus human sequenceif the
`glycosylation site is reasonably expected to be important.
`If only the
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`

`consensus sequence, and not the import, bears the glycosylation site, it is
`preferred to eliminate that glycosylation site or substitute therefor the ,
`corresponding amino acid residues from the import sequence.
`
`Another embodiment of this invention comprises aligning import
`
`\
`
`identifying. import
`antibody and the consensus antibody FR sequences,
`_ antibody FR residues which are non-homologous with the aligned consensus
`FR sequence, and for each such non-homologous import antibody FR residue,
`determining if the corresponding consensus antibody residue represents a
`residue which is highly conserved acrossall species at that site, and if it is
`so conserved, preparing a humanized _antibody which comprises the
`consensus antibody amino acid residue at that site..
`Certain alternate embodiments of the methods of this invention
`comprise obtaining the amino acid sequence of at least a portion. of an
`import, non-human antibody variable domain having a CDR and a FR,
`_ obtaining the amino acid sequence of at least a portion of a consensus
`human antibody variable domain having a CDR and a FR, substituting the
`non-human CDR for the human CDRin the consensus human antibody
`variable domain, and then substituting
`an amino acid residue for the .
`consensus aminoacid residue at at least one of the following sites:
`a.
`(in the FR of the variable domainof the light chain) 4L,
`35L, 36L, 38L, 43L, 44L, 58L, 46L, 62L, 63L, 64L, 65L,
`66L, B7L, BBL, GOL, 7OL, 71L, 73L, BSL, 87L, BL,or
`"(in the FR of the variable domain of the heavy chain) 2H,
`4H, 24H, 36H, 37H, 39H, 43H, 45H, 49H, 58H, 60H,-
`68H, 69H, 70H, 73H, 74H, 75H, 76H, 78H, 91H, 92H, |
`93H, and 103H.
`in preferred embodiments, the non-CDRresidue substituted at the consensus
`FR site is the residue found at the corresponding location of the non-human
`antibody.
`,
`|
`Optionally, this just-recited embodiment comprises the additional
`steps of following the method steps appearing at the beginning of this
`summary and determining whether aparticular amino acid residue can
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`b.
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`reasonably be expected to have undesirable effects.
`This invention also relates to a humanized antibody comprising the
`
`-
`
`CDR sequence of an import, non-human antibody and the FR sequenceof a
`human antibody, wherein an amino acid residue within the human FR
`sequence located at any one. of the sites 4L, 35L, 36L, 38L, 43L, 44L, 46L,
`58L, 62L, 63L, 64L, 65L, GEL, G7L, 6BL, 69L, 7OL, 7IL, 73L, BBL, 87L,
`98L, 2H, 4H, 24H, 36H, 37H, 39H, 43H, 45H, 49H, 58H, 6OH, 68H, 69H,
`70H, 73H, 74H, 75H, 76H, 78H, 91H, 92H, 93H, and 103H has been
`substituted by another residue.
`In preferred embodiments,
`the residue
`_ substituted at the human FRsite is the residue found at the corresponding
`location of the non-human antibody from which the non-human CDR was _
`obtained.
`In other embodiments, no human FRresidue other than those set
`forth in this group has been substituted.
`- This invention also encompasses specific humanized antibody
`variable domains, and isolated polypeptides having homology with the
`following sequences.
`4. SEQ.
`ID NO. 1, which is thelight ‘chain variable domain of a
`humanized version of muMAb4D5:
`DIOMTOSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAP
`KLLIY SASFLESGVPSRFSGSRSGTDFTLTISSLOPEDFATYYCQQHY
`TTPPTFGOGTKVEIKRT
`,
`
`_
`;
`
`2. SEQ. ID NO. 2, which is the heavy chain variable domain ofa
`humanized version of muMAb4D5):
`- EVOLVESGGGLVOPGGSLRLSCAASGFNIKDTYIHWVROAPGKGLE
`WVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLOMNSLRAEDT
`AVYYCSRWGGDGFYAMDVWGOGTLVTVSS
`
`In another aspect, this invention provides a consensus human
`antibody variable domain amino acid sequencefor use in the preparation of
`humanized antibodies, methods for obtaining, using, and storing a computer .
`representation of such a consensus sequence, and computers comprising the
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`In one embodiment, the following
`sequence data of such a sequence.
`consensus human antibody variable domain. amino acid sequences are
`
`provided:
`
`SEQ. ID NO. 3 light chain):
`DIOMTOSPSSLSASVGDRVTITCRASQDVSSYLAWYQOKPGKAPK
`LLIYAASSLESGVPSRFSGSGSGTDFTLTISSLOPEDFATYYCQQYN
`SLPYTFGQGTKVEIKRT, and
`.
`
`;
`SEQ..ID NO. 4 (heavy chain):
`EVOLVESGGGLVOPGGSLRLSCAASGFTFSDYAMSWVRQAPGKG
`LEWVAVISENGGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAE
`DTAVYYCSRWGGDGFYAMDVWGQGTLVTVSS
`
`Brief Description of the Drawings
`
`FIGURE 1A shows the comparison of the V; domain amino acid
`residues of muUMAb4D5, huMAb4D5, and a consensus human sequence (Fig.
`1A, SEQ.ID NO. 5, SEQ. ID NO. 1 and SEQ. ID NO. 3, respectively). FIGURE
`1B shows the comparison between the Vi, domain aminoacid residues of the
`muMAb4d5, huMAb4D5, and a consensus human sequence (Fig. 1B, SEQ.
`ID NO. 6, SEQ. ID NO. 2:and SEQ.ID NO. 4, respectively). Both Figs 1A and
`1B use the generally accepted numbering scheme from Kabat, E. A., et a/.,
`Sequences of Proteins of Immunological Interest (National Institutes of
`Health, Bethesda, MD (1987)).
`In both Fig. 1A and Fig. 1B, the CDR
`residues determined according to a standard sequencedefinition (as in Kabat,
`E. A. et al., Sequences of Proteins of Immunological Interest (National
`“Institutes of ‘Health, Bethesda, MD, 1987)) are indicated by the first
`underlining beneath the sequences, and the CDR residues determined
`according to a structural definition (as in Chothia, C. & Lesk, A. M., J. Mol.
`
`Biol. 196:901-917 (1987)) are indicated by the second, lower underlines.
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`Pod
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`are shownby the verticallines.
`ie The mismatches between
`FIGURE 2 shows a scheme for humanization of muMAb4D5 V,and
`Vy, by gene conversion mutagenesis.
`FIGURE 3 showstheinhibition of SK-BR-3 proliferation by MAb4D5
`variants. Relative cell proliferation was determined as described (Hudziak,R.
`M. et a/., Molec. Cell. Biol. 9:1165-1172 (1989)) and data (average of
`triplicate determinations) are presented as a percentage of results with
`untreated cultures for MUMAb4D5(}), huMAb4D5-8 (n) and huMAb4D5-1 ();
`FIGURE 4 showsa stereo view of'a-carbon tracing for model of
`huMAb4D5-8 V, and Vy. The CDR residues (Kabat, E. A. et a/., Sequences
`of Proteins ofImmunologicalInterest (NationalInstitutes of Health, Bethesda,
`MD, 1987)) are shownin bold and. side chains of Vi residues A71, 773,
`A78, $93, Y102 and Vy residues Y55 plus R66 (see Table 1) are shown.
`
`Detailed Description of the Invention
`
`Definitions
`the following words or phrases have the indicated:
`In general,
`definitions when used in the description, examples, and claims:
`The murine monoclonal antibody known as muMAb4D5 (Fendly, B
`M. et al., Cancer Res. 50:1550-1558 (1990)) is directed against
`the
`extracellular domain (ECD) of p1gsHeR2, The muMAb4D5 and its uses are
`described in
`copending U.S. patent
`applications 07/143,912 and
`_07/147,461, and in corresponding PCT application WO 89/06692 published
`' 27 July 1989. This murine antibody was deposited with the ATCC and
`designated ATCC CRL 10463.
`In this description and claims, the terms
`muMAb4D5, chMAb4D5 and huMAb4D5represent murine, chimerized and
`humanized versions of the monoclonal antibody 4D5, respectively.
`A humanized antibody for the purposes hereinis an immunoglobulin
`amino acid sequence variant or fragment thereof which is capable of binding
`toa predetermined antigen and which comprises a FR region having
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`substantially the amino acid sequence of a human immunoglobulin and a CDR
`having
`substantially
`the
`amino acid
`sequence
`of
`a
`non-human
`immunoglobulin.
`In general, the humanized antibody will comprise substantially all of
`at least one, and typically two, variable domains (Fab)
`in which all or
`
`- substantially all of the CDR regions correspond to those of a non-human
`immunoglobulin and all or substantially all of the FR regions are those of a
`human immunoglobulin consensus sequence.
`‘The humanized antibody
`optimally also will comprise at least a.portion of an immunoglobulin constant
`region (Fo),
`typically that of a human immunoglobulin. Ordinarily,
`the
`_antibody will contain both the light chain as well as at least the variable
`domain of a heavy chain. The antibody also may include the CH?1, hinge,
`CH2, CH3, and CH4 regions of the heavy chain.
`The humanized antibody will be selected from any class of
`immunoglobulins,
`including IgM, IgG, IgD, IgA and IgE, and any isotype,
`including IgG1, IgG2, IgG3 and IgG4. Usually the constant domain is a °
`complement fixing constant domain whereit is desired that the humanized
`antibody exhibit cytotoxic activity, and the classis typically IgG,. Where
`such cytotoxic activity is not desirable, the constant domain maybe of the
`igG, class. The humanized antibody may comprise sequences. from more.
`than one class or isotype, and selecting particular constant domains to
`optimize desired effector functions is within the ordinary skill in the art..
`The FR and CDR regions of the humanized antibody need not
`
`—
`
`correspond precisely to the parental sequences, e.g., the import CDR or the
`consensus FR may be mutagenized by substitution, insertion or deletion of
`a residue so that the CDR or FR residue at that site does not correspond to.
`
`‘either the consensus or the import antibody. Such mutations, however, will
`not be extensive. Usually, at least 75% of the humanized antibody residues
`will correspond to those of the parental FR and CDR sequences, more often
`' 90%, and most preferably greater than 95%.
`in general, humanized antibodies prepared by the methodofthis
`invention are produced by a process of analysis of the parental sequences
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`_ and various conceptual humanized products using three dimensional models
`of
`the
`parental
`and
`humanized
`sequences.
`Three
`dimensional
`immunoglobulin models are commonly available and are familiar to those
`’ skilled in the art. Computer programs are available which illustrate and
`display probable three dimensional conformational structures of selected ~
`candidate immunoglobulin sequences.
`Inspection of these displays permits
`analysis of the likely role of the residues in the functioning of-the candidate
`immunoglobulin sequence, i.e., the analysisofresidues that influence the
`ability of the candidate immunoglobulin to bind its antigen.
`Residues that influence antigen binding are defined to be residues -
`that are substantially responsible for the antigen affinity or antigen specificity |
`of acandidate immunoglobulin, in a positive or a negative sense, The object
`here is toselect FR residues from the consensus and import sequence so that
`the desired immunoglobulin characteristic is achieved. Such desired
`characteristics include increases in affinity and greater specificity for the
`target antigen, although itis conceivable that in some circumstances the
`opposite. effects might be desired. - In general, the CDR residues are directly _
`and most substantially involved in influencing antigen binding (although not
`all CDR residues are so involved and therefore need not be substituted into ©
`the consensus sequence). However, FR residues also have a significant
`effect and can exert their influence in. at least three ways: They may .-
`noncovalently directly bind to antigen, they mayinteract with CDR residues
`and they may affect the interface between the heavy and light chains.
`A residue that noncovalently directly binds to antigen is one that,
`by three dimensional analysis,
`is reasonably expected to noncovalently
`directly bind to antigen. Typically, it is necessary to impute the position of
`antigen from the spatial location of neighboring CDRsandthe dimensionsand
`structure of the target antigen. In general, only those humanized antibody
`‘residues that are capable of
`forming salt bridges, hydrogen bonds, or
`“hydrophobic interactions arelikely to be involved in non-covalent antigen
`binding, however residues which are2SeparatedS|spatially by,3.2{Angstroms )
`ee
`~~|angrier
`_orless may also non-covalently interact.
`Suchresidues typically are the
`essMaya'soNon’covereyeee
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`relatively larger aminoacids,suchastyrosine,arginine,andlysine. Antigen-
`binding FR residuesalso typically will have side chains that are oriented into
`an envelope surrounding the solvent oriented face of a CDR which extends
`about 7 Angstroms into the solvent from the CDR domain and about 7
`Angstroms on either side of the CDR domain, again as visualized by three
`dimensional modeling.
`.
`,
`-
`A residue that interacts with a CDR generally.is a residue that either
`affects the conformation of the CDR polypeptide backbone or forms a
`noncovalent bond with a CDR residue side chain. Conformation-affecting
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`residues ordinarily are those that change the spatial position of any CDR 7
`backbone atom (N, Ca, C, O, Cf) by more, than about 0.2 Angstroms.
`Backbone atoms of CDR sequences are displaced for example by residues ,
`that interrupt or modify organized structures such as beta sheets,helices o