O
`(12) Ulllted States Patent
`Gegg et al.
`
`(54) MODIFIED FC MOLECULES
`
`(75)
`
`Inventors: Colin Gegg, Newbury Park, CA (US);
`Fei Xi6ng7 Thousand Oaks, CA (US);
`Karen C. Sitney, Weston, CT (US)
`.
`(73) Assignee: Amgen Inc., Thousand Oaks, CA (US)
`( * ) Notice‘
`Subject to any disclaimer the term ofthis
`'
`’
`patent is extended or adjusted under 35
`USC. 15403) by 145 days.
`
`(21) App1.No.: 11/234,731
`
`US007442778B2
`
`(10) Patent No.:
`(45) Date of Patent:
`
`US 7,442,778 B2
`Oct. 28, 2008
`
`5,480,981 A
`5,498,530 A
`5,514,582 A
`5,608,035 A
`ggfig’ :
`5,733,731 A
`577397277 A
`:
`,
`,
`577867331 A
`5,792,451 A
`5,800,096 A
`
`1/1996 Goodwin etal.
`3/1996 Schatz et al.
`5/1995 C3P0I1 e1 31-
`3/1997 Yanofsky et al.
`g:17'4:?ye7t,,a7174
`3/1998 S ht
`t
`l.
`4/1998 Pfeftazfi :17
`Eva-lgflstky ett all’
`II
`OH 6 3.
`.
`7/1998 Barrett 61417
`8/1998 Saiubbi et al.
`9/1998 Barrow
`,
`(Continued)
`
`(22)
`
`Ffledi
`
`S°P- 23: 2005
`
`FOREIGN PATENT DOCUMENTS
`
`(65)
`
`Prior Publication Data
`
`US 2006/0140934 A1
`
`Jun. 29, 2006
`
`Related U.S. Application Data
`
`AU
`EP
`Ep
`EP
`Ep
`
`(60) Provisional application No. 60/612,680, filed on Sep.
`24, 2004.
`
`64763/98
`0 315 062 A2
`0 315 456 A2
`0714 912 A2
`0 325 224 131
`
`7/1998
`5/1989
`571989
`6/1996
`7/1995
`
`(Continued)
`OTHER PUBLICATIONS
`
`(51)
`
`Int‘ Cl‘
`(2006.01)
`C0711’ 16/00
`(2006-01)
`C07H 21/02
`(52) U.S. Cl.
`................ .. 530/391.7; 530/350; 530/391.1
`(58) Field of Classification Search ..................... .. None
`See application file for complete search history.
`References Cited
`
`(56)
`
`U.S. PATENT DOCUMENTS
`
`9/1972 Patel
`3,691,016 A
`6/1974 Rubenstein et al.
`3,817,837 A
`11/1974 Hermanus
`3,850,752 A
`2/1975 Kronick e131,
`3,939,350 A
`3/1976 Sarantakis
`3,941,763 A
`7/1976 Jaworek et al.
`3,969,287 A
`12/1976 Ullman et al.
`3,996,345 A
`5/1978 Merz e131,
`4,087,778 A
`12/1979 Davis et al.
`4,179,337 A
`3/ 1930 Hildebrand e1a1~
`4,195,128 A
`10/1980 Hodgins 9131
`4329537 A
`1/1981 Hirohara
`4 247 642 A
`7,198, Ma
`,0
`4’277’437 A
`gg.
`’
`’
`11/1981 Iwashita et al.
`4,301,144 A
`5/1983 Ayers 6, 517
`473367446 A
`1/1985 Mimi et 347
`474967689 A
`2/1937 ghimizu e1 31,
`4,540,335 A
`6/1987 Iwasakj et a1,
`4,670,417 A
`1/1988 Schneider et a1.
`4,719,192 A
`5/ 1990 Steiner e131.
`4,925,673 A
`gag A A E‘/Oodle 9:131
`5416664 A
`5,1992 Casky et,
`,
`,
`apone
`,
`57216713, A
`6/1993 Lasky e, 7717
`5,223,409 A
`6/1993 Ladner et al.
`5 225 538 A
`7/1993 Ca
`7 ,4
`’
`’
`‘’°“ °
`5,284,656 A
`2/1994 Platz et al.
`573367663 A
`8/1994 Capon et 347
`573387665 A
`8/1994 Schatz et 417
`5,428,130 A
`6/1995 Capon et al.
`5,432,018 A
`7/1995 Dower et al.
`5,455,165 A
`10/1995 CaP0I1 e131
`
`'
`
`Kuby Immunology Eds. Freeman and Co. 1992 p. 104*
`U.S.App1. No. 60/641,144, filed Jan. 5, 2005, Ruker et al.
`Abuchowski and Davis, “Soluble Polyrner-Enzyme Adducts”,
`Enzymes as Drugs, pp. 362-383 (1981).7
`7
`7
`7
`Adey & Kay’ Idemlficatlon °fC3_1m°du1m'Bmdmg PePt_‘de C‘_’nSen'
`ilgjnjicggénlcgegs fr3°7E1,’919I6)1)1age'DlSP1ayed Random Peptlde Llbmry’
`Adey & Kay, “Isolation of Peptides From Phage-Displayed Random
`Peptide Libraries That Interact With the Talin-Binding Domain of
`Vinculin”, Biochem. J. 324: 523-528 (1997).
`
`(Continued)
`
`7
`7
`7
`Primary Exammer—Shee71a J H1111
`(74) Attorney, Agent, or F1rm—Nisan A. Steinberg
`
`(57)
`
`ABSTRACT
`
`7
`7
`7
`The present invention concerns molecules and a process in
`which one or more biologically active peptides are incorpo-
`rated into an Fc domain. In this invention, pharrnacologically
`active compounds may be prepared by a process comprising
`~
`~
`~
`~
`(a) selecting7 at least one peptide that modulates the activity of
`a protein of interest; and (b) preparing a pharmacologic agent
`.
`.
`.
`.d
`fth
`1
`t d
`t.d .
`comprising anamino aci
`sequence o
`e se ec e pep i e in
`a loop r7egion ofan Fc domain.7 This process may be employed
`to modify 7an Fc domain that is already linked through an7N-
`or C-terminus or sidechain to a peptide or to a polypeptide
`(e.g., etanercept). This process may also be employed to
`modify an Fc domain that is part of an antibody (e.g., adali-
`mumab, epratuzumab, infliximab, Herceptin®, and the like).
`In this way, different molecules can be produced that have
`.
`.
`.
`.
`.
`.
`.
`.
`. _
`?dditional functionalities, such as a7binding domain to a dif
`erent epitope or an additional binding domain to the precur-
`,
`.
`.
`.
`.
`sor molecule s existing epitope. The peptide can be selected,
`1“
`1
`b
`ha e dis la E coli dis la
`ribosome
`9“ eXamP es
`Y P . g
`P .3’:
`'
`P Y’
`.
`display, RNA7-peptide 7screeni7ng, yeast-based screening,
`chemical-peptide screening, rational design, or protein struc-
`111181 aI1a1YS1S~
`
`14 Claims, 22 Drawing Sheets
`
`APOTEX EX1046
`
`Page 1
`
`APOTEX EX1046
`
`Page 1
`
`

`

`US 7,442,778 B2
`Page 2
`
`U.S. PATENT DOCUMENTS
`
`9/1998 Bruckhous et al.
`5,808,029 A
`11/1998 Lasky et al.
`5,840,844 A
`12/1998 Sledzlewski et al.
`5,843,725 A
`12/1998 Takenaka et al.
`5,849,452 A
`2/1999 Dower et al.
`5,869,451 A
`2/ 1999 Ng etal.
`5869452 A
`3/1999 Pereira
`5,877,151 A
`3/1999 Thorpe et al.
`5,877,289 A
`3/1999 Barret et al.
`5,880,096 A
`3/1999 Urban et al.
`5,880,103 A
`3/1999 Duchesne et al.
`5,886,150 A
`3/1999 Hanafusa et al.
`5,888,763 A
`7/1999 Matheakis et al.
`5,922,545 A
`8/1999 Barrett et al.
`5,932,546 A
`8/1999 Montelaro et al.
`5,945,507 A
`11/1999 Keller
`5,985,450 A
`12/1999 Thorpe et al.
`6,004,555 A
`8/2000 Corbett
`6,108,026 A
`9/2000 Capon et al.
`6,117,655 A
`10/2000 Thorpe et al.
`6,132,730 A
`10/2000 Gonzalez et al.
`6,133,426 A
`12/2000 Thorpe et al.
`6,156,321 A
`9/2001 Sledziewski et al.
`6,291,212 B1
`9/2001 Sledziewski et al.
`6,291,646 B1
`10/2001 Sledziewski et al.
`6,300,099 B1
`11/2001 Sledziewski et al.
`6,323,323 B1
`6/2002 Capon et al.
`6,406,697 B1
`12/2003 Feige et al.
`6,660,843 B1
`7/2003 Capon et al.
`2003/0143220 A1
`9/2003 Min et al.
`2003/0176352 A1
`10/2003 Min et al.
`2003/0195156 A1
`2003/0215914 A1* 11/2003 Houtzager et al.
`2003/0229023 A1
`12/2003 Oliner et
`
`....... .. 435/69.1
`
`12/2003 Olrner et al.
`2003/0236193 A1
`5/2004 Feige et al.
`2004/0087778 A1
`9/2004 Han et al.
`2004/0181033 A1
`FOREIGN PATENT DOCUMENTS
`0 911 393 A1
`4/1999
`0 585 287 B1
`10/1999
`0 958 829 A1
`11/1999
`1 029 870 A2
`8/2000
`0 526 452 B1
`2/2001
`0 770 524 B1
`5/2003
`0 988 055 B1
`7/2003
`1 752 471 A1
`1/2005
`1 772 465 A1
`1/2006
`WO 91/08298
`6/1981
`
`EP
`EP
`EP
`EP
`EP
`EP
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`WO 89/09622
`WO 00/12727
`WO 94/04689
`WO 94/07921
`W0 95/09917
`W0 95/14714
`W0 95/13353
`wo 95/21919
`WO 95/21920
`WO 95/26746
`WO 96/05309
`WO 96/11214
`WO 96/11953
`WO 96/17942
`WO 96/18412
`WO 96/23899
`WO 96/30057
`WO 96/32478
`WO 96/40772
`WO 96/40987
`WO 97/00270
`
`10/1989
`3/1990
`3/1994
`4/1994
`4/1995
`6/1995
`7/1995
`3/1995
`8/1995
`10/1995
`2/1996
`4/1996
`4/1996
`6/1996
`6/1996
`8/1996
`10/1996
`10/1996
`12/1996
`12/1996
`1/1997
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`WO 97/08203
`WO 97/08553
`W0 97/23514
`W0 97/28328
`W0 97/31019
`W0 97/34631
`W0 97/35959
`W0 97/40070
`W0 97/4122()
`W0 97/44453
`W0 98/09985
`W0 93/10795
`W0 98/15833
`W0 93/24477
`W0 93/28427
`W0 93/31820
`W0 93/3381;
`W0 98/46257
`W0 93/5384;
`W0 98/55620
`W0 99/02711
`W0 99/0530;
`W0 99/14244
`W0 99/17739
`W0 99/18243
`W0 99/1375“
`W0 99/2445;
`W0 99/2473;
`W0 99/38008
`W0 99/38526
`W0 99/42592
`W0 99/45944
`W0 99/46233
`W0 99/47151
`WO 99/50282
`
`3/1997
`3/1997
`7/1997
`3/1997
`3/1997
`9/1997
`10/1997
`10/1997
`11/1997
`11/1997
`3/1998
`3/1993
`4/1998
`6/1998
`7/1993
`7/1993
`3/1993
`10/1998
`12/1993
`12/1998
`1/1999
`2/1999
`3/1999
`4/1999
`4/1999
`4/1999
`5/1999
`5/1999
`7/1999
`8/1999
`3/1999
`9/1999
`9/1999
`9/1999
`10/1999
`
`WO 99/51720
`
`10/1999
`
`$8 $2 1
`WO 99/62539
`12/1999
`WO 00/01402
`1/2000
`WO 00/04048
`1/2000
`W0 00/09560
`2/2000
`W0 00/11027
`3/2000
`W0 00/11028
`3/2000
`W0 00/17226
`3/2000
`W0 00/17358
`3/2000
`W0 00/17370
`3/2000
`WO 00/17648
`3/2000
`WO 00/18895
`4/2000
`WO 00/23585
`4/2000
`WO 00/24770
`5/2000
`WO 00/24782 A2
`5/2000
`W001/02440 A1
`1/2001
`WO 01/04296 A1
`1/2001
`WO 01/83525 A2
`11/2001
`WO 02/32925 A2
`4/2002
`WO 02/32925 A3
`4/2002
`02/44215
`6/2002
`W0 02/092620 A2
`11/2002
`W0 02/092620 A3
`11/2002
`W0 03/031589 A2
`4/2003
`W0 03/057134 A2
`7/2003
`WO 2004/002417 A2
`1/2004
`WO 2004/002424 A2
`1/2004
`WO 2004/026329 A1
`4/2004
`WO 2004/058988
`7/2004
`WO 2004/092215
`10/2004
`WO 2005/047337
`5/2005
`
`Page 2
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`
`

`

`US 7,442,778 B2
`Page 3
`
`W0
`
`WO 2006/072620 A1
`
`1/2006
`
`OTHER PUBLICATIONS
`
`Adjei & Garren, Pulmonary Delivery of Peptide Drugs: Effect of
`Particle Size on Bioavailability of Leuprolide Acetate in Healthy
`Male Volunteers, Pharma. Res. 7: 556-569 (1990).
`Adjei, et al., “Bioavailability of Leuprolide Following Intratracheal
`Administration to Beagle Dogs”, Internatl. ./'. Pharmaceutics, 63:
`135-144 (1990).
`Ahern, et al., “Special Report: The Peptide-Oligonucleotide Partner-
`ship”, The Scientist 4(19): 24-25 (1990).
`Akerstrom, “Protein G: A Powerful Tool for Binding and Detection of
`Monoclonal and Ployclonal Antibodies”, J'. Immunol. 135(4): 2589-
`2592 (1985).
`Akeson, et al., “AF12198, a Novel Low Molecular Weight Antago-
`nist, Selectively Binds the Human Type I Interleukin (IL)-1 Receptor
`and Blocks in vivo Responses to IL-1”, .1. Biol Chem. 271: 30517-
`20523 (1996).
`Asai, et al. , Methods in cell Biology, vol. 37, Academic Press, Inc.,
`New York (1993) (Table of Contents Provided Only).
`Ball, et al., “Cell Cycle Arrest and Inhibition of Cdk4 Activity by
`Small Peptides Based on the Carboxy-Terminal Domain of
`p2lWAFl”, Current Biology 7(1): 71-80 (1997).
`Barna, et al., “Combination Therapy with a Synthetic Peptide of
`C-Reactive Protein and Interleukin 2: Augmented Survival and
`Eradication
`of Pulmonary Metastases”, Cancer
`Immunol.
`Immunotherapy 38: 38-42 (1994).
`Bhatnagar, et al., “Structure-Activity Relationships of Novel
`Hematoregulatory Pepticides”, .1. Med. Chem. 39: 3814-3 819 (1996).
`Bottger, et al., Molecular Characterization of the hdm2-p53 Interac-
`tion, .1. Mol. Biol. 269: 744-756 (1997).
`Bottger, et al., “Identification of novel mdm2 binding peptides by
`phage display”, Oncogene 13: 2141-2147 (1996).
`Brocks, et al., “A TNF Receptor Antagonistic scFv, which is not
`Secreted in Mammalian Cells, is Expressed as a Soluble Mono- and
`Bivalent scFv Derivative in Insect Cells”, Immunotechnology , 3(3):
`173-184 (1997).
`Burstein, et al., “Thymic Humoral Factor «/2: Purification and Amino
`Acid Sequence of an Immunoregulatory Peptide From Calf Thy-
`mus”, Biochemistry 27: 4066-4071 (1988).
`Capon et al., “Designing CD4 Immunoadhesins for AIDS Therapy”,
`Nature 337: 525-531 (1989).
`Carillo, et al., “The Multiple Sequence Alignment Problem in Biol-
`ogy”, SIAM./'. Applied Math 48 : 1073-1082 (1988).
`Chamow, S. M., et al., “Immunoadhesins, Principles and Applica-
`tions”, Tibtech 14: 52-60 (1996).
`Chan and Kim, et al, “HIV Entry and Its Inhibition” Cell 93: 681-684
`(1998).
`Chaubert, et al., “Simultaneous Double Immunoenzymatic Labeling:
`A New Procedure for the Histopathlogic Routine”, Mod. Pathol. 10:
`585 (1997).
`Chirinos-Rojas, et al., “A Peptidomimetic Antagonist of TNF-oL-
`Mediated Cytotoxicity Identified from a Phage-Displayed Random
`Peptide Library”, Journal oflmmunology 161: 5621-5626 (1998).
`Chou, et al., “Prediction of the [3-Turns”, ./'. Biophys. 26: 367-384
`(1979).
`Chou, et al., “Prediction ofthe Secondary Structure of Proteins From
`Their Amino Acid Sequence”, Adv. Enzymol. Related. Areas Mol.
`Biol. 47: 45-148 (1978).
`Chou, et al., “Empirical Predictions of Protein Conformation”, Ann.
`Rev. Biochem. 47: 251-276 (1979).
`Clackson, et al. “A Hot Spot of Binding Energy in a Hormone-
`Receptor Interface”, Science 267: 383-336 (1995).
`Cooper, et al., “Purification and Characterization of a peptide from
`Anyloid-Rich Pancreases of Type 2 Diabetic Patients”, PNAS 84:
`8628-8632 (1987).
`Cortese, et al. , “Selection of Biologically Active Peptides by Phage
`Display of Random Peptide Libraries”, Current Opinion In
`Biotechnology 7: 616-621 (1996).
`Couet, et al., “Identification of Peptide and Protein Ligands for the
`Caveolin-Scaffolding Domain”, TheJournal ofBiological Chemistry
`272(10): 6525-6533 (1997).
`
`Couet, et al., “Interaction of a Receptor Tyosine Kinase, EGF -R, with
`Caveolins”, The Journal of Biological Chemistry 272(48): 30429-
`30438 (1997).
`Creighton, “Proteins: Structures and Molecular Principles”, (W. H.
`Freeman & Co., San Francisco) pp. 70-86 (1983).
`Cuthbertson,
`et
`al.,
`“Design
`of Low Molecular Weight
`Hematoregulatory Agents from the Structure-Activity Relationship
`ofa Dimeric Pentapeptide”, .1. Med Chem. 40 : 2876-2882 (1997).
`Cwirla, et al., “Peptide Agonist of the Thrombopoietin Receptor as
`Potent as the Natural Cytokine”, Science 276: 1696-1699 (1997).
`Davis, et al., “Preparation and Characterization of Antibodies with
`Specificity for the Amino-Terminal Tetrapeptide Sequence of the
`Platelet-Derived Connective Tissue”, Biochem Intl. 10: 395-404
`(1985).
`Dayhoff, et al., Atlas of Protein Sequence and Structure, Nat’l
`Biomed. Research Foundation, 5(Supp. 3) (1978) (Table of Contents
`Provide Only).
`Debs, et al., “Lung-Specific Delivery of Cytokines Induces Sustained
`Pulmonary and Systemic Immunomodulation in Rats”, J'. Immunol.
`140: 3482-3488, (1988).
`Dedman, et al., “Selection of Targeted Biological Modifiers from a
`Bacteriophage Library of Random Peptides” .1. Biol. Chem. 268(31):
`23025-23030 (1993).
`Devereux, et al., “A Comprehensive Set of Sequence Analysis Pro-
`grams for the VAX” NucleidAcids Research., 12: 387-395 (1984).
`Devlin, et al., “Random Peptide Libraries: A Source of Specific
`Protein Binding Molecules”, Science 249: 404-406 (1990).
`Duncan, et al. “Localization of the Binding Site for the Human
`High-Affinity Fc Receptor on IgG”, Nature 332: 563-564 (1988).
`Dysan & Murray, “Selection of Peptide Inhibitors of Interactions
`Involved in Complex Protein Assemblies: Association of the Core
`and Surface Antigens of Hepatitis B Virus”, Proc. Natl. Acad Sci.
`USA 92: 2194-2198 (1995).
`Ellison, et al., “The Nucleotide Sequence ofHuman Immunoglobulin
`Cyl Gene”, Nucleic Acids Res. 10: 4071-4079 (1982).
`Engel, et al., “Insertion ofCarrier Proteins Into Hydrophilic Loops of
`the Escherichia coli Lactose Permease”, Biochimica et Biophysica
`Acta 1564: 38-46 (2002).
`Erickson, et al., The Proteins, “Solid-Phase Peptide Synthesis”, (3rd
`ed.), Vol. II, pp. 257-527 (1976).
`Fahraeus, et al., “Inhibition of pRb Phosphorylation and Cell-Cycle
`Progression by a 20-Residue Peptide Derived from PISCDKN”
`INK4A”, Current Biology. 6: 84-91 (1996).
`Fairbrother, et al., “Novel Peptides Selected to Find Vascular
`Endothelial Growth Factor Target the Receptor-Binding Site”, Bio-
`chemistry 37: 17754-17764 (1998).
`Finn, et al., The Proteins, “The Synthesis Peptides by Solution Meth-
`ods with Emphasis on Peptide Hormones”, (3rd ed.), vol. II, pp.
`105-253 (1976).
`Fisher, et al., “Treatment of Septic Shock with the Tumor Necrosis
`Factor Receptor : Fc Fusion Protein”, N England J.; Med. 334(26):
`1697-1702 (1996).
`Francis, Gillian E., “Protein Modification and Fusion Proteins”,
`Royal Free Hospital School ofMedicine 3: 4-10 (1992).
`Fukimoto, et al., “Peptide Mimics of The CTLAA4-Bindining
`Domain Stimulate T-Cell Proliferation”, Nature Biotechnology 16:
`267-270 (1998).
`Gan, et al., “Echistatin”, .1. Biol. Chem. 263: 19827-19832 (1988).
`Ghetie, et al., “Increasing the Serum Persistence of an IgG Fragment
`by Random Mutagenesis”, Nature Biotechnology 15: 637-640
`(1997).
`Gibbs, et al., “Farnesyltransferase Inhibitors: Ras Research Yields a
`Potential Cancer Therapeutic”, Cell 77: 175-178 (1994).
`Gibbs, et al., “Pharmaceutical Research in Molecular Oncology”,
`Cell 79: 193-198 (1994).
`Golub, E. S. and Gren D. R., eds., Immunology—A Synthesis,
`Sinauer Associates, Sunderland, Mass. ,' 3”} Edition, “The Structure
`of Immunoglobulins”, Chapter 3, pp. 42-52; “The Constant Region”,
`Chapter 6, pp. 92-107; “Amino Acid Abbreviations”, Appendix 1, p.
`7 16 (199 1).
`Gonzalez, et al., “Organization of the Human Myostatin Gene and
`Expression in Healthy Men and HIV-Infected Men with Muscle
`Wasting” Proc. Natl. Acad. Sci. 95114938-14943 (1998).
`
`Page 3
`
`Page 3
`
`

`

`US 7,442,778 B2
`Page 4
`
`Goodson, et al., “High-Affinity Urokinase Receptor Antagonists
`Identified with Bacteriophase Peptide Display”, Proc. Natl. Acad.
`Sci. 91: 7129-7133 (1994).
`Graf and Kastin, “Delta-Sleep-Inducing Peptide (DSIP): An
`Update”, Peptides 7: 1165- 1 1 87(1986).
`Gribskov, M. and Devereux, Sequence Anab/sis Primer, Stockton
`Press, New York (1991) (Table of Contents Provided Only).
`Gribskov, et al., “Profile Analysis”, Meth. Enzym. 183: 146-159
`(1990).
`Gribskov, et al., “Profile Analysis: Detection of Distantly Related
`Proteins”, Proc. Nat. Acad. Sci. 84(13): 4355-4358 (1987).
`Griffin, A.M., and Griffin, H.G., Computer Anab/sis of Sequence
`Data, Part 1, Humana Press, New Jersey (1994) (Table of Contents
`Provided Only).
`Halaby, et al ., “The Immunoglobulin Fold Family Sequence Analysis
`and 3D Structure Comparisons”, Protein Engineering, 12(7): 563-
`571 (1999).
`Harnrick, et al., “Bone Mineral Content and Destiny in the Huen1rous
`of Adult Myostatin-Feficient Mice” Calcif Tissue Int. 71(1): 63-68
`(2002).
`Harvill, et al., “An IgG3-IL2 Fusion Protein Activiates Compleme-
`ment, Binds FcyRI, Generates LAK Activity and Shows Enhanced
`Binding to the High Affinity IL-2R”, Immunotech 1: 95-105 (1995).
`Harwig, et al., “Neutrophi Defenses: Purification , Characterization,
`and Antimicrobial Testing”, Methods Enzymology 236: 160-172
`(1994).
`Henikoff, et al., Proc. NalAcad. Sci. USA 89: 10915-10919 (1992).
`Herz, et al., “Molecular Approaches to Receptor as Targets for Drug
`Discovery”, J ofReceptor & Signal Transduction Research 17(5):
`671-776 (1997).
`Holm, et al., “Protein Folds and Families: Sequence and Structure
`Alignments”, Nucleic Acids Research., 27(1): 244-247 (1999).
`Hong, et al., Protein Ligands of the Human Adenovirus Type 2 Outer
`Capsid Identified by Biopanning of a Phage-Displayed Peptide
`Library on Separate Domains of Wild-Type and Mutant Penton
`Capsomers, The EMBO Journal 14: 4714-4727 (1995).
`Hubbard, et al., “Anti-Neutrophil-Elastase Defenses of the Lower
`Respiratory Tract in oil-Antitrypsin Deficiency Directly Augmented
`with an Aerosol ofotl-Antitrypsin”, Annals Int. Med. 3(3): 206-212
`(1989).
`Hughes, David, “Therapeutic Antibodies Make a Comeback”, Drug
`Discovery Today 3(10): 439-442 (1998).
`Inagaki -Ohara, “Effects ofa Nonapeptide Thymic Hormone on Intes-
`tinal Intraepithelial Lymphocytes in Mice Following Administration
`of 5-Fluorouracil”, Cellular Immunol. 17: 30-40 (1996).
`Inglot, Anna, D., “Classification of Cytokines According to the
`Receptor
`Code”, Archivum Immunologies
`et
`Therapine
`Experimentalis, 45: 353-357 (1997).
`Ishikawa, et al., “GD1oL-Replica Peptides Functionally Mimic
`CD101, and Adhesion Molecule of Metastatic Tumor Cell, And Sup-
`press the Tumor Metastasis”, FEBS 441: 20-24 (1998).
`Jeffries, D., “Selection ofNovel Ligands from Phage Display Librar-
`ies: An Alternative Approach to Drug and Vaccine Discovery. ”,
`Parasitology Today 14(5): 202-206 (1988).
`Jefferis, et al., “Recognition Sites on Human IgG for Fey Receptors:
`the Role of Glycosylation”, ImmunologyLetters 44: 111-117 (1995).
`Jefferis, et al., Molecular Definition of Interaction Sites on Human
`IgG Fe Receptors (huFey R), Molecular Immunology 27(12): 1237-
`1240 (1990).
`Johnson, et al., Identification of a 13 Amino Acid Peptide Mimetic of
`Erythropoietin and Description of Amino Acids, Critical for the
`Mimetic Activity of EMP1 , Biochemistry 37(11): 3699-3710 (1998).
`Jones, et al., “Stromal Expression of Jagged 1 Promotes Colony
`Formation by Fetal Hen1atopoietic Progenitor Cells”, Blood , 92(5):
`1505-1511 (1998).
`Jones, D., “Progress in Protein Structure Prediction”, Curr Opin.
`Struct. Biol. 7(3): 377-387 (1997).
`Junghans, R. P, “Finally! The Branbell Receptor (FcRB)”, Immuno-
`logic Research 16(1): 29-57 (1997).
`Kay, et al., “From Peptides to Drugs Via Phage Display”, Drug Disc.
`Today 3: 370-378 (1998).
`
`King, et al., “Modulation ofBone Marrow Stromal Cell Production of
`Colony Stimulating Activity by the Synthetic Peptide”, Exp. Hematol
`19: 481 (1991).
`King, et al., “Hematoregulatory Peptide, SK&F Induced Stromal
`Cell Production of KC Enhances CFU-GM Growth and Effector Cell
`Function”, Blood 86(1): 309a (1995).
`Kitamura, et al., “Adrenomedullin: A Novel Hypotensive Peptide
`Isolated From Human Pheochromocytoma”, BBRC. 192: 553-560
`(1993).
`Klucyk, et al., “Immunomodulatory Activity of Oligopeptides
`Related to Interleukin 1 Receptor Antagonist Sequence”, Archivum
`Immunologiac et Therapiae Experimentalis 45: 427-433 (1997).
`Koivunen, et al., “Tumor Targeting with a Selective Gelatinase
`Inhibitor”, Nat. Biotech. 17: 768-774 (1999).
`Kraft, et al., “Definition of an Unexpected Ligand Recognition Motif
`for av[36 Integrin”, Journal ofBiological Chemistry 274(4): 1979-
`1985 (1999).
`Kyte, et al., “A Simple Method for Displaying the Hydropathic Char-
`acter ofa Protein”, J Mol Biol., 157: 105-131 (1982).
`Kreeger, Karen Young, “Immunological Applications Top List of
`Peptide-Synthesis Services”, The Scientist 10(13): 19-20 (1998).
`Kuai, et al., “Plasminogen Activator
`Inhibitor-1 Fused With
`Erythropoietin (EPO) Mimetic Peptide (EMP) Enhances the EPO
`Activity of EMP”, J Peptide Research 56: 59-61 (2000).
`Laerum, et al., “The Dimer of Hemoregulatory Peptide (HP5B)
`Stimulates Mouse and Human Myelpoiesis in Vitro”, Exp. Hemat.
`16: 274-280 (1988).
`Lalani, et al., “Myostatin and Insulin-Like Growth Factor-I and -II
`Expression in the Muscle of Rats Exposed to the Microgravity Envi-
`ronment of the NeuroLab Space Shuttle Flight”, J Endocrin 167(3):
`417-428 (2000).
`Lesk, A. M., Computational Molecular Biology—Sources and Meth-
`ods for Sequence Analysis, Oxford University Press (1988) (Table of
`Contents Provided Only).
`Lewin, B., Genes V., Oxford University Press, p. 11 (1994).
`Lin, et al., “Myostatin Knockout in Mice Increases Myogenesis and
`Decreases Adipogenesis” Biochem Biophys. Res. Commun. 291(3):
`701-706 (2002).
`Linse, et al., “A Region ofVitamin K-Dependent Protein S That binds
`to C4b Binding Protein (C4BP) Identified Using Bacteriophage
`Peptide Display Libraries”, The Journal Biological Chemistry
`272(23): 14658-14665 (1997).
`Linsley, et al., “CTLA-4 is a Second Receptor for the B Cell Activa-
`tion Antigen B7”, J Exp. Med. 174: 561-569 (1991).
`Livnah, et al., “Functional Mimicry of a Protein Hormone by a
`Peptide Agonist: The EPO Receptor Complex at 2.8 A”, Science 273:
`464-471 (1996).
`Loetscher, et al., “Efficacy of a Chimeric TNFR-IgG Fusion Protein
`to Inhibit TNF Activity in Animal Models of Septic Shock”, Int’l
`Congress Series 2.‘ Elsevier Science Publishers pp. 455-462 (1993).
`Lowman, H. B., “Bacteriophage Display and Discovery of Peptide
`Leads for Drug Development”, Annu. Rev. Biophys. Biomol. Struct.
`26: 401-424(1997).
`Lundergan, et al., “Angiotensin-II Increases Cyctoplasmic Calcium,
`Cell Number and Total DNA or Human Periodontal Ligamental Cells
`In Vitro”, J Periodontal Res. 34(4): 223-228 (1999).
`Vlariuzza, Roy A. and Winter, Greg; “Secretion of a Homodimeric
`V.C.T-cell Receptor-Immunoglobulin Chimeric Protein” TheJ Biol.
`Chem. 13: 7310-7316 (1989).
`Vlarshall, K., “Solid Oral Dosage forms” Modern Pharmaceutics,
`edited by G.S. Banker and C.T. Thodes, Chap. 10 (1979).
`\/Iartens, et al., “Peptides Which Bind to E-Selectin and Block
`\Ieutrophil Adhesion”, TheJournal ofBiological Chemistry 270(36):
`21129-21136 (1995).
`\/Iaurer, et al. “Autodisplay: One-Component System for Efficient
`Surface Display and Release of Soluble Recombinant Proteins from
`Escherichia coli”, Journal ofBacteriology179(3): 794-780 (1997).
`VIcGregor, Duncan, “Selection of Proteins and Peptides from Librar-
`ies Displayed
`on
`Filamentous Bacteriophage”, Molecular
`Biotechnology 6: 155-162 (1996).
`\/Ierrifield, R.B.,
`“Solid-Phase
`Pob/peptides 335-361 (1973).
`
`Synthesis”, Chem.
`
`Peptide
`
`Page 4
`
`Page 4
`
`

`

`US 7,442,778 B2
`Page 5
`
`\/Ierrifield, R.B., “Solid-Phase Peptide Synthesis. I. The Synthesis of
`a Tetrapeptide”, .1. Am. Chem. Soc. 85: 2149-2154 (1963).
`Vliura, Y, Kirito, K. and Komatsu, N., “Regulation of Both Erythroid
`and Megakaryocytic Differentiation ofa Human Leukemia Cell Line,
`UT-7,”Acta Haematologica, 99; 180-184 (1998).
`\/Ioodie, et al., “The 3Rs of life: Ras, Raf and Growth Regulation”,
`TIG 10(2): 44-48 (1994).
`VIoonga,et al., Effects of Peptide Fragments of Protein Kinase C on
`Isolated Rat Osteoclasts, Experimental Physiology 83: 717-725
`(1998).
`\/Iorikis, et al., “Solution Structure of Compstatin, a Potent Comple-
`ment Inhibitor”, Protein Science 7: 619-627 (1998).
`Vloult, J., “The Current State of the Art in Protein Structure Predic-
`tion”, Curr Op. in Biotech. 7(4): 422-427 (1996).
`\Iachman, et al., “Pseudodipeptide Analogs of the Pyrokinin/PBAN
`(FXPRLa) Insect Neuropeptide Family Containing Carbocyclic Pro-
`\/Iimetic Conformational Components”, Reglatory Peptides 57: 3 59-
`370 (1995).
`\Iaranda, et al., “Activation of Erythropoietin Receptor in the
`Absence of Hormone by a Peptide that Binds to a Domain Different
`from the Hormone Binding Site”, Proc. Natl. Acad, Sci. USA 96:
`7569-7574 (1999).
`\Ieed1eman, et al., “A General Method Applicable to the Search for
`Similarities in the Amino Acid Sequence of Two Proteins”, .1. Mol.
`Biol. 48:443-453 (1970).
`\Iewmark, eta1.,./'. Appl. Biochem 4: 185-189 (1982).
`\Iishi, et al., “Tight-Binding Inhibitory Sequences Against pp60°'“‘°
`Identified Using a Random 15-Amino-Acid Peptide Library”, FEBS
`399: 237-240 (1996).
`Park, et al., “Rationally Designed Anti-HER2/neu Peptide Mimetic
`Disables P185HER2/“E” Tyrosine Kinases In Vitro and In Vivo”, Nat.
`Biotechnol. 18: 194-198 (2000).
`Pasquaimi, et al., “Organ Targeting In Vivo Using Phage Display
`Peptide Libraries”, Nature 380: 364-366 (1996).
`Paukovitis, et al., Structural Investigations on a Peptide Regulating
`Hemopoiesis In Vitro and In Vivo Hoppe—Seylers Z. Physio. Chem.
`365: 303-311 (1984).
`Pawson, et al., “SH2 and SH3 Domains”, Current Biology, 3: 434-
`442 (1993).
`Picksley, et al., “Immunochemical Analysis of the Interaction of p53
`with MDM2;—Fine Mapping of the MDM2 Binding Site on p53
`Using Synthetic Peptides”, Oncogene 9: 2523-2529 (1994).
`Pierce, et al., “Identification of Cyclized Calmodulin Antagonists
`From a Phage Display Random Peptide Library”, Molec. Diversity 1:
`259-265 (1995).
`Piette, et al., “Mdm2: Keeping p53 Under Control”, Oncogene 15:
`1001-1010 (1997).
`Powis, Garth, “Signaling Targets for Anticancer Drug Development”,
`TIPS 12: 188-194 (1991).
`RCSB, Protein Data Book File 1I1C PDB.
`RCSB, Protein Data Book File 1IGY PDB.
`RCSB, Protein Data Book File 1H3T PDB.
`Rickles, et al., “Identification of Src, Fyn, Lyn, PI3K and AbI SH3
`Domain Ligands Using Phagel Display Libraries”, TheEMBOJour—
`nal 13(23): 5598-5604 (1994).
`Roberts & Szostak, “RNA-Peptide Fusions for the In Vitro Selection
`of Peptides and Proteins”, Proc. Natl. Acad Sci. USA, 94: 12297-
`12303 (1997).
`Rodriguez-Viciana, et al., “Phosphatidylinositol-3-OH Kinase as a
`Direct Target of Ras”, Nature 370: 527-532 (1994).
`Sahu, et al., “Inhibition of Human Complement by a C3-Binding
`Peptide Isolated from a Phage-Displayed Random Peptide Library”,
`The Journal ofI. Immunology 157: 884-891 (1996).
`Sarmay, et al., “Mapping and Comparison of the Interaction Sites on
`the Fe Region of IgG Responsible for Triggering Antibody Depen-
`dent Cellular Cytotoxicity (ADCC) Through Different Types of
`Human Fcy Receptor”, Molecular Immunology 29(5): 633-639
`(1993).
`Scott, et al., “Searching for Peptide Ligands with an Epitope
`Library”, Science 249: 386-390 (1990).
`
`Sharma, et al., “Myostatin, a Transforming Growth Factor-[3
`Superfamily Member,
`Is Expressed in Heart Muscle and Is
`Upregulated in Carciomyocytes After Infarct”,
`.1. Cell Physiol.
`180(1): 1-9 (1999).
`Shinmei, et al., “Quantitation of Chondroitin 4-Sulfate and
`Chondroitin 6-Sulfate in Pathologic Joint Fluid”, Athritis Rheum. 35:
`1304-1308 (1992).
`Siemion, et al., “The Evidence on the Possible Interleukin-lot Tuftsin
`Competition”,
`Archivium
`Immunologiae
`et
`Therapiae
`Experimentalis 39: 605-611 (1991).
`Silberberg, Anderson’s Pathology, Kissane (ed.), II: 1828 (1985).
`Sippl, et al., “Threading Thrills and Threats”, Structure 4(1): 15-19
`(1996).
`Smith, et al., “Pulmonary Depositoni and Clearance of Aerosolized
`Alpha-1-Proteinase Inhibitor Administered to Dogs and to Sheep” L.
`Clin. Invest. .84: 1145-1146 (oil-proteinase) (1989).
`Smith, et al., “Isolation of Glucagon Antagonists by Random
`Molecular Mutagenesis and Screening”, Mol. Pharmacol, 43: 741-
`748 (1993).
`Sparks, et al., Distinct Ligand Preferences of Src Homology 3
`Domains from Src, Yes, Abl, Cortactin, p53bp2, PLCy, Crk, and
`Grb2, Proc. Natl. Acad Sci. USA 93: 1540-1544 (1996).
`Sparks, et al., “Identification and Characterization of Src SH3
`Ligands from Phage-Displayed Random Peptide Libraries”, The
`Journal Biological Chemistry 269(39): 23853-23856 (1994).
`Staufer, eta1., “Inhibition of Lyn Function in Mast Cell Activation by
`SH3 Domain Binding Peptides”, Biochemestry 36: 9388-9394
`(1997).
`Stewart and Young, Solid Phase Peptide Synthesis, WH. Freeman
`and Co. (1969) (Table of Contents Provided Only).
`Suzuki, and Yoshino, “The Relationship Between Amino Acid
`Sequences of Sperm-Activiating Peptides and the Taxonomy of
`Echinoids” Comp. Biochem. Physiol. 102B: 679 (1992).
`Tai, Mei-Sheng, “A Bifunctional Fusion Protein Containing Fc -Bind-
`ing Fragment B of Staphylococcal Protein A Amino Terminal to
`Antidigoxin Single-Chain Fvl”, Biochemistry 29: 8024-8030 (1990).
`Takasaki, et al., “Structure-Based Design and Characterization of
`Exocyclic Peptidomimetics that Inhibit TNFOL Binding to its Recep-
`tor”, Nature Biotechnology 15: 1266-1270 (1997).
`Thonar, et al., “Body Fluid Markers of Cartilege Changes in
`Osteoarthritis”, Rheumatoid Disease Clinics ofNorth America, 19:
`635-657 (1993).
`Van Zee, et al., “Protection Against Lethal Escherichia coli
`Bacteremia in Baboons (Papio anubis) by Pretreatment with a
`55-kDa TNF Receptor (CD120a)-Ig. Fusion Protein, Ro 45-2081”, J'.
`Immunol. 156: 2221-2230 (1996).
`Von Heinje, G., Sequence Analysis in Molecular Biology, Academic
`Press (1987) (Table of Contents Provided Only).
`Wells, et al., “Rapid Evolution of Peptide and Protein Binding Prop-
`erties InVivo”, Current Opinion ofBiotechnology 3: 355-362 (1992).
`Whitty, et al., “Small Molecular Cytokine Mimetics”, Chemistry &
`Biology 6: R107-R118 (1996).
`Wieczorek, et al., “The Immunomodulatory Activity of Tetra- and
`Tripeptides of Tuftsin_Kentsin Group”, Peptides 15(2): 215-221
`(1994).
`Williams, G. T. and Neuberger, M. S.; “Production of Antibody-
`Tagged Enzymes by Myeloma Cells: Application to DNA
`Polymerase I Klenow Fragmont”, Gene 43: 319-324 (1986).
`Wilson, et al., “Phage Display: Applications, Innovations, and Issues
`in Phage and Host Biology”, Can. J'. Microbiol. 44: 313-329 (1998).
`Wright, et al., “The Importance of Loop Length in the Folding of an
`Immunoglobulin Domain”, Protein Engin. Design & Selection 17:
`443-453 (2004).
`Wrighton, et al., “Small Peptides as Potent Mimetics of the Protein
`Hormone Erythropoietin”, Science 273: 458-463 (1996).
`Wrighton, et al., “Increased Potency of an Erythropoietin Peptide
`Mimetic through Covalent Dimerization”, Nature Biotechnology 15:
`1261-1265 (1997).
`Van Zee, K. et al., “Protection Against Lethal Escherichia coli
`Bacteremia ni Baboons (Papio anubis) by Pretreatment with a
`55-kDa TNF Receptor (CD120 a)-Ig Fusion Protein, Ro 45-2081”, J'.
`Immunol. 156: 2221-2230 (1996).
`
`Page 5
`
`Page 5
`
`

`

`US 7,442,778 B2
`Page 6
`
`Yanofsky, et al., “High Affinity Type I Interleukin 1 ReceptorAntago-
`nists Discovered by Screening Recombinant Peptide Libraries”,
`Proc. Natl. Acad. Sci. 93: 7381-7386 (1996).
`Yarasheskj et 31., J Num Aging 5(5);343_g (2002).
`Yen, et al., “Obsesity, Diabetes, and Neoplasia inYellow Avy /-Mice:
`Ectopic Expression Ofthe Agouti Gene», FASEB J. 8, 479 (1994).
`Yoshida, et al., “The Activity of Synthetic Analogs ofSerum Thymic
`Factor (FTS) to Convert Mouse Pre-T Cells into Thy-1 Positive
`Cells”, Int. 1. Immunopharmac 6(2): 141-146 (1984).
`
`Yu, et al., “Structural Basis for the Binding of Proline-Rich Peptides
`to SH3 Domains”, Cell. 76; 933-945 (1994).
`Zachwieja, et al., “Plasma Myostatin-Immunoreactive Protein is
`Increased After Prolonged Bed Rest with Low-Dow T, Administra-
`lion’: ‘I’ Gm”-I Phys}-0_l' 6(2): 11 (1999)
`_
`_
`_
`Zheng, et al., “Administration of Noncytolytic IL-10/Fc in Murine
`?:1:(ti?f1rSa:fS L1:L1:1(:::::)SI1l1,fc3a;rlr(lir€r:lfil1g;1c1e:;i4.S:1;t;)§1g:):)k(?I;;guogenelc
`P
`’
`'
`'
`'
`'
`* Cited by examiner
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