WO2000023564A3 - Protein design automation for protein libraries - Google Patents

Protein design automation for protein libraries Download PDF

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Publication number
WO2000023564A3
WO2000023564A3 PCT/US1999/024229 US9924229W WO0023564A3 WO 2000023564 A3 WO2000023564 A3 WO 2000023564A3 US 9924229 W US9924229 W US 9924229W WO 0023564 A3 WO0023564 A3 WO 0023564A3
Authority
WO
WIPO (PCT)
Prior art keywords
protein
libraries
design automation
protein design
pda
Prior art date
Application number
PCT/US1999/024229
Other languages
French (fr)
Other versions
WO2000023564A2 (en
Inventor
Klaus M Fiebig
Robert J Hayes
Bassil I Dahiyat
Joerg Bentzien
Original Assignee
Xencor Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Xencor Inc filed Critical Xencor Inc
Priority to CA002347214A priority Critical patent/CA2347214A1/en
Priority to JP2000577277A priority patent/JP2003527072A/en
Priority to AU11190/00A priority patent/AU774334B2/en
Priority to EP99954972A priority patent/EP1157093A1/en
Publication of WO2000023564A2 publication Critical patent/WO2000023564A2/en
Publication of WO2000023564A3 publication Critical patent/WO2000023564A3/en
Priority to AU2004203224A priority patent/AU2004203224B2/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1044—Preparation or screening of libraries displayed on scaffold proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/78—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • C12N9/86—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5) acting on amide bonds in cyclic amides, e.g. penicillinase (3.5.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/02—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amides (3.5.2)
    • C12Y305/02006—Beta-lactamase (3.5.2.6)

Abstract

The invention relates to the use of protein design automation (PDA) to generate computationally prescreened secondary libraries of proteins, and to methods and compositions utilizing the libraries.
PCT/US1999/024229 1998-10-16 1999-10-15 Protein design automation for protein libraries WO2000023564A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
CA002347214A CA2347214A1 (en) 1998-10-16 1999-10-15 Protein design automation for protein libraries
JP2000577277A JP2003527072A (en) 1998-10-16 1999-10-15 Protein design automation for protein libraries
AU11190/00A AU774334B2 (en) 1998-10-16 1999-10-15 Protein design automation for protein libraries
EP99954972A EP1157093A1 (en) 1998-10-16 1999-10-15 Protein design automation for protein libraries
AU2004203224A AU2004203224B2 (en) 1998-10-16 2004-07-16 Protein design automation for protein libraries

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US10461298P 1998-10-16 1998-10-16
US60/104,612 1998-10-16
US15870099P 1999-10-08 1999-10-08

Publications (2)

Publication Number Publication Date
WO2000023564A2 WO2000023564A2 (en) 2000-04-27
WO2000023564A3 true WO2000023564A3 (en) 2001-12-13

Family

ID=26801737

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1999/024229 WO2000023564A2 (en) 1998-10-16 1999-10-15 Protein design automation for protein libraries

Country Status (5)

Country Link
EP (1) EP1157093A1 (en)
JP (1) JP2003527072A (en)
AU (2) AU774334B2 (en)
CA (1) CA2347214A1 (en)
WO (1) WO2000023564A2 (en)

Cited By (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7662925B2 (en) 2002-03-01 2010-02-16 Xencor, Inc. Optimized Fc variants and methods for their generation
US7973136B2 (en) 2005-10-06 2011-07-05 Xencor, Inc. Optimized anti-CD30 antibodies
US8039592B2 (en) 2002-09-27 2011-10-18 Xencor, Inc. Optimized Fc variants and methods for their generation
US8084582B2 (en) 2003-03-03 2011-12-27 Xencor, Inc. Optimized anti-CD20 monoclonal antibodies having Fc variants
US8101720B2 (en) 2004-10-21 2012-01-24 Xencor, Inc. Immunoglobulin insertions, deletions and substitutions
US8124731B2 (en) 2002-03-01 2012-02-28 Xencor, Inc. Optimized Fc variants and methods for their generation
US8188231B2 (en) 2002-09-27 2012-05-29 Xencor, Inc. Optimized FC variants
US8318907B2 (en) 2004-11-12 2012-11-27 Xencor, Inc. Fc variants with altered binding to FcRn
US8388955B2 (en) 2003-03-03 2013-03-05 Xencor, Inc. Fc variants
US8394374B2 (en) 2006-09-18 2013-03-12 Xencor, Inc. Optimized antibodies that target HM1.24
US8524867B2 (en) 2006-08-14 2013-09-03 Xencor, Inc. Optimized antibodies that target CD19
US8546543B2 (en) 2004-11-12 2013-10-01 Xencor, Inc. Fc variants that extend antibody half-life
US8802820B2 (en) 2004-11-12 2014-08-12 Xencor, Inc. Fc variants with altered binding to FcRn
US9040041B2 (en) 2005-10-03 2015-05-26 Xencor, Inc. Modified FC molecules
US9200079B2 (en) 2004-11-12 2015-12-01 Xencor, Inc. Fc variants with altered binding to FcRn
US9475881B2 (en) 2010-01-19 2016-10-25 Xencor, Inc. Antibody variants with enhanced complement activity

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AU751331B2 (en) 1997-04-11 2002-08-15 California Institute Of Technology Apparatus and method for automated protein design
US7315786B2 (en) 1998-10-16 2008-01-01 Xencor Protein design automation for protein libraries
US20020048772A1 (en) 2000-02-10 2002-04-25 Dahiyat Bassil I. Protein design automation for protein libraries
US7024312B1 (en) 1999-01-19 2006-04-04 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides having desired characteristics
US20070065838A1 (en) 1999-01-19 2007-03-22 Maxygen, Inc. Oligonucleotide mediated nucleic acid recombination
US8457903B1 (en) 1999-01-19 2013-06-04 Codexis Mayflower Holdings, Llc Method and/or apparatus for determining codons
US7702464B1 (en) 2001-08-21 2010-04-20 Maxygen, Inc. Method and apparatus for codon determining
US7873477B1 (en) 2001-08-21 2011-01-18 Codexis Mayflower Holdings, Llc Method and system using systematically varied data libraries
US6946265B1 (en) 1999-05-12 2005-09-20 Xencor, Inc. Nucleic acids and proteins with growth hormone activity
US6746853B1 (en) 1999-05-19 2004-06-08 Xencor, Inc. Proteins with insulin-like activity useful in the treatment of diabetes
US7430477B2 (en) 1999-10-12 2008-09-30 Maxygen, Inc. Methods of populating data structures for use in evolutionary simulations
DK1255826T3 (en) * 2000-02-10 2006-01-30 Xencor Inc Automation of protein design for protein libraries
EP1621617A1 (en) * 2000-02-10 2006-02-01 Xencor, Inc. Protein design automation for protein libraries
US7446174B2 (en) 2001-03-02 2008-11-04 Xencor, Inc. Protein based TNF-α variants for the treatment of TNF-α related disorders
US7244823B2 (en) 2000-03-02 2007-07-17 Xencor TNF-alpha variants proteins for the treatment of TNF-alpha related disorders
US7687461B2 (en) 2000-03-02 2010-03-30 Xencor, Inc. Treatment of TNF-α related disorders with TNF-α variant proteins
US7101974B2 (en) 2000-03-02 2006-09-05 Xencor TNF-αvariants
US7056695B2 (en) 2000-03-02 2006-06-06 Xencor TNF-α variants
US7662367B2 (en) 2000-03-02 2010-02-16 Xencor, Inc. Pharmaceutical compositions for the treatment of TNF-α related disorders
AU2001278872A1 (en) * 2000-07-06 2002-01-21 Genvec, Inc. Method of identifying a binding partner of a gene product
ATE396539T1 (en) 2000-07-13 2008-06-15 Ct Concept Technologie Ag METHOD AND DEVICE FOR STATE-DEPENDENT CONTROL OF THE TRANSIENT BEHAVIOR OF POWER SEMICONDUCTOR SWITCHES
AU2002211624A1 (en) * 2000-10-10 2002-04-22 Genencor International, Inc. Information rich libraries
US7351690B2 (en) 2000-12-19 2008-04-01 Palatin Technologies, Inc. Knockout identification of target-specific sites in peptides
AU2002251999A1 (en) * 2001-02-22 2002-09-12 Xencor Methods and compositions for the construction and use of fusion libraries using computational protein design methods
JP2005505250A (en) 2001-05-04 2005-02-24 ゼンコー Nucleic acid and protein having thioredoxin reductase activity
US7381792B2 (en) 2002-01-04 2008-06-03 Xencor, Inc. Variants of RANKL protein
DE10233047A1 (en) * 2002-07-19 2004-02-26 Amaxa Gmbh Preparing synthetic polypeptides, particularly fluorescent proteins, useful in pharmaceutical compositions, by aligning sequences of known proteins to define an average sequence
US20090010920A1 (en) 2003-03-03 2009-01-08 Xencor, Inc. Fc Variants Having Decreased Affinity for FcyRIIb
US9051373B2 (en) 2003-05-02 2015-06-09 Xencor, Inc. Optimized Fc variants
US9714282B2 (en) 2003-09-26 2017-07-25 Xencor, Inc. Optimized Fc variants and methods for their generation
EP1697741A4 (en) 2003-12-04 2008-02-13 Xencor Inc Methods of generating variant proteins with increased host string content and compositions thereof
US20150010550A1 (en) 2004-07-15 2015-01-08 Xencor, Inc. OPTIMIZED Fc VARIANTS
EP1836223B1 (en) * 2005-01-03 2011-11-23 F. Hoffmann-La Roche AG Method for identifying a nucleic acid encoding a hemopexin-like structure which specifically binds a predetermined target molecule.
EP2808343B8 (en) 2007-12-26 2020-01-15 Xencor, Inc. Fc variants with altered binding to FcRn
EP2332424B1 (en) 2008-09-26 2014-06-18 Nippon Suisan Kaisha, Ltd. Method for producing lipid
US9493578B2 (en) 2009-09-02 2016-11-15 Xencor, Inc. Compositions and methods for simultaneous bivalent and monovalent co-engagement of antigens

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Cited By (31)

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Publication number Priority date Publication date Assignee Title
US8093357B2 (en) 2002-03-01 2012-01-10 Xencor, Inc. Optimized Fc variants and methods for their generation
US7662925B2 (en) 2002-03-01 2010-02-16 Xencor, Inc. Optimized Fc variants and methods for their generation
US8734791B2 (en) 2002-03-01 2014-05-27 Xencor, Inc. Optimized fc variants and methods for their generation
US8124731B2 (en) 2002-03-01 2012-02-28 Xencor, Inc. Optimized Fc variants and methods for their generation
US8809503B2 (en) 2002-09-27 2014-08-19 Xencor, Inc. Optimized Fc variants and methods for their generation
US8039592B2 (en) 2002-09-27 2011-10-18 Xencor, Inc. Optimized Fc variants and methods for their generation
US8188231B2 (en) 2002-09-27 2012-05-29 Xencor, Inc. Optimized FC variants
US9353187B2 (en) 2002-09-27 2016-05-31 Xencor, Inc. Optimized FC variants and methods for their generation
US9193798B2 (en) 2002-09-27 2015-11-24 Xencor, Inc. Optimized Fc variants and methods for their generation
US8093359B2 (en) 2002-09-27 2012-01-10 Xencor, Inc. Optimized Fc variants and methods for their generation
US8858937B2 (en) 2002-09-27 2014-10-14 Xencor, Inc. Optimized Fc variants and methods for their generation
US8383109B2 (en) 2002-09-27 2013-02-26 Xencor, Inc. Optimized Fc variants and methods for their generation
US8084582B2 (en) 2003-03-03 2011-12-27 Xencor, Inc. Optimized anti-CD20 monoclonal antibodies having Fc variants
US8388955B2 (en) 2003-03-03 2013-03-05 Xencor, Inc. Fc variants
US8735545B2 (en) 2003-03-03 2014-05-27 Xencor, Inc. Fc variants having increased affinity for fcyrllc
US8101720B2 (en) 2004-10-21 2012-01-24 Xencor, Inc. Immunoglobulin insertions, deletions and substitutions
US8338574B2 (en) 2004-11-12 2012-12-25 Xencor, Inc. FC variants with altered binding to FCRN
US8367805B2 (en) 2004-11-12 2013-02-05 Xencor, Inc. Fc variants with altered binding to FcRn
US8318907B2 (en) 2004-11-12 2012-11-27 Xencor, Inc. Fc variants with altered binding to FcRn
US9200079B2 (en) 2004-11-12 2015-12-01 Xencor, Inc. Fc variants with altered binding to FcRn
US8802820B2 (en) 2004-11-12 2014-08-12 Xencor, Inc. Fc variants with altered binding to FcRn
US8324351B2 (en) 2004-11-12 2012-12-04 Xencor, Inc. Fc variants with altered binding to FcRn
US8852586B2 (en) 2004-11-12 2014-10-07 Xencor, Inc. Fc variants with altered binding to FcRn
US8546543B2 (en) 2004-11-12 2013-10-01 Xencor, Inc. Fc variants that extend antibody half-life
US8883973B2 (en) 2004-11-12 2014-11-11 Xencor, Inc. Fc variants with altered binding to FcRn
US9040041B2 (en) 2005-10-03 2015-05-26 Xencor, Inc. Modified FC molecules
US7973136B2 (en) 2005-10-06 2011-07-05 Xencor, Inc. Optimized anti-CD30 antibodies
US9574006B2 (en) 2005-10-06 2017-02-21 Xencor, Inc. Optimized anti-CD30 antibodies
US8524867B2 (en) 2006-08-14 2013-09-03 Xencor, Inc. Optimized antibodies that target CD19
US8394374B2 (en) 2006-09-18 2013-03-12 Xencor, Inc. Optimized antibodies that target HM1.24
US9475881B2 (en) 2010-01-19 2016-10-25 Xencor, Inc. Antibody variants with enhanced complement activity

Also Published As

Publication number Publication date
WO2000023564A2 (en) 2000-04-27
JP2003527072A (en) 2003-09-16
CA2347214A1 (en) 2000-04-27
AU1119000A (en) 2000-05-08
AU2004203224B2 (en) 2007-07-05
AU774334B2 (en) 2004-06-24
EP1157093A1 (en) 2001-11-28
AU2004203224A1 (en) 2004-08-12

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