CA2485732A1 - Production et selection d'une banque de proteines dans de la silice - Google Patents

Production et selection d'une banque de proteines dans de la silice Download PDF

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Publication number
CA2485732A1
CA2485732A1 CA002485732A CA2485732A CA2485732A1 CA 2485732 A1 CA2485732 A1 CA 2485732A1 CA 002485732 A CA002485732 A CA 002485732A CA 2485732 A CA2485732 A CA 2485732A CA 2485732 A1 CA2485732 A1 CA 2485732A1
Authority
CA
Canada
Prior art keywords
library
sequence
lead
amino acid
antibody
Prior art date
Legal status (The legal status 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 status listed.)
Abandoned
Application number
CA002485732A
Other languages
English (en)
Inventor
Peizhi Luo
Mark Hsieh
Pingyu Zhong
Caili Wang
Yicheng Cao
Shengjiang Liu
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Abmaxis Inc
Original Assignee
Individual
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
Priority claimed from US10/153,176 external-priority patent/US20030022240A1/en
Priority claimed from US10/153,159 external-priority patent/US7117096B2/en
Application filed by Individual filed Critical Individual
Publication of CA2485732A1 publication Critical patent/CA2485732A1/fr
Abandoned legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/22—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against growth factors ; against growth regulators
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30—Detection of binding sites or motifs
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G16B35/20—Screening of libraries
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry
    • 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
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/50—Mutagenesis

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Library & Information Science (AREA)
  • Biochemistry (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Immunology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Computing Systems (AREA)
  • Peptides Or Proteins (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

L'invention concerne un procédé de production et de criblage de banques de protéines pour détecter des protéines optimisées qui possèdent les fonctions biologiques recherchées, telles qu'une affinité de liaison améliorée pour des molécules cibles biologiquement et/ou thérapeutiquement intéressantes. Ce procédé consiste à appliquer des calculs à grand débit pour extraire des bases de données toujours croissantes de séquences de protéines de tous les organismes, plus particulièrement, des organismes humains. Dans un mode de réalisation, un procédé permettant de produire une banque de protéines spécifiquement conçues, consiste à : fournir une séquence d'acides aminés dérivée d'une protéine de tête, cette séquence d'acides aminés étant conçue comme une séquence de tête ; comparer la séquence de tête à une pluralité de séquences de protéines d'essai; sélectionner parmi la pluralité des séquences de protéines d'essai au moins deux segments de peptides qui partagent au moins 15% de l'identité de séquence avec la séquence de tête, les segments de peptides sélectionnés formant une banque cible; et enfin, former une banque de protéines spécifiquement conçues en substituant la séquence de tête à la banque cible. La banque de protéines spécifiquement conçues peut être exprimée in vitro ou in vivo pour produire une banque de protéines recombinées pouvant être criblée pour détecter de nouvelles fonctions ou des fonctions améliorées par rapport à la protéine de tête, par exemple, un anticorps agissant contre une cible thérapeutiquement importante.
CA002485732A 2002-05-20 2003-05-20 Production et selection d'une banque de proteines dans de la silice Abandoned CA2485732A1 (fr)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US10/153,176 US20030022240A1 (en) 2001-04-17 2002-05-20 Generation and affinity maturation of antibody library in silico
US10/153,159 2002-05-20
US10/153,159 US7117096B2 (en) 2001-04-17 2002-05-20 Structure-based selection and affinity maturation of antibody library
US10/153,176 2002-05-20
PCT/US2003/016037 WO2003099999A2 (fr) 2002-05-20 2003-05-20 Production et selection d'une banque de proteines dans de la silice

Publications (1)

Publication Number Publication Date
CA2485732A1 true CA2485732A1 (fr) 2003-12-04

Family

ID=29586304

Family Applications (1)

Application Number Title Priority Date Filing Date
CA002485732A Abandoned CA2485732A1 (fr) 2002-05-20 2003-05-20 Production et selection d'une banque de proteines dans de la silice

Country Status (7)

Country Link
EP (1) EP1514216A4 (fr)
JP (1) JP2005526518A (fr)
CN (1) CN1672160B (fr)
AU (1) AU2003248548B2 (fr)
CA (1) CA2485732A1 (fr)
SG (1) SG135053A1 (fr)
WO (1) WO2003099999A2 (fr)

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US7667004B2 (en) * 2001-04-17 2010-02-23 Abmaxis, Inc. Humanized antibodies against vascular endothelial growth factor
AU2004202566B2 (en) * 2004-06-11 2011-07-21 Li-Te Chin Method for Producing Human Antibodies with Properties of Agonist, Antagonist, or Inverse Agonist
MX2007001015A (es) 2004-07-26 2007-04-12 Biogen Idec Inc Anticuerpos anti-cd154.
WO2006055778A2 (fr) 2004-11-16 2006-05-26 Kalobios, Inc. Echange de cassettes d'une region variable de l'immunoglobuline
CA2600929A1 (fr) 2005-03-04 2006-09-14 Biogen Idec Ma Inc. Methodes d'humanisation de regions variables d'immunoglobuline par modification rationnelle de residus determinant une complementarite
NZ591252A (en) * 2006-03-17 2012-06-29 Biogen Idec Inc Methods of designing antibody or antigen binding fragments thereof with substituted non-covarying amino acids
EP2069558B1 (fr) 2006-10-02 2013-05-01 Sea Lane Biotechnologies,llc. Conception et construction de diverses banques de peptides et de polypeptides synthétiques
WO2008094547A2 (fr) * 2007-01-31 2008-08-07 Jiaan Yang Procédés, systèmes, algorithmes et moyens permettant la description de conformations possibles de protéines réelles ou théoriques et d'évaluer des protéines réelles et théoriques par rapport au repli, à la forme globale et de motifs structurels
AU2009313560B2 (en) 2008-11-07 2016-04-14 Fabrus Llc Combinatorial antibody libraries and uses thereof
CA2765755C (fr) * 2009-06-17 2018-01-02 Abbott Biotherapeutics Corp. Anticorps anti-vegf et leurs utilisations
WO2011047146A2 (fr) * 2009-10-14 2011-04-21 Centocor Ortho Biotech Inc. Procédés de maturation d'affinité d'anticorps
JPWO2013171810A1 (ja) 2012-05-14 2016-01-07 パナソニックＩｐマネジメント株式会社 耐熱性抗体提示ファージを得る方法
US20140154255A1 (en) 2012-11-30 2014-06-05 Abbvie Biotherapeutics Inc. Anti-vegf antibodies and their uses
CN105074463B (zh) * 2013-01-31 2018-09-25 科德克希思公司 使用相乘形式的模型鉴定生物分子的方法、系统和软件
CN104805507B (zh) * 2014-01-29 2019-01-22 杭州康万达医药科技有限公司 噬菌体展示文库及其应用和制备方法
EP3167395B1 (fr) * 2014-07-07 2020-09-02 Yeda Research and Development Co., Ltd. Procedé de conception informatique des proteines
GB201500464D0 (en) * 2015-01-12 2015-02-25 Crescendo Biolog Ltd Method of producing optimised therapeutic molecules
WO2016137992A2 (fr) * 2015-02-24 2016-09-01 Academia Sinica Banque de fragments variables monocaténaires présentés sur phage
CN104789555A (zh) * 2015-04-29 2015-07-22 江南大学 一种基于合成单链dna文库进化基因表达调控元件的方法
JP6558754B2 (ja) 2015-08-07 2019-08-14 富士通株式会社 情報処理装置、指標次元抽出方法、および指標次元抽出プログラム
US10072075B2 (en) * 2015-09-23 2018-09-11 Genentech, Inc. Optimized variants of anti-VEGF antibodies and methods of treatment thereof by reducing or inhibiting angiogenesis
CN106290908A (zh) * 2016-08-07 2017-01-04 查文娟 一种用于肾脏损伤检测用试剂盒
WO2018052131A1 (fr) * 2016-09-16 2018-03-22 国立大学法人大阪大学 Logiciel de regroupement d'entités immunologiques
CN106905435B (zh) * 2017-03-13 2020-04-10 武汉海沙百得生物技术有限公司 一种制备基于蛋白a突变体的结合蛋白的方法
CN110730822B (zh) * 2017-04-18 2024-03-08 X-化学有限公司 鉴定化合物的方法
EP3669018A4 (fr) 2017-08-18 2021-05-26 Nautilus Biotechnology, Inc. Procédés de sélection de réactifs de liaison
US11015188B2 (en) * 2017-11-20 2021-05-25 NantBio Inc. MRNA display antibody library and methods
CN108304691B (zh) * 2018-02-09 2021-05-18 北京矿冶科技集团有限公司 基于片段的浮选药剂分子设计方法
CN108491692B (zh) * 2018-03-09 2023-07-21 中国科学院生态环境研究中心 一种构建抗生素抗性基因数据库的方法
CN108763870B (zh) * 2018-05-09 2021-08-03 浙江工业大学 一种多域蛋白质Linker构建方法
CN109002690B (zh) * 2018-06-08 2021-05-18 济南大学 通过构建charmm rotamers力场预测突变氨基酸侧链结构的方法
CN108959846B (zh) * 2018-07-03 2021-09-14 南昌立德生物技术有限公司 一种计算机辅助先导药物优化设计的亲和自由能分解算法
CN109243526B (zh) * 2018-07-12 2021-08-03 浙江工业大学 一种基于特定片段交叉的蛋白质结构预测方法
CN109086568B (zh) * 2018-08-16 2022-03-11 福建工程学院 计算机抗体组合突变进化系统及方法、信息数据处理终端
CN109801679B (zh) * 2019-01-15 2021-02-02 广州柿宝生物科技有限公司 一种用于长链分子的数学序列重建方法
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CN111370074B (zh) * 2020-02-27 2023-07-07 北京晶泰科技有限公司 一种分子序列的生成方法、装置和计算设备
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CN112102883B (zh) * 2020-08-20 2023-12-08 深圳华大生命科学研究院 一种fastq文件压缩中的碱基序列编码方法和系统

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Also Published As

Publication number Publication date
WO2003099999A2 (fr) 2003-12-04
AU2003248548B2 (en) 2010-03-11
AU2003248548A1 (en) 2003-12-12
JP2005526518A (ja) 2005-09-08
WO2003099999A3 (fr) 2004-09-16
EP1514216A4 (fr) 2010-01-06
CN1672160A (zh) 2005-09-21
SG135053A1 (en) 2007-09-28
CN1672160B (zh) 2010-06-09
EP1514216A2 (fr) 2005-03-16

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Legal Events

Date Code Title Description
EEER Examination request
FZDE Discontinued

Effective date: 20140228