WO2004083427A3 - Ligational encoding of small molecules - Google Patents

Ligational encoding of small molecules Download PDF

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Publication number
WO2004083427A3
WO2004083427A3 PCT/DK2004/000195 DK2004000195W WO2004083427A3 WO 2004083427 A3 WO2004083427 A3 WO 2004083427A3 DK 2004000195 W DK2004000195 W DK 2004000195W WO 2004083427 A3 WO2004083427 A3 WO 2004083427A3
Authority
WO
WIPO (PCT)
Prior art keywords
chemical entities
template
encoded molecule
codon
identifier polynucleotide
Prior art date
Application number
PCT/DK2004/000195
Other languages
French (fr)
Other versions
WO2004083427A2 (en
Inventor
Thomas Franch
Soeren Nyboe Jacobsen
Torben Rasmussen
Soeren Neve
Henrik Pedersen
Alex Haahr Gouliaev
Original Assignee
Nuevolution As
Thomas Franch
Soeren Nyboe Jacobsen
Torben Rasmussen
Soeren Neve
Henrik Pedersen
Alex Haahr Gouliaev
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 to EP04722237A priority Critical patent/EP1608748B1/en
Priority to DK04722237T priority patent/DK1608748T3/en
Priority to US10/549,619 priority patent/US7915201B2/en
Priority to DE602004019764T priority patent/DE602004019764D1/en
Application filed by Nuevolution As, Thomas Franch, Soeren Nyboe Jacobsen, Torben Rasmussen, Soeren Neve, Henrik Pedersen, Alex Haahr Gouliaev filed Critical Nuevolution As
Publication of WO2004083427A2 publication Critical patent/WO2004083427A2/en
Publication of WO2004083427A3 publication Critical patent/WO2004083427A3/en
Priority to EP05715120A priority patent/EP1730277B1/en
Priority to AT05715120T priority patent/ATE447020T1/en
Priority to DK05715120.1T priority patent/DK1730277T3/en
Priority to DE602005017370T priority patent/DE602005017370D1/en
Priority to US10/593,868 priority patent/US7704925B2/en
Priority to PCT/DK2005/000199 priority patent/WO2005090566A2/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • 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
    • C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P21/00—Preparation of peptides or proteins
    • C12P21/02—Preparation of peptides or proteins having a known sequence of two or more amino acids, e.g. glutathione
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/04—Methods of creating libraries, e.g. combinatorial synthesis using dynamic combinatorial chemistry techniques

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Biotechnology (AREA)
  • Wood Science & Technology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Biomedical Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Heterocyclic Carbon Compounds Containing A Hetero Ring Having Oxygen Or Sulfur (AREA)

Abstract

The invention relates to a method for synthesising a bifunctional complex comprising an encoded molecule and an identifier polynucleotide identifying the chemical entities having participated in the synthesis of the encoded molecule, said method comprising the steps of i) providing a) at least one template comprising one or more codons capable of hybridising to an anti-codon, wherein said template is optionally associated with one or more chemical entities, and b) a plurality of building blocks each comprising an anti-codon associated with one or more chemical entities, and ii) hybridising the anti-codon of one or more of the provided building blocks to the template, iii) covalently linking said anti-codons and/or linking the at least one template with the anti-codon of at least one building block, thereby generating an identifier polynucleotide capable of identifying chemical entities having participated in the synthesis of the encoded molecule, iv) separating the template from one or more of the anti-codons hybridised thereto, thereby generating an at least partly single stranded identifier polynucleotide associated with a plurality of chemical entities, v) generating a bifunctional complex comprising an encoded molecule and an identifier polynucleotide identifying the chemical entities having participated in the synthesis of the encoded molecule, wherein said encoded molecule is generated by reacting at least two of said plurality of chemical entities associated with the identifier polynucleotide, and wherein said at least two chemical entities are provided by separate building blocks.
PCT/DK2004/000195 2003-03-20 2004-03-22 Ligational encoding of small molecules WO2004083427A2 (en)

Priority Applications (10)

Application Number Priority Date Filing Date Title
EP04722237A EP1608748B1 (en) 2003-03-20 2004-03-22 Ligational encoding of small molecules
DK04722237T DK1608748T3 (en) 2003-03-20 2004-03-22 Ligation coding of small molecules
US10/549,619 US7915201B2 (en) 2003-03-20 2004-03-22 Ligational encoding of small molecules
DE602004019764T DE602004019764D1 (en) 2003-03-20 2004-03-22 LIGATION-RELATED CODING OF SMALL MOLECULES
PCT/DK2005/000199 WO2005090566A2 (en) 2004-03-22 2005-03-22 Ligational encoding using building block oligonucleotides
EP05715120A EP1730277B1 (en) 2004-03-22 2005-03-22 Ligational encoding using building block oligonucleotides
US10/593,868 US7704925B2 (en) 2004-03-22 2005-03-22 Ligational encoding using building block oligonucleotides
AT05715120T ATE447020T1 (en) 2004-03-22 2005-03-22 LIGATION CODING USING OLIGONUCLEOTIDE BUILDING BLOCKS
DK05715120.1T DK1730277T3 (en) 2004-03-22 2005-03-22 Coding by ligation using building block oligonucleotides
DE602005017370T DE602005017370D1 (en) 2004-03-22 2005-03-22 LIGATION CODING USING OLIGONUCLEOTIDE COMPONENTS

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US45585803P 2003-03-20 2003-03-20
DKPA200300430 2003-03-20
DKPA200300430 2003-03-20
US60/455,858 2003-03-20

Related Parent Applications (2)

Application Number Title Priority Date Filing Date
US10/549,619 Continuation-In-Part US7915201B2 (en) 2003-03-20 2004-03-22 Ligational encoding of small molecules
PCT/DK2004/000195 Continuation-In-Part WO2004083427A2 (en) 2003-03-20 2004-03-22 Ligational encoding of small molecules

Related Child Applications (3)

Application Number Title Priority Date Filing Date
US10/549,619 A-371-Of-International US7915201B2 (en) 2003-03-20 2004-03-22 Ligational encoding of small molecules
PCT/DK2004/000195 Continuation-In-Part WO2004083427A2 (en) 2003-03-20 2004-03-22 Ligational encoding of small molecules
US10/593,868 Continuation-In-Part US7704925B2 (en) 2004-03-22 2005-03-22 Ligational encoding using building block oligonucleotides

Publications (2)

Publication Number Publication Date
WO2004083427A2 WO2004083427A2 (en) 2004-09-30
WO2004083427A3 true WO2004083427A3 (en) 2005-02-17

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/DK2004/000195 WO2004083427A2 (en) 2003-03-20 2004-03-22 Ligational encoding of small molecules

Country Status (6)

Country Link
US (1) US7915201B2 (en)
EP (2) EP1608748B1 (en)
AT (1) ATE424455T1 (en)
DE (1) DE602004019764D1 (en)
DK (2) DK1608748T3 (en)
WO (1) WO2004083427A2 (en)

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RU2459869C2 (en) * 2005-06-09 2012-08-27 ГЛЭКСОСМИТКЛАЙН ЭлЭлСи Compound containing coding oligonucleotide, production method thereof, library of compounds, production method thereof, method of identifying compound bound with biological target (versions)
US8808984B2 (en) 2002-03-15 2014-08-19 Neuvolution A/S Method for synthesising templated molecules
US8932992B2 (en) 2001-06-20 2015-01-13 Nuevolution A/S Templated molecules and methods for using such molecules
US9096951B2 (en) 2003-02-21 2015-08-04 Nuevolution A/S Method for producing second-generation library
US9121110B2 (en) 2002-12-19 2015-09-01 Nuevolution A/S Quasirandom structure and function guided synthesis methods
US9574189B2 (en) 2005-12-01 2017-02-21 Nuevolution A/S Enzymatic encoding methods for efficient synthesis of large libraries
JP7010875B2 (en) 2009-02-13 2022-01-26 エックス－ケム インコーポレイテッド How to make and screen a DNA coding library

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AU2003266932B2 (en) * 2002-09-27 2009-04-09 Mpm-Holding Aps Spatially encoded polymer matrix
DE602004019764D1 (en) 2003-03-20 2009-04-16 Nuevolution As LIGATION-RELATED CODING OF SMALL MOLECULES
US8017323B2 (en) * 2003-03-26 2011-09-13 President And Fellows Of Harvard College Free reactant use in nucleic acid-templated synthesis
WO2005026387A1 (en) 2003-09-18 2005-03-24 Nuevolution A/S A method for obtaining structural information concerning an encoded molecule and method for selecting compounds
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DE602005012319D1 (en) 2004-11-22 2009-02-26 Peter Birk Rasmussen MATRESSED SPLIT AND MIX SYNTHESIS OF LIBRARY LIBRARIES
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US11225655B2 (en) 2010-04-16 2022-01-18 Nuevolution A/S Bi-functional complexes and methods for making and using such complexes
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JP7283727B2 (en) 2016-06-16 2023-05-30 ヘイスタック サイエンシィズ コーポレーション Oligonucleotides Directed and Recorded for Combinatorial Synthesis of Code Probe Molecules
US11795580B2 (en) 2017-05-02 2023-10-24 Haystack Sciences Corporation Molecules for verifying oligonucleotide directed combinatorial synthesis and methods of making and using the same
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US8932992B2 (en) 2001-06-20 2015-01-13 Nuevolution A/S Templated molecules and methods for using such molecules
US8808984B2 (en) 2002-03-15 2014-08-19 Neuvolution A/S Method for synthesising templated molecules
US8206901B2 (en) 2002-10-30 2012-06-26 Nuevolution A/S Method for the synthesis of a bifunctional complex
US8722583B2 (en) 2002-10-30 2014-05-13 Nuevolution A/S Method for selecting a chemical entity from a tagged library
US9109248B2 (en) 2002-10-30 2015-08-18 Nuevolution A/S Method for the synthesis of a bifunctional complex
US9284600B2 (en) 2002-10-30 2016-03-15 Neuvolution A/S Method for the synthesis of a bifunctional complex
US9121110B2 (en) 2002-12-19 2015-09-01 Nuevolution A/S Quasirandom structure and function guided synthesis methods
US9096951B2 (en) 2003-02-21 2015-08-04 Nuevolution A/S Method for producing second-generation library
RU2459869C2 (en) * 2005-06-09 2012-08-27 ГЛЭКСОСМИТКЛАЙН ЭлЭлСи Compound containing coding oligonucleotide, production method thereof, library of compounds, production method thereof, method of identifying compound bound with biological target (versions)
US9574189B2 (en) 2005-12-01 2017-02-21 Nuevolution A/S Enzymatic encoding methods for efficient synthesis of large libraries
JP7010875B2 (en) 2009-02-13 2022-01-26 エックス－ケム インコーポレイテッド How to make and screen a DNA coding library

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US20060246450A1 (en) 2006-11-02
ATE424455T1 (en) 2009-03-15
WO2004083427A2 (en) 2004-09-30
EP1608748B1 (en) 2009-03-04
US7915201B2 (en) 2011-03-29
EP2236606A2 (en) 2010-10-06
EP1608748A2 (en) 2005-12-28
EP2236606A3 (en) 2010-10-20
DK1608748T3 (en) 2009-06-29
DE602004019764D1 (en) 2009-04-16
DK2236606T3 (en) 2014-02-10

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