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Ep001402024b1* (19) *EP001402024B1* (11) EP 1 402 024 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/10 (2006.01) C12P 1/00 (2006.01) 22.08.2007 Bulletin 2007/34 C12P 19/34 (2006.01) C07H 21/00 (2006.01) C12P 21/02 (2006.01) (21) Application number: 02740409.4 (86) International application number: (22) Date of filing: 20.06.2002 PCT/DK2002/000419 (87) International publication number: WO 2002/103008 (27.12.2002 Gazette 2002/52) (54) TEMPLATED MOLECULES AND METHODS FOR USING SUCH MOLECULES EINE METHODE ZUR SYNTHESE VON MATRIZENABHÄNGIGEN MOLEKÜLEN MOLECULES A MATRICE ET PROCEDES D’UTILISATION DE CES DERNIERES (84) Designated Contracting States: • FRANCH, Thomas AT BE CH CY DE DK ES FI FR GB GR IE IT LI LU DK-5000 Odense C (DK) MC NL PT SE TR • THISTED, Thomas Designated Extension States: DK-3600 Frederikssund (DK) AL LT LV MK RO SI • HYLDTOFT, Lene DK-2830 Virum (DK) (30) Priority: 20.06.2001 DK 200100962 • NØRREGAARD-MADSEN, Mads 15.03.2002 DK 200200415 DK-3460 Birkerød (DK) • ANDERS GODSKESEN, Michael (43) Date of publication of application: DK-2950 Vedbæk (DK) 31.03.2004 Bulletin 2004/14 • SCHRØDER GLAD, Sanne DK-2750 Ballerup (DK) (73) Proprietor: Nuevolution A/S 2100 Copenhagen (DK) (74) Representative: HOEIBERG A/S European Patent & Trademark Attorneys (72) Inventors: Store Kongensgade 59A • PEDERSEN, Henrik 1264 Copenhagen K (DK) DK-2880 Bagsværd (DK) • GOUILAEV, Alex, Haahr (56) References cited: 3670 Veksø Sjælland (DK) WO-A-00/23458 WO-A-00/61775 • SAMS, Klarner, Christian WO-A-93/03172 WO-A-98/56904 DK-1973 Frederiksberg C (DK) WO-A-02/074929 DE-C- 19 646 372 • SLØK, Frank, Abilgaard DK-2200 København N (DK) • WALDER J A ET AL: "COMPLEMENTARY • FRESKGÅRD, PER-OLA CARRIER PEPTIDE SYNTHESIS: GENERAL DK-235 93 Vellinge (SE) STRATEGY AND IMPLICATIONS FOR • HOLTMANN, Anette PREBIOTIC ORIGIN OF PEPTIDE SYNTHESIS" DK-2750 Ballerup (DK) PROCEEDINGS OF THE NATIONAL ACADEMY • KAMPMANN OLSEN, Eva OF SCIENCES OF USA, NATIONAL ACADEMY OF DK-2730 Herlev (DK) SCIENCE. WASHINGTON, US, vol. 76, no. 1, • HUSEMOEN, Gitte, Nystrup January 1979 (1979-01), pages 51-55, DK-2200 København N (DK) XP000857351 ISSN: 0027-8424 • FELDING, Jakob DK-2920 Charlottenlund (DK) Note: Within nine months from the publication of the mention of the grant of the European patent, any person may give notice to the European Patent Office of opposition to the European patent granted. Notice of opposition shall be filed in a written reasoned statement. It shall not be deemed to have been filed until the opposition fee has been paid. (Art. 99(1) European Patent Convention). EP 1 402 024 B1 Printed by Jouve, 75001 PARIS (FR) (Cont. next page) EP 1 402 024 B1 • VISSCHER J ET AL: "TEMPLATE-DIRECTED • BRENNER S ET AL: "ENCODED SYNTHESIS OF ACYCLIC OLIGONUCLEOTIDE COMBINATORIAL CHEMISTRY" PROCEEDINGS ANALOGUES" JOURNAL OF MOLECULAR OF THE NATIONAL ACADEMY OF SCIENCES OF EVOLUTION, SPRINGER VERLAG, NEW YORK, USA, NATIONAL ACADEMY OF SCIENCE. NY, US, vol. 28, no. 1/2, 1988, pages 3-6, WASHINGTON, US, vol. 89, no. 12, 1 June 1992 XP000857353 ISSN: 0022-2844 (1992-06-01), pages 5381-5383, XP000647936 • KEILER K C ET AL: "ROLE OF A PEPTIDE ISSN: 0027-8424 TAGGING SYSTEM IN DEGRADATION OF • BRUICK R K ET AL: "TEMPLATE-DIRECTED PROTEINS SYNTHESIZED FROM DAMAGED LIGATION OF PEPTIDES TO MESSENGER RNA" SCIENCE, AMERICAN OLIGONUCLEOTIDES" CHEMISTRY AND ASSOCIATION FOR THE ADVANCEMENT OF BIOLOGY, CURRENT BIOLOGY, LONDON, GB, SCIENCE,, US, vol. 271, 16 February 1996 vol. 3, no. 1, January 1996 (1996-01), pages 49-56, (1996-02-16), pages 990-993, XP002041752 ISSN: XP000856876 ISSN: 1074-5521 0036-8075 • BERGER MARKUS ET AL: "Universal bases for • SALAS J ET AL: "BIOSYNTHETIC hybridization, replication and chain termination" POLYDEOXYNUCLEOTIDES AS DIRECT NUCLEIC ACIDS RESEARCH, OXFORD TEMPLATES FOR POLYPEPTIDE SYNTHESIS" UNIVERSITY PRESS, SURREY, GB, vol. 28, no. JOURNAL OF BIOLOGICAL CHEMISTRY, THE 15, 1 August 2000 (2000-08-01), pages 2911-2914, AMERICAN SOCIETY OF BIOLOGICAL XP002194275 ISSN: 0305-1048 cited in the CHEMISTS, INC.,, US, vol. 243, no. 6, 1968, pages application 1012-1015, XP000857332 ISSN: 0021-9258 2 EP 1 402 024 B1 Description Technical Field of the Invention 5 [0001] Biological systems allow template-directed synthesis of α-peptides. The present invention enables a system that allows template-directed synthesis of other types of polymers as well as α-peptides. The present invention relates to templated molecules and templated molecules linked to a predetermined template. The templated molecules comprise a sequence of functional groups that are linked together. Each functional group is initially linked to an element capable of complementing a predetermined coding element of the template. Following complementation of a coding element, or 10 complementation of a plurality of coding elements, the appended functional groups are linked and the templated mole- culed is formed. Background 15 [0002] The central dogma in biology describes the flow of information as a one-way process from DNA to RNA to polypeptide. Accordingly, DNA is transcribed by a RNA polymerase into mRNA; and the mRNA is subsequently then translated into protein by the ribosomes and tRNAs. [0003] The direct relation between the, DNA and the protein, i.e., the fact that the sequence of triplet codons defines the sequence of α-amino acid residues in a polypeptide, has allowed the development of numerous molecular biological 20 methods, in which the experimenter manipulates the DNA (mutagenizes, recombines, deletes, inserts, etc), and then uses in vivo systems (e.g., microbes) or in vitro systems (e.g., Zubay in vitro expression systems) to transfer the resulting changes from the DNA level to the level of the templated polypeptide, i.e., to mutate, recombine, delete, insert, etc. the polypeptide. [0004] Several systems have been invented that allows a flow of information from polypeptide to DNA. These systems 25 are phage display, ribosome/polysome display, peptides-on-plasmid display, and other.systems. These systems intro- duce a physical link between the template (e.g., DNA) and the templated molecule (polypeptide). As a result, it is possible, from a-population of templated molecules linked to the template that templated the synthesis of the molecule, to first enrich for a desired characteristic of the templated molecule (e.g., binding of the templated molecule to an affinity column), and then amplify the enriched population of templated molecules through amplification of its template (DNA or RNA), 30 followed by translation of the amplified templates. These methods have been used to identify polypeptides with novel and/or improved features from libraries consisting of from a million to about 1015 polypeptides. [0005] The critical feature of the prior art systems is the amplifiability of the templated molecule, through amplification of its template. Thus, after the selection step in which molecules with the desired property are enriched, the enriched population may be amplified and then taken through yet a selection step, etc. - the process of selection-and-amplification 35 may be repeated many times. In this way the "noise" of the selection assay is averaged out over several selection-and- amplification rounds, and even if the individual selection step only enriches e.g. 10-fold, a theoretical enrichment of 1012 can be reached after 12 selection-and-amplification rounds. Had the molecules not been amplifiable, the same enrichment would have had to be achieved in a single screening step, which means that the enrichment in this one step would have had to be 1012, and the assay should still have the same overall stringency (accuracy). This is practically impossible 40 with current technologies. [0006] In the field of chemistry, a different combinatorial approach has been developed. This approach involved the parallel synthesis of millions of related compounds, in an array (where each position defined a specific compound), or on beads (where one bead carried many copies of the same compound). The population of compounds were then screened for desired characteristics. Importantly, this type of combinatorial library has no means for amplification, and 45 therefore requires the use of very stringent screening methods, as explained above. Recently, the trend in for example medicinal chemistry has therefore been to use less diverse, but better characterized libraries. [0007] Principles for tagging chemical libraries have also been developed. For example, systems that employed DNA oligos to tag molecule libraries have been developed as exemplified herein below. The tag is used as a means of identification, but cannot be used to template the synthesis of the tagged molecule. Therefore, despite the tag, these 50 systems still require a very efficient screening method. [0008] The below listed references illustrate some of the above-mentioned short-comings of the prior art methods in the field of the invention. [0009] EP 0 604 552 B1 relates to a method for synthesizing diverse collections of oligomers. The invention involves the use of an identifier tag to identify the sequence of monomers in an oligomer. The identifier tags facilitate subsequent 55 identification of reactions through which members of a library of different synthetic compounds have been synthesised in a component by component fashion. [0010] EP 0 643 778 B1 relates to encoded combinatorial chemical libraries. Each of a collection of polypeptides is labelled by an appended "genetic" tag, itself constructed by chemical synthesis, to provide a "retro-genetic" way of 3 EP 1 402 024 B1 specifying each polypeptide. [0011] EP 0 773 227 A1 relates to a method for preparing a new pharmaceutical drug or diagnostic reagent, which includes the step of screening, against a ligand or receptor, a library of different synthetic compounds obtainable by synthesis in a component by component fashion.
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