Method for synthesising templated molecules

• US 7,413,854 B2
• Filed: 03/14/2003
• Issued: 08/19/2008
• Est. Priority Date: 03/15/2002
• Status: Expired due to Term

• Current Assignee: Nuevolution A/S (Amgen Inc.)
• Original Assignee: Nuevolution A/S (Amgen Inc.)
• Inventors: Franch, Thomas, Gouliaev, Alex Haahr, Pedersen, Henrik, Holtmann, Anette, Felding, Jakob
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US10/507,121
• Publication Number:
  US 20050221316A1
• Time in Patent Office: 1,985 Days
• Field of Search: 435/6, 536/22.1, 536/25.3
• US Class Current: 435/6.16
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07D 405/04 directly linked by a ring-member-to-ring-member bond
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12N 15/1068 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
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/14 Libraries containing macromolecular compounds and not covered by groups C40B40/06 - C40B40/12

Abstract

The invention relates to a method for synthesizing templated molecules attached to the templated which directed the synthesis thereof. The method involves a template, a scaffold functional entity and a functional entity attached to a building block, which, in turn, is attached the template. The scaffold functional entity and the functional entity of the building block are both provided with complementary dimerization domains allowing the functional entities to come into close proximity when the complementary domains interact with to each other. The method may be used for generating libraries of templated molecules which may be selected for biological activity.

Claims

1. A method for synthesizing a templated molecule, comprising the steps of:

a) providing at least one template comprising of one or more codons,

b) providing a first functional entity attached to a first zipping oligonucleotide capable of reversible interaction with a second zipping oligonucleotide,

c) providing one or more building blocks, each building block comprising a further functional entity linked to an anti-codon by a linker,

wherein the anti-codon complements a codon of the template,

wherein the further functional entity is connected to the second zipping oligonucleoticle capable of reversible interaction with the first zipping oligonucleotide attached to the first functional entity provided in step b), and

wherein the further functional entity is capable of being chemically connected to the first functional entity provided in step b),

d) contacting the components provided in steps a), b) and c) with each other under conditions allowing for i) specific hybridization of building block anti-codon(s) to the codon(s) of the template(s) and ii) dimerization of two zipping oligonucleotides attached to different functional entities,

e) allowing a further functional entity of the one or more building blocks provided in step c) to form a chemical connection to the first functional entity provided in step b), and

f) obtaining a templated molecule attached to the template which directed the synthesis thereof.

2. The method of claim 1, wherein steps d) and e) are repeated one or more times prior to obtaining in step f) the templated molecule attached to the template which directed the synthesis thereof.

3. The method of claim 1, wherein the first functional entity is covalently connected to the template.

4. The method of claim 1, wherein the first functional entity is hybridized to the template.

5. The method of claim 1, wherein the first functional entity forms part of a building block further comprising

an anti-codon complementing a template codon,

a linker connecting the anti-codon and the first functional entity, and

a first zipping oligonucleotide connected to the first functional entity.

6. The method of claim 3, wherein the first functional entity forms part of a building block further comprising

an anti-codon complementing a template codon,

a linker connecting the anti-codon and the first functional entity, and

a first zipping oligonucleotide connected to the first functional entity.

7. The method of claim 4, wherein the first functional entity forms part of a building block further comprising

an anti-codon complementing a template codon,

a linker connecting the anti-codon and the first functional entity, and

a first zipping oligonucleotide connected to the first functional entity.

8. The method of claim 1, wherein the zipping oligonucleotide of the first functional entity is present in the template.

9. The method of claim 3, wherein the zipping oligonucleotide of the first functional entity is present in the template.

10. The method of claim 5, wherein the zipping oligonucleotide of the first functional entity is present in the template.

11. The method of claim 1, wherein the zipping oligonucleotides comprise complementary sequences of nucleic acids or nucleic acid analogs.

12. The method of claim 3, wherein the zipping oligonucleotides comprise complementary sequences of nucleic acids or nucleic acid analogs.

13. The method of claim 4, wherein the zipping oligonucleotides comprise complementary sequences of nucleic acids or nucleic acid analogs.

14. The method of claim 1, wherein the first functional entity is further connected to a sequence of nucleic acids complementing a sequence of nucleic acids harbored by the template.

15. The method of claim 3, wherein the first functional entity is further connected to a sequence of nucleic acids complementing a sequence of nucleic acids harbored by the template.

16. The method of claim 4, wherein the first functional entity is further connected to a sequence of nucleic acids complementing a sequence of nucleic acids harbored by the template.

17. The method of claim 1, wherein the zipping oligonucleotide forms part of the linker of the building block.

18. The method of claim 5, wherein the zipping oligonucleotide forms part of the linker of the building block.

19. The method of claim 8, wherein the zipping oligonucleotide is proximal to the functional entity.

20. The method of claim 17, wherein the zipping oligonucleotide is proximal to the functional entity.

21. The method of claim 17, wherein the zipping oligonucleotide is spaced from the first or further functional entity by no more than 2 nucleotides.

22. The method of claim 19, wherein the zipping oligonucleotide is spaced from the first or further functional entity by no more than 2 nucleotides.

23. The method of claim 21, wherein the zipping oligonucleotide and the first functional entity is spaced by no more than 2 nucleotides.

24. The method of claim 1, wherein the number of nucleotides which distance the first functional entity from the first zipping oligonucleotide is the same as the number of nucleotides which distance the further functional entity from the second zipping oligonucleotide.

25. The method of claim 1, wherein the zipping oligonucleotides comprise from 3 to 20 nucleotides.

26. The method of claim 25, wherein the zipping oligonucleotides comprise from 4 to 16 nucleotides.

27. The method of claim 26, wherein the zipping oligonucleotides comprise from 5 to 10 nucleotides.

28. The method of claim 1, wherein the linker in the building block between the anti-codon and the zipping oligonucleotide is a single bond.

29. The method of claim 5, wherein the linker in the building block between the anti-codon and the zipping oligonucleotide is a single bond.

30. The method of claim 1, wherein the hybridization of the building block anti-codon(s) to the template codons results in the formation of a codon:

anti-codon hybrid, characterized by an annealing temperature, and the annealing temperature of the codon;

anti-codon hybrid is higher than the annealing temperature of the hybridized zipping oligonucleotides.

31. The method of claim 30, wherein the difference between the annealing temperatures is 10°

C. or more.

32. The method of claim 30, wherein the difference between the annealing temperatures is 25°

C. or more.

33. The method of claim 1, wherein the conditions for allowing specific hybridization of the building block anticodon(s) to the codon(s) of the template(s) are distinct from the conditions allowing for optimal dimerisation of the two zipping oligonucleotides.

34. The method of claim 33, wherein the conditions for allowing specific hybridization of the building block anti-codon(s) to the codon(s) of the template include a concentration of codons and/or anticodons, which is higher than the concentration of codons and/or anticodons used for dimerisation of the two zipping oligonucleotides.

35. The method of claim 34, wherein the concentration during hybridization of codon(s) and anti-codons is at least 10 times higher than the concentration used for dimerisation of the two zipping oligonucleotides.

36. The method of claim 1, wherein the contacting according to step d) is performed by alternating the temperature below and above the annealing temperature of the hybridized zipping oligonucleotides.

37. The method of claim 36, wherein a plurality of temperature alternations are performed.

38. The method of claim 36, wherein the highest temperature is below the annealing temperature of the codon:

anti-codon hybrid.

39. The method of claim 1, wherein the template codons have from 3 to 30 nucleotides.

40. The method of claim 1, wherein at least two codons of the template are arranged in sequence next to each other and are separated by a spacer group.

41. The method of claim 40, wherein the template comprises further codons.

42. The method of claim 41, wherein each further codon is separated by a spacer nucleotide sequence.

43. The method of claim 40, wherein each spacer nucleotide sequence identifies the position of a corresponding codon.

44. The method of claim 40, wherein the spacer nucleotide sequence contains a region of high affinity ensuring that the hybridization of the template with the anti-codon(s) occur in frame.

45. The method of claim 40, wherein the spacer nucleotide sequence adjusts the codon:

anti-codon annealing temperature.

46. The method of claim 1, wherein the number of template codons is from 2 to 100.

47. The method of claim 46, wherein the number of template codons is from 3 to 15.

48. The method of claim 1, wherein the functional entity of the building block is a precursor of the functional entity which is incorporated into the templated molecule.

49. The method of claim 48, wherein the structure of the functional entity is changed as a result of the incorporation of the functional entity into the templated molecule during its synthesis.

50. The method of claim 1, wherein a functional entity of the one or more building blocks has from 1 to 10 reactive groups.

51. The method of claim 50, wherein a building block featuring only one reactive group is used for generating end positions of polymers.

52. The method of claim 50, wherein building blocks having two reactive groups are used for generating the body part of a polymer.

53. The method of claim 50, wherein building blocks having two reactive groups are used for generating scaffolds capable of being reacted with further functional entities.

54. The method of claim 53, wherein functional entities having two or more reactive groups are used for reactions with a scaffold in the form of a core structure comprising several reactive groups, wherein said reactions result in the formation of different templated molecules.

55. The method of claim 53, wherein the reactions of the reactive groups are aided by fill-in groups or catalysts.

56. The method of claim 1, wherein the anti-codon, the linker and the second zipping oligonucleotide of the one or more building block(s) forms a contiguous, linear oligonucleotide.

57. The method of claim 1, wherein building block anti-codons are annealed to the template before the functional entities are connected to each other through a chemical reaction.

58. The method of claim 1, wherein individual building blocks are added separately and contacted with the template.

59. The method of claim 2, wherein building blocks contacting the template in a first reaction cycle result in the formation of codon:

anti-codon hybrids with a lower annealing temperature than the annealing temperature of the codon;

anti-codon hybrids which are formed when subsequently added, further building blocks are contacting the template in a second or further reaction cycle.

60. The method of claim 59, wherein the annealing temperature of codon:

anti-codon hybrids in the second or further reaction cycle results in maintaining only second or further round building blocks in contact with the template, while the majority of the anti-codons of previous synthesis round building blocks, or anti-codons of non-reacted building blocks, become single stranded and are displaced from the template.

61. The method of claim 2, wherein the anti-codon of a building block remain annealed to the template after the transfer of a building block functional entity to a scaffold and during a subsequent reaction cycle.

62. The method of claim 2, wherein the anti-codon of a reacted building block is removed from the template prior to a repetition of steps d) and e).

63. The method of claim 1 comprising the further step of transferring the templated molecule to an anchorage point on the template, or to a nucleotide sequence complementing the template, to establish a chemical connection between the template and the templated molecule which allows the even further steps of denaturing enrichment or denaturing post-templating modification of the templated molecule to be performed.

64. The method of claim 63, wherein the chemical connection is a covalent chemical bond.

65. The method of claim 63, wherein the hybrid formed between the complementing nucleotide sequence and the template has a higher annealing temperature than the annealing temperature of hybrid(s) formed between any of the building block anticodons and the template.

66. The method of claim 65, wherein stringency conditions are used during templated molecule enrichment which result in the clearance of used building blocks from the template.

67. The method of claim 1, wherein the first functional entity is a scaffold which is reacted with two or more functional entities.

68. The method of claim 67, wherein the scaffold is reacted with functional entities emanating from building blocks.

69. The method of claim 67, wherein the scaffold comprises two or more reactive groups.

70. The method of claim 67, wherein the scaffold remains attached to the template through-out the synthesis of the templated molecule.

71. The method of claim 1, wherein the scaffold forms part of a building block the anti-codon of which is annealed to a flanking position of the template, which flanking position is not located between the template codons.

72. The method of claim 1, wherein the template comprises two or more codons, and wherein said building blocks attached to said two or more codons through their anti-codons have identical, complementary zipping oligonucleotides capable of dimerising in an ordered way.

73. The method of claim 72, wherein the hybridization of codon(s) to anti-codon(s) and the dimerisation of zipping oligonucleotides occur in separate steps, wherein the conditions for specific hybridization of codon(s) to anti-codon(s) of the template(s) are distinct from the conditions for dimerisation of the zipping oligonucleotides.

74. The method of claim 73, wherein the step of dimerisation of the zipping oligonucleotides is carried out under conditions ensuring that codons and anti-codons remain attached and under conditions allowing a reaction between functional entities on different building blocks.

75. The method of claim 1, wherein the codon is a series of nucleotides in the form of nucleobases on a backbone, wherein said nucleobases are selected from the group consisting of natural nucleobases and non-natural nucleobases obeying Watson-Crick hydrogen bonding rules.

76. The method of claim 75, wherein the nucleobases are selected from the group consisting of adenine, guanine, thymine, cytosine, uracil, purine, xanthine, diaminopurine, 8-oxo-N⁶-methyladenine, 7-deazaxanthine, 7-deazaguanine, N⁴N⁴-ethanocytosin, N⁶,N⁶-ethano-2,6-diamino-purine, 5-methylcytosine, 5-(C³C⁶)-alkynylcytosine, 5-fluorouracil, 5-bromouracil, pseudoisocytosine, 2-hydroxy-5-methyl-4-triazolopyridine, isocytosine, isoguanine and inosine.

77. The method of claim 75, wherein the backbone contains a sugar moiety and an internucleoside linker.

78. The method of claim 77, wherein the backbone is a pentose selected from ribose, 2′

-deoxyribose, 2′

-O-methyl-ribose, 2′

-flour-ribose and 2′

-4′

-O-methylene-ribose (LNA).

79. The method of claim 78, wherein the nucleobase is attached to the 1′

position of the pentose.

80. The method of claim 78, wherein the internucleoside linker connects the 3′

end of a preceding monomer to a 5′

end of a succeeding monomer when the sugar moiety of the backbone is a pentose.

81. The method of claim 80, wherein the internucleoside linker is a phosphodiester bond.

82. The method of claim 80, wherein the internucleoside linker is a bond selected from phosphorothioate bonds, methylphosphonate bonds, phosphoramidate bonds, phosphotriester bonds and phosphodithioate bonds.

83. The method of claim 1, wherein the template is immobilised on a solid support.

84. The method of claim 83, wherein the solid support is a bead.

85. The method of claim 83, wherein a biotin group is incorporated in the template, and wherein the solid support is as matrix material coated with streptavidin.

86. The method of claim 1, wherein the first functional entity is linked to the template through a selectively cleavable linker which enables the separation of the synthesized, template-directed molecule from the template at a predetermined time.

87. The method of claim 86, wherein the first functional entity is a scaffold.

88. A method for generating a library of different bifunctional complexes, said method comprising the steps of subjecting a plurality of templates to the method according to claim 1, thereby generating a library of different bifunctional complexes each comprising a templated molecule attached to the template or complementary template which directed the synthesis of the templated molecule.

89. The method of claim 88, wherein the number of different bifunctional complexes in the library is at least 10³.

90. The method of claim 88, wherein the number of different bifunctional complexes in the library is at least 10⁶.

91. The method of claim 88, wherein the number of different bifunctional complexes in the library is at least 10⁹.

92. The method of claim 88, wherein a plurality of different templates is provided in step a) and wherein a plurality of different building blocks is provided in step c).

93. A method for generating a library of different bifunctional complexes, said method comprising the steps of subjecting a plurality of templates simultaneously to the method according to claim 1, thereby generating a library of different bifunctional complexes each comprising a templated molecule attached to the template or complementary template which directed the synthesis of the templated molecule.

94. The method of claim 88, wherein the templated molecules of the library are synthesized by sequentially contacting the templates with subsets of building blocks to be used in the synthesis if the templated molecules.

95. The method of claim 88, wherein each template comprises a number of coding sections, and wherein each coding section specifies one or more unique codons.

96. The method of claim 95, wherein the coding sections are positioned in a linear sequence with individual coding sections positioned immediately next to each other.

97. The method of claim 96, wherein the coding sections are interspaced by a spacer sequence.

98. The method of claim 95, wherein the template is branched.

99. The method of claim 95, wherein each template has from 2 to 50 coding regions.

100. The method of claim 95, wherein each template has from 3 to 30 coding regions.

101. The method of claim 95, wherein each template has from 4 to 15 coding regions.

102. The method of claim 99, wherein the number of unique codons in each coding region is the same.

103. The method of claim 99, wherein each coding region contains a different number of unique codons.

104. The method of claim 99, wherein each coding region contains a single unique codon.

105. The method of claim 88, comprising the further step of subjecting the library of bifunctional complexes to an enrichment comprising the steps of:

i) exposing the library to conditions enriching the library with complexes having a predetermined activity,

ii) amplifying the complexes of the enriched library, thereby obtaining amplification product(s),

iii) obtaining an enriched library having a higher ratio of complexes comprising templated molecules with the predetermined activity.

106. The method of claim 105, wherein the amplification of the complexes of the enriched library comprises the steps of contacting the library of complexes with amplification means, amplifying the templates or the complementing templates, and conducting the method using the amplification product(s) as templates.

107. The method of claim 105, wherein steps i) and ii) are repeated from 2 to 5 times.

108. The method of claim 107, wherein generated complexes are identified after the completion of each cycle of repetition.

109. The method of claim 107, wherein the complexes are identified after the last repetition cycle.

110. The method of claim 108, wherein the identification after the enrichment involves determination of the sequence of the template and/or structural determination of the templated molecule and/or the entire complex having the predetermined activity.

116. The method of claim 1, comprising the further step of contacting the templated molecule with a target molecule selected from receptors, enzymes, hormones, transcription factors, ion channels and DNA, and identifying a templated molecule contacting a target molecule as an agonist or an antagonist for the target molecule.

117. A bifunctional complex comprising a templated molecule attached to the template which directed the synthesis thereof, wherein said template is further attached to at least two zipping oligonucleotides capable of reversibly dimerizing in an ordered way, said bifunctional complex being obtainable by the method of claim 1, wherein at least one of the following conditions applies:

(i) the templated molecule is a beta-peptide,

(ii) the templated molecule is a gamma-peptide,

(iii) the templated molecule is an omega-peptide,

(iv) the templated molecule is a cyclohexane- and cyclopentanebackbone modified beta-peptide,

(v) the templated molecule is a vinylogous polypeptide,

(vi) the templated molecule is a peptide having prosthetic group(s),

(vii) the templated molecule is an aliphatic polycycle,

(viii) the templated molecule is an aromatic polycycle,

(ix) the templated molecule is a polyheterocycle,

(x) the templated molecule is a monofunctional, difunctional or trifunctional, nonaromatic carbocycle,

(xi) the templated molecule is a monocyclic, bicyclic or tricyclic hydrocarbon,

(xii) the templated molecule is a monofunctional, difunctional or trifunctional nonaromatic heterocycle,

(xiii) the templated molecule is a monocyclic, bicyclic or tricyclic heterocycles,

(xiv) the templated molecule is a bridged polycyclic heterocycle,

(xv) the templated molecule is a monofunctional, difunctional or trifunctional aromatic carbocycle,

(xvi) the templated molecule is a monocyclic, bicyclic or tricyclic aromatic carbocycle,

(xvii) the templated molecule is a monofunctional, difunctional or trifunctional aromatic heterocycle,

(xviii) the templated molecule is a monocyclic, bicyclic or tricyclic heterocycle, or

(xix) the templated molecule is a steroid.

118. The bifunctional complex according to claim 117, wherein the templated molecule is a beta-peptide.

119. The bifunctional complex according to claim 117, wherein the templated molecule is a gamma-peptide.

120. The bifunctional complex according to claim 117, wherein the templated molecule is an omega-peptide.

121. The bifunctional complex according to claim 117, wherein the templated molecule is a cyclohexane and cyclopentane-backbone modified beta-peptide.

122. The bifunctional complex according to claim 117, wherein the templated molecule is a vinylogous polypeptide.

123. The bifunctional complex according to claim 117, wherein the templated molecule is a peptide having prosthetic group(s).

124. The bifunctional complex according to claim 117, wherein the templated molecule is an aliphatic polycycle.

125. The bifunctional complex according to claim 117, wherein the templated molecule is an aromatic polycycle.

126. The bifunctional complex according to claim 117, wherein the templated molecule is a polyheterocycle.

127. The bifunctional complex according to claim 117, wherein the templated molecule is a monofunctional, difunctional or trifunctional, nonaromatic carbocycle.

128. The bifunctional complex according to claim 117, wherein the templated molecule is a monocyclic, bicyclic or tricyclic hydrocarbon.

129. The bifunctional complex according to claim 117, wherein the templated molecule is a monofunctional, difunctional or trifunctional nonaromatic heterocycle.

130. The bifunctional complex according to claim 117, wherein the templated molecule is a monocyclic, bicyclic or tricyclic heterocycles.

131. The bifunctional complex according to claim 117, wherein the templated molecule is a bridged polycyclic heterocycle.

132. The bifunctional complex according to claim 117, wherein the templated molecule is a monofunctional, difunctional or trifunctional aromatic carbocycle.

133. The bifunctional complex according to claim 117, wherein the templated molecule is a monocyclic, bicyclic or tricyclic aromatic carbocycle.

134. The bifunctional complex according to claim 117, wherein the templated molecule is a monofunctional, difunctional or trifunctional aromatic heterocycle.

135. The bifunctional complex according to claim 117, wherein the templated molecule is a monocyclic, bicyclic or tricyclic heterocycle.

136. The bifunctional complex according to claim 117, wherein the templated molecule is a steroid.

137. A library of different bifunctional complexes according to claim 117.

138. The library according to claim 137, wherein each bifunctional complex comprises a different templated molecule.

139. The library according to claim 137, wherein the number of different bifunctional complexes in the library is at least 10³.

140. The library according to claim 137, wherein the number of different bifunctional complexes in the library is at least 10⁶.

141. The library according to claim 137, wherein the number of different bifunctional complexes in the library is at least 10⁹.

142. A bifunctional complex comprising a templated molecule attached to the template which directed the synthesis thereof, wherein said template is further attached to at least two zipping oligonucleotides capable of reversibly dimerizing in an ordered way, said bifunctional complex being obtainable by the method of claim 1, wherein the templated molecule is not a polynucleotide.

143. The bifunctional complex according to claim 141, wherein the templated molecule is a monofunctional, difunctional or trifunctional open-chain hydrocarbon.

144. The bifunctional complex according to claim 141 wherein the templated molecule is a bridged polycyclic hydrocarbon.

145. The method of claim 1 wherein the chemical connection of the further functional entity to the first functional entity, referred to in steps (c) and (e), is a covalent connection.

111. The method of 105, wherein enrichment of library complexes is obtained by screening for complexes having an affinity for or an effect on a target molecule.

112. The method of claim 111, wherein the target molecule is selected from soluble receptors, cell surface receptors, enzyme inhibitors and surface epitopes.

113. The method of claim 111, wherein the target molecule is selected from receptors, enzymes, hormones, transcription factors, ion channels and DNA.

114. The method of claim 113, wherein the target molecule is selected from receptors and enzymes.

115. The method of claim 114, wherein the target molecule is selected from G protein coupled receptors and proteases.