Fused cyclooctyne compounds and their use in metal-free click reactions

Patent metadata

Field	Value
Publication number	US-12180145-B2
Application number	US-202217839202-A
Country	US
Kind code	B2
Filing date	Jun 13, 2022
Priority date	Apr 27, 2010
Publication date	Dec 31, 2024
Grant date	Dec 31, 2024

Abstract

The invention relates to fused cyclooctyne compounds, and to a method for their preparation. The invention also relates to a conjugate wherein a fused cyclooctyne compound according to the invention is conjugated to a label, and to the use of these conjugates in bioorthogonal labeling, imaging and/or modification, such as for example surface modification, of a target molecule. The invention further relates to a method for the modification of a target molecule, wherein a conjugate according to the invention is reacted with a compound comprising a 1,3-dipole or a 1,3-(hetero)diene.

First claim

The invention claimed is:

1. A method for producing a modified target molecule, the method comprising reacting a conjugate with a target molecule, wherein the target molecule comprises a 1,3-dipole which is an azide or a nitrone, and the conjugate is a compound of Formula (IIa), (IIb) or (IIc):

wherein:
n is 0 to 8;
p is 0 or 1;
R 3 is selected from the group consisting of [(L) p -Q], hydrogen, halogen, C 1 -C 24 alkyl groups, C 6 -C 24 (hetero)aryl groups, C 7 -C 24 alkyl(hetero)aryl groups and C 7 -C 24 (hetero)arylalkyl groups, the alkyl groups optionally being interrupted by one of more hetero-atoms selected from the group consisting of O, N and S, wherein the alkyl groups, (hetero)aryl groups, alkyl(hetero)aryl groups and (hetero)arylalkyl groups are independently optionally substituted with one or more substituents independently selected from the group consisting of C 1 -C 12 alkyl groups, C 2 -C 12 alkenyl groups, C 2 -C 12 alkynyl groups, C 3 -C 12 cycloalkyl groups, C 1 -C 12 alkoxy groups, C 2 -C 12 alkenyloxy groups, C 2 -C 12 alkynyloxy groups, C 3 -C 12 cycloalkyloxy groups, halogens, amino groups, oxo groups and silyl groups, wherein the alkyl groups, alkenyl groups, alkynyl groups, cycloalkyl groups, alkoxy groups, alkenyloxy groups, alkynyloxy groups and cycloalkyloxy groups are optionally substituted, the alkyl groups, the alkoxy groups, the cycloalkyl groups and the cycloalkoxy groups being optionally interrupted by one of more hetero-atoms selected from the group consisting of O, N and S, wherein the silyl groups are represented by the formula (R 4 ) 3 Si—, wherein R 4 is independently selected from the group consisting of C 1 -C 12 alkyl groups, C 2 -C 12 alkenyl groups, C 2 -C 12 alkynyl groups, C 3 -C 12 cycloalkyl groups, C 1 -C 12 alkoxy groups, C 2 -C 12 alkenyloxy groups, C 2 -C 12 alkynyloxy groups and C 3 -C 12 cycloalkyloxy groups, wherein the alkyl groups, alkenyl groups, alkynyl groups, cycloalkyl groups, alkoxy groups, alkenyloxy groups, alkynyloxy groups and cycloalkyloxy groups are optionally substituted, the alkyl groups, the alkoxy groups, the cycloalkyl groups and the cycloalkoxy groups being optionally interrupted by one of more hetero-atoms selected from the group consisting of O, N and S;
L is a linking group selected from linear or branched C 1 -C 24 alkylene groups, C 2 -C 24 alkenylene groups, C 2 -C 24 alkynylene groups, C 3 -C 24 cycloalkylene groups, C 5 -C 24 cycloalkenylene groups, C 8 -C 24 cycloalkynylene groups, C 7 -C 24 alkyl(hetero)arylene groups, C 7 -C 24 (hetero)arylalkylene groups, C 8 -C 24 (hetero)arylalkenylene groups, C 9 -C 24 (hetero)arylalkynylene groups, the alkylene groups, alkenylene groups, alkynylene groups, cycloalkylene groups, cycloalkenylene groups, cycloalkynylene groups, alkyl(hetero)arylene groups, (hetero)arylalkylene groups, (hetero)arylalkenylene groups and (hetero)arylalkynylene groups optionally being substituted with one or more substituents independently selected from the group consisting of C 1 -C 12 alkyl groups, C 2 -C 12 alkenyl groups, C 2 -C 12 alkynyl groups, C 3 -C 12 cycloalkyl groups, C 5 -C 12 cycloalkenyl groups, C 8 -C 12 cycloalkynyl groups, C 1 -C 12 alkoxy groups, C 2 -C 12 alkenyloxy groups, C 2 -C 12 alkynyloxy groups, C 3 -C 12 cycloalkyloxy groups, halogens, amino groups, oxo and silyl groups, wherein the silyl groups can be represented by the formula (R 4 ) 3 Si—, wherein R 4 is defined as above;
Q is bonded to a label or is a functional group selected from the group consisting of hydrogen, halogen, R 6 , —CH═C(R 6 ) 2 , —C≡CR 6 , —[C(R 6 ) 2 C(R 6 ) 2 O] q —R 6 , wherein q is in the range of 1 to 200, —CN, —N 3 , —NCX, —XCN, —XR 6 , —N(R 6 ) 2 , — + N(R 6 ) 3 , —C(X)N(R 6 ) 2 , —C(R 6 ) 2 XR 6 , —C(X)R 6 , —C(X)XR 6 , —S(O)R 6 , —S(O) 2 R 6 , —S(O)OR 6 , —S(O) 2 OR 6 , —S(O)N(R 6 ) 2 , —S(O) 2 N(R 6 ) 2 , —OS(O)R 6 , —OS(O) 2 R 6 , —OS(O)OR 6 , —OS(O) 2 OR 6 , —P(O)(R 6 )(OR 6 ), —P(O)(OR 6 ) 2 , —OP(O)(OR 6 ) 2 , —Si(R 6 ) 3 , —XC(X)R 6 , —XC(X)XR 6 , —XC(X)N(R 6 ) 2 , —N(R 6 )C(X)R 6 , —N(R 6 )C(X)XR 6 and —N(R 6 )C(X)N(R 6 ) 2 , wherein X is oxygen or sulphur and wherein R 6 is independently selected from the group consisting of hydrogen, halogen, C 1 -C 24 alkyl groups, C 6 -C 24 (hetero)aryl groups, C 7 -C 24 alkyl(hetero)aryl groups and C 7 -C 24 (hetero)arylalkyl groups;
R 1 is independently selected from the group consisting of hydrogen, C 1 -C 24 alkyl groups, C 6 -C 24 (hetero)aryl groups, C 7 -C 24 alkyl(hetero)aryl groups and C 7 -C 24 (hetero)arylalkyl groups; and
R 2 is independently selected from the group consisting of halogen, —OR 6 , —NO 2 , —CN, —S(O) 2 R 6 , C 1 -C 12 alkyl groups, C 1 -C 12 aryl groups, C 1 -C 12 alkylaryl groups and C 1 -C 12 arylalkyl groups, wherein R 6 is as defined above, and wherein the alkyl groups, aryl groups, alkylaryl groups and arylalkyl groups are optionally substituted;
wherein
the label is selected from the group consisting of nucleotides, peptides, glycans and pharmaceutical compounds; and
the target molecule is selected from the group consisting of peptides, proteins, glycans, lipids and nucleic acids.

2. The method according to claim 1 , wherein the label is a nucleotide selected from the group consisting of oligonucleotides and polynucleotides.

3. The method according to claim 1 , wherein the label is a glycan selected from the group consisting of oligosaccharides and polysaccharides.

4. The method according to claim 1 , wherein the target molecule is selected from the group consisting of peptides and proteins.

5. The method according to claim 4 , wherein the 1,3-dipole is an azide.

6. The method according to claim 1 , wherein the label is selected from the group consisting of nucleotides and peptides.

7. The method according to claim 1 , wherein the target molecule is selected from peptides and proteins, and wherein Q is bonded to the label.

8. The method according to claim 1 , wherein the 1,3-dipole is an N-methyl nitrone.

9. The method according to claim 1 , wherein the modified target molecule is of Formula (VIIIa), (VIIIb1), (VIIIb2), (VIIIc1) or (VIIIc2):

10. The method according to claim 1 , wherein the modified target molecule is of Formula (VIIIa) or (IXa):

11. The method according to claim 1 , wherein the modified target molecule is of Formula (VIIIa):

12. The method according to claim 1 , wherein p is 1 and L is CH 2 .

13. The method according to claim 1 , wherein R 1 is hydrogen.

14. The method according to claim 1 , wherein n is 0.

15. A modified target molecule produced by the method according to claim 1 .

16. The modified target molecule according to claim 15 , wherein the modified target molecule is of the Formula (VIIIa), (VIIIb1), (VIIIb2), (VIIIc1), (VIIIc2), (IXa), (IXb1), (IXb2), (IXc1) or (IXc2):

wherein:
n is 0 to 8;
p is 0 or 1;
R 3 is selected from the group consisting of [(L) p -Q], hydrogen, halogen, C 1 -C 24 alkyl groups, C 6 -C 24 (hetero)a

Assignees

• Synaffix Bv

Inventors

• Van Delft Floris Louis
• Theodorus Rutjes Floris Petrus Johannes
• Dommerholt Frederik Jan

Classifications

• G01N2021/6439

  with indicators, stains, dyes, tags, labels, marks · CPC title

• G01N21/6428

  Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" (in vivo A61B5/00; immunoassay G01N33/53) · CPC title

• G01N33/582

  with fluorescent label · CPC title

• C07K14/47

  from mammals · CPC title

• C07D495/04

  Ortho-condensed systems · CPC title