Granted Patent B2

US 12,649,918 · App. 17/542,196 · Granted Jun 9, 2026

Inventors: Alex Haahr Gouliaev (Veksø Sjælland, DK); Thomas Franch (Snekkersten, DK); Michael Anders Godskesen (Vedbæk, DK); Kim Birkebæk Jensen (Rødovre, DK)

Assignee: Nuevolution A/S

C12N15/1065C12N15/1068

Abstract

Claims (53)

1 . A method for the synthesis of a bi-functional complex comprising a molecule part and an identifier oligonucleotide part identifying the molecule part, the identifier oligonucleotide part comprising a first identifier oligonucleotide tag and a second identifier oligonucleotide tag which identify a first reactive compound building block and a second reactive compound building block, respectively,

said method comprising the steps of

i) linking the first identifier oligonucleotide tag comprising a chemical reaction site to a solid support,

ii) reacting in an organic solvent the first reactive compound building block with the chemical reaction site,

iii) reacting in an organic solvent the second reactive compound building block with the chemical reaction site and/or with the first reactive compound building block, and

iv) enzymatically ligating in an aqueous medium the first identifier oligonucleotide tag and the second identifier oligonucleotide tag,

wherein said reactive compound building block reactions generate the molecule part of the bi-functional complex, and wherein said enzymatic ligation of said oligonucleotide tags generates the identifier oligonucleotide part of the bi-functional complex, and wherein the bifunctional complex is linked to the solid support.

2 . The method of claim 1 , wherein the link between the first identifier oligonucleotide tag and the solid support is a non-covalent linker.

3 . The method of claim 1 , wherein the first identifier oligonucleotide tag is protected by one or more protection groups.

4 . The method of claim 1 , wherein reactive groups of the first identifier oligonucleotide tag are protected by protection groups during reaction of one or more reactive compound building blocks.

5 . The method of claim 1 , wherein the first identifier oligonucleotide tag is synthesised on the solid support.

6 . The method of claim 1 , wherein the first identifier oligonucleotide tag is protected by one or more protection groups in at least one reactive compound building block reaction to prevent interaction between an oligonucleotide tag and at least one reactive compound building block.

7 . The method of claim 1 , wherein the first identifier oligonucleotide tag is protected by one or more protection groups from the organic solvent used in the reaction of a reactive compound building block.

8 . The method of claim 1 , wherein the molecule part has a molecular weight of less than 500 Da.

9 . The method of claim 1 , wherein the molecule part has a c log P value of from-1 to 5.

10 . The method of claim 1 , wherein the molecule part comprises a scaffold comprising a cyclic or non-cyclic structure.

11 . The method of claim 1 , wherein the molecule part comprises structural elements selected from linear, branched and cyclical structural elements, including a combination thereof.

12 . The method of claim 1 , wherein the molecule part comprises a single ring system or fused ring system, wherein one or more heteroatoms are optionally present in the system.

13 . The method of claim 12 , wherein the single ring system is a cycloalkyl, heterocycloalkyl, aryl, or a heteroaryl ring having from three to eight ring atoms.

14 . The method of claim 12 , wherein the fused ring system is a fused aryl or cyclyl ring having from two to six fused rings independently selected from aryl, heteroaryl, cycloalkyl, heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl, wherein each ring is substituted or unsubstituted and has from four to fourteen ring atoms.

15 . The method of claim 1 , wherein the molecule part comprises a system selected from a monocyclic system, a bicyclic system, a tricyclic system, a spirocyclic system and a fused bicyclic system, wherein said cyclic systems optionally comprise carbon atoms, silicon atoms, nitrogen atoms, phosphorous atoms, oxygen atoms, sulfur atoms, and wherein each cyclic system is optionally substituted by one or more substituents.

16 . The method of claim 1 , wherein one or more reactive compound building blocks are reacted using one or more reactions selected from the group of chemical reactions consisting of an acylation reaction, an alkylation reaction, a vinylation reaction, an alkenylidation reaction, a HWE reaction, a Wittig reaction, a transition metal catalyzed reaction, a transition metal catalyzed arylation reaction, a transition metal catalyzed hetarylation reaction, a transition metal catalyzed vinylation compound building block under suitable conditions to form one or more carbon-nitrogen bond(s);

e) isocyanate groups and complementary hydroxyl groups; wherein a reactive compound building block comprising one or more isocyanate-group(s) react with a complementary reactive compound building block comprising one or more hydroxyl-groups under suitable conditions to form one or more carbon-oxygen bond(s);

f) amino groups and complementary carbonyl groups; wherein a reactive compound building block comprising one or more amino groups react with a complementary reactive compound building block comprising one or more carbonyl-group(s), including aldehyde and/or ketone group(s); wherein the amines react with said carbonyl group(s) via reductive amination to form a carbon-nitrogen bond;

g) phosphorous ylide groups and complementary aldehyde and/or ketone groups;

wherein a reactive compound building block comprising a phosphorus-ylide-group react with an aldehyde and/or a ketone-group of a complementary reactive compound building block under suitable conditions to form a carbon-carbon double bond;

h) reactive alkynes and organic azides, which react under suitable conditions to form a triazole ring structure;

i) alkyl halide groups and one or more nucleophile group(s) selected from the group consisting of amino groups, hydroxyl groups and carboxyl group; wherein such groups react under suitable conditions to form a carbon-nitrogen bond or a carbon oxygen bond; and

j) halogenated heteroaromatic groups and one or more nucleophile group(s), wherein said groups are linked under suitable conditions via aromatic nucleophilic substitution,

reaction, a palladium catalyzed reaction, a palladium catalyzed arylation reaction, a palladium catalyzed hetarylation reaction, a palladium catalyzed vinylation reaction, a reaction using boronic acid or boronic acid ester, a reaction using aryl iodide, a reaction using an enamine, a reaction using enolether, a Diels-Alder reaction, a 1,3-dipolar cycloaddition reaction, a reaction using EDC, and a reaction using 4-(4,6-dimethoxy-1,3,5-thiazin-2-yl)-4-methylmorpholinium chloride (DMTMM), including combinations of the aforementioned reactions.

17 . The method of claim 1 , wherein reactive groups of the chemical reaction site and/or reactive group(s) of one or more reactive compound building blocks reacting with each other and/or with the chemical reaction site are selected from the group consisting of:

a) activated carboxyl groups, reactive sulfonyl groups and reactive phosphonyl groups, or a combination thereof, and complementary primary or secondary amino groups; wherein the complementary reactive groups react under suitable conditions to form amide, sulfonamide and/or phosphoramidate bonds;

b) epoxide groups and complementary primary and/or secondary amino groups; wherein a reactive compound building block comprising one or more epoxide reactive group(s) react with one or more amine-group(s) of a complementary reactive compound building block under suitable conditions to form one or more carbon-nitrogen bond(s);

c) aziridine groups and complementary primary or secondary amino groups; wherein, under suitable conditions, a reactive compound building block comprising one or more aziridine-group(s) react with one or more amine-group(s) of a complementary reactive compound building block to form one or more carbon-nitrogen bond(s);

d) isocyanate groups and complementary primary or secondary amino groups, wherein a reactive compound building block comprising one or more isocyanate-group(s) react with one or more amino-group(s) of a complementary reactive compound building block under suitable conditions to form one or more carbon-nitrogen bond(s);

e) isocyanate groups and complementary hydroxyl groups; wherein a reactive compound building block comprising one or more isocyanate-group(s) react with a complementary reactive compound building block comprising one or more hydroxyl-groups under suitable conditions to form one or more carbon-oxygen bond(s);

f) amino groups and complementary carbonyl groups; wherein a reactive compound building block comprising one or more amino groups react with a complementary reactive compound building block comprising one or more carbonyl-group(s), including aldehyde and/or ketone group(s); wherein the amines react with said carbonyl group(s) via reductive amination to form a carbon-nitrogen bond;

g) phosphorous ylide groups and complementary aldehyde and/or ketone groups; wherein a reactive compound building block comprising a phosphorus-ylide-group react with an aldehyde and/or a ketone-group of a complementary reactive compound building block under suitable conditions to form a carbon-carbon double bond;

h) reactive alkynes and organic azides, which react under suitable conditions to form a triazole ring structure;

i) alkyl halide groups and one or more nucleophile group(s) selected from the group consisting of amino groups, hydroxyl groups and carboxyl group; wherein such groups react under suitable conditions to form a carbon-nitrogen bond or a carbon oxygen bond; and

j) halogenated heteroaromatic groups and one or more nucleophile group(s), wherein said groups are linked under suitable conditions via aromatic nucleophilic substitution.

18 . The method of claim 1 comprising the further step of cleaving the bi-functional complex from the solid support.

19 . The method of claim 18 comprising the further steps of reacting the bi-functional complex with one or more further reaction compound building blocks and one or more oligonucleotide tags identifying said building block(s).

20 . The method of claim 18 comprising the further step of binding the bi-functional complex to a biological target.

21 . The method of claim 19 comprising the further step of binding the bi-functional complex to a biological target.

22 . The method of claim 1 , wherein the first reactive compound building block and the second reactive compound building block are not a nucleotide, an oligonucleotide, or a polynucleotide.

23 . The method of claim 1 , wherein the first identifier oligonucleotide tag and the second identifier oligonucleotide tag are linked by a covalent bond.

24 . The method of claim 1 , wherein the first identifier oligonucleotide tag and the second identifier oligonucleotide tag are directly linked by a covalent bond.

25 . The method of claim 1 , wherein the first identifier oligonucleotide tag and the second identifier oligonucleotide tag are directly linked by a covalent bond through a 3′ end of the first identifier oligonucleotide tag and a 5′ end of the second identifier oligonucleotide tag.

26 . The method of claim 1 , wherein the second identifier oligonucleotide tag is not directly linked to the molecule part.

27 . The method of claim 1 , wherein the first identifier oligonucleotide tag is linked to the second identifier oligonucleotide tag and the molecule part.

28 . The method of claim 1 , wherein the molecule part and the identifier oligonucleotide part are linked by a selectively cleavable linker moiety.

29 . The method of claim 1 , wherein the first identifier oligonucleotide tag is linked to the solid support through a non-covalent bond.

Assignments (1)

Priority Claims (1)

Continuity (3)

References Cited (400)