Encoded self-assembling chemical libraries (ESACHEL)
View Patent ↗The invention provides a chemical compound comprising a chemical moiety (p) capable of performing a binding interaction with a target molecule, and an oligonucleotide (b) or functional analogue thereof. The oligonucleotide (b) or functional analogue comprises at least one self-assembly sequence (b1) capable of performing a combination reaction with at least one self-assembly sequence (b1′) of a complementary oligonucleotide or functional analogue bound to another chemical compound comprising a chemical moiety (q). In some embodiments, the chemical compound comprises a coding sequence (b1) coding for the identification of the chemical moiety (p) and further comprises at least one self-assembly moiety (m) capable of performing a combination reaction with at least one self-assembly moiety (m′) of a similar chemical compound comprising a chemical moiety (q). The invention also provides corresponding libraries of chemical compounds as well as methods of biopanning of for target molecules and of identifying such targets.
1. A chemical library comprising stable combination reaction products between a first number of chemical compounds of a sub-library A with a sub-library B of chemical compounds, wherein the compounds of the sub-library A comprise:
(i) a chemical moiety (p) capable of performing a binding interaction with a single target molecule, and
(ii) an oligonucleotide (b) or functional analogue thereof, which comprises a variable, unique distinctive sequence tag (b2) coding for the identification of the chemical moiety (p) of its compound and a common self-assembly sequence (b1) capable of performing a combination reaction and of building a stable combination reaction product with a common self-assembly sequence (b1′) of a plurality of chemical compounds of the sub-library B, wherein the sub-library B comprises a second number of chemical compounds each comprising:
(i) a chemical moiety (q) capable of performing a binding interaction with a single target molecule, and
(ii) an oligonucleotide (b′) or functional analogue thereof, which comprises a variable, unique distinctive sequence tag (b2′) coding for the identification of the chemical moiety (q) of its compound, and the common self-assembly sequence (b 1′),
wherein the chemical moieties (p,q) are peptides or globular proteins.
2. The chemical library of claim 1 , wherein the chemical compounds of sub-library A and sub-library B are capable to form stable combination reaction products in the absence of said target molecule(s).
3. The chemical library of claim 1 , wherein sub-library A and sub-library B each comprise at least four chemical compounds.
4. The chemical library of claim 1 , wherein the chemical compounds of each sub-library comprise a different chemical moiety (p,q) than other members of the respective sub-library.
5. The chemical library of claim 1 , wherein the chemical moieties (p) of sub-library A are coupled to a 3′ extremity of the oligonucleotide (b1), and wherein the chemical moieties (q) of sub-library B are coupled to a 5′ extremity of the oligonucleotide (b1′).
6. The chemical library of claim 1 , wherein said stable combination reaction products are derived by forming oligomers selected from the group comprising dimers, trimers, and tetramers, by hetero-oligomerization of the self-assembly sequences (b1,b1′) of the oligonucleotides (b,b′), thereby forming heteroduplexes, heterotriplexes or heteroquadruplexes.
7. The chemical library of claim 1 , wherein in sub-library A or in sub-library B, iodoacetamido- or maleimido-derivatives of the respective chemical moieties have been coupled to individual DNA oligonucleotides which carry a thiol group at the 3′ or 5′ extremity.
8. The chemical library of claim 1 , wherein in sub-library A or in sub-library B, amide derivatives —forming chemical structures according to the formula —O—P(O) 2 —O—(CH 2 )n-NH—CO—R, where R corresponds to a number of different chemical entities, and n ranges between 1 and 10—are coupled to the oligonucleotides carrying a phosphodiester bond at one extremity.
9. The chemical library of claim 1 , wherein in sub-library A the self-assembly sequence (b1) is interrupted by a d-spacer, the d-spacer preventing any undesired pairing to the bases of distinctive sequence tag (b2′) which encodes sub-library B, and wherein the oligonucleotide (b) of sub-library A has its distinctive sequence tag (b2) towards the 5′ extremity.
10. The chemical library of claim 1 , wherein each chemical compound of sub-library A further comprises at least one chemical group that is capable of forming a covalent bond with at least one chemical group of a chemical compound of sub-library B with which had been formed a stable combination reaction product.
11. The chemical library of claim 1 , wherein in sub-library A, each oligonucleotide (b) or functional analogue thereof is directly and covalently linked to a chemical moiety (p) and wherein in sub-library B, each oligonucleotide (b′) of or functional analogue thereof is directly and covalently linked to a chemical moiety (q).
12. The chemical library of claim 1 , wherein in the chemical compounds of sub-library A and sub-library B, the respective oligonucleotides (b,b′) or functional analogues thereof further each comprise a linking portion which is situated between the respective self-assembly sequences (b1,b1′) and the respective chemical moieties (p,q).
13. The chemical library of claim 1 , wherein the sequences of the distinctive sequence tags (b2,b2′) of each oligonucleotide (b,b′) or the functional analogues thereof are situated between their respective chemical moieties (p,q) and their respective self-assembly sequences (b1,b1′).
14. The chemical library of claim 1 , wherein in the stable combination reaction products between members of a sub-library A with a sub-library B, the respective members in each stable combination reaction product are covalently linked to each other.
15. A chemical compound or sub-library A of chemical compounds, the chemical compound or each chemical compound of said sub-library A comprising:
(i) a chemical moiety (p) capable of performing a binding interaction with a single target molecule, and
(ii) an oligonucleotide (b) or functional analogue thereof, both of which comprise a variable, unique distinctive sequence tag (b2) coding for the identification of the chemical moiety (p),
wherein the chemical compound or each chemical compound of said sub-library A further comprises a common self-assembly sequence (b1) capable of performing a combination reaction and of building, in the absence of said target molecule, a stable combination reaction product with a common self-assembly sequence (b1′) of a plurality of chemical compounds of a sub-library B with a chemical moiety (q) and an oligonucleotide (b′) or functional analogue thereof, and
wherein the chemical moieties (p,q) are peptides or globular proteins.
16. The chemical library of claim 1 , wherein both chemical moieties (p,q) of the stable combination reaction product of one chemical compound of sub-library A and of one chemical compound of sub-library B bind to the same target molecule.
17. The chemical library of claim 1 , wherein the chemical moiety (p) and the chemical moiety (q) are not covalently linked.