Bio-oligomer libraries and a method of use thereof

• US 5,858,670 A
• Filed: 10/23/1996
• Issued: 01/12/1999
• Est. Priority Date: 07/02/1990
• Status: Expired due to Fees

• Current Assignee: Aventis Pharmaceuticals Incorporated (Sanofi )
• Original Assignee: Arizona Board of Regents (University of Arizona)
• Inventors: Lam, Kit Sang, Salmon, Sydney E.
• Primary Examiner(s): Sisson, Bradley L.
• Application Number:
  US08/735,623
• Time in Patent Office: 811 Days
• Field of Search: 435/6, 435/7.1, 435/7.5, 435/7.92, 435/91.1, 436/501, 436/523, 436/524, 436/531, 530/300, 530/322, 530/333, 530/335, 530/344, 530/387.1, 536/23.1, 536/24.3, 536/24.33, 536/25.3, 935/77, 935/5, 935/17
• US Class Current: 435/6.16
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61K 39/00 Medicinal preparations containing antigens or antibodies materials for immunoassay G01N33/53
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00592 Split-and-pool, mix-and-divide processes
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00729 Peptide nucleic acids [PNA]
• CPC Class Codes: C07K 1/047 Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C07K 14/70 Enkephalins
• CPC Class Codes: C07K 14/82 Translation products from oncogenes
• CPC Class Codes: C07K 16/26 against hormones ; against hormone releasing or inhibiting factors
• CPC Class Codes: C07K 16/32 against translation products of oncogenes
• CPC Class Codes: C07K 2317/34 Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
• CPC Class Codes: C07K 2317/92 Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
• CPC Class Codes: C12N 15/1062 mRNA-Display, e.g. polypeptide and encoding template are connected covalently
• CPC Class Codes: C12N 15/1075 by coupling phenotype to genotype, not provided for in other groups of this subclass
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: Y02P 20/55 : Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
• CPC Class Codes: Y10S 530/806 : Antigenic peptides or proteins
• CPC Class Codes: Y10S 530/812 : Peptides or proteins is immobilized on, or in, an organic carrier
• CPC Class Codes: Y10S 530/817 : Entrapped within the carrier, e.g. gel, hollow fibre

Abstract

The instant invention provides a library of bio-oligomers of defined size and known composition, in which the library contains all of the possible sequences of the bio-oligomers, and a method of synthesis thereof. The bio-oligomers of the library may be peptides, nucleic acids, or a combination of the foregoing. The instant invention also provides methods to identify bio-oligomers from a library that demonstrate desired characteristics such as binding, bioactivity and catalytic activity. Thus the instant invention provides a unique and powerful method to identify a useful bio-oligomer sequences from a library more quickly than current state-of-the-art technology allows. Effector molecules for use in treatment or diagnosis of disease are also provided.

Claims

1. A method for determining the chemical structure of a bio-oligomer ligand for an acceptor molecule comprising the steps of:

(a) introducing to a library of bio-oligomers attached to solid phase supports wherein each solid chase support is attached to a single wholly deprotected bio-oligomer species, an acceptor molecule of interest such that said acceptor molecule will recognize and bind to one or more solid phase support/bio-oligomer species within the library;

(b) isolating a solid phase support/bio-oligomer combination that exhibits binding with the acceptor molecule; and

(c) determining the chemical structure of the bio-oligomer of the solid phase support/bio-oligomer isolated in step (b).

2. The method of claim 1 in which the acceptor molecule is selected from the group consisting of antibodies, receptors, viruses, bacteria, proteins, carbohydrates, nucleic acids, lipids, drugs, metals and small molecules.

3. The method according to claim 2 in which the acceptor molecule is an antibody.

4. The method according to claim 2 in which the acceptor molecule is a receptor.

10. A method for determining the chemical structure of a bio-oligomer which inhibits an enzyme catalyzed reaction comprising:

(a) generating a bio-oligomer library of claim 1 in which the solid phase support is modified;

(b) releasing a portion of the bio-oligomers from the solid phase support/bio-oligomer combination in situ;

(c) detecting inhibition of the enzyme catalyzed reaction of interest in situ;

(d) isolating a solid phase support/bio-oligomer combination detected in step (c);

(e) determining the chemical structure of the bio-oligomer remaining on the solid phase support/bio-oligomer isolated in step (d).

12. The method according to claim 1, 5, 10, or 11 in which the subunits are selected from the group consisting of amino acids, amino acid analogs, and peptidomimetics.

13. The method according to claim 1, 5, 10, or 11 in which the subunits are linked by a bond selected from the group consisting of amide, ester, ether bonds and combinations thereof.

5. A method for determining the chemical structure of a biologically active bio-oligomer ligand comprising the steps of:

(a) subdividing a bio-oligomer library comprising a multiplicity of solid phase supports, wherein a single deprotected bio-oligomer species is attached to each solid phase support, and in which the library is prepared by a method comprising repeating k times, wherein k is at least three, the steps of;

(i) providing at least two aliquots of a solid phase support, in which the solid phase support comprises a linker selected from the group consisting of a selectively cleavable linker, a plurality of selectively cleavable linkers, or a combination of a non-cleavable linker and a selectively cleavable linker, by means of which the bio-oligomer can be attached covalently;

(ii) separately introducing a species of subunits of the bio-oligomers to each of the aliquots of solid phase supports such that a different subunit is introduced to each aliquot, at least one of said subunits having a protecting group or a plurality of protecting groups;

(iii) completely covalently coupling the subunit to the reactive sites of the solid phase support;

(iv) thoroughly mixing and deprotecting the aliquots of the solid phase supports whereby a reactive site is provided; and

, after repeating steps (ii) through (iv) k times, a final step of removing any protecting groups such that the deprotected bio-oligomer remains covalently attached to the solid phase supports in which the solid phase support is modified so that a portion of bio-oligomer can be released;

(b) releasing a portion of the bio-oligomers from the solid phase support/bio-oligomer by cleavage of a clearable linker;

(c) detecting the biological activity of the released bio-oligomer interest in situ;

(d) isolating a solid phase support/bio-oligomer combination that exhibits the specific biological activity of interest; and

(e) determining the chemical structure of the bio-oligomer remaining on the solid phase support/bio-oligomer isolated in step (d).

6. The method according to claim 5 in which the solid support is modified to be acid-sensitive, base-sensitive, nucleophilic-sensitive, photosensitive, electrophilic-sensitive, oxidation-sensitive, or reduction-sensitive.

7. The method according to claim 5 in which the solid phase support comprises a linker which is acid-sensitive, base-sensitive, nucleophilic-sensitive, electrophilic-sensitive, photosensitive, oxidation-sensitive, or reduction-sensitive.

8. The method according to claim 5 in which the in situ release of step (b) is affected by enzymatic cleavage, chemical clevage or a photochemical cleavage.

9. The method according to claim 5 in which the detection of step (c) is of a biological activity selected from the group consisting of cytotoxicity, antitumor activity, antibacterial activity, antiviral activity, antifungal activity, anti-parasite activity, growth factor activity, growth inhibitory activity, hormone activity, neurotransmitter activity, immunomodulator activity and regulatory activity.

11. A method for determining the chemical structure of a bio-oligomer ligand for an acceptor molecule comprising the steps of:

(a) introducing, to a bio-oligomer library comprising a multiplicity of solid phase supports, wherein a single deprotected bio-oligomer species is attached to each solid phase support, and which the library is prepared by a method comprising repeating k times, wherein k is at least three, the steps of;

(i) providing at least two aliquots of a solid phase support said supports having a reactive site to which a species of subunit of the bio-oligomer can be covalently coupled;

(ii) separately introducing a species of subunits of the bio-oligomers to each of the aliquots of solid phase supports such that a different subunit is introduced to each aliquot, at least one of said subunits having a protecting group or a plurality of protecting groups;

(iii) completely covalently coupling the subunit to the reactive sites of the solid phase support;

(iv) thoroughly mixing and deprotecting the aliquots of the solid phase supports whereby a reactive site is provided; and

, after repeating steps (ii) through (iv) k times, a final step of removing any protecting groups such that the deprotected bio-oligomer remains covalently attached to the solid phase supports,

an acceptor molecule of interest such that said acceptor molecule will recognize and bind to one or more solid phase support/bio-oligomer species within the library;

(b) isolating a solid phase support/bio-oligomer combination that exhibits binding with the acceptor molecule; and

(c) determining the chemical structure of the bio-oligomer of the solid phase support/bio-oligomer isolated in step (b).