Morpholino-subunit combinatorial library and method

• US 5,698,685 A
• Filed: 03/31/1995
• Issued: 12/16/1997
• Est. Priority Date: 03/15/1985
• Status: Expired due to Fees

• Current Assignee: AntiVirals, Inc. (Sarepta Therapeutics, Inc.)
• Original Assignee: AntiVirals, Inc. (Sarepta Therapeutics, Inc.)
• Inventors: Weller, Dwight D., Summerton, James E.
• Primary Examiner(s): Nutter, Nathan M.
• Application Number:
  US08/414,018
• Time in Patent Office: 991 Days
• Field of Search: 536/24.3, 435/6
• US Class Current: 506/2
• CPC Class Codes: A61K 47/545 Heterocyclic compounds A61K47/558 takes precedence
• CPC Class Codes: A61K 47/548 Phosphates or phosphonates, e.g. bone-seeking phospholipids A61K47/544
• CPC Class Codes: A61K 47/59 obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
• CPC Class Codes: A61K 47/60 the organic macromolecular compound being a polyoxyalkylene oligomer, polymer or dendrimer, e.g. PEG, PPG, PEO or polyglycerol
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: C07D 417/14 containing three or more hetero rings
• CPC Class Codes: C07D 473/00 Heterocyclic compounds containing purine ring systems
• 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: C07K 14/003 Peptide-nucleic acids (PNAs)
• CPC Class Codes: C08G 79/02 a linkage containing phosphorus
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6839 Triple helix formation or other higher order conformations in hybridisation assays

Abstract

A method of generating a compound capable of interacting specifically with a selected macromolecular ligand is disclosed. The method involves contacting the ligand with a combinatorial library of oligomers composed of morpholino subunits with a variety of nucleobase and non-nucleobase side chains. Oligomer molecules that bind specifically to the receptor are isolated and their sequence of base moieties is determined. Also disclosed is a combinatorial library of oligomers useful in the method and novel morpholino-subunit polymer compositions.

Claims

1. A method of generating a compound capable of interacting specifically with a selected receptor, comprising

(a) contacting the receptor with a combinatorial library of oligomers, each formed of at least four morpholino subunits of the form:

##STR4## in which (i) morpholino subunits are linked together by oligomer linkages L one to four atoms long joining the morpholino nitrogen of one subunit to the 4'"'"' cyclic carbon of an adjacent subunit, (ii) X_i is a side chain in subunit i in each oligomer of the library, (iii) the different oligomers in the library have different sequences of side chains in at least three subunit positions, (iv) X_i is selected from the group consisting of purines, pyrimidines, non-nucleobase aromatic side chains, aliphatic side chains, and mixed aromatic/aliphatic side chains, and (v) said library contains at least 1,000 different side chain sequence oligomers,

(b) isolating oligomer molecules that bind specifically to the receptor, and

(c) determining the sequence of oligomer side chains in the isolated oligomer molecules.

2. The method of claim 1, wherein oligomer linkages in the library include one-atom linkages of the form:

##STR5## where X_i+1 is a side chain in a subunit adjacent subunit i.

3. The method of claim 1, wherein oligomer linkages in the library include amide-containing linkages of the form:

##STR6##

4. The method of claim 1, wherein oligomer side chains in the library include some side chains selected from the group consisting of purines and pyrimidines, and some side chains selected from the group consisting of a non-nucleobase aromatic side chains, aliphatic side chains, and mixed aromatic/aliphatic side chains.

5. The method of claim 1, wherein said oligomers are designed to hybridize, by Watson-Crick base pairing, to random-sequence oligonucleotides, and said determining includes reacting the isolated oligomer molecules with a combinatorial library of oligonucleotides, under conditions effective to produce hybridization between the isolated oligomer molecules and complementary-base oligonucleotides, and determining the sequence of the oligonucleotides hybridized to the isolated oligomer molecules.

6. The method of claim 1, wherein the combinatorial library is formed on a plurality of particles, each particle having a surface coating of oligomer molecules containing one of the side chain-sequences in the library, said isolating includes isolating a particle having surface-bound receptor, and said determining includes determining the sequence of side chains of the oligomer molecules on the isolated particle.

7. The method of claim 6, wherein said isolating includes contacting particles having surface-bound receptor with a solid surface having surface-bound anti-receptor molecules effective to bind specifically to the receptor, and isolating particles bound to the solid surface.

8. The method of claim 7, wherein the oligomer molecules on each bead are carried on dendritic polymers attached to the particles and coupled to the oligomer molecules through cleavable linkages.

9. The method of claim 8, wherein said determining includes analyzing the side chain sequence of the isolated oligomer molecules by mass spectrometry.

10. The method of claim 1, for use in generating an oligomer effective to bind selectively to an known antibody, wherein each oligomer forming the library is bivalent, and said isolating includes immunoprecipitating antibody-bound oligomers from a solution of the library oligomers.