Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving antigen-antibody binding – specific binding protein...
Reexamination Certificate
1996-11-22
2001-04-03
Venkat, Jyothsna (Department: 1627)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving antigen-antibody binding, specific binding protein...
C435S004000, C436S501000, C436S518000, C436S524000, C436S528000, C436S529000, C436S530000, C436S531000, C436S164000, C436S182000
Reexamination Certificate
active
06210900
ABSTRACT:
FIELD OF THE INVENTION
The field of this invention concerns combinatorial chemistry which involves the syntheses of one or more encoded combinatorial libraries where large numbers of products having varying compositions are obtained. This invention also relates to methods of encoding combinatorial libraries.
BACKGROUND OF THE INVENTION
In the continuing search for new chemical moieties that can effectively modulate a variety of biological processes, the standard method for conducting a search is to screen a variety of pre-existing chemical moieties, for example, naturally occurring compounds or compounds which exist in synthetic libraries or databanks. The biological activity of the pre-existing chemical moieties is determined by applying the moieties to an assay which has been designed to test a particular property of the chemical moiety being screened, for example, a receptor binding assay which tests the ability of the moiety to bind to a particular receptor site.
In an effort to reduce the time and expense involved in screening a large number of randomly chosen compounds for biological activity, several developments have been made to provide libraries of compounds for the discovery of lead compounds. The chemical generation of molecular diversity has become a major tool in the search for novel lead structures. Currently, the known methods for chemically generating large numbers of molecularly diverse compounds generally involve the use of solid phase synthesis, in particular to synthesize and identify peptides and peptide libraries. See, for example, Lebl et al.,
Int. J. Pept. Prot. Res.,
41, p. 201 (1993) which discloses methodologies providing selectively cleavable linkers between peptide and resin such that a certain amount of peptide can be liberated from the resin and assayed in soluble form while some of the peptide still remains attached to the resin, where it can be sequenced; Lam et al.,
Nature,
354, p. 82 (1991) and (WO 92/00091) which disclose a method of synthesis of linear peptides on a solid support such as polystyrene or polyacrylamide resin; Geysen et al.,
J. Immunol. Meth.,
102, p. 259 (1987) which discloses the synthesis of peptides on derivatized polystyrene pins which are arranged on a block in such a way that they correspond to the arrangement of wells in a 96-well microtiter plate; and Houghten et al.,
Nature,
354, p. 84 (1991) and WO 92/09300 which disclose an approach to de novo determination of antibody or receptor binding sequences involving soluble peptide pools.
The major drawback, aside from technical considerations, with all of these methods for lead generation is the quality of the lead. Linear peptides historically have represented relatively poor leads for pharmaceutical design. In particular, there is no rational strategy for conversion of a linear peptide into a non-peptide lead. As noted above, one must resort to screening large databanks of compounds, with each compound being tested individually, in order to determine non-peptide leads for peptide receptors.
It is known that a wide variety of organic reactions can be carried out on substrates immobilized on resins. These include, in addition to peptide synthesis reactions which are well known to those of ordinary skill in the art, nucleophilic displacements on benzylic halides, halogenation, nitration, sulfonation, oxidation, hydrolysis, acid chloride formation, Friedel-Crafts reactions, reduction with LiAlH
4
, metallation, and reaction of the organometallic polymer with a wide variety of reagents. See, for example, N. K. Mathur et al.,
Polymers as Aids in Organic Chemistry,
Academic Press, New York, p. 18 (1980). In addition, Farrall et al.,
J. Org. Chem.,
41, p. 3877 (1976) describe the experimental details of some of these reactions carried out with resins.
Nonpeptidic organic compounds, such as peptide mimetics, can often surpass peptide ligands in affinity for a certain receptor of enzyme. An effective strategy for rapidly identifying high affinity biological ligands, and ultimately new and important drugs, requires rapid construction and screening of diverse libraries of non-peptidic structures containing a variety of structural units capable of establishing one or more types of interactions with a biological acceptor (e.g., a receptor or enzyme), such as hydrogen bonds, salt bridges, pi-complexation, hydrophobic effects, etc. However, work on the generation and screening of synthetic test compound libraries containing nonpeptidic molecules is now in its infancy. one example from this area is the work of Ellman and Bunin on a combinatorial synthesis of benzodiazepines on a solid support (J. Am. Chem. Soc. 114, 10997, (1992); see
Chemical and Engineering News,
Jan. 18, 1993, page 33).
A key unsolved problem in the area of generation and use of nonpeptide libraries is the generation and use of nonpeptide libraries is the elucidation of the structure of molecules selected from a library that show promising biological activity.
An attempt to uncover the structures of peptides selected from a library using unique nucleotide sequence codes. which are synthesized in tandem with the peptide library, has been described by Brenner and Lerner (Brenner, S. and Lerner, R. A.
Proc. Nat'l. Acad. Sci. USA,
1992 89. 5381-5383). The nucleotide sequence of the code attached to each peptide must be amplifiable via the polymerase chain reaction (PCR). However, nucleotide synthesis techniques are not compatible with all of the synthetic techniques required for synthesis of many types of molecular libraries. Furthermore, the close proximity of nucleotide and synthetic test compound in the library, which can result in interactions between these molecules interfering with the binding of the ligand with a target receptor of enzyme during the biological assay, also limits this approach. The nucleotide component of the library can also interfere during biological assays in a variety of other ways.
Kerr et al. (
J. Am. Chem. Soc.,
1993, 115, 2520-2531) reported synthesizing solution phase libraries of peptides, containing non-natural amino acid residues, in parallel with peptide coding strands. The peptide ligand and its coding strand in this library are covalently joined together, which allows isolation and sequence determination of pairs of synthetic test compound and corresponding code. However, as with the nucleic-acid-encoded library described by Brenner and Lerner, above, the coding peptide may interfere with the screening assay.
PCT/US93/09345 describes a method of identifying actives in a combinatorial library by attaching multiple tags in a predetermined binary coding system.
PCT/HU93/0030 describes fluorescently labeled sub-library peptide kits for use in peptide synthesis.
PCT/US94/06078 describes methods of encoding combinatorial libraries using polymeric sequences.
Many of the disadvantages of the known methods as well as many of the needs not met by them are addressed by the present invention which, as described more fully hereinafter, provides numerous advantages over the known methods.
SUMMARY OF THE INVENTION
This invention relates to a method for identifying compounds having desired characteristics and identifying essential moieties in a lead structure which comprises preparing one or more encoded combinatorial libraries from a specified set of reaction sequences and testing compounds therein for biological activity.
This invention also relates to a method of encoding a single registry in each combinatorial library of a series of combinatorial libraries and combinatorial libraries with a single encoded registry.
This invention also relates to a method of encoding combinatorial libraries which comprises utilization of tagged beads.
This invention also relates to a method of encoding each choice of a combinatorial library and combinatorial libraries encoded thereby.
This invention also relates to beads with fluorescently labeled identifiers attached thereto.
DETAILED DESCRIPTION OF THE INVENTION
As used herein, the term “beads” means any solid support material capable o
Weinstock Joseph
Yamashita Dennis Shinji
Dustman Wayne J.
King William T.
Kinzig Charles M.
Ricigliano Joseph W.
SmithKline Beecham Corporation
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