Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
  • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00277—Apparatus
  • B01J2219/0054—Means for coding or tagging the apparatus or the reagents
  • B01J2219/00572—Chemical means
• • C—CHEMISTRY; METALLURGY
  • C40—COMBINATORIAL TECHNOLOGY
  • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
  • C40B70/00—Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes

Definitions

• This invention relates to the fields of biopolymer synthesis and drug design. More particularly, the invention relates to methods for synthesizing libraries of biologically active polymers in association with an included polymer which is encoded to facilitate deciphering.
• Rational drug design achieves results by intensive analysis of the molecular structure of binding sites, and designing compounds specifically to complement a desired binding site.
• one interested in preparing new antihypertensive compounds might analyze the molecular structure of the ⁇ - adrenergic receptor binding site using X-ray crystallography and/or advanced NMR techniques, and then synthesize compounds calculated to fit within the binding site and complement the charge distribution.
• the other approach is to prepare an enormous library of compounds and select only those compounds which exhibit a desired activity.
• This approach differs from the traditional pharmaceutical cycle of design/synthesize/test/synthesize variants by conducting the screening step in a massively parallel fashion, screening an enormous number of different compounds simultaneously.
• the challenge to this approach is first to provide a group of compounds for screening that is sufficiently numerous and diverse to insure that the activity sought is represented in the group, and second to identify the active compounds at low concentration within the group.
• Rutter et al., US 5,010,175 disclosed a method of making diverse mixtures of peptides by adjusting the concentration of each activated peptide in proportion to its reaction rate, in order to obtain a substantially eguimolar mixture of peptides. Rutter also disclosed the process of providing a mixture of peptides (having at least 50 different peptides) , and selecting one or more peptides having a desired property and separating them from the rest of the peptides.
• This method also facilitates the preparation of oligopeptides wherein some positions within the peptide chain are held constant, and where some posi ⁇ tions are restricted to less than all amino acids.
• this method may use this method to prepare a pep ⁇ tide of the formula X ⁇ X ⁇ X j -Glu-Ala-X ⁇ Xs-X, ; , where X,. can be any amino acid. If desired, one could limit, for example, X 3 and X 5 to hydrophobic residues.
• this method may be applied to the synthesis of oligonucleotides, which may then be inserted into cloning and expression vectors for biological expression.
• Peptoids sample a different region of physico-chemical parameter space than traditional oligopeptides, depending on the type of linkage between monomers, and may be able to exhibit activities unavailable to peptide libraries due to the diversity (or difference) in side chains.
• Houghten US 4,631,211 disclosed a "tea-bag” peptide synthesis method.
• the "tea bags” are mesh bags containing resin beads for peptide synthesis. Houghten's method enables one to add the same amino acid to a number of different oligopeptides without mixing the products: a number of "tea bags” may be reacted with an amino acid in a common pot, then separated physically.
• Cook, EP 383620 described synthesis of COP-
• COP-1 a random polymer of Ala, Glu, Lys, and Tyr, having an average molecular weight of 23 kDa having activity in the treatment of multiple sclerosis.
• COP-1 is made in the prior art by chemical polymerization of the amino acids. However, Cook described expression from genes made by random polymerization of oligonucleotides, and selection for those clones expressing COP-1 with the highest activity.
• Lebl et al., EP 445915 described a machine for performing multiple simultaneous peptide syntheses using a planar support surface.
• the planar support is, for example, paper or cotton.
• Kauffman et al., O86/05803 disclosed production of peptide libraries by expression from synthetic genes which are partially or wholly "stochastic.”
• Stochastic genes are prepared by polym- erizing a mixture of at least three oligonucleotides (at least heptamers) to form a double-stranded stochastic sequence, and ligating the stochastic sequence into an expression vector.
• Lam et al., WO92/00091 disclosed libraries of oligonucleotides, oligopeptides, and peptide/nucleotide chimeras, and methods for screening the libraries for active compounds. However, Lam did not disclose conjugates having an active sequence and a coding sequence. K.M. Derbyshire et al.. Gene (1986) 46:145-
• J.F. Reidhaar-Olson et al.. Science (1988) 241:53-57 disclosed the generation of mutant ⁇ repressor proteins by replacing two codons with random nucleotides (NNG/C) .
• NNG/C random nucleotides
• A.R. Oliphant & K. Struhl, Nuc Acids Res (1988) JL6:7673-83 disclosed the use of random poly- nucleotides to investigate promoter function.
• a section of random polynucleotide was inserted into the -35 to -10 region of a gene conferring drug resistance in E. coli, and the transformants screened for resis ⁇ tance. Survivors were cloned and sequenced to provide a functional consensus sequence.
• Oligopeptides are typically sequenced by stepwise cleavage of each amino acid from the parent compound (which is usually immobilized on a resin) , with chromatographic analysis of the cleaved moiety. Sensitive techniques are required to distinguish between twenty or more amino acids. Analysis is further complicated when uncommon amino acids are employed (using current techniques) , especially when monomers are linked without using amide bonds.
• the present invention provides a method of synthesizing true mixtures of diverse oligopeptides and/or peptide-like compounds along with an associated encoding polymer making it possible to easily analyze those compounds exhibiting a desired activity.
• the invention involves synthesizing an encoding DNA strand simultaneously with the peptide/peptoid. Each unique peptide/peptoid sequence associated with its own unique DNA strand to provide the conjugates of the invention.
• conjugates are screened to determine which peptide/ peptoid compounds exhibit a desired activity, and the active conjugates analyzed by DNA sequencing methods to determine the attached peptide/peptoid sequence by deduc-tion, i.e., since each DNA sequence is associated with a known peptide/peptoid, once the DNA sequence is deter ⁇ mined, the sequence of the peptide/peptoid can be deduced.
• Another aspect of the invention is a conjugate comprising a peptide or peptoid coupled to and/or directly associated with a coding polymer (CP) , e.g. a nucleic acid (NA) .
• CP coding polymer
• NA nucleic acid
• the peptide/peptoid/CP conjugate may be linked directly (i.e., covalently bound either directly or through a small organic mol- ecule) , or by linkage to the same support (e.g., by synthesizing both peptide/peptoid and CP strand on the same particle or bead of resin) .
• An important object of the invention is to provide a chemical synthesis method which allows the production of libraries of peptides and/or peptoids along with a unique encoded polymer such as a DNA strand which makes it possible to readily determine the sequence of the peptide or peptoid.
• An advantage of the present invention is that the methodology makes it possible to readily identify and sequence peptides and/or peptoids having desirable biological activities.
• a feature of the present invention is that sequences of peptoids or peptides which contain nonconventional amino acids can still be readily determined by sequencing associated polymers such as DNA sequences which are simultaneously synthesized with the peptoids and encode them.
• Figure 1 is a schematic diagram showing a specific embodiment of a conjugate of the invention which conjugate includes a "binding" strand or active polymer attached to a solid-support substrate which substrate is also bound to an information storage or "coding" strand;
• Figure 2 is a schematic flow diagram demonstrating how encoded libraries can be synthesized on beads as the solid-support substrate;
• Figure 3 is a schematic diagram showing methods of the synthesis of both solid-phase and solution-phase libraries
• Figure 4 is a schematic diagram showing resin-bound libraries generated by the derivatization of non-hydrolyzable resins
• Figure 5 is an HPLC chromatogram of binding and coding peptide strands simultaneously synthesized via non-hydrolyzable resin linkage
• Figure 6 is an HPLC chromatogram of a coding and binding strand adduct which was synthesized via a hydrolyzable resin linker
• Figure 7 is a plotted graph resulting from ELISA competition of binding sequences versus binding/encoding sequences
• Figure 8 is a schematic diagram showing the analysis of a solid-phase amptide.
• Figure 9 is a schematic flow diagram showing the analysis of a solution-phase amptide.
• the invention provides a rapid method of synthesizing large numbers of conjugates which conjugates are comprised of a peptide/peptoid sequence, e.g., an amino acid sequence associated with a unique encoding sequence, e.g., a DNA sequence.
• the conjugates can be readily synthesized and thereafter screened for biological activity, and when activity is found, the particular peptide/peptoid sequence found to be active can be readily identified by its associated encoding (DNA) strand.
• Each conjugate of the invention is comprised of at least two components with one of the components being the peptide or peptoid sequence which binds to a receptor of interest and the other sequence being a polymer which encodes the binding sequence.
• the invention may utilize standard amino acids and DNA as encoding monomers to produce a chemically diverse library of solution-phase or solid-phase conjugates. In order to further describe the invention in detail, the following definitions are provided.
• nucleic acid and nucleic acid refer to oligomers constructed from DNA and/or RNA bases which may be sequenced using standard DNA sequencing tech ⁇ niques.
• the NAs used herein may include uncommon bases so long as such bases are distinguishable from the other bases employed under the DNA sequencing methods to be used and include peptide-nucleic acids (PNAs) (disclosed by Nielsen, P.E., Egholm, M. , Berg, R.H. & Buchardt, 0. , Science (1991) 254, 1497-1500).
• PNAs peptide-nucleic acids
• Such PNAs could serve as coding strands and the detection would be by hybridi-zation.
• NAs will usually be constructed from monomers linked by phos- phodiester bonds, but other similar linkages may be substituted if desired.
• phosphorothioates may be employed to reduce lability.
• the term "peptide” as used herein refers to the 20 commonly-occurring amino acids: alanine (A) , cysteine (C) , aspartic acid (D) , glutamic acid (E) , phenylalanine (F) , glycine (G) , histidine (H) , isoleucine (I) , lysine (K) , leucine (L) , methionine (M) , asparagine (N) , proline (P) , gluta ine (Q) , arginine (R) , serine (S) , threonine (T) , valine (V) , tryptophan ( ) , and tyrosine (Y) .
• eptoid refers to a non-peptide monomer of the general formula (R) n -X- (L) m , where R is a side chain group, n is at least 1, L is a linking group, m is at least 2, and X is a small organic radical. It is preferred to select L radicals that may be individually protected and deprotected. Preferably n will be 1 or 2 and m will be 2. Monomers wherein m is 3 or greater may be used to form branched active polymers. Presently preferred monomers are N-substituted glycine derivatives of the formula
• R is alkyl of 2-6 carbon atoms, haloalkyl of 1-6 carbon atoms wherein halo is F, Cl, Br, or I, alkenyl of 2-6 carbon atoms, alkynyl of 2-6 carbon atoms, cyclolkyl of 3-8 carbon atoms, alkoxyalkyl of 2-8 carbon atoms, aryl of 6-10 carbon atoms, arylalkyl of 7-12 carbon atoms, arylalkyl of 7-12 carbon atoms substituted with 1-3 radicals independently selected from halo and nitro and hydroxy, aminoalkyl of 1-6 carbon atoms, hydroxyalkyl of 1-6 carbon atoms, carboxy, carboxyalkyl of 2-6 carbon atoms, carboalkoxy-alkyl of 3-10 carbon atoms, carbamyl, carbamylalkyl of 2-6 carbon atoms, imidazolyl, imid- azolylalkyl of 4-10 carbon atoms
• coding and “encoding” indicated that one or more coding monomers corresponds directly and uniquely to a given active monomer, e.g., conventional nucleic acids encode (in groups of three) the 20 natural amino acids.
• the number of coding monomers used for each code depends on the number of different coding mono ⁇ mers and the number of different active monomers. Typically, the number of different active monomers used will range from about 5 to about 30.
• a basis set of 4 coding monomers can encode up to 16 active monomers taken in "codons" of 2 coding monomers. By increasing the coding monomer basis set to five distinct monomers, one can encode up to 25 different peptide/peptoid monomers.
• a basis set of 4 coding monomers can encode up to 64 peptide/peptoid monomers taken in "codons" of 3 coding monomers. Note that one can make the code degenerate or nondegenerate, and can insert additional coding information into the sequence. For example, one may wish to begin each codon with the same base (e.g. , G) , using that base only in the first position, thus unambiguously identi ⁇ fying the beginning of each codon.
• the group of monomers selected for use as coding monomers will form polymers that are easier to sequence than the active polymers, i.e., the coding monomers may be more readily identified using present day sequencing technology as compared to the monomer of the active polymers.
• nucleic acids With current technology, the order of preference for coding monomers is nucleic acids > peptides > peptoids. Nucleic acids have the additional advantage that the coding sequence may be amplified by cloning or PCR (polymerase chain reaction) methods known in the art.
• active polymer and/or “binding polymer” refers to a polymer having a desired biological activity. Suitable biological activities include binding to natural receptors, pharmaceutical effects, immunogenicity/antigenicity, and the like. "Immunogenicity” refers to the ability to stimulate an immune response (whole or partial serum-mediated immunity and/or cell-mediated immunity) in a bird or mammal following administration.
• Antigenicity requires only that the active polymer bind to the antigen-binding site of an antibody.
• Pharmaceutical activities will generally depend on the ability of the active polymer to bind a protein, carbohydrate, lipid, nucleic acid, or other compound present in the subject.
• an active polymer may bind to a cell surface receptor and compete with the receptor's natural ligand, with or without activation of the receptor.
• Other useful pharmaceutical activities include cleavage of endogenous molecules (e.g.
• Active polymers comprise a series of monomers which are linked sequentially.
• the monomers will generally be peptides, peptoids, or carbohydrates in the practice of the instant invention.
• mixture refers to a composition having a plurality of similar components in a single vessel.
• Couple refers to formation of a covalent bond.
• Coupled moiety refers to a soluble or insoluble support to which can be attached one or more active monomers and the corresponding encoding monomers.
• Insoluble supports (“solid support means") may be any solid or semi-solid surface which is stable to the reaction conditions required for synthesis of the active and coding polymers, and is suitable for covalently attaching and immobilizing both polymers, for example, most resins commonly employed in DNA and peptide synthesis, such as MBHA, Rink, and the like. The particular resin used will depend upon the choice of coding and active polymers and their associated synthetic chemistries.
• Soluble coupling moieties are molecules having functional groups to which active and coding monomers may be attached.
• Each soluble coupling moiety must be able to accommodate at least one coding polymer and at least one active polymer, although the active and coding polymers need not be present in a 1:1 ratio.
• the soluble coupling moiety may be as simple as an amino acid having an functional group in its side chain, or may be as complex as a functionalized (soluble) polymer.
• conjugate refers to the combination of any "active polymer” and its associated “coding” polymer.
• the conjugate may be formed using a “coupling moiety” or by binding both the “active polymer” and “encoding polymer” to the same support surface in close proximity with each other so that the two polymers are “associated” with each other.
• both polymers are bound to the same support surface, such as a small bead, the encoding polymer can be readily sequenced off of the bead and the other "active polymers” remaining on the bead will be identified once the encoding sequence is known.
• Filamentous bacteriophage libraries offer the largest source of peptide diversity ( «10 7 -10 8 different components) of any current technology to date (Scott, J. & Smith, G. , Science. (1990), 249, 386-390; Devlin, J. , Panganiban, L. & Devlin, P., Science. (1990), 249, 404-406; Cwirla, S., Peters, E., Barret, R. & Dower, W. , Proc. Natl. Acad. Sci. U.S.A.. (1990), 87, 6378-6382).
• the sequence of a biologically active protein can be determined even without isolating the protein of interest. This can be done by synthesizing large numbers of different proteins on large numbers of different support surfaces such as small beads. An encoding polymer is attached to beads to identify each protein. A sample to be tested is then brought into contact with the beads and the beads are observed with respect to which proteins bind to a receptor site in the sample. The bead having the receptor bound thereon is analyzed by sequencing the coding polymer which has also been synthesized on the bead. When the encoding polymer has been sequenced, the sequence of the active polymer, which may be a peptide, can be readily deduced. Thus, the present invention makes it possible to determine the activity and sequence an active polymer, such as a biologically active peptide, without ever isolating the peptide.
• This invention describes a methodology for the synthesis and screening of large synthetic polymer libraries that contain non-standard amino acids and even non-amide based polymers.
• the strategy utilizes a modified mixed-resin peptide synthesis methodology to simultaneously synthesize two polymer sequences: one polymer strand (the "binding" strand) is synthesized for the intended purpose of receptor binding, and the second strand (the "coding” strand) contains standard amino acids or deoxyribonucleotides that encodes for the binding strand ( Figure 1) .
• the ability to decipher the binding sequence by analysis of the coding strand with standard peptide or oligonucleotide techniques allow the inclusion of a wide variety of novel building blocks and conformational constraints into a diverse ligand library.
• This invention also describes a methodology to increase the size (>10 8 ) and screening rate of a ligand library.
• the method uses two polymers as above, but specifically utilizes an oligodeoxyribonucleotide for the "coding" strand.
• the use of DNA as the coding strand allows for an increased sensitivity of detection (fmol vs pmol for peptide analysis) .
• This increased sensitivity allows for a larger library size since the amount of polymer needed for detection is reduced dramatically.
• the rate of sequence determination of receptor binders is increased since many samples can be analyzed in parallel.
• Two synthesis formats are possible for amptide libraries, one that generates resin-bound libraries and one that generates solution-phase libraries ( Figure 3) .
• Resin-bound libraries can be synthesized using non-hydrolyzable linkers that are derivatized with the "binding" and "coding" monomers strands.
• Solution-phase libraries can be synthesized as a 1:1 polymer:peptide/DNA conjugate via a hydrolyzable linker attached to the resin.
• Peptide as the "Coding" strand
• base-labile Fmoc-protected monomers and acid-labile (l-P-Ddz-protected amino acids (Birr, C, Nassal, M. , Pipkorn, R. , Int. J. Peptide Protein Res.. (1979), 13, 287-295), for example, allow for selective deprotection and coupling to two individual polymer strands.
• Resin-bound libraries can be generated by the derivatization of non-hydrolyzable resins with a 1:1 ratio (or any desired ratio) of Fmoc:Ddz monomers ( Figure 4) . This introduces two differently protected amino acids that an be extended independently.
• Solution-phase libraries that contain a 1:1 ratio of binding:coding strands can be synthesized by using a hydrolyzable Fmoc-Lysine(Moz)- OH linker that allowed for chain growth at both the ⁇ - and ⁇ -amino groups. Amino acids which do not contain functional groups are preferred for the "coding" strand in order to minimize unwanted binding interactions.
• the receptor-binding ligand can be identified by bead staining techniques (Lam, K. , Salmon, S., Hersh, E., Hruby, V., Kazmiersky, W. & Knapp, R. , Nature, (1991), 354, 82-84) and the sequence determined by N-terminal Edman degradation. In order to ensure that only the "coding" strand is sequenced, it is essential that the N-terminus of the "binding" strand be acetylated or otherwise made non- sequencable.
• the construction of libraries with DNA as the coding strand is similar to those with peptides but offers several advantages: the information storage and replicative properties of DNA allow for increased sensitivity of detection, a larger library size and an increased rate of sequence determination.
• the synthesis of DNA as the coding polymer requires compatibility between the assembly of Fmoc- based monomers and standard DNA chemistry. These synthesis strategies are likely to be compatible ((a) Juby, C, Richardson, C. & Brousseau, R., Tet. Letters. (1991), 32, 879-882. (b) Haralambidis, J. , Duncan, L., Angus, B. & Tregear W., Nucleic Acid Res.. (1990), 18, 493-499) (see Table 2) .
• allyl-based protection strategies exists for both peptide (Lyttle, M.H.; Hudson, D. , Peptides: Chemistry and Biology fProceedings of the 12th American Peptide Sym osiuml.: Smith, J. and Rivier, J.E., Eds.; ESCOM, Leiden, 1992, pp. 583-584) and oligodeoxyribonucleotide (Hayakawa, Y., Wakabayashi, S., Kato, H. & Noyori, R. , J. Am. Chem. Soc. r (1990), 112, 1691-1696) synthesis.
• the assay of solution- phase libraries can be facilitated by using only pyrimidines in the coding strand, thereby avoiding the potential problem of base pairing between individual strands.
• SUBSTITUTE SHEET Resin-bound libraries can be synthesized by using non-hydrolyzable linkers to attach both the C- terminus of the peptide and the 3'-end of the oligonucleotide to the same bead.
• Solution-phase libraries can be synthesized as a 1:1 peptide- oligonucleotide conjugate, in which the C-terminus of the peptide is attached to the 3'-end of the oligonucleotide through a hydrolyzable Fmoc-Ser(O-Dmt) linker which is attached to the resin.
• the identification of binders in the resin- bound peptide libraries can be detected by the bead staining methodology (Lam, K.
• Example 1 The independent synthesis of two unambiguously correlated sequences has been successfully completed. The subsequent sequence analysis of the "coding" strand has also been demonstrated. For convenience, two peptide sequences were chosen. The "binding" strand was synthesized with N ⁇ -Fmoc-protected amino acids and the "coding” strand was synthesized with IT-Ddz-protected amino acids.
• the model library bead has two independently synthesized sequences and is ready for assay. Only the coding strand has a free ⁇ -amino group and can be characterized by N-terminal Edman degradation. The binding strand is acetylated and there-fore will not interfere with the sequencing. The two peptides were cleaved from the resin with HF thereby providing both the "binding" and "coding" sequences as free peptides. The amino acid composition, mass spectro-scopy and N- terminal sequencing data are consistent with the correct products. (See Figures 5, 6 and 7.) Mass Spectrometry:
• the model solution-phase library contains a 1:1 Fmoc/Ddz conjugate peptide.
• One peptide sequence was synthesized and not a mixture in order to fully characterize the reaction product. The amino acid composition and mass spectroscopy data are consistent with the correct product.
• the "binding" and "coding” hybrid peptides were tested in a competition ELISA format. The ELSTRPnL "binding" sequence binds to an anti-gpl20 antibody with submicromolar affinity. This value was not affected by the presence of the "coding" peptide.

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