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Lee HK, Chui WK. Combinatorial mixture synthesis and biological evaluation of dihydrophenyl triazine antifolates. Bioorg Med Chem 1999; 7:1255-62. [PMID: 10428399 DOI: 10.1016/s0968-0896(99)00051-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The traditional 'one-pot' three component synthesis was adapted successfully for combinatorial mixtures synthesis of dihydrophenyl triazines, which are nonclassical, dihydrofolate reductase (DHFR) inhibitors. Each library was designed to comprise eight reaction mixture pots and in every pot there were three dihydrophenyl triazines. A total of three libraries were synthesized and the final number of compounds harvested was 64. The products precipitated out of the reaction mixture and could be collected easily and cleansed by washing. Solid supports and further purification processes were not required. The reactions were monitored by TLC and a HPLC method was developed to determine the number of products in each pot. All 24 pots were screened for inhibitory activity against the rat liver DHFR. Two pots showed good inhibitory activity and the products in them were individually synthesized, characterized and biologically tested again. One lead compound was identified amongst all the compounds synthesized, and would be further optimized.
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Affiliation(s)
- H K Lee
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
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53
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Wong DW, Robertson GH. Combinatorial chemistry and its applications in agriculture and food. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1999; 464:91-105. [PMID: 10335388 DOI: 10.1007/978-1-4615-4729-7_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Combinatorial chemistry has become a major focus of research activity in the pharmaceutical industry for development new therapeutic compounds. The same techniques could be potentially applied to benefit agricultural and food research. This article reviews the various procedures used in combinatorial chemistry, outlines some of the strengths and limitations of the various methods, and proposes potential areas in agriculture and food that could be benefited by this technology. These areas include developing new antimicrobial agents, antioxidants, and other additives, creating antigen-binding molecules for the detection or removal of food pathogens or toxicants, engineering food proteins and enzymes for specific functions, and modifying biosynthetic pathways for the production of novel natural products.
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Affiliation(s)
- D W Wong
- Western Regional Research Center, United States Department of Agriculture, Albany, California 94710, USA
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54
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Boutin JA, Lambert PH, Bertin S, Volland JP, Fauchère JL. Physico-chemical and biological analysis of true combinatorial libraries. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 725:17-37. [PMID: 10226875 DOI: 10.1016/s0378-4347(98)00569-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Combinatorial libraries offer new sources of compounds for the research of pharmacological agents such as receptor ligands, enzyme inhibitors or substrates and antibody-binding epitopes. The present review stresses the main roles played by both physico-chemical analysis, particularly when complex mixture of compounds are synthesized as libraries, and biological analysis from which active compounds are identified. After a brief discussion of semantic problems related to the designation of the product mixtures, the physico-chemical analysis of mixtures is reviewed with special emphasis on mass spectrometric techniques. These methods are able both to give a representative view of a library composition and to identify single critical compounds in large libraries. Then the biological screening of such combinatorial libraries is critically discussed with respect to the power and limitations of the methods used for the identification of the active components. Special attention is given to the complex process of library deconvolution. It is pointed out that while combinatorial techniques have evolved towards sophisticated high-tech methods, simple and robust biochemical tests should be used to deconvolute. From a large panel of published examples, a set of trends are identified which should help investigators to choose the most appropriate assay for the discovery of new entities.
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Affiliation(s)
- J A Boutin
- Department of Molecular and Cellular Pharmacology, Institut de Recherches SERVIER, Croissy-sur-Seine, France
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55
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Van Hijfte L, Marciniak G, Froloff N. Combinatorial chemistry, automation and molecular diversity: new trends in the pharmaceutical industry. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 725:3-15. [PMID: 10226874 DOI: 10.1016/s0378-4347(99)00007-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Combinatorial chemistry has emerged as a set of novel strategies for the synthesis of large sets of compounds (combinatorial libraries) for biological evaluation. Within a few years combinatorial chemistry has undergone a series of changes in trends, which are closely related to two important factors in libraries: numbers and quality. While the number of compounds in a library may be easily expressed, it is a lot more difficult to indicate the degree of quality of a library. This degree of quality can be split into two aspects: purity and diversity. The changing trends in combinatorial chemistry with respect to the strategies, the technologies, the libraries themselves (numbers and purity aspects) and the molecular diversity are outlined in this paper.
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Affiliation(s)
- L Van Hijfte
- Synthélabo Biomoléculaire, Department of Combinatorial Chemistry, Strasbourg, France
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Molecular recognition and solid phase organic synthesis: Synthesis of unnatural oligomers, techniques for monitoring reactions, and the analysis of combinatorial libraries. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1068-7459(99)80013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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59
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Mondorf K, Kaufman DB, Carbonell RG. Screening of combinatorial peptide libraries: identification of ligands for affinity purification of proteins using a radiological approach. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1998; 52:526-36. [PMID: 9924997 DOI: 10.1111/j.1399-3011.1998.tb01257.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Peptides deduced from peptide libraries may serve as affinity ligands for protein purification. Identification of a ligand that binds the protein of interest depends highly on the screening method used. One approach which offers simple and direct detection involves screening a solid-phase peptide library against a radiolabeled target protein. We have developed a radiological screening method, using 14C as a radioactive label, that offers high resolution and sensitivity. Less than 100 DPM/bead are detectable after a one-day exposure using autoradiography. The validity of the technique was illustrated by screening a solid-phase hexameric-peptide library spiked with YNFEVL-beads against 14C-labeled ribonuclease S-protein. For this particular system, the amount of protein bound to a single bead was estimated to be in the femtomolar range with a peptide:protein ratio of 500:1. Finally, a portion of the library was screened against 14C-labeled fibrinogen. Three peptides deduced from the library, WQEHYN, WQETYQ, and YENYGY, purified fibrinogen from a mixture with albumin.
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Affiliation(s)
- K Mondorf
- Department of Chemical Engineering, North Carolina State University, Raleigh 27695-7905, USA
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60
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Hiemstra HS, van Veelen PA, Schloot NC, Geluk A, van Meijgaarden KE, Willemen SJM, Leunissen JAM, Benckhuijsen WE, Amons R, de Vries RRP, Roep BO, Ottenhoff THM, Drijfhout JW. Definition of Natural T Cell Antigens with Mimicry Epitopes Obtained from Dedicated Synthetic Peptide Libraries. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.161.8.4078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Progress has recently been made in the use of synthetic peptide libraries for the identification of T cell-stimulating ligands. T cell epitopes identified from synthetic libraries are mimics of natural epitopes. Here we show how the mimicry epitopes obtained from synthetic peptide libraries enable unambiguous identification of natural T cell Ags. Synthetic peptide libraries were screened with Mycobacterium tuberculosis-reactive and -autoreactive T cell clones. In two cases, database homology searches with mimicry epitopes isolated from a dedicated synthetic peptide library allowed immediate identification of the natural antigenic protein. In two other cases, an amino acid pattern that reflected the epitope requirements of the T cell was determined by substitution and omission mixture analysis. Subsequently, the natural Ag was identified from databases using this refined pattern. This approach opens new perspectives for rapid and reliable Ag definition, representing a feasible alternative to the biochemical and genetic approaches described thus far.
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Affiliation(s)
- Hoebert S. Hiemstra
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. van Veelen
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Nanette C. Schloot
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Geluk
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Krista E. van Meijgaarden
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Sabine J. M. Willemen
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Jack A. M. Leunissen
- †National Center for Computer-Aided Chemistry and Bioinformatics (CAOS/CAMM), Catholic University Nijmegen, Nijmegen, The Netherlands; and
| | - Willemien E. Benckhuijsen
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Reinout Amons
- ‡Department of Medical Biochemistry, Sylvius Laboratory, Leiden University Medical Center, Leiden, The Netherlands
| | - René R. P. de Vries
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Bart O. Roep
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom H. M. Ottenhoff
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan W. Drijfhout
- *Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
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Boutin JA, Gesson I, Henlin JM, Bertin S, Lambert PH, Volland JP, Fauchère JL. Limitations of the coupling of amino acid mixtures for the preparation of equimolar peptide libraries. Mol Divers 1998; 3:43-60. [PMID: 9527476 DOI: 10.1023/a:1009602707067] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The standard method of peptide library synthesis involves coupling steps in which a single amino acid is reacted with a mixture of resin-bound amino acids. The more recently described positional scanning strategy (in which each position in the peptide sequence is occupied in turn by a single residue) is different since it involves the coupling of mixtures of amino acids to mixtures of resin-bound amino acids. In the present study, we analyze the compounds produced under these conditions measuring coupling rates and amounts of formed products, using mainly UV, HPLC, LC/MS and MS/MS techniques. Our data do not permit to conclude that the resulting libraries are complete. Indeed, our analytical data indicate that a large part of the di-, tri- and tetrapeptides synthesized with this method are not present in the final mixture. Although chemical compensation (in which poor coupling kinetics is compensated by a larger excess of the incoming amino acid) has been thought to counterbalance these biases, our experiments show that the compensation method does not take into account the crucial influence of the resin-bound amino acid and that even the dipeptide libraries obtained in this way are far from completeness. The present work provides strong evidence that the coupling of mixtures of amino acids to resin-bound residues, which is required by the positional scanning strategy, results in incomplete and/or non-equimolar libraries. It also clearly confirms that coupling rates in solid-phase peptide synthesis are dependent on the nature of both the incoming and the immobilized amino acid.
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Affiliation(s)
- J A Boutin
- Department of Peptide and Combinatorial Chemistry, Institut de Recherches SERVIER, Suresnes, France
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64
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Konings DA, Wyatt JR, Ecker DJ, Freier SM. Strategies for rapid deconvolution of combinational libraries: comparative evaluation using a model system. J Med Chem 1997; 40:4386-95. [PMID: 9435908 DOI: 10.1021/jm970503o] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Synthesis and testing of complex mixtures maximize the number of compounds that can be prepared and tested in a combinatorial library. When mixtures of compounds are screened, however, the identity of the compound(s) selected may depend on the deconvolution procedure employed. Previously, we developed a model system for evaluation of deconvolution procedures and used it to compare pooling strategies for iterative and noniterative deconvolution [Freier et al. J. Med. Chem. 1995, 38, 344-352]. We have now extended the model studies to include simulations of procedures with overlapping subsets such as subtractive pooling [Carell et al. Angew, Chem., Int. Ed. Engl. 1994, 33, 2061-2064], bogus coin pooling [Blake and Litzi-Davis. Bioconjugate Chem. 1992, 3, 510-513], and orthogonal pooling [D'Prez et al. J. Am. Chem. Soc. 1995, 117, 5405-5406]. These strategies required synthesis and testing of fewer subsets than did the more traditional nonoverlapping iterative strategies. The compounds identified using simulations of these strategies, however, were not the most active compounds in the library and were substantially less active than those identified by simulations of more traditional strategies.
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Affiliation(s)
- D A Konings
- ISIS Pharmaceuticals, Carlsbad, California 92008, USA
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65
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Affiliation(s)
- M Lebl
- Trega Biosciences, Inc., San Diego, California 92121, USA
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66
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Keifer PA. High-resolution NMR techniques for solid-phase synthesis and combinatorial chemistry. Drug Discov Today 1997. [DOI: 10.1016/s1359-6446(97)01104-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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67
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Abstract
Using the newly developed combinatorial peptide library methods, D-amino acid containing peptides that are specific against pan-B cell markers such as CD19, CD20, and CD22 can potentially be identified. These peptides can then be used as targeting agents for human lymphoma.
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Affiliation(s)
- K S Lam
- Arizona Cancer Center, Tucson, USA
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68
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Hiemstra HS, Duinkerken G, Benckhuijsen WE, Amons R, de Vries RR, Roep BO, Drijfhout JW. The identification of CD4+ T cell epitopes with dedicated synthetic peptide libraries. Proc Natl Acad Sci U S A 1997; 94:10313-8. [PMID: 9294207 PMCID: PMC23359 DOI: 10.1073/pnas.94.19.10313] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
For a large number of T cell-mediated immunopathologies, the disease-related antigens are not yet identified. Identification of T cell epitopes is of crucial importance for the development of immune-intervention strategies. We show that CD4+ T cell epitopes can be defined by using a new system for synthesis and screening of synthetic peptide libraries. These libraries are designed to bind to the HLA class II restriction molecule of the CD4+ T cell clone of interest. The screening is based on three selection rounds using partial release of 14-mer peptides from synthesis beads and subsequent sequencing of the remaining peptide attached to the bead. With this approach, two peptides were identified that stimulate the beta cell-reactive CD4+ T cell clone 1c10, which was isolated from a newly diagnosed insulin-dependent diabetes mellitus patient. After performing amino acid-substitution studies and protein database searches, a Haemophilus influenzae TonB-derived peptide was identified that stimulates clone 1c10. The relevance of this finding for the pathogenesis of insulin-dependent diabetes mellitus is currently under investigation. We conclude that this system is capable of determining epitopes for (autoreactive) CD4+ T cell clones with previously unknown peptide specificity. This offers the possibility to define (auto)antigens by searching protein databases and/or to induce tolerance by using the peptide sequences identified. In addition the peptides might be used as leads to develop T cell receptor antagonists or anergy-inducing compounds.
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Affiliation(s)
- H S Hiemstra
- Department of Immunohematology and Blood Bank, Leiden University Hospital, University of Leiden, 2300 RC Leiden, The Netherlands
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69
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Scott RH, Balasubramanian S. Properties of fluorophores on solid phase resins; implications for screening, encoding and reaction monitoring. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00263-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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70
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Osborne SE, Ellington AD. Nucleic Acid Selection and the Challenge of Combinatorial Chemistry. Chem Rev 1997; 97:349-370. [PMID: 11848874 DOI: 10.1021/cr960009c] [Citation(s) in RCA: 425] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Scott E. Osborne
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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71
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Weinberger H, Lichte E, Griesinger C, Kutscher B. Small peptide libraries: combinatorial split-mix synthesis followed by combinatorial amino acid analysis of selected variants. Arch Pharm (Weinheim) 1997; 330:109-11. [PMID: 9230529 DOI: 10.1002/ardp.19973300406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Peptides from small combinatorial libraries, covalently attached to polymeric TentaGel beads, can be directly sequenced using amino acid analysis. For libraries with restricted diversity, generated by the split-mix synthesis method, the amino acids on a selected single bead identified by pre-column derivatization with o-phthaldialdehyde (OPA) correlate directly with the sequence of a given peptide. This is shown on a tripeptide (343 different compounds) and a tetrapeptide (4096 different compounds) library. This method allows for rapid peptide sequence determination without relying on complex encoding strategies.
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Affiliation(s)
- H Weinberger
- Institute of Organic Chemistry, J.W. Goethe-University of Frankfurt, Frankfurt/Main, Germany
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72
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Lam KS, Lebl M, Krchnák V. The "One-Bead-One-Compound" Combinatorial Library Method. Chem Rev 1997; 97:411-448. [PMID: 11848877 DOI: 10.1021/cr9600114] [Citation(s) in RCA: 514] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kit S. Lam
- Arizona Cancer Center, Department of Medicine, Department of Microbiology and Immunology, 1501 N. Campbell Avenue, Tucson, Arizona 85724, and Houghten Pharmaceuticals Inc., 3550 General Atomics Court, San Diego, California 92121
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73
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Gennari C, Nestler HP, Piarulli U, Salom B. Combinatorial Libraries: Studies in Molecular Recognition and the Quest for New Catalysts. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/jlac.199719970405] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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74
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Abstract
In an effort to increase the probability of finding novel peptides in resin-bound combinatorial libraries displaying affinity to various macromolecular targets, we increased the diversity of a solid-phase library considerably by synthesizing multiple structures on each bead - a motif-library - including 45 building blocks. The building blocks consist of L-aa, D-aa and eight hydrophobic non-proteinogenic alpha-amino acids. A library with the format O-Z0-1-O-Z0-1-O-XX-resin was synthesized giving the four motifs OOOXX, OZOOXX, OOZOXX, OZOZOXX corresponding to 364.500 different motifs (45(3) x 4 theoretical combinations). The positions O are defined amino acids while Z represents three mixtures pi, omega, phi, where pi is a mixture of polar and charged residues, omega is a mixture of aliphatic residues and phi is a mixture of aromatic residues. X represents a mixture of all 45 residues. The library was screened with the macromolecular target streptavidin which served as a model receptor. Binding peptides were sequenced by microsequencing. We included small amounts of norvaline and norleucine in the library, which served as index residues to be able to distinguish between LD-amino acids and other residues with the same retention time in the HPLC system. Beads that interact with the receptor were found, and the binding motifs that appeared had no homology to known binding motifs found in either L-aa or D-aa libraries, instead motifs with the non-proteinogenic residues L-phenylglycine, O-benzyl-L-hydroxyproline and O-benzyl-L-tyrosine dominated. The novel peptides inhibit binding of biotin to streptavidin but do not bind to avidin, and the affinity is higher than the peptides found in linear all L-aa peptide libraries.
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Affiliation(s)
- S Ostergaard
- Research Center of Medical Biotechnology, Chemistry Department Royal Veterinary and Agricultural University, Frederiksberg, Denmark
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76
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Ferry G, Boutin JA, Atassi G, Fauchère JL, Tucker GC. Selection of a histidine-containing inhibitor of gelatinases through deconvolution of combinatorial tetrapeptide libraries. Mol Divers 1997; 2:135-46. [PMID: 9238644 DOI: 10.1007/bf01682201] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A fully automated peptide synthesizer was used to generate tetrapeptide sublibraries from 24 natural and nonnatural amino acids, from which new inhibitors of gelatinases (matrix metalloproteinases MMP-2 and MMP-9) were selected as potential anticancer drugs. MMP-2 and MMP-9 from mouse Balbc/3T3 fibroblasts conditioned media were assayed in their linear range response by zymography to quantify inhibition at each step of the tetrapeptide library deconvolution. The histidine-epsilon-amino caproic acid-beta-alanine-histidine (His-epsilon Ahx-beta Ala-His) sequence was found to yield optimal inhibition of both MMP-2 and MMP-9. Inhibition by selected tetrapeptides was also evaluated with two other techniques, a native type IV collagen degradation assay and a fluorogenic enzymatic assay, confirming the tetrapeptide potency. The His-epsilon Ahx-beta Ala-His tetrapeptide also inhibited purified human MMP-2 and MMP-9 and the corresponding enzymes present in conditioned media from human tumour cells. Finally, the length of the spacer between the two terminal histidines was found to be crucial to the inhibitory potential. This approach may thus be considered as a-successful strategy to yield specific peptide or pseudopeptide inhibitors, although their potency remains moderate, since it was measured before any chemical optimization was undertaken.
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Affiliation(s)
- G Ferry
- Department of Tumour Biology, Institut de Recherches Servier, Suresnes, France
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79
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Crews CM. Deciphering isozyme function: exploring cell biology with chemistry in the post-genomic era. CHEMISTRY & BIOLOGY 1996; 3:961-5. [PMID: 9000005 DOI: 10.1016/s1074-5521(96)90162-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genome sequencing projects are identifying protein sequences faster than it is possible to discover their functions. Fortunately, combinatorial chemistry offers an opportunity to develop new biological reagents with which to determine the roles of related isozymes.
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Affiliation(s)
- C M Crews
- Biology Department, Yale University, New Haven, CT 06520-8103, USA.
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80
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Wess G, Bock K, Kleine H, Kurz M, Guba W, Hemmerle H, Lopez-Calle E, Baringhaus KH, Glombik H, Enhsen A, Kramer W. Design und Synthese eines Gerüstes aus Gallensäure für die kombinatorische Chemie. Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961081914] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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81
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Abstract
The decreasing reactivity of tri-, di- and monochlorotriazine was utilized for the solid-phase construction of a combinatorial library with three randomized positions, using 20 amino acids and 50 amines as building blocks. The first chlorine atom was selectively substituted by coupling a large excess of trichlorotriazine to the support-bound amino acid, thus avoiding simultaneous substitution of the second chlorine. The second and third diversity positions were selectively introduced by coupling amines at different temperatures. Mixtures of model compounds were synthesized and analyzed, showing the correct representation of all expected components. A library composed of 12,000 compounds was generated using this method.
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Affiliation(s)
- M Stanková
- Selectide Corporation, Tucson, AZ 85737, USA
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82
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Abstract
Tweezer-like receptor molecules have proven their potential for molecular recognition on several occasions. We decided to make twofold use of this receptor design: firstly to learn whether simple molecular forceps consisting of two peptide chains linked by a spacer are able to selectively bind to small peptides, and secondly to investigate the importance of structural preorganization for the characteristics of the receptors. We prepared two encoded combinatorial libraries based on this design, featuring two combinatorial tripeptide chains held by different scaffolds: the use of chenodeoxycholic acid as spacer provided a rigid scaffold for the forceps, whereas linking the peptide chains by a pentamethylene chain yielded a very flexible forceps structure. Molecules from the cholic acid library recognize and discriminate various enkephalins with micromolar affinities. Molecules from the flexible library show distinct interactions with the enkephalins as well, but the specificity and affinity are clearly diminished. Thus, although the interactions of molecular forceps with peptides are not crucially dependent on structural preorganization, receptors with a rigid design are clearly superior to flexible molecular forceps.
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Affiliation(s)
- H P Nestler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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83
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Pennington ME, Lam KS, Cress AE. The use of a combinatorial library method to isolate human tumor cell adhesion peptides. Mol Divers 1996; 2:19-28. [PMID: 9238629 DOI: 10.1007/bf01718696] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tumor cell progression is dependent in part on the successful adhesive interactions of the cells with the extracellular matrix. In this study, a new approach is described to isolate linear peptide ligand candidates involved in cellular adhesion. A synthetic combinatorial peptide library based on the 'one-bead-one-peptide' concept was incubated with live human prostate cancer cells for 90 min at 37 degrees C. The peptide bead coated with a monolayer of cells was then isolated for microsequencing. The DU145 (DU-H) cells were chosen since they have been previously characterized as containing elevated levels of a laminin receptor for cell adhesion, the alpha 6 beta 1 integrin on the cell surface. The use of a function-blocking antibody (GoH3) allows for the detection of peptides which are alpha 6-specific ligand candidates. From two different libraries (linear 9-mer and 11-mer) of a total of 1,500,000 beads, 68 peptide beads containing attached cells were isolated. These positive beads were then retested to determine the ability of the GoH3 antibody to block binding of the cells to the peptide beads. The alpha 6 integrin candidate peptide beads (five in total) were recovered and two of the beads were microsequenced. These two peptides, RU-1 (LNIVS-VNGRHX) and RX-1 (DNRIRLQAKXX), resemble the previously reported active peptide sequences (GD-2 and AG-73) from native laminin. The RU-1, RX-1 and AG-73 peptides were tested for their ability to support cell attachment and to bind the cell surface of DU-H prostate carcinoma cells in suspension using fluorescence-activated cell-sorting (FACS) analysis. Both RU-1 and AG-73 peptides supported cellular attachment within 1 h. In contrast, after 1 h, EHS laminin supported both cellular attachment and spreading. The RX-1 peptide exhibited only weak binding to the DU-H prostate carcinoma cells. FACS analysis indicated that AG-73 peptide attached to tumor cell surfaces over a range of concentrations, whereas the RU-1 peptide showed a homogeneous concentration required for attachment. The described strategy for screening a random peptide library offers three advantages: (i) ligands for conformationally sensitive receptors of adhesion can be isolated using live cells; (ii) specific binding can be selected for using function-blocking antibodies; and (iii) peptides supporting adhesion independent of spreading properties can be distinguished. In principle, specific adhesive peptides without prior knowledge of the sequence could be isolated for any epithelial cell surface receptor for which a function-blocking reagent is available.
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Affiliation(s)
- M E Pennington
- Department of Radiation Oncology, University of Arizona, Tucson 85824, USA
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84
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Salmon SE, Liu-Stevens RH, Zhao Y, Lebl M, Krchñák V, Wertman K, Sepetov N, Lam KS. High-volume cellular screening for anticancer agents with combinatorial chemical libraries: a new methodology. Mol Divers 1996; 2:57-63. [PMID: 9238634 DOI: 10.1007/bf01718701] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A single-step cancer cell cytotoxic assay system for anticancer drug discovery has been developed which facilitates rapid screening of large combinatorial chemical libraries synthesized using the 'one-bead-one-compound' (OBOC) methodology. Each OBOC library bead incorporates two orthogonally cleavable linkers that release the bead-bound compound at a different pH. The assay utilizes high concentrations of tumor cells mixed directly with OBOC beads and plated in soft agarose containing tissue culture medium. One of the orthogonal linkers is cleaved at neutral pH in tissue culture releasing an aliquot of compound to diffuse at a relatively high local concentration into the soft agarose immediately surrounding the bead. Active compounds are identified visually from a clear ring of tumor cell lysis which forms within 48 h around just the rare bead releasing a cytotoxic compound. The bead releasing a cytotoxin is then plucked from the agar and the remaining compound still linked to the bead can be released for structural analysis, followed by compound resynthesis and confirmatory testing. This assay system has been successfully applied to identification of lead cytotoxic compounds from model peptidic and non-peptidic combinatorial chemical libraries. Use of this methodology may facilitate anticancer drug discovery.
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Affiliation(s)
- S E Salmon
- Arizona Cancer Center, University of Arizona, Tucson 85724, USA
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85
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Abstract
With the advent of combinatorial chemistry a new paradigm is evolving in the field of drug discovery. The approach is based on an integration of chemistry, high-throughput screening and automation engineering. The chemistry arm is usually based on solid-phase synthesis technology as the preferred approach to library construction. One of the most powerful of the solid-phase methods is encoded split synthesis, in which the reaction history experience by each polymeric bead is unambiguously recorded. This split-and-pool approach, employing chemically robust tags, was used to construct a 85,000-membered dihydrobenzopyran library.
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86
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87
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Vágner J, Barany G, Lam KS, Krchnák V, Sepetov NF, Ostrem JA, Strop P, Lebl M. Enzyme-mediated spatial segregation on individual polymeric support beads: application to generation and screening of encoded combinatorial libraries. Proc Natl Acad Sci U S A 1996; 93:8194-9. [PMID: 8710846 PMCID: PMC38645 DOI: 10.1073/pnas.93.16.8194] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Proteolysis of short N alpha-protected peptide substrates bound to polyoxyethylene-polystyrene beads releases selectively free amino sites in the enzyme-accessible "surface" area. The substantial majority of functional sites in the "interior" of the polymeric support are not reached by the enzyme and remain uncleaved (protected). Subsequent synthesis with two classes of orthogonal protecting groups-N alpha-tert-butyloxycarbonyl (Boc) and N alpha-9-fluorenylmethyloxy-carbonyl (Fmoc)-allows generation of two structures on the same bead. The surface structure is available for receptor interactions, whereas the corresponding interior structure is used for coding. Coding structures are usually readily sequenceable peptides. This "shaving" methodology was illustrated by the preparation of a peptide-encoded model peptide combinatorial library containing 1.0 x 10(5) members at approximately 6-fold degeneracy. From this single library, good ligands were selected for three different receptors: anti-beta-endorphin anti-body, streptavidin, and thrombin, and the binding structures were deduced correctly by sequencing the coding peptides present on the same beads.
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Affiliation(s)
- J Vágner
- Department of Chemistry, University of Minnesota, Minneapolis 55455, USA
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88
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Combinatorial chemistry and natural products. Teicoplanin aglycone as a molecular scaffold for solid phase synthesis of combinatorial libraries. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)01350-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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89
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Konings DA, Wyatt JR, Ecker DJ, Freier SM. Deconvolution of combinatorial libraries for Drug discovery: theoretical comparison of pooling strategies. J Med Chem 1996; 39:2710-9. [PMID: 8709101 DOI: 10.1021/jm960168o] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Synthesis and testing of mixtures of compounds in a combinatorial library allow much greater throughput than synthesis and testing of individual compounds. When mixtures of compounds are screened, however, the possibility exists that the most active compound will not be identified. The specific strategies employed for pooling and deconvolution will affect the likelihood of success. We have used a nucleic acid hybridization example to develop a theoretical model of library deconvolution for a library of more than 250,000 compounds. This model was used to compare various strategies for pooling and deconvolution. Simulations were performed in the absence and presence of experimental error. We found iterative deconvolution to be most reliable when active molecules were assigned to the same subset in early rounds. Reliability was reduced only slightly when active molecules were assigned randomly to all subsets. Iterative deconvolution with as many as 65,536 compounds per subset did not drastically reduce the reliability compared to one-at-a-time testing. Pooling strategies compared using this theoretical model are compared experimentally in an accompanying paper.
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Affiliation(s)
- D A Konings
- ISIS Pharmaceuticals, Carlsbad, California 92008, USA
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90
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Nestler H, Wennemers H, Sherlock R, Dong DLY. Microautoradiographic identification of receptor-ligand interactions in bead-supported combinatorial libraries. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00228-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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91
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Krchnák V, Weichsel AS, Cabel D, Flegelova Z, Lebl M. Structurally homogeneous and heterogeneous synthetic combinatorial libraries. Mol Divers 1996; 1:149-64. [PMID: 9237206 DOI: 10.1007/bf01544953] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have designed and synthesized structurally homogeneous and heterogeneous nonpeptide libraries. Structurally homogeneous libraries are characterized by the presence of one common structural unit, a scaffold, in all library compounds (e.g. cyclopentane, cyclohexane, diketopiperazine, thiazolidine). In structurally heterogeneous libraries different organic reactions (acylation, etherification, reductive amination, nucleophilic displacement) were applied to connect bifunctional building blocks unrelated in structure (aromatic hydroxy acids, aromatic hydroxy aldehydes, amino alcohols, diamines, and amino acids). The focus of this communication is to document the use of bifunctional building blocks for the design and synthesis of structurally heterogeneous libraries of N-(alkoxy acyl)amino acids, N,N'-bis-(alkoxy acyl)diamino acids, N-acylamino ethers, N-(alkoxy acyl)amino alcohols, N-alkylamino ethers, and N-(alkoxy aryl)diamines.
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Affiliation(s)
- V Krchnák
- Selectide Corporation, Hoechst Marion Roussel, Tucson, AZ 85737, USA
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92
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Lou Q, Leftwich ME, Lam KS. Identification of GIYWHHY as a novel peptide substrate for human p60c-src protein tyrosine kinase. Bioorg Med Chem 1996; 4:677-82. [PMID: 8804533 DOI: 10.1016/0968-0896(96)00063-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have recently determined that -Ile-Tyr- were the two critical residues as a peptide substrate for p60c-src protein tyrosine kinase (Lou, Q. et al., Lett. Peptide Sci., 1995, 2, 289). Here, we report on the design and synthesis of a secondary 'one-bead, one-compound' combinatorial peptide library based on this dipeptide motif (XIYXXXX, where X = all 19 eukaryotic amino acids except for cysteine). This secondary library was screened for its ability to be phosphorylated by p60c-src PTK using [gamma 32P]ATP as a tracer. Five of the strongest [32P]-labeled peptide-beads were identified and microsequenced: GIYWHHY, KIYDDYE, EIYEENG, EIYEEYE, and YIYEEED. A solid-phase phosphorylation assay was used to evaluate the structure-activity relationship of GIYWHHY. It was determined that Ile2, Tyr3, His5, and His6 were crucial for its activity as a substrate.
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Affiliation(s)
- Q Lou
- Arizona Cancer Center, Tucson, USA
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93
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Freier SM, Konings DA, Wyatt JR, Ecker DJ. 'Mutational SURF': a strategy for improving lead compounds identified from combinatorial libraries. Bioorg Med Chem 1996; 4:717-25. [PMID: 8804538 DOI: 10.1016/0968-0896(96)00068-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Synthesis and testing of mixtures of compounds in a combinatorial library offers the potential of much greater throughput than the 'one compound, one well' approach. When mixtures of compounds are screened, however, pooling and deconvolution strategies must be employed to identify the most active compound in the library. The possibility exists that the most active compound will not be identified. We have developed a theoretical model of library deconvolution using the well characterized properties of nucleic acid hybridization to calculate activities of individual molecules in libraries of more than 250,000 compounds. Calculations using this model have been employed to evaluate strategies for pooling and deconvolution. In the presence of errors in synthesis and testing, iterative deconvolution or position scanning sometimes identified a compound with sub-optimal activity. We describe a procedure called 'mutational SURF' in which 'mutants' of the selected compound are individually synthesized and tested. Simulations of mutational SURF using our model libraries suggest that mutational SURF provides an efficient method for improving the activity of lead compounds identified from combinatorial libraries.
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Affiliation(s)
- S M Freier
- ISIS Pharmaceuticals, Carlsbad, CA 92008, USA
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94
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Krchnák V, Weichsel AS, Issakova O, Lam KS, Lebl M. Bifunctional scaffolds as templates for synthetic combinatorial libraries. Mol Divers 1996; 1:177-82. [PMID: 9237208 DOI: 10.1007/bf01544955] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A small-molecule synthetic combinatorial library was designed and synthesized that features potential pharmacophores attached to a variety of small cyclic scaffolds. The synthesis of the library involved randomization of three types of building blocks: 20 amino acids, 10 aromatic hydroxy acids and 21 alcohols, totaling a library complexity of 4200 compounds. Mitsunobu polymer-supported etherification was used in the last randomization. The library compounds were attached to beads via an ester-bond linkage enabling both on-bead as well as in-solution screening. When the library was tested against a model target, streptavidin, specific binders were found. The structures of the most active compounds were determined from the fragmentation pattern in MS/MS experiments.
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Affiliation(s)
- V Krchnák
- Selectide Corporation, Hoechst Marion Roussel, Tucson, AZ 85737, USA
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95
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Krchnák V, Lebl M. Synthetic library techniques: subjective (biased and generic) thoughts and views. Mol Divers 1996; 1:193-216. [PMID: 9237211 DOI: 10.1007/bf01544958] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Various aspects of synthetic diversity generation and screening are discussed. Controversial issues are raised and different points of view are presented. We hope the article will stimulate thinking about the utilization of library techniques and start a discussion about questions concerning their application.
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Affiliation(s)
- V Krchnák
- Selectide Corporation, Hoechst Marion Roussel, Tucson, AZ 85737, USA
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96
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Evans DM, Williams KP, McGuinness B, Tarr G, Regnier F, Afeyan N, Jindal S. Affinity-based screening of combinatorial libraries using automated, serial-column chromatography. Nat Biotechnol 1996; 14:504-7. [PMID: 9630929 DOI: 10.1038/nbt0496-504] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have developed an automated serial chromatographic technique for screening a library of compounds based upon their relative affinity for a target molecule. A "target" column containing the immobilized target molecule is set in tandem with a reversed-phase column. A combinatorial peptide library is injected onto the target column. The target-bound peptides are eluted from the first column and transferred automatically to the reversed-phase column. The target-specific peptide peaks from the reversed-phase column are identified and sequenced. Using a monoclonal antibody (3E-7) against beta-endorphin as a target, we selected a single peptide with sequence YGGFL from approximately 5800 peptides present in a combinatorial library. We demonstrated the applicability of the technology towards selection of peptides with predetermined affinity for bacterial lipopolysaccharide (LPS, endotoxin). We expect that this technology will have broad applications for high throughout screening of chemical libraries or natural product extracts.
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Affiliation(s)
- D M Evans
- PerSeptive Biosystems, Framingham, MA 01701, USA
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97
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Keifer PA. Influence of Resin Structure, Tether Length, and Solvent upon the High-Resolution (1)H NMR Spectra of Solid-Phase-Synthesis Resins. J Org Chem 1996; 61:1558-1559. [PMID: 11667018 DOI: 10.1021/jo952001t] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul A. Keifer
- Varian NMR Instruments, 3120 Hansen Way, Palo Alto, California 94304
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98
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Sarkar SK, Garigipati RS, Adams JL, Keifer PA. An NMR Method To Identify Nondestructively Chemical Compounds Bound to a Single Solid-Phase-Synthesis Bead for Combinatorial Chemistry Applications. J Am Chem Soc 1996. [DOI: 10.1021/ja952434d] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susanta K. Sarkar
- SmithKline Beecham Pharmaceuticals 709 Swedeland Road King of Prussia, Pennsylvania 19406 Varian NMR Instruments, 3120 Hansen Way Palo Alto, California 94304
| | - Ravi S. Garigipati
- SmithKline Beecham Pharmaceuticals 709 Swedeland Road King of Prussia, Pennsylvania 19406 Varian NMR Instruments, 3120 Hansen Way Palo Alto, California 94304
| | - Jerry L. Adams
- SmithKline Beecham Pharmaceuticals 709 Swedeland Road King of Prussia, Pennsylvania 19406 Varian NMR Instruments, 3120 Hansen Way Palo Alto, California 94304
| | - Paul A. Keifer
- SmithKline Beecham Pharmaceuticals 709 Swedeland Road King of Prussia, Pennsylvania 19406 Varian NMR Instruments, 3120 Hansen Way Palo Alto, California 94304
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99
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Affiliation(s)
- Lorin A. Thompson
- Department of Chemistry, University of California, Berkeley, California 94720
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100
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Chen CL, Strop P, Lebl M, Lam KS. One bead-one compound combinatorial peptide library: different types of screening. Methods Enzymol 1996; 267:211-9. [PMID: 8743318 DOI: 10.1016/s0076-6879(96)67014-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- C L Chen
- Hoechst Marion Roussel, Tucson, Arizona 85737, USA
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