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Peptide Sequencing Directly on Solid Surfaces Using MALDI Mass Spectrometry. Sci Rep 2017; 7:17811. [PMID: 29259225 PMCID: PMC5736625 DOI: 10.1038/s41598-017-18105-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/05/2017] [Indexed: 11/08/2022] Open
Abstract
There are an increasing variety of applications in which peptides are both synthesized and used attached to solid surfaces. This has created a need for high throughput sequence analysis directly on surfaces. However, common sequencing approaches that can be adapted to surface bound peptides lack the throughput often needed in library-based applications. Here we describe a simple approach for sequence analysis directly on solid surfaces that is both high speed and high throughput, utilizing equipment available in most protein analysis facilities. In this approach, surface bound peptides, selectively labeled at their N-termini with a positive charge-bearing group, are subjected to controlled degradation in ammonia gas, resulting in a set of fragments differing by a single amino acid that remain spatially confined on the surface they were bound to. These fragments can then be analyzed by MALDI mass spectrometry, and the peptide sequences read directly from the resulting spectra.
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2
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The hidden potential of small synthetic molecules and peptides as affinity ligands for bioseparations. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.54] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Boschetti E, Righetti P. Mixed Beds. ADVANCES IN CHROMATOGRAPHY 2012. [DOI: 10.1201/b11636-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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Millward SW, Henning RK, Kwong GA, Pitram S, Agnew HD, Deyle KM, Nag A, Hein J, Lee SS, Lim J, Pfeilsticker JA, Sharpless KB, Heath JR. Iterative in situ click chemistry assembles a branched capture agent and allosteric inhibitor for Akt1. J Am Chem Soc 2011; 133:18280-8. [PMID: 21962254 DOI: 10.1021/ja2064389] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We describe the use of iterative in situ click chemistry to design an Akt-specific branched peptide triligand that is a drop-in replacement for monoclonal antibodies in multiple biochemical assays. Each peptide module in the branched structure makes unique contributions to affinity and/or specificity resulting in a 200 nM affinity ligand that efficiently immunoprecipitates Akt from cancer cell lysates and labels Akt in fixed cells. Our use of a small molecule to preinhibit Akt prior to screening resulted in low micromolar inhibitory potency and an allosteric mode of inhibition, which is evidenced through a series of competitive enzyme kinetic assays. To demonstrate the efficiency and selectivity of the protein-templated in situ click reaction, we developed a novel QPCR-based methodology that enabled a quantitative assessment of its yield. These results point to the potential for iterative in situ click chemistry to generate potent, synthetically accessible antibody replacements with novel inhibitory properties.
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Affiliation(s)
- Steven W Millward
- Nanosystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, MC-127-72, California Institute of Technology, Pasadena, California 91125, United States
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5
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Schnur DM, Beno BR, Tebben AJ, Cavallaro C. Methods for combinatorial and parallel library design. Methods Mol Biol 2011; 672:387-434. [PMID: 20838978 DOI: 10.1007/978-1-60761-839-3_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Diversity has historically played a critical role in design of combinatorial libraries, screening sets and corporate collections for lead discovery. Large library design dominated the field in the 1990s with methods ranging anywhere from purely arbitrary through property based reagent selection to product based approaches. In recent years, however, there has been a downward trend in library size. This was due to increased information about the desirable targets gleaned from the genomics revolution and to the ever growing availability of target protein structures from crystallography and homology modeling. Creation of libraries directed toward families of receptors such as GPCRs, kinases, nuclear hormone receptors, proteases, etc., replaced the generation of libraries based primarily on diversity while single target focused library design has remained an important objective. Concurrently, computing grids and cpu clusters have facilitated the development of structure based tools that screen hundreds of thousands of molecules. Smaller "smarter" combinatorial and focused parallel libraries replaced those early un-focused large libraries in the twenty-first century drug design paradigm. While diversity still plays a role in lead discovery, the focus of current library design methods has shifted to receptor based methods, scaffold hopping/bio-isostere searching, and a much needed emphasis on synthetic feasibility. Methods such as "privileged substructures based design" and pharmacophore based design still are important methods for parallel and small combinatorial library design. This chapter discusses some of the possible design methods and presents examples where they are available.
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Affiliation(s)
- Dora M Schnur
- Computer Aided Drug Design, Pharmaceutical Research Institute, Bristol-Myers Squibb Company, Princeton, NJ, USA
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6
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Fierabracci A. Unravelling autoimmune pathogenesis by screening random peptide libraries with human sera. Immunol Lett 2009; 124:35-43. [PMID: 19375456 DOI: 10.1016/j.imlet.2009.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 04/01/2009] [Accepted: 04/04/2009] [Indexed: 12/20/2022]
Abstract
The incidence of autoimmunity is increasing worldwide. The long preclinical period of autoimmune disorders is characterised by an enhanced exposure over time of autoreactive T cells to an increased number of autoantigenic determinants and autoantibodies production. The discovery of novel autoimmune-disease related epitopes is a task that remains extremely challenging in order to establish predictive and preventive strategies of the disease onset. In this Opinion article we highlight the contribution of screening combinatorial random peptide libraries with patients sera in unravelling the etiopathogenesis of autoimmunity.
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Affiliation(s)
- Alessandra Fierabracci
- Autoimmunity and Organ Regeneration Laboratory, Ospedale Pediatrico Bambino Gesu', Research Institute, Piazza S. Onofrio 4, 00165 Rome, Italy.
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7
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Boschetti E, Righetti PG. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 2009; 9:1492-510. [DOI: 10.1002/pmic.200800389] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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8
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Morgan RE, Westwood NJ. Screening and synthesis: high throughput technologies applied to parasitology. Parasitology 2008; 128 Suppl 1:S71-9. [PMID: 16454900 DOI: 10.1017/s0031182004007073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
High throughput technologies continue to develop in response to the challenges set by the genome projects. This article discusses how the techniques of both high throughput screening (HTS) and synthesis can influence research in parasitology. Examples of the use of targeted and phenotype-based HTS using unbiased compound collections are provided. The important issue of identifying the protein target(s) of bioactive compounds is discussed from the synthetic chemist's perspective. This article concludes by reviewing recent examples of successful target identification studies in parasitology.
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Affiliation(s)
- R E Morgan
- School of Chemistry, Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
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9
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Floyd CD, Leblanc C, Whittaker M. Combinatorial chemistry as a tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2000; 36:91-168. [PMID: 10818672 DOI: 10.1016/s0079-6468(08)70046-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.
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Affiliation(s)
- C D Floyd
- British Biotech Pharmaceuticals Limited, Oxford, U.K
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Dolle RE. Comprehensive survey of chemical libraries yielding enzyme inhibitors, receptor agonists and antagonists, and other biologically active agents: 1992 through 1997. ACTA ACUST UNITED AC 1999. [DOI: 10.1007/978-94-017-0735-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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11
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Dolle RE. Comprehensive survey of chemical libraries yielding enzyme inhibitors, receptor agonists and antagonists, and other biologically active agents: 1992 through 1997. Mol Divers 1998; 3:199-233. [PMID: 9850519 DOI: 10.1023/a:1009699413828] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This review is a historical accounting of chemical libraries from which biologically active agents have been obtained. The comprehensive tabulation includes citations as early as 1992, when the first descriptions of biologically active libraries were disclosed, and continues through 1997. Four tables are provided listing libraries screened against (1) proteolytic enzymes, (2) non-proteolytic enzymes, (3) G-protein coupled receptors (GPCRs), and (4) other targets not classified in the first three tables (e.g. non-GPCRs, integrins, antiinfectives). A name, generic structure, and size is provided for each library citation, accompanied by the molecular screen and the structure and potency of the most active library member. In total, 86 libraries are presented with 60% of the contributions reported from pharmaceutical and biotechnology companies. Approximately 70% of the libraries have used alpha-amino acid synthons in their construction and 85% of the libraries include one or more amide bonds.
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Affiliation(s)
- R E Dolle
- Department of Chemistry, Pharmacopeia, Inc., Princeton, NJ 08540, USA.
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12
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Babcock B, Anderson BW, Papayannopoulos I, Castilleja A, Murray JL, Stifani S, Kudelka AP, Wharton JT, Ioannides CG. Ovarian and breast cytotoxic T lymphocytes can recognize peptides from the amino enhancer of split protein of the Notch complex. Mol Immunol 1998; 35:1121-33. [PMID: 10395201 DOI: 10.1016/s0161-5890(98)00100-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study we investigated recognition by ovarian tumor associated lymphocyte (OVTAL), and breast tumor associated lymphocytes (BRTAL), of peptides corresponding to the sequence 125-135 of the Aminoenhancer of split (AES) protein. Three of these peptides designated as G75:AES1/2 (128-135), G60: AES1/2 (127-137) and G61: AES1/2 (125-133) correspond to the wildtype AES sequence, while the fourth G76:GPLTPLPV, AES1/2 (128-135) corresponds to a variant sequence of the peptide G75 with the N-terminal Leu substituted to glycine. These sequences were chosen for study because mass-spectrometric analysis (MS) of a CTL active HPLC peptide fraction eluted from immunoaffinity precipitated HLA-A2 molecule, revealed: (a) the presence of an ion with a mass-to-charge ratio (m/z) of 793 which was more abundant than other ions of similar masses; (b) the tentatively reconstituted sequence of the ion 793 matched the sequence of peptide G76. We found that AES peptides G75 (128-135) and G76 (128-135) (L128G) reconstituted CTL recognition at concentrations ranging between 200-500 nM. These concentrations are lower than concentrations reported to activate effector function of CTL recognizing other epithelial tumor Ag. Furthermore, analysis with cloned CD8+ T cells indicated that G75 and G76 were not cross-reactive specificities, suggesting a key role for the N-terminal residues of the variant peptide in dictating specificities. Since the AES proteins are part of a set of transcriptional repressors encoded by the Enhancer of split [E(spl)] genes, and since these repressors are activated to suppress cell differentiation in response to Notch receptors signalling, the AES peptides may represent a novel class of self-antigens that deserve further consideration as tumor Ag in epithelial cancers.
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Affiliation(s)
- B Babcock
- Department of Gynecologic Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, USA
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Samson I, Rozenski J, Samyn B, Van Aerschot A, Van Beeumen J, Herdewijn P. Screening a random pentapeptide library, composed of 14 D-amino acids, against the COOH-terminal sequence of fructose-1,6-bisphosphate aldolase from Trypanosoma brucei. J Biol Chem 1997; 272:11378-83. [PMID: 9111046 DOI: 10.1074/jbc.272.17.11378] [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] Open
Abstract
A random pentapeptide library composed of 14 D-amino acids, including two unusual amino acids, thus representing 537,824 different peptide sequences anchored on polystyrene beads was created with each bead bearing a single pentapeptide sequence. This library was used for affinity screening against the fructose-1, 6-bisphosphate aldolase of Trypanosoma brucei labeled with biotin as well as versus the COOH-terminal labeled with fluorescein isothiocyanate. The thus selected peptide beads were identified and the appropriate sequences synthesized as peptide amides and evaluated for enzyme activity inhibition. Screening against the whole enzyme did not result in selection of an enzyme inhibitor. However, we demonstrate here that screening against a part of the enzyme involved in the catalytic activity may lead to the discovery of an enzyme inhibitor as well as an enzyme activator. Two low affinity inhibitors, RRVKF-NH2 and KThiKAR-NH2, with an IC50 of approximately 1 mM and approximately 0.2 mM, respectively, were identified. Two other pentapeptides with the sequence SWChaKK-NH2 and SKChaKM-NH2 are able to activate the enzyme fructose-1, 6-bisphosphate aldolase. Thus, successful screening of solid phase libraries can be accomplished using selected sequences of the target enzyme.
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Affiliation(s)
- I Samson
- Laboratory of Medicinal Chemistry (F. F. W.), Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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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: 507] [Impact Index Per Article: 18.8] [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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Samson I, Rozenski J, van Aerschot A, Samyn B, van Beeumen J, Herdewijn P. Screening of a synthetic pentapeptide library composed of d-amino acids against fructose-1,6-biphosphate aldolase. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf00119166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Samson I, van Aerschot A, Samyn B, van Beeumen J, Herdewijn P. Screening of a synthetic peptide library against glycosomal phosphoglycerate kinase of Trypanosoma brucei. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf00119157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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