Generation and screening of combinatorial peptide libraries designed for rapid sequencing by mass spectrometry

Youngquist, R.S.; Fuentes, Gary R.; Lacey, Martin P.; Keough, T.

doi:10.1021/ja00119a002

Cited by 219 publications

(186 citation statements)

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“…Glycopeptides can be generated in a library format via a combinatorial approach [7,8]. The most frequently implemented method for the generation of ''one-bead-one-compound" (glyco)peptide libraries [9,10] is the split-and-mix method [11,12]. This method, combined with the ladder synthesis strategy, offers facile synthesis and characterization of thousands of possible ligands that can be used for interaction studies or the development of new therapeutic agents.…”

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confidence: 99%

Assessing the inhibitory potency of galectin ligands identified from combinatorial (glyco)peptide libraries using surface plasmon resonance spectroscopy

Maljaars¹,

André²,

Halkes³

et al. 2008

Analytical Biochemistry

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a b s t r a c tCombinatorial (glyco)peptide libraries offer the possibility to define effective inhibitors of protein (lectin)-glycan interactions. If a (glyco)peptide surpasses the inhibitory potency of the free sugar, then the new peptide-lectin contacts underlying the affinity enhancement may guide further rational drug design. Focusing on the adhesion/growth regulatory human galectins 1 and 3, a screening of three combinatorial solid-phase (glyco)peptide libraries, containing Gal(b1-O)Thr, Gal(b1-S)Cys/Gal(b1-N)Asn, and Lac(b1-O)Thr, with the fluorescently labeled lectins had led to a series of lead compounds. To define the inhibitory potency of a selection of resynthesized (glyco)peptides systematically, a surface plasmon resonance-based inhibition assay with immobilized asialofetuin was set up. (Glyco)Peptides with up to 66-fold potency relative to free lactose as inhibitor were characterized. The presence of lactose in the most effective glycopeptides indicated the presence of affinity-enhancing peptide-lectin contacts. In addition to drug design, they may be helpful for fine-structural analysis of the binding sites.

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confidence: 99%

Assessing the inhibitory potency of galectin ligands identified from combinatorial (glyco)peptide libraries using surface plasmon resonance spectroscopy

Maljaars¹,

André²,

Halkes³

et al. 2008

Analytical Biochemistry

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“…[9][10][11]; (ii) spatially addressable syntheses in which the structure of a compound is deduced from its position on an array (2,(12)(13)(14); and (iii) split synthesis procedures, whereby compounds are built up on solid-phase beads, each of which has a unique history throughout the randomization steps and hence a unique structure-e.g., "one-bead-one-peptide" (4,6). The appropriate synthetic strategies can be modified in a number of ways so that with each component introduced by a combinatorial step, a conjugate "tag" is added in a parallel step; these coding sequences or tags are read subsequently to decode the steps used for the construction of the structure on any given bead.…”

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confidence: 99%

Enzyme-mediated spatial segregation on individual polymeric support beads: application to generation and screening of encoded combinatorial libraries.

Vagner

Bárány

Lam

et al. 1996

Proc. Natl. Acad. Sci. U.S.A.

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Proteolysis of short NO-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 groupsNa_tert-butyloxycarbonyl (Boc) and Na_9-fluorenylmethyloxycarbonyl (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 105 members at -6-fold degeneracy. From this single library, good ligands were selected for three different receptors: anti-.8-endorphin antibody, streptavidin, and thrombin, and the binding structures were deduced correctly by sequencing the coding peptides present on the same beads.

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“…Besides NMR spectroscopy, mass spectrometry has played an important role in library screening for determining the bound molecule either by MALDI-TOF 12 or ESI-MS. 13 Recently CSI-MS, a variant of ESI-MS operating at low temperature, was developed. 14,15 It facilitates observation of weaker associations among proteins, since the temperature at the spray interface is much lower.…”

Section: Introductionmentioning

confidence: 99%

Application of Difference NOE-pumping NMR Technique and Cold-Spray Ionization Mass Spectrometry to Identify a Ligand Binding with a Protein Receptor

et al. 2004

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The identification of compounds with a desired biological activity is a key step in the drug discovery process. There is a growing need for efficient methods, capable of reliably identifying compounds in a relatively short time span with desired binding affinity.Several NMR-based screening methods have been developed using chemical shift perturbation, 1-3 transferred NOE 4,5 and diffusion and relaxation editing methods. [6][7][8] In the development of NMR techniques for measuring binding affinity, one of the main aims is the reduction of experiment time and of sample usage without isotope enrichment. Although a high resolution structure of protein-ligand complex is preferable in rational drug design, the mapping of specific interaction sites obtained by NMR techniques often provides valuable insights for identifying lead compounds or analyzing their mode of binding.In designing NMR-based screening methods, it is critical to develop the technique capable of screening a large pool of new drug candidates and capable of identifying lead compounds with high affinity towards the target proteins. The most straightforward way to achieve this is by detecting only ligand signals while suppressing signals from target proteins. Recently, it has been shown that diffusion-based NOE-pumping experiment 9-11 can effectively be used to directly detect ligands that bind to the macromolecules. One of the disadvantages in this method is the technical difficulty to quickly optimize a diffusion filter for suppressing the ligand signals at a short NOE mixing time in preparation of the acquisition. For aim of developing an efficient and practical screening method to identify a lead compound with high affinity towards the protein receptor, a simple approach using the difference NOE-pumping experiment is implemented in this study.Besides NMR spectroscopy, mass spectrometry has played an important role in library screening for determining the bound molecule either by MALDI-TOF 12 or ESI-MS. 13 Recently CSI-MS, a variant of ESI-MS operating at low temperature, was developed.14,15 It facilitates observation of weaker associations among proteins, since the temperature at the spray interface is much lower. Although ESI-MS has been used for the detection of non-covalent macromolecular associations, [16][17][18][19] it is shown that CSI-MS is more sensitive in observations of macromolecular interaction. CSI-MS was successfully used to observe hyper-stranded DNA molecules that were unable to be detected by the ESI method 20 indicating the significant advance Pharmacy and Life Science, Hachioji, Japan *5 NM Application & Research Group, Application & Research Center, Analytical Instruments Division, JEOL Ltd., Musashino, Akishima, Japan *6 Department of Chemistry, Faculty of Science, Tokyo Metropolitan University, Hachioji, Japan A difference diffusion-based NMR technique and cold-spray ionization mass spectrometry were employed as a solutionbased approach for identifying a ligand binding with a protein receptor. The difference diffusion-b...

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Generation and screening of combinatorial peptide libraries designed for rapid sequencing by mass spectrometry

Cited by 219 publications

References 0 publications

Assessing the inhibitory potency of galectin ligands identified from combinatorial (glyco)peptide libraries using surface plasmon resonance spectroscopy

Assessing the inhibitory potency of galectin ligands identified from combinatorial (glyco)peptide libraries using surface plasmon resonance spectroscopy

Enzyme-mediated spatial segregation on individual polymeric support beads: application to generation and screening of encoded combinatorial libraries.

Application of Difference NOE-pumping NMR Technique and Cold-Spray Ionization Mass Spectrometry to Identify a Ligand Binding with a Protein Receptor

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