1
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Peker T, Zagiel B, Rocard L, Bich C, Sachon E, Moumné R. Analytical Tools for Dynamic Combinatorial Libraries of Cyclic Peptides. Chembiochem 2023; 24:e202300688. [PMID: 37815502 DOI: 10.1002/cbic.202300688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
Target-directed dynamic combinatorial chemistry is a very attractive strategy for the discovery of bioactive peptides. However, its application has not yet been demonstrated, presumably due to analytical challenges that arise from the diversity of a peptide library with combinatorial side-chains. We previously reported an efficient method to generate, under biocompatible conditions, large dynamic libraries of cyclic peptides grafted with amino acid's side-chains, by thiol-to-thioester exchanges. In this work, we present analytical tools to easily characterize such libraries by HPLC and mass spectrometry, and in particular to simplify the isomers' distinction requiring sequencing by MS/MS fragmentations. After structural optimization, the cyclic scaffold exhibits a UV-tag, absorbing at 415 nm, and an ornithine residue which favors the regioselective ring-opening and simultaneous MS/MS fragmentation, in the gas-phase.
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Affiliation(s)
- Taleen Peker
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Benjamin Zagiel
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Lou Rocard
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Emmanuelle Sachon
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
- MS3U Platform, Fédération de Chimie Moléculaire de Paris Centre - FR2769, Sorbonne Université, 4 Place Jussieu, 75005, Paris, France
| | - Roba Moumné
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
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2
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Li H, Hou Z, Wang Y, Zhou Z, Cai J, Xin Q, Yin F, Li Z, Xu N. Methodology of stable peptide based on propargylated sulfonium. Biochem Biophys Rep 2023; 35:101508. [PMID: 37448811 PMCID: PMC10336417 DOI: 10.1016/j.bbrep.2023.101508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Peptides can be used as effective molecular tool for covalent modification of proteins and play important roles in ligand directed covalent modification. Tyr-selective protein modifications exert a profound impact on protein functionality. Here, we developed a general strategy that involves nucleophilic addition of alkyne for tyrosine modification. The terminal alkyne of propargyl sulfonium is motivated by the sulfonium center to react with phenolic hydroxyl. This approach provides a straightforward method for tyrosine modification due to its high yield in aqueous solution at physiological temperature. In addition, cyclic peptides could be obtained via adjusting pH to 8.0 from peptides consisting of tyrosine and methionine modified by propargyl bromide, and the resulting cyclic peptides are proved to have better stability, excellent 2-mercaptopyridine resistance and improved cellular uptakes. Furthermore, molecules made from the propargylated sulfonium have the potential to be used as warheads against tyrosine containing biomolecules. Collectively, we develop a direct and uncomplicated technique for modifying tyrosine residues, the strategy concerned can be widely utilized to construct stable peptides and biomolecules imaging.
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Affiliation(s)
- Heng Li
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhanfeng Hou
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Ziyuan Zhou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jin Cai
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Qilei Xin
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Naihan Xu
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
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3
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Price S, Mehta R, Tan D, Hinojosa A, Thomas PW, Cummings T, Fast W, Que EL. Structural insights into the design of reversible fluorescent probes for metallo-β-lactamases NDM-1, VIM-2, and IMP-1. J Inorg Biochem 2022; 233:111869. [PMID: 35653820 PMCID: PMC9216179 DOI: 10.1016/j.jinorgbio.2022.111869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 12/31/2022]
Abstract
Metallo-β-lactamases (MBLs) are enzymes that are capable of hydrolyzing most β-lactam antibiotics and all clinically relevant carbapenems. We developed a library of reversible fluorescent turn-on probes that are designed to directly bind to the dizinc active site of these enzymes and can be used to study their dynamic metalation state and enzyme-inhibitor interactions. Structure-function relationships with regards to inhibitory strength and fluorescence turn-on response were evaluated for three representative MBLs.
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Affiliation(s)
- Sky Price
- Department of Chemistry, University of Texas at Austin, 105 E 24th St Stop A5300, Austin, TX 78712, United States of America
| | - Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 E 24th St Stop A5300, Austin, TX 78712, United States of America
| | - Dominique Tan
- Department of Chemistry, University of Texas at Austin, 105 E 24th St Stop A5300, Austin, TX 78712, United States of America
| | - Abigail Hinojosa
- Department of Chemistry, University of Texas at Austin, 105 E 24th St Stop A5300, Austin, TX 78712, United States of America
| | - Pei W. Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, and the LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, United States of America
| | - Tawanda Cummings
- Department of Chemistry, University of Texas at Austin, 105 E 24th St Stop A5300, Austin, TX 78712, United States of America
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, and the LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, United States of America
| | - Emily L. Que
- Department of Chemistry, University of Texas at Austin, 105 E 24th St Stop A5300, Austin, TX 78712, United States of America,Corresponding author. (E.L. Que)
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4
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Murphy SA, Phelan C, Shanmugaraju S, Blasco S, Gunnlaugsson T. Fluorescent 3-amino-1,8-naphthalimide Tröger’s bases (3-amino-TBNaps) incorporating protected α-amino acids. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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5
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Murphy SA, Phelan CA, Veale EB, Kotova O, Comby S, Gunnlaugsson T. Fluorescent 4-amino-1,8-naphthalimide Tröger's bases (TBNaps) possessing (orthogonal) 'α-amino acids', esters and di-peptides and their solvent dependent photophysical properties. Org Biomol Chem 2021; 19:6817-6833. [PMID: 34308464 DOI: 10.1039/d1ob00973g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of fifteen luminescent bis-naphthalimide based Tröger's bases (TBNaps) derived from 4-amino-1,8-naphthalimide (4-Amino-Nap) precursors is described; these scaffolds possess α-amino acids, esters or di-peptides conjugated at the imide site and show minor fluorescence in aqueous solution while being highly emissive in organic solvents. The investigation shows that these TBNaps possessing ICT excited state properties are capable of generating either positive or negative solvatochromic effects in response to changes in polarity and/or the hydrogen bonding capabilities of the medium.
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Affiliation(s)
- Samantha A Murphy
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
| | - Caroline A Phelan
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
| | - Emma B Veale
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
| | - Oxana Kotova
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland. and Advanced Materials and BioEngineering Research (AMBER) Centre, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Steve Comby
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
| | - Thorfinnur Gunnlaugsson
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland. and Advanced Materials and BioEngineering Research (AMBER) Centre, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
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6
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Zhang Y, Wang Y, Yan Z, Song C, Miao G, Zhang L. Design, Synthesis, and Use of Novel Photoaffinity Probes in Measuring the Serum Concentration of Glycogen Phosphorylase. Molecules 2019; 24:E798. [PMID: 30813328 PMCID: PMC6413153 DOI: 10.3390/molecules24040798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 11/17/2022] Open
Abstract
A procedure to measure the serum concentration of glycogen phosphorylase during acute myocardial infarction is presented. This method was based on the synthesis of photoaffinity probes, and used the semiquantitative protein electrophoretic mobility shift technique. Three novel photoaffinity probes bearing different secondary tags were synthesized. Their potency was evaluated in an enzyme inhibition assay against rabbit muscle glycogen phosphorylase a (RMGPa). The inhibitory activity of probe 1 was only 100-fold less potent than the mother compound CP-320626. The photoaffinity labeling experiments were also performed, and a protein with molecular weight (MW) of about 90⁻100 kDa, which was consistent with the MW of GP, was clearly labeled by probe 1. A semiquantitative evaluation of the GP level in serum with probe 1 was also performed. The results showed that the protein band with a MW of about 90⁻100 kDa was tagged, and the concentration of the protein in serum was found to be between 25 and 50 ng/mL. Mass spectrometric analysis revealed that alpha-1,4 glucan phosphorylase (GPMM) was well-preserved in the bands.
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Affiliation(s)
- Yuchao Zhang
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde 067000, China.
| | - Youde Wang
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde 067000, China.
| | - Zhiwei Yan
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde 067000, China.
| | - Chengjun Song
- Department of Human Anatomy, Chengde Medical University, Chengde 067000, China.
| | - Guangxin Miao
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde 067000, China.
| | - Liying Zhang
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde 067000, China.
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7
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Battista E, Scognamiglio PL, Di Luise N, Raucci U, Donati G, Rega N, Netti PA, Causa F. Turn-on fluorescence detection of protein by molecularly imprinted hydrogels based on supramolecular assembly of peptide multi-functional blocks. J Mater Chem B 2018; 6:1207-1215. [PMID: 32254181 DOI: 10.1039/c7tb03107f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Synthetic receptors for biomacromolecules lack the supramolecular self-assembly behavior typical of biological systems. Here we propose a new method for the preparation of protein imprinted polymers based on the specific interaction of a peptide multi-functional block with a protein target. This peptide block contains a protein-binding peptide domain, a polymerizable moiety at the C-terminus and an environment-sensitive fluorescent molecule at the N-terminus. The method relies on a preliminary step consisting of peptide/protein supramolecular assembly, followed by copolymerization with the most common acrylate monomers (acrylamide, acrylic acid and bis-acrylamide) to produce a protein imprinted hydrogel polymer. Such a peptide block can function as an active assistant recognition element to improve affinity, and guarantees its effective polymerization at the protein/cavity interface, allowing for proper placement of a dye. As a proof of concept, we chose Bovine Serum Albumin (BSA) as the protein target and built the peptide block around a BSA binding dodecapeptide, with an allyl group as the polymerizable moiety and a dansyl molecule as the responsive dye. Compared to conventional approaches these hydrogels showed higher affinity (more than 45%) and imprinted sensitivity (about twenty fold) to the target, with a great BSA selectivity with respect to ovalbumin (α = 1.25) and lysozyme (α = 6.02). Upon protein binding, computational and experimental observations showed a blue shift of the emission peak (down to 440 nm) and an increase of fluorescence emission (twofold) and average lifetime (Δτ = 4.3 ns). Such an approach generates recognition cavities with controlled chemical information and represents an a priori method for self-responsive materials. Provided a specific peptide and minimal optimization conditions are used, such a method could be easily implemented for any protein target.
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Affiliation(s)
- Edmondo Battista
- Interdisciplinary Research Centre on Biomaterials (CRIB) Università degli studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy.
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8
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Erak M, Bellmann-Sickert K, Els-Heindl S, Beck-Sickinger AG. Peptide chemistry toolbox - Transforming natural peptides into peptide therapeutics. Bioorg Med Chem 2018; 26:2759-2765. [PMID: 29395804 DOI: 10.1016/j.bmc.2018.01.012] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/09/2018] [Accepted: 01/18/2018] [Indexed: 01/27/2023]
Abstract
The development of solid phase peptide synthesis has released tremendous opportunities for using synthetic peptides in medicinal applications. In the last decades, peptide therapeutics became an emerging market in pharmaceutical industry. The need for synthetic strategies in order to improve peptidic properties, such as longer half-life, higher bioavailability, increased potency and efficiency is accordingly rising. In this mini-review, we present a toolbox of modifications in peptide chemistry for overcoming the main drawbacks during the transition from natural peptides to peptide therapeutics. Modifications at the level of the peptide backbone, amino acid side chains and higher orders of structures are described. Furthermore, we are discussing the future of peptide therapeutics development and their impact on the pharmaceutical market.
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Affiliation(s)
- Miloš Erak
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Kathrin Bellmann-Sickert
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Sylvia Els-Heindl
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany.
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9
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Haque N, Baratam K, Prabhu NP. Analysing the microenvironment of 2-p-toluidinylnaphthalene-6-sulfonate (TNS) in solvents and in different conformational states of proteins in relation to its fluorescence properties: a computational study. Phys Chem Chem Phys 2017; 19:24656-24666. [PMID: 28857104 DOI: 10.1039/c7cp03951d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Characterization of different conformational states of proteins is essential to understand their stability and activity. Biophysical techniques aid in analysing these conformational states and molecular fluorescence is one of the most reliable and quickly accessible methods. Apart from the intrinsic fluorescence of proteins, external fluorescence dyes such as TNS, ANS, nile red and thioflavin are also used to characterize partially unfolded, aggregated and fibrillar states of proteins, though their exact molecular-level interactions with proteins are yet to be completely unravelled. The present study attempts to investigate the binding of TNS molecules on different conformational states of proteins. Unconstrained molecular dynamics simulation of 50 molecules of TNS with the native state of BSA, native and two partially unfolded states of RNase A and α-lactalbumin in water was carried out. Dynamics simulation of TNS alone in different solvents such as water, ethanol, DMF and DMSO was also performed. Binding environments in all the proteins and the solvents were analysed in terms of H-bonding interactions, order of contacts, amino acid specificity and conformational changes of TNS, and correlated with experimentally observed fluorescence changes of the dye. The results suggest that TNS forms aggregates in water whereas in non-aqueous solvents the order of aggregates is lower which might result in an enhancement of its fluorescence intensity. Further, TNS preferably interacts with basic and aromatic amino acid residues of the proteins. In RNase A and α-lactalbumin, most of the TNS molecules tend to form aggregates even with the unfolded conformations of the proteins. However in BSA, the number of aggregated TNS molecules is less and TNS molecules in monomeric form are found in the hydrophobic crevices of the protein. This might result in an enhancement of the fluorescence in BSA compared to the other proteins. The distributions of angles and dihedrals of TNS in different environments suggest that the bending movement between the naphthyl and tolyl rings is constrained whereas significant planar rotations could be observed both in solvents and in protein-bound states.
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Affiliation(s)
- Neshatul Haque
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad - 500046, India.
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10
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Sainlos M, Iskenderian-Epps WS, Olivier NB, Choquet D, Imperiali B. Caged Mono- and Divalent Ligands for Light-Assisted Disruption of PDZ Domain-Mediated Interactions. J Am Chem Soc 2013; 135:4580-3. [DOI: 10.1021/ja309870q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Matthieu Sainlos
- Departments of Chemistry and
Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- University of Bordeaux, IINS, CNRS, UMR 5297, F-33000 Bordeaux, France
- CNRS, IINS, UMR 5297,
F-33000 Bordeaux, France
| | - Wendy S. Iskenderian-Epps
- Departments of Chemistry and
Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nelson B. Olivier
- Departments of Chemistry and
Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel Choquet
- University of Bordeaux, IINS, CNRS, UMR 5297, F-33000 Bordeaux, France
- CNRS, IINS, UMR 5297,
F-33000 Bordeaux, France
| | - Barbara Imperiali
- Departments of Chemistry and
Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Penas C, Pazos E, Mascareñas JL, Vázquez ME. A Folding-Based Approach for the Luminescent Detection of a Short RNA Hairpin. J Am Chem Soc 2013; 135:3812-4. [DOI: 10.1021/ja400270a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Cristina Penas
- Centro Singular
de Investigación en Química
Biolóxica e Materiais Moleculares (CIQUS), Departamento de
Química Orgánica and Unidad Asociada al CSIC, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Elena Pazos
- Centro Singular
de Investigación en Química
Biolóxica e Materiais Moleculares (CIQUS), Departamento de
Química Orgánica and Unidad Asociada al CSIC, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - José L. Mascareñas
- Centro Singular
de Investigación en Química
Biolóxica e Materiais Moleculares (CIQUS), Departamento de
Química Orgánica and Unidad Asociada al CSIC, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - M. Eugenio Vázquez
- Centro Singular
de Investigación en Química
Biolóxica e Materiais Moleculares (CIQUS), Departamento de
Química Orgánica and Unidad Asociada al CSIC, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
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12
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Jeong HS, Choi SM, Kim HW, Park JW, Park HN, Park SM, Jang SK, Rhee YM, Kim BH. Fluorescent peptide indicator displacement assay for monitoring interactions between RNA and RNA binding proteins. ACTA ACUST UNITED AC 2013; 9:948-51. [DOI: 10.1039/c2mb25470k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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13
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Goguen BN, Loving GS, Imperiali B. Development of a fluorogenic sensor for activated Cdc42. Bioorg Med Chem Lett 2011; 21:5058-61. [PMID: 21549598 DOI: 10.1016/j.bmcl.2011.04.051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 04/08/2011] [Accepted: 04/12/2011] [Indexed: 11/30/2022]
Abstract
Cdc42, a member of the Rho GTPase family, is a fundamental regulator of the actin cytoskeleton during cell migration. To generate a sensor for Cdc42 activation, we employed a multi-pronged approach, utilizing cysteine labeling and expressed protein ligation, to incorporate the environment sensitive fluorophore 4-N,N-dimethylamino-1,8-naphthalimide (4-DMN) into the GTPase binding domain of the WASP protein. These constructs bind only the active, GTP-bound conformation of Cdc42 to produce a fluorescence signal. Studies with a panel of five sensor analogs revealed a derivative that exhibits a 32-fold increase in fluorescence intensity in the presence of activated Cdc42 compared to incubation with the inactive GDP-bound form of the protein. We demonstrate that this sensor can be exploited to monitor Cdc42 nucleotide exchange and GTPase activity in a continuous, fluorescence assay.
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Affiliation(s)
- Brenda N Goguen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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14
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Iskenderian-Epps WS, Imperiali B. Modulation of Shank3 PDZ domain ligand-binding affinity by dimerization. Chembiochem 2011; 11:1979-84. [PMID: 20715264 DOI: 10.1002/cbic.201000246] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Pazos E, Pérez M, Gutiérrez-de-Terán H, Orzáez M, Guevara T, Mascareñas JL, Vázquez ME. Rational design of a cyclin A fluorescent peptide sensor. Org Biomol Chem 2011; 9:7629-32. [DOI: 10.1039/c1ob06009k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Sainlos M, Tigaret C, Poujol C, Olivier NB, Bard L, Breillat C, Thiolon K, Choquet D, Imperiali B. Biomimetic divalent ligands for the acute disruption of synaptic AMPAR stabilization. Nat Chem Biol 2010; 7:81-91. [DOI: 10.1038/nchembio.498] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 11/08/2010] [Indexed: 11/09/2022]
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17
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Sainlos M, Imperiali B. Tools for investigating peptide-protein interactions: peptide incorporation of environment-sensitive fluorophores through SPPS-based 'building block' approach. Nat Protoc 2008; 2:3210-8. [PMID: 18079721 DOI: 10.1038/nprot.2007.443] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol presents the synthesis and peptide incorporation of environment-sensitive fluorescent amino acids derived from the dimethylamino-phthalimide family. The procedure uses anhydride precursors of 4-dimethylaminophthalimide (4-DMAP) or 6-dimethylaminonaphthalimide (6-DMN), whose syntheses are described in a related protocol by these authors. In this study, the corresponding fluorescent amino acids can be readily obtained in Fmoc-protected form for convenient use as building blocks in solid phase peptide synthesis (SPPS). The time required to complete the procedure depends on the size and the number of peptides targeted. Alternatively, the chromophores can be incorporated directly after SPPS via on-resin derivatization of peptides, which is an option described in a related protocol by these authors.
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Affiliation(s)
- Matthieu Sainlos
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
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18
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Sainlos M, Imperiali B. Synthesis of anhydride precursors of the environment-sensitive fluorophores 4-DMAP and 6-DMN. Nat Protoc 2008; 2:3219-25. [PMID: 18079722 DOI: 10.1038/nprot.2007.444] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the synthesis of cyclic anhydride precursors of the environment-sensitive fluorophores 4-dimethylaminophthalimide (4-DMAP) and 6-dimethylaminonaphthalimide (6-DMN). The condensation of these anhydrides with a primary amino group confers on molecules of interest solvatochromic properties. In particular, two strategies for the insertion of the chromophores into peptides are presented in two companion protocols. The anhydride syntheses can be completed on the gram scale in 2 d for the 4-DMAP precursor and 10-15 d for the 6-DMN precursor.
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Affiliation(s)
- Matthieu Sainlos
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
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