1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Maujean T, Wagner P, Valencia C, Riché S, Iturrioz X, Villa P, Girard N, Karpenko J, Gulea M, Bonnet D. Rapid and Highly Selective Fluorescent Labeling of Peptides via a Thia-Diels-Alder Cycloaddition: Application to Apelin. Bioconjug Chem 2023; 34:162-168. [PMID: 36534753 DOI: 10.1021/acs.bioconjchem.2c00500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Herein, we describe a catalyst-free thia-Diels-Alder cycloaddition for the chemoselective labeling of fully deprotected phosphonodithioester-peptides in solution with fluorophores functionalized with an exocyclic diene. The reaction was optimized on the model tripeptide 1 containing a lysine residue, which enabled its rapid and straightforward labeling with three different fluorophores (fluorescein, lissamine rhodamine B, and squaraine) in very mild conditions (H2O/iPrOH, 37 °C, 1 h). The reaction was then successfully applied to the chemoselective labeling of fully deprotected apelin-13 with squaraine dye. The resulting fluorescent ligand 18 exhibited a high affinity (0.17 ± 0.03 nM) for apelinR. It enabled the development of time-resolved FRET-based competition assays for high-throughput screening and drug discovery. Thanks to its fluorogenic properties, ligand 18 was also successfully involved in the live-cell optical imaging of apelinR in no-wash conditions.
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Affiliation(s)
- Timothé Maujean
- Université de Strasbourg, CNRS, Laboratoire d'Innovation Thérapeutique, LIT UMR 7200, F-67400 Strasbourg, France
| | - Patrick Wagner
- Université de Strasbourg, CNRS, Laboratoire d'Innovation Thérapeutique, LIT UMR 7200, F-67400 Strasbourg, France
| | - Christel Valencia
- Université de Strasbourg, CNRS, PCBIS Plateforme de chimie biologie intégrative de Strasbourg, UAR 3286, F-67412 Illkirch, France
| | - Stéphanie Riché
- Université de Strasbourg, CNRS, Laboratoire d'Innovation Thérapeutique, LIT UMR 7200, F-67400 Strasbourg, France
| | - Xavier Iturrioz
- CEA, Institute of Biology and Technology, Service d'Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France
| | - Pascal Villa
- Université de Strasbourg, CNRS, PCBIS Plateforme de chimie biologie intégrative de Strasbourg, UAR 3286, F-67412 Illkirch, France
| | - Nicolas Girard
- Université de Strasbourg, CNRS, Laboratoire d'Innovation Thérapeutique, LIT UMR 7200, F-67400 Strasbourg, France
| | - Julie Karpenko
- Université de Strasbourg, CNRS, Laboratoire d'Innovation Thérapeutique, LIT UMR 7200, F-67400 Strasbourg, France
| | - Mihaela Gulea
- Université de Strasbourg, CNRS, Laboratoire d'Innovation Thérapeutique, LIT UMR 7200, F-67400 Strasbourg, France
| | - Dominique Bonnet
- Université de Strasbourg, CNRS, Laboratoire d'Innovation Thérapeutique, LIT UMR 7200, F-67400 Strasbourg, France
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3
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Larsen JB, Taebnia N, Dolatshahi-Pirouz A, Eriksen AZ, Hjørringgaard C, Kristensen K, Larsen NW, Larsen NB, Marie R, Mündler AK, Parhamifar L, Urquhart AJ, Weller A, Mortensen KI, Flyvbjerg H, Andresen TL. Imaging therapeutic peptide transport across intestinal barriers. RSC Chem Biol 2021; 2:1115-1143. [PMID: 34458827 PMCID: PMC8341777 DOI: 10.1039/d1cb00024a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Oral delivery is a highly preferred method for drug administration due to high patient compliance. However, oral administration is intrinsically challenging for pharmacologically interesting drug classes, in particular pharmaceutical peptides, due to the biological barriers associated with the gastrointestinal tract. In this review, we start by summarizing the pharmacological performance of several clinically relevant orally administrated therapeutic peptides, highlighting their low bioavailabilities. Thus, there is a strong need to increase the transport of peptide drugs across the intestinal barrier to realize future treatment needs and further development in the field. Currently, progress is hampered by a lack of understanding of transport mechanisms that govern intestinal absorption and transport of peptide drugs, including the effects of the permeability enhancers commonly used to mediate uptake. We describe how, for the past decades, mechanistic insights have predominantly been gained using functional assays with end-point read-out capabilities, which only allow indirect study of peptide transport mechanisms. We then focus on fluorescence imaging that, on the other hand, provides opportunities to directly visualize and thus follow peptide transport at high spatiotemporal resolution. Consequently, it may provide new and detailed mechanistic understanding of the interplay between the physicochemical properties of peptides and cellular processes; an interplay that determines the efficiency of transport. We review current methodology and state of the art in the field of fluorescence imaging to study intestinal barrier transport of peptides, and provide a comprehensive overview of the imaging-compatible in vitro, ex vivo, and in vivo platforms that currently are being developed to accelerate this emerging field of research.
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Affiliation(s)
- Jannik Bruun Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nayere Taebnia
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Alireza Dolatshahi-Pirouz
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Anne Zebitz Eriksen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Claudia Hjørringgaard
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kasper Kristensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nanna Wichmann Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Niels Bent Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Rodolphe Marie
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ann-Kathrin Mündler
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ladan Parhamifar
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Andrew James Urquhart
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Arjen Weller
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kim I Mortensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Henrik Flyvbjerg
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Thomas Lars Andresen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
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4
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Wu Y, Tam WS, Chau HF, Kaur S, Thor W, Aik WS, Chan WL, Zweckstetter M, Wong KL. Solid-phase fluorescent BODIPY-peptide synthesis via in situ dipyrrin construction. Chem Sci 2020; 11:11266-11273. [PMID: 34094367 PMCID: PMC8162834 DOI: 10.1039/d0sc04849f] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/23/2020] [Indexed: 12/28/2022] Open
Abstract
Traditional fluorescent peptide chemical syntheses hinge on the use of limited fluorescent/dye-taggable unnatural amino acids and entail multiple costly purifications. Here we describe a facile and efficient protocol for in situ construction of dipyrrins on the N-terminus with 20 natural and five unnatural amino acids and the lysine's side chain of selected peptides/peptide drugs through Fmoc-based solid-phase peptide synthesis. The new strategy enables the direct formation of boron-dipyrromethene (BODIPY)-peptide conjugates from simple aldehyde and pyrrole derivatives without pre-functionalization, and only requires a single-time chromatographic purification at the final stage. As a model study, synthesized EBNA1-targeting BODIPY1-Pep4 demonstrates intact selectivity in vitro, responsive fluorescence enhancement, and higher light cytotoxicity due to the photo-generation of cytotoxic singlet oxygen. This work offers a novel practical synthetic platform for fluorescent peptides for multifaceted biomedical applications.
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Affiliation(s)
- Yue Wu
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Wing-Sze Tam
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Ho-Fai Chau
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Simranjeet Kaur
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Waygen Thor
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Wei Shen Aik
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
| | - Wai-Lun Chan
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- German Center for Neurodegenerative Diseases (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Germany
| | - Markus Zweckstetter
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- German Center for Neurodegenerative Diseases (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Germany
| | - Ka-Leung Wong
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR China
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5
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Synthesis of a HyCoSuL peptide substrate library to dissect protease substrate specificity. Nat Protoc 2017; 12:2189-2214. [PMID: 28933778 DOI: 10.1038/nprot.2017.091] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many biologically and chemically based approaches have been developed to design highly active and selective protease substrates and probes. It is, however, difficult to find substrate sequences that are truly selective for any given protease, as different proteases can demonstrate a great deal of overlap in substrate specificities. In some cases, better enzyme selectivity can be achieved using peptide libraries containing unnatural amino acids such as the hybrid combinatorial substrate library (HyCoSuL), which uses both natural and unnatural amino acids. HyCoSuL is a combinatorial library of tetrapeptides containing amino acid mixtures at the P4-P2 positions, a fixed amino acid at the P1 position, and an ACC (7-amino-4-carbamoylmethylcoumarin) fluorescent tag occupying the P1' position. Once the peptide is recognized and cleaved by a protease, the ACC is released and produces a readable fluorescence signal. Here, we describe the synthesis and screening of HyCoSuL for human caspases and legumain. We also discuss possible modifications and adaptations of this approach that make it a useful tool for developing highly active and selective reagents for a wide variety of proteolytic enzymes. The protocol can be divided into three major parts: (i) solid-phase synthesis of the fluorescence-labeled HyCoSuL, (ii) screening of protease P4-P2 preferences, and (iii) synthesis of the optimized activity probes equipped with an AOMK (acyloxymethyl ketone) reactive group and a biotin label for easy detection. Beginning with the library design, the entire protocol can be completed in 4-8 weeks (HyCoSuL synthesis: 3-5 weeks; HyCoSuL screening per enzyme: 4-8 d; and activity-based probe synthesis: 1-2 weeks).
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6
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Mendive-Tapia L, Subiros-Funosas R, Zhao C, Albericio F, Read ND, Lavilla R, Vendrell M. Preparation of a Trp-BODIPY fluorogenic amino acid to label peptides for enhanced live-cell fluorescence imaging. Nat Protoc 2017; 12:1588-1619. [PMID: 28703788 DOI: 10.1038/nprot.2017.048] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fluorescent peptides are valuable tools for live-cell imaging because of the high specificity of peptide sequences for their biomolecular targets. When preparing fluorescent versions of peptides, labels must be introduced at appropriate positions in the sequences to provide suitable reporters while avoiding any impairment of the molecular recognition properties of the peptides. This protocol describes the preparation of the tryptophan (Trp)-based fluorogenic amino acid Fmoc-Trp(C2-BODIPY)-OH and its incorporation into peptides for live-cell fluorescence imaging-an approach that is applicable to most peptide sequences. Fmoc-Trp(C2-BODIPY)-OH contains a BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) fluorogenic core, which works as an environmentally sensitive fluorophore, showing high fluorescence in lipophilic conditions. It is attached to Trp via a spacer-free C-C linkage, resulting in a labeled amino acid that can mimic the molecular interactions of Trp, enabling wash-free imaging. This protocol covers the chemical synthesis of the fluorogenic amino acid Fmoc-Trp(C2-BODIPY)-OH (3-4 d), the preparation of the labeled antimicrobial peptide BODIPY-cPAF26 by solid-phase synthesis (6-7 d) and its spectral and biological characterization as a live-cell imaging probe for different fungal pathogens. As an example, we include a procedure for using BODIPY-cPAF26 for wash-free imaging of fungal pathogens, including real-time visualization of Aspergillus fumigatus (5 d for culturing, 1-2 d for imaging).
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Affiliation(s)
- Lorena Mendive-Tapia
- Department of Inorganic and Organic Chemistry, University of Barcelona, Barcelona, Spain
| | - Ramon Subiros-Funosas
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK
| | - Can Zhao
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Fernando Albericio
- Department of Inorganic and Organic Chemistry, University of Barcelona, Barcelona, Spain.,Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Nick D Read
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Rodolfo Lavilla
- Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain.,Laboratory of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Marc Vendrell
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK
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7
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de Picciotto S, Dickson PM, Traxlmayr MW, Marques BS, Socher E, Zhao S, Cheung S, Kiefer JD, Wand AJ, Griffith LG, Imperiali B, Wittrup KD. Design Principles for SuCESsFul Biosensors: Specific Fluorophore/Analyte Binding and Minimization of Fluorophore/Scaffold Interactions. J Mol Biol 2016; 428:4228-4241. [PMID: 27448945 PMCID: PMC5048519 DOI: 10.1016/j.jmb.2016.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 11/18/2022]
Abstract
Quantifying protein location and concentration is critical for understanding function in situ. Scaffold conjugated to environment-sensitive fluorophore (SuCESsFul) biosensors, in which a reporting fluorophore is conjugated to a binding scaffold, can, in principle, detect analytes of interest with high temporal and spatial resolution. However, their adoption has been limited due to the extensive empirical screening required for their development. We sought to establish design principles for this class of biosensor by characterizing over 400 biosensors based on various protein analytes, binding proteins, and fluorophores. We found that the brightest readouts are attained when a specific binding pocket for the fluorophore is present on the analyte. Also, interaction of the fluorophore with the binding protein it is conjugated to can raise background fluorescence, considerably limiting sensor dynamic range. Exploiting these two concepts, we designed biosensors that attain a 100-fold increase in fluorescence upon binding to analyte, an order of magnitude improvement over the previously best-reported SuCESsFul biosensor. These design principles should facilitate the development of improved SuCESsFul biosensors.
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Affiliation(s)
- Seymour de Picciotto
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Paige M Dickson
- Department of Chemistry, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Michael W Traxlmayr
- Koch Institute for Integrative Cancer Research, 500 Main Street, Cambridge, MA 02139, USA
| | - Bryan S Marques
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elke Socher
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA
| | - Sixing Zhao
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Stephanie Cheung
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA
| | - Jonathan D Kiefer
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Barbara Imperiali
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - K Dane Wittrup
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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8
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Qvit N, Kornfeld OS. Development of a Backbone Cyclic Peptide Library as Potential Antiparasitic Therapeutics Using Microwave Irradiation. J Vis Exp 2016:e53589. [PMID: 26863382 DOI: 10.3791/53589] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is a major effort to target PPIs in basic research and in the pharmaceutical industry. Protein-protein interfaces are usually large, flat, and often lack pockets, complicating the discovery of small molecules that target such sites. Alternative targeting approaches using antibodies have limitations due to poor oral bioavailability, low cell-permeability, and production inefficiency. Using peptides to target PPI interfaces has several advantages. Peptides have higher conformational flexibility, increased selectivity, and are generally inexpensive. However, peptides have their own limitations including poor stability and inefficiency crossing cell membranes. To overcome such limitations, peptide cyclization can be performed. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, predicting the bioactive conformation of a cyclic peptide is not trivial. To overcome this challenge, one attractive approach it to screen a focused library to screen in which all backbone cyclic peptides have the same primary sequence, but differ in parameters that influence their conformation, such as ring size and position. We describe a detailed protocol for synthesizing a library of backbone cyclic peptides targeting specific parasite PPIs. Using a rational design approach, we developed peptides derived from the scaffold protein Leishmania receptor for activated C-kinase (LACK). We hypothesized that sequences in LACK that are conserved in parasites, but not in the mammalian host homolog, may represent interaction sites for proteins that are critical for the parasites' viability. The cyclic peptides were synthesized using microwave irradiation to reduce reaction times and increase efficiency. Developing a library of backbone cyclic peptides with different ring sizes facilitates a systematic screen for the most biological active conformation. This method provides a general, fast, and facile way to synthesize cyclic peptides.
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Affiliation(s)
- Nir Qvit
- Department of Chemical and Systems Biology, Stanford University School of Medicine;
| | - Opher S Kornfeld
- Department of Chemical and Systems Biology, Stanford University School of Medicine
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9
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Fujii M, Namba M, Yamaji M, Okamoto H. Solvent-induced multicolour fluorescence of amino-substituted 2,3-naphthalimides studied by fluorescence and transient absorption measurements. Photochem Photobiol Sci 2016; 15:842-50. [DOI: 10.1039/c6pp00048g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amino-substituted 2,3-naphthalimide derivatives showed marked positive solvatofluorochromism, and the fluorescence emission was effectively quenched in methanol via the internal conversion process.
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Affiliation(s)
- Mayu Fujii
- Division of Earth
- Life
- and Molecular Sciences
- Graduate School of Natural Science and Technology
- Okayama University
| | - Misa Namba
- Division of Earth
- Life
- and Molecular Sciences
- Graduate School of Natural Science and Technology
- Okayama University
| | - Minoru Yamaji
- Division of Molecular Science
- Graduate School of Science and Engineering
- Gunma University
- Kiryu
- Japan
| | - Hideki Okamoto
- Division of Earth
- Life
- and Molecular Sciences
- Graduate School of Natural Science and Technology
- Okayama University
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10
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Aihara K, Inokuma T, Komiya C, Shigenaga A, Otaka A. Synthesis of lactam-bridged cyclic peptides using sequential olefin metathesis and diimide reduction reactions. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.04.093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Pivovarenko VG, Zamotaiev OM, Shvadchak VV, Postupalenko VY, Klymchenko AS, Mély Y. Quantification of local hydration at the surface of biomolecules using dual-fluorescence labels. J Phys Chem A 2012; 116:3103-9. [PMID: 22394312 DOI: 10.1021/jp2101732] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By using four labels of the 3-hydroxyflavone family displaying selective sensitivity to hydrogen bond (HB) donors and poor response to other polar molecules, we developed an approach for measuring local water concentration [H(2)O](L) (or partial volume of water: W(A) = [H(2)O](L)/55.6) in the label surrounding both in solvent mixtures and in biomolecules by the intensity ratio of two emissive forms of the label, N*/T*. Using a series of binary water/solvent mixtures with limited preferential solvation effects, a linear dependence of log(N*/T*) on the local concentration of HB donor was obtained and then used as a calibration curve for estimating the W(A) values in the surroundings of the probes conjugated to biomolecules. By this approach, we estimated the hydration of the labels in different peptides and their complexes with DNAs. We found that W(A) values for the label at the peptide N-terminus are lower (0.63-0.91) than for free labels and depend strongly on the nature of the N-terminal amino acid. When complexed with different DNAs, the estimated hydration of the labels conjugated to the labeled peptides was much lower (W(A) = 0-0.47) and depended on the DNA nature and linker-label structure. Thus, the elaborated method allows a site-specific evaluation of hydration at the surface of a biomolecule through the determination of the partial volume of water. We believe the developed procedure can be successfully applied for monitoring hydration at the surface of any biomolecule or nanostructure.
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Affiliation(s)
- Vasyl G Pivovarenko
- Organic Chemistry Chair, Chemistry Faculty, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
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12
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Baathulaa K, Xu Y, Qian X. Short and scalable synthesis of an anhydride precursor of the environment-sensitive fluorophore 6-dimethylaminonaphthalimide. Nat Protoc 2011; 6:1990-7. [DOI: 10.1038/nprot.2011.415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Loving G, Imperiali B. A versatile amino acid analogue of the solvatochromic fluorophore 4-N,N-dimethylamino-1,8-naphthalimide: a powerful tool for the study of dynamic protein interactions. J Am Chem Soc 2008; 130:13630-8. [PMID: 18808123 DOI: 10.1021/ja804754y] [Citation(s) in RCA: 197] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a new unnatural amino acid based on the solvatochromic fluorophore 4-N,N-dimethylamino-1,8-naphthalimide (4-DMN) for application in the study of protein-protein interactions. The fluorescence quantum yield of this chromophore is highly sensitive to changes in the local solvent environment, demonstrating "switch-like" emission properties characteristic of the dimethylaminophthalimide family of fluorophores. In particular, this new species possesses a number of significant advantages over related fluorophores, including greater chemical stability under a wide range of conditions, a longer wavelength of excitation (408 nm), and improved synthetic accessibility. This amino acid has been prepared as an Fmoc-protected building block and may readily be incorporated into peptides via standard solid-phase peptide synthesis. A series of comparative studies are presented to demonstrate the advantageous properties of the 4-DMN amino acid relative to those of the previously reported 4-N,N-dimethylaminophthalimidoalanine and 6-N,N-dimethylamino-2,3-naphthalimidoalanine amino acids. Other commercially available solvatochromic fluorophores are also include in these studies. The potential of this new probe as a tool for the study of protein-protein interactions is demonstrated by introducing it into a peptide that is recognized by calcium-activated calmodulin. The binding interaction between these two components yields an increase in fluorescence emission greater than 900-fold.
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Affiliation(s)
- Galen Loving
- Department of Chemistry, Massachusetts Institute of Technology, 77 Mass Avenue, Cambridge, Massachusetts 02139, USA
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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: 17] [Impact Index Per Article: 1.1] [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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Sainlos M, Imperiali B. Tools for investigating peptide–protein interactions: peptide incorporation of environment-sensitive fluorophores via on-resin derivatization. Nat Protoc 2007; 2:3201-9. [DOI: 10.1038/nprot.2007.442] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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