1
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Huang X, Yang Z, Yang X, Liang Z, Zhong Q, Hu L, Huang Z, Zhang Z. New Wine in Old Bottle: Crown Ether-Functionalized Digital Polymer toward Efficient MALDI-TOF MS/MS Decoding via a Classical Supramolecular Interaction. ACS Macro Lett 2024:979-986. [PMID: 39042378 DOI: 10.1021/acsmacrolett.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Digital polymers (DPs), which serve as promising molecular-level storage media, have increasingly garnered interest. Their application significantly depends on the efficiency of the information writing (synthesis) and reading processes (sequencing). For reading, rational incorporation of weak bonds in the main chain was applied in most cases in order to improve readability of the tandem mass spectra (MS/MS), which would limit the chain length of DPs, thus reducing the information storage capacity. In this study, the introduction of commercially available crown ether (CE) at the terminus of digital oligo(γ-butyrolactone)s (DOBLs) significantly enhances the predictability and fidelity of matrix-assisted laser desorption/ionization time-of-flight tandem mass spectra (MALDI-TOF MS/MS), thus improving the decoding process. The use of crown ether, leveraging a well-established supramolecular interaction with alkali cations known since 1967, offers a strong affinity between ionization agents and CE motifs, to form a selective effect of the desired fragments during the tandem MS. This method is particularly effective for long-chain DPs, extending up to 32-mer, and allows for customizable fragmentation patterns. The incorporation of CE at the DP chain end presents a novel and efficient strategy for enhancing MS/MS readability and amplifying the information storage capacity of polymers.
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Affiliation(s)
- Xiaoman Huang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
| | - Zhilin Yang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
- Jiangsu Yangnong Chemical Group Co., Ltd., Yangzhou 225009, China
| | - Xiaojie Yang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
| | - Zhishan Liang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
| | - Qinmeng Zhong
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
| | - Lihua Hu
- Analysis and Testing Center, Soochow University, Suzhou 215123, China
| | - Zhihao Huang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, Suzhou 215123, China
| | - Zhengbiao Zhang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
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2
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Shi Q, Zhang Z, Liu S. Precision Sequence-Defined Polymers: From Sequencing to Biological Functions. Angew Chem Int Ed Engl 2024; 63:e202313370. [PMID: 37875462 DOI: 10.1002/anie.202313370] [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: 09/08/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
Precise sequence-defined polymers (SDPs) with uniform chain-to-chain structure including chain length, unit sequence, and end functionalities represent the pinnacle of sophistication in the realm of polymer science. For example, the absolute control over the unit sequence of SDPs allows for the bottom-up design of polymers with hierarchical microstructures and functions. Accompanied with the development of synthetic techniques towards precision SDPs, the decoding of SDP sequences and construction of advanced functions irreplaceable by other synthetic materials is of central importance. In this Minireview, we focus on recent advances in SDP sequencing techniques including tandem mass spectrometry (MS), chemically assisted primary MS, as well as other non-destructive sequencing methods such as nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD), and nanopore sequencing. Additionally, we delve into the promising prospects of SDP functions in the area of cutting-edge biological research. Topics of exploration include gene delivery systems, the development of hybrid materials combining SDPs and nucleic acids, protein recognition and regulation, as well as the interplay between chirality and biological functions. A brief outlook towards the future directions of SDPs is also presented.
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Affiliation(s)
- Qiangqiang Shi
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and Key Laboratory of Precision and Intelligent Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Zhengbiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Shiyong Liu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and Key Laboratory of Precision and Intelligent Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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3
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Day EC, Chittari SS, Bogen MP, Knight AS. Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows. ACS POLYMERS AU 2023; 3:406-427. [PMID: 38107416 PMCID: PMC10722570 DOI: 10.1021/acspolymersau.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/19/2023]
Abstract
Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a "user guide" for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure-property relationships in soft materials.
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Affiliation(s)
| | | | - Matthew P. Bogen
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Abigail S. Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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4
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Soete M, Mertens C, Badi N, Du Prez FE. Reading Information Stored in Synthetic Macromolecules. J Am Chem Soc 2022; 144:22378-22390. [PMID: 36454647 DOI: 10.1021/jacs.2c10316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The storage of information in synthetic (macro)molecules provides an attractive alternative for current archival storage media, and the advancements made within this area have prompted the investigation of such molecules for numerous other applications (e.g., anti-counterfeiting tags, steganography). While different strategies have been described for storing information at the molecular level, this Perspective aims to provide a critical overview of the most prominent approaches that can be utilized for retrieving the encoded information. The major part will focus on the sequence determination of synthetic macromolecules, wherein information is stored by the precise arrangement of constituting monomers, with an emphasis on chemically aided strategies, (tandem) mass spectrometry, and nanopore sensing. In addition, recent progress in utilizing (mixtures of) small molecules for information storage will be discussed. Finally, the closing remarks aim to highlight which strategy we believe is the most suitable for a series of specific applications, and will also touch upon the future research avenues that can be pursued for reading (macro)molecular information.
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Affiliation(s)
- Matthieu Soete
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Chiel Mertens
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Nezha Badi
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Filip E Du Prez
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
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5
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Clapperton A, Babi J, Tran H. A Field Guide to Optimizing Peptoid Synthesis. ACS POLYMERS AU 2022; 2:417-429. [PMID: 36536890 PMCID: PMC9756346 DOI: 10.1021/acspolymersau.2c00036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 12/19/2022]
Abstract
N-Substituted glycines (peptoids) are a class of peptidomimetic molecules used as materials for health, environmental, and drug delivery applications. Automated solid-phase synthesis is the most widely used approach for preparing polypeptoids, with a range of published protocols and modifications for selected synthetic targets. Simultaneously, emerging solution-phase syntheses are being leveraged to overcome limitations in solid-phase synthesis and access high-molecular weight polypeptoids. This Perspective aims to outline strategies for the optimization of both solid- and solution-phase synthesis, provide technical considerations for robotic synthesizers, and offer an outlook on advances in synthetic methodologies. The solid-phase synthesis sections explore steps for protocol optimization, accessing complex side chains, and adaptation to robotic synthesizers; the sections on solution-phase synthesis cover the selection of initiators, side chain compatibility, and strategies for controlling polymerization efficiency and scale. This text acts as a "field guide" for researchers aiming to leverage the flexibility and adaptability of peptoids in their research.
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Affiliation(s)
- Abigail
Mae Clapperton
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S
3H6, Canada
| | - Jon Babi
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S
3H6, Canada
| | - Helen Tran
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S
3H6, Canada,Department
of Chemical Engineering, University of Toronto, 200 College St, Toronto, Toronto, ON M5S
3E5, Canada,
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6
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Affinity Selection from Synthetic Peptide Libraries Enabled by De Novo MS/MS Sequencing. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10370-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractRecently, de novo MS/MS peptide sequencing has enabled the application of affinity selections to synthetic peptide mixtures that approach the diversity of phage libraries (> 108 random peptides). In conjunction with ‘split-mix’ solid phase synthesis to access equimolar peptide mixtures, this approach provides a straightforward means to examine synthetic peptide libraries of considerably higher diversity than has been feasible historically. Here, we offer a critical perspective on this work, report emerging data, and highlight opportunities for further methods refinement. With continued development, ‘affinity selection–mass spectrometry’ may become a complimentary approach to phage display, in vitro selection, and DNA-encoded libraries for the discovery of synthetic ligands that modulate protein function.
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7
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Avital-Shmilovici M, Liu X, Shaler T, Lowenthal A, Bourbon P, Snider J, Tambo-Ong A, Repellin C, Yniguez K, Sambucetti L, Madrid PB, Collins N. Mega-High-Throughput Screening Platform for the Discovery of Biologically Relevant Sequence-Defined Non-Natural Polymers. ACS CENTRAL SCIENCE 2022; 8:86-101. [PMID: 35106376 PMCID: PMC8796305 DOI: 10.1021/acscentsci.1c01041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 06/14/2023]
Abstract
Combinatorial methods enable the synthesis of chemical libraries on scales of millions to billions of compounds, but the ability to efficiently screen and sequence such large libraries has remained a major bottleneck for molecular discovery. We developed a novel technology for screening and sequencing libraries of synthetic molecules of up to a billion compounds in size. This platform utilizes the fiber-optic array scanning technology (FAST) to screen bead-based libraries of synthetic compounds at a rate of 5 million compounds per minute (∼83 000 Hz). This ultra-high-throughput screening platform has been used to screen libraries of synthetic "self-readable" non-natural polymers that can be sequenced at the femtomole scale by chemical fragmentation and high-resolution mass spectrometry. The versatility and throughput of the platform were demonstrated by screening two libraries of non-natural polyamide polymers with sizes of 1.77M and 1B compounds against the protein targets K-Ras, asialoglycoprotein receptor 1 (ASGPR), IL-6, IL-6 receptor (IL-6R), and TNFα. Hits with low nanomolar binding affinities were found against all targets, including competitive inhibitors of K-Ras binding to Raf and functionally active uptake ligands for ASGPR facilitating intracellular delivery of a nonglycan ligand.
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8
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Herlan CN, Feser D, Schepers U, Bräse S. Bio-instructive materials on-demand - combinatorial chemistry of peptoids, foldamers, and beyond. Chem Commun (Camb) 2021; 57:11131-11152. [PMID: 34611672 DOI: 10.1039/d1cc04237h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry allows for the rapid synthesis of large compound libraries for high throughput screenings in biology, medicinal chemistry, or materials science. Especially compounds from a highly modular design are interesting for the proper investigation of structure-to-activity relationships. Permutations of building blocks result in many similar but unique compounds. The influence of certain structural features on the entire structure can then be monitored and serve as a starting point for the rational design of potent molecules for various applications. Peptoids, a highly diverse class of bioinspired oligomers, suit perfectly for combinatorial chemistry. Their straightforward synthesis on a solid support using repetitive reaction steps ensures easy handling and high throughput. Applying this modular approach, peptoids are readily accessible, and their interchangeable side-chains allow for various structures. Thus, peptoids can easily be tuned in their solubility, their spatial structure, and, consequently, their applicability in various fields of research. Since their discovery, peptoids have been applied as antimicrobial agents, artificial membranes, molecular transporters, and much more. Studying their three-dimensional structure, various foldamers with fascinating, unique properties were discovered. This non-comprehensive review will state the most interesting discoveries made over the past years and arouse curiosity about what may come.
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Affiliation(s)
- Claudine Nicole Herlan
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Dominik Feser
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
| | - Stefan Bräse
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. .,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
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9
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DeStefano A, Segalman RA, Davidson EC. Where Biology and Traditional Polymers Meet: The Potential of Associating Sequence-Defined Polymers for Materials Science. JACS AU 2021; 1:1556-1571. [PMID: 34723259 PMCID: PMC8549048 DOI: 10.1021/jacsau.1c00297] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 05/08/2023]
Abstract
Polymers with precisely defined monomeric sequences present an exquisite tool for controlling material properties by harnessing both the robustness of synthetic polymers and the ability to tailor the inter- and intramolecular interactions so crucial to many biological materials. While polymer scientists traditionally synthesized and studied the physics of long molecules best described by their statistical nature, many biological polymers derive their highly tailored functions from precisely controlled sequences. Therefore, significant effort has been applied toward developing new methods of synthesizing, characterizing, and understanding the physics of non-natural sequence-defined polymers. This perspective considers the synergistic advantages that can be achieved via tailoring both precise sequence control and attributes of traditional polymers in a single system. Here, we focus on the potential of sequence-defined polymers in highly associating systems, with a focus on the unique properties, such as enhanced proton conductivity, that can be attained by incorporating sequence. In particular, we examine these materials as key model systems for studying previously unresolvable questions in polymer physics including the role of chain shape near interfaces and how to tailor compatibilization between dissimilar polymer blocks. Finally, we discuss the critical challenges-in particular, truly scalable synthetic approaches, characterization and modeling tools, and robust control and understanding of assembly pathways-that must be overcome for sequence-defined polymers to attain their potential and achieve ubiquity.
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Affiliation(s)
- Audra
J. DeStefano
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A. Segalman
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department
of Materials, University of California, Santa Barbara, California 93106, United States
| | - Emily C. Davidson
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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10
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Lin W, Gandhi S, Oviedo Lara AR, Thomas AK, Helbig R, Zhang Y. Controlling Surface Wettability for Automated In Situ Array Synthesis and Direct Bioscreening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102349. [PMID: 34309086 DOI: 10.1002/adma.202102349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Indexed: 06/13/2023]
Abstract
The in situ synthesis of biomolecules on glass surfaces for direct bioscreening can be a powerful tool in the fields of pharmaceutical sciences, biomaterials, and chemical biology. However, it is still challenging to 1) achieve this conventional multistep combinatorial synthesis on glass surfaces with small feature sizes and high yields and 2) develop a surface which is compatible with solid-phase syntheses, as well as the subsequent bioscreening. This work reports an amphiphilic coating of a glass surface on which small droplets of polar aprotic organic solvents can be deposited with an enhanced contact angle and inhibited motion to permit fully automated multiple rounds of the combinatorial synthesis of small-molecule compounds and peptides. This amphiphilic coating can be switched into a hydrophilic network for protein- and cell-based screening. Employing this in situ synthesis method, chemical space can be probed via array technology with unprecedented speed for various applications, such as lead discovery/optimization in medicinal chemistry and biomaterial development.
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Affiliation(s)
- Weilin Lin
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Shanil Gandhi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alan Rodrigo Oviedo Lara
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alvin K Thomas
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Ralf Helbig
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Hohe Strasse 6, 01069, Dresden, Germany
| | - Yixin Zhang
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence "Physics of Life", Technische Universität Dresden, 01062, Dresden, Germany
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11
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Shariatgorji R, Nilsson A, Strittmatter N, Vallianatou T, Zhang X, Svenningsson P, Goodwin RJA, Andrén PE. Bromopyrylium Derivatization Facilitates Identification by Mass Spectrometry Imaging of Monoamine Neurotransmitters and Small Molecule Neuroactive Compounds. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2553-2557. [PMID: 32633532 DOI: 10.1021/jasms.0c00166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry imaging using matrix-assisted laser desorption/ionization and desorption electrospray ionization has recently been employed to investigate the distribution of neurotransmitters, including biogenic amines and amino acids, directly in brain tissue sections. Ionization is facilitated by charge-tagging through pyrylium derivatization of primary amine containing neurotransmitters directly in tissue sections, significantly improving the limit of detection. Since the derivatization adds carbon and hydrogen to the target compounds, the resulting isotopic patterns of the products are not distinctive from those of the nonderivatized species. Here, we describe an approach for chemically modifying the reactive pyrylium ion to introduce the distinct isotopic signature of bromine in mass spectra of chemically derivatized substances in tissue sections. The method enables monoamine compounds to be distinguished directly in tissue sections, facilitating their identification.
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Affiliation(s)
- Reza Shariatgorji
- Medical Mass Spectrometry Imaging, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 75124, Sweden
- Science for Life Laboratory, National Resource for Mass Spectrometry Imaging, Uppsala University, Uppsala 75124, Sweden
| | - Anna Nilsson
- Medical Mass Spectrometry Imaging, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 75124, Sweden
- Science for Life Laboratory, National Resource for Mass Spectrometry Imaging, Uppsala University, Uppsala 75124, Sweden
| | - Nicole Strittmatter
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Theodosia Vallianatou
- Medical Mass Spectrometry Imaging, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 75124, Sweden
- Science for Life Laboratory, National Resource for Mass Spectrometry Imaging, Uppsala University, Uppsala 75124, Sweden
| | - Xiaoqun Zhang
- Section of Neurology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Per Svenningsson
- Section of Neurology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Richard J A Goodwin
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Per E Andrén
- Medical Mass Spectrometry Imaging, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 75124, Sweden
- Science for Life Laboratory, National Resource for Mass Spectrometry Imaging, Uppsala University, Uppsala 75124, Sweden
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12
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McEnaney P, Balzarini M, Park H, Kodadek T. Structural characterization of a peptoid-inspired conformationally constrained oligomer (PICCO) bound to streptavidin. Chem Commun (Camb) 2020; 56:10560-10563. [PMID: 32785302 DOI: 10.1039/d0cc02588g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A high affinity Streptavidin ligand was mined from a DNA-encoded library of non-peptidic oligimers and characterized structurally.
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Affiliation(s)
- Patrick McEnaney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 3345, USA.
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13
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Xuan S, Zuckermann RN. Engineering the atomic structure of sequence-defined peptoid polymers and their assemblies. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122691] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Bottom-Up Design Approach for OBOC Peptide Libraries. Molecules 2020; 25:molecules25153316. [PMID: 32707811 PMCID: PMC7435479 DOI: 10.3390/molecules25153316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 11/27/2022] Open
Abstract
One-bead-one-compound peptide libraries, developed following the top-down experimental approach, have attracted great interest in the identification of potential ligands or active peptides. By exploiting a reverse experimental design approach based on the bottom-up strategy, we aimed to develop simplified, maximally diverse peptide libraries that resulted in the successful characterization of mixture components. We show that libraries of 32 and 48 components can be successfully detected in a single run using chromatography coupled to mass spectrometry (UPLC-MS). The proposed libraries were further theoretically evaluated in terms of their composition and physico-chemical properties. By combining the knowledge obtained on single libraries we can cover larger sequence spaces and provide a controlled exploration of the peptide chemical space both theoretically and experimentally. Designing libraries by using the bottom-up approach opens up the possibility of rationally fine-tuning the library complexity based on the available analytical methods.
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15
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Ren J, Tian Y, Hossain E, Ho JS, Mann YS, Zhang Y, Browne MD, Connolly MD, Zuckermann RN. Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids. Biopolymers 2020; 111:e23358. [DOI: 10.1002/bip.23358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Jianhua Ren
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuan Tian
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Ekram Hossain
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Joshua S. Ho
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yadwinder S. Mann
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuntao Zhang
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Browne
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Connolly
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
| | - Ronald N. Zuckermann
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
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16
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Morisaki T, Shigenaga A, Otaka A. Development of a Turn-On Fluorescent Traceable Linker Employing N-Sulfanylethylcoumarinyl Amide for the Enrichment and Visualization of Target Proteins. Chem Pharm Bull (Tokyo) 2020; 68:216-219. [PMID: 32115528 DOI: 10.1248/cpb.c19-00726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A turn-on fluorescent traceable linker based on N-sulfanylethylcoumarinyl amide (SECmide) has been developed as an advanced cleavable linker. It was successfully employed for the enrichment and selective visualization of a target protein in cell lysate. The results demonstrated that the SECmide-based traceable linker is potentially applicable to the identification of low molecular weight target proteins, a factor which has been problematic for a previously developed N-sulfanylethylanilide-based traceable linker.
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Affiliation(s)
- Takuya Morisaki
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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17
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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Abstract
Peptides, as a large group of molecules, are composed of amino acid residues and can be divided into linear or cyclic peptides according to the structure. Over 13,000 molecules of natural peptides have been found and many of them have been well studied. In artificial peptide libraries, the number of peptide diversity could be up to 1 × 1013. Peptides have more complex structures and higher affinity to target proteins comparing with small molecular compounds. Recently, the development of targeting cancer immune checkpoint (CIP) inhibitors is having a very important role in tumor therapy. Peptides targeting ligands or receptors in CIP have been designed based on three-dimensional structures of target proteins or directly selected by random peptide libraries in biological display systems. Most of these targeting peptides work as inhibitors of protein-protein interaction and improve CD8+ cytotoxic T-lymphocyte (CTL) activation in the tumor microenvironment, for example, PKHB1, Ar5Y4 and TPP1. Peptides could be designed to regulate CIP protein degradation in vivo, such as PD-LYSO and PD-PALM. Besides its use in developing therapeutic drugs for targeting CIP, targeting peptides could be used in drug's targeted delivery and diagnosis in tumor immune therapy.
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19
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Liu B, Shi Q, Hu L, Huang Z, Zhu X, Zhang Z. Engineering digital polymer based on thiol–maleimide Michael coupling toward effective writing and reading. Polym Chem 2020. [DOI: 10.1039/c9py01939a] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Based on thiol–maleimide Michael coupling, a digital polymer allowing efficient message writing and reading was rationally designed.
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Affiliation(s)
- Baolei Liu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
| | - Qiunan Shi
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
| | - Lihua Hu
- Analysis and Testing Center
- Soochow University
- Suzhou 215123
- China
| | - Zhihao Huang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
| | - Xiulin Zhu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
- Global Institute of Software Technology
| | - Zhengbiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
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20
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Shigenaga A. Development of Chemical Biology Tools Focusing on Peptide/Amide Bond Cleavage Reaction. Chem Pharm Bull (Tokyo) 2019; 67:1171-1178. [PMID: 31685746 DOI: 10.1248/cpb.c19-00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peptides and proteins are involved in almost all biological events. In this review, three chemical biology tools, which were developed for peptide/protein sciences from a viewpoint of peptide/amide bond cleavage, are overviewed. First, study on an artificial amino acid that enables stimulus-responsive functional control of peptides/proteins is briefly described. Two N-S acyl transfer reaction-based tools, one a linker molecule for facile identification of target proteins of bioactive compounds and the other a reagent for selective labeling of proteins of interest, are then discussed.
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Affiliation(s)
- Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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21
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Pei D, Kubi GA. Developments with bead-based screening for novel drug discovery. Expert Opin Drug Discov 2019; 14:1097-1102. [PMID: 31335229 PMCID: PMC7301614 DOI: 10.1080/17460441.2019.1647164] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/19/2019] [Indexed: 01/24/2023]
Abstract
Introduction: Combinatorial chemistry provides a cost-effective method for rapid discovery of drug hits/leads. The one-bead-one-compound (OBOC) library method is in principle ideally suited for this application, because it permits a large number of structurally diverse compounds to be rapidly synthesized and simultaneously screened for binding to a target of interest. However, application of OBOC libraries in drug discovery has encountered significant technical challenges. Areas covered: This Special Report covers the challenges associated with first-generation OBOC libraries (difficulty in structural identification of non-peptidic hits, screening biases and high false positive rates, and poor scalability). It also covers the many strategies developed over the past two decades to overcome these challenges. Expert opinion: With most of the technical challenges now overcome and the advent of powerful intracellular delivery technologies, OBOC libraries of metabolically stable and conformationally rigidified molecules (macrocyclic peptides and peptidomimetics, rigidified acyclic oligomers, and D-peptides) can be routinely synthesized and screened to discover initial hits against previously undruggable targets such as intracellular protein-protein interactions. On the other hand, further developments are still needed to expand the utility of the OBOC method to non-peptidic chemical scaffolds.
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Affiliation(s)
- Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - George Appiah Kubi
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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22
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Erharuyi O, Simanski S, McEnaney PJ, Kodadek T. Screening one bead one compound libraries against serum using a flow cytometer: Determination of the minimum antibody concentration required for ligand discovery. Bioorg Med Chem Lett 2018; 28:2773-2778. [PMID: 29395976 PMCID: PMC6064678 DOI: 10.1016/j.bmcl.2018.01.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/17/2018] [Accepted: 01/18/2018] [Indexed: 10/18/2022]
Abstract
One bead one compound (OBOC) libraries can be screened against serum samples to identify ligands to antibodies in this mixture. In this protocol, hit beads are identified by staining with a fluorescent labeled secondary antibody. When screens are conducted against two different sets of serum, antibodies, and ligands to them, can be discovered that distinguish the two populations. The application of DNA-encoding technology to OBOC libraries has allowed the use of 10 µm beads for library preparation and screening, which pass through a standard flow cytometer, allowing the fluorescent hit beads to be separated from beads displaying non-ligands easily. An important issue in using this approach for the discovery of antibody biomarkers is its analytical sensitivity. In other words, how abundant must an IgG be to allow it to be pulled out of serum in an unbiased screen using a flow cytometer? We report here a model study in which monoclonal antibodies with known ligands of varying affinities are doped into serum. We find that for antibody ligands typical of what one isolates from an unbiased combinatorial library, the target antibody must be present at 10-50 nM. True antigens, which bind with significantly higher affinity, can detect much less abundant serum antibodies.
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Affiliation(s)
- Osayemwenre Erharuyi
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott Simanski
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Patrick J McEnaney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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23
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Komnatnyy VV, Nielsen TE, Qvortrup K. Bead-based screening in chemical biology and drug discovery. Chem Commun (Camb) 2018; 54:6759-6771. [PMID: 29888365 DOI: 10.1039/c8cc02486c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput screening is an important component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds requires assays amenable to miniaturisation and automization. Combinatorial chemistry holds a unique promise to deliver structurally diverse libraries for early drug discovery. Among the various library forms, the one-bead-one-compound (OBOC) library, where each bead carries many copies of a single compound, holds the greatest potential for the rapid identification of novel hits against emerging drug targets. However, this potential has not yet been fully realized due to a number of technical obstacles. In this feature article, we review the progress that has been made in bead-based library screening and its application to the discovery of bioactive compounds. We identify the key challenges of this approach and highlight key steps needed for making a greater impact in the field.
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Affiliation(s)
- Vitaly V Komnatnyy
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
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24
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Shu K, Kodadek T. Solid-Phase Synthesis of β-Hydroxy Ketones Via DNA-Compatible Organocatalytic Aldol Reactions. ACS COMBINATORIAL SCIENCE 2018; 20:277-281. [PMID: 29578681 DOI: 10.1021/acscombsci.8b00001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One-bead one-compound (OBOC) libraries constructed by solid-phase split-and-pool synthesis are a valuable source of protein ligands. Most OBOC libraries are composed of oligoamides, particularly peptides, peptoids, and peptoid-inspired molecules. Further diversification of the chemical space covered by OBOC libraries is desirable. Toward this end, we report here that the proline-catalyzed asymmetric aldol reaction, developed by List and Barbas for solution-phase synthesis, also works well for coupling immobilized aldehydes and soluble ketones. These reaction conditions do not compromise the amplification of DNA by the polymerase chain reaction. Thus, this chemistry should be useful for the construction of novel DNA-encoded OBOC libraries by solid-phase synthesis.
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Affiliation(s)
- Keitou Shu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto 606-8306, Japan
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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25
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Ren J, Mann YS, Zhang Y, Browne MD. Synthesis and Mass Spectrometry Analysis of Oligo-peptoids. J Vis Exp 2018. [PMID: 29553518 DOI: 10.3791/56652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques. The sample peptoid is a nonamer consisting of alternating N-(2-methyloxyethyl)glycine (Nme) and N-(2-phenylethyl)glycine (Npe), as well as an N-(2-aminoethyl)glycine (Nae) at the N-terminus. The sequence formula of the peptoid is Ac-Nae-(Npe-Nme)4-NH2, where Ac is the acetyl group. The synthesis takes place in a commercially available solid-phase reaction vessel. The rink amide resin is used as the solid support to yield the peptoid with an amide group at the C-terminus. The resulting peptoid product is subjected to sequence analysis using a triple-quadrupole mass spectrometer coupled to an electrospray ionization source. The MS/MS measurement produces a spectrum of fragment ions resulting from the dissociation of charged peptoid. The fragment ions are sorted out based on the values of their mass-to-charge ratio (m/z). The m/z values of the fragment ions are compared against the nominal masses of theoretically predicted fragment ions, according to the scheme of peptoid fragmentation. The analysis generates a fragmentation pattern of the charged peptoid. The fragmentation pattern is correlated to the monomer sequence of the neutral peptoid. In this regard, MS analysis reads out the sequence information of the peptoids.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific;
| | | | - Yuntao Zhang
- Department of Chemistry, University of the Pacific
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26
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Tran-Hoang N, Kodadek T. Solid-Phase Synthesis of β-Amino Ketones Via DNA-Compatible Organocatalytic Mannich Reactions. ACS COMBINATORIAL SCIENCE 2018; 20:55-60. [PMID: 29316387 PMCID: PMC7074847 DOI: 10.1021/acscombsci.7b00151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
One-bead-one-compound (OBOC) libraries constructed by solid-phase split-and-pool synthesis are a valuable source of protein ligands. Most OBOC libraries are comprised of oligoamides, particularly peptides, peptoids, and peptoid-inspired molecules. Further diversification of the chemical space covered by OBOC libraries is desirable. Toward this end, we report here the efficient proline-catalyzed asymmetric Mannich reaction between immobilized aldehydes and soluble ketones and anilines. The reaction conditions do not compromise the amplification of DNA by the PCR. Thus, this chemistry will likely be useful for the construction of novel DNA-encoded libraries by solid-phase synthesis.
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Affiliation(s)
- Nam Tran-Hoang
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, Florida 33458, United States
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27
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Charles L, Cavallo G, Monnier V, Oswald L, Szweda R, Lutz JF. MS/MS-Assisted Design of Sequence-Controlled Synthetic Polymers for Improved Reading of Encoded Information. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1149-1159. [PMID: 27914016 DOI: 10.1007/s13361-016-1543-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information. Changing the tri(ethylene glycol) spacer to an alkyl group of the same size allowed this unwanted fragmentation pathway to be avoided, hence greatly simplifying the MS/MS reading step for such undecyl-based poly(triazole amide)s. In poly(alkoxyamine phosphodiester)s, a single dissociation pathway was achieved with repeating units containing an alkoxyamine linkage, which, by very low dissociation energy, made any other chemical bonds MS/MS-silent. Structure of these polymers was further tailored to enhance the stability of those precursor ions with a negatively charged phosphate group per monomer in order to improve their MS/MS readability. Increasing the size of both the alkyl coding moiety and the nitroxide spacer allowed sufficient distance between phosphate groups for all of them to be deprotonated simultaneously. Because the charge state of product ions increased with their polymerization degree, MS/MS spectra typically exhibited groups of fragments at one or the other side of the precursor ion depending on the original α or ω end-group they contain, allowing sequence reconstruction in a straightforward manner. Graphical Abstract ᅟ.
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Affiliation(s)
- Laurence Charles
- Aix Marseille University, CNRS, ICR Institut de Chimie Radicalaire, Marseille, France.
| | - Gianni Cavallo
- Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, Strasbourg, France
| | - Valérie Monnier
- Aix Marseille University, CNRS, Fédération des Sciences Chimiques de Marseille, Marseille, France
| | - Laurence Oswald
- Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, Strasbourg, France
| | - Roza Szweda
- Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, Strasbourg, France
| | - Jean-François Lutz
- Precision Macromolecular Chemistry, Institut Charles Sadron, UPR22-CNRS, Strasbourg, France.
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28
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Wu H, An H, Mo SC, Kodadek T. Asymmetric synthesis of vinylogous β-amino acids and their incorporation into mixed backbone oligomers. Org Biomol Chem 2017; 15:3255-3264. [PMID: 28346549 PMCID: PMC7243482 DOI: 10.1039/c7ob00333a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chiral vinylogous β-amino acids (VBAA) were synthesized using enantioselective Mannich reactions of aldehydes with in situ generated N-carbamoyl imines followed by a Horner-Wadsworth-Emmons reaction. The efficiency with which these units could be incorporated into oligomers with different moieties on the C- and N-terminal sides was established, as was the feasibility of sequencing oligomers containing VBAAs by tandem mass spectrometry. The data show that VBAAs will be useful building blocks for the construction of combinatorial libraries of peptidomimetic compounds.
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Affiliation(s)
- Hao Wu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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29
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Abstract
Molecular imaging allows for the visualization of changes at the cellular level in diseases such as cancer. A successful molecular imaging agent must rely on disease-selective targets and ligands that specifically interact with those targets. Unfortunately, the translation of novel target-specific ligands into the clinic has been frustratingly slow with limitations including the complex design and screening approaches for ligand identification, as well as their subsequent optimization into useful imaging agents. This review focuses on combinatorial library approaches towards addressing these two challenges, with particular focus on phage display and one-bead one-compound (OBOC) libraries. Both of these peptide-based techniques have proven successful in identifying new ligands for cancer-specific targets and some of the success stories will be highlighted. New developments in screening methodology and sequencing technology have pushed the bounds of phage display and OBOC even further, allowing for even faster and more robust discovery of novel ligands. The combination of multiple high-throughput technologies will not only allow for more accurate identification, but also faster affinity maturation, while overall streamlining the process of translating novel ligands into clinical imaging agents.
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30
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Liu R, Li X, Xiao W, Lam KS. Tumor-targeting peptides from combinatorial libraries. Adv Drug Deliv Rev 2017; 110-111:13-37. [PMID: 27210583 DOI: 10.1016/j.addr.2016.05.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 02/07/2023]
Abstract
Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors.
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Affiliation(s)
- Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Wenwu Xiao
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; Division of Hematology & Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, USA
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31
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Nalband DM, Warner BP, Zahler NH, Kirshenbaum K. Rapid identification of metal-binding peptoid oligomers by on-resin X-ray fluorescence screening. Biopolymers 2016; 102:407-15. [PMID: 25059748 DOI: 10.1002/bip.22528] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 12/18/2022]
Abstract
N-Substituted glycine peptoid oligomers have recently attracted attention for their metal binding capabilities. Due to their efficient synthesis on solid phase, peptoids are well suited for generation of compound libraries, followed by screening for molecular recognition and other diverse functional attributes. Ideally, peptoids could be simultaneously screened for binding to a number of metal species. Here, we demonstrate the use of bench-top X-ray fluorescence (XRF) instrumentation to screen rapidly, on solid support, a library of peptoid oligomers incorporating metal-binding functionalities. A subset of the peptoid sequences exhibited significant metal binding capabilities, including a peptoid pentamer and a nonamer that were shown to selectively bind nickel. The binding capabilities were validated by colorimetric assay and by depletion of Ni(2+) ion concentration from solution, establishing bench-top XRF as a rapid, practicable high-throughput screening technique for peptoid oligomers. This protocol will facilitate discovery of metallopeptoids with unique material properties.
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32
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Morisaki T, Denda M, Yamamoto J, Tsuji D, Inokuma T, Itoh K, Shigenaga A, Otaka A. An N-sulfanylethylanilide-based traceable linker for enrichment and selective labelling of target proteins. Chem Commun (Camb) 2016; 52:6911-3. [PMID: 27146590 DOI: 10.1039/c6cc01229a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
An N-sulfanylethylanilide-based traceable linker, developed to facilitate identification of target proteins of bioactive compounds, was introduced into an alkynylated target protein. Subsequent adsorption onto streptavidin beads allowed it to be treated with a cysteine-fluorophore conjugate in the presence of phosphate. This induced the N-S acyl transfer reaction of the N-sulfanylethylanilide unit. The subsequent native chemical ligation of the fluorophore resulted in cleavage of the linker for target elution and fluorescence labelling of the target, allowing it to be distinguished from non-target proteins.
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Affiliation(s)
- Takuya Morisaki
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan.
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33
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Doran TM, Sarkar M, Kodadek T. Chemical Tools To Monitor and Manipulate Adaptive Immune Responses. J Am Chem Soc 2016; 138:6076-94. [PMID: 27115249 PMCID: PMC5332222 DOI: 10.1021/jacs.6b02954] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Methods to monitor and manipulate the immune system are of enormous clinical interest. For example, the development of vaccines represents one of the earliest and greatest accomplishments of the biomedical research enterprise. More recently, drugs capable of "reawakening" the immune system to cancer have generated enormous excitement. But, much remains to be done. All drugs available today that manipulate the immune system cannot distinguish between "good" and "bad" immune responses and thus drive general and systemic immune suppression or activation. Indeed, with the notable exception of vaccines, our ability to monitor and manipulate antigen-specific immune responses is in its infancy. Achieving this finer level of control would be highly desirable. For example, it might allow the pharmacological editing of pathogenic immune responses without restricting the ability of the immune system to defend against infection. On the diagnostic side, a method to comprehensively monitor the circulating, antigen-specific antibody population could provide a treasure trove of clinically useful biomarkers, since many diseases expose the immune system to characteristic molecules that are deemed foreign and elicit the production of antibodies against them. This Perspective will discuss the state-of-the-art of this area with a focus on what we consider seminal opportunities for the chemistry community to contribute to this important field.
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Affiliation(s)
- Todd M. Doran
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Mohosin Sarkar
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Thomas Kodadek
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
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Kodadek T, McEnaney PJ. Towards vast libraries of scaffold-diverse, conformationally constrained oligomers. Chem Commun (Camb) 2016; 52:6038-59. [PMID: 26996593 PMCID: PMC4846527 DOI: 10.1039/c6cc00617e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is great interest in the development of probe molecules and drug leads that would bind tightly and selectively to protein surfaces that are difficult to target with traditional molecules, such as those involved in protein-protein interactions. The currently available evidence suggests that this will require molecules that are larger and have quite different chemical properties than typical Lipinski-compliant molecules that target enzyme active sites. We describe here efforts to develop vast libraries of conformationally constrained oligomers as a potentially rich source of these molecules.
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Affiliation(s)
- Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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35
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Ren J, Tian Y, Hossain E, Connolly MD. Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:646-661. [PMID: 26832347 DOI: 10.1007/s13361-016-1341-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 01/07/2016] [Accepted: 01/09/2016] [Indexed: 06/05/2023]
Abstract
Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry. Graphical Abstract ᅟ.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA.
| | - Yuan Tian
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Ekram Hossain
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael D Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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36
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Helmer D, Schmitz K. Peptides and Peptide Analogs to Inhibit Protein-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:147-83. [PMID: 27236556 DOI: 10.1007/978-3-319-32805-8_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Protein-protein interactions are governed by relatively few amino acid residues at the binding interface. Peptides derived from these protein regions may serve as mimics of one of the interaction partners in structural studies or as inhibitors to disrupt the respective interaction and investigate its biological consequences. Inhibitory peptides may also be lead structures for drug development if the respective protein-protein interaction is essential for a pathogen or disease mechanism. Binding peptides may be systematically derived from one of the binding partners or found in the screen of combinatorial peptide libraries. Molecular modelling based on structural data helps to refine existing peptides or even design novel binding peptides. This chapter gives an outline of the binding peptide discovery process and subsequent chemical modifications to further enhance affinity and specificity and to increase stability against degradation in vivo. Examples from the past three decades illustrate the great diversity of applications for protein binding peptides and peptide analogs.
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Affiliation(s)
- Dorothea Helmer
- Technische Universität Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Katja Schmitz
- Technische Universität Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany.
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37
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Mendes K, Ndungu JM, Clark LF, Kodadek T. Optimization of the Magnetic Recovery of Hits from One-Bead-One-Compound Library Screens. ACS COMBINATORIAL SCIENCE 2015. [PMID: 26221913 DOI: 10.1021/acscombsci.5b00090] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
On-bead screening of one-bead-one-compound (OBOC) libraries is a useful procedure for the identification of protein ligands. An important aspect of this experiment is the method by which beads that bind the target protein are separated from those that do not. Ideally, such a method would be rapid and convenient and result in the isolation of 100% of the "hits" with no false positives (beads that display compounds that are not good ligands for the target). We introduced a technique in which beads that have bound a labeled target protein can be magnetized, thus allowing their convenient isolation ( Astle et al. Chem. Biol. 2010 , 17 , 38 - 45 ). However, recent work in our laboratory and others has shown that magnetic hit recovery can result in the isolation of large numbers of false positives and has also suggested that many true hit beads are missed. In this study, we employ a well-defined model system to examine the efficiency of various magnetic hit isolation protocols. We show that the choice of reagents and the particular operations employed are critical for optimal results.
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Affiliation(s)
- Kimberly Mendes
- Opko Health, Inc., RF Building, Jupiter, Florida 33458, United States
| | - J. M. Ndungu
- Opko Health, Inc., RF Building, Jupiter, Florida 33458, United States
| | - Lorraine F. Clark
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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38
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Lutz JF. Coding Macromolecules: Inputting Information in Polymers Using Monomer-Based Alphabets. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00890] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jean-François Lutz
- Precision Macromolecular
Chemistry, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, BP84047, 67034 Strasbourg, Cedex
2, France
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39
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Charles L, Laure C, Lutz JF, Roy RK. MS/MS Sequencing of Digitally Encoded Poly(alkoxyamine amide)s. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01051] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Laurence Charles
- Aix-Marseille
Université − CNRS, UMR 7273, Institute of Radical Chemistry, 13397 Marseille Cedex 20, France
| | - Chloé Laure
- Precision
Macromolecular Chemistry, UPR22-CNRS, BP84047, Institut Charles Sadron, 23 rue du Loess, 67034 Strasbourg, Cedex 2, France
| | - Jean-François Lutz
- Precision
Macromolecular Chemistry, UPR22-CNRS, BP84047, Institut Charles Sadron, 23 rue du Loess, 67034 Strasbourg, Cedex 2, France
| | - Raj Kumar Roy
- Precision
Macromolecular Chemistry, UPR22-CNRS, BP84047, Institut Charles Sadron, 23 rue du Loess, 67034 Strasbourg, Cedex 2, France
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40
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Yamamoto J, Denda M, Maeda N, Kita M, Komiya C, Tanaka T, Nomura W, Tamamura H, Sato Y, Yamauchi A, Shigenaga A, Otaka A. Development of a traceable linker containing a thiol-responsive amino acid for the enrichment and selective labelling of target proteins. Org Biomol Chem 2015; 12:3821-6. [PMID: 24806338 DOI: 10.1039/c4ob00622d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A traceable linker that is potentially applicable to identification of a target protein of bioactive compounds was developed. It enabled not only thiol-induced cleavage of the linker for enrichment of the target protein but also selective labelling to pick out the target from contaminated non-target proteins for facile identification.
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Affiliation(s)
- Jun Yamamoto
- Institute of Health Biosciences and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi, Tokushima 770-8505, Japan.
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41
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Helmer D, Rink I, Dalton JAR, Brahm K, Jöst M, Nargang TM, Blum W, Wadhwani P, Brenner-Weiss G, Rapp BE, Giraldo J, Schmitz K. Rational design of a peptide capture agent for CXCL8 based on a model of the CXCL8:CXCR1 complex. RSC Adv 2015. [DOI: 10.1039/c4ra13749c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A CXCL8-binding peptide designed from the interaction sites of CXCR1 with CXCL8 serves as a capture agent and inhibits neutrophil migration.
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42
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Wolfram S, Würfel H, Habenicht SH, Lembke C, Richter P, Birckner E, Beckert R, Pohnert G. A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection. Beilstein J Org Chem 2014; 10:2470-9. [PMID: 25383118 PMCID: PMC4222447 DOI: 10.3762/bjoc.10.258] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/08/2014] [Indexed: 11/23/2022] Open
Abstract
Molecular probes are widely used tools in chemical biology that allow tracing of bioactive metabolites and selective labeling of proteins and other biomacromolecules. A common structural motif for such probes consists of a reporter that can be attached by copper(I)-catalyzed 1,2,3-triazole formation between terminal alkynes and azides to a reactive headgroup. Here we introduce the synthesis and application of the new thiazole-based, azide-tagged reporter 4-(3-azidopropoxy)-5-(4-bromophenyl)-2-(pyridin-2-yl)thiazole for fluorescence, UV and mass spectrometry (MS) detection. This small fluorescent reporter bears a bromine functionalization facilitating the automated data mining of electrospray ionization MS runs by monitoring for its characteristic isotope signature. We demonstrate the universal utility of the reporter for the detection of an alkyne-modified small molecule by LC–MS and for the visualization of a model protein by in-gel fluorescence. The novel probe advantageously compares with commercially available azide-modified fluorophores and a brominated one. The ease of synthesis, small size, stability, and the universal detection possibilities make it an ideal reporter for activity-based protein profiling and functional metabolic profiling.
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Affiliation(s)
- Stefanie Wolfram
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstr. 8, 07743 Jena, Germany
| | - Hendryk Würfel
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University, Humboldtstr. 10, 07743 Jena, Germany
| | - Stefanie H Habenicht
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University, Humboldtstr. 10, 07743 Jena, Germany
| | - Christine Lembke
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstr. 8, 07743 Jena, Germany
| | - Phillipp Richter
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstr. 8, 07743 Jena, Germany
| | - Eckhard Birckner
- Institute for Physical Chemistry, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Rainer Beckert
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University, Humboldtstr. 10, 07743 Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Lessingstr. 8, 07743 Jena, Germany
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43
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Mutlu H, Lutz JF. Reading Polymers: Sequencing of Natural and Synthetic Macromolecules. Angew Chem Int Ed Engl 2014; 53:13010-9. [DOI: 10.1002/anie.201406766] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/24/2014] [Indexed: 11/07/2022]
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44
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Mutlu H, Lutz JF. “Lesen” von Polymeren: Die Sequenzierung natürlicher und synthetischer Makromoleküle. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406766] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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45
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Yamamoto J, Maeda N, Komiya C, Tanaka T, Denda M, Ebisuno K, Nomura W, Tamamura H, Sato Y, Yamauchi A, Shigenaga A, Otaka A. Development of a fluoride-responsive amide bond cleavage device that is potentially applicable to a traceable linker. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.05.110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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46
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Bogdanov B, Zhao X, Robinson DB, Ren J. Electron capture dissociation studies of the fragmentation patterns of doubly protonated and mixed protonated-sodiated peptoids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1202-1216. [PMID: 24845348 DOI: 10.1007/s13361-014-0869-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 06/03/2023]
Abstract
The fragmentation patterns of a group of doubly protonated ([P + 2H](2+)) and mixed protonated-sodiated ([P + H + Na](2+)) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C'-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z(•)-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z(•)'-series of ions in addition to the C'-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H](•+)) and the sodiated peptoids ([P + H + Na](•+)). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.
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Affiliation(s)
- Bogdan Bogdanov
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
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47
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Doran TM, Gao Y, Mendes K, Dean S, Simanski S, Kodadek T. Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits. ACS COMBINATORIAL SCIENCE 2014; 16:259-70. [PMID: 24749624 PMCID: PMC4053090 DOI: 10.1021/co500030f] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Large
one-bead one-compound (OBOC) combinatorial libraries can
be constructed relatively easily by solid-phase split and pool synthesis.
The use of resins with hydrophilic surfaces, such as TentaGel, allows
the beads to be used directly in screens for compounds that bind selectively
to labeled proteins, nucleic acids, or other biomolecules. However,
we have found that this method, while useful, has a high false positive
rate. In other words, beads that are scored as hits often display
compounds that prove to be poor ligands for the target of interest
when they are resynthesized and carried through validation trials.
This results in a significant waste of time and resources in cases
where putative hits cannot be validated without resynthesis. Here,
we report that this problem can be largely eliminated through the
use of redundant OBOC libraries, where more than one bead displaying
the same compound is present in the screen. We show that compounds
isolated more than once are likely to be high quality ligands for
the target of interest, whereas compounds isolated only once have
a much higher likelihood of being poor ligands. While the use of redundant
libraries does limit the number of unique compounds that can be screened
at one time in this format, the overall savings in time, effort, and
materials makes this a more efficient route to the isolation of useful
ligands for biomolecules.
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Affiliation(s)
- Todd M. Doran
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Yu Gao
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Kimberly Mendes
- OPKO Health, Inc., 555 Heritage
Drive, Jupiter, Florida 33458, United States
| | - Sonja Dean
- OPKO Health, Inc., 555 Heritage
Drive, Jupiter, Florida 33458, United States
| | - Scott Simanski
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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48
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Knight AS, Zhou EY, Pelton JG, Francis MB. Selective chromium(VI) ligands identified using combinatorial peptoid libraries. J Am Chem Soc 2013; 135:17488-93. [PMID: 24195610 PMCID: PMC4136388 DOI: 10.1021/ja408788t] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hexavalent chromium [Cr(VI)] is a worldwide water contaminant that is currently without cost-effective and efficient remediation strategies. This is in part due to a lack of ligands that can bind it amid an excess of innocuous ions in aqueous solution. We present herein the design and application of a peptoid-based library of ligand candidates for toxic metal ions. A selective screening process was used to identify members of the library that can bind to Cr(VI) species at neutral pH and in the presence of a large excess of spectator ions. There were 11 sequences identified, and their affinities were compared using titrations monitored with UV-vis spectroscopy. To identify the interactions involved in coordination and specificity, we evaluated the effects of sequence substitutions and backbone variation in the highest affinity structure. Additional characterization of the complex formed between this sequence and Cr(VI) was performed using NMR spectroscopy. To evaluate the ability of the developed sequences to remediate contaminated solutions, the structures were synthesized on a solid-phase resin and incubated with environmental water samples that contained simulated levels of chromium contamination. The synthetic structures demonstrated the ability to reduce the amount of toxic chromium to levels within the range of the EPA contamination guidelines. In addition to providing some of the first selective ligands for Cr(VI), these studies highlight the promise of peptoid sequences as easily prepared components of environmental remediation materials.
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Affiliation(s)
- Abigail S. Knight
- Department of Chemistry, University of California, Berkeley, CA, 94720
| | - Effie Y. Zhou
- Department of Chemistry, University of California, Berkeley, CA, 94720
| | - Jeffrey G. Pelton
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, CA, 94720
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
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49
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Sun J, Zuckermann RN. Peptoid polymers: a highly designable bioinspired material. ACS NANO 2013; 7:4715-32. [PMID: 23721608 DOI: 10.1021/nn4015714] [Citation(s) in RCA: 307] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Bioinspired polymeric materials are attracting increasing attention due to significant advantages over their natural counterparts: the ability to precisely tune their structures over a broad range of chemical and physical properties, increased stability, and improved processability. Polypeptoids, a promising class of bioinspired polymer based on a N-substituted glycine backbone, have a number of unique properties that bridge the material gap between proteins and bulk polymers. Peptoids combine the sequence specificity of biopolymers with the simpler intra/intermolecular interactions and robustness of traditional synthetic polymers. They are highly designable because hundreds of chemically diverse side chains can be introduced from simple building blocks. Peptoid polymers can be prepared by two distinct synthetic techniques offering access to two material subclasses: (1) automated solid-phase synthesis which enables precision sequence control and near absolute monodispersity up to chain lengths of ~50 monomers, and (2) a classical polymerization approach which allows access to higher molecular weights and larger-scale yields, but with less control over length and sequence. This combination of facile synthetic approaches makes polypeptoids a highly tunable, rapid polymer prototyping platform to investigate new materials that are intermediate between proteins and bulk polymers, in both their structure and their properties. In this paper, we review the methods to synthesize peptoid polymers and their applications in biomedicine and nanoscience, as both sequence-specific materials and as bulk polymers.
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Affiliation(s)
- Jing Sun
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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50
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El-Mahdi O, Melnyk O. α-Oxo aldehyde or glyoxylyl group chemistry in peptide bioconjugation. Bioconjug Chem 2013; 24:735-65. [PMID: 23578008 DOI: 10.1021/bc300516f] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since the 1990s, α-oxo aldehyde or glyoxylic acid chemistry has inspired a vast array of synthetic tools for tailoring peptide or protein structures, for developing peptides endowed with novel physicochemical properties or biological functions, for assembling a large diversity of bioconjugates or hybrid materials, or for designing peptide-based micro or nanosystems. This past decade, important developments have enriched the α-oxo aldehyde synthetic tool box in peptide bioconjugation chemistry and explored novel applications. The aim of this review is to give a large overview of this creative field.
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Affiliation(s)
- Ouafâa El-Mahdi
- Université Sidi Mohamed Ben Abdellah, Faculté Polydisciplinaire de Taza, Morocco
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