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Gilad AA, Bar-Shir A, Bricco AR, Mohanta Z, McMahon MT. Protein and peptide engineering for chemical exchange saturation transfer imaging in the age of synthetic biology. NMR IN BIOMEDICINE 2023; 36:e4712. [PMID: 35150021 PMCID: PMC10642350 DOI: 10.1002/nbm.4712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 05/23/2023]
Abstract
At the beginning of the millennium, the first chemical exchange saturation transfer (CEST) contrast agents were bio-organic molecules. However, later, metal-based CEST agents (paraCEST agents) took center stage. This did not last too long as paraCEST agents showed limited translational potential. By contrast, the CEST field gradually became dominated by metal-free CEST agents. One branch of research stemming from the original work by van Zijl and colleagues is the development of CEST agents based on polypeptides. Indeed, in the last 2 decades, tremendous progress has been achieved in this field. This includes the design of novel peptides as biosensors, genetically encoded recombinant as well as synthetic reporters. This was a result of extensive characterization and elucidation of the theoretical requirements for rational designing and engineering of such agents. Here, we provide an extensive overview of the evolution of more precise protein-based CEST agents, review the rationalization of enzyme-substrate pairs as CEST contrast enhancers, discuss the theoretical considerations to improve peptide selectivity, specificity and enhance CEST contrast. Moreover, we discuss the strong influence of synthetic biology on the development of the next generation of protein-based CEST contrast agents.
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Affiliation(s)
- Assaf A. Gilad
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, USA
- Department of Radiology, Michigan State University, East Lansing, Michigan, USA
| | - Amnon Bar-Shir
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander R. Bricco
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Zinia Mohanta
- Division of MR Research, The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, Maryland, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Michael T. McMahon
- Division of MR Research, The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, Maryland, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
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2
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Huang Y, Li Y, Li X. Strategies for developing DNA-encoded libraries beyond binding assays. Nat Chem 2022; 14:129-140. [PMID: 35121833 DOI: 10.1038/s41557-021-00877-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
DNA-encoded chemical libraries (DELs) have emerged as a powerful technology in drug discovery. The wide adoption of DELs in the pharmaceutical industry and the rapid advancements of DEL-compatible chemistry have further fuelled its development and applications. In general, a DEL has been considered as a massive binding assay to identify physical binders for individual protein targets. However, recent innovations demonstrate the capability of DELs to operate in the complex milieu of biological systems. In this Perspective, we discuss the recent progress in using DNA-encoded chemical libraries to interrogate complex biological targets and their potential to identify structures that elicit function or possess other useful properties. Future breakthroughs in these aspects are expected to catapult DEL to become a momentous technology platform not only for drug discovery but also to explore fundamental biology.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
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3
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Daguer JP, Gonse A, Shchukin Y, Farrera-Soler L, Barluenga S, Winssinger N. Dual Bcl-X L /Bcl-2 inhibitors discovered from DNA-encoded libraries using a fragment pairing strategy. Bioorg Med Chem 2021; 44:116282. [PMID: 34216984 DOI: 10.1016/j.bmc.2021.116282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022]
Abstract
A dual Bcl-XL / Bcl-2 inhibitor was discovered from DNA-encoded libraries using a two steps process. In the first step, DNA was used to pair PNA-encoded fragments exploring > 250 000 combinations. In the second step, a focused library combining the selected fragments with linkers of different lengths and geometries led to the identification of tight binding adducts that were further investigated for their selective target engagement in pull-down assays, for their affinity by SPR, and their selectivity in a cytotoxicity assay. The best compound showed comparable cellular activity to venetoclax, the first-in-class therapeutic targeting Bcl-2.
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Affiliation(s)
- Jean-Pierre Daguer
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Arthur Gonse
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Yevhenii Shchukin
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Lluc Farrera-Soler
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.
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4
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Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
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Phan NN, Li C, Alabi CA. Intracellular Delivery via Noncharged Sequence-Defined Cell-Penetrating Oligomers. Bioconjug Chem 2018; 29:2628-2635. [PMID: 29953207 DOI: 10.1021/acs.bioconjchem.8b00336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intracellular drug delivery systems are often limited by their poor serum stability and delivery efficiency. Cell-penetrating peptides (CPPs), particularly those derived from basic protein subunits, have been studied extensively in this regard and used for the delivery of a variety of cargoes in vitro. Although promising, traditional cationic CPPs have some drawbacks that hinder their therapeutic application such as rapid proteolytic degradation and undesired interactions with the biological milieu. To overcome these limitations, this article details the discovery of a new class of noncharged cell-penetrating oligoTEAs (CPOTs) that undergo extensive and rapid cellular entry across different cell lines with low cytotoxicity. CPOTs outperform a widely used CPP, R9 peptide. This new class of highly efficient noncharged macromolecular transporters are distinct from their cationic counterparts and show strong promise for the intracellular delivery of hydrophilic small-molecule therapeutics.
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Affiliation(s)
- Ngoc N Phan
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall , Ithaca , New York 14853 , United States
| | - Connie Li
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall , Ithaca , New York 14853 , United States
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall , Ithaca , New York 14853 , United States
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Portal C, Hintersteiner M, Barbeau O, Dodd P, Huggett M, Pérez‐Pi I, Evans D, Auer M. Facile Synthesis of a Next Generation Safety-Catch Acid-Labile Linker, SCAL-2, Suitable for Solid-Phase Synthesis, On-Support Display and for Post-Synthesis Tagging. ChemistrySelect 2017; 2:6658-6662. [PMID: 29104911 PMCID: PMC5661701 DOI: 10.1002/slct.201701519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 11/27/2022]
Abstract
The SCAL linker, a safety catch linker, is amongst the most versatile linkers for solid phase synthesis. It was originally described in 1991 by Pátek and Lebl. Yet, its application has been hindered by the low yields of published synthetic routes. Over time, the exceptional versatility of this linker has been demonstrated in several applications of advanced solid phase synthesis of peptides and peptidomimetics. Recently, an updated synthesis of the original linker has also been presented at the 22nd American Peptide Symposium, comprising 10 steps. Herein, the design and synthesis of a next generation SCAL linker, SCAL-2, is reported. SCAL-2 features a simplified molecular architecture, which allows for a more efficient synthesis in 8 steps with superior yields. Both linkers, SCAL and SCAL-2 are compared in terms of their cleavage properties adding valuable information on how to best utilize the versatility of these linkers for solid phase synthesis.
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Affiliation(s)
- Christophe Portal
- Edinburgh BioQuarter9 Little France Road, EdinburghScotland EH16 4UXU.K.
| | - Martin Hintersteiner
- School of Biological Sciences and Edinburgh Medical School: Biomedical SciencesUniversity of Edinburgh, The King's Buildings, EdinburghScotland EH9 3BFU.K.
| | - Olivier Barbeau
- School of Biological Sciences and Edinburgh Medical School: Biomedical SciencesUniversity of Edinburgh, The King's Buildings, EdinburghScotland EH9 3BFU.K.
| | - Peter Dodd
- School of Biological Sciences and Edinburgh Medical School: Biomedical SciencesUniversity of Edinburgh, The King's Buildings, EdinburghScotland EH9 3BFU.K.
| | - Margaret Huggett
- School of Biological Sciences and Edinburgh Medical School: Biomedical SciencesUniversity of Edinburgh, The King's Buildings, EdinburghScotland EH9 3BFU.K.
| | - Irene Pérez‐Pi
- School of Biological Sciences and Edinburgh Medical School: Biomedical SciencesUniversity of Edinburgh, The King's Buildings, EdinburghScotland EH9 3BFU.K.
| | - David Evans
- School of Biological Sciences and Edinburgh Medical School: Biomedical SciencesUniversity of Edinburgh, The King's Buildings, EdinburghScotland EH9 3BFU.K.
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School: Biomedical SciencesUniversity of Edinburgh, The King's Buildings, EdinburghScotland EH9 3BFU.K.
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7
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Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
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8
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Gilad Y, Firer M, Gellerman G. Recent Innovations in Peptide Based Targeted Drug Delivery to Cancer Cells. Biomedicines 2016; 4:E11. [PMID: 28536378 PMCID: PMC5344250 DOI: 10.3390/biomedicines4020011] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 12/21/2022] Open
Abstract
Targeted delivery of chemotherapeutics and diagnostic agents conjugated to carrier ligands has made significant progress in recent years, both in regards to the structural design of the conjugates and their biological effectiveness. The goal of targeting specific cell surface receptors through structural compatibility has encouraged the use of peptides as highly specific carriers as short peptides are usually non-antigenic, are structurally simple and synthetically diverse. Recent years have seen many developments in the field of peptide based drug conjugates (PDCs), particularly for cancer therapy, as their use aims to bypass off-target side-effects, reducing the morbidity common to conventional chemotherapy. However, no PDCs have as yet obtained regulatory approval. In this review, we describe the evolution of the peptide-based strategy for targeted delivery of chemotherapeutics and discuss recent innovations in the arena that should lead in the near future to their clinical application.
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Affiliation(s)
- Yosi Gilad
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel.
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Michael Firer
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Gary Gellerman
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel.
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9
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Zambaldo C, Daguer JP, Saarbach J, Barluenga S, Winssinger N. Screening for covalent inhibitors using DNA-display of small molecule libraries functionalized with cysteine reactive moieties. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00242k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Discriminating between non-covalent and covalent inhibitors with SDS wash in microarray-based screen.
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Affiliation(s)
- C. Zambaldo
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - J.-P. Daguer
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - J. Saarbach
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - S. Barluenga
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - N. Winssinger
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
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10
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Novel PTP1B inhibitors identified by DNA display of fragment pairs. Bioorg Med Chem Lett 2015; 26:1080-1085. [PMID: 26691757 DOI: 10.1016/j.bmcl.2015.11.102] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 11/27/2015] [Accepted: 11/28/2015] [Indexed: 12/15/2022]
Abstract
DNA display of PNA-encoded libraries was used to pair fragments containing different phosphotyrosine surrogates with diverse triazoles. Microarray-based screening of the combinatorially paired fragment sets (62,500 combinations) against a prototypical phosphatase, PTP1B, was used to identify the fittest fragments. A focused library (10,000 members) covalently pairing identified fragments with linkers of different length and geometry was synthesized. Screening of the focused library against PTP1B and closely related TCPTP revealed orthogonal inhibitors. The selectivity of the identified inhibitors for PTP1B versus TCPT was confirmed by enzymatic inhibition assay.
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11
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Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, Zimmermann M, Samain F, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D. Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410736] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, Zimmermann M, Samain F, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D. Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library. Angew Chem Int Ed Engl 2015; 54:3927-31. [DOI: 10.1002/anie.201410736] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Indexed: 11/10/2022]
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13
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Li G, Zheng W, Liu Y, Li X. Novel encoding methods for DNA-templated chemical libraries. Curr Opin Chem Biol 2015; 26:25-33. [PMID: 25635927 DOI: 10.1016/j.cbpa.2015.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/08/2015] [Indexed: 12/12/2022]
Abstract
Among various types of DNA-encoded chemical libraries, DNA-templated library takes advantage of the sequence-specificity of DNA hybridization, enabling not only highly effective DNA-templated chemical reactions, but also high fidelity in library encoding. This brief review summarizes recent advances that have been made on the encoding strategies for DNA-templated libraries, and it also highlights their respective advantages and limitations for the preparation of DNA-encoded libraries.
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Affiliation(s)
- Gang Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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14
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Zambaldo C, Barluenga S, Winssinger N. PNA-encoded chemical libraries. Curr Opin Chem Biol 2015; 26:8-15. [PMID: 25621730 DOI: 10.1016/j.cbpa.2015.01.005] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/08/2015] [Indexed: 01/04/2023]
Abstract
Peptide nucleic acid (PNA)-encoded chemical libraries along with DNA-encoded libraries have provided a powerful new paradigm for library synthesis and ligand discovery. PNA-encoding stands out for its compatibility with standard solid phase synthesis and the technology has been used to prepare libraries of peptides, heterocycles and glycoconjugates. Different screening formats have now been reported including selection-based and microarray-based methods that have yielded specific ligands against diverse target classes including membrane receptors, lectins and challenging targets such as Hsp70.
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Affiliation(s)
- Claudio Zambaldo
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland.
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15
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Franzini RM, Nauer A, Scheuermann J, Neri D. Interrogating target-specificity by parallel screening of a DNA-encoded chemical library against closely related proteins. Chem Commun (Camb) 2015; 51:8014-6. [DOI: 10.1039/c5cc01230a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Screening a DNA-encoded chemical library against closely related proteins enabled us to predict target specificity as illustrated for serum albumins from different species.
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Affiliation(s)
| | - Angela Nauer
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
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16
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Reissmann S. Cell penetration: scope and limitations by the application of cell-penetrating peptides. J Pept Sci 2014; 20:760-84. [DOI: 10.1002/psc.2672] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/06/2014] [Accepted: 06/10/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Siegmund Reissmann
- Friedrich Schiller University, Biological and Pharmaceutical Faculty; Institute of Biochemistry and Biophysics; Dornburger Strasse 25 07743 Jena Germany
- Jena Bioscience GmbH; Loebstedter Strasse 80 07749 Jena Germany
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17
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Zhao P, Chen Z, Li Y, Sun D, Gao Y, Huang Y, Li X. Selection of DNA-Encoded Small Molecule Libraries Against Unmodified and Non-Immobilized Protein Targets. Angew Chem Int Ed Engl 2014; 53:10056-9. [DOI: 10.1002/anie.201404830] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 11/07/2022]
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18
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Zhao P, Chen Z, Li Y, Sun D, Gao Y, Huang Y, Li X. Selection of DNA-Encoded Small Molecule Libraries Against Unmodified and Non-Immobilized Protein Targets. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404830] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Suppo JS, Subra G, Bergès M, Marcia de Figueiredo R, Campagne JM. Inverse Peptide Synthesis via Activated α-Aminoesters. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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20
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Suppo JS, Subra G, Bergès M, Marcia de Figueiredo R, Campagne JM. Inverse Peptide Synthesis via Activated α-Aminoesters. Angew Chem Int Ed Engl 2014; 53:5389-93. [DOI: 10.1002/anie.201402147] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/21/2022]
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21
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Chouikhi D, Ciobanu M, Zambaldo C, Duplan V, Barluenga S, Winssinger N. Expanding the scope of PNA-encoded synthesis (PES): Mtt-protected PNA fully orthogonal to fmoc chemistry and a broad array of robust diversity-generating reactions. Chemistry 2012; 18:12698-704. [PMID: 22915361 DOI: 10.1002/chem.201201337] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/15/2012] [Indexed: 01/11/2023]
Abstract
Nucleic acid-encoded libraries are emerging as an attractive and highly miniaturized format for the rapid identification of protein ligands. An important criterion in the synthesis of nucleic acid encoded libraries is the scope of reactions that can be used to introduce molecular diversity and devise divergent pathways for diversity-oriented synthesis (DOS). To date, the protecting group strategies that have been used in peptide nucleic acid (PNA) encoded synthesis (PES) have limited the choice of reactions used in the library synthesis to just a few prototypes. Herein, we describe the preparation of PNA monomers with a protecting group combination (Mtt/Boc) that is orthogonal to Fmoc-based synthesis and compatible with a large palette of reactions that have been productively used in DOS (palladium cross-couplings, metathesis, reductive amination, amidation, heterocycle formation, nucleophilic addition, conjugate additions, Pictet-Spengler cyclization). We incorporate γ-modifications in the PNA backbone that are known to enhance hybridization and solubility. We demonstrate the robustness of this strategy with a library synthesis that is characterized by MALDI MS analysis at every step.
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Affiliation(s)
- Dalila Chouikhi
- Institut de Science et Ingénierie Supramoléculaires, ISIS - UMR, Université de Strasbourg - CNRS, France
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22
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Winssinger N. DNA display of PNA-tagged ligands: a versatile strategy to screen libraries and control geometry of multidentate ligands. ARTIFICIAL DNA, PNA & XNA 2012; 3:105-8. [PMID: 22871882 PMCID: PMC3581508 DOI: 10.4161/adna.21108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past decade, several technologies have emerged to access nucleic acid-tagged libraries and select the fittest compound within such libraries. This perspective focuses on recent development with PNA-tagged small molecules displayed on DNA templates for screening purposes and to probe the optimal geometry in multivalent interactions.
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Affiliation(s)
- Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires, Université de Strasbourg, CNRS, Strasbourg, France.
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23
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Lee KH, Lee KY, Byun JY, Kim BG, Kim DM. On-bead expression of recombinant proteins in an agarose gel matrix coated on a glass slide. LAB ON A CHIP 2012; 12:1605-1610. [PMID: 22410788 DOI: 10.1039/c2lc21239k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A system for expression and in situ display of recombinant proteins on a microbead surface is described. Biotinylated PCR products were immobilized on microbead surfaces, which were then embedded in a gel matrix and supplied with translation machinery and substrates. Upon the incubation of the gel matrix, target proteins encoded on the bead-immobilized DNA were expressed and captured on the same bead, thus allowing bead-mediated linkage of DNA and encoded proteins. The new method combines the simplicity and convenience of solid-phase separation of genetic information with the benefits of cell-free protein synthesis, such as instant translation of genetic information, unrestricted substrate accessibility and flexible assay configuration design.
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Affiliation(s)
- Kyung-Ho Lee
- Interdisciplinary Program for Nano-Technology, Chungnam National University, Daejeon 305-764, Korea
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Decoding a PNA encoded peptide library by PCR: the discovery of new cell surface receptor ligands. ACTA ACUST UNITED AC 2012; 18:1284-9. [PMID: 22035797 DOI: 10.1016/j.chembiol.2011.07.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 07/05/2011] [Accepted: 07/06/2011] [Indexed: 12/18/2022]
Abstract
The ability to screen and identify new ligands for cell surface receptors has been a long-standing goal as it might allow targeting of pharmaceutically relevant receptors, such as integrins or G protein coupled receptors. Here, we present a method to amplify hits from a library of PNA-tagged peptides. To this end, human cells, overexpressing either integrins or the CCR6 receptor, were treated with a 10,000 member PNA-encoded peptide library. Extraction of the PNA tags from the surface of the cells was followed by a PNA-tag to DNA translation and amplification enabling decoding of the tags via microarray hybridization. This approach to ligand discovery facilitates screening for differences in surface-receptor ligands and/or receptor expression between different cell types, and opens up a practical approach to PNA-tag amplification.
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Svensen N, Walton JG, Bradley M. Peptides for cell-selective drug delivery. Trends Pharmacol Sci 2012; 33:186-92. [DOI: 10.1016/j.tips.2012.02.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/14/2012] [Accepted: 02/14/2012] [Indexed: 10/28/2022]
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26
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Daguer JP, Ciobanu M, Barluenga S, Winssinger N. Discovery of an entropically-driven small molecule streptavidin binder from nucleic acid-encoded libraries. Org Biomol Chem 2012; 10:1502-5. [DOI: 10.1039/c2ob06880j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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27
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Auld D, Lea W, Davis MI, Simeonov A. Literature Search and Review. Assay Drug Dev Technol 2011. [DOI: 10.1089/adt.2011.0906.lr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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