1
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Trobe M, Blesl J, Vareka M, Schreiner T, Breinbauer R. Modular Synthesis of Teraryl‐based alpha‐Helix Mimetics, Part 4: Core Fragments with two Halide Leaving Groups Featuring Side Chains of Proteinogenic Amino Acids. European J Org Chem 2022; 2022:e202101279. [PMID: 35910460 PMCID: PMC9304293 DOI: 10.1002/ejoc.202101279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/08/2022] [Indexed: 12/03/2022]
Abstract
Teraryl‐based α‐helix mimetics have proven to be useful compounds for the inhibition of protein‐protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl‐based α‐helix mimetics using a benzene core unit featuring two halide leaving groups of differentiated reactivity in the Pd‐catalyzed cross‐coupling used for teraryl assembly. The use of para‐bromo iodoarene core fragments resolved the issue of hydrolysis during cross‐coupling that was observed when using triflate as a leaving group. We report a complete set of para‐bromoiodoarene core fragments decorated with side chains of all proteinogenic amino acids relevant for PPI (Ala, Arg, Asn, Asp, Cys, Gln, Glu, His, Ile, Leu, Lys, Met, Phe, Ser, Thr, Trp, Tyr and Val). In order to be compatible with general cross‐coupling conditions, some of the nucleophilic side chains had to be provided in a protected form to serve as stable building blocks.
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Affiliation(s)
- Melanie Trobe
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Julia Blesl
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Martin Vareka
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Till Schreiner
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Rolf Breinbauer
- Technische Universitat Graz Institute of Organic Chemistry Stremayrgasse 9 A-8010 Graz AUSTRIA
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2
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Maity D, Kumar S, Curreli F, Debnath AK, Hamilton AD. α‐Helix‐Mimetic Foldamers for Targeting HIV‐1 TAR RNA. Chemistry 2019; 25:7265-7269. [DOI: 10.1002/chem.201900139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/22/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Debabrata Maity
- Department of ChemistryNew York University New York New York 10003 USA
| | - Sunil Kumar
- Department of ChemistryNew York University New York New York 10003 USA
| | - Francesca Curreli
- Lindsey F. Kimball Research InstituteNew York Blood Center New York New York 10065 USA
| | - Asim K. Debnath
- Lindsey F. Kimball Research InstituteNew York Blood Center New York New York 10065 USA
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3
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Tan J, Zhao M, Wang J, Li Z, Liang L, Zhang L, Yuan Q, Tan W. Regulation of Protein Activity and Cellular Functions Mediated by Molecularly Evolved Nucleic Acids. Angew Chem Int Ed Engl 2019; 58:1621-1625. [PMID: 30556364 PMCID: PMC6442720 DOI: 10.1002/anie.201809010] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 11/07/2018] [Indexed: 01/05/2023]
Abstract
Regulation of protein activity is essential for revealing the molecular mechanisms of biological processes. DNA and RNA achieve many uniquely efficient functions, such as genetic expression and regulation. The chemical capability to synthesize artificial nucleotides can expand the chemical space of nucleic acid libraries and further increase the functional diversity of nucleic acids. Herein, a versatile method has been developed for modular expansion of the chemical space of nucleic acid libraries, thus enabling the generation of aptamers able to regulate protein activity. Specifically, an aptamer that targets integrin alpha3 was identified and this aptamer can inhibit cell adhesion and migration. Overall, this chemical-design-assisted in vitro selection approach enables the generation of functional nucleic acids for elucidating the molecular basis of biological activities and uncovering a novel basis for the rational design of new protein-inhibitor pharmaceuticals.
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Affiliation(s)
- Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China,
| | - Mengmeng Zhao
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China
| | - Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhihao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Ling Liang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China
| | - Liqin Zhang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China,
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China, Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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4
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Tan J, Zhao M, Wang J, Li Z, Liang L, Zhang L, Yuan Q, Tan W. Regulation of Protein Activity and Cellular Functions Mediated by Molecularly Evolved Nucleic Acids. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Mengmeng Zhao
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 China
| | - Zhihao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 China
| | - Ling Liang
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Liqin Zhang
- Department of Chemistry and Department of Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute and McKnight Brain Institute University of Florida Gainesville FL 32611-7200 USA
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
- Department of Chemistry and Department of Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute and McKnight Brain Institute University of Florida Gainesville FL 32611-7200 USA
- Institute of Molecular Medicine (IMM) Renji Hospital Shanghai Jiao Tong University School of Medicine College of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai China
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5
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Martínez-Crespo L, Escudero-Adán EC, Costa A, Rotger C. The Role of N
-Methyl Squaramides in a Hydrogen-Bonding Strategy to Fold Peptidomimetic Compounds. Chemistry 2018; 24:17802-17813. [DOI: 10.1002/chem.201803930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/18/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Luís Martínez-Crespo
- Department of Chemistry; University of Balearic Islands; Cra Valldemossa km 7.5 07122 Palma Spain
| | - Eduardo C. Escudero-Adán
- Institute of Chemical Research of Catalonia (ICIQ); Av. Països Catalans 16 43007 Tarragona Spain
| | - Antonio Costa
- Department of Chemistry; University of Balearic Islands; Cra Valldemossa km 7.5 07122 Palma Spain
| | - Carmen Rotger
- Department of Chemistry; University of Balearic Islands; Cra Valldemossa km 7.5 07122 Palma Spain
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6
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Trobe M, Burke MD. The Molecular Industrial Revolution: Automated Synthesis of Small Molecules. Angew Chem Int Ed Engl 2018; 57:4192-4214. [PMID: 29513400 PMCID: PMC5912692 DOI: 10.1002/anie.201710482] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/05/2017] [Indexed: 11/10/2022]
Abstract
Today we are poised for a transition from the highly customized crafting of specific molecular targets by hand to the increasingly general and automated assembly of different types of molecules with the push of a button. Creating machines that are capable of making many different types of small molecules on demand, akin to that which has been achieved on the macroscale with 3D printers, is challenging. Yet important progress is being made toward this objective with two complementary approaches: 1) Automation of customized synthesis routes to different targets by machines that enable the use of many reactions and starting materials, and 2) automation of generalized platforms that make many different targets using common coupling chemistry and building blocks. Continued progress in these directions has the potential to shift the bottleneck in molecular innovation from synthesis to imagination, and thereby help drive a new industrial revolution on the molecular scale.
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Affiliation(s)
- Melanie Trobe
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin D. Burke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
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7
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Trobe M, Burke MD. Die molekulare industrielle Revolution: zur automatisierten Synthese organischer Verbindungen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710482] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Melanie Trobe
- Department of Chemistry University of Illinois Urbana-Champaign 600 S. Mathews, 454 RAL Urbana-Champaign IL 61801 USA
| | - Martin D. Burke
- Department of Chemistry University of Illinois Urbana-Champaign 600 S. Mathews, 454 RAL Urbana-Champaign IL 61801 USA
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8
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Martin C, Moors SLC, Danielsen M, Betti C, Fabris C, Sejer Pedersen D, Pardon E, Peyressatre M, Fehér K, Martins JC, Mosolff Mathiesen J, Morris MC, Devoogdt N, Caveliers V, De Proft F, Steyaert J, Ballet S. Rational Design of Nanobody80 Loop Peptidomimetics: Towards Biased β 2 Adrenergic Receptor Ligands. Chemistry 2017; 23:9632-9640. [PMID: 28449310 DOI: 10.1002/chem.201701321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Indexed: 01/10/2023]
Abstract
G protein-coupled receptors (GPCRs) play an important role in many cellular responses; as such, their mechanism of action is of utmost interest. To gain insight into the active conformation of GPCRs, the X-ray crystal structures of nanobody (Nb)-stabilized β2 -adrenergic receptor (β2 AR) have been reported. Nb80, in particular, is able to bind the intracellular G protein binding site of β2 AR and stabilize the receptor in an active conformation. Within Nb80, the complementarity-determining region 3 (CDR3) is responsible for most of the binding interactions. Hence, we hypothesized that peptidomimetics of the CDR3 loop might be sufficient for binding to the receptor, inhibiting the interaction of β2 AR with intracellular GPCR interacting proteins (e.g., G proteins). Based on previous crystallographic data, a set of peptidomimetics were synthesized that, similar to the Nb80 CDR3 loop, adopt a β-hairpin conformation. Syntheses, conformational analysis, binding and functional in vitro assays, as well as internalization experiments, were performed. We demonstrate that peptidomimetics can structurally mimic the CDR3 loop of a nanobody and its function by inhibiting G protein coupling as measured by partial inhibition of cAMP production.
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Affiliation(s)
- Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Samuel L C Moors
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
| | - Mia Danielsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cecilia Betti
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cecilia Fabris
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Els Pardon
- Structural Biology Brussels, VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Marion Peyressatre
- Institut des Biomolécules Max Mousseron-IBMM-CNRS-UMR 5247, Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Krisztina Fehér
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Gent, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Gent, Belgium
| | - Jesper Mosolff Mathiesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - May C Morris
- Institut des Biomolécules Max Mousseron-IBMM-CNRS-UMR 5247, Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Nick Devoogdt
- In Vivo Cellular and Molecular Imaging lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Vicky Caveliers
- In Vivo Cellular and Molecular Imaging lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
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9
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Tashiro S, Chiba M, Shionoya M. Arrangement of Proteinogenic α-Amino Acids on a Cyclic Peptide Comprising Alternate Biphenyl-Cored ζ-Amino Acids. Chem Asian J 2017; 12:1087-1094. [DOI: 10.1002/asia.201700203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/25/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Shohei Tashiro
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Masayuki Chiba
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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10
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Wilch C, Talbiersky P, Berchner‐Pfannschmidt U, Schaller T, Kirsch M, Klärner F, Schrader T. Molecular Tweezers Inhibit PARP‐1 by a New Mechanism. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Constanze Wilch
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Peter Talbiersky
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | | | - Torsten Schaller
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Michael Kirsch
- Institute of Physiological Chemistry University Hospital Essen Hufelandstr. 55 45122 Essen Germany
| | - Frank‐Gerrit Klärner
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Thomas Schrader
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
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11
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Goyal B, Srivastava KR, Durani S. Examination of the Effect of N-terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine-based Short Peptides: A Molecular Dynamics Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201601381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University, Fatehgarh; Sahib-140406, Punjab India
| | - Kinshuk Raj Srivastava
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Life Sciences Institute; University of Michigan; Ann Arbor, MI USA 48105
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
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12
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Sonzini S, Marcozzi A, Gubeli RJ, van der Walle CF, Ravn P, Herrmann A, Scherman OA. High Affinity Recognition of a Selected Amino Acid Epitope within a Protein by Cucurbit[8]uril Complexation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Silvia Sonzini
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Formulation Sciences, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | - Alessio Marcozzi
- Zernike Institute for Advanced Materials; Dept. of Polymer Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Raphael J. Gubeli
- Formulation Sciences, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | | | - Peter Ravn
- Antibody Discovery and Protein Engineering, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials; Dept. of Polymer Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Oren A. Scherman
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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13
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Sonzini S, Marcozzi A, Gubeli RJ, van der Walle CF, Ravn P, Herrmann A, Scherman OA. High Affinity Recognition of a Selected Amino Acid Epitope within a Protein by Cucurbit[8]uril Complexation. Angew Chem Int Ed Engl 2016; 55:14000-14004. [DOI: 10.1002/anie.201606763] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/18/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Silvia Sonzini
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Formulation Sciences, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | - Alessio Marcozzi
- Zernike Institute for Advanced Materials; Dept. of Polymer Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Raphael J. Gubeli
- Formulation Sciences, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | | | - Peter Ravn
- Antibody Discovery and Protein Engineering, MedImmune Ltd.; Granta Park Cambridge CB21 6GH UK
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials; Dept. of Polymer Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Oren A. Scherman
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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14
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Hu K, Geng H, Zhang Q, Liu Q, Xie M, Sun C, Li W, Lin H, Jiang F, Wang T, Wu YD, Li Z. An In-tether Chiral Center Modulates the Helicity, Cell Permeability, and Target Binding Affinity of a Peptide. Angew Chem Int Ed Engl 2016; 55:8013-7. [PMID: 27167181 DOI: 10.1002/anie.201602806] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Indexed: 11/11/2022]
Abstract
The addition of a precisely positioned chiral center in the tether of a constrained peptide is reported, yielding two separable peptide diastereomers with significantly different helicity, as supported by circular dichroism (CD) and NMR spectroscopy. Single crystal X-ray diffraction analysis suggests that the absolute configuration of the in-tether chiral center in helical form is R, which is in agreement with theoretical simulations. The relationship between the secondary structure of the short peptides and their biochemical/biophysical properties remains elusive, largely because of the lack of proper controls. The present strategy provides the only method for investigating the influence of solely conformational differences upon the biochemical/biophysical properties of peptides. The significant differences in permeability and target binding affinity between the peptide diastereomers demonstrate the importance of helical conformation.
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Affiliation(s)
- Kuan Hu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Hao Geng
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Qingzhou Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Qisong Liu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Mingsheng Xie
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chengjie Sun
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wenjun Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Huacan Lin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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15
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Hu K, Geng H, Zhang Q, Liu Q, Xie M, Sun C, Li W, Lin H, Jiang F, Wang T, Wu YD, Li Z. An In-tether Chiral Center Modulates the Helicity, Cell Permeability, and Target Binding Affinity of a Peptide. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602806] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kuan Hu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Hao Geng
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Qingzhou Zhang
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Qisong Liu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Mingsheng Xie
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Chengjie Sun
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Wenjun Li
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Huacan Lin
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Tao Wang
- Department of Biology; Southern University of Science and Technology; Shenzhen 518055 China
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Zigang Li
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
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16
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Nissinkorn Y, Lahav‐Mankovski N, Rabinkov A, Albeck S, Motiei L, Margulies D. Sensing Protein Surfaces with Targeted Fluorescent Receptors. Chemistry 2015; 21:15981-7. [DOI: 10.1002/chem.201502069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Yael Nissinkorn
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Naama Lahav‐Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Aharon Rabinkov
- Department of Biological Services, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
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17
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Holvey RS, Valkov E, Neal D, Stewart M, Abell C. Selective Targeting of the TPX2 Site of Importin-α Using Fragment-Based Ligand Design. ChemMedChem 2015; 10:1232-9. [PMID: 25899172 PMCID: PMC4515083 DOI: 10.1002/cmdc.201500014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 01/05/2023]
Abstract
Protein-protein interactions are difficult therapeutic targets, and inhibiting pathologically relevant interactions without disrupting other essential ones presents an additional challenge. Herein we report how this might be achieved for the potential anticancer target, the TPX2-importin-α interaction. Importin-α is a nuclear transport protein that regulates the spindle assembly protein TPX2. It has two binding sites--major and minor-to which partners bind. Most nuclear transport cargoes use the major site, whereas TPX2 binds principally to the minor site. Fragment-based approaches were used to identify small molecules that bind importin-α, and crystallographic studies identified a lead series that was observed to bind specifically to the minor site, representing the first ligands specific for this site. Structure-guided synthesis informed the elaboration of these fragments to explore the source of ligand selectivity between the minor and major sites. These ligands are starting points for the development of inhibitors of this protein-protein interaction.
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Affiliation(s)
- Rhian S Holvey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Eugene Valkov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH (UK)
| | - David Neal
- University of Cambridge, Department of Oncology, Box 279, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ (UK)
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH (UK)
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW (UK).
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18
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Barnard A, Long K, Martin HL, Miles JA, Edwards TA, Tomlinson DC, Macdonald A, Wilson AJ. Selective and Potent Proteomimetic Inhibitors of Intracellular Protein-Protein Interactions. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 127:3003-3008. [PMID: 26877561 PMCID: PMC4737265 DOI: 10.1002/ange.201410810] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/15/2014] [Indexed: 01/07/2023]
Abstract
Inhibition of protein-protein interactions (PPIs) represents a major challenge in chemical biology and drug discovery. α-Helix mediated PPIs may be amenable to modulation using generic chemotypes, termed "proteomimetics", which can be assembled in a modular manner to reproduce the vectoral presentation of key side chains found on a helical motif from one partner within the PPI. In this work, it is demonstrated that by using a library of N-alkylated aromatic oligoamide helix mimetics, potent helix mimetics which reproduce their biophysical binding selectivity in a cellular context can be identified.
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Affiliation(s)
- Anna Barnard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Kérya Long
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Heather L. Martin
- Leeds Institute of Biomedical and Clinical Sciences, Wellcome Trust Brenner Building, University of Leeds, St. James's University Hospital, Leeds LS9 7TF (UK)
| | - Jennifer A. Miles
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Thomas A. Edwards
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Darren C. Tomlinson
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Andrew Macdonald
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Andrew J. Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
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Barnard A, Long K, Martin HL, Miles JA, Edwards TA, Tomlinson DC, Macdonald A, Wilson AJ. Selective and potent proteomimetic inhibitors of intracellular protein-protein interactions. Angew Chem Int Ed Engl 2015; 54:2960-5. [PMID: 25651514 PMCID: PMC4506525 DOI: 10.1002/anie.201410810] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/15/2014] [Indexed: 12/30/2022]
Abstract
Inhibition of protein–protein interactions (PPIs) represents a major challenge in chemical biology and drug discovery. α-Helix mediated PPIs may be amenable to modulation using generic chemotypes, termed “proteomimetics”, which can be assembled in a modular manner to reproduce the vectoral presentation of key side chains found on a helical motif from one partner within the PPI. In this work, it is demonstrated that by using a library of N-alkylated aromatic oligoamide helix mimetics, potent helix mimetics which reproduce their biophysical binding selectivity in a cellular context can be identified.
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Affiliation(s)
- Anna Barnard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK); Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
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20
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Chen L, Wang H, Zhang DW, Zhou Y, Li ZT. Quadruple Switching of Pleated Foldamers of Tetrathiafulvalene-Bipyridinium Alternating Dynamic Covalent Polymers. Angew Chem Int Ed Engl 2015; 54:4028-31. [PMID: 25651411 DOI: 10.1002/anie.201410757] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Lan Chen
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Fudan University, 220 Handan Road, Shanghai 200433 (China)
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21
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Chen L, Wang H, Zhang DW, Zhou Y, Li ZT. Quadruple Switching of Pleated Foldamers of Tetrathiafulvalene-Bipyridinium Alternating Dynamic Covalent Polymers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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22
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Hydrogen-Bonding-Driven Aromatic Foldamers: Their Structural and Functional Evolution. CHEM REC 2014; 15:233-51. [DOI: 10.1002/tcr.201402046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Indexed: 12/16/2022]
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23
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 305] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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24
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Latza P, Gilles P, Schaller T, Schrader T. Affinity Polymers Tailored for the Protein A Binding Site of Immunoglobulin G Proteins. Chemistry 2014; 20:11479-87. [DOI: 10.1002/chem.201402399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 01/01/2023]
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26
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Motiei L, Pode Z, Koganitsky A, Margulies D. Targeted Protein Surface Sensors as a Tool for Analyzing Small Populations of Proteins in Biological Mixtures. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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27
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Motiei L, Pode Z, Koganitsky A, Margulies D. Targeted Protein Surface Sensors as a Tool for Analyzing Small Populations of Proteins in Biological Mixtures. Angew Chem Int Ed Engl 2014; 53:9289-93. [DOI: 10.1002/anie.201402501] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 01/11/2023]
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28
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Vargas C, Radziwill G, Krause G, Diehl A, Keller S, Kamdem N, Czekelius C, Kreuchwig A, Schmieder P, Doyle D, Moelling K, Hagen V, Schade M, Oschkinat H. Small-molecule inhibitors of AF6 PDZ-mediated protein-protein interactions. ChemMedChem 2014; 9:1458-62. [PMID: 24668962 DOI: 10.1002/cmdc.201300553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/13/2014] [Indexed: 10/25/2022]
Abstract
PDZ (PSD-95, Dlg, ZO-1) domains are ubiquitous interaction modules that are involved in many cellular signal transduction pathways. Interference with PDZ-mediated protein-protein interactions has important implications in disease-related signaling processes. For this reason, PDZ domains have gained attention as potential targets for inhibitor design and, in the long run, drug development. Herein we report the development of small molecules to probe the function of the PDZ domain from human AF6 (ALL1-fused gene from chromosome 6), which is an essential component of cell-cell junctions. These compounds bind to AF6 PDZ with substantially higher affinity than the peptide (Ile-Gln-Ser-Val-Glu-Val) derived from its natural ligand, EphB2. In intact cells, the compounds inhibit the AF6-Bcr interaction and interfere with epidermal growth factor (EGF)-dependent signaling.
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Affiliation(s)
- Carolyn Vargas
- Leibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Str. 10, 13125 Berlin (Germany); Current address: Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern (Germany)
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29
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Xin D, Perez LM, Ioerger TR, Burgess K. A multifaceted secondary structure mimic based on piperidine-piperidinones. Angew Chem Int Ed Engl 2014; 53:3594-8. [PMID: 24591004 DOI: 10.1002/anie.201400927] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Indexed: 11/07/2022]
Abstract
Minimalist secondary structure mimics are typically made to resemble one interface in a protein-protein interaction (PPI), and thus perturb it. We recently proposed suitable chemotypes can be matched with interface regions directly, without regard for secondary structures. Here we describe a modular synthesis of a new chemotype 1, simulation of its solution-state conformational ensemble, and correlation of that with ideal secondary structures and real interface regions in PPIs. Scaffold 1 presents amino acid side-chains that are quite separated from each other, in orientations that closely resemble ideal sheet or helical structures, similar non-ideal structures at PPI interfaces, and regions of other PPI interfaces where the mimic conformation does not resemble any secondary structure. 68 different PPIs where conformations of 1 matched well were identified. A new method is also presented to determine the relevance of a minimalist mimic crystal structure to its solution conformations. Thus DLD-1 faf crystallized in a conformation that is estimated to be 0.91 kcal mol(-1) above the minimum energy solution state.
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Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77841-3012 (USA)
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30
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Xin D, Perez LM, Ioerger TR, Burgess K. A Multifaceted Secondary Structure Mimic Based On Piperidine-piperidinones. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Guan JY, Foerster JM, Drijfhout JW, Timmer M, Blok A, Ullmann GM, Ubbink M. An Ensemble of Rapidly Interconverting Orientations in Electrostatic Protein-Peptide Complexes Characterized by NMR Spectroscopy. Chembiochem 2014; 15:556-66. [DOI: 10.1002/cbic.201300623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Indexed: 12/21/2022]
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32
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Hassanpour A, De Carufel CA, Bourgault S, Forgione P. Synthesis of 2,5-diaryl-substituted thiophenes as helical mimetics: towards the modulation of islet amyloid polypeptide (IAPP) amyloid fibril formation and cytotoxicity. Chemistry 2014; 20:2522-8. [PMID: 24488624 DOI: 10.1002/chem.201303928] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Indexed: 11/08/2022]
Abstract
A range of 2,5-diarylated thiophenes were synthesised as small molecule mimetics of the α-helix to modulate the amyloidogenesis and cytotoxic effect of islet amyloid polypeptide (IAPP). 3-Substituted thiophene-2-carboxylic acids were used as key intermediates and functionalised by palladium decarboxylative cross-coupling and direct C-H activation successively with overall yields ranging from 23 to 95 %. The effect of the ligands on IAPP amyloid fibril formation was evaluated with the thioflavin T (ThT) fluorescence-based assay. Furthermore, the capacity of these compounds to inhibit the cytotoxic effect of IAPP was assessed using β-pancreatic cells.
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Affiliation(s)
- Avid Hassanpour
- Concordia University, Department of Chemistry and Biochemistry, Pharmaqam, 7141 rue Sherbrooke O., Montréal, QC H4B 1R6 (Canada)
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33
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Wu CF, Li ZM, Xu XN, Zhao ZX, Zhao X, Wang RX, Li ZT. Folding-Induced Folding: The Assembly of Aromatic Amide and 1,2,3-Triazole Hybrid Helices. Chemistry 2014; 20:1418-26. [DOI: 10.1002/chem.201304161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 12/15/2022]
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34
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Buratto J, Colombo C, Stupfel M, Dawson SJ, Dolain C, Langlois d'Estaintot B, Fischer L, Granier T, Laguerre M, Gallois B, Huc I. Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution. Angew Chem Int Ed Engl 2013; 53:883-7. [DOI: 10.1002/anie.201309160] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Indexed: 11/06/2022]
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35
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Buratto J, Colombo C, Stupfel M, Dawson SJ, Dolain C, Langlois d'Estaintot B, Fischer L, Granier T, Laguerre M, Gallois B, Huc I. Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201309160] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Hack V, Reuter C, Opitz R, Schmieder P, Beyermann M, Neudörfl JM, Kühne R, Schmalz HG. Efficient α-Helix Induction in a Linear Peptide Chain byN-Capping with a Bridged-tricyclic Diproline Analogue. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Hack V, Reuter C, Opitz R, Schmieder P, Beyermann M, Neudörfl JM, Kühne R, Schmalz HG. Efficient α-Helix Induction in a Linear Peptide Chain byN-Capping with a Bridged-tricyclic Diproline Analogue. Angew Chem Int Ed Engl 2013; 52:9539-43. [DOI: 10.1002/anie.201302014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 04/11/2013] [Indexed: 11/11/2022]
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38
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Prabhakaran P, Barnard A, Murphy NS, Kilner CA, Edwards TA, Wilson AJ. Aromatic Oligoamide Foldamers with a “Wet Edge” as Inhibitors of the α-Helix-Mediated p53-hDM2 Protein-Protein Interaction. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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39
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Murphy NS, Prabhakaran P, Azzarito V, Plante JP, Hardie MJ, Kilner CA, Warriner SL, Wilson AJ. Solid-phase methodology for synthesis of O-alkylated aromatic oligoamide inhibitors of α-helix-mediated protein-protein interactions. Chemistry 2013; 19:5546-50. [PMID: 23508712 PMCID: PMC3743211 DOI: 10.1002/chem.201204098] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 01/18/2023]
Abstract
Rapid access to rigid rods: A method is described for the synthesis of 3-O-alkylated aromatic oligobenzamide foldamers that could be used for assembly of libraries of α-helix mimetic inhibitors of protein-protein interactions (see scheme; Fmoc=9-fluorenylmethoxycarbonyl).
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Affiliation(s)
- Natasha S Murphy
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK
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40
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Yoshimatsu K, Lesel BK, Yonamine Y, Beierle JM, Shea KJ. Temperature-responsive "catch and release" of proteins by using multifunctional polymer-based nanoparticles. Angew Chem Int Ed Engl 2012; 51:2405-8. [PMID: 22287126 PMCID: PMC3425610 DOI: 10.1002/anie.201107797] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 01/10/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Keiichi Yoshimatsu
- Department of Chemistry University of California, Irvine Irvine, CA 92697 (USA)
| | - Benjamin K. Lesel
- Department of Chemistry University of California, Irvine Irvine, CA 92697 (USA)
| | - Yusuke Yonamine
- Department of Chemistry University of California, Irvine Irvine, CA 92697 (USA)
| | - John M. Beierle
- Department of Chemistry University of California, Irvine Irvine, CA 92697 (USA)
| | - Kenneth J. Shea
- Department of Chemistry University of California, Irvine Irvine, CA 92697 (USA)
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41
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Thiel P, Kaiser M, Ottmann C. Small-molecule stabilization of protein-protein interactions: an underestimated concept in drug discovery? Angew Chem Int Ed Engl 2012; 51:2012-8. [PMID: 22308055 DOI: 10.1002/anie.201107616] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Indexed: 11/08/2022]
Abstract
The modulation of protein-protein interactions (PPIs) has been recognized as one of the most challenging tasks in drug discovery. While their systematic development has long been considered as intractable, this view has changed over the last years, with the first drug candidates undergoing clinical studies. To date, the vast majority of PPI modulators are interaction inhibitors. However, in many biological contexts a prolonged lifespan of a PPI might be desirable, calling for the complementary approach of PPI stabilization. In fact, nature offers impressive examples of this concept and some PPI-stabilizing natural products have already found application as important drugs. Moreover, directed small-molecule stabilization has recently been demonstrated. Therefore, it is time to take a closer look at the constructive side of modulating PPIs.
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Affiliation(s)
- Philipp Thiel
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
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42
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Thiel P, Kaiser M, Ottmann C. Niedermolekulare Stabilisatoren von Protein-Protein-Wechselwirkungen: ein unterschätztes Konzept in der Wirkstoffentwicklung? Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107616] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Yoshimatsu K, Lesel BK, Yonamine Y, Beierle JM, Hoshino Y, Shea KJ. Temperature-Responsive “Catch and Release” of Proteins by using Multifunctional Polymer-Based Nanoparticles. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107797] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Gordo S, Martos V, Vilaseca M, Menéndez M, de Mendoza J, Giralt E. On the role of flexibility in protein-ligand interactions: the example of p53 tetramerization domain. Chem Asian J 2011; 6:1463-9. [PMID: 21626703 DOI: 10.1002/asia.201000938] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The recognition of protein surfaces by designed ligands has become an attractive approach in drug discovery. However, the variable nature and irregular behavior of protein surfaces defy this new area of research. The easy to understand "lock-and-key" model is far from being the ideal paradigm in biomolecular interactions and, hence, any new finding on how proteins and ligands behave in recognition events paves a step of the way. Herein, we illustrate a clear example on how an increase in flexibility of both protein and ligand can result in an increase in the stability of the macromolecular complex. The biophysical study of the interaction between a designed flexible tetraguanidinium-calix[4]arene and the tetramerization domain of protein p53 (p53TD) and its natural mutant p53TD-R337H shows how the floppy mutant domain interacts more tightly with the ligand than the well-packed wild-type protein. Moreover, the flexible calixarene ligand interacts with higher affinity to both wild-type and mutated protein domains than a conformationally rigid calixarene analog previously reported. These findings underscore the crucial role of flexibility in molecular recognition processes, for both small ligands and large biomolecular surfaces.
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Affiliation(s)
- Susana Gordo
- Institute for Research in Biomedicine, Baldiri Reixac 10, 08028 Barcelona, Spain
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Liu L, Ghosh N, Slivka PF, Fiorini Z, Hutchinson MR, Watkins LR, Yin H. An MD2 hot-spot-mimicking peptide that suppresses TLR4-mediated inflammatory response in vitro and in vivo. Chembiochem 2011; 12:1827-31. [PMID: 21678541 PMCID: PMC3374877 DOI: 10.1002/cbic.201100211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Indexed: 01/11/2023]
Abstract
A truncated peptide was shown to retain the structure of the TLR4-binding hot-spot region of MD2, disrupting with the TLR4/MD2 interactions. The peptide not only demonstrated strong binding affinity in the fluorescence polarization assay, but also showed high specificity in macrophage cells. Furthermore, MD2-I was able to suppress neuropathic pain in animal models.
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Affiliation(s)
- Liping Liu
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado at Boulder Boulder, CO 80309-0215 (USA), Fax: (+1)303-492-5894
| | - Nilanjan Ghosh
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado at Boulder Boulder, CO 80309-0215 (USA), Fax: (+1)303-492-5894
| | - Peter F. Slivka
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado at Boulder Boulder, CO 80309-0215 (USA), Fax: (+1)303-492-5894
| | - Zeno Fiorini
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado at Boulder Boulder, CO 80309-0215 (USA), Fax: (+1)303-492-5894
| | - Mark R. Hutchinson
- Discipline of Physiology School of Medical Sciences, University of Adelaide, Adelaide, South Australia (Australia)
| | - Linda R. Watkins
- Department of Psychology and Neuroscience, University of Colorado at Boulder, Boulder, CO 80309-0345 (USA)
| | - Hang Yin
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado at Boulder Boulder, CO 80309-0215 (USA), Fax: (+1)303-492-5894
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46
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Liskamp RMJ, Rijkers DTS, Kruijtzer JAW, Kemmink J. Peptides and proteins as a continuing exciting source of inspiration for peptidomimetics. Chembiochem 2011; 12:1626-53. [PMID: 21751324 DOI: 10.1002/cbic.201000717] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Indexed: 12/17/2022]
Abstract
Despite their enormous diversity in biological function and structure, peptides and proteins are endowed with properties that have induced and stimulated the development of peptidomimetics. Clearly, peptides can be considered as the "stem" of a phylogenetic molecular development tree from which branches of oligomeric peptidomimetics such as peptoids, peptidosulfonamides, urea peptidomimetics, as well as β-peptides have sprouted. It is still a challenge to efficiently synthesize these oligomeric species, and study their structural and biological properties. Combining peptides and peptidomimetics led to the emergence of peptide-peptidomimetic hybrids in which one or more (proteinogenic) amino acid residues have been replaced with these mimetic residues. In scan-like approaches, the influence of these replacements on biological activity can then be studied, to evaluate to what extent a peptide can be transformed into a peptidomimetic structure while maintaining, or even improving, its biological properties. A central issue, especially with the smaller peptides, is the lack of secondary structure. Important approaches to control secondary structure include the introduction of α,α-disubstituted amino acids, or (di)peptidomimetic structures such as the Freidinger lactam. Apart from intra-amino acid constraints, inter-amino acid constraints for formation of a diversity of cyclic peptides have shaped a thick branch. Apart from the classical disulfide bridges, the repertoire has been extended to include sulfide and triazole bridges as well as the single-, double- and even triple-bond replacements, accessible by the extremely versatile ring-closing alkene/alkyne metathesis approaches. The latter approach is now the method of choice for the secondary structure that presents the greatest challenge for structural stabilization: the α-helix.
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Affiliation(s)
- Rob M J Liskamp
- Medicinal Chemistry and Chemical Biology, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
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47
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Urbach AR, Ramalingam V. Molecular Recognition of Amino Acids, Peptides, and Proteins by Cucurbit[n]uril Receptors. Isr J Chem 2011. [DOI: 10.1002/ijch.201100035] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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48
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Henchey LK, Porter JR, Ghosh I, Arora PS. High specificity in protein recognition by hydrogen-bond-surrogate α-helices: selective inhibition of the p53/MDM2 complex. Chembiochem 2011; 11:2104-7. [PMID: 20821791 DOI: 10.1002/cbic.201000378] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Laura K Henchey
- Department of Chemistry, New York University, New York, NY 10003, USA
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49
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Peñalver P, Marcelo F, Jiménez-Barbero J, Vicent C. Carbohydrate recognition at the minor-groove of the self-complementary duplex d(CGCGAATTCGCG)2 by a synthetic glyco-oligoamide. Chemistry 2011; 17:4561-70. [PMID: 21259350 DOI: 10.1002/chem.201003027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Indexed: 12/20/2022]
Abstract
The structure of a neutral glyco-conjugate β-Gal-Py-γ-Py-Ind (1), designed as a probe for analyzing sugar-DNA interactions, when bound to a self-complementary oligonucleotide duplex d(CGCG AATT CGCG)(2) has been deduced by employing (1)H NMR techniques. Analysis of the formed 1:1 complex demonstrated that the glycol ligand is bound in a hairpin-like conformation in which both pyrrole amino acid moieties are stacked, whereas the indole and the sugar residues are spatially close. The binding site is defined by the minor groove formed by the -AATT- stretch. In particular, the -Py-γ-Py- region of the ligand is sited near the A5-A6 oligonucleotide residues, whereas the indole and the sugar rings are next to the T7-T8 base pairs. More relevant, the existence of a variety of intermolecular NOE correlations permitted the close proximity of the sugar to the minor groove to be assessed, thus showing that the binding of the glycoconjugate at the minor groove is the origin of the specificity of the glycoconjugate-DNA interaction. The experimental NMR data have been combined with restrained and unrestrained molecular dynamics calculations, to provide the 3D structure of the complex.
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Affiliation(s)
- Pablo Peñalver
- Departamento de Síntesis, Estructura y Propiedades de Compuestos Orgánicos (SEPCO), Instituto de Química Orgánica general CSIC, c/Juan de la Cierva 3, 28006, Madrid, Spain
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50
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Rasmussen JE, Schiødt CB, Christensen SF, Nørskov-Lauritsen L, Meldal M, St Hilaire PM, Jensen KJ. Small-molecule affinity ligands for protein purification: combined computational enrichment and automated in-line screening of an optically encoded library. Angew Chem Int Ed Engl 2010; 49:3477-80. [PMID: 20301150 DOI: 10.1002/anie.200906602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jakob E Rasmussen
- Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark.
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