1
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Minnee H, Rack JGM, van der Marel GA, Overkleeft HS, Codée JDC, Ahel I, Filippov DV. Solid-Phase Synthesis and Biological Evaluation of Peptides ADP-Ribosylated at Histidine. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 136:e202313317. [PMID: 38516349 PMCID: PMC10952255 DOI: 10.1002/ange.202313317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Indexed: 03/23/2024]
Abstract
The transfer of an adenosine diphosphate (ADP) ribose moiety to a nucleophilic side chain by consumption of nicotinamide adenine dinucleotide is referred to as ADP-ribosylation, which allows for the spatiotemporal regulation of vital processes such as apoptosis and DNA repair. Recent mass-spectrometry based analyses of the "ADP-ribosylome" have identified histidine as ADP-ribose acceptor site. In order to study this modification, a fully synthetic strategy towards α-configured N(τ)- and N(π)-ADP-ribosylated histidine-containing peptides has been developed. Ribofuranosylated histidine building blocks were obtained via Mukaiyama-type glycosylation and the building blocks were integrated into an ADP-ribosylome derived peptide sequence using fluorenylmethyloxycarbonyl (Fmoc)-based solid-phase peptide synthesis. On-resin installation of the ADP moiety was achieved using phosphoramidite chemistry, and global deprotection provided the desired ADP-ribosylated oligopeptides. The stability under various chemical conditions and resistance against (ADP-ribosyl) hydrolase-mediated degradation has been investigated to reveal that the constructs are stable under various chemical conditions and non-degradable by any of the known ADP-ribosylhydrolases.
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Affiliation(s)
- Hugo Minnee
- Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityRA-2300LeidenThe Netherlands
| | - Johannes G. M. Rack
- Sir William Dunn School of PathologyUniversity of OxfordSouth Parks RoadOxfordOX1 3REUK
- Current address: Medical Research Council Centre for Medical Mycology at the University of ExeterUniversity of Exeter, Geoffrey Pope BuildingStocker RoadExeterEX4 4QDUK
| | | | - Herman S. Overkleeft
- Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityRA-2300LeidenThe Netherlands
| | - Jeroen D. C. Codée
- Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityRA-2300LeidenThe Netherlands
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordSouth Parks RoadOxfordOX1 3REUK
| | - Dmitri V. Filippov
- Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityRA-2300LeidenThe Netherlands
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2
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Minnee H, Rack JGM, van der Marel GA, Overkleeft HS, Codée JDC, Ahel I, Filippov DV. Solid-Phase Synthesis and Biological Evaluation of Peptides ADP-Ribosylated at Histidine. Angew Chem Int Ed Engl 2024; 63:e202313317. [PMID: 37903139 PMCID: PMC10952301 DOI: 10.1002/anie.202313317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
The transfer of an adenosine diphosphate (ADP) ribose moiety to a nucleophilic side chain by consumption of nicotinamide adenine dinucleotide is referred to as ADP-ribosylation, which allows for the spatiotemporal regulation of vital processes such as apoptosis and DNA repair. Recent mass-spectrometry based analyses of the "ADP-ribosylome" have identified histidine as ADP-ribose acceptor site. In order to study this modification, a fully synthetic strategy towards α-configured N(τ)- and N(π)-ADP-ribosylated histidine-containing peptides has been developed. Ribofuranosylated histidine building blocks were obtained via Mukaiyama-type glycosylation and the building blocks were integrated into an ADP-ribosylome derived peptide sequence using fluorenylmethyloxycarbonyl (Fmoc)-based solid-phase peptide synthesis. On-resin installation of the ADP moiety was achieved using phosphoramidite chemistry, and global deprotection provided the desired ADP-ribosylated oligopeptides. The stability under various chemical conditions and resistance against (ADP-ribosyl) hydrolase-mediated degradation has been investigated to reveal that the constructs are stable under various chemical conditions and non-degradable by any of the known ADP-ribosylhydrolases.
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Affiliation(s)
- Hugo Minnee
- Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityRA-2300Leiden (TheNetherlands
| | - Johannes G. M. Rack
- Sir William Dunn School of PathologyUniversity of OxfordSouth Parks RoadOxfordOX1 3REUK
- Current address: Medical Research Council Centre for Medical Mycology at the University of ExeterUniversity of Exeter, Geoffrey Pope BuildingStocker RoadExeterEX4 4QDUK
| | | | - Herman S. Overkleeft
- Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityRA-2300Leiden (TheNetherlands
| | - Jeroen D. C. Codée
- Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityRA-2300Leiden (TheNetherlands
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordSouth Parks RoadOxfordOX1 3REUK
| | - Dmitri V. Filippov
- Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityRA-2300Leiden (TheNetherlands
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3
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Voorneveld J, Kloet MS, Wijngaarden S, Kim RQ, Moutsiopoulou A, Verdegaal M, Misra M, Đikić I, van der Marel GA, Overkleeft HS, Filippov DV, van der Heden van Noort GJ. Arginine ADP-Ribosylation: Chemical Synthesis of Post-Translationally Modified Ubiquitin Proteins. J Am Chem Soc 2022; 144:20582-20589. [DOI: 10.1021/jacs.2c06249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Jim Voorneveld
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Max S. Kloet
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Sven Wijngaarden
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Robbert Q. Kim
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Angeliki Moutsiopoulou
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Marnix Verdegaal
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Mohit Misra
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Ivan Đikić
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Gijsbert A. van der Marel
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Dmitri V. Filippov
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gerbrand J. van der Heden van Noort
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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4
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Mikhailov SN, Drenichev MS, Oslovsky VE, Kulikova IV, Herdewijn P. Synthesis of Poly(ADP-ribose) Monomer Containing 2'-O-α-D-Ribofuranosyl Adenosine. ACTA ACUST UNITED AC 2020; 78:e92. [PMID: 31529780 DOI: 10.1002/cpnc.92] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this article, the earlier reported procedure for the synthesis of 2'-O-β-D-ribofuranosyl nucleosides was extended to the synthesis of 2'-O-α-D-ribofuranosyl adenosine, a monomeric unit of poly(ADP-ribose). It consists in condensation of a small excess of 1-O-acetyl-2,3,5-tri-O-benzoyl-α,β-D-arabinofuranose activated with tin tetrachloride with 3',5'-O-tetra-isopropyldisiloxane-1,3-diyl-ribonucleosides in 1,2-dichloroethane. The following debenzoylation and silylation of arabinofuranosyl residue and inversion of configuration at C-2'' atom of arabinofuranosyl residue and final removal of silyl protective groups gave 2'-O-α-D-ribofuranosyl adenosine in overall 13% to 21% yield. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sergey N Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S Drenichev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir E Oslovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Irina V Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Piet Herdewijn
- Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
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5
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van
der Heden van
Noort GJ. Chemical Tools to Study Protein ADP-Ribosylation. ACS OMEGA 2020; 5:1743-1751. [PMID: 32039309 PMCID: PMC7003193 DOI: 10.1021/acsomega.9b03591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/08/2020] [Indexed: 05/03/2023]
Abstract
Post-translational modification of substrate proteins plays crucial roles in the regulation of their activity, cellular localization, and ability to be recognized by other proteins. One of those modifications involves the installment of adenosine-diphosphate-ribose (ADPr) onto nucleophilic side-chain groups of amino acid residues. This highly dynamic process is regulated by ADP-ribosyl transferases (ARTs) that install the ADPr-molecules on selected proteins and poly(ADP-ribosyl) glycohydrolases (PARGs) and (ADP-ribosyl)hydrolases (ARHs) that trim down and remove ADPr-chains. In this mini-review, the most recent advances in the chemical synthesis of ADPr-conjugates, poly-ADP-ribose, ADPr-peptides, and -proteins, and other tools to investigate ADPr-biology are discussed.
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6
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Liu Q, van der Marel GA, Filippov DV. Chemical ADP-ribosylation: mono-ADPr-peptides and oligo-ADP-ribose. Org Biomol Chem 2020; 17:5460-5474. [PMID: 31112180 DOI: 10.1039/c9ob00501c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
ADP-ribosylation is an important post-translational modification that plays a pivotal role in many cellular processes, including cell signaling, DNA repair, gene regulation and apoptosis. Although chemical synthesis of mono- or poly-ADP-ribosylated biomolecules is extremely difficult due to the challenges in regio- and stereoselective glycosylation, suitable protective group manipulations and pyrophosphate construction, synthetic procedures towards these bio-related targets have been reported in recent years. Chemically synthesized well-defined ADP-ribose derivatives serve as useful tools in biological experiments aimed to further elucidate native ADP-ribosylation. In this review, we will discuss the synthetic studies on mono-ADP-ribosylated proteins and oligo-ADP-ribose chains. Future possible synthetic targets and upcoming new methods for the synthesis of these molecules are also included.
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Affiliation(s)
- Qiang Liu
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
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7
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O'Neill S, Rodriguez J, Walczak MA. Direct Dehydrative Glycosylation of C1-Alcohols. Chem Asian J 2018; 13:2978-2990. [PMID: 30019854 PMCID: PMC7326538 DOI: 10.1002/asia.201800971] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Indexed: 12/15/2022]
Abstract
Due to the central role played by carbohydrates in a multitude of biological processes, there has been a sustained interest in developing effective glycosylation methods to enable more thorough investigation of their essential functions. Among the myriad technologies available for stereoselective glycoside bond formation, dehydrative glycosylation possesses a distinct advantage given the unique properties of C1-alcohols such as straightforward preparation, stability, and a general reactivity compatible with a diverse set of reaction conditions. In this Focus Review, a survey of direct dehydrative glycosylations of C1-alcohols is provided with an emphasis on recent achievements, pervading limitations, mechanistic insights, and applications in total synthesis.
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Affiliation(s)
- Sloane O'Neill
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Jacob Rodriguez
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Maciej A Walczak
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
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8
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Hems ES, Nepogodiev SA, Rejzek M, Field RA. Synthesis of glyceryl glycosides related to A-type prymnesin toxins. Carbohydr Res 2018; 463:14-23. [PMID: 29698849 PMCID: PMC5999359 DOI: 10.1016/j.carres.2018.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 11/23/2022]
Abstract
A suite of glycosylated glycerol derivatives representing various fragments of the glycosylated ichthyotoxins called prymnesins were chemically synthesised. Glycerol was used to represent a small fragment of the prymnesin backbone, and was glycosylated at the 2° position with the sugars currently reported to be present on prymnesin toxins. Neighbouring group participation was utilised to synthesise 1,2-trans-glycosides. SnCl2-promoted glycosylation with furanosyl fluorides gave 1,2-cis-furanosides with moderate stereocontrol, whilst TMSOTf promoted glycosylation with a furanosyl imidate gave a 1,2-cis-furanoside with good stereocontrol. The chemical synthesis of two larger glyceryl diglycoside fragments of prymnesin-1, glycosylated with α-ʟ-arabinopyranose and α-ᴅ-ribofuranose, is also described. As the stereochemistry of the prymnesin backbones at this region is undefined, both the 2R- and 2S- glycerol isomers were synthesised. The separated diastereoisomers were distinguished by comparing NOESY NMR with computational models.
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Affiliation(s)
- Edward S Hems
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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9
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Liu Q, Kistemaker HAV, Overkleeft HS, van der Marel GA, Filippov DV. Synthesis of ribosyl-ribosyl-adenosine-5',5'',5'''(triphosphate)-the naturally occurring branched fragment of poly(ADP ribose). Chem Commun (Camb) 2018; 53:10255-10258. [PMID: 28868552 DOI: 10.1039/c7cc05755e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Poly-adenosine diphosphate ribose (PAR) is a branched biopolymer that occurs as a result of post-translational modification of proteins. In 1981 Miwa et al. determined the structure of enzymatically prepared branched PAR. We present the first synthesis of the same branched PAR fragment and have shown by NMR that the structure proposed by Miwa is correct.
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Affiliation(s)
- Qiang Liu
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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10
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Dyapa R, Dockery LT, Walczak MA. Dehydrative glycosylation with cyclic phosphonium anhydrides. Org Biomol Chem 2018; 15:51-55. [PMID: 27722396 DOI: 10.1039/c6ob01812b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic phosphonium anhydrides generated from bis-phosphine oxides and trifluoromethanesulfonic anhydride are shown as general coupling reagents in a dehydrative glycosylation reaction of C1-hemiacetals. This reaction protocol is characterized by a broad substrate scope and high yields, including reactions of O-, C-, N-, and S-based nucleophiles with furanose, pyranose, and deoxysugar donors.
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Affiliation(s)
- Rajendar Dyapa
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
| | - Lance T Dockery
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
| | - Maciej A Walczak
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
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11
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Shirinfar B, Ahmed N. Chemical Glycosylations for the Synthesis of Building Units of Post-Translational Modifications. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201700226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Bahareh Shirinfar
- School of Chemistry; University of Bristol; Bristol BS8 1TS United Kingdom
- Organic Chemistry Institute; University of Zürich; Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Nisar Ahmed
- School of Chemistry; University of Bristol; Bristol BS8 1TS United Kingdom
- Organic Chemistry Institute; University of Zürich; Winterthurerstrasse 190 8057 Zürich Switzerland
- School of Chemistry; Cardiff University; Cardiff CF10 3AT United Kingdom
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12
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Drenichev MS, Mikhailov SN. Poly(ADP-ribose): From chemical synthesis to drug design. Bioorg Med Chem Lett 2016; 26:3395-403. [PMID: 27318540 DOI: 10.1016/j.bmcl.2016.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 12/17/2022]
Abstract
Poly(ADP-ribose) (PAR) is an important biopolymer, which is involved in various life processes such as DNA repair and replication, modulation of chromatin structure, transcription, cell differentiation, and in pathogenesis of various diseases such as cancer, diabetes, ischemia and inflammations. PAR is the most electronegative biopolymer and this property is essential for its binding with a wide range of proteins. Understanding of PAR functions in cell on molecular level requires chemical synthesis of regular PAR oligomers. Recently developed methodologies for chemical synthesis of PAR oligomers, will facilitate the study of various cellular processes, involving PAR.
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Affiliation(s)
- Mikhail S Drenichev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation
| | - Sergey N Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation.
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13
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Affiliation(s)
- Yonglian Zhang
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Spencer Knapp
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
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Kistemaker HA, Meeuwenoord NJ, Overkleeft HS, Marel GA, Filippov DV. Solid‐Phase Synthesis of Oligo‐ADP‐Ribose. ACTA ACUST UNITED AC 2016; 64:4.68.1-4.68.27. [DOI: 10.1002/0471142700.nc0468s64] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hans A.V. Kistemaker
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
| | - Herman S. Overkleeft
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
| | - Gijsbert A. Marel
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
| | - Dmitri V. Filippov
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
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15
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Drenichev MS, Mikhailov SN. Poly(ADP-ribose)--a unique natural polymer structural features, biological role and approaches to the chemical synthesis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:258-76. [PMID: 25774719 DOI: 10.1080/15257770.2014.984073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Poly(ADP-ribose) (PAR) is a natural polymer, taking part in numerous important cellular processes. Several enzymes are involved in biosynthesis and degradation of PAR. One of them, poly(ADP-ribose)polymerase-1 (PARP-1) is considered to be a perspective target for the design of new drugs, affecting PAR metabolism. The structure of PAR was established by enzymatic hydrolysis and further analysis of the products, but total chemical synthesis of PAR hasn't been described yet. Several approaches have been developed on the way to chemical synthesis of this unique biopolymer.
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Affiliation(s)
- Mikhail S Drenichev
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russian Federation
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16
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Kistemaker HAV, Overkleeft HS, van der Marel GA, Filippov DV. Branching of poly(ADP-ribose): Synthesis of the Core Motif. Org Lett 2015; 17:4328-31. [PMID: 26307949 DOI: 10.1021/acs.orglett.5b02143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The synthesis of the core motif of branched poly(adenosine diphosphate ribose) (poly(ADPr)) is described, and structural analysis reasserted the proposed stereochemistry for branching. For the synthesis, a ribose trisaccharide was first constructed with only α-O-glycosidic linkages. Finally, the adenine nucleobase was introduced via a Vorbrüggen-type glycosylation reaction. The orthogonality of the selected protecting groups was demonstrated, allowing for the construction of branched poly(ADPr) oligomers in the near future.
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Affiliation(s)
- Hans A V Kistemaker
- Leiden Institute of Chemistry, Leiden University , P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University , P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University , P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University , P.O. Box 9502, 2300 RA Leiden, The Netherlands
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17
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Lambrecht MJ, Brichacek M, Barkauskaite E, Ariza A, Ahel I, Hergenrother PJ. Synthesis of dimeric ADP-ribose and its structure with human poly(ADP-ribose) glycohydrolase. J Am Chem Soc 2015; 137:3558-64. [PMID: 25706250 PMCID: PMC6089346 DOI: 10.1021/ja512528p] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Poly(ADP-ribosyl)ation is a common post-translational modification that mediates a wide variety of cellular processes including DNA damage repair, chromatin regulation, transcription, and apoptosis. The difficulty associated with accessing poly(ADP-ribose) (PAR) in a homogeneous form has been an impediment to understanding the interactions of PAR with poly(ADP-ribose) glycohydrolase (PARG) and other binding proteins. Here we describe the chemical synthesis of the ADP-ribose dimer, and we use this compound to obtain the first human PARG substrate-enzyme cocrystal structure. Chemical synthesis of PAR is an attractive alternative to traditional enzymatic synthesis and fractionation, allowing access to products such as dimeric ADP-ribose, which has been detected but never isolated from natural sources. Additionally, we describe the synthesis of an alkynylated dimer and demonstrate that this compound can be used to synthesize PAR probes including biotin and fluorophore-labeled compounds. The fluorescently labeled ADP-ribose dimer was then utilized in a general fluorescence polarization-based PAR-protein binding assay. Finally, we use intermediates of our synthesis to access various PAR fragments, and evaluation of these compounds as substrates for PARG reveals the minimal features for substrate recognition and enzymatic cleavage. Homogeneous PAR oligomers and unnatural variants produced from chemical synthesis will allow for further detailed structural and biochemical studies on the interaction of PAR with its many protein binding partners.
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Affiliation(s)
- Michael J. Lambrecht
- University of Illinois, Department of Chemistry, Roger Adams Laboratory, 600 South Mathews, Urbana, Illinois 61801, USA
| | - Matthew Brichacek
- University of Illinois, Department of Chemistry, Roger Adams Laboratory, 600 South Mathews, Urbana, Illinois 61801, USA
| | - Eva Barkauskaite
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul J. Hergenrother
- University of Illinois, Department of Chemistry, Roger Adams Laboratory, 600 South Mathews, Urbana, Illinois 61801, USA
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18
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Kistemaker HAV, Lameijer LN, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Synthesis of Well-Defined Adenosine Diphosphate Ribose Oligomers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kistemaker HAV, Lameijer LN, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Synthesis of well-defined adenosine diphosphate ribose oligomers. Angew Chem Int Ed Engl 2015; 54:4915-8. [PMID: 25704172 DOI: 10.1002/anie.201412283] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/10/2022]
Abstract
The post-translational modification of proteins that is known as adenosine diphosphate ribosylation (ADPr) regulates a wide variety of important biological processes, such as DNA-damage repair and cellular metabolism. This modification is also involved in carcinogenesis and the process of aging. Therefore, a better understanding of the function of ADP-ribosylation is crucial for the development of novel therapeutics. To facilitate the elucidation of the biology of ADPr, the availability of well-defined fragments of poly(ADP-ribose) is essential. Herein we report a solid-phase synthetic approach for the preparation of ADP-ribose oligomers of exactly defined length. The methodology is exemplified by the first reported synthesis of an ADP-ribose dimer and trimer.
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Affiliation(s)
- Hans A V Kistemaker
- Leiden Institute of Chemistry, Department of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC Leiden (The Netherlands) http://biosyn.lic.leidenuniv.nl/
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Sylla B, Gauthier C, Legault J, Fleury PY, Lavoie S, Mshvildadze V, Muzashvili T, Kemertelidze E, Pichette A. Isolation of a new disaccharide nucleoside from Helleborus caucasicus: structure elucidation and total synthesis of hellecaucaside A and its β-anomer. Carbohydr Res 2014; 398:80-9. [DOI: 10.1016/j.carres.2014.06.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 11/30/2022]
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Oka N, Kajino R, Takeuchi K, Nagakawa H, Ando K. α-Selective Ribofuranosylation of Alcohols with Ribofuranosyl Iodides and Triphenylphosphine Oxide. J Org Chem 2014; 79:7656-64. [DOI: 10.1021/jo500632h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Natsuhisa Oka
- Department of Chemistry and
Biomolecular Science, Faculty of Engineering, Gifu University, 1-1
Yanagido, Gifu 501-1193, Japan
| | - Rin Kajino
- Department of Chemistry and
Biomolecular Science, Faculty of Engineering, Gifu University, 1-1
Yanagido, Gifu 501-1193, Japan
| | - Kaoru Takeuchi
- Department of Chemistry and
Biomolecular Science, Faculty of Engineering, Gifu University, 1-1
Yanagido, Gifu 501-1193, Japan
| | - Haruna Nagakawa
- Department of Chemistry and
Biomolecular Science, Faculty of Engineering, Gifu University, 1-1
Yanagido, Gifu 501-1193, Japan
| | - Kaori Ando
- Department of Chemistry and
Biomolecular Science, Faculty of Engineering, Gifu University, 1-1
Yanagido, Gifu 501-1193, Japan
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Efremova AS, Zakharenko AL, Shram SI, Kulikova IV, Drenichev MS, Sukhanova MV, Khodyreva SN, Myasoedov NF, Lavrik OI, Mikhailov SN. Disaccharide pyrimidine nucleosides and their derivatives: a novel group of cell-penetrating inhibitors of poly(ADP-ribose) polymerase 1. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:510-28. [PMID: 24079274 DOI: 10.1080/15257770.2013.827793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nearly 30 synthetic nucleosides were tested with human recombinant poly(ADP-ribose) polymerase 1 as potential inhibitors of this enzyme. The most active compounds were some disaccharide analogues of thymidine: 3'-O-β-D-ribofuranosyl-5-iodo-dUrd (2d; IC₅₀ = 45 μM), 3'-O-β-D-ribofuranosyl-2'-deoxythymidine (2e; IC₅₀ = 38 μM), and 3'-O-β-D-ribofuranosyl-2'-deoxythymidine oxidized (4; IC₅₀ = 25 μM). These compounds also reduced H₂O₂-induced synthesis of poly(ADP-ribose) in cultured human ovarian carcinoma (SKOV-3) cells in a dose-dependent manner. Furthermore, compounds 2d or 2e until a concentration of 1 mM did not affect growth of SKOV-3 cells, whereas dialdehyde compound 4, as well as thymidine, exhibited a significant cytotoxicity.
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Affiliation(s)
- Anna S Efremova
- a Institute of Molecular Genetics , Russian Academy of Sciences , Moscow , Russia
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Kistemaker HAV, van Noort GJVDH, Overkleeft HS, van der Marel GA, Filippov DV. Stereoselective ribosylation of amino acids. Org Lett 2013; 15:2306-9. [PMID: 23614697 DOI: 10.1021/ol400929c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The glycosylation properties of ribofuranosyl N-phenyltrifluoroacetimidates toward carboxamide side chains of asparagine and glutamine were investigated. Conditions were found that promote nearly exclusive formation of the α-anomerically configured N-glycosides. The strategy allows for the synthesis of Fmoc-amino acids suitably modified for the preparation of ADP-ribosylated peptides. Furthermore, ribosylation of serine with these donors proved to be completely α-selective, and for the first time, α-ribosylated glutamic and aspartic acid, the naturally occurring sites for poly-ADP-ribosylation, were synthesized.
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Affiliation(s)
- Hans A V Kistemaker
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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