1
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Engelsma SB, Nardozza AP, de Saint Aulaire P, Overkleeft HS, van der Marel GA, Ladurner AG, Filippov DV. Synthesis and Macrodomain Binding of Gln-carba-ADPr-peptide. Chembiochem 2024; 25:e202300865. [PMID: 38442082 DOI: 10.1002/cbic.202300865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Mono-ADP-ribosylation is a dynamic post-translational modification (PTM) with important roles in cell signalling. This modification occurs on a wide variety of amino acids, and one of the canonical modification sites within proteins is the side chain of glutamic acid. Given the transient nature of this modification (acylal linkage) and the high sensitivity of ADP-ribosylated glutamic acid, stabilized isosteres are required for structural and biochemical studies. Here, we report the synthesis of a mimic of ADP-ribosylated peptide derived from histone H2B that contains carba-ADP-ribosylated glutamine as a potential mimic for Glu-ADPr. We synthesized a cyclopentitol-ribofuranosyl derivative of 5'-phosphoribosylated Fmoc-glutamine and used this in the solid-phase synthesis of the carba-ADPr-peptide mimicking the ADP-ribosylated N-terminal tail of histone H2B. Binding studies with isothermal calorimetry demonstrate that the macrodomains of human MacroD2 and TARG1 bind to carba-ADPr-peptide in the same way as ADPr-peptides containing the native ADP-riboside moiety connected to the side chain of glutamine in the same peptide sequence.
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Affiliation(s)
- Sander B Engelsma
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Faculty of Science, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Aurelio Pio Nardozza
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Street 9, 82152, Planegg-Martinsried, Germany
| | - Pieter de Saint Aulaire
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Faculty of Science, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Herman S Overkleeft
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Faculty of Science, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Gijsbert A van der Marel
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Faculty of Science, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Andreas G Ladurner
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Street 9, 82152, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Butenandt Street 5-13, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, Feodor Lynen Street 17, 81377, Munich, Germany
| | - Dmitri V Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Faculty of Science, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
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2
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Zhang Z, Fu J, Rack JGM, Li C, Voorneveld J, Filippov DV, Ahel I, Luo ZQ, Das C. Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain. Nat Commun 2024; 15:2452. [PMID: 38503748 PMCID: PMC10951314 DOI: 10.1038/s41467-024-46649-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster. Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.
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Affiliation(s)
- Zhengrui Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jiaqi Fu
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, UK
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, EX4 4QD, Exeter, UK
| | - Chuang Li
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Jim Voorneveld
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Dmitri V Filippov
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, UK
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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3
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Nouwen LV, Breeuwsma M, Zaal EA, van de Lest CHA, Buitendijk I, Zwaagstra M, Balić P, Filippov DV, Berkers CR, van Kuppeveld FJM. Modulation of nucleotide metabolism by picornaviruses. PLoS Pathog 2024; 20:e1012036. [PMID: 38457376 PMCID: PMC10923435 DOI: 10.1371/journal.ppat.1012036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Viruses actively reprogram the metabolism of the host to ensure the availability of sufficient building blocks for virus replication and spreading. However, relatively little is known about how picornaviruses-a large family of small, non-enveloped positive-strand RNA viruses-modulate cellular metabolism for their own benefit. Here, we studied the modulation of host metabolism by coxsackievirus B3 (CVB3), a member of the enterovirus genus, and encephalomyocarditis virus (EMCV), a member of the cardiovirus genus, using steady-state as well as 13C-glucose tracing metabolomics. We demonstrate that both CVB3 and EMCV increase the levels of pyrimidine and purine metabolites and provide evidence that this increase is mediated through degradation of nucleic acids and nucleotide recycling, rather than upregulation of de novo synthesis. Finally, by integrating our metabolomics data with a previously acquired phosphoproteomics dataset of CVB3-infected cells, we identify alterations in phosphorylation status of key enzymes involved in nucleotide metabolism, providing insight into the regulation of nucleotide metabolism during infection.
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Affiliation(s)
- Lonneke V. Nouwen
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Martijn Breeuwsma
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Esther A. Zaal
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Chris H. A. van de Lest
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Inge Buitendijk
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Pascal Balić
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Dmitri V. Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Celia R. Berkers
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank J. M. van Kuppeveld
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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4
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Remmerswaal WA, de Jong T, van de Vrande KNA, Louwersheimer R, Verwaal T, Filippov DV, Codée JDC, Hansen T. Backside versus Frontside S N 2 Reactions of Alkyl Triflates and Alcohols. Chemistry 2024:e202400590. [PMID: 38385647 DOI: 10.1002/chem.202400590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/23/2024]
Abstract
Nucleophilic substitution reactions are elementary reactions in organic chemistry that are used in many synthetic routes. By quantum chemical methods, we have investigated the intrinsic competition between the backside SN 2 (SN 2-b) and frontside SN 2 (SN 2-f) pathways using a set of simple alkyl triflates as the electrophile in combination with a systematic series of phenols and partially fluorinated ethanol nucleophiles. It is revealed how and why the well-established mechanistic preference for the SN 2-b pathway slowly erodes and can even be overruled by the unusual SN 2-f substitution mechanism going from strong to weak alcohol nucleophiles. Activation strain analyses disclose that the SN 2-b pathway is favored for strong alcohol nucleophiles because of the well-known intrinsically more efficient approach to the electrophile resulting in a more stabilizing nucleophile-electrophile interaction. In contrast, the preference of weaker alcohol nucleophiles shifts to the SN 2-f pathway, benefiting from a stabilizing hydrogen bond interaction between the incoming alcohol and the leaving group. This hydrogen bond interaction is strengthened by the increased acidity of the weaker alcohol nucleophiles, thereby steering the mechanistic preference toward the frontside SN 2 pathway.
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Affiliation(s)
- Wouter A Remmerswaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Tjeerd de Jong
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Koen N A van de Vrande
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Rick Louwersheimer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Thomas Verwaal
- 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
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Thomas Hansen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The, Netherlands
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5
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Doelman W, Ligthart NAM, van de Plassche MAT, de Geus MAR, Reinalda L, Isendoorn MME, Filippov DV, van Kasteren SI. Synthesis of Peptides Containing a Combination of Free and 2-trans-Cyclooctene Carbamate Protected Lysine Residues. Chembiochem 2024; 25:e202300786. [PMID: 38126970 DOI: 10.1002/cbic.202300786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023]
Abstract
The allylic trans-cyclooctene (TCO) functionality facilitates powerful control over the spatiotemporal activity of bio-active molecules, enabling precision targeting of druglike and imaging modalities. However, the introduction of this function onto molecules remains chemically challenging, particularly for peptides. Modification with TCOs of this important class of biomolecules remains a challenge, primarily due to the sensitivity of the TCO group to the strong acids typically used in global deprotection during solid phase peptide synthesis. Here, we present a novel synthetic approach to site-selectively introduce TCO-groups in peptides. Our approach utilizes azide groups to mask amine functions, enabling selective introduction of the TCO on a single lysine residue. Staudinger reduction of the azides back to the corresponding amines proceeds without disturbing the sensitive TCO. We show that using our method, we can produce TCO-inactivated antigenic peptides of previously unseen complexity.
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Affiliation(s)
- W Doelman
- Leiden Institute of Chemistry, Leiden, the Netherlands
| | | | | | - M A R de Geus
- Leiden Institute of Chemistry, Leiden, the Netherlands
| | - L Reinalda
- Leiden Institute of Chemistry, Leiden, the Netherlands
| | | | - D V Filippov
- Leiden Institute of Chemistry, Leiden, the Netherlands
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6
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Guo J, Balić P, Borodkin VS, Filippov DV, Codée JDC. Synthesis of Unsymmetrical Difluoromethylene Bisphosphonates. Org Lett 2024; 26:739-744. [PMID: 38215221 PMCID: PMC10825822 DOI: 10.1021/acs.orglett.3c04211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/14/2024]
Abstract
We demonstrate the use of the symmetrical diethyl(dimethyl)difluoromethylene bisphosphonate reagent for the synthesis of terminal and unsymmetrical difluoromethylene bisphosphonates, close analogues of biologically important molecules. The difference in reactivity of the methyl and ethyl groups in the symmetrical diethyl(dimthyl)difluoromethylene bisphosphonate is exploited in a stepwise demethylation-condensation sequence to functionalize either side of the reagent to allow the generation of a series of close bioisosteres of natural pyrophosphate molecules, including ADPr, CDP-glycerol and CDP-ribitol.
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Affiliation(s)
- Jianyun Guo
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Pascal Balić
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Vladimir S. Borodkin
- Division
of Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH Dundee, U.K.
| | - Dmitri V. Filippov
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Jeroen D. C. Codée
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
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7
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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 Weinheim Bergstr Ger 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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Wijngaarden S, Yang C, Vela-Rodríguez C, Lehtiö L, Overkleeft HS, Paschal BM, Filippov DV. Synthetic Dual Cysteine-ADP Ribosylated Peptides from the Androgen Receptor are Recognized by the DTX3L/PARP9 Complex. ACS Chem Biol 2023; 18:2377-2384. [PMID: 37939374 PMCID: PMC10660311 DOI: 10.1021/acschembio.3c00305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023]
Abstract
Androgen signaling in prostate cancer cells involves multisite cysteine ADP-ribosylation of the androgen receptor (AR) by PARP7. The AR modification is read by ADP-ribosyl binding macrodomains in PARP9, but the reason that multiple cysteines are modified is unknown. Here, we use synthetic peptides to show that dual ADP-ribosylation of closely spaced cysteines mediates recognition by the DTX3L/PARP9 complex. Mono and dual ADP-ribosylated cysteine peptides were prepared using a novel solid-phase synthetic strategy utilizing a key, Boc-protected, ribofuranosylcysteine building block. This synthetic strategy allowed us to synthesize fluorescently labeled peptides containing a dual ADP-ribosylation motif. It was found that the DTX3L/PARP9 complex recognizes the dual ADP-ribosylated AR peptide (Kd = 80.5 nM) with significantly higher affinity than peptides with a single ADP-ribose. Moreover, oligomerization of the DTX3L/PARP9 complex proved crucial for ADP-ribosyl-peptide interaction since a deletion mutant of the complex that prevents its oligomer formation dramatically reduced peptide binding. Our data show that features of the substrate modification and the reader contribute to the efficiency of the interaction and imply that multivalent interactions are important for AR-DTX3L/PARP9 assembly.
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Affiliation(s)
- Sven Wijngaarden
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Chunsong Yang
- Department
of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Carlos Vela-Rodríguez
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Aapistie 7B, Oulu 90220, Finland
| | - Lari Lehtiö
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Aapistie 7B, Oulu 90220, Finland
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Bryce M. Paschal
- Department
of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Dmitri V. Filippov
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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10
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Đukić N, Strømland Ø, Elsborg JD, Munnur D, Zhu K, Schuller M, Chatrin C, Kar P, Duma L, Suyari O, Rack JGM, Baretić D, Crudgington DRK, Groslambert J, Fowler G, Wijngaarden S, Prokhorova E, Rehwinkel J, Schüler H, Filippov DV, Sanyal S, Ahel D, Nielsen ML, Smith R, Ahel I. PARP14 is a PARP with both ADP-ribosyl transferase and hydrolase activities. Sci Adv 2023; 9:eadi2687. [PMID: 37703374 PMCID: PMC10499325 DOI: 10.1126/sciadv.adi2687] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023]
Abstract
PARP14 is a mono-ADP-ribosyl transferase involved in the control of immunity, transcription, and DNA replication stress management. However, little is known about the ADP-ribosylation activity of PARP14, including its substrate specificity or how PARP14-dependent ADP-ribosylation is reversed. We show that PARP14 is a dual-function enzyme with both ADP-ribosyl transferase and hydrolase activity acting on both protein and nucleic acid substrates. In particular, we show that the PARP14 macrodomain 1 is an active ADP-ribosyl hydrolase. We also demonstrate hydrolytic activity for the first macrodomain of PARP9. We reveal that expression of a PARP14 mutant with the inactivated macrodomain 1 results in a marked increase in mono(ADP-ribosyl)ation of proteins in human cells, including PARP14 itself and antiviral PARP13, and displays specific cellular phenotypes. Moreover, we demonstrate that the closely related hydrolytically active macrodomain of SARS2 Nsp3, Mac1, efficiently reverses PARP14 ADP-ribosylation in vitro and in cells, supporting the evolution of viral macrodomains to counteract PARP14-mediated antiviral response.
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Affiliation(s)
- Nina Đukić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Jonas Damgaard Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Pulak Kar
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Domagoj Baretić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | | | - Gerissa Fowler
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sven Wijngaarden
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Herwig Schüler
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Rebecca Smith
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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11
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van de Vrande KN, Filippov DV, Codée JDC. Formation of Glycosyl Trichloroacetamides from Trichloroacetimidate Donors Occurs through an Intermolecular Aglycon Transfer Reaction. Org Lett 2023; 25:6128-6132. [PMID: 37578204 PMCID: PMC10463224 DOI: 10.1021/acs.orglett.3c02196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Indexed: 08/15/2023]
Abstract
To probe the reaction mechanism, underlying the rearrangement of oft-used trichloroacetimidate glycosyl donors into the corresponding anomeric trichloroacetamides, we have used a combination of 13C- and 15N-labeled glycosyl trichloroacetimidate donors in a series of crossover experiments. These unambiguously show that trichloroacetamides are formed via an intermolecular aglycon transfer mechanism. This insight enables the design of more effective glycosylation protocols, preventing the formation of dead-end side products.
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Affiliation(s)
| | - Dmitri V. Filippov
- Leiden Institute
of Chemistry, Leiden University, Einsteinweg 55, 2333
CC Leiden, Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute
of Chemistry, Leiden University, Einsteinweg 55, 2333
CC Leiden, Netherlands
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12
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Minnee H, Chung H, Rack JG, van der Marel GA, Overkleeft HS, Codée JDC, Ahel I, Filippov DV. Four of a Kind: A Complete Collection of ADP-Ribosylated Histidine Isosteres Using Cu(I)- and Ru(II)-Catalyzed Click Chemistry. J Org Chem 2023; 88:10801-10809. [PMID: 37464783 PMCID: PMC10407933 DOI: 10.1021/acs.joc.3c00827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 07/20/2023]
Abstract
Adenosine diphosphate ribosylation (ADP-ribosylation) is a crucial post-translational modification involved in important regulatory mechanisms of numerous cellular pathways including histone maintenance and DNA damage repair. To study this modification, well-defined ADP-ribosylated peptides, proteins, and close analogues thereof have been invaluable tools. Recently, proteomics studies have revealed histidine residues to be ADP-ribosylated. We describe here the synthesis of a complete set of triazole-isosteres of ADP-ribosylated histidine to serve as probes for ADP-ribosylating biomachinery. By exploiting Cu(I)- and Ru(II)-catalyzed click chemistry between a propargylglycine building block and an α- or β-configured azidoribose, we have successfully assembled the α- and β-configured 1,4- and 1,5-triazoles, mimicking N(τ)- and N(π)-ADP-ribosylated histidine, respectively. The ribosylated building blocks could be incorporated into a peptide sequence using standard solid-phase peptide synthesis and transformed on resin into the ADP-ribosylated fragments to provide a total of four ADP-ribosyl triazole conjugates, which were evaluated for their chemical and enzymatic stability. The 1,5-triazole analogues mimicking the N(π)-substituted histidines proved susceptible to base-induced epimerization and the ADP-ribosyl α-1,5-triazole linkage could be cleaved by the (ADP-ribosyl)hydrolase ARH3.
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Affiliation(s)
- Hugo Minnee
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Hayley Chung
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | | | - Gijsbert A. van der Marel
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Herman S. Overkleeft
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Jeroen D. C. Codée
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Ivan Ahel
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
| | - Dmitri V. Filippov
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
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13
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Madern J, Voorneveld J, Rack JGM, Kistemaker HAV, Ahel I, van der Marel GA, Codée JDC, Filippov DV. 4-Thioribose Analogues of Adenosine Diphosphate Ribose (ADPr) Peptides. Org Lett 2023; 25:4980-4984. [PMID: 37338412 PMCID: PMC10353035 DOI: 10.1021/acs.orglett.3c01554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Indexed: 06/21/2023]
Abstract
Adenosine diphosphate (ADP) ribosylation is an important post-translational modification (PTM) that plays a role in a wide variety of cellular processes. To study the enzymes responsible for the establishment, recognition, and removal of this PTM, stable analogues are invaluable tools. We describe the design and synthesis of a 4-thioribosyl APRr peptide that has been assembled by solid phase synthesis. The key 4-thioribosyl serine building block was obtained in a stereoselective glycosylation reaction using an alkynylbenzoate 4-thioribosyl donor.
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Affiliation(s)
- Jerre
M. Madern
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Jim Voorneveld
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Johannes G. M. Rack
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Hans A. V. Kistemaker
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ivan Ahel
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | | | - Jeroen D. C. Codée
- 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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14
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Tashiro K, Wijngaarden S, Mohapatra J, Rack JGM, Ahel I, Filippov DV, Liszczak G. Chemoenzymatic and Synthetic Approaches To Investigate Aspartate- and Glutamate-ADP-Ribosylation. J Am Chem Soc 2023; 145:14000-14009. [PMID: 37315125 DOI: 10.1021/jacs.3c03771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We report here chemoenzymatic and fully synthetic methodologies to modify aspartate and glutamate side chains with ADP-ribose at specific sites on peptides. Structural analysis of aspartate and glutamate ADP-ribosylated peptides reveals near-quantitative migration of the side chain linkage from the anomeric carbon to the 2″- or 3″-ADP-ribose hydroxyl moieties. We find that this linkage migration pattern is unique to aspartate and glutamate ADP-ribosylation and propose that the observed isomer distribution profile is present in biochemical and cellular environments. After defining distinct stability properties of aspartate and glutamate ADP-ribosylation, we devise methods to install homogenous ADP-ribose chains at specific glutamate sites and assemble glutamate-modified peptides into full-length proteins. By implementing these technologies, we show that histone H2B E2 tri-ADP-ribosylation is able to stimulate the chromatin remodeler ALC1 with similar efficiency to histone serine ADP-ribosylation. Our work reveals fundamental principles of aspartate and glutamate ADP-ribosylation and enables new strategies to interrogate the biochemical consequences of this widespread protein modification.
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Affiliation(s)
- Kyuto Tashiro
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Sven Wijngaarden
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jugal Mohapatra
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Johannes G M Rack
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K
| | - Dmitri V Filippov
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Glen Liszczak
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
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15
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Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawłowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler M. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J 2022; 289:7399-7410. [PMID: 34323016 PMCID: PMC9027952 DOI: 10.1111/febs.16142] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/13/2023]
Abstract
ADP-ribosylation, a modification of proteins, nucleic acids, and metabolites, confers broad functions, including roles in stress responses elicited, for example, by DNA damage and viral infection and is involved in intra- and extracellular signaling, chromatin and transcriptional regulation, protein biosynthesis, and cell death. ADP-ribosylation is catalyzed by ADP-ribosyltransferases (ARTs), which transfer ADP-ribose from NAD+ onto substrates. The modification, which occurs as mono- or poly-ADP-ribosylation, is reversible due to the action of different ADP-ribosylhydrolases. Importantly, inhibitors of ARTs are approved or are being developed for clinical use. Moreover, ADP-ribosylhydrolases are being assessed as therapeutic targets, foremost as antiviral drugs and for oncological indications. Due to the development of novel reagents and major technological advances that allow the study of ADP-ribosylation in unprecedented detail, an increasing number of cellular processes and pathways are being identified that are regulated by ADP-ribosylation. In addition, characterization of biochemical and structural aspects of the ARTs and their catalytic activities have expanded our understanding of this protein family. This increased knowledge requires that a common nomenclature be used to describe the relevant enzymes. Therefore, in this viewpoint, we propose an updated and broadly supported nomenclature for mammalian ARTs that will facilitate future discussions when addressing the biochemistry and biology of ADP-ribosylation. This is combined with a brief description of the main functions of mammalian ARTs to illustrate the increasing diversity of mono- and poly-ADP-ribose mediated cellular processes.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Peter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Hungary
| | | | - Michael Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Daniela Corda
- Department of Biomedical Sciences, National Research Council, Rome, Italy
| | | | - Matthew D Daugherty
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Anthony R Fehr
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | | | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | | | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Nicolas C Hoch
- Department of Biochemistry, University of São Paulo, Brazil
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Ladurner
- Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Germany
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, Norway
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Joel Moss
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Friedrich Nolte
- Institut für Immunologie, Universitätsklinikum Hamburg-Eppendorf, Germany
| | - John Pascal
- Biochemistry and Molecular Medicine, Université de Montréal, Canada
| | - Bryce M Paschal
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, NY, USA
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller University of Jena, Germany
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Roko Zaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Weixler L, Ikenga NJ, Voorneveld J, Aydin G, Bolte TMHR, Momoh J, Bütepage M, Golzmann A, Lüscher B, Filippov DV, Žaja R, Feijs KLH. Protein and RNA ADP-ribosylation detection is influenced by sample preparation and reagents used. Life Sci Alliance 2022; 6:6/1/e202201455. [PMID: 36368907 PMCID: PMC9652768 DOI: 10.26508/lsa.202201455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
The modification of substrates with ADP-ribose (ADPr) is important in, for example, antiviral immunity and cancer. Recently, several reagents were developed to detect ADP-ribosylation; however, it is unknown whether they recognise ADPr, specific amino acid-ADPr linkages, or ADPr with the surrounding protein backbone. We first optimised methods to prepare extracts containing ADPr-proteins and observe that depending on the amino acid modified, the modification is heatlabile. We tested the reactivity of available reagents with diverse ADP-ribosylated protein and RNA substrates and observed that not all reagents are equally suited for all substrates. Next, we determined cross-reactivity with adenylylated RNA, AMPylated proteins, and metabolites, including NADH, which are detected by some reagents. Lastly, we analysed ADP-ribosylation using confocal microscopy, where depending on the fixation method, either mitochondrion, nucleus, or nucleolus is stained. This study allows future work dissecting the function of ADP-ribosylation in cells, both on protein and on RNA substrates, as we optimised sample preparation methods and have defined the reagents suitable for specific methods and substrates.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Nonso Josephat Ikenga
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Gülcan Aydin
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Timo MHR Bolte
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Alexandra Golzmann
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Karla LH Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany,Correspondence: ;
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18
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Speetjens FM, Welters MJP, Slingerland M, van Poelgeest MIE, de Vos van Steenwijk PJ, Roozen I, Boekestijn S, Loof NM, Zom GG, Valentijn ARPM, Krebber WJ, Meeuwenoord NJ, Janssen CAH, Melief CJM, van der Marel GA, Filippov DV, van der Burg SH, Gelderblom H, Ossendorp F. Intradermal vaccination of HPV-16 E6 synthetic peptides conjugated to an optimized Toll-like receptor 2 ligand shows safety and potent T cell immunogenicity in patients with HPV-16 positive (pre-)malignant lesions. J Immunother Cancer 2022; 10:jitc-2022-005016. [PMID: 36261215 PMCID: PMC9582304 DOI: 10.1136/jitc-2022-005016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Amplivant is a molecularly optimized Toll-like receptor 2 ligand that can be covalently conjugated to tumor peptide antigens. In preclinical models, amplivant-adjuvanted synthetic long peptides (SLPs) strongly enhanced antigen presentation by dendritic cells, T cell priming and induction of effective antitumor responses. The current study is a first-in-human trial to investigate safety and immunogenicity of amplivant conjugated to human papillomavirus (HPV) 16-SLP. METHODS A dose escalation phase I vaccination trial was performed in 25 patients treated for HPV16 positive (pre-)malignant lesions. Amplivant was conjugated to two SLPs derived from the two most immunodominant regions of the HPV16 E6 oncoprotein. The vaccine, containing a mix of these two conjugates in watery solution without any other formulation, was injected intradermally three times with a 3-week interval in four dose groups (1, 5, 20 or 50 µg per conjugated peptide). Safety data were collected during the study. Peptide-specific T cell immune responses were determined in blood samples taken before, during and after vaccination using complementary immunological assays. RESULTS Toxicity after three amplivant-conjugated HPV16-SLP vaccinations was limited to grade 1 or 2, observed as predominantly mild skin inflammation at the vaccination site and sometimes mild flu-like symptoms. Adverse events varied from none in the lowest dose group to mild/moderate vaccine-related inflammation in all patients and flu-like symptoms in three out of seven patients in the highest dose group, after at least one injection. In the lowest dose group, vaccine-induced T cell responses were observed in the blood of three out of six vaccinated persons. In the highest dose group, all patients displayed a strong HPV16-specific T cell response after vaccination. These HPV16-specific T cell responses lasted until the end of the trial. CONCLUSIONS Amplivant-conjugated SLPs can safely be used as an intradermal therapeutic vaccine to induce robust HPV16-specific T cell immunity in patients previously treated for HPV16 positive (pre-) malignancies. Increased vaccine dose was associated with a higher number of mild adverse events and with stronger systemic T cell immunity. TRIAL REGISTRATION NUMBERS NCT02821494 and 2014-000658-12.
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Affiliation(s)
- Frank M Speetjens
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marij J P Welters
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Marije Slingerland
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Inge Roozen
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sanne Boekestijn
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Nikki M Loof
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Gijs G Zom
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - A Rob P M Valentijn
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Nico J Meeuwenoord
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | | | | | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
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19
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Remmerswaal WA, Houthuijs KJ, van de Ven R, Elferink H, Hansen T, Berden G, Overkleeft HS, van der Marel GA, Rutjes FPJT, Filippov DV, Boltje TJ, Martens J, Oomens J, Codée JDC. Stabilization of Glucosyl Dioxolenium Ions by "Dual Participation" of the 2,2-Dimethyl-2-( ortho-nitrophenyl)acetyl (DMNPA) Protection Group for 1,2- cis-Glucosylation. J Org Chem 2022; 87:9139-9147. [PMID: 35748115 PMCID: PMC9295149 DOI: 10.1021/acs.joc.2c00808] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
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The stereoselective
introduction of glycosidic bonds is of paramount
importance to oligosaccharide synthesis. Among the various chemical
strategies to steer stereoselectivity, participation by either neighboring
or distal acyl groups is used particularly often. Recently, the use
of the 2,2-dimethyl-2-(ortho-nitrophenyl)acetyl (DMNPA)
protection group was shown to offer enhanced stereoselective steering
compared to other acyl groups. Here, we investigate the origin of
the stereoselectivity induced by the DMNPA group through systematic
glycosylation reactions and infrared ion spectroscopy (IRIS) combined
with techniques such as isotopic labeling of the anomeric center and
isomer population analysis. Our study indicates that the origin of
the DMNPA stereoselectivity does not lie in the direct participation
of the nitro moiety but in the formation of a dioxolenium ion that
is strongly stabilized by the nitro group.
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Affiliation(s)
- Wouter A Remmerswaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kas J Houthuijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Roel van de Ven
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Hidde Elferink
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas Hansen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Departament de Química Inorgànica i Orgànica & IQTUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Herman S Overkleeft
- 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
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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20
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Minnee H, Rack JGM, van der Marel GA, Overkleeft HS, Codée JDC, Ahel I, Filippov DV. Mimetics of ADP-Ribosylated Histidine through Copper(I)-Catalyzed Click Chemistry. Org Lett 2022; 24:3776-3780. [PMID: 35587229 PMCID: PMC9171823 DOI: 10.1021/acs.orglett.2c01300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 11/28/2022]
Abstract
A convergent synthesis provided nearly perfect τ-ADP-ribosylated histidine isosteres (His*-τ-ADPr) via a copper(I)-catalyzed cycloaddition between an azido-ADP-ribosyl analogue and an oligopeptide carrying a propargyl glycine. Both α- and β-configured azido-ADP-ribosyl analogues have been synthesized. The former required participation of the C-2 ester functionality during glycosylation, while the latter was obtained in high stereoselectivity from an imidate donor with a nonparticipating para-methoxy benzyl ether. Four His*-τ-ADPr peptides were screened against a library of human ADP-ribosyl hydrolases.
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Affiliation(s)
- Hugo Minnee
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes G. M. Rack
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Gijsbert A. van der Marel
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Herman S. Overkleeft
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jeroen D. C. Codée
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Ivan Ahel
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Dmitri V. Filippov
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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21
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Kliza KW, Liu Q, Roosenboom LWM, Jansen PWTC, Filippov DV, Vermeulen M. Reading ADP-ribosylation signaling using chemical biology and interaction proteomics. Mol Cell 2021; 81:4552-4567.e8. [PMID: 34551281 DOI: 10.1016/j.molcel.2021.08.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/23/2021] [Accepted: 08/26/2021] [Indexed: 01/12/2023]
Abstract
ADP-ribose (ADPr) readers are essential components of ADP-ribosylation signaling, which regulates genome maintenance and immunity. The identification and discrimination between monoADPr (MAR) and polyADPr (PAR) readers is difficult because of a lack of suitable affinity-enrichment reagents. We synthesized well-defined ADPr probes and used these for affinity purifications combined with relative and absolute quantitative mass spectrometry to generate proteome-wide MAR and PAR interactomes, including determination of apparent binding affinities. Among the main findings, MAR and PAR readers regulate various common and distinct processes, such as the DNA-damage response, cellular metabolism, RNA trafficking, and transcription. We monitored the dynamics of PAR interactions upon induction of oxidative DNA damage and uncovered the mechanistic connections between ubiquitin signaling and ADP-ribosylation. Taken together, chemical biology enables exploration of MAR and PAR readers using interaction proteomics. Furthermore, the generated MAR and PAR interaction maps significantly expand our current understanding of ADPr signaling.
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Affiliation(s)
- Katarzyna W Kliza
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Qiang Liu
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, Netherlands
| | - Laura W M Roosenboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
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22
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Liu Q, Knobloch G, Voorneveld J, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Ladurner AG, Filippov DV. Chemical synthesis of linear ADP-ribose oligomers up to pentamer and their binding to the oncogenic helicase ALC1. Chem Sci 2021; 12:12468-12475. [PMID: 34603678 PMCID: PMC8480336 DOI: 10.1039/d1sc02340c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/12/2021] [Indexed: 11/21/2022] Open
Abstract
ADP-ribosylation is a pivotal post-translational modification that mediates various important cellular processes producing negatively charged biopolymer, poly (ADP-ribose), the functions of which need further elucidation. Toward this end, the availability of well-defined ADP-ribose (ADPr) oligomers in sufficient quantities is a necessity. In this work, we demonstrate the chemical synthesis of linear ADPr oligomers of defined, increasing length using a modified solid phase synthesis method. An advanced phosphoramidite building block temporarily protected with the base sensitive Fm-group was designed and implemented in the repeating pyrophosphate formation via a P(v)-P(iii) coupling procedure on Tentagel solid support. Linear ADPr oligomers up to a pentamer were successfully synthesized and their affinity for the poly-(ADP-ribose)-binding macrodomain of the human oncogenic helicase and chromatin remodeling enzyme ALC1 was determined. Our data reveal a length-dependent binding manner of the nucleic acid, with larger ADPr oligomers exhibiting higher binding enthalpies for ALC1, illustrating how the activity of this molecular machine is gated by PAR.
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Affiliation(s)
- Qiang Liu
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Gunnar Knobloch
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine LMU Munich 82152 Planegg-Martinsried Germany
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Nico J Meeuwenoord
- 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
| | | | - Andreas G Ladurner
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine LMU Munich 82152 Planegg-Martinsried Germany
- Eisbach Bio GmbH Am Klopferspitz 19, Planegg-Martinsried 82152 Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
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23
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Reijneveld JF, Marino L, Cao TP, Cheng TY, Dam D, Shahine A, Witte MD, Filippov DV, Suliman S, van der Marel GA, Moody DB, Minnaard AJ, Rossjohn J, Codée JDC, Van Rhijn I. Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells. J Biol Chem 2021; 297:101197. [PMID: 34536421 PMCID: PMC8511953 DOI: 10.1016/j.jbc.2021.101197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/25/2022] Open
Abstract
Whereas proteolytic cleavage is crucial for peptide presentation by classical major histocompatibility complex (MHC) proteins to T cells, glycolipids presented by CD1 molecules are typically presented in an unmodified form. However, the mycobacterial lipid antigen mannosyl-β1-phosphomycoketide (MPM) may be processed through hydrolysis in antigen presenting cells, forming mannose and phosphomycoketide (PM). To further test the hypothesis that some lipid antigens are processed, and to generate antigens that lead to defined epitopes for future tuberculosis vaccines or diagnostic tests, we aimed to create hydrolysis-resistant MPM variants that retain their antigenicity. Here, we designed and tested three different, versatile synthetic strategies to chemically stabilize MPM analogs. Crystallographic studies of CD1c complexes with these three new MPM analogs showed anchoring of the lipid tail and phosphate group that is highly comparable to nature-identical MPM, with considerable conformational flexibility for the mannose head group. MPM-3, a difluoromethylene-modified version of MPM that is resistant to hydrolysis, showed altered recognition by cells, but not by CD1c proteins, supporting the cellular antigen processing hypothesis. Furthermore, the synthetic analogs elicited T cell responses that were cross-reactive with nature-identical MPM, fulfilling important requirements for future clinical use.
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Affiliation(s)
- Josephine F Reijneveld
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands; Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Laura Marino
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Thinh-Phat Cao
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tan-Yun Cheng
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Dennis Dam
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Adam Shahine
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Martin D Witte
- Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Dmitri V Filippov
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Sara Suliman
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Gijsbert A van der Marel
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - D Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff, United Kingdom
| | - Jeroen D C Codée
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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24
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Rack JGM, Liu Q, Zorzini V, Voorneveld J, Ariza A, Honarmand Ebrahimi K, Reber JM, Krassnig SC, Ahel D, van der Marel GA, Mangerich A, McCullagh JSO, Filippov DV, Ahel I. Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal. Nat Commun 2021; 12:4581. [PMID: 34321462 PMCID: PMC8319183 DOI: 10.1038/s41467-021-24723-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/30/2021] [Indexed: 12/17/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PAR) is a versatile and complex posttranslational modification composed of repeating units of ADP-ribose arranged into linear or branched polymers. This scaffold is linked to the regulation of many of cellular processes including the DNA damage response, alteration of chromatin structure and Wnt signalling. Despite decades of research, the principles and mechanisms underlying all steps of PAR removal remain actively studied. In this work, we synthesise well-defined PAR branch point molecules and demonstrate that PARG, but not ARH3, can resolve this distinct PAR architecture. Structural analysis of ARH3 in complex with dimeric ADP-ribose as well as an ADP-ribosylated peptide reveal the molecular basis for the hydrolysis of linear and terminal ADP-ribose linkages. We find that ARH3-dependent hydrolysis requires both rearrangement of a catalytic glutamate and induction of an unusual, square-pyramidal magnesium coordination geometry.
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Affiliation(s)
| | - Qiang Liu
- Leiden University, Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Valentina Zorzini
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jim Voorneveld
- Leiden University, Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Julia M Reber
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sarah C Krassnig
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Aswin Mangerich
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - James S O McCullagh
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, UK
| | - Dmitri V Filippov
- Leiden University, Leiden Institute of Chemistry, Leiden, The Netherlands.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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25
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Voorneveld J, Rack JGM, van Gijlswijk L, Meeuwenoord NJ, Liu Q, Overkleeft HS, van der Marel GA, Ahel I, Filippov DV. Molecular Tools for the Study of ADP-Ribosylation: A Unified and Versatile Method to Synthesise Native Mono-ADP-Ribosylated Peptides. Chemistry 2021; 27:10621-10627. [PMID: 33769608 PMCID: PMC8360141 DOI: 10.1002/chem.202100337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 01/13/2023]
Abstract
ADP-ribosylation (ADPr), as a post-translational modification, plays a crucial role in DNA-repair, immunity and many other cellular and physiological processes. Serine is the main acceptor for ADPr in DNA damage response, whereas the physiological impact of less common ADPr-modifications of cysteine and threonine side chains is less clear. Generally, gaining molecular insights into ADPr recognition and turn-over is hampered by the availability of homogeneous, ADP-ribosylated material, such as mono-ADP-ribosylated (MARylated) peptides. Here, a new and efficient solid-phase strategy for the synthesis of Ser-, Thr- and Cys-MARylated peptides is described. ADP-ribosylated cysteine, apart from being a native post-translational modification in its own right, proved to be suitable as a stabile bioisostere for ADP-ribosylated serine making it a useful tool to further biochemical research on serine ADP-ribosylation. In addition, it was discovered that the Streptococcus pyogenes encoded protein, SpyMacroD, acts as a Cys-(ADP-ribosyl) hydrolase.
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Affiliation(s)
- Jim Voorneveld
- Leiden Institute of ChemistryLeiden UniversityDepartment of Bioorganic SynthesisEinsteinweg 552333CCLeidenThe Netherlands
| | | | - Luke van Gijlswijk
- Leiden Institute of ChemistryLeiden UniversityDepartment of Bioorganic SynthesisEinsteinweg 552333CCLeidenThe Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of ChemistryLeiden UniversityDepartment of Bioorganic SynthesisEinsteinweg 552333CCLeidenThe Netherlands
| | - Qiang Liu
- Leiden Institute of ChemistryLeiden UniversityDepartment of Bioorganic SynthesisEinsteinweg 552333CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of ChemistryLeiden UniversityDepartment of Bioorganic SynthesisEinsteinweg 552333CCLeidenThe Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of ChemistryLeiden UniversityDepartment of Bioorganic SynthesisEinsteinweg 552333CCLeidenThe Netherlands
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordSouth Parks RoadOxfordOX1 3REUnited Kingdom
| | - Dmitri V. Filippov
- Leiden Institute of ChemistryLeiden UniversityDepartment of Bioorganic SynthesisEinsteinweg 552333CCLeidenThe Netherlands
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26
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Ali S, Hendriks A, van Dalen R, Bruyning T, Meeuwenoord N, Overkleeft HS, Filippov DV, van der Marel GA, van Sorge NM, Codée JDC. (Automated) Synthesis of Well-defined Staphylococcus Aureus Wall Teichoic Acid Fragments. Chemistry 2021; 27:10461-10469. [PMID: 33991006 PMCID: PMC8361686 DOI: 10.1002/chem.202101242] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 02/03/2023]
Abstract
Wall teichoic acids (WTAs) are important components of the cell wall of the opportunistic Gram‐positive bacterium Staphylococcus aureus. WTAs are composed of repeating ribitol phosphate (RboP) residues that are decorated with d‐alanine and N‐acetyl‐d‐glucosamine (GlcNAc) modifications, in a seemingly random manner. These WTA‐modifications play an important role in shaping the interactions of WTA with the host immune system. Due to the structural heterogeneity of WTAs, it is impossible to isolate pure and well‐defined WTA molecules from bacterial sources. Therefore, here synthetic chemistry to assemble a broad library of WTA‐fragments, incorporating all possible glycosylation modifications (α‐GlcNAc at the RboP C4; β‐GlcNAc at the RboP C4; β‐GlcNAc at the RboP C3) described for S. aureus WTAs, is reported. DNA‐type chemistry, employing ribitol phosphoramidite building blocks, protected with a dimethoxy trityl group, was used to efficiently generate a library of WTA‐hexamers. Automated solid phase syntheses were used to assemble a WTA‐dodecamer and glycosylated WTA‐hexamer. The synthetic fragments have been fully characterized and diagnostic signals were identified to discriminate the different glycosylation patterns. The different glycosylated WTA‐fragments were used to probe binding of monoclonal antibodies using WTA‐functionalized magnetic beads, revealing the binding specificity of these WTA‐specific antibodies and the importance of the specific location of the GlcNAc modifications on the WTA‐chains.
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Affiliation(s)
- Sara Ali
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Astrid Hendriks
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht (The, Netherlands
| | - Rob van Dalen
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht (The, Netherlands
| | - Thomas Bruyning
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Nico Meeuwenoord
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Herman S Overkleeft
- 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
| | - Gijs A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Nina M van Sorge
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht (The, Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
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27
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Speetjens FM, Welters MJP, Slingerland M, de Vos van Steenwijk P, Roozen IC, Boekestijn S, Loof N, Zom GG, Valentijn R, Krebber WJ, Melief CJM, Filippov DV, Gelderblom H, van der Burg SH, Ossendorp F. Phase I trial to determine safety and immunogenicity of amplivant, a synthetic toll-like receptor 2 ligand, conjugated to two HPV16 E6 synthetic long peptides. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.2614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2614 Background: Therapeutic vaccines based on synthetic long peptides (SLPs) have a great potential for immunotherapy of cancer patients as these SLPs include both human leukocyte antigen (HLA) class I and II epitopes and no patient selection for HLA types is required. The antigen-induced immune response can be strengthened with immune stimulating additives. Amplivant (AV) is a synthetic Toll-like receptor 2 ligand which can be directly conjugated to tumor peptide antigens. In preclinical studies, AV-conjugation to antigens led to both enhanced antigen presentation by dendritic cells and T-cell priming and caused superior induction of effective anti-tumor responses. Moreover, AV-conjugated SLPs showed a 100 times higher immune response compared to unconjugated SLP. The current study is a first-in-human trial to investigate safety and immunogenicity of AV-conjugated human papillomavirus (HPV)16-SLPs. Methods: A dose escalation phase I trial was performed in 24 patients with HPV16 positive (pre-) malignant lesions. AV was conjugated to two SLPs derived from the most immunodominant regions of the HPV16 E6 oncoprotein. Four dose groups (1, 5, 20 or 50 μg of each peptide) in 6 patients each were studied. The vaccine was injected three times intradermally in DMSO / water with a three-week interval. Adverse events (AE) were collected according to CTCAE v4.0 up to 26 weeks. Peptide-specific T-cell immune responses were determined in blood samples taken before and after vaccination using complementary immunological assays (proliferation assay, IFNγ-ELISPOT and cytokine bead array). Results: Toxicity after three AV-conjugated HPV16-SLP vaccinations was limited to CTCAE grade 1 or 2, with predominantly inflammation at the vaccination site and sometimes flu-like symptoms, which generally resolved within one day. Dose increase resulted from no AE in the lowest dose group to mild/moderate AE in all vaccinated persons in the highest dose group. In the lowest dose group, minor vaccine-induced T-cell responses were observed in three of six vaccinated persons. In the highest dose group, all patients displayed a strong HPV16-specific T-cell response after vaccination. The induced T-cell response against HPV16 lasted until the end of the trial. Conclusions: This first-in-human study showed that AV conjugated to SLPs can safely be used as an intradermal therapeutic vaccine. AV-conjugated HPV16-SLP was able to induce robust HPV16-specific T-cell immunity in patients treated for HPV16 positive (pre-) malignancies without any other vaccine adjuvant or formulation. Increase in dose resulted in both a higher number of mild adverse events as well as stronger T-cell immunity. Clinical trial information: NCT02821494.
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Affiliation(s)
- Frank M. Speetjens
- Leiden University Medical Center, Department of Medical Oncology, Leiden, Netherlands
| | - Marij JP Welters
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Marije Slingerland
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Peggy de Vos van Steenwijk
- GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Inge C.F.M. Roozen
- Leiden University Medical Center, Department of Medical Oncology, Leiden, Netherlands
| | - Sanne Boekestijn
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Nikki Loof
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Gijs G Zom
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Rob Valentijn
- Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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28
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Affiliation(s)
- Alex Ham
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden, The Netherlands
| | - Hermen S. Overkleeft
- 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
| | - Grégory F. Schneider
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden, The Netherlands
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29
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Hansen T, Vermeeren P, Yoshisada R, Filippov DV, van der Marel GA, Codée JDC, Hamlin TA. How Lewis Acids Catalyze Ring-Openings of Cyclohexene Oxide. J Org Chem 2021; 86:3565-3573. [PMID: 33538169 PMCID: PMC7901664 DOI: 10.1021/acs.joc.0c02955] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 11/29/2022]
Abstract
We have quantum chemically studied the Lewis acid-catalyzed epoxide ring-opening reaction of cyclohexene epoxide by MeZH (Z = O, S, and NH) using relativistic dispersion-corrected density functional theory. We found that the reaction barrier of the Lewis acid-catalyzed epoxide ring-opening reactions decreases upon ascending in group 1 along the series Cs+ > Rb+ > K+ > Na+ > Li+ > H+. Our activation strain and Kohn-Sham molecular orbital analyses reveal that the enhanced reactivity of the Lewis acid-catalyzed ring-opening reaction is caused by the reduced steric (Pauli) repulsion between the filled orbitals of the epoxide and the nucleophile, as the Lewis acid polarizes the filled orbitals of the epoxide more efficiently away from the incoming nucleophile. Furthermore, we established that the regioselectivity of these ring-opening reactions is, aside from the "classical" strain control, also dictated by a hitherto unknown mechanism, namely, the steric (Pauli) repulsion between the nucleophile and the substrate, which could be traced back to the asymmetric orbital density on the epoxide. In all, this work again demonstrates that the concept of Pauli-lowering catalysis is a general phenomenon.
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Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry, Amsterdam
Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling
(ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081
HV Amsterdam, The Netherlands
- Leiden Institute of Chemistry, Leiden
University, Einsteinweg 55, 2333 CC Leiden, The
Netherlands
| | - Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam
Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling
(ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081
HV Amsterdam, The Netherlands
| | - Ryoji Yoshisada
- 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
| | | | - Jeroen D. C. Codée
- Leiden Institute of Chemistry, Leiden
University, Einsteinweg 55, 2333 CC Leiden, The
Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry, Amsterdam
Institute of Molecular and Life Sciences (AIMSS), Amsterdam Center for Multiscale Modeling
(ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081
HV Amsterdam, The Netherlands
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30
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Kim RQ, Misra M, Gonzalez A, Tomašković I, Shin D, Schindelin H, Filippov DV, Ovaa H, Đikić I, van der Heden van Noort GJ. Development of ADPribosyl Ubiquitin Analogues to Study Enzymes Involved in Legionella Infection. Chemistry 2021; 27:2506-2512. [PMID: 33075184 PMCID: PMC7898697 DOI: 10.1002/chem.202004590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Indexed: 11/18/2022]
Abstract
Legionnaires' disease is caused by infection with the intracellularly replicating Gram-negative bacterium Legionella pneumophila. This pathogen uses an unconventional way of ubiquitinating host proteins by generating a phosphoribosyl linkage between substrate proteins and ubiquitin by making use of an ADPribosylated ubiquitin (UbADPr ) intermediate. The family of SidE effector enzymes that catalyze this reaction is counteracted by Legionella hydrolases, which are called Dups. This unusual ubiquitination process is important for Legionella proliferation and understanding these processes on a molecular level might prove invaluable in finding new treatments. Herein, a modular approach is used for the synthesis of triazole-linked UbADPr , and analogues thereof, and their affinity towards the hydrolase DupA is determined and hydrolysis rates are compared to natively linked UbADPr . The inhibitory effects of modified Ub on the canonical eukaryotic E1-enzyme Uba1 are investigated and rationalized in the context of a high-resolution crystal structure reported herein. Finally, it is shown that synthetic UbADPr analogues can be used to effectively pull-down overexpressed DupA from cell lysate.
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Affiliation(s)
- Robbert Q. Kim
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Mohit Misra
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
- Rudolf Virchow Center for Integrative and Translational BioimagingUniversity of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Alexis Gonzalez
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
| | - Ines Tomašković
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
| | - Donghyuk Shin
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
- Current Address: Department of Nano-BioengineeringIncheon National UniversityAcademyro 11922012IncheonSouth Korea
| | - Hermann Schindelin
- Rudolf Virchow Center for Integrative and Translational BioimagingUniversity of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Dmitri V. Filippov
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Ivan Đikić
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
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31
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Reintjens NRM, Tondini E, Vis C, McGlinn T, Meeuwenoord NJ, Hogervorst TP, Overkleeft HS, Filippov DV, van der Marel GA, Ossendorp F, Codée JDC. Multivalent, Stabilized Mannose-6-Phosphates for the Targeted Delivery of Toll-Like Receptor Ligands and Peptide Antigens. Chembiochem 2021; 22:434-440. [PMID: 32864819 PMCID: PMC7894537 DOI: 10.1002/cbic.202000538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/29/2020] [Indexed: 02/03/2023]
Abstract
Mannose-6-phosphate (M6P) is recognized by the mannose-6-phosphate receptor and plays an important role in the transport of cargo to the endosomes, making it an attractive tool to improve endosomal trafficking of vaccines. We describe herein the assembly of peptide antigen conjugates carrying clusters of mannose-6-C-phosphonates (M6Po). The M6Po's are stable M6P mimics that are resistant to cleavage of the phosphate group by endogenous phosphatases. Two different strategies for the incorporation of the M6Po clusters in the conjugate have been developed: the first relies on a "post-assembly" click approach employing an M6Po bearing an alkyne functionality; the second hinges on an M6Po C-glycoside amino acid building block that can be used in solid-phase peptide synthesis. The generated conjugates were further equipped with a TLR7 ligand to stimulate dendritic cell (DC) maturation. While antigen presentation is hindered by the presence of the M6Po clusters, the incorporation of the M6Po clusters leads to increased activation of DCs, thus demonstrating their potential in improving vaccine adjuvanticity by intraendosomally active TLR ligands.
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Affiliation(s)
- Niels R. M. Reintjens
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenNetherlands
| | - Elena Tondini
- Department of ImmunologyLeiden University Medical CenterLeiden UniversityAlbinusdreef 22333 ZALeidenNetherlands
| | - Christopher Vis
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenNetherlands
| | - Toroa McGlinn
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenNetherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenNetherlands
| | - Tim P. Hogervorst
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenNetherlands
| | - Herman S. Overkleeft
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenNetherlands
| | - Dmitri V. Filippov
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenNetherlands
| | | | - Ferry Ossendorp
- Department of ImmunologyLeiden University Medical CenterLeiden UniversityAlbinusdreef 22333 ZALeidenNetherlands
| | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenNetherlands
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32
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Hansen T, Ofman TP, Vlaming JGC, Gagarinov IA, van Beek J, Goté TA, Tichem JM, Ruijgrok G, Overkleeft HS, Filippov DV, van der Marel GA, Codée JDC. Reactivity-Stereoselectivity Mapping for the Assembly of Mycobacterium marinum Lipooligosaccharides. Angew Chem Int Ed Engl 2021; 60:937-945. [PMID: 32856761 PMCID: PMC7821131 DOI: 10.1002/anie.202010280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Indexed: 01/08/2023]
Abstract
The assembly of complex bacterial glycans presenting rare structural motifs and cis-glycosidic linkages is significantly obstructed by the lack of knowledge of the reactivity of the constituting building blocks and the stereoselectivity of the reactions in which they partake. We here report a strategy to map the reactivity of carbohydrate building blocks and apply it to understand the reactivity of the bacterial sugar, caryophyllose, a rare C12-monosaccharide, containing a characteristic tetrasubstituted stereocenter. We mapped reactivity-stereoselectivity relationships for caryophyllose donor and acceptor glycosides by a systematic series of glycosylations in combination with the detection and characterization of different reactive intermediates using experimental and computational techniques. The insights garnered from these studies enabled the rational design of building blocks with the required properties to assemble mycobacterial lipooligosaccharide fragments of M. marinum.
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Affiliation(s)
- Thomas Hansen
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Tim P. Ofman
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Joey G. C. Vlaming
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Ivan A. Gagarinov
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jessey van Beek
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Tessa A. Goté
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jacoba M. Tichem
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Gijs Ruijgrok
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Dmitri V. Filippov
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | | | - Jeroen D. C. Codée
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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33
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van den Ende TC, Heuts JMM, Gential GPP, Visser M, van de Graaff MJ, Ho NI, Jiskoot W, Valentijn ARPM, Meeuwenoord NJ, Overkleeft HS, Codée JDC, van der Burg SH, Verdegaal EME, van der Marel GA, Ossendorp F, Filippov DV. Simplified Monopalmitoyl Toll-like Receptor 2 Ligand Mini-UPam for Self-Adjuvanting Neoantigen-Based Synthetic Cancer Vaccines. Chembiochem 2020; 22:1215-1222. [PMID: 33180981 PMCID: PMC8049070 DOI: 10.1002/cbic.202000687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/04/2020] [Indexed: 12/14/2022]
Abstract
Synthetic vaccines, based on antigenic peptides that comprise MHC-I and MHC-II T-cell epitopes expressed by tumors, show great promise for the immunotherapy of cancer. For optimal immunogenicity, the synthetic peptides (SPs) should be adjuvanted with suitable immunostimulatory additives. Previously, we have shown that improved immunogenicity in vivo is obtained with vaccine modalities in which an SP is covalently connected to an adjuvanting moiety, typically a ligand to Toll-like receptor 2 (TLR2). SPs were covalently attached to UPam, which is a derivative of the classic TLR2 ligand Pam3 CysSK4 . A disadvantage of the triply palmitoylated UPam is its high lipophilicity, which precludes universal adoption of this adjuvant for covalent modification of various antigenic peptides as it renders the synthetic vaccine insoluble in several cases. Here, we report a novel conjugatable TLR2 ligand, mini-UPam, which contains only one palmitoyl chain, rather than three, and therefore has less impact on the solubility and other physicochemical properties of a synthetic peptide. In this study, we used SPs that contain the clinically relevant neoepitopes identified in a melanoma patient who completely recovered after T-cell therapy. Homogeneous mini-UPam-SP conjugates have been prepared in good yields by stepwise solid-phase synthesis that employed a mini-UPam building block pre-prepared in solution and the standard set of Fmoc-amino acids. The immunogenicity of the novel mini-UPam-SP conjugates was demonstrated by using the cancer patient's T-cells.
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Affiliation(s)
- Thomas C van den Ende
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jeroen M M Heuts
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Geoffroy P P Gential
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marten Visser
- Department of Medical Oncology and Oncode Institute, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Michel J van de Graaff
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Nataschja I Ho
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Wim Jiskoot
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - A Rob P M Valentijn
- Clinical Pharmacy and Toxicology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Nico J Meeuwenoord
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology and Oncode Institute, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Els M E Verdegaal
- Department of Medical Oncology and Oncode Institute, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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34
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Hansen T, Ofman TP, Vlaming JGC, Gagarinov IA, Beek J, Goté TA, Tichem JM, Ruijgrok G, Overkleeft HS, Filippov DV, Marel GA, Codée JDC. Reactivity–Stereoselectivity Mapping for the Assembly of
Mycobacterium marinum
Lipooligosaccharides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Thomas Hansen
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Tim P. Ofman
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Joey G. C. Vlaming
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Ivan A. Gagarinov
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jessey Beek
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Tessa A. Goté
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jacoba M. Tichem
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijs Ruijgrok
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. Marel
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jeroen D. C. Codée
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
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35
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Madern JM, Kim RQ, Misra M, Dikic I, Zhang Y, Ovaa H, Codée JDC, Filippov DV, van der Heden van Noort GJ. Synthesis of Stable NAD + Mimics as Inhibitors for the Legionella pneumophila Phosphoribosyl Ubiquitylating Enzyme SdeC. Chembiochem 2020; 21:2903-2907. [PMID: 32421893 PMCID: PMC7687180 DOI: 10.1002/cbic.202000230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/15/2020] [Indexed: 12/14/2022]
Abstract
Stable NAD+ analogues carrying single atom substitutions in either the furanose ring or the nicotinamide part have proven their value as inhibitors for NAD+ -consuming enzymes. To investigate the potential of such compounds to inhibit the adenosine diphosphate ribosyl (ADPr) transferase activity of the Legionella SdeC enzyme, we prepared three NAD+ analogues, namely carbanicotinamide adenosine dinucleotide (c-NAD+ ), thionicotinamide adenosine dinucleotide (S-NAD+ ) and benzamide adenosine dinucleotide (BAD). We optimized the chemical synthesis of thionicotinamide riboside and for the first time used an enzymatic approach to convert all three ribosides into the corresponding NAD+ mimics. We thus expanded the known scope of substrates for the NRK1/NMNAT1 enzyme combination by turning all three modified ribosides into NAD+ analogues in a scalable manner. We then compared the three NAD+ mimics side-by-side in a single assay for enzyme inhibition on Legionella effector enzyme SdeC. The class of SidE enzymes to which SdeC belongs was recently identified to be important in bacterial virulence, and we found SdeC to be inhibited by S-NAD+ and BAD with IC50 values of 28 and 39 μM, respectively.
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Affiliation(s)
- Jerre M. Madern
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Robbert Q. Kim
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Mohit Misra
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt amMainGermany
| | - Ivan Dikic
- Institute of Biochemistry IIGoethe University Faculty of MedicineTheodor-Stern-Kai 760590Frankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesGoethe University Frankfurt, Riedberg CampusMax-von-Laue-Strasse 1560438Frankfurt amMainGermany
| | - Yong Zhang
- Department of Pharmacology and Pharmaceutical SciencesSchool of PharmacyUniversity of Southern California1985 Zonal AvenueLos AngelesCA 90089USA
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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36
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Reintjens NRM, Tondini E, de Jong AR, Meeuwenoord NJ, Chiodo F, Peterse E, Overkleeft HS, Filippov DV, van der Marel GA, Ossendorp F, Codée JDC. Self-Adjuvanting Cancer Vaccines from Conjugation-Ready Lipid A Analogues and Synthetic Long Peptides. J Med Chem 2020; 63:11691-11706. [PMID: 32960056 PMCID: PMC7586330 DOI: 10.1021/acs.jmedchem.0c00851] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Self-adjuvanting
vaccines, wherein an antigenic
peptide is covalently bound to an immunostimulating agent, have been
shown to be promising tools for immunotherapy. Synthetic Toll-like
receptor (TLR) ligands are ideal adjuvants for covalent linking to
peptides or proteins. We here introduce a conjugation-ready TLR4 ligand,
CRX-527, a potent powerful lipid A analogue, in the generation of
novel conjugate-vaccine modalities. Effective chemistry has been developed
for the synthesis of the conjugation-ready ligand as well as the connection
of it to the peptide antigen. Different linker systems and connection
modes to a model peptide were explored, and in vitro evaluation of the conjugates showed them to be powerful immune-activating
agents, significantly more effective than the separate components.
Mounting the CRX-527 ligand at the N-terminus of the model peptide
antigen delivered a vaccine modality that proved to be potent in activation
of dendritic cells, in facilitating antigen presentation, and in initiating
specific CD8+ T-cell-mediated killing of antigen-loaded
target cells in vivo. Synthetic TLR4 ligands thus
show great promise in potentiating the conjugate vaccine platform
for application in cancer vaccination.
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Affiliation(s)
- Niels R M Reintjens
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Elena Tondini
- Department of Immunology, Leiden University Medical Center, Leiden University, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Ana R de Jong
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Nico J Meeuwenoord
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Fabrizio Chiodo
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Evert Peterse
- 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
| | - Gijsbert A van der Marel
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Center, Leiden University, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Jeroen D C Codée
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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37
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Enotarpi J, Tontini M, Balocchi C, van der Es D, Auberger L, Balducci E, Carboni F, Proietti D, Casini D, Filippov DV, Overkleeft HS, van der Marel GA, Colombo C, Romano MR, Berti F, Costantino P, Codeé JDC, Lay L, Adamo R. A stabilized glycomimetic conjugate vaccine inducing protective antibodies against Neisseria meningitidis serogroup A. Nat Commun 2020; 11:4434. [PMID: 32895393 PMCID: PMC7477203 DOI: 10.1038/s41467-020-18279-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/09/2020] [Indexed: 12/15/2022] Open
Abstract
Neisseria meningitidis serogroup A capsular polysaccharide (MenA CPS) consists of (1 → 6)-2-acetamido-2-deoxy-α-D-mannopyranosyl phosphate repeating units, O-acetylated at position C3 or C4. Glycomimetics appear attractive to overcome the CPS intrinsic lability in physiological media, due to cleavage of the phosphodiester bridge, and to develop a stable vaccine with longer shelf life in liquid formulation. Here, we generate a series of non-acetylated carbaMenA oligomers which are proven more stable than the CPS. An octamer (DP8) inhibits the binding of a MenA specific bactericidal mAb and polyclonal serum to the CPS, and is selected for further in vivo testing. However, its CRM197 conjugate raises murine antibodies towards the non-acetylated CPS backbone, but not the natural acetylated form. Accordingly, random O-acetylation of the DP8 is performed, resulting in a structure (Ac-carbaMenA) showing improved inhibition of anti-MenA CPS antibody binding and, after conjugation to CRM197, eliciting anti-MenA protective murine antibodies, comparably to the vaccine benchmark.
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MESH Headings
- Animals
- Antibodies, Bacterial/analysis
- Antibodies, Neutralizing/chemistry
- Bacterial Capsules/immunology
- Biomimetics/methods
- Glycoconjugates/chemical synthesis
- Glycoconjugates/immunology
- Mice
- Neisseria meningitidis, Serogroup A/chemistry
- Neisseria meningitidis, Serogroup A/drug effects
- Neisseria meningitidis, Serogroup A/immunology
- Polysaccharides, Bacterial/chemical synthesis
- Polysaccharides, Bacterial/chemistry
- Polysaccharides, Bacterial/immunology
- Vaccines, Conjugate/chemistry
- Vaccines, Conjugate/microbiology
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Affiliation(s)
- Jacopo Enotarpi
- Department of Chemistry and CRC Polymeric Materials (LaMPo), University of Milan, Milan, Italy
- Department of Bioorganic Synthesis, Leiden University, 2333, Leiden, The Netherlands
| | | | | | - Daan van der Es
- Department of Bioorganic Synthesis, Leiden University, 2333, Leiden, The Netherlands
| | - Ludovic Auberger
- Department of Chemistry and CRC Polymeric Materials (LaMPo), University of Milan, Milan, Italy
| | | | | | | | | | - Dmitri V Filippov
- Department of Bioorganic Synthesis, Leiden University, 2333, Leiden, The Netherlands
| | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden University, 2333, Leiden, The Netherlands
| | | | - Cinzia Colombo
- Department of Chemistry and CRC Polymeric Materials (LaMPo), University of Milan, Milan, Italy
| | | | | | | | - Jeroen D C Codeé
- Department of Bioorganic Synthesis, Leiden University, 2333, Leiden, The Netherlands.
| | - Luigi Lay
- Department of Chemistry and CRC Polymeric Materials (LaMPo), University of Milan, Milan, Italy.
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38
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Voorneveld J, Florea BI, Bakkum T, Mendowicz RJ, van der Veer MS, Gagestein B, van Kasteren SI, van der Stelt M, Overkleeft HS, Filippov DV. Olaparib-Based Photoaffinity Probes for PARP-1 Detection in Living Cells. Chembiochem 2020; 21:2431-2434. [PMID: 32282108 PMCID: PMC7496120 DOI: 10.1002/cbic.202000042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/11/2020] [Indexed: 12/31/2022]
Abstract
The poly-ADP-ribose polymerase (PARP) is a protein from the family of ADP-ribosyltransferases that catalyzes polyadenosine diphosphate ribose (ADPR) formation in order to attract the DNA repair machinery to sites of DNA damage. The inhibition of PARP activity by olaparib can cause cell death, which is of clinical relevance in some tumor types. This demonstrates that quantification of PARP activity in the context of living cells is of great importance. In this work, we present the design, synthesis and biological evaluation of photo-activatable affinity probes inspired by the olaparib molecule that are equipped with a diazirine for covalent attachment upon activation by UV light and a ligation handle for the addition of a reporter group of choice. SDS-PAGE, western blotting and label-free LC-MS/MS quantification analysis show that the probes target the PARP-1 protein and are selectively outcompeted by olaparib; this suggests that they bind in the same enzymatic pocket. Proteomics data are available via ProteomeXchange with identifier PXD018661.
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Affiliation(s)
- Jim Voorneveld
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bogdan I Florea
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Thomas Bakkum
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Rafal J Mendowicz
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Miriam S van der Veer
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Berend Gagestein
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Sander I van Kasteren
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mario van der Stelt
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Dmitri V Filippov
- Bio-organic Synthesis Group Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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39
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de Geus MAR, Maurits E, Sarris AJC, Hansen T, Kloet MS, Kamphorst K, ten Hoeve W, Robillard MS, Pannwitz A, Bonnet SA, Codée JDC, Filippov DV, Overkleeft HS, van Kasteren SI. Fluorogenic Bifunctional trans-Cyclooctenes as Efficient Tools for Investigating Click-to-Release Kinetics. Chemistry 2020; 26:9900-9904. [PMID: 32154603 PMCID: PMC7496853 DOI: 10.1002/chem.201905446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/09/2020] [Indexed: 12/11/2022]
Abstract
The inverse electron demand Diels-Alder pyridazine elimination reaction between tetrazines and allylic substituted trans-cyclooctenes (TCOs) is a key player in bioorthogonal bond cleavage reactions. Determining the rate of elimination of alkylamine substrates has so far proven difficult. Here, we report a fluorogenic tool consisting of a TCO-linked EDANS fluorophore and a DABCYL quencher for accurate determination of both the click and release rate constants for any tetrazine at physiologically relevant concentrations.
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Affiliation(s)
- Mark A. R. de Geus
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Elmer Maurits
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Alexi J. C. Sarris
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Thomas Hansen
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Max S. Kloet
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Kiki Kamphorst
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | | | - Marc S. Robillard
- Tagworks PharmaceuticalsGeert Grooteplein Zuid 106525 GANijmegenThe Netherlands
| | - Andrea Pannwitz
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Sylvestre A. Bonnet
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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40
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Li RJE, Hogervorst TP, Achilli S, Bruijns SCM, Spiekstra S, Vivès C, Thépaut M, Filippov DV, van der Marel GA, van Vliet SJ, Fieschi F, Codée JDC, van Kooyk Y. Targeting of the C-Type Lectin Receptor Langerin Using Bifunctional Mannosylated Antigens. Front Cell Dev Biol 2020; 8:556. [PMID: 32760719 PMCID: PMC7371993 DOI: 10.3389/fcell.2020.00556] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
Langerhans cells (LCs) are antigen-presenting cells that reside in the skin. They uniquely express high levels of the C-type lectin receptor Langerin (CD207), which is an attractive target for antigen delivery in immunotherapeutic vaccination strategies against cancer. We here assess a library of 20 synthetic, well-defined mannoside clusters, built up from one, two, and three of six monomannosides, dimannosides, or trimannosides, appended to an oligopeptide backbone, for binding with Langerin using surface plasmon resonance and flow cytometric quantification. It is found that Langerin binding affinity increases with increasing number of mannosides. Hexavalent presentation of the mannosides resulted in binding affinities ranging from 3 to 12 μM. Trivalent presentation of the dimannosides and trimannosides led to Langerin affinity in the same range. The model melanoma gp100 antigenic peptide was subsequently equipped with a hexavalent cluster of the dimannosides and trimannosides as targeting moieties. Surprisingly, although the bifunctional conjugates were taken up in LCs in a Langerin-dependent manner, limited antigen presentation to cytotoxic T cells was observed. These results indicate that targeting glycan moieties on immunotherapeutic vaccines should not only be validated for target binding, but also on the continued effects on biology, such as antigen presentation to both CD8+ and CD4+ T cells.
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Affiliation(s)
- Rui-Jun Eveline Li
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Tim P Hogervorst
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Silvia Achilli
- Univ. Grenoble Alpes, CEA, CRNS, Institut de Biologie Structurale, Grenoble, France
| | - Sven C M Bruijns
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Sander Spiekstra
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Corinne Vivès
- Univ. Grenoble Alpes, CEA, CRNS, Institut de Biologie Structurale, Grenoble, France
| | - Michel Thépaut
- Univ. Grenoble Alpes, CEA, CRNS, Institut de Biologie Structurale, Grenoble, France
| | - Dmitri V Filippov
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Gijs A van der Marel
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Sandra J van Vliet
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Franck Fieschi
- Univ. Grenoble Alpes, CEA, CRNS, Institut de Biologie Structurale, Grenoble, France
| | - Jeroen D C Codée
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Yvette van Kooyk
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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41
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Reintjens NRM, Koemans TS, Zilverschoon N, Castelli R, Cordfunke RA, Drijfhout JW, Meeuwenoord NJ, Overkleeft HS, Filippov DV, Marel GA, Codée JDC. Synthesis of
C
‐Glycosyl Amino Acid Building Blocks Suitable for the Solid‐Phase Synthesis of Multivalent Glycopeptide Mimics. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Niels R. M. Reintjens
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Tony S. Koemans
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nick Zilverschoon
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Riccardo Castelli
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Robert A. Cordfunke
- Dept. of Immunohematology and Blood Transfusion Leiden University Medical Center Leiden University Albinusdreef 2 2333 ZA Leiden The Netherlands
| | - Jan Wouter Drijfhout
- Dept. of Immunohematology and Blood Transfusion Leiden University Medical Center Leiden University Albinusdreef 2 2333 ZA Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- 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
| | - Gijsbert A. Marel
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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42
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Hansen T, Elferink H, van Hengst JMA, Houthuijs KJ, Remmerswaal WA, Kromm A, Berden G, van der Vorm S, Rijs AM, Overkleeft HS, Filippov DV, Rutjes FPJT, van der Marel GA, Martens J, Oomens J, Codée JDC, Boltje TJ. Characterization of glycosyl dioxolenium ions and their role in glycosylation reactions. Nat Commun 2020; 11:2664. [PMID: 32471982 PMCID: PMC7260182 DOI: 10.1038/s41467-020-16362-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/22/2020] [Indexed: 12/28/2022] Open
Abstract
Controlling the chemical glycosylation reaction remains the major challenge in the synthesis of oligosaccharides. Though 1,2-trans glycosidic linkages can be installed using neighboring group participation, the construction of 1,2-cis linkages is difficult and has no general solution. Long-range participation (LRP) by distal acyl groups may steer the stereoselectivity, but contradictory results have been reported on the role and strength of this stereoelectronic effect. It has been exceedingly difficult to study the bridging dioxolenium ion intermediates because of their high reactivity and fleeting nature. Here we report an integrated approach, using infrared ion spectroscopy, DFT computations, and a systematic series of glycosylation reactions to probe these ions in detail. Our study reveals how distal acyl groups can play a decisive role in shaping the stereochemical outcome of a glycosylation reaction, and opens new avenues to exploit these species in the assembly of oligosaccharides and glycoconjugates to fuel biological research.
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Affiliation(s)
- Thomas Hansen
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Hidde Elferink
- Radboud University Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jacob M A van Hengst
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Kas J Houthuijs
- Radboud University Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Wouter A Remmerswaal
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Alexandra Kromm
- Radboud University Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED, Nijmegen, The Netherlands
| | - Stefan van der Vorm
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anouk M Rijs
- Radboud University Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED, Nijmegen, The Netherlands
| | - Hermen S Overkleeft
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Dmitri V Filippov
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Floris P J T Rutjes
- Radboud University Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Gijsbert A van der Marel
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jonathan Martens
- Radboud University Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED, Nijmegen, The Netherlands.
| | - Jeroen D C Codée
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| | - Thomas J Boltje
- Radboud University Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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43
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van Mechelen J, Voorneveld J, Overkleeft HS, Filippov DV, van der Marel GA, Codée JDC. Synthesis of orthogonally protected and functionalized bacillosamines. Org Biomol Chem 2020; 18:2834-2837. [PMID: 32236232 DOI: 10.1039/d0ob00256a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2,4-Diamino-2,4,6-trideoxyglucose (bacillosamine) is a monosaccharide found in many pathogenic bacteria, variation in the functionalities appended to the amino groups occurs depending on the species the sugar is derived from. We here report the first synthesis of bacillosamine synthons that allow for the incorporation of two different functionalities at the C-2-N-acetyl and C-4-amines. We have developed chemistry to assemble a set of conjugation ready Neisseria meningitidis C-2-N-acetyl bacillosamine saccharides, carrying either an acetyl or (R)- or (S)-glyceroyl at the C-4 amine. The glyceroyl bacillosamines have been further extended at the C-3-OH with an α-d-galactopyranose to provide structures that occur as post-translational modifications of N. meningitidis PilE proteins, which make up the bacterial pili.
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Affiliation(s)
- Jeanine van Mechelen
- Bioorganic synthesis group, Leiden University, Einsteinweg 55, 2333 CC Leiden, Leiden, The Netherlands.
| | - Jim Voorneveld
- Bioorganic synthesis group, Leiden University, Einsteinweg 55, 2333 CC Leiden, Leiden, The Netherlands.
| | - Hermen S Overkleeft
- Bioorganic synthesis group, Leiden University, Einsteinweg 55, 2333 CC Leiden, Leiden, The Netherlands.
| | - Dmitri V Filippov
- Bioorganic synthesis group, Leiden University, Einsteinweg 55, 2333 CC Leiden, Leiden, The Netherlands.
| | - Gijsbert A van der Marel
- Bioorganic synthesis group, Leiden University, Einsteinweg 55, 2333 CC Leiden, Leiden, The Netherlands.
| | - Jeroen D C Codée
- Bioorganic synthesis group, Leiden University, Einsteinweg 55, 2333 CC Leiden, Leiden, The Netherlands.
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44
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Hogervorst TP, Li RJE, Marino L, Bruijns SCM, Meeuwenoord NJ, Filippov DV, Overkleeft HS, van der Marel GA, van Vliet SJ, van Kooyk Y, Codée JDC. C-Mannosyl Lysine for Solid Phase Assembly of Mannosylated Peptide Conjugate Cancer Vaccines. ACS Chem Biol 2020; 15:728-739. [PMID: 32045202 PMCID: PMC7091534 DOI: 10.1021/acschembio.9b00987] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Dendritic
cells (DCs) are armed with a multitude of Pattern Recognition
Receptors (PRRs) to recognize pathogens and initiate pathogen-tailored
T cell responses. In these responses, the maturation of DCs is key,
as well as the production of cytokines that help to accomplish T cell
responses. DC-SIGN is a frequently exploited PRR that can effectively
be targeted with mannosylated antigens to enhance the induction of
antigen-specific T cells. The natural O-mannosidic
linkage is susceptible to enzymatic degradation, and its chemical
sensitivity complicates the synthesis of mannosylated antigens. For
this reason, (oligo)mannosides are generally introduced in a late
stage of the antigen synthesis, requiring orthogonal conjugation handles
for their attachment. To increase the stability of the mannosides
and streamline the synthesis of mannosylated peptide antigens, we
here describe the development of an acid-stable C-mannosyl lysine, which allows for the inline introduction of mannosides
during solid-phase peptide synthesis (SPPS). The developed amino acid
has been successfully used for the assembly of both small ligands
and peptide antigen conjugates comprising an epitope of the gp100
melanoma-associated antigen and a TLR7 agonist for DC activation.
The ligands showed similar internalization capacities and binding
affinities as the O-mannosyl analogs. Moreover, the
antigen conjugates were capable of inducing maturation, stimulating
the secretion of pro-inflammatory cytokines, and providing enhanced
gp100 presentation to CD8+ and CD4+ T cells,
similar to their O-mannosyl counterparts. Our results
demonstrate that the C-mannose lysine is a valuable
building block for the generation of anticancer peptide-conjugate
vaccine modalities.
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Affiliation(s)
- Tim P. Hogervorst
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - R. J. Eveline Li
- Amsterdam UMC-Location Vrije Universiteit Amsterdam, Deptartment of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Laura Marino
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Sven C. M. Bruijns
- Amsterdam UMC-Location Vrije Universiteit Amsterdam, Deptartment of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Nico J. Meeuwenoord
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Dmitri V. Filippov
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Gijsbert A. van der Marel
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Sandra J. van Vliet
- Amsterdam UMC-Location Vrije Universiteit Amsterdam, Deptartment of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Yvette van Kooyk
- Amsterdam UMC-Location Vrije Universiteit Amsterdam, Deptartment of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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45
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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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46
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Xin BT, Espinal C, de Bruin G, Filippov DV, van der Marel GA, Florea BI, Overkleeft HS. Two-Step Bioorthogonal Activity-Based Protein Profiling of Individual Human Proteasome Catalytic Sites. Chembiochem 2020; 21:248-255. [PMID: 31597011 DOI: 10.1002/cbic.201900551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Indexed: 12/12/2022]
Abstract
Bioorthogonal chemistry allows the selective modification of biomolecules in complex biological samples. One application of this methodology is in two-step activity-based protein profiling (ABPP), a methodology that is particularly attractive where direct ABPP using fluorescent or biotinylated probes is ineffective. Herein we describe a set of norbornene-modified, mechanism-based proteasome inhibitors aimed to be selective for each of the six catalytic sites of human constitutive proteasomes and immunoproteasomes. The probes developed for β1i, β2i, β5c, and β5i proved to be useful two-step ABPs that effectively label their developed proteasome subunits in both Raji cell extracts and living Raji cells through inverse-electron-demand Diels-Alder (iEDDA) ligation. The compound developed for β1c proved incapable of penetrating the cell membrane, but effectively labels β1c in vitro. The compound developed for β2c proved not selective, but its azide-containing analogue LU-002c proved effective in labeling of β2c via azide-alkyne click ligation chemistry both in vitro and in situ. In total, our results contribute to the growing list of proteasome activity tools to include five subunit-selective activity-based proteasome probes, four of which report on proteasome activities in living cells.
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Affiliation(s)
- Bo-Tao Xin
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Christofer Espinal
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gerjan de Bruin
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.,Present address, Acerta Pharma B.V., Industrielaan 63, 5349 AE, Oss, The Netherlands
| | - Dmitri V Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bogdan I Florea
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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47
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Zurlo E, Gorroño Bikandi I, Meeuwenoord NJ, Filippov DV, Huber M. Tracking amyloid oligomerization with monomer resolution using a 13-amino acid peptide with a backbone-fixed spin label. Phys Chem Chem Phys 2019; 21:25187-25195. [PMID: 31696167 DOI: 10.1039/c9cp01060b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amyloid oligomers are suspected as toxic agents in neurodegenerative disease, and are transient and often heterogeneous, making them difficult to detect. Here we show an approach to track the development of amyloid oligomers in situ by room temperature, continuous wave (cw) 9 and 95 GHz EPR. Three amyloid peptides with the 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid (TOAC) spin label were synthesized by solid phase peptide synthesis: T0EZ (TKVKVLGDVIEVGG) with TOAC (T) at the N-terminus, T5EZ with TOAC in the middle (KVKVTGDVIEVG) and T12EZ with TOAC at the C-terminus (KVKVLGDVIEVTG). These sequences are derived from the K11V (KVKVLGDVIEV) amyloid peptide, which self-aggregates to oligomers with a β-sheet configuration (A. Laganowsky, et al., Science, 2012, 335, 1228-1231). To monitor oligomerization, the rotational correlation time (τr) is measured by cw-EPR. For the backbone-fixed TOAC label that is devoid of local mobility τr should reflect the rotation and thereby the size of the peptide, resp. oligomer. For T5EZ a good match between the measured τr and the size of the peptide is obtained, showing the validity of the approach. One of the three peptides (T0EZ) aggregates (circular dichroism), whereas the other two do not. Since also the respective MTSL (S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate) labelled peptides fail to aggregate, molecular crowding due to the label, rather than the helix-inducing properties of TOAC, seems to be responsible. Following in situ oligomer formation of T0EZ by the change in rotational correlation time, two oligomers are observed, a 5-6 mer and a 15-18 mer. The EPR approach, particularly 95 GHz EPR, enables following oligomerization of one monomer at a time, suggesting that the cw-EPR approach presented is a novel tool to follow amyloid oligomerization with high resolution.
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Affiliation(s)
- E Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| | - I Gorroño Bikandi
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| | - N J Meeuwenoord
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, 2300 RA Leiden, The Netherlands
| | - D V Filippov
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, 2300 RA Leiden, The Netherlands
| | - M Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
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48
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Hos BJ, Camps MG, van den Bulk J, Tondini E, van den Ende TC, Ruano D, Franken K, Janssen GM, Ru A, Filippov DV, Arens R, van Veelen PA, Miranda N, Ossendorp F. Identification of a neo-epitope dominating endogenous CD8 T cell responses to MC-38 colorectal cancer. Oncoimmunology 2019; 9:1673125. [PMID: 32923109 PMCID: PMC7458608 DOI: 10.1080/2162402x.2019.1673125] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/13/2019] [Accepted: 09/22/2019] [Indexed: 02/08/2023] Open
Abstract
The murine MC-38 colorectal cancer model is a commonly used model for cancer with high mutational burden, which is sensitive for immune checkpoint immunotherapy. We set out to analyze endogenous CD8+ T cell responses to MC-38 neo-antigens in tumor-bearing mice and after anti-PD-L1 checkpoint therapy. Through combination of whole-exome sequencing analysis with mass spectrometry of MHC class I eluted peptides we could identify eight candidate epitopes. Of these, a neo-epitope encoded by a point-mutation in the sequence of the ribosomal protein L18 (Rpl18) strongly dominated the CD8+ T cell response to our MC-38 cell-line in comparison to a previously described neo-epitope in the Adpgk protein. Therapeutic vaccination with synthetic peptides induced CD8+ T cell responses against the mutated Rpl18 epitope, which controlled tumor growth in vivo. This immunologically dominant response to mutated Rpl18 is of great importance in the development and optimization of immunotherapeutic strategies with the MC-38 tumor model.
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Affiliation(s)
- Brett J. Hos
- Leiden University Medical Center, Immunohematology and Blood Transfusion, Leiden, The Netherlands
| | - Marcel G.M. Camps
- Leiden University Medical Center, Immunohematology and Blood Transfusion, Leiden, The Netherlands
| | | | - Elena Tondini
- Leiden University Medical Center, Immunohematology and Blood Transfusion, Leiden, The Netherlands
| | | | - Dina Ruano
- Leiden University Medical Center, Pathology, Leiden, The Netherlands
| | - Kees Franken
- Leiden University Medical Center, Immunohematology and Blood Transfusion, Leiden, The Netherlands
| | - George M.C. Janssen
- Leiden University Medical Center, Center for Proteomics & Metabolomics, Leiden, The Netherlands
| | - Arnoud Ru
- Leiden University Medical Center, Center for Proteomics & Metabolomics, Leiden, The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Ramon Arens
- Leiden University Medical Center, Immunohematology and Blood Transfusion, Leiden, The Netherlands
| | - Peter A. van Veelen
- Leiden University Medical Center, Center for Proteomics & Metabolomics, Leiden, The Netherlands
| | - Noel Miranda
- Leiden University Medical Center, Pathology, Leiden, The Netherlands
| | - Ferry Ossendorp
- Leiden University Medical Center, Immunohematology and Blood Transfusion, Leiden, The Netherlands
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49
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Li RJE, Hogervorst TP, Achilli S, Bruijns SC, Arnoldus T, Vivès C, Wong CC, Thépaut M, Meeuwenoord NJ, van den Elst H, Overkleeft HS, van der Marel GA, Filippov DV, van Vliet SJ, Fieschi F, Codée JDC, van Kooyk Y. Systematic Dual Targeting of Dendritic Cell C-Type Lectin Receptor DC-SIGN and TLR7 Using a Trifunctional Mannosylated Antigen. Front Chem 2019; 7:650. [PMID: 31637232 PMCID: PMC6787163 DOI: 10.3389/fchem.2019.00650] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/11/2019] [Indexed: 01/22/2023] Open
Abstract
Dendritic cells (DCs) are important initiators of adaptive immunity, and they possess a multitude of Pattern Recognition Receptors (PRR) to generate an adequate T cell mediated immunity against invading pathogens. PRR ligands are frequently conjugated to tumor-associated antigens in a vaccination strategy to enhance the immune response toward such antigens. One of these PPRs, DC-SIGN, a member of the C-type lectin receptor (CLR) family, has been extensively targeted with Lewis structures and mannose glycans, often presented in multivalent fashion. We synthesized a library of well-defined mannosides (mono-, di-, and tri-mannosides), based on known "high mannose" structures, that we presented in a systematically increasing number of copies (n = 1, 2, 3, or 6), allowing us to simultaneously study the effect of mannoside configuration and multivalency on DC-SIGN binding via Surface Plasmon Resonance (SPR) and flow cytometry. Hexavalent presentation of the clusters showed the highest binding affinity, with the hexa-α1,2-di-mannoside being the most potent ligand. The four highest binding hexavalent mannoside structures were conjugated to a model melanoma gp100-peptide antigen and further equipped with a Toll-like receptor 7 (TLR7)-agonist as adjuvant for DC maturation, creating a trifunctional vaccine conjugate. Interestingly, DC-SIGN affinity of the mannoside clusters did not directly correlate with antigen presentation enhancing properties and the α1,2-di-mannoside cluster with the highest binding affinity in our library even hampered T cell activation. Overall, this systematic study has demonstrated that multivalent glycan presentation can improve DC-SIGN binding but enhanced binding cannot be directly translated into enhanced antigen presentation and the sole assessment of binding affinity is thus insufficient to determine further functional biological activity. Furthermore, we show that well-defined antigen conjugates combining two different PRR ligands can be generated in a modular fashion to increase the effectiveness of vaccine constructs.
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Affiliation(s)
- Rui-Jun Eveline Li
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam Universitair Medische Centra, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Tim P. Hogervorst
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Silvia Achilli
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Sven C. Bruijns
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam Universitair Medische Centra, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Tim Arnoldus
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam Universitair Medische Centra, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Corinne Vivès
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Chung C. Wong
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Nico J. Meeuwenoord
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Hans van den Elst
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Gijs A. van der Marel
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Dmitri V. Filippov
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Sandra J. van Vliet
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam Universitair Medische Centra, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Jeroen D. C. Codée
- Department of Bio-organic Synthesis, Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Yvette van Kooyk
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam Universitair Medische Centra, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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50
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van der Ham A, Hansen T, Lodder G, Codée JDC, Hamlin TA, Filippov DV. Computational and NMR Studies on the Complexation of Lithium Ion to 8-Crown-4. Chemphyschem 2019; 20:2103-2109. [PMID: 31282054 PMCID: PMC6772996 DOI: 10.1002/cphc.201900496] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/01/2019] [Indexed: 01/09/2023]
Abstract
Lithium ion selective crown ethers have been the subject of much research for a multitude of applications. Current research is aimed at structurally rigidifying crown ethers, as restructuring of the crown ether ring upon ion binding is energetically unfavorable. In this work, the lithium ion binding ability of the relatively rigid 8-crown-4 was investigated both computationally by density functional theory calculations and experimentally by 1 H and 7 Li NMR spectroscopy. Although both computational and experimental results showed 8-crown-4 to bind lithium ion, this binding was found to be weak compared to larger crown ethers. The computational analysis revealed that the complexation is driven by enthalpy rather than entropy, illustrating that rigidity is only of nominal importance. To elucidate the origin of the favorable interaction of lithium ion with crown ethers, activation strain analyses and energy decomposition analyses were performed pointing to the favorable interaction being mainly electrostatic in nature. 8-crown-4 presents the smallest crown ether reported to date capable of binding lithium ion, possessing two distinct conformations from which it is able to do so.
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Affiliation(s)
- Alex van der Ham
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Thomas Hansen
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Gerrit Lodder
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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