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... Show moreAndrogen 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. Show less
Minnee, H.; Rack, J.G.M.; Marel, G.A. van der; Overkleeft, H.S.; Codée, J.D.C.; Ahel, I.; Filippov, D.V. 2023
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... Show moreThe 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. Show less
Đukić, N.; Strømland, Ø.; Elsborg, J.D.; Munnur, D.; Zhu, K.; Schuller, M.; ... ; Ahel, I. 2023
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... Show morePARP14 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. Show less
Vrande, K.N.A. van de; Filippov, D.V.; Codee, J.D.C. 2023
To probe the reaction mechanism, underlying the rearrangementofoft-used trichloroacetimidate glycosyl donors into the correspondinganomeric trichloroacetamides, we have used a combination of C-13-... Show moreTo probe the reaction mechanism, underlying the rearrangementofoft-used trichloroacetimidate glycosyl donors into the correspondinganomeric trichloroacetamides, we have used a combination of C-13- and N-15-labeled glycosyl trichloroacetimidate donorsin a series of crossover experiments. These unambiguously show thattrichloroacetamides are formed via an intermolecular aglycon transfermechanism. This insight enables the design of more effective glycosylationprotocols, preventing the formation of dead-end side products. Show less
Minnee, H.; Chung, H.W.; Rack, J.G.M.; Marel, G.A. van der; Overkleeft, H.S.; Codee, J.D.C.; ... ; Filippov, D.V. 2023
Adenosine diphosphateribosylation (ADP-ribosylation) is a crucialpost-translational modification involved in important regulatory mechanismsof numerous cellular pathways including histone... Show moreAdenosine diphosphateribosylation (ADP-ribosylation) is a crucialpost-translational modification involved in important regulatory mechanismsof numerous cellular pathways including histone maintenance and DNAdamage repair. To study this modification, well-defined ADP-ribosylatedpeptides, proteins, and close analogues thereof have been invaluabletools. Recently, proteomics studies have revealed histidine residuesto be ADP-ribosylated. We describe here the synthesis of a completeset of triazole-isosteres of ADP-ribosylated histidine to serve asprobes for ADP-ribosylating biomachinery. By exploiting Cu(I)- andRu(II)-catalyzed click chemistry between a propargylglycine buildingblock and an & alpha;- or & beta;-configured azidoribose, we have successfullyassembled the & alpha;- and & beta;-configured 1,4- and 1,5-triazoles,mimicking N(& tau;)- and N(& pi;)-ADP-ribosylated histidine, respectively.The ribosylated building blocks could be incorporated into a peptidesequence using standard solid-phase peptide synthesis and transformedon resin into the ADP-ribosylated fragments to provide a total offour ADP-ribosyl triazole conjugates, which were evaluated for theirchemical and enzymatic stability. The 1,5-triazole analogues mimickingthe N(& pi;)-substituted histidines proved susceptible to base-inducedepimerization and the ADP-ribosyl & alpha;-1,5-triazole linkage couldbe cleaved by the (ADP-ribosyl)hydrolase ARH3. Show less
Madern, J.M.; Voorneveld, J.; Rack, J.G.M.; Kistemaker, H.A.V.; Ahel, I.; Marel, G.A. van der; ... ; Filippov, D.V. 2023
Adenosine diphosphate (ADP) ribosylation is an importantpost-translationalmodification (PTM) that plays a role in a wide variety of cellularprocesses. To study the enzymes responsible for the... Show moreAdenosine diphosphate (ADP) ribosylation is an importantpost-translationalmodification (PTM) that plays a role in a wide variety of cellularprocesses. To study the enzymes responsible for the establishment,recognition, and removal of this PTM, stable analogues are invaluabletools. We describe the design and synthesis of a 4-thioribosyl APRrpeptide that has been assembled by solid phase synthesis. The key4-thioribosyl serine building block was obtained in a stereoselectiveglycosylation reaction using an alkynylbenzoate 4-thioribosyl donor. Show less
We report here chemoenzymatic and fully synthetic methodologiesto modify aspartate and glutamate side chains with ADP-ribose at specificsites on peptides. Structural analysis of aspartate and... Show moreWe report here chemoenzymatic and fully synthetic methodologiesto modify aspartate and glutamate side chains with ADP-ribose at specificsites on peptides. Structural analysis of aspartate and glutamateADP-ribosylated peptides reveals near-quantitative migration of theside chain linkage from the anomeric carbon to the 2 ''- or 3 ''-ADP-ribosehydroxyl moieties. We find that this linkage migration pattern isunique to aspartate and glutamate ADP-ribosylation and propose thatthe observed isomer distribution profile is present in biochemicaland cellular environments. After defining distinct stability propertiesof aspartate and glutamate ADP-ribosylation, we devise methods toinstall homogenous ADP-ribose chains at specific glutamate sites andassemble glutamate-modified peptides into full-length proteins. Byimplementing these technologies, we show that histone H2B E2 tri-ADP-ribosylationis able to stimulate the chromatin remodeler ALC1 with similar efficiencyto histone serine ADP-ribosylation. Our work reveals fundamental principlesof aspartate and glutamate ADP-ribosylation and enables new strategiesto interrogate the biochemical consequences of this widespread proteinmodification. Show less
The modification of substrates with ADP-ribose (ADPr) is im-portant in, for example, antiviral immunity and cancer. Recently, several reagents were developed to detect ADP-ribosylation; however, it... Show moreThe modification of substrates with ADP-ribose (ADPr) is im-portant 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 con-taining ADPr-proteins and observe that depending on the amino acid modified, the modification is heatlabile. We tested the re-activity of available reagents with diverse ADP-ribosylated pro-tein 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 me-tabolites, 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 prepa-ration methods and have defined the reagents suitable for specific methods and substrates. Show less
Voorneveld, J.; Kloet, M.S.; Wijngaarden, S.; Kim, R.Q.; Moutsiopoulou, A.; Verdegaal, M.; ... ; Noort, G.J.V. van 2022
We describe the development and optimization of a methodology to prepare peptides and proteins modified on the arginine residue with an adenosine-di-phosphate-ribosyl (ADPr) group. Our method... Show moreWe describe the development and optimization of a methodology to prepare peptides and proteins modified on the arginine residue with an adenosine-di-phosphate-ribosyl (ADPr) group. Our method comprises reacting an ornithine containing polypeptide on-resin with an alpha-linked anomeric isothiourea N-riboside, ensuing installment of a phosphomonoester at the 5 '- hydroxyl of the ribosyl moiety followed by the conversion into the adenosine diphosphate. We use this method to obtain four regioisomers of ADP-ribosylated ubiquitin (UbADPr), each modified with an ADP-ribosyl residue on a different arginine position within the ubiquitin (Ub) protein (Arg42, Arg54, Arg72, and Arg74) as the first reported examples of fully synthetic arginine-linked ADPr-modified proteins. We show the chemically prepared Arg-linked UbADPr to be accepted and processed by Legionella enzymes and compare the entire suite of four Arg-linked UbADPr regioisomers in a variety of biochemical experiments, allowing us to profile the activity and selectivity of Legionella pneumophila ligase and hydrolase enzymes. Show less
Voorneveld, J.; Kloet, M.S.; Wijngaarden, S.; Kim, R.Q.; Moutsiopoulou, A.; Verdegaal, M.; ... ; Noort, G.J.V. van 2022
We describe the development and optimization of a methodology to prepare peptides and proteins modified on the arginine residue with an adenosine-di-phosphate-ribosyl (ADPr) group. Our method... Show moreWe describe the development and optimization of a methodology to prepare peptides and proteins modified on the arginine residue with an adenosine-di-phosphate-ribosyl (ADPr) group. Our method comprises reacting an ornithine containing polypeptide on-resin with an alpha-linked anomeric isothiourea N-riboside, ensuing installment of a phosphomonoester at the 5 '- hydroxyl of the ribosyl moiety followed by the conversion into the adenosine diphosphate. We use this method to obtain four regioisomers of ADP-ribosylated ubiquitin (UbADPr), each modified with an ADP-ribosyl residue on a different arginine position within the ubiquitin (Ub) protein (Arg42, Arg54, Arg72, and Arg74) as the first reported examples of fully synthetic arginine-linked ADPr-modified proteins. We show the chemically prepared Arg-linked UbADPr to be accepted and processed by Legionella enzymes and compare the entire suite of four Arg-linked UbADPr regioisomers in a variety of biochemical experiments, allowing us to profile the activity and selectivity of Legionella pneumophila ligase and hydrolase enzymes. Show less
Speetjens, F.M.; Welters, M.J.P.; Slingerland, M.; Poelgeest, M.I.E. van; Steenwijk, P.J.D. van; Roozen, I.; ... ; Ossendorp, F. 2022
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... Show moreBackground: 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 mu g 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. Show less
Speetjens, F.M.; Welters, M.J.P.; Slingerland, M.; Poelgeest, M.I.E. van; Steenwijk, P.J.D. van; Roozen, I.; ... ; Ossendorp, F. 2022
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... Show moreBackground: 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 mu g 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. Show less
Remmerswaal, W.A.; Houthuijs, K.J.; Ven, R. van de; Elferink, H.; Hansen, T.; Berden, G.; ... ; Codee, J.D.C. 2022
The stereoselective introduction of glycosidic bonds is of paramount importance to oligosaccharide synthesis. Among the various chemical strategies to steer stereoselectivity, participation by... Show moreThe 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. Show less
Tondini, E.; Reintjens, N.R.M.; Castello, G.; Arakelian, T.; Isendoorn, M.; Camps, M.; ... ; Ossendorp, F. 2022
Adjuvants play a determinant role in cancer vaccination by optimally activating APCs and shaping the T cell response. Bacterial-derived lipid A is one of the most potent immune-stimulators known,... Show moreAdjuvants play a determinant role in cancer vaccination by optimally activating APCs and shaping the T cell response. Bacterial-derived lipid A is one of the most potent immune-stimulators known, and is recognized via Toll-like receptor 4 (TLR4). In this study, we explore the use of the synthetic, non-toxic, lipid A analog CRX-527 as an adjuvant for peptide cancer vaccines. This well-defined adjuvant was covalently conjugated to antigenic peptides as a strategy to improve vaccine efficacy. We show that coupling of this TLR4 agonist to peptide antigens improves vaccine uptake by dendritic cells (DCs), maturation of DCs and T cell activation in vitro, and stimulates DC migration and functional T cell priming in vivo. This translates into enhanced tumor protection upon prophylactic and therapeutic vaccination via intradermal injection against B16-OVA melanoma and HPV-related TC1 tumors. These results highlight the potential of CRX-527 as an adjuvant for molecularly defined cancer vaccines, and support the design of adjuvant-peptide conjugates as a strategy to optimize vaccine formulation. Show less
Tondini, E.; Reintjens, N.R.M.; Castello, G.; Arakelian, T.; Isendoorn, M.M.E.; Camps, M.; ... ; Ossendorp, F. 2022
Adjuvants play a determinant role in cancer vaccination by optimally activating APCs and shaping the T cell response. Bacterial-derived lipid A is one of the most potent immune-stimulators known,... Show moreAdjuvants play a determinant role in cancer vaccination by optimally activating APCs and shaping the T cell response. Bacterial-derived lipid A is one of the most potent immune-stimulators known, and is recognized via Toll-like receptor 4 (TLR4). In this study, we explore the use of the synthetic, non-toxic, lipid A analog CRX-527 as an adjuvant for peptide cancer vaccines. This well-defined adjuvant was covalently conjugated to antigenic peptides as a strategy to improve vaccine efficacy. We show that coupling of this TLR4 agonist to peptide antigens improves vaccine uptake by dendritic cells (DCs), maturation of DCs and T cell activation in vitro, and stimulates DC migration and functional T cell priming in vivo. This translates into enhanced tumor protection upon prophylactic and therapeutic vaccination via intradermal injection against B16-OVA melanoma and HPV-related TC1 tumors. These results highlight the potential of CRX-527 as an adjuvant for molecularly defined cancer vaccines, and support the design of adjuvant-peptide conjugates as a strategy to optimize vaccine formulation. Show less
Minnee, H.; Rack, J.G.M.; Marel, G.A. van der; Overkleeft, H.S.; Codee, J.D.C.; Ahel, I.; Filippov, D.V. 2022
A convergent synthesis provided nearly perfect tau-ADP-ribosylated histidine isosteres (His*-tau-ADPr) via a copper(I)-catalyzed cycloaddition between an azido-ADP-ribosyl analogue and an... Show moreA convergent synthesis provided nearly perfect tau-ADP-ribosylated histidine isosteres (His*-tau-ADPr) via a copper(I)-catalyzed cycloaddition between an azido-ADP-ribosyl analogue and an oligopeptide carrying a propargyl glycine. Both alpha- and beta-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*-tau-ADPr peptides were screened against a library of human ADP-ribosyl hydrolases. Show less
Ham, A. van der; Liu, X.; Calvani, D.; Melcrová, A.; Kozdra, M.; Buda, F.; ... ; Schneider, G.F. 2022
Molecularly thin, nanoporous thin films are of paramount importance in material sciences. Their use in a wide range of applications requires control over their chemical functionalities, which is... Show moreMolecularly thin, nanoporous thin films are of paramount importance in material sciences. Their use in a wide range of applications requires control over their chemical functionalities, which is difficult to achieve using current production methods. Here, the small polycyclic aromatic hydrocarbon decacyclene is used to form molecular thin films, without requiring covalent crosslinking of any kind. The 2.5 nm thin films are mechanically stable, able to be free-standing over micrometer distances, held together solely by supramolecular interactions. Using a combination of computational chemistry and microscopic imaging techniques, thin films are studied on both a molecular and microscopic scale. Their mechanical strength is quantified using AFM nanoindentation, showing their capability of withstanding a point load of 26 ± 9 nN, when freely spanning over a 1 μm aperture, with a corresponding Young's modulus of 6 ± 4 GPa. Our thin films constitute free-standing, non-covalent thin films based on a small PAH. Show less
Peterse, E.; Meeuwenoord, N.J.; Elst, H. van den; Marel, G.A. van der; Overkleeft, H.S.; Filippov, D.V. 2022
Cyclic peptides represent a popular class of macrocyclic drug candidates and therefore their solid phase synthesis has attracted much attention. In this contribution we present an efficient method... Show moreCyclic peptides represent a popular class of macrocyclic drug candidates and therefore their solid phase synthesis has attracted much attention. In this contribution we present an efficient method of side-chain anchoring for ornithine and lysine residues to be used in the standard Fmoc-based synthesis of cyclic peptides via on-resin cyclization. We demonstrate that the side chain of ornithine and lysine protected with N-Bocgroup can efficiently be converted to the isocyanate which is then immobilized on Wang-type resin in almost quantitative yield. We further show the synthesis of four biologically active cyclic peptides employing the side chain ornithine anchoring. Our method is at least on a par with the previously reported methodologies in terms of yield and the purity of the final products and is arguably operationally more straightforward. Show less
