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
Madern, J.M.; Hansen, T.; Rijssel, E.R. van; Kistemaker, H.A.V.; Vorm, S. van der; Overkleeft, H.S.; ... ; Codee, J.D.C. 2019
Thiosugars, sugars that have their endocyclic oxygen substituted for a sulfur atom, have been used as stable bioisosteres of naturally occurring glycans because the thiosugar glycosydic linkage is... Show moreThiosugars, sugars that have their endocyclic oxygen substituted for a sulfur atom, have been used as stable bioisosteres of naturally occurring glycans because the thiosugar glycosydic linkage is supposed to be stabilized toward chemical and enzymatic hydrolysis. We have performed an in-depth investigation into the stability and reactivity of furanosyl thiacarbenium ions, by assessing all four diastereoisomeric thiofuranosides experimentally and computationally. We show that all furanosyl thiacarbenium ions react in a 1,2-cis-selective manner with triethylsilane, reminiscent of their oxo counterparts. The computed conformational space occupied by the thiacarbenium ions is strikingly similar to that of the corresponding furanosyl oxycarbenium ions, indicating that the stereoelectronic substituent effects governing the stability of furanosyl oxocarbenium ions and thiacarbenium ions are very similar. While the thio-ribo-furanose appears to be less reactive than its oxo counterpart, the thio-ara-, lyxo-, and xylo-furanosides appear to be more reactive than their oxygen equivalents. These differences are accounted for using the conformational preference of the donors and the carbocation intermediates. The lower reactivity of the thio-ribo furanosides in (Lewis) acid-mediated reactions and the similarity of the thia- and oxocarbenium ions make thio-ribofuranosides excellent stabilized analogues of the naturally occurring ribo-furanose sugars. Show less
Liu, Q.; Kistemaker, H.A.V.; Bhogaraju, S.; Dikic, I.; Overkleeft, H.S.; Marel, G.A. van der; ... ; Filippov, D.V. 2018
Current methods to prepare adenosine diphosphate ribosylated (ADPr) peptides are not generally applicable due to the labile nature of this post-translational modification and its incompatibility... Show moreCurrent methods to prepare adenosine diphosphate ribosylated (ADPr) peptides are not generally applicable due to the labile nature of this post-translational modification and its incompatibility with strong acidic conditions used in standard solid-phase peptide synthesis. A general strategy is presented to prepare ADPr peptide analogues based on a copper-catalyzed click reaction between an azide-modified peptide and an alkyne-modified ADPr counterpart. The scope of this approach was expanded to proteins by preparing two ubiquitin ADPr analogues carrying the biological relevant α-glycosidic linkage. Biochemical validation using Legionella effector enzyme SdeA shows that clicked ubiquitin ADPr is well-tolerated and highlights the potential of this strategy to prepare ADPr proteins. Show less
DNA damage triggers chromatin remodeling by mechanisms that are poorly understood. The oncogene and chromatin remodeler ALC1/CHD1L massively decompacts chromatin in vivo yet is inactive prior to... Show moreDNA damage triggers chromatin remodeling by mechanisms that are poorly understood. The oncogene and chromatin remodeler ALC1/CHD1L massively decompacts chromatin in vivo yet is inactive prior to DNA-damage-mediated PARP1 induction. We show that the interaction of the ALC1 macrodomain with the ATPase module mediates auto-inhibition. PARP1 activation suppresses this inhibitory interaction. Crucially, release from auto-inhibition requires a poly-ADP-ribose (PAR) binding macrodomain. We identify tri-ADP-ribose as a potent PAR-mimic and synthetic allosteric effector that abrogates ATPase-macrodomain interactions, promotes an ungated conformation, and activates the remodeler’s ATPase. ALC1 fragments lacking the regulatory macrodomain relax chromatin in vivo without requiring PARP1 activation. Further, the ATPase restricts the macrodomain’s interaction with PARP1 under non-DNA damage conditions. Somatic cancer mutants disrupt ALC1’s auto-inhibition and activate chromatin remodeling. Our data show that the NAD+-metabolite and nucleic acid PAR triggers ALC1 to drive chromatin relaxation. Modular allostery in this oncogene tightly controls its robust, DNA-damage-dependent activation. Show less
Liu, Q.; Kistemaker, H.A.V.; Overkleeft, H.S.; Marel, G.A. van der; Filippov, D.V. 2017
Poly-adenosine diphosphate ribose (PAR) is a branched biopolymer that occurs as a result of post-translational modification of proteins. In 1981 Miwa et al. determined the structure of... Show morePoly-adenosine diphosphate ribose (PAR) is a branched biopolymer that occurs as a result of post-translational modification of proteins. In 1981 Miwa et al. determined the structure of enzymatically prepared branched PAR. We present the first synthesis of the same branched PAR fragment and have shown by NMR that the structure proposed by Miwa is correct. Show less
The post-translational modification of proteins known as adenosine diphosphate ribosylation (ADPr) is involved in a wide variety of important biological processes and is also associated with... Show moreThe post-translational modification of proteins known as adenosine diphosphate ribosylation (ADPr) is involved in a wide variety of important biological processes and is also associated with carcinogenesis and the process of aging. Therefore, a better understanding of the biology of ADP-ribosylation is crucial for the development of novel therapeutics. To facilitate this research, the availability of well-defined fragments of mono- and poly-ADP-ribose is essential. This Thesis describes the development of new synthetic methodologies to achieve this and the successful synthesis of well-defined ADP-ribosylated biomolecules. Show less
Kistemaker, H.A.V.; Meeuwenoord, N.J.; Overkleeft, H.S.; Marel, G.A. van der; Filippov, D.V. 2015
