Carbohydrates, alongside proteins and nucleic acids, constitute a crucial and versatile family of biomolecules present in all life forms. They manifest as monosaccharides, oligosaccharides, and... Show moreCarbohydrates, alongside proteins and nucleic acids, constitute a crucial and versatile family of biomolecules present in all life forms. They manifest as monosaccharides, oligosaccharides, and polysaccharides, covalently bonded to proteins and fats. Carbohydrates are integral to plant and arthropod cell walls and traditionally viewed as the primary source and storage of energy, but also play a vital role in many fundamental biological processes. To study the structure and biological activity of specific carbohydrates, it is essential to synthesize them in a pure and well-defined form, as current natural extraction techniques are often limiting.The work of this thesis is focused on a specific type of glycomimetics: thiosugars, i.e. sugar analogues which have their endocylic oxygen replaced by a sulfur atom. These analogues are of interest because of their unique stability and stereoelectronic effects, which closely mimick their natural O-counterparts. The glycosidic linkage of thioglycosides (i.e. 4-S-furanosides and 5-S-pyranosides) shows improved resistance towards chemical and enzymatic hydrolysis. 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
Madern, J.M.; Kim, R.Q.; Misra, M.; Dikic, I.; Zhang, Y.; Ovaa, H.; ... ; Noort, G.J.V. van 2021
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... Show moreStable 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 IC(50)values of 28 and 39 mu M, respectively. Show less
Vorm, S. van der; Hansen, T.; Rijssel, E.R. van; Dekkers, R.; Madern, J.M.; Overkleeft, H.S.; ... ; Codée, J.D.C. 2019
The 3D shape of glycosyl oxocarbenium ions determines their stability and reactivity and the stereochemical course of SN1-reactions taking place on these reactive intermediates is dictated by the... Show moreThe 3D shape of glycosyl oxocarbenium ions determines their stability and reactivity and the stereochemical course of SN1-reactions taking place on these reactive intermediates is dictated by the conformation of these species. The nature and configuration of functional groups on the carbohydrate ring effect the stability of glycosyl oxocarbenium ions and they control the overall shape of the cations. We here map the stereoelectronic substituent effects of the C2-azide, C2-fluoride and C4-carboxylic acid ester on the stability and reactivity of the complete suite of diastereoisomeric furanoses using a combined computational and experimental approach. Surprisingly all furanosyl donors studied react in a highly stereoselective manner to provide the 1,2-cis products, except for the reactions in the xylose series. The 1,2-cis selectivity in the ribo-, arabino- and lyxo-configured furanosides can be traced back to the lowest energy 3E or E3-conformers of the intermediate oxocarbenium ions. The lack of selectivity of the xylosyl donors is related to the occurrence of oxocarbenium ions, adopting other conformations. 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
