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
The development of novel anti-infectives requires unprecedented strategies targeting pathways which are solely present in pathogens but absent in humans. Following this principle, we developed... Show moreThe development of novel anti-infectives requires unprecedented strategies targeting pathways which are solely present in pathogens but absent in humans. Following this principle, we developed inhibitors of lipoic acid (LA) salvage, a crucial pathway for the survival of LA auxotrophic bacteria and parasites but non-essential in human cells. An LA-based probe was selectively transferred onto substrate proteins via lipoate protein ligase (LPL) in intact cells, and their binding sites were determined by mass spectrometry. Probe labeling served as a proxy of LPL activity, enabling in situ screenings for cell-permeable LPL inhibitors. Profiling a focused compound library revealed two substrate analogs (LAMe and C3) as inhibitors, which were further validated by binding studies and co-crystallography. Importantly, LAMe exhibited low toxicity in human cells and achieved killing of Plasmodium falciparum in erythrocytes with an EC50 value of 15 μM, making it the most effective LPL inhibitor reported to date. Show less
Ham, M.P.J.M. van der.; Keulen, E. van; Koper, M.T.M.; Tashvigh, A.A.; Bitter, J.H. 2023
Non-activated esters are prominently featured functional groups in polymer science, as ester functional monomers display great structural diversity and excellent compatibility with a wide range of... Show moreNon-activated esters are prominently featured functional groups in polymer science, as ester functional monomers display great structural diversity and excellent compatibility with a wide range of polymerization mechanisms. Yet, their direct use as a reactive handle in post-polymerization modification has been typically avoided due to their low reactivity, which impairs the quantitative conversion typically desired in post-polymerization modification reactions. While activated ester approaches are a well-established alternative, the modification of non-activated esters remains a synthetic and economically valuable opportunity. In this review, we discuss past and recent efforts in the utilization of non-activated ester groups as a reactive handle to facilitate transesterification and aminolysis/amidation reactions, and the potential of the developed methodologies in the context of macromolecular engineering. Show less
Molecular-level insight into interfacial water at a buried electrode interface is essential in electrochemistry, but spectroscopic probing of the interface remains challenging. Here, using surface... Show moreMolecular-level insight into interfacial water at a buried electrode interface is essential in electrochemistry, but spectroscopic probing of the interface remains challenging. Here, using surface-specific heterodyne-detected sum-frequency generation (HD-SFG) spectroscopy, we directly access the interfacial water in contact with the graphene electrode supported on calcium fluoride (CaF2). We find phase transition-like variations of the HD-SFG spectra vs. applied potentials, which arises not from the charging/discharging of graphene but from the charging/discharging of the CaF2 substrate through the pseudocapacitive process. The potential-dependent spectra are nearly identical to the pH-dependent spectra, evidencing that the pseudocapacitive behavior is associated with a substantial local pH change induced by water dissociation between the CaF2 and graphene. Our work evidences the local molecular-level effects of pseudocapacitive charging at an electrode/aqueous electrolyte interface. Show less
Heijden O. van der; Park S.; Eggebeen J.J.J.; Koper M.T.M. 2023
We herein report the first total synthesis of the Streptococcus pneumoniae serotype 1 (Sp1) oligosaccharide, a unique zwitterionic capsular polysaccharide carrying labile O-acetyl esters. The... Show moreWe herein report the first total synthesis of the Streptococcus pneumoniae serotype 1 (Sp1) oligosaccharide, a unique zwitterionic capsular polysaccharide carrying labile O-acetyl esters. The target oligosaccharides, featuring rare α-2,4-diamino-2,4,6-trideoxy galactose (AAT) and α-galacturonic acids, were assembled up to the 9-mer level, in a highly stereoselective manner using trisaccharide building blocks. The lability of the O-acetyl esters imposed a careful deprotection scheme to prevent migration and hydrolysis. The migration was investigated in detail at various pD values using NMR spectroscopy, to show that migration and hydrolysis of the C-3-O-acetyl esters readily takes place under neutral conditions. Structural investigation showed the oligomers to adopt a right-handed helical structure with the acetyl esters exposed on the periphery of the helix in close proximity of the neighboring AAT residues, thereby imposing conformational restrictions on the AATα1-4GalA(3OAc) glycosidic linkages, supporting the helical shape of the polysaccharide, that has been proposed to be critical for its unique biological activity. Show less
In the field of lipid research, bioorthogonal chemistry has made the study of lipid uptake and processing in living systems possible, whilst minimising biological properties arising from detectable... Show moreIn the field of lipid research, bioorthogonal chemistry has made the study of lipid uptake and processing in living systems possible, whilst minimising biological properties arising from detectable pendant groups. To allow the study of unsaturated free fatty acids in live cells, we here report the use of sterculic acid, a 1,2-cyclopropene-containing oleic acid analogue, as a bioorthogonal probe. We show that this lipid can be readily taken up by dendritic cells without toxic side effects, and that it can subsequently be visualised using an inverse electron-demand Diels-Alder reaction with quenched tetrazine-fluorophore conjugates. In addition, the lipid can be used to identify changes in protein oleoylation after immune cell activation. Finally, this reaction can be integrated into a multiplexed bioorthogonal reaction workflow by combining it with two sequential copper-catalysed Huisgen ligation reactions. This allows for the study of multiple biomolecules in the cell simultaneously by multimodal confocal imaging. Show less
The successful integration of 2D nanomaterials into functional devices hinges on developing fabrication methods that afford hierarchical control across length scales of the entire assembly. We... Show moreThe successful integration of 2D nanomaterials into functional devices hinges on developing fabrication methods that afford hierarchical control across length scales of the entire assembly. We demonstrate structural control over a class of crystalline 2D nanosheets assembled from collagen triple helices. By lengthening the triple helix unit through sequential additions of Pro-Hyp-Gly triads, we achieved sub-angstrom tuning over the 2D lattice. These subtle changes influence the overall nanosheet size, which can be adjusted across the mesoscale size regime. The internal structure was observed by cryo-TEM with direct electron detection, which provides real-space high-resolution images, in which individual triple helices comprising the lattice can be clearly discerned. These results establish a general strategy for tuning the structural hierarchy of 2D nanomaterials that employ rigid, cylindrical structural units. Show less
