Chain‐Terminating and Clickable NAD+ Analogues for Labeling the Target Proteins of ADP‐Ribosyltransferases

ADP‐ribosyltransferases (ARTs) use NAD⁺ as a substrate and play important roles in numerous biological processes, such as the DNA damage response and cell cycle regulation, by transferring multiple ADP‐ribose units onto target proteins to form poly(ADP‐ribose) (PAR) chains of variable sizes. Efforts to identify direct targets of PARylation, as well as the specific ADP‐ribose acceptor sites, must all tackle the complexity of PAR. Herein, we report new NAD⁺ analogues that are efficiently processed by wild‐type ARTs and lead to chain termination owing to a lack of the required hydroxy group, thereby significantly reducing the complexity of the protein modification. Due to the presence of an alkyne group, these NAD⁺ analogues allow subsequent manipulations by click chemistry for labeling with dyes or affinity markers. This study provides insight into the substrate scope of ARTs and might pave the way for the further developments of chemical tools for investigating PAR metabolism.     

Fragmentation behavior of Amadori‐peptides obtained by non‐enzymatic glycosylation of lysine residues with ADP‐ribose in tandem mass spectrometry

Mono‐ and poly‐adenosine diphosphate (ADP)‐ribosylation are common post‐translational modifications incorporated by sequence‐specific enzymes at, predominantly, arginine, asparagine, glutamic acid or aspartic acid residues, whereas non‐enzymatic ADP‐ribosylation (glycation) modifies lysine and cysteine residues. These glycated proteins and peptides (Amadori‐compounds) are commonly found in organisms, but have so far not been investigated to any great degree. In this study, we have analyzed their fragmentation characteristics using different mass spectrometry (MS) techniques. In matrix‐assisted laser desorption/ionization (MALDI)‐MS, the ADP‐ribosyl group was cleaved, almost completely, at the pyrophosphate bond by in‐source decay. In contrast, this cleavage was very weak in electrospray ionization (ESI)‐MS. The same fragmentation site also dominated the MALDI‐PSD (post‐source decay) and ESI‐CID (collision‐induced dissociation) mass spectra. The remaining phospho‐ribosyl group (formed by the loss of adenosine monophosphate) was stable, providing a direct and reliable identification of the modification site via the b‐ and y‐ion series. Cleavage of the ADP‐ribose pyrophosphate bond under CID conditions gives access to both neutral loss (347.10 u) and precursor‐ion scans (m/z 348.08), and thereby permits the identification of ADP‐ribosylated peptides in complex mixtures with high sensitivity and specificity. With electron transfer dissociation (ETD), the ADP‐ribosyl group was stable, providing ADP‐ribosylated c‐ and z‐ions, and thus allowing reliable sequence analyses. Copyright © 2010 John Wiley & Sons, Ltd.     

A General Approach Towards Triazole‐Linked Adenosine Diphosphate Ribosylated Peptides and Proteins

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 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.     

Synthesis and Macrodomain Binding of Mono‐ADP‐Ribosylated Peptides

Mono‐ADP‐ribosylation is a dynamic posttranslational modification (PTM) with important roles in signaling. Mammalian proteins that recognize or hydrolyze mono‐ADP‐ribosylated proteins have been described. We report the synthesis of ADP‐ribosylated peptides from the proteins histone H2B, RhoA and, HNP‐1. An innovative procedure was applied that makes use of pre‐phosphorylated amino acid building blocks. Binding assays revealed that the macrodomains of human MacroD2 and TARG1 exhibit distinct specificities for the different ADP‐ribosylated peptides, thus showing that the sequence surrounding ADP‐ribosylated residues affects the substrate selectivity of macrodomains.     

Molecular Tools for the Study of ADP-Ribosylation: A Unified and Versatile Method to Synthesise Native Mono-ADP-Ribosylated Peptides

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.     

Chemical synthesis of linear ADP-ribose oligomers up to pentamer and their binding to the oncogenic helicase ALC1

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.

We report the synthesis of linear ADPr oligomers of defined length up to a pentamer using an improved solid phase method. Binding study with human oncogenic helicase ALC1 shows that ADPr oligomers bind to ALC1 in a length-dependent manner.     

MicroITIES Detection of Adenosine Phosphates

The complexation between a triamide ligand derived from tris‐2‐(aminoethyl)amine: N‐{2‐[bis‐(2‐(4‐tert‐butylbenzoyl)‐aminoethyl)‐amino]‐ethyl}4‐tert‐butylbenzamide, L , and the three adenosine‐containing nucleotides, ATP, ADP, and AMP, was investigated by facilitated ion transfer processes through a microhole array film. Differential pulse voltammetry (DPV) was used to measure the transfer currents for the respective nucleotides. The three nucleotides were found to have different transfer potentials with transfer currents proportional to their aqueous concentrations. Based on the differences of the transfer potentials, it is concluded that the host ligand, L, interacts with the phosphate moiety and the Gibbs transfer energy is dominated by the charge generated by the phosphate groups. The linear relationship between the current response and nucleotide concentration forms the basis of an anion sensor with a dynamic range from 0.1 mM to 5 mM .     

Damit Blut nicht verklumpt

Inhibitors of platelet aggregation (“anti‐platelets”) constitute a remarkably heterogeneous family of drugs, with regard to both chemistry and biochemistry. The rather uncommon diversity and the continuing search for new anti‐platelet drugs results from the particular requirements: high efficacy associated with good tolerability especially during long‐term treatment, marginal side effects and easy administration. Sophisticated structural modifications to lead compounds are employed to meet these requirements and improve bio‐availability and efficacy. While thromboxane synthesis and ADP receptors are currently the most prominent targets of anti‐platelet drugs, a number of other promising targets are now evaluated and new drugs are on the verge.     

Cyclic Adenosine 5′‐Diphosphoribose (cADPR) Mimics Used as Molecular Probes in Cell Signaling

Cyclic adenosine 5′‐diphosphate ribose (cADPR) is a second messenger in the Ca²⁺ signaling pathway. To elucidate its molecular mechanism in calcium release, a series of cADPR analogues with modification on ribose, nucleobase, and pyrophosphate have been investigated. Among them, the analogue with the modification of the northern ribose by ether linkage substitution (cIDPRE) exhibits membrane‐permeate Ca²⁺ agonistic activity in intact HeLa cells, human T cells, mouse cardiac myocytes and neurosecretory PC12 cell lines; thus, cIDPRE and coumarin‐caged cIDPRE are valuable probes to investigate the cADPR‐mediated Ca²⁺ signal pathway.     

Replacement of Water Molecules in a Phosphate Binding Site by Furanoside‐Appended lin‐Benzoguanine Ligands of tRNA‐Guanine Transglycosylase (TGT)

The enzyme tRNA‐guanine transglycosylase has been identified as a drug target for the foodborne illness shigellosis. A key challenge in structure‐based design for this enzyme is the filling of the polar ribose‐34 pocket. Herein, we describe a novel series of ligands consisting of furanoside‐appended lin‐benzoguanines. They were designed to replace a conserved water cluster and differ by the functional groups at C(2) and C(3) of the furanosyl moiety being either OH or OMe. The unfavorable desolvation of Asp102 and Asp280, which are located close to the ribose‐34 pocket, had a significant impact on binding affinity. While the enzyme has tRNA as its natural substrate, X‐ray co‐crystal structures revealed that the furanosyl moieties of the ligands are not accommodated in the tRNA ribose‐34 site, but at the location of the adjacent phosphate group. A remarkable similarity of the position of the oxygen atoms in these two structures suggests furanosides as a potential phosphate isoster.     

Discovery of Cell‐Permeable Inhibitors That Target the BRCT Domain of BRCA1 Protein by Using a Small‐Molecule Microarray

BRCTs are phosphoserine‐binding domains found in proteins involved in DNA repair, DNA damage response and cell cycle regulation. BRCA1 is a BRCT domain‐containing, tumor‐suppressing protein expressed in the cells of breast and other human tissues. Mutations in BRCA1 have been found in ca. 50 % of hereditary breast cancers. Cell‐permeable, small‐molecule BRCA1 inhibitors are promising anticancer agents, but are not available currently. Herein, with the assist of microarray‐based platforms, we have discovered the first cell‐permeable protein–protein interaction (PPI) inhibitors against BRCA1. By targeting the (BRCT)₂ domain, we showed compound 15 a and its prodrug 15 b inhibited BRCA1 activities in tumor cells, sensitized these cells to ionizing radiation‐induced apoptosis, and showed synergistic inhibitory effect when used in combination with Olaparib (a small‐molecule inhibitor of poly‐ADP‐ribose polymerase) and Etoposide (a small‐molecule inhibitor of topoisomerase II). Unlike previously reported peptide‐based PPI inhibitors of BRCA1, our compounds are small‐molecule‐like and could be directly administered to tumor cells, thus making them useful for future studies of BRCA1/PARP‐related pathways in DNA damage and repair response, and in cancer therapy.     

Design and synthesis of novel polycycles based on the 3H‐pyrrolo/6,7‐dihydropyrido[1,2‐a]indole scaffold as templates for pharmaceutical development

In the course of our work aimed at developing novel heterocycles of pharmaceutical interest, we designed and synthesized several polycyclic templates as potential substrates to be used in drug design. We obtained a set of condensed ring systems as versatile structural platforms to generate potential DNA‐interactive agents and/or reversible inhibitors of enzymes such as topoisomerases, poly(ADP‐ribose) polymerase‐1 (PARP‐1), telomerase, and, in particular, cyclin dependent kinases. Herein, we report the design, synthesis, structural investigation, and preliminary DNA‐binding affinity of these heteroaromatic systems. J. Heterocyclic Chem., (2011).     

Well‐Defined Thermoresponsive Polymethacrylamide Copolymers with Ester Pendent Groups through One‐Pot Statistical Postpolymerization Modification of Poly(2‐Isopropenyl‐2‐Oxazoline) with Multiple Carboxylic Acids

Thermoresponsive polymers that undergo a solubility phase transition in water are important as basis for the development for a wide variety of responsive and smart materials. In this study, the synthesis of thermoresponsive copolymers is demonstrated by the straightforward one‐pot statistical postpolymerization modification of well‐defined poly(2‐isopropenyl‐2‐oxazoline) (PiPOx) by ring‐opening reaction with multiple carboxylic acids. The reactions are carried out using dual, triple, and quadruple mixtures of up to four different aliphatic carboxylic acids. The cloud point temperatures of the resulting polymethacrylamide copolymers with ester pendent groups can be finely tuned by adjusting the feed ratio and the hydrophilic–hydrophobic balance of the acids that are used for the ring‐opening modification of PiPOx. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 360–366     

Total synthesis of a cyclic adenosine 5'-diphosphate ribose receptor agonist

Stable cyclic adenosine 5'-diphosphate ribose (cADPR) analogues are chemical biology tools that can probe the Ca(2+) release mechanism and structure-activity relationships of this emerging potent second messenger. However, analogues with an intact "northern" ribose have been inaccessible due to the difficulty of generating the sensitive N1-ribosyl link. We report the first total synthesis of the membrane permeant, hydrolytically stable, cADPR receptor agonist 8-Br-N1-cIDPR via regio- and stereoselective N1-ribosylation of protected 8-bromoinosine.     

Asperflavipine A: A Cytochalasan Heterotetramer Uniquely Defined by a Highly Complex Tetradecacyclic Ring System from Aspergillus flavipes QCS12

Asperflavipines A ( 1 ) and B ( 2 ), two structurally complex merocytochalasans, were isolated from Aspergillus flavipes . Asperflavipine A ( 1 ), which contains two cytochalasan moieties and two epicoccine moieties, is the first cytochalasan heterotetramer to be discovered. It is uniquely defined by 5/6/11/5/6/5/6/5/6/5/5/11/6/5 fused tetradecacyclic rings with three continuous bridged ring systems. Asperflavipine B ( 2 ) is a cytochalasan heterotrimer containing a cytochalasan and two epicoccine moieties with a 5/6/11/5/5/6/5/6/5 nonacyclic ring system. The hypothetical biosynthesis of 1 and 2 is proposed to involve Diels–Alder and [3+2] cycloaddition reactions as key steps and reveals unparalleled plasticity in the biosynthesis of merocytochalasans. The existence of 1 adds a new dimension to the diversity of the cytochalasan family. Compound 1 showed moderate cytotoxicity and induced apoptosis in Jurkat, NB4, and HL60 cells through the activation of caspase‐3 and degradation of poly(ADP‐ribose) polymerase (PARP).     

Separation of tryptic peptides of native and glycated BSA using open‐tubular CEC with salophene–lanthanide–Zn2+ complex as stationary phase

Open‐tubular CEC (OT‐CEC) with a new stationary phase, salophene–lanthanide–Zn²⁺ complex, has been applied to the separation of tryptic peptides of native BSA and BSA glycated by glucose and ribose. Glycation of proteins (non‐enzymatic modification by sugars) significantly affects their properties and it is of great importance from a physiological point of view. Separation of tryptic peptides of glycated BSA by CZE was poor because of their strong adsorption to the bare fused silica capillary. An improved separation of tryptic peptides of both native and glycated BSA was achieved by OT‐CEC in the fused silica capillary non‐covalently coated with salophene–lanthanide–Zn²⁺ complex, which suppressed the adsorption of peptides to the capillary and via specific interactions with some (glyco)peptides enhanced selectivity of the separation. Significant differences have been found in OT‐CEC analyses of tryptic hydrolysates of native and glycated BSA. In OT‐CEC‐UV profile of tryptic peptides of native BSA, 44 peaks could be resolved, whereas a reduced number of 38 peaks were observed in the profile of tryptic peptides of glucose‐glycated BSA and only 30 peaks were found in the case of ribose‐glycated BSA. The developed OT‐CEC can be potentially used for monitoring of protein glycation.     

PARP‐1/PAR Activity in Cultured Human Lens Epithelial Cells Exposed to Two Levels of UVB Light

This study investigated poly(ADP ‐ribose) polymerase‐1 (PARP ‐1) activation in cultured human lens epithelial cells exposed to two levels of UVB light (312 nm peak wavelength), 0.014 and 0.14 J cm⁻² (“low” and “high” dose, respectively). At the low dose, PARP ‐1 and poly(ADP ‐ribose) (PAR ) polymers acted to repair DNA strand breaks rapidly with no subsequent major effects on either cell morphology or viability. However, following the high UVB dose, there was a dramatic second phase of PARP ‐1 activation, 90 min later, which included a sudden reappearance of DNA strand breaks, bursts of reactive oxygen species (ROS ) formation within both the mitochondria and nucleus, a translocation of PAR from the nucleus to the mitochondria and an ultimate 70% loss of cell viability occurring after 24 h. The results provide evidence for an important role for PARP ‐1 in protecting the human lens epithelium against low levels of UVB light, and possibly participating in the triggering of cell death following exposure to toxic levels of radiation.     

Conformation of ATP and ADP Molecules in Aqueous Solutions Determined by High-Energy X-ray Diffraction

High-energy X-ray diffraction measurements were carried out at 26 °C for aqueous 1.0, 2.0 and 2.05 mol% disodium adenosine 5′-triphosphate (ATP) and 2.0 and 2.05 mol% disodium adenosine 5′-diphosphate (ADP) solutions in order to obtain direct experimental information on the intramolecular conformations of ATP and ADP molecules in aqueous solutions. Observed interference terms were analyzed in terms of the intramolecular geometry of the ATP and ADP molecules. Dihedral angles between adenine and the ribose group (t ₁), ribose-ring and methylene group of ribose (t ₂), and the methylene group of ribose and triphosphate (or diphosphate) group (t ₃), were determined through the least-squares fitting procedure of the observed interference term.     

Profiling of Ribose Methylations in RNA by High‐Throughput Sequencing

Ribose methylations are the most abundant chemical modifications of ribosomal RNA and are critical for ribosome assembly and fidelity of translation. Many aspects of ribose methylations have been difficult to study due to lack of efficient mapping methods. Here, we present a sequencing‐based method (RiboMeth‐seq) and its application to yeast ribosomes, presently the best‐studied eukaryotic model system. We demonstrate detection of the known as well as new modifications, reveal partial modifications and unexpected communication between modification events, and determine the order of modification at several sites during ribosome biogenesis. Surprisingly, the method also provides information on a subset of other modifications. Hence, RiboMeth‐seq enables a detailed evaluation of the importance of RNA modifications in the cells most sophisticated molecular machine. RiboMeth‐seq can be adapted to other RNA classes, for example, mRNA, to reveal new biology involving RNA modifications.     

Solution Structure of a RNA Decamer Duplex,Containing 9‐[2‐O‐(β‐D‐ribofuranosyl)‐β‐D‐ribofuranosyl]adenine,a Special Residue in Lower Eukaryotic Initiator tRNAs

The solution structure of the self‐complementary deca‐ribonucleotide 5′‐r(GCGA*AUUCGC)‐3′ containing 9‐[2‐O‐(β‐D ‐ribofuranosyl)‐β‐D ‐ribofuranosyl]adenine (A*), a modified nucleotide that occurs in lower eukaryotic methionine initiator tRNAs (tRNAs_i^Met), was determined by NMR spectroscopy. Unexpectedly, the modification has no effect on the thermal stability of the duplex. However, the extra ribose moiety is in the C(3′)‐endo conformation and takes up a well‐defined position in the minor groove, which is in agreement with its position in tRNAs_i^Met as determined by X‐ray crystallography. Molecular‐dynamics simulations on the RNA duplex in H₂O show that the position of the extra ribofuranose moiety seems to be stabilized by bridged H‐bonds (mediated by two H₂O molecules) to the backbone of the complementary chain.