4‐(N,N‐Dimethylamino)pyridine‐Embedded Nanoporous Conjugated Polymer as a Highly Active Heterogeneous Organocatalyst

We report herein for the first time the incorporation of a versatile organocatalyst, 4‐(N,N‐dimethylamino)pyridine (DMAP), into the network of a nanoporous conjugated polymer (NCP) by the “bottom‐up” approach. The resulting DMAP‐NCP material possesses highly concentrated and homogeneously distributed DMAP catalytic sites (2.02 mmol g^?1). DMAP‐NCP also exhibits enhanced stability and permanent porosity due to the strong covalent linkage and the rigidity of the “bottom‐up” monomers. As a result, DMAP‐NCP shows excellent catalytic activity in the acylation of alcohols with yields of 92–99 %. The DMAP‐NCP catalyst could be easily recovered from the reaction mixture and reused in at least 14 consecutive cycles without measurable loss of activity. Moreover, the catalytic acylation reaction could be performed under neat and continuous‐flow conditions for at least 536 h of continuous work with the same catalyst activity.     

Highly Selective Lysine Acylation in Proteins Using a Lys-His Tag Sequence

Chemical modification of proteins has numerous applications, but it has been challenging to achieve the required high degree of selectivity on lysine amino groups. Recently, we described the highly selective acylation of proteins with an N-terminal Gly-His₆ segment. This tag promoted acylation of the N-terminal N^α-amine resulting in stable conjugates. Herein, we report the peptide sequences His_n-Lys-His_m, which we term Lys-His tags. In combination with simple acylating agents, they facilitate the acylation of the designated Lys N^ϵ-amine under mild conditions and with high selectivity over native Lys residues. We show that the Lys-His tags, which are 7 to 10 amino acids in length and still act as conventional His tags, can be inserted in proteins at the C-terminus or in loops, thus providing high flexibility regarding the site of modification. Finally, the selective and efficient acylation of the therapeutic antibody Rituximab, pure or mixed with other proteins, demonstrates the scope of the Lys-His tag acylation method.     

A Versatile Approach for Site‐Specific Lysine Acylation in Proteins

Using amber suppression in coordination with a mutant pyrrolysyl‐tRNA synthetase‐tRNA^Pyl pair, azidonorleucine is genetically encoded in E. coli . Its genetic incorporation followed by traceless Staudinger ligation with a phosphinothioester allows the convenient synthesis of a protein with a site‐specifically installed lysine acylation. By simply changing the phosphinothioester identity, any lysine acylation type could be introduced. Using this approach, we demonstrated that both lysine acetylation and lysine succinylation can be installed selectively in ubiquitin and synthesized histone H3 with succinylation at its K4 position (H3K4su). Using an H3K4su‐H4 tetramer as a substrate, we further confirmed that Sirt5 is an active histone desuccinylase. Lysine succinylation is a recently identified post‐translational modification. The reported technique makes it possible to explicate regulatory functions of this modification in proteins.     

Site‐Selective Acylations with Tailor‐Made Catalysts

The acylation of alcohols catalyzed by N,N‐dimethylamino pyridine (DMAP) is, despite its widespread use, sometimes confronted with substrate‐specific problems: For example, target compounds with multiple hydroxy groups may show insufficient selectivity for one hydroxyl, and the resulting product mixtures are hardly separable. Here we describe a concept that aims at tailor‐made catalysts for the site‐specific acylation. To this end, we introduce a catalyst library where each entry is constructed by connecting a variable and readily tuned peptide scaffold with a catalytically active unit based on DMAP. For selected examples, we demonstrate how library screening leads to the identification of optimized catalysts, and the substrates of interest can be converted with a markedly enhanced site‐selectivity compared with only DMAP. Furthermore, substrate‐optimized catalysts of this type can be used to selectively convert “their” substrate in the presence of structurally similar compounds, an important requisite for reactions with mixtures of substances.     

Integrative Chemical Biology Approaches for Identification and Characterization of “Erasers” for Fatty‐Acid‐Acylated Lysine Residues within Proteins

Acylation of proteins with fatty acids is important for the regulation of membrane association, trafficking, subcellular localization, and activity of many cellular proteins. While significant progress has been made in our understanding of the two major forms of protein acylation with fatty acids, N‐myristoylation and S‐palmitoylation, studies of the acylation of lysine residues, within proteins, with fatty acids have lagged behind. Demonstrated here is the use of integrative chemical biology approaches to examine human sirtuins as de‐fatty‐acid acylases in vitro and in cells. Photo‐crosslinking chemistry is used to investigate enzymes which recognize fatty‐acid acylated lysine. Human Sirt2 was identified as a robust lysine de‐fatty‐acid acylase in vitro. The results also show that Sirt2 can regulate the acylation of lysine residues, of proteins, with fatty acids within cells.     

Visible Light-Gated Organocatalysis Using a RuII-Photocage

The light-gated organocatalysis via the release of 4-N,N-dimethylaminopyridine (DMAP) by irradiation of the [Ru(bpy)₂(DMAP)₂]²⁺ complex with visible light was investigated. As model reaction the acetylation of benzyl alcohols with acetic anhydride was chosen. The pre-catalyst releases one DMAP molecule on irradiation at wavelengths longer than 455 nm. The photochemical process was characterized by steady-state irradiation and ultrafast transient absorption spectroscopy. The latter enabled the observation of the ³MLCT state and the spectral features of the penta-coordinated intermediate [Ru(bpy)₂(DMAP)]²⁺. The released DMAP catalyzes the acetylation of a wide range of benzyl alcohols with chemical yields of up to 99 %. Control experiments revealed unequivocally that it is the released DMAP which takes the role of the catalyst.     

An Enzymatic N‐Acylation Step Enables the Biocatalytic Synthesis of Unnatural Sialosides

Chitin is one of the most abundant and cheaply available biopolymers in Nature. Chitin has become a valuable starting material for many biotechnological products through manipulation of its N‐acetyl functionality, which can be cleaved under mild conditions using the enzyme family of de‐N‐acetylases. However, the chemoselective enzymatic re‐acylation of glucosamine derivatives, which can introduce new stable functionalities into chitin derivatives, is much less explored. Herein we describe an acylase (CmCDA from Cyclobacterium marinum) that catalyzes the N‐acylation of glycosamine with a range of carboxylic acids under physiological reaction conditions. This biocatalyst closes an important gap in allowing the conversion of chitin into complex glycosides, such as C5‐modified sialosides, through the use of highly selective enzyme cascades.     

Highly Selective Vapor-Phase Acylation of Veratrole over H_3PO_4/TiO_2-ZrO_2: Using Ethyl Acetate as a Green and Efficient Acylating Agent

A simple sol‐gel method with and without surfactant was applied to prepare TiO₂‐ZrO₂ mixed oxides containing Ti and Zr at a molar ratio of 1:1. Several catalysts containing w=15% –35% H₃PO₄ were set up using these mixed oxides. The physical and chemical properties of catalysts were investigated by BET, SEM and pyridine adsorption‐desorption. The catalytic performance of each material was determined for the vapor‐phase acylation of veratrole (1,2‐dimethoxybenzene) to 3,4‐dimethoxyacetophenone (3,4‐DMAP), which was found to be the major product of the reaction of veratrole with ethyl acetate, with alkylated products being the minor products. 2,3‐Dimethoxyacetophenone (2,3‐DMAP) was not detected in the product stream. In the best experimental conditions, the alkylated products were less than 0.7%. This reaction may represent an environmentally friendly alternative to use the ethyl acetate as the acylating reagent. The feed molar ratios of veratrole/ethyl acetate were varied over a wide range of 0.1 to 1, and the optimum feed ratio of veratrole/ethyl acetate was 1:3. Space velocity employed in the veratrole acylation reported as WHSV (veratrole) was 1.2 h^?1. The acylation reactions were carried out in the temperature range of 423 to 673 K and the optimum H₃PO₄ content for acylation was w=15%.     

Evolved,Selective Erasers of Distinct Lysine Acylations

Lysine acylations, a family of diverse protein modifications varying in acyl‐group length, charge, and saturation, are linked to many important physiological processes. Only a small set of substrate‐promiscuous lysine acetyltransferases and deacetylases (KDACs) install and remove this vast variety of modifications. Engineered KDACs that remove only one type of acylation would help to dissect the different contributions of distinct acylations. We developed a bacterial selection system for the directed evolution of KDACs and identified variants up to 400 times more selective for butyryl‐lysine compared to crotonyl‐lysine. Structural analyses revealed that the enzyme adopts different conformational states depending on the type of acylation of the bound peptide. We used the butyryl‐selective KDAC variant to shift the cellular acylation spectrum towards increased lysine crotonylation. These new enzymes will help in dissecting the roles of different lysine acylations in cell physiology.     

S‐Adamantyl Group Directed Site‐Selective Acylation: Applications in Streamlined Assembly of Oligosaccharides

The site‐selective functionalization of carbohydrates is an active area of research. Reported here is the surprising observation that the sterically encumbered adamantyl group directed site‐selective acylation at the C2 position of S‐glycosides through dispersion interactions between the adamantyl C?H bonds and the π system of the cationic acylated catalyst, which may have broad implications in many other chemical reactions. Because of their stability, chemical orthogonality, and ease of activation for glycosylation, the site‐selective acylation of S‐glycosides streamlines oligosaccharide synthesis and will have wide applications in complex carbohydrate synthesis.     

Arylfluorosulfate‐Based Electrophiles for Covalent Protein Labeling: A New Addition to the Arsenal

Selective covalent modification of a targeted protein is a powerful tool in chemical biology and drug discovery, with applications ranging from identification and characterization of proteins and their functions to the development of targeted covalent inhibitors. Most covalent ligands contain an affinity motif and an electrophilic warhead that reacts with a nucleophilic residue of the targeted protein. Because the electrophilic warhead is prone to react and modify off‐target nucleophiles, its reactivity should be balanced carefully to maximize target selectivity. Arylfluorosulfates have recently emerged as latent electrophiles for selective labeling of context‐specific tyrosine and lysine residues in protein pockets. Here, we review the recent but intense introduction of arylfluorosulfates into the arsenal of available warheads for selective covalent modification of proteins. We highlight the untapped potential of this functional group for use in chemical biology and drug discovery.     

Chemical Biology Approaches for Investigating the Functions of Lysine Acetyltransferases

The side‐chain acetylation of lysine residues in histones and non‐histone proteins catalyzed by lysine acetyltransferases (KATs) represents a widespread posttranslational modification (PTM) in the eukaryotic cells. Lysine acetylation plays regulatory roles in major cellular pathways inside and outside the nucleus. In particular, KAT‐mediated histone acetylation has an effect on all DNA‐templated epigenetic processes. Aberrant expression and activation of KATs are commonly observed in human diseases, especially cancer. In recent years, the study of KAT functions in biology and disease has greatly benefited from chemical biology tools and strategies. In this Review, we present the past and current accomplishments in the design of chemical biology approaches for the interrogation of KAT activity and function. These methods and probes are classified according to their mechanisms of action and respective applications, with both strengths and limitations discussed.     

A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants

The core histones, H2A, H2B, H3 and H4, undergo post‐translational modifications (PTMs) including lysine acetylation, methylation and ubiquitylation, arginine methylation and serine phosphorylation. Lysine residues may be mono‐, di‐ and trimethylated, the latter resulting in an addition of mass to the protein that differs from acetylation by only 0.03639 Da, but that can be distinguished either on high‐performance mass spectrometers with sufficient mass accuracy and mass resolution or via retention times. Here we describe the use of chemical derivatization to quantify methylated and acetylated histone isoforms by forming deuteroacetylated histone derivatives prior to tryptic digestion and bottom‐up liquid chromatography‐mass spectrometric analysis. The deuteroacetylation of unmodified or mono‐methylated lysine residues produces a chemically identical set of tryptic peptides when comparing the unmodified and modified versions of a protein, making it possible to directly quantify lysine acetylation. In this work, the deuteroacetylation technique is used to examine a single histone H3 peptide with methyl and acetyl modifications at different lysine residues and to quantify the relative abundance of each modification in different deacetylase and methylase knockout yeast strains. This application demonstrates the use of the deuteroacetylation technique to characterize modification ‘cross‐talk’ by correlating different PTMs on the same histone tail. Copyright © 2013 John Wiley & Sons, Ltd.     

A Silyliumylidene Cation Stabilized by an Amidinate Ligand and 4‐Dimethylaminopyridine

The synthesis and reactivity of a silyliumylidene cation stabilized by an amidinate ligand and 4‐dimethylaminopyridine (DMAP) are described. The reaction of the amidinate silicon(I) dimer [ L Si:]₂ ( 1 ; L =PhC(NtBu)₂) with one equivalent of N‐trimethylsilyl‐4‐dimethylaminopyridinium triflate [4‐NMe₂C₅H₄NSiMe₃]OTf and two equivalents of DMAP in THF afforded [ L Si(DMAP)]OTf ( 2 ). The ambiphilic character of 2 is demonstrated from its reactivity. Treatment of 2 with 1 in THF afforded the disilylenylsilylium triflate [ L′ ₂( L )Si]OTf ( 3 ; L′ = L Si:) with the displacement of DMAP. The reaction of 2 with [K{HB(iBu)₃}] and elemental sulfur in THF afforded the silylsilylene [ L SiSi(H){(NtBu)₂C(H)Ph}] ( 4 ) and the base‐stabilized silanethionium triflate [ L Si(S)DMAP]OTf ( 5 ), respectively. Compounds 2 , 3 , and 5 have been characterized by X‐ray crystallography.     

Rhodium‐Catalyzed Stereoselective Amination of Thioethers with N‐Mesyloxycarbamates: DMAP and Bis(DMAP)CH2Cl2 as Key Additives

A stereoselective Rh‐catalyzed intermolecular amination of thioethers using a readily available chiral N‐mesyloxycarbamate to produce sulfilimines in excellent yields and diastereomeric ratio is described. A catalytic mixture of 4‐dimethylaminopyridine (DMAP) and bis(DMAP)CH₂Cl₂ proved pivotal in achieving high selectivity. The X‐ray crystal structure of the (DMAP)₂?[Rh₂{(S)‐nttl}₄] complex was obtained and mechanistic studies suggested a Rh^II‐Rh^III complex as the catalytically active species.     

Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos

Lysine acetylation is an important post‐translational modification (PTM). Since the development of MS‐based proteomics technology, important roles of lysine acetylation beyond histones have focused on chromatin remodeling during the cell cycle and regulation of nuclear transport, metabolism, and translation. Zebrafish (Danio rerio) is a widely used vertebrate model in genetics and biologic studies. Although studies in several mammalian species have been performed, the mechanism of lysine acetylation in D. rerio embryos is incompletely understood. Here, we investigated the global acetylome in D. rerio embryos by using an MS‐based proteomics approach. We identified 351 acetylated peptides and 377 nonredundant acetylation sites on 189 lysine‐acetylated proteins in 5‐day postfertilization (hpf) embryos of D. rerio. Among lysine‐acetylated peptides, 40.2% indicated three motifs: (ac)KxxxK, (ac)KxxxxK, and Lx(ac)K. Of 190 acetylated proteins, 81 (42.6%) were mainly distributed in the cytoplasm. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that lysine acetylation in D. rerio was enriched in metabolic pathways. Additionally, 17 of 30 acetylated ribosomal proteins were evolutionarily conserved between zebrafish and humans. Our results indicate that acetyllysine might have regulatory effects on ribosomal proteins involved in protein biosynthesis.     

Selective Halogenation Using an Aniline Catalyst

Electrophilic halogenation is used to produce a wide variety of halogenated compounds. Previously reported methods have been developed mainly using a reagent‐based approach. Unfortunately, a suitable “catalytic” process for halogen transfer reactions has yet to be achieved. In this study, arylamines have been found to generate an N‐halo arylamine intermediate, which acts as a highly reactive but selective catalytic electrophilic halogen source. A wide variety of heteroaromatic and aromatic compounds are halogenated using commercially available N‐halosuccinimides, for example, NCS, NBS, and NIS, with good to excellent yields and with very high selectivity. In the case of unactivated double bonds, allylic chlorides are obtained under chlorination conditions, whereas bromocyclization occurs for polyolefin. The reactivity of the catalyst can be tuned by varying the electronic properties of the arene moiety of catalyst.     

Functionality,Effectiveness, and Mechanistic Evaluation of a Multicatalyst‐Promoted Reaction Sequence by Electrospray Ionization Mass Spectrometry

A multicatalytic three‐step reaction consisting of epoxidation, hydrolysis, and enantioselective monoacylation of cyclohexene was studied by using mass spectrometry (MS). The reaction sequence was carried out in a one‐pot reaction using a multicatalyst. All reaction steps were thoroughly analyzed by electrospray ionization (ESI) MS (and MS/MS), as well as high‐resolution MS for structure elucidation. These studies allow us to shed light on the individual mode of action of each catalytic moiety. Thus, we find that under the epoxidation conditions, the catalytically active N‐methyl imidazole for the terminal acylation step is partially deactivated through oxidation. This observation helps to explain the lower efficiency of the catalyst in the last step compared to the monoacylation performed separately. All reactive intermediates and products of the reaction sequence, as well as of the side‐reactions, were monitored, and we present a working mechanism of the reaction.     

Mechanochromism,Twisted/Folded Structure Determination,and Derivatization of (N‐Phenylfluorenylidene)acridane

(N‐Phenylfluorenylidene)acridane (Ph‐FA) compounds with electron‐withdrawing and ‐donating substituents (H, MeO, Ph, NO₂, Br, F) at the para position of the phenyl group were successfully synthesized by Barton–Kellogg reactions of N‐aryl thioacridones and diazofluorene. By using the substituent on the nitrogen atom to alter the electronic properties, both the folded and twisted conformers of p‐NO₂‐C₆H₄‐FA could be crystallographically characterized, which enabled the charge transfer from the electron‐donating acridane moiety to the electron‐accepting fluorenylidene moiety to be understood. Ground‐state mechanochromism, thermochromism, vapochromism, and proton‐induced chromism were demonstrated between the folded and twisted conformations of the conformers. Protonation and chemical oxidation of Ph‐FA gave two stable acridinium compounds, namely, the fluorenylacridinium and acridinium radical cations. The present study will contribute to the development of functional dyes and organic semiconductors.     

Mechanochromism,Twisted/Folded Structure Determination,and Derivatization of (N‐Phenylfluorenylidene)acridane

(N‐Phenylfluorenylidene)acridane (Ph‐FA) compounds with electron‐withdrawing and ‐donating substituents (H, MeO, Ph, NO₂, Br, F) at the para position of the phenyl group were successfully synthesized by Barton–Kellogg reactions of N‐aryl thioacridones and diazofluorene. By using the substituent on the nitrogen atom to alter the electronic properties, both the folded and twisted conformers of p‐NO₂‐C₆H₄‐FA could be crystallographically characterized, which enabled the charge transfer from the electron‐donating acridane moiety to the electron‐accepting fluorenylidene moiety to be understood. Ground‐state mechanochromism, thermochromism, vapochromism, and proton‐induced chromism were demonstrated between the folded and twisted conformations of the conformers. Protonation and chemical oxidation of Ph‐FA gave two stable acridinium compounds, namely, the fluorenylacridinium and acridinium radical cations. The present study will contribute to the development of functional dyes and organic semiconductors.