An E1‐Catalyzed Chemoenzymatic Strategy to Isopeptide‐N‐Ethylated Deubiquitylase‐Resistant Ubiquitin Probes

Triazole‐based deubiquitylase (DUB)‐resistant ubiquitin (Ub) probes have recently emerged as effective tools for the discovery of Ub chain‐specific interactors in proteomic studies, but their structural diversity is limited. A new family of DUB‐resistant Ub probes is reported based on isopeptide‐N‐ethylated dimeric or polymeric Ub chains, which can be efficiently prepared by a one‐pot, ubiquitin‐activating enzyme (E1)‐catalyzed condensation reaction of recombinant Ub precursors to give various homotypic and even branched Ub probes at multi‐milligram scale. Proteomic studies using label‐free quantitative (LFQ) MS indicated that the isopeptide‐N‐ethylated Ub probes may complement the triazole‐based probes in the study of Ub interactome. Our study highlights the utility of modern protein synthetic chemistry to develop structurally and new families of tool molecules needed for proteomic studies.     

Synthetic studies on chemotherapeutics. II. Synthesis of phenyl-substituted 1,4-dihydro-4-oxonicotinic acid derivatives. [Studies on the syntheses of heterocyclic compounds. Part 704]

The thermal cyclization of the arninomethylenemalonates (8) gave the 4-hydroxynicotinates ( 9 ), ethylation of which yieldedN-ethylated ( 11 ) and O-ethylated products ( 12 ). Hydrolysis of 9, 11 , and 12 led to the desired nicotinic acids (10, 4, and 13), respectively.     

Sulfonylation of 1,4-Diazabicyclo[2.2.2]octane: Charge-Transfer Complex Triggered C−N Bond Cleavage

A novel charge-transfer complex triggered sulfonylation of 1,4-diazabicyclo[2.2.2]octane (DABCO) with mild reaction conditions has been developed. The formation of a charge-transfer complex between electron-withdrawing (hetero)aryl sulfonyl chloride and DABCO allows the synthesis of N-ethylated piperazine sulfonamide in good yields. The reaction has a high functional group tolerance. Spectroscopic studies confirmed the charge-transfer complex formation between sulfonyl chlorides and DABCO, which facilitates the C−N bond cleavage of DABCO.     

Ion Mobility-Mass Spectrometry Study of Folded Ubiquitin Conformers Induced By Treatment with <Emphasis Type="Italic">cis</Emphasis>-[Pd(en)(H<Subscript>2</Subscript>O)<Subscript>2</Subscript>]<Superscript>2+</Superscript>

Ion mobility-mass spectrometry is used to study the new conformers of bovine ubiquitin (Ub) and the palladium(II) binding sites after the incubation with cis-[Pd(en)(H₂O)₂]²⁺ where en = ethylenediamine. Palladium(II) complexes are potentially useful proteomic reagents because they selectively bind to the side groups of methionine and histidine and hydrolytically cleave the peptide bond. Incubating 1.0 mM solution of Ub with 10.0 molar excess of cis-[Pd(en)(H₂O)₂]²⁺ results with one to four Pd²⁺ or Pd(en)²⁺ being attached to intact Ub and two conformer families at each of the 4+ to 11+ charge states. The 4+ and 5+ species exhibit a compact form, which is also observed in untreated Ub, and a new highly folded conformer. The 6+ to 10+ exhibit an elongated form, also observed in Ub, and a new partially folded conformer. The new conformers are shown to be more stable if they contain at least one Pd²⁺, rather than all Pd(en)²⁺. IM-MS/MS of [UbPd₂en+5H]⁹⁺ shows that both the partially folded and elongated conformers first lose the en ligand, followed by dissociating into product ions that indicate that Met1, Glu51/Asp52, His68, and Glu16 are binding sites for Pd²⁺. These results suggest that Pd²⁺ is simultaneously binding to multiple side groups across different regions of Ub. This type of sequestering of Pd²⁺ probably reduces the efficiency of Pd²⁺ ions to selectively cleave Ub because it prevents Pd²⁺ anchoring to only Met or His and to an adjacent backbone amide nitrogen and forming the “activated complex” necessary for specific peptide bond cleavage.     

Efficient Semi-Synthesis of Atypical Ubiquitin Chains and Ubiquitin-Based Probes Forged by Thioether Isopeptide Bonds

The development of powerful and general methods to acquire ubiquitin (Ub) chains has prompted the deciphering of Ub-mediated processes. Herein, the cysteine-aminoethylation assisted chemical ubiquitination (CAACU) strategy is extended and improved to enable the efficient semi-synthesis of atypical Ub chain analogues and Ub-based probes. Combining the Cys aminoethylation and the auxiliary-mediated protein ligation, several linkage- and length-defined atypical Ub chains including di-Ubs, K27C-linked tri-Ub, K11/K48C-branched tri-Ub, and even the SUMOlated Ub are successfully prepared from recombinantly expressed starting materials at about a 9–20 mg L⁻¹ expression level. In addition, the utility of this strategy is demonstrated with the synthesis of a novel non-hydrolyzable di-Ub PA probe, which may provide a new useful tool for the mechanistic studies of deubiquitinase (DUB) recognition.     

Chemical Synthesis of Diubiquitin‐Based Photoaffinity Probes for Selectively Profiling Ubiquitin‐Binding Proteins

Biochemical studies of cellular processes involving polyubiquitin have gained increasing attention. More tools are needed to identify ubiquitin (Ub)‐binding proteins. We report diazirine‐based photoaffinity probes that can capture Ub‐binding proteins in cell lysates, and show that diazirines are preferable to aryl azides as the photo‐crosslinking group, since they decrease non‐selective capture. Photoaffinity probes containing at least two Ub units were required to effectively capture Ub‐binding proteins. Different capture selectivity was observed for probes containing diubiquitin moieties with different types of linkages, thus indicating the potential to develop linkage‐dependent probes for selectively profiling Ub‐binding proteins under various cellular conditions.     

Polyhydrazides. IV. Preparation and properties of poly-N-ethyl- and isopropylhydrazide oxadiazoles

High molecular weight poly-N-alkylhydrazide-oxadiazoles have been prepared in poly-phosphoric acid by alkylation of poly-1,3,4-oxadiazole which was synthesized from terephthalic acid and hydrazine sulfate. Various kinds of reagents having an alkoxy group were used as alkylating agent, and N-ethylated and N-propylated polyhydrazides containing oxadiazole units were obtained. The thermal properties of the polymers obtained were investigated by using infrared spectroscopy, viscometry, differential thermometric and thermogravimetric techniques. Soluble poly-N-alkylhydrazide-oxadiazole are thermally cyclized to poly-1,3,4-oxadiazole with elimination of olefins and water at 226–330°C for propylated polydrazide and at 240–360°C for ethylated polyhydrazide. For both, weight loss in polyhydrazides occurs in two distinct stages corresponding, respectively, to cyclization and decomposition of the poly-1,3,4-oxadiazole formed in situ.     

Comparing Cyclophellitol N‐Alkyl and N‐Acyl Cyclophellitol Aziridines as Activity‐Based Glycosidase Probes

The synthesis and evaluation as activity‐based probes (ABPs) of three configurationally distinct, fluorescent N‐alkyl cyclophellitol aziridine isosteres for profiling GH1 β‐glucosidase (GBA), GH27 α‐galactosidase (GLA) and GH29 α‐fucosidase (FUCA) is described. In comparison with the corresponding acyl aziridine ABPs reported previously, the alkyl aziridine ABPs are synthesized easily and are more stable in mild acidic and basic media, and are thus easier to handle. The β‐glucose‐configured alkyl aziridine ABP proves equally effective in labeling GBA as its N‐acyl counterpart, whereas the N‐acyl aziridines targeting GLA and FUCA outperform their N‐alkyl counterparts. Alkyl aziridines can therefore be an attractive alternative in retaining glycosidase ABP design, but in targeting a new retaining glycosidase both N‐alkyl and N‐acyl aziridines are best considered at the onset of a new study.     

Synthesis of and Specific Antibody Generation for Glycopeptides with Arginine N‐GlcNAcylation

As a unique and unappreciated protein posttranslational modification, arginine N‐glycosylation was recently discovered to play an important role in the process that bacteria counteract host defenses. To provide chemical tools for further proteomic and biochemical studies on arginine N‐glycosylation, we report the first general strategy for a rapid and cost‐effective synthesis of glycopeptides carrying single or multiple arginine N‐GlcNAcyl groups. These glycopeptides were successfully utilized to generate the first antibodies that can specifically recognize arginine N‐GlcNAcylated peptides or proteins in a sequence‐independent manner.     

Mobility-sensitive fluorescence probes for quantitative monitoring of water sorption and diffusion in polymer coatings

The fluorescent molecular rotor probes 4-tricyanovinyl-[N-(2-hydroxyethyl)-N-ethyl]-aniline, tricyano-4-(dimethylamino) benzylidene, and tricyanovinyljulolidene have been used as extrinsic fluorescence probes for quantitative monitoring of water uptake in polymeric coatings. The presence of water causes plasticization of the polymer, which results in increased local mobility within the film. The nonradiative decay pathways of the rotor probes are increased as local mobility increases, and the resulting decrease in fluorescence intensity of the probes is directly proportional to the amount of water sorbed. Beyond allowing for the characterization of sorbent content, this fluorescence technique can be used to determine the diffusion coefficient of water in a polymer film. The relative change in fluorescence fits well to a Fickian diffusion model, yielding a diffusion coefficient for water of 3 × 10^-8 cm²/s in poly(vinyl acetate), and a value of 6 × 10^-9 cm²/s in a room-temperature cured epoxypolyamide, in excellent agreement with diffusion coefficient values determined from gravimetric analysis. Preliminary studies also demonstrate the utility of molecular rotor probes to monitor water uptake in individual layers of multilayered polymer systems. © 1995 John Wiley & Sons, Inc.     

Ubiquitin Associates with the N‐Terminal Domain of Nerve Growth Factor: The Role of Copper(II) Ions

Many biochemical pathways involving nerve growth factor (NGF), a neurotrophin with copper(II) binding abilities, are regulated by the ubiquitin (Ub) proteasome system. However, whether NGF binds Ub and the role played by copper(II) ions in modulating their interactions have not yet been investigated. Herein NMR spectroscopy, circular dichroism, ESI‐MS, and titration calorimetry are employed to characterize the interactions of NGF with Ub. NGF_1–14, which is a short model peptide encompassing the first 14 N‐terminal residues of NGF, binds the copper‐binding regions of Ub (K_D=8.6 10^?5 m ). Moreover, the peptide undergoes a random coil–polyproline type II helix structural conversion upon binding to Ub. Notably, copper(II) ions inhibit NGF_1–14/Ub interactions. Further experiments performed with the full‐length NGF confirmed the existence of a copper(II)‐dependent association between Ub and NGF and indicated that the N‐terminal domain of NGF was a valuable paradigm that recapitulated many traits of the full‐length protein.     

N-terminal Cyclization of Peptides in Large-scale Protein Identification Based on Biological Mass Spectrometry

Biological mass spectrometry has been developed for the large-scale protein identification. The successful identification of protein in proteomic study is based on an effective match of MS data to the sequence in database. At times, because of the diversity and heterogeneity of protein modification, the experimental data obtained by mass spectrometry does not match the theoretical value; hence, approximately 90 percent or more of the tandem mass spectra cannot be identified effectively. This has become one of the most important technique issues to be resolved in current proteome research. The N-terminal cyclization of peptides, as one of a variety of modification introduced in sample preparation, has been preliminarily studied in this work. The result showed that N-terminal cyclization occurred in most of the glutamine (Q) or carbamoylmethyl-cysteine (CAM_C) residues, and the reaction is often incomplete or partial; both types of peptides can often exist in its respective state at the same time, and the behavior of modified peptides in reversion phase chromatography is changed. The success rate of protein identification could be obviously improved by the addition of the N-terminal cyclization modification in the database searching. These results will be very helpful in the mass spectrometric data analysis of proteomic study.     

Integration of the 1,2,3‐Triazole “Click” Motif as a Potent Signalling Element in Metal Ion Responsive Fluorescent Probes

In a systematic approach we synthesized a new series of fluorescent probes incorporating donor–acceptor (D‐A) substituted 1,2,3‐triazoles as conjugative π‐linkers between the alkali metal ion receptor N‐phenylaza‐[18]crown‐6 and different fluorophoric groups with different electron‐acceptor properties (4‐naphthalimide, meso‐phenyl‐BODIPY and 9‐anthracene) and investigated their performance in organic and aqueous environments (physiological conditions). In the charge‐transfer (CT) type probes 1 , 2 and 7 , the fluorescence is almost completely quenched by intramolecular CT (ICT) processes involving charge‐separated states. In the presence of Na⁺ and K⁺ ICT is interrupted, which resulted in a lighting‐up of the fluorescence in acetonitrile. Among the investigated fluoroionophores, compound 7 , which contains a 9‐anthracenyl moiety as the electron‐accepting fluorophore, is the only probe which retains light‐up features in water and works as a highly K⁺/Na⁺‐selective probe under simulated physiological conditions. Virtually decoupled BODIPY‐based 6 and photoinduced electron transfer (PET) type probes 3 – 5 , where the 10‐substituted anthracen‐9‐yl fluorophores are connected to the 1,2,3‐triazole through a methylene spacer, show strong ion‐induced fluorescence enhancement in acetonitrile, but not under physiological conditions. Electrochemical studies and theoretical calculations were used to assess and support the underlying mechanisms for the new ICT and PET 1,2,3‐triazole fluoroionophores.     

Probing Conformational Changes of Ubiquitin by Host–Guest Chemistry Using Electrospray Ionization Mass Spectrometry

We report mechanistic studies of structural changes of ubiquitin (Ub) by host–guest chemistry with cucurbit[6]uril (CB[6]) using electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism spectroscopy and molecular dynamics (MD) simulation. CB[6] binds selectively to lysine (Lys) residues of proteins. Low energy collision-induced dissociation (CID) of the protein-CB[6] complex reveals CB[6] binding sites. We previously reported (Anal. Chem. 2011, 83, 7916–7923) shifts in major charge states along with Ub-CB[6] complexes in the ESI-MS spectrum with addition of CB[6] to Ub from water. We also reported that CB[6] is present only at Lys₆ or Lys₁₁ in high charge state (+13) complex. In this study, we provide additional information to explain unique conformational change mechanisms of Ub by host–guest chemistry with CB[6] compared with solvent-driven conformational change of Ub. Additional CID study reveals that CB[6] is bound only to Lys₄₈ and Lys₆₃ in low charge state (+7) complex. MD simulation studies reveal that the high charge state complexes are attributed to the CB[6] bound to Lys₁₁. The complexation prohibits salt bridge formation between Lys₁₁ and Glu₃₄ and induces conformational change of Ub. This results in formation of high charge state complexes in the gas phase. Then, by utilizing stronger host–guest chemistry of CB[6] with pentamethylenediamine, refolding of Ub via detaching CB[6] from the protein is performed. Overall, this study gives an insight into the mechanism of denatured Ub ion formation via host-guest interactions with CB[6]. Furthermore, this provides a direction for designing function-controllable supramolecular system comprising proteins and synthetic host molecules.      

DMAP‐BODIPY Alkynes: A Convenient Tool for Labeling Biomolecules for Bimodal PET–Optical Imaging

Several new boron dipyrromethene/N,N‐dimethylaminopyridine (BODIPY‐DMAP) assemblies were synthesized as precursors for bimodal imaging probes (optical imaging, OI/positron emission tomography, PET). The photophysical properties of the new compounds were also studied. The first proof‐of‐concept was obtained with the preparation of several new BODIPY‐labeled bombesins and evaluation of the affinity for bombesin receptors by using a competition binding assay. Fluorination reactions were investigated on DMAP‐BODIPY precursors as well as on DMAP‐BODIPY‐labeled bombesins. Chemical modifications on the BODIPY core were also performed to obtain luminescent dyes emitting in the therapeutic window (650–900 nm), suitable for in vivo imaging, making these compounds promising precursors for PET/optical dual‐modality imaging agents.     

Pseudo-poly(amino acid)s: study on construction and characterization of novel chiral and thermally stable nanostructured poly(ester-imide)s containing different trimellitylimido-amino acid-based diacids and pyromellitoyl-tyrosine-based diol

A new class of chiral and potentially biodegradable poly(ester-imide)s (PEI)s as pseudo-poly(amino acid)s (PAA)s bearing natural amino acids in the main chain was synthesized. In this investigation, N,N′-(pyromellitoyl)-bis-(L-tyrosine dimethyl ester) as a biodegradable optically active diphenol and synthesized trimellitic anhydride-derived dicarboxylic acids containing different natural amino acids such as S-valine, L-methionine, L-leucine, L-isoleucine, and L-phenylalanine were used for direct polyesterification. With the aim of tosyl chloride/pyridine/N,N′-dimethylformamide system as a condensing agent, the new optically active PEIs were obtained in good yields and moderate inherent viscosity up to 0.42 dL/g. The obtained polymers were characterized with FT-IR, ¹H-NMR, X-ray diffraction (XRD), field emission scanning electron microscopy, elemental, and thermogravimetric analysis techniques. These polymers show high solubility in organic solvents, such as N,N′-dimethyl acetamide, N-methyl-2-pyrrolidone, and sulfuric acid at room temperature, and are insoluble in solvents, such as methylene chloride, cyclohexane, and water. Morphology probes showed these pseudo-poly(amino acid)s were noncrystalline and nanostructured polymers. On the basis of thermogravimetric analysis data, such PAAs are thermally stable and can be classified as self-extinguishing polymers. In addition due to the existence of amino acids in the polymer backbones these pseudo-PAAs not only are optically active but also are expected to be biodegradable and therefore could be classified under eco-friendly polymers.     

Unravelling RNA–Substrate Interactions in a Ribozyme‐Catalysed Reaction Using Fluorescent Turn‐On Probes

The Diels–Alder reaction is one of the most important C?C bond‐forming reactions in organic chemistry, and much effort has been devoted to controlling its enantio‐ and diastereoselectivity. The Diels–Alderase ribozyme (DAse) catalyses the reaction between anthracene dienes and maleimide dienophiles with multiple‐turnover, stereoselectivity, and up to 1100‐fold rate acceleration. Here, a new generation of anthracene‐BODIPY‐based fluorescent probes was developed to monitor catalysis by the DAse. The brightness of these probes increases up to 93‐fold upon reaction with N‐pentylmaleimide (NPM), making these useful tools for investigating the stereochemistry of the ribozyme‐catalysed reaction. With these probes, we observed that the DAse catalyses the reaction with >91 % de and >99 % ee. The stereochemistry of the major product was determined unambiguously by rotating‐frame nuclear Overhauser NMR spectroscopy (ROESY‐NMR) and is in agreement with crystallographic structure information. The pronounced fluorescence change of the probes furthermore allowed a complete kinetic analysis, which revealed an ordered bi uni type reaction mechanism, with the dienophile binding first.     

Design,Preparation and Application of a New π‐Basic Chiral Stationary Phase for the Liquid Chromatographic Separation of Enantiomers

A new reciprocal π‐basic chiral stationary phase (CSP) was designed based on the reciprocity conception of chiral recognition and prepared starting from (S)‐leucine. The CSP thus prepared was applied in resolving various π‐acidic N‐(3,5‐dinitrobenzoyl)‐α‐amino amides and esters and found to be very effective. Especially, N‐(3,5‐dinitrobenzoyl)‐α‐amino N,N‐dialkyl amides were resolved very well on the new reciprocal CSP. From the chromatographic resolution results and based on the reciprocity conception of chiral recognition with the aid of Corey/Pauling/Koltan (CPK) molecular model studies, a chiral recognition mechanism which utilizes π‐π interaction and simultaneously two hydrogen bonding interactions between the CSP and the analyte has been proposed. The CSP prepared in this study was also successful in resolving 3,5‐dinitrophenylcarbamate derivatives of 2‐hydroxycarboxylic acid esters.     

Characterization of Crystalline Complexes between Heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin and Various Alkanes or Alkenes (5 ≤ C ≤ 10)°

Crystallization, at room temperature under normal pressure, of heptakis (2,3,6-tri-O-methyl)--cyclodextrin (TRIMEB) in the presence of various hydrocarbons (n-pentane, n-hexane, cyclohexane, methylcyclohexane, (RS)--pinene, (S)--pinene and (R)--pinene) gave two series of isomorphous crystalline phases: Ua (metastable) and Ub (stable). In this study, the molar guest/host ratio is defined as the variable x. On the one hand, the experiments carried out in solution at high supersaturations led to the Ua phase, with x < 1 for linear alkanes (non-stoichiometric and efflorescent phases) and x = 1 for cyclic guests. On the other hand, by slow evaporation, the Ub phase obtained with cyclic components was stoichiometric (x = 1) and non-efflorescent; whereas the Ub phase with n-pentane and n-hexane as guestsdisplayed efflorescent character and was non-stoichiometric (x approx 0.15). Temperature-resolved X-ray powder diffraction allowed the irreversible transition from Ua to Ub to be observed. Following this thermal process and whatever the nature of the cyclic guest molecule, Ub was non-stoichiometric (x 0.7 for methylcyclohexane); thus, x was significantly lower than that of the mother phase Ua with x = 1. This suggests a destructive-reconstructive solid-solid transition. The crystal structure solved at 120K of Ub obtained from solution, with methylcyclohexane, reveals that the guest molecule is totally buried within the cavity. The methylcyclohexane mean plane, defined by the C(2), C(3), C(5) and C(6) atoms, is 45° away from the pseudo seven-fold axis of the macrocycle. The methylcyclohexane molecule is disordered within the cavity, and its possible conformations were twisted chair and twisted boat.These results differ from the conformations reported by Rontoyianni et al., J. Incl. Phenom. 32, 415–428 (1998) for the structure of the same complex solved at 293K. Molecular simulations of n-alkane (C(5) and C(6)) movements along the a axis showed that the Ub phase structure can easily undergo a partial release of this linear alkane, due to the presence of channels in this structure. Comparison between solid stateconformations observed for the TRIMEB molecule in itscomplexes does not support the notion of `induced fit' inthe inclusion process.     

A Unified Strategy for the Synthesis of Mucin Cores 1–4 Saccharides and the Assembled Multivalent Glycopeptides

By displaying different O‐glycans in a multivalent mode, mucin and mucin‐like glycoproteins are involved in a plethora of protein binding events. The understanding of the roles of the glycans and the identification of potential glycan binding proteins are major challenges. To enable future binding studies of mucin glycan and glycopeptide probes, a method that gives flexible and efficient access to all common mucin core‐glycosylated amino acids was developed. Based on a convergent synthesis strategy starting from a shared early stage intermediate by differentiation in the glycoside acceptor reactivity, a common disaccharide building block allows for the creation of extended glycosylated amino acids carrying the mucin type‐2 cores 1–4 saccharides. Formation of a phenyl‐sulfenyl‐N‐Troc (Troc=trichloroethoxycarbonyl) byproduct during N‐iodosuccinimide‐promoted thioglycoside couplings was further characterized and a new methodology for the removal of the Troc group is described. The obtained glycosylated 9‐fluorenylmethoxycarbonyl (Fmoc)‐protected amino acid building blocks are incorporated into peptides for multivalent glycan display.