Two-Step Bioorthogonal Activity-Based Protein Profiling of Individual Human Proteasome Catalytic Sites

Bioorthogonal chemistry allows the selective modification of biomolecules in complex biological samples. One application of this methodology is in two-step activity-based protein profiling (ABPP), a methodology that is particularly attractive where direct ABPP using fluorescent or biotinylated probes is ineffective. Herein we describe a set of norbornene-modified, mechanism-based proteasome inhibitors aimed to be selective for each of the six catalytic sites of human constitutive proteasomes and immunoproteasomes. The probes developed for β1i, β2i, β5c, and β5i proved to be useful two-step ABPs that effectively label their developed proteasome subunits in both Raji cell extracts and living Raji cells through inverse-electron-demand Diels–Alder (iEDDA) ligation. The compound developed for β1c proved incapable of penetrating the cell membrane, but effectively labels β1c in vitro. The compound developed for β2c proved not selective, but its azide-containing analogue LU-002c proved effective in labeling of β2c via azide–alkyne click ligation chemistry both in vitro and in situ. In total, our results contribute to the growing list of proteasome activity tools to include five subunit-selective activity-based proteasome probes, four of which report on proteasome activities in living cells.     

Two‐Step Protein Labeling by Using Lipoic Acid Ligase with Norbornene Substrates and Subsequent Inverse‐Electron Demand Diels–Alder Reaction

Inverse‐electron‐demand Diels–Alder cycloaddition (DA_inv) between strained alkenes and tetrazines is a highly bio‐orthogonal reaction that has been applied in the specific labeling of biomolecules. In this work we present a two‐step labeling protocol for the site‐specific labeling of proteins based on attachment of a highly stable norbornene derivative to a specific peptide sequence by using a mutant of the enzyme lipoic acid ligase A (LplA^W37V), followed by the covalent attachment of tetrazine‐modified fluorophores to the norbornene moiety through the bio‐orthogonal DA_inv . We investigated 15 different norbornene derivatives for their selective enzymatic attachment to a 13‐residue lipoic acid acceptor peptide (LAP) by using a standardized HPLC protocol. Finally, we used this two‐step labeling strategy to label proteins in cell lysates in a site‐specific manner and performed cell‐surface labeling on living cells.     

Protein Spin Labeling with a Photocaged Nitroxide Using Diels–Alder Chemistry

EPR spectroscopy of diamagnetic bio-macromolecules is based on site-directed spin labeling (SDSL). Herein, a novel labeling strategy for proteins is presented. A nitroxide-based spin label has been developed and synthesized that can be ligated to proteins by an inverse-electron-demand Diels–Alder (DA_inv) cycloaddition to genetically encoded noncanonical amino acids. The nitroxide moiety is shielded by a photoremovable protecting group with an attached tetra(ethylene glycol) unit to achieve water solubility. SDSL is demonstrated on two model proteins with the photoactivatable nitroxide for DA_inv reaction (PaNDA) label. The strategy features high reaction rates, combined with high selectivity, and the possibility to deprotect the nitroxide in Escherichia coli lysate.     

Diels–Alder reaction in water for the straightforward preparation of thermoresponsive hydrogels

Because the properties and applications of hydrogels are determined by the formation principle and conditions of the hydrogels, novel methods for preparing hydrogels have increasingly triggered scientists' interest. Here the Diels–Alder reaction was applied to the preparation of hydrogels. For the resultant polymeric diene and dienophile, the Diels–Alder reaction could be performed in water. The gelation time was found to be closely related to the temperature. The gelation time decreased with the temperature increasing. Moreover, the hydrogels were stable in water, and the retro‐Diels–Alder reaction could be performed in N,N‐dimethylformamide easily. A study of the swelling ratio indicated that the hydrogels were responsive to the temperature. The hydrogel formation method described here provides several advantages, such as mild reaction conditions, no initiator or catalyst, a tunable gelation rate, and thermal reversibility, and it has great potential for the preparation of biomaterials. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011     

Free‐radical copolymerization of [(4‐isopropyl phenyl) oxycarbonyl] methyl methacrylate with acrylonitrile and methyl methacrylate

The present investigation has been achieved in accordance with the Diels–Alder reaction (1,4 cycloaddition) to produce a new halogenated bicyclic adduct. ortho‐Bromoallylbenzoate is a new dienophile that was prepared in a pure form, and its structure was confirmed. The Diels–Alder syntheses of hexachlorocyclopentadiene and the new dienophile were studied to determine the optimum condensation reaction conditions under a temperature range of 90–160°C, reaction times of 1–8 h, and molar diene/dienophile ratios from 1:1 to 5:1 as a consequence. The optimum conditions reached were a temperature of 140°C, an initial diene/dienophile molar ratio of 3:1, and a duration time of 6 h. The maximum stoichometric yield under these optimum conditions (82.5%) was obtained. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 2331–2338, 2003     

Diastereo‐ and Enantioselective Synthesis of trans‐2,3‐Disubstituted 2,3‐Dihydropyran‐4‐one Derivatives

trans‐Diastereoselective hetero‐Diels–Alder reactions took place in the presence of SiCl₄/activator systems. The reactions of aldehydes with a derivative of Danishefsky’s diene afforded the corresponding pyrones with high yields and diastereoselectivity upon activating SiCl₄ with suitable neutral Lewis bases. Aldol intermediates deriving from a Mukaiyama‐type pathway were isolated in many cases. The employment of a chiral activator allowed us to convert Danishefsky’s diene (or its disubstituted derivative) into both aldols and pyrones in good to high enantiomeric excesses.     

Coordination‐Assisted Bioorthogonal Chemistry: Orthogonal Tetrazine Ligation with Vinylboronic Acid and a Strained Alkene

Bioorthogonal chemistry can be used for the selective modification of biomolecules without interfering with any other functionality that might be present. Recent developments in the field include orthogonal bioorthogonal reactions to modify multiple biomolecules simultaneously. During our research, we observed that the reaction rates for the bioorthogonal inverse‐electron‐demand Diels–Alder (iEDDA) reactions between nonstrained vinylboronic acids (VBAs) and dipyridyl‐s‐tetrazines were exceptionally higher than those between VBAs and tetrazines bearing a methyl or phenyl substituent. As VBAs are mild Lewis acids, we hypothesised that coordination of the pyridyl nitrogen atom to the boronic acid promoted tetrazine ligation. Herein, we explore the molecular basis and scope of VBA–tetrazine ligation in more detail and benefit from its unique reactivity in the simultaneous orthogonal tetrazine labelling of two proteins modified with VBA and norbornene, a widely used strained alkene. We further show that the two orthogonal iEDDA reactions can be performed in living cells by labelling the proteasome by using a nonselective probe equipped with a VBA and a subunit‐selective VBA bearing a norbornene moiety.     

Cyclopentadiene‐functionalized polyketone as self‐cross‐linking thermo‐reversible thermoset with increased softening temperature

Self‐cross‐linkable thermo‐reversible thermosets were obtained by a two‐steps post‐functionalization of aliphatic alternating polyketones yielding two different cyclopentadiene functionalization degree of 9 and 22% (with the respect of initial 1,4‐dicarbonyl units). Thermo‐reversibility was verified by gelation experiments and differential scanning calorimetry (DSC) scans displayed a broad transition varying from 75–100°C till 160°C that can be related to retro‐Diels Alder de‐bonding of the dicyclopentadienyl moieties. The dynamic mechanical thermal (DMTA) analysis showed the complete thermo‐mechanical recovery of the material up to six thermal cycles with a softening temperature around 210°C, thereby ensuring a suitable application window for high‐temperature resistant thermosets. Independently of the exact mechanism at the molecular level and in addition to previous studies which used the same Diels‐Alder diene‐dienophile system, it must be noticed that all prepared materials retained their mechanical behavior during at least six consecutive thermal cycles, thus indicating the re‐workability of the system. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 133, 42924.     

1,2,3,4‐Tetrachloro‐5,5‐dimethoxy‐cyclopenta‐1,3‐diene: Diels Alder Reactions and Applications of the Products Formed

Readily available 1,2,3,4‐tetrachloro‐5,5‐dimethoxy‐ cyclopenta‐1,3‐diene ( 2 ) is an excellent cyclic diene for Diels—Alder reaction with a vast variety of dienophiles. The products so formed (norbornene derivatives) constitute important building blocks for the synthesis of diverse complex natural as well as non‐natural products. Apart from very high endo selectivity associated with Diels—Alder reactions, there are several other fascinating features associated with these bicyclic products which make them convenient entities in the synthesis of complex molecules. The most important is the rigid framework that act as a powerful template to provide high degree of selectivity and directional nature to various substituents. The proposed article is intended to focus on Diels‐Alder reactions of 2 and the applications of norbornene derivatives in organic synthesis.     

Irreversible Protein Labeling by Paal–Knorr Conjugation

The application of new chemical reactions in a biological context has advanced bioconjugation methods for both fundamental research and commercial arenas. Recent adaptations of reactions such as Huisgen 1,3‐dipolar or Diels–Alder cycloadditions have enabled the labeling of specific residues in biomolecules by the attachment of molecules carrying azides, alkynes, or strained alkenes. Although these are fundamental tools, there is a need for the discovery of reactions that can label native proteins. We report herein the adaptation of the Paal–Knorr reaction to label lysine residues in proteins via pyrrole linkages.     

Synthesis of a Tetrasubstituted Cyclohexene from a Bicyclo[2.2.2]octa‐2,5‐diene

A palladium‐catalyzed cross‐coupling reaction between the arylstannane 5c and the bicyclic vinyl bromide 3 , which was obtained by a Diels—Alder reaction, provided the substituted bicyclo[2.2.2]octa‐2,5‐diene 6 . A subsequent ozonolysis of the less substituted double bond of 6 followed by reduction of the intermediate with sodium borohydride provided the highly functionalized cyclohexene 8 . This compound can be viewed as a substructure of the antitumor antibiotic dynemicin A.     

Synthesis and polymerization of anthracene‐based itaconimides

Two new anthracene‐based itaconimides, ie N‐(1‐ and 2‐anthryl) itaconimides, were synthesized by the reaction of aromatic amines with itaconic anhydride, followed by itaconamic acid imidization. The same reaction failed in the case of anthracene‐ring substitution at the position 9′. Radical and thermal polymerization of N‐(1‐ and 2‐anthryl) itaconimides led to polymers with anthracene pendant groups. No self‐polymerization by Diels–Alder cycloaddition of the itaconic function (dienophile) and anthracene nucleus (diene) was observed, as is the case for N‐(anthryl) maleimides and citraconimides. Copyright © 2004 Society of Chemical Industry     

Polyurethane adhesives containing Diels–Alder‐based thermoreversible bonds

A facile two‐step process is developed to obtain polyester urethanes that contain various concentrations of thermoreversible Diels–Alder adduct–based bonds for the development of adhesives. Besides linear systems thermoreversible networks have been included in the study. The reactions are verified using IR‐spectroscopy and gel permeation chromatography analysis. The material properties are characterized with solvent exposure tests, dynamic scanning calorimetry, microindentation and rheology and the potential for application as adhesives is tested with an elcometer. Material properties have been found highly tunable for the system, and high adhesive strengths (off‐scale) are found for polyester urethanes that are doped with an intermediate level Diels–Alder functional groups. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134, 44972.     

Retro‐Diels–Alder Reactions of Masked Cyclopentadienones Catalyzed by Heterogeneous Brønsted Acids

The zeolite H‐Beta catalyzes the retro‐Diels–Alder reaction of a range of cyclopentadiene cyclo‐adducts at moderate temperatures and ambient pressure, in the presence of an active dienophile. The active catalyst was identified and optimum reaction conditions established after screening a range of zeolites in the retro‐Diels–Alder reaction of the cyclopentadiene adduct of cyclopentenone. Our results suggest that retro‐Diels–Alder reactions of tricyclodecadienones are catalyzed by Brønsted acids and the high catalytic performance of H‐Beta catalysts can be ascribed to the optimal balance between the number of acid sites and their strength as well as to the accessibility of these sites. The methodology was then applied to a series of alkyl derivatives of cyclopentadienylcyclopentenones to provide a viable alternative synthetic route to 4‐alkylcyclopentenones and the versatility of the approach was demonstrated by the successful cycloreversion of N‐cyclohexyl‐2‐azanorborn‐5‐ene.     

Reversibly crosslinked self‐healing PCL‐based networks

Poly(ε‐caprolactone) (PCL)‐based thermoreversible networks with self‐healing properties were prepared through Diels–Alder (DA) and retro‐DA reactions. Bis‐ or Tris‐maleimide compounds and a series of copolymer(caprolactone‐diene) PCL_XF_Y (X: degree of polymerization and Y: furan‐average functionality) with Y between 2.4 and 4.9 were used. The successive sequences of formation and dissociation of polycaprolactone networks via DA and retro‐DA reactions were observed repeatedly by dynamic mechanical analyses (DMA) and their gel‐temperatures determined. The cross‐linking densities, thermal properties, and thermal reversibility of the PCL_XF_Y/multimaleimide polymers have been modulated by the structure and functionalities of the used diene and dienophile moieties. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013     

Click‐Chemistry‐Mediated Rapid Microbubble Capture for Acute Thrombus Ultrasound Molecular Imaging

Bioorthogonal coupling chemistry has been studied as a potentially advantageous approach for molecular imaging because it offers rapid, efficient, and strong binding, which might also benefit stability, production, and chemical conjugation. The inverse‐electron‐demand Diels–Alder reaction between a 1,2,4,5‐tetrazine and trans‐cyclooctene (TCO) is an example of a highly selective and rapid bioorthogonal coupling reaction that has been used successfully to prepare targeted molecular imaging probes. Here we report a fast, reliable, and highly sensitive approach, based on a two‐step pretargeting bioorthogonal approach, to achieving activated‐platelet‐specific CD62p‐targeted thrombus ultrasound molecular imaging. Tetrazine‐modified microbubbles (tetra‐MBs) could be uniquely and rapidly captured by subsequent click chemistry of thrombus tagged with a trans‐cyclooctene‐pretreated CD62p antibody. Moreover, such tetra‐MBs showed great long‐term stability under physiological conditions, thus offering the ability to monitor thrombus changes in real time. We demonstrated for the first time that a bioorthogonal targeting molecular ultrasound imaging strategy based on tetra‐MBs could be a simple but powerful tool for rapid diagnosis of acute thrombosis.     

No Evidence Found for Diels–Alder Reaction Products in Soybean Oil Oxidized at the Frying Temperature by NMR Study

It has been generally accepted that the Diels–Alder reaction mechanism is one of the major reaction mechanisms to produce dimers and polymers during heating process of vegetable oil. Soybean oil oxidized at 180 °C for 24 h with 1.45 surface area-to-volume ratio showed 36 % polymer peak area in gel permeation chromatogram. However, the NMR DEPT (Distortionless Enhancement by Polarization Transfer) 135 spectrum did not show any signals of possible Diels–Alder products. A fraction separated from the oxidized soybean oil by column chromatography contained 98 % polymers, but again, showed no signals of proposed Diels–Alder products in the DEPT 135 spectrum. Methyl oleate and triolein without a diene required for the Diels–Alder reaction produced 27 and 63 % of total polymers, respectively, under the same condition. This indicates that the polymers must be produced by reactions other than the Diels–Alder reaction for these oils. This study shows that the Diels–Alder reaction is not the major reaction to produce polymers during oxidation of soybean oil, within the DEPT 135 spectroscopy sensitivity level, about 5 mol %.     

1,2,4‐Triazine‐Modified 2′‐Deoxyuridine Triphosphate for Efficient Bioorthogonal Fluorescent Labeling of DNA

In order to establish the Diels–Alder reaction with inverse electron demand for postsynthetic DNA modification, a 1,2,4‐triazine‐modified 2′‐deoxyuridine triphosphate was synthesized. The bioorthogonally reactive 1,2,4‐triazine group was attached at the 5‐position of 2′‐deoxyuridine by a flexible alkyl linker to facilitate its acceptance by DNA polymerases. The screening of four DNA polymerases showed successful primer extensions, using a mixture of dATP, dGTP, dCTP, and the modified 2′‐deoxyuridine triphosphate, by using KOD XL or Vent polymerase. The triazine moiety was stable under the conditions of primer extension, which was evidenced by labeling with a BCN‐modified rhodamine at room temperature in yields of up to 82 %. Two or three modified bases could be incorporated in quantitative yields when the modification sites were separated by three base pairs. These results establish the 1,2,4‐triazene group as a bioorthogonally reactive moiety in DNA, thereby replacing the problematic 1,2,4,5‐tetrazine for postsynthetic labeling by the Diels–Alder reaction with inverse electron demand.     

Polyimides containing s‐triazine rings

A series of new polyimides containing s‐triazine rings have been synthesized via Diels–Alder intermolecular polymerization of 2,6‐bis(2‐furanylmethylimino)‐4‐isopropoxy‐1,3,5‐triazine with various bis(maleimide)s. All the poly(imino‐s‐triazine imide)s were characterized by elemental analyses, FTIR spectral studies, number average molecular weight ( M _n) by non‐aqueous conductometric titration and thermogravimetry. Glass‐fibre reinforced composites were prepared via an in situ Diels–Alder intermolecular reaction between 2,6‐bis(2‐furanylmethylimino)‐4‐isopropoxy‐1,3,5‐triazine and various bis(maleimide)s. The composites were characterized for chemical resistivity and mechanical properties. © 2003 Society of Chemical Industry     

Diels–Alder‐based crosslinked self‐healing polyurethane/urea from polymeric methylene diphenyl diisocyanate

Crosslinked self‐healing polyurethane/urea based on a Diels–Alder reaction (C‐PMPU–DA) was synthesized from a multiple‐furan monomer and a commercial bismaleimide. The multiple‐furan monomer (PMPU–furan) was obtained from a functionalized prepolymer (polymeric MDI: PBA‐2000 = 2:1) by furfuryl amine. The structures of both the PMPU–furan and C‐PMPU–DA were characterized by attenuated total reflectance (ATR)–Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry, thermogravimetric analysis, and ¹H‐NMR. The Diels–Alder bonds enabled C‐PMPU–DA thermal reversibility, which was investigated by ATR–FTIR spectroscopy, ¹H‐NMR, gel–solution–gel experiments, and viscosity tests. Meanwhile, the self‐healing properties of C‐PMPU–DA were also investigated by the recovery of the mechanical properties. The results showed that C‐PMPU–DA exhibited good thermal reversibility and self‐healing properties. C‐PMPU–DA exhibited thermosetting properties at room temperature, although it exhibited thermoplastic properties at higher temperatures and may find applications in self‐healing materials, recyclable materials, or removable materials. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 40234.