Inverse Electron Demand Diels-Alder Reaction Research Articles

DNA Logic Gates for Small Molecule Activation Circuits in Cells.

DNA-based devices such as DNA logic gates self-assemble into supramolecular structures, as dictated by the sequences of the constituent oligonucleotides and their predictable Watson-Crick base pairing interactions. The programmable nature of DNA-based devices permits the design and implementation of DNA circuits that interact in a dynamic and sequential manner capable of spatially arranging disparate DNA species. Here, we report the application of an activatable fluorescence reporter based on a proximity-driven inverse electron demand Diels-Alder (IEDDA) reaction and its robust integration with DNA strand displacement circuits. In response to specific DNA input patterns, sequential strand displacement reactions are initiated and culminate in the hybridization of two modified DNA strands carrying probes capable of undergoing an IEDDA reaction between a vinyl-ether-caged fluorophore and its reactive partner tetrazine, leading to the activation of fluorescence. This approach provides a major advantage for DNA computing in mammalian cells since circuit degradation does not induce fluorescence, in contrast to traditional fluorophore-quencher designs. We demonstrate the robustness and sensitivity of the reporter by testing its ability to serve as a readout for DNA logic circuits of varying complexity inside cells.

Tetrazine cyclized peptides for one-bead-one-compound library: Synthesis and sequencing.

While most FDA-approved peptide drugs are cyclic, robust cyclization chemistry of peptides and the deconvolution of the cyclic peptide sequences using tandem mass spectrometry render cyclic peptide drug discovery difficult. In this chapter, the protocol for the successful synthesis of tetrazine-linked cyclic peptide library in solid phase, which shows both robust cyclization and easy sequence deconvolution, is described. The protocol for the linearization and cleavage of cyclic peptides from the solid phase by simple UV light irradiation, followed by accurate sequencing using tandem mass spectrometry, is described. We describe the troubleshooting for this dithiol bis-arylation reaction and for the successful cleavage of the aryl cyclic peptide into linear form. This method for efficient solid-phase macrocyclization can be used for the rapid production of loop-based peptides and screening for inhibition of protein-protein interactions, by using the covalent inverse electron-demand Diels Alder reaction to supplement the non-covalent interaction between a protein and its peptide binder, isolating highly selective peptides in the process.

Annealing 1,2,4-triazine to iridium(III) complexes induces luminogenic behaviour in bioorthogonal reactions with strained alkynes.

A phenanthroline-type ligand containing an annealed 1,2,4-triazine ring was used to prepare novel Ir(III) complexes 3 and 4. The complexes are non-luminescent but show luminogenic behaviour following the inverse electron demand Diels-Alder (IEDDA) reaction with bicyclononyne (BCN) derivatives. It was observed that the complexes react with BCN-C10 faster than the corresponding free ligands. The magnitude of this accelerating metal-coordination effect, however, is less profound than in previously reported Ir(III) complexes of 1,2,4-triazines, in which the triazine was directly coordinated to the Ir(III) metal centre. Nevertheless, luminogenic behaviour opens prospects for the use of such complexes in bioimaging applications, which was demonstrated by developing a convenient methodology using the "chemistry on the complex" concept for labelling antibodies with luminescent Ir(III) complexes. The bioorthogonal reactivity of complex 4 was demonstrated by metabolically labelling live cells with BCN groups, followed by a luminogenic IEDDA reaction with the triazine iridium complex.

An electrochemical access to 2-amino-2,3-dihydro-1,4-benzodioxanes derived from hydroxytyrosol.

The anodic oxidation of a natural antioxidative catechol, hydroxytyrosol, was developed in an acetonitrile/dimethylsulfoxide (or acetonitrile/water) solvent mixture to produce in a stable way the resulting non-activated o-quinone and generate structural analogues. 2-Amino-2,3-dihydro-1,4-benzodioxane derivatives were obtained as two regioisomers in good to high overall yields (65-90%) and 1 : 3 ratios, through an inverse electron demand Diels-Alder (IEDDA) reaction between the electrogenerated o-quinone and tertiary enamines. The insertion of an electron withdrawing (or electron donating) group on the catechol modified their relative proportions, so that the reaction became regiospecific. With some aliphatic enamines, a competitive 1,6-Michael addition took place, affording 2-hydroxy-1,2,4,5-tetrahydrobenzo[d]oxepine compounds.

Site-selective peptide functionalisation mediated via vinyl-triazine linchpins.

Herein we introduce 3-vinyl-1,2,4-triazines derivatives as dual-reactive linkers that exhibit selectivity towards cysteine and specific strained alkynes, enabling conjugate addition and inverse electron-demand Diels-Alder (IEDDA) reactions. This approach facilitates site-selective bioconjugation of biologically relevant peptides, followed by rapid and highly selective reactions with bicyclononyne (BCN) reagents.

Cascade In Situ Self-Assembly and Bioorthogonal Reaction Enable the Enrichment of Photosensitizers and Carbonic Anhydrase Inhibitors for Pretargeted Cancer Theranostics.

We report here a tumor-pretargted theranostic approach for multimodality imaging-guided synergistic cancer PDT by cascade alkaline phosphatase (ALP)-mediated in situ self-assembly and bioorthogonal inverse electron demand Diels-Alder (IEDDA) reaction. Using the enzymatic catalysis of ALP that continuously catalyses the dephosphorylation and self-assembly of trans-cyclooctene (TCO)-bearing P-FFGd-TCO, a high density of fluorescent and magnetic TCO-containing nanoparticles (FMNPs-TCO) can be synthesized and retained on the membrane of tumor cells. They can act as 'artificial antigens' amenable to concurrently capture lately administrated tetrazine (Tz)-decorated PS (775NP-Tz) and carbonic anhydrase (CA) inhibitor (SA-Tz) via the fast IEDDA reaction. This two-step pretargeting process can further induce FMNPs-TCO regrowth into microparticles (FMNPs-775/SA) directly on tumor cell membranes, which is analyzed by bio-SEM and fluorescence imaging. Thus, efficient enrichment of both SA-Tz and 775NP-Tz in tumors can be achieved, allowing to alleviate hypoxia by continuously inhibiting CA activity and improving PDT of tumors. Findings show that subcutaneous HeLa tumors could be completely eradicated and no tumor recurred after irradiation with an 808 nm laser (0.33 W cm-2 , 10 min). This pretargeted approach may be applied to enrich other therapeutic agents in tumors to improve targeted therapy.

Cascade In Situ Self‐Assembly and Bioorthogonal Reaction Enable the Enrichment of Photosensitizers and Carbonic Anhydrase Inhibitors for Pretargeted Cancer Theranostics

AbstractWe report here a tumor‐pretargted theranostic approach for multimodality imaging‐guided synergistic cancer PDT by cascade alkaline phosphatase (ALP)‐mediated in situ self‐assembly and bioorthogonal inverse electron demand Diels–Alder (IEDDA) reaction. Using the enzymatic catalysis of ALP that continuously catalyses the dephosphorylation and self‐assembly of trans‐cyclooctene (TCO)‐bearing P‐FFGd‐TCO, a high density of fluorescent and magnetic TCO‐containing nanoparticles (FMNPs‐TCO) can be synthesized and retained on the membrane of tumor cells. They can act as ‘artificial antigens’ amenable to concurrently capture lately administrated tetrazine (Tz)‐decorated PS (775NP‐Tz) and carbonic anhydrase (CA) inhibitor (SA‐Tz) via the fast IEDDA reaction. This two‐step pretargeting process can further induce FMNPs‐TCO regrowth into microparticles (FMNPs‐775/SA) directly on tumor cell membranes, which is analyzed by bio‐SEM and fluorescence imaging. Thus, efficient enrichment of both SA‐Tz and 775NP‐Tz in tumors can be achieved, allowing to alleviate hypoxia by continuously inhibiting CA activity and improving PDT of tumors. Findings show that subcutaneous HeLa tumors could be completely eradicated and no tumor recurred after irradiation with an 808 nm laser (0.33 W cm−2, 10 min). This pretargeted approach may be applied to enrich other therapeutic agents in tumors to improve targeted therapy.

Synthesis of Densely Substituted Pyridines through 1,2‐Oxazine‐6‐ones Inverse Electron Demand Diels–Alder Reaction

AbstractDensely substituted pyridines are synthesized from available 1,2‐oxazin‐6‐ones and enamines through tandem hetero‐Diels–Alder and retro‐Diels–Alder reaction in 45–98 % yield.

Bidentate Lewis Acid-Catalyzed Inverse Electron-Demand Diels–Alder Reaction of Phthalazines and Cyclooctynes

AbstractHerein we report a method for facilitating the inverse-electron-demand Diels–Alder reaction of 1,2-diazines and cyclooctynes by utilizing a boron-based bidentate Lewis acid catalyst. Readily available electron-deficient and electron-rich phthalazines proved to be suitable substrates in this transformation. The described method enables the facile construction of diversely substituted polycyclic aromatic hydrocarbons fused to eight-membered carbocycles.

Synthesis and characterization of novel polyurethanes, polypyridazine, and polyamide based on s‐1,2,4,5‐tetrazine

AbstractThe synthesis and analysis of new polymeric materials based on 1,2,4,5‐tetrazine are discussed in this study. Tetrazine was mixed with thermoplastic polyurethane in dimethylformamide (DMF) as solvent and dibutyl tin dilaurate as catalyst at 50°C for 24 h to create brush polyurethane‐urea, which was then reacted with an unsaturated center in dimethyl sulfoxide as solvent at 60°C for 48 h made of either polyenol or thermoplastic polyurethane through π–π interaction. Because 1,2,4,5‐tetrazine (red color) is known to act as an electron‐deficient dine in inverse electron demand Diels–Alder reactions and can be easily converted to pyridazine (peach color) via [4 + 2] cycloaddition with suitable followed by expulsion of molecular nitrogen (cycloreversion), we observed a highly colored red shift to peach and this monitor for this reaction. Additionally, polyamide was prepared via reaction of 3,6‐diamino‐1,2,4,5‐tetrazine with terephthaloyl chloride in DMF as a suitable solvent and triethylamine as basic catalyst at 0°C for 3 h and then 36 h at room temperature. The new polymers that were produced were elucidated by spectral data.

P-040 - Radiosynthesis of [18F]AmBF3-Tyr3-Octreotides with Tetrazine Ligation Based on the Inverse Electron-Demand Diels–Alder Reaction: Rapid, Catalyst-free and Mild Conversion of 1,4-Dihydropyridazines to Pyridazines

P-040 - Radiosynthesis of [18F]AmBF3-Tyr3-Octreotides with Tetrazine Ligation Based on the Inverse Electron-Demand Diels–Alder Reaction: Rapid, Catalyst-free and Mild Conversion of 1,4-Dihydropyridazines to Pyridazines

One-Pot Synthesis of Polycyclic 4,5-Dihydropyridazine-3(2H)-ones by Inverse Electron-Demand Diels-Alder (IEDDA) Reactions from Alkenes.

In the classical Inverse Electron-Demand Diels-Alder (IEDDA) reactions between alkenes and tetrazines, 4,5-dihydropyridazines are formed. 4,5-Dihydropyridazines are rapidly converted to the more energetically stable 1,4-dihydropyridazines by 1,3-prototropic isomerization. In this study, instead of 1,4-dihydropyridazines, 4,5-dihydropyridazine-3(2H)-ones were obtained as a result of IEDDA reactions between tetrazines with leaving groups at the 3,6-positions, and norbornene and barrelene-derived polycyclic alkenes in the presence of moisture in air or solvent. To show that this new method works not only on strained polycyclic alkenes but also on monocyclic and linear alkenes, the corresponding 4,5-dihydropyridazine-3(2H)-ones were obtained in high yields from the reactions performed with styrene and cyclopentene as well. The chemical structures of the polycyclic 4,5-dihydropyridazine-3(2H)-ones were determined by NMR and HRMS analyses. In addition, the exact structures of the polycyclic 4,5-dihydropyridazine-3(2H)-ones were also experimentally proven by converting them to pyridazine-3(2H)-ones known in the literature.

Click Chemistry and Radiochemistry: An Update.

The term "click chemistry" describes a class of organic transformations that were developed to make chemical synthesis simpler and easier, in essence allowing chemists to combine molecular subunits as if they were puzzle pieces. Over the last 25 years, the click chemistry toolbox has swelled from the canonical copper-catalyzed azide-alkyne cycloaddition to encompass an array of ligations, including bioorthogonal variants, such as the strain-promoted azide-alkyne cycloaddition and the inverse electron-demand Diels-Alder reaction. Without question, the rise of click chemistry has impacted all areas of chemical and biological science. Yet the unique traits of radiopharmaceutical chemistry have made it particularly fertile ground for this technology. In this update, we seek to provide a comprehensive guide to recent developments at the intersection of click chemistry and radiopharmaceutical chemistry and to illuminate several exciting trends in the field, including the use of emergent click transformations in radiosynthesis, the clinical translation of novel probes synthesized using click chemistry, and the advent of click-based in vivo pretargeting.

Evaluation of Tetrazine Tracers for Pretargeted Imaging within the Central Nervous System.

The pretargeting approach separates the biological half-life of an antibody from the physical half-life of the radioisotope label, providing a strategy for reducing the radiation burden. A widely explored pretargeting approach makes use of the bioorthogonal click reaction between tetrazines (Tzs) and trans-cyclooctenes (TCOs), combining the targeting specificity of monoclonal antibodies (mAbs) with the rapid clearance and precise reaction of Tzs and TCOs. Such a strategy can allow for the targeting and imaging (e.g., by positron emission tomography (PET)) of molecular markers, which cannot be addressed by solely relying on small molecules. Tz derivatives that undergo inverse electron-demand Diels-Alder (IEDDA) reactions with an antibody bearing TCO moieties have been investigated. This study describes the synthesis and characterization of 11 cold Tz imaging agent candidates. These molecules have the potential to be radiolabeled with 18F or 3H, and with the former label, they could be of use as imaging tracers for positron emission tomography studies. Selection was made using a multiparameter optimization score for the central nervous system (CNS) PET tracers. Novel tetrazines were tested for their pH-dependent chemical stability. Those which turned out to be stable in a pH range of 6.5-8 were further characterized in in vitro assays with regard to their passive permeability, microsomal stability, and P-glycoprotein transport. Furthermore, selected Tzs were examined for their systemic clearance and CNS penetration in a single-dose pharmacokinetic study in rats. Two tetrazines were successfully labeled with 18F, one of which showed brain penetration in a biodistribution study in mice. Another Tz was successfully tritium-labeled and used to demonstrate a bioorthogonal click reaction on a TCO-modified antibody. As a result, we identified one Tz as a potential fluorine-18-labeled CNS-PET agent and a second as a 3H-radioligand for an IEDDA-based reaction with a modified brain-penetrating antibody.

2'-Modified Thymidines with Bioorthogonal Cyclopropene or Sydnone as Building Blocks for Copper-Free Postsynthetic Functionalization of Chemically Synthesized Oligonucleotides.

The development of facile methods for conjugating relevant probes, ligands, or delivery agents onto oligonucleotides (ONs) is highly desirable both for fundamental studies in chemical biology and for improving the pharmacology of ONs in medicinal chemistry. Numerous efforts have been focused on the introduction of bioorthogonal groups onto phosphoramidite building blocks, allowing the controlled chemical synthesis of reactive ONs for postsynthetic modifications. Among these building blocks, alkyne, cyclooctynes, trans-cyclooctene, and norbornene have been proved to be compatible with automated solid-phase chemistry. Herein, we present the development of novel 2'-functionalized nucleoside phosphoramidite monomers comprising bioorthogonal methylcyclopropene or sydnone moieties and their introduction for the first time to ON solid-phase synthesis. Traceless ON postsynthetic modifications with reactive complementary probes were successfully achieved through either inverse electron-demand Diels-Alder (iEDDA) reactions or strain-promoted sydnone-alkyne cycloaddition (SPSAC). These results expand the set of bioorthogonal phosphoramidite building blocks to generate ONs for postsynthetic labeling.

A Triphosphate Pronucleotide (TriPPPro)Reporter with Optimized Cell-Permeable Dyes for Metabolic Labeling of Cellular and Viral DNA in Living Cells.

The metabolic labeling of nucleic acids in living cells is highly desirable to track the dynamics of nucleic acid metabolism in real-time and has the potential to provide novel insights into cellular biology as well as pathogen-host interactions. Catalyst-free inverse electron demand Diels-Alder reactions (iEDDA) with nucleosides carrying highly reactive moieties such as axial 2-trans-cyclooctene (2TCOa) would be an ideal tool to allow intracellular labeling of DNA. However, cellular kinase phosphorylation of the modified nucleosides is needed after cellular uptake as triphosphates are not membrane permeable. Unfortunately, the narrow substrate window of most endogenous kinases limits the use of highly reactive moieties. Here, we apply our TriPPPro (triphosphate pronucleotide) approach to directly deliver a highly reactive 2TCOa-modified 2'-deoxycytidine triphosphate reporter into living cells. We show that this nucleoside triphosphate is metabolically incorporated into de novo synthesized cellular and viral DNA and can be labeled with highly reactive and cell-permeable fluorescent dye-tetrazine conjugates via iEDDA to visualize DNA in living cells directly. Thus, we present the first comprehensive method for live-cell imaging of cellular and viral nucleic acids using a two-step labeling approach.

Iso-Pentadienyl Carbonate as a Five Carbon Synthon in Manganese(I)-Catalyzed Selective Linear 1,3-Dienylation.

Selective linear 1,3-dienylations are essential transformations, and numerous synthetic efforts have been documented. However, a general method enabling access to electron-rich, -poor, and biologically relevant dienyl molecules is in high demand. Hence, we report a straightforward method of manganese(I)-catalyzed C-H dienylation of arenes by using iso-pentadienyl carbonate as a five carbon synthon. This is a highly unprecedented report for selective linear 1,3-dienylation using manganese C-H activation catalysis. Our method facilitates the synthesis of varieties of dienes, including those suitable for normal or inverse electron demand Diels-Alder reactions, dienyl glycoconjugates, and unnatural amino acids. Extensive mechanistic studies, including isolation of C-H activated organo-manganese complex and isotopic analyses, have supported the proposed mechanism of this dienylation. The synthetic applicability of this method eased to deliver a 6/6/5-fused tricyclic nagilactone scaffold.

Two-Way Catalysis in a Diels-Alder Reaction Limits Inhibition Induced by an External Electric Field.

Oriented external electric fields (EEFs) act as catalysts that can induce selectivity in chemical reactions. The responses of the Diels-Alder (DA) reaction between butadiene and ethylene (BDE-DA) as well as cyclopentadiene and ethylene (CPDE-DA) towards EEF stimuli are investigated here using density functional theory (B3LYP) calculations. EEF is a vector that catalyzes the reaction in one direction while inhibiting it in the opposite direction. Here we report that the inhibitive direction becomes rate-enhancing after some increase in the EEF. The EEF value that brings about the maximum possible inhibition for the reaction is defined as the electrostatic resistance point (ERP). The possibility of both normal and inverse electron-demand DA reactions causes catalytic activity in both directions of the EEF starting at a unique ERP value. The C5 substituents of cyclopentadiene control the ERP values depending upon the resistance power that the functional group provides against the EEF. The endo and exo diastereomeric transition states of the DA reaction have distinct ERP values and the difference (ΔERP) provides the through-space electrostatic contribution to the stereoselectivity on a relative scale. Thus, the ERP values can be used as a gauge for the electrostatic interactions between substituent groups and external stimuli.

Targeted delivery of PROTAC-based prodrug activated by bond-cleavage bioorthogonal chemistry for microneedle-assisted cancer therapy

Proteolysis-targeting chimera (PROTAC) is emerging as a new strategy to degrade target proteins in a precise way by taking advantage of the cellular ubiquitin-proteasome system. However, the potential cytotoxicity of PROTAC should be avoided to mitigate the off-target degradation of proteins in healthy tissues or cells. To address this issue, we herein present a strategy to cage a PROTAC with 4-(vinyloxy) benzyl carbonate (MZ1-O), which can be eliminated through a 3,6-dimethyl-1,2,4,5-tetrazine (Tz)-mediated inverse electron-demand Diels-Alder (iEDDA) reaction to generate a BRD4 (bromodomain-containing protein 4) degrader, MZ1. We further propose a dissolvable microneedle-assisted strategy for site-specific activation of MZ1-O that is delivered by a targeted delivery vector through systemic route in vivo, and demonstrate such a bioorthogonal strategy is efficient and precise for tumor treatment. Our study suggests that the bioorthogonal activation of PROTAC-based prodrug offers a highly specific and precise approach for cancer therapy.

DNA templated Click Chemistry via 5-vinyl-2′-deoxyuridine and an acridine-tetrazine conjugate induces DNA damage and apoptosis in cancer cells

AimsClick Chemistry is providing valuable tools to biomedical research, but its direct use in therapies remains nearly unexplored. For cancer treatment, nucleoside analogues (NA) such as 5-vinyl-2′-deoxyuridine (VdU) can be metabolically incorporated into cancer cell DNA and subsequently “clicked” to form a toxic product. The inverse electron-demand Diels-Alder (IEDDA) reaction between VdU and an acridine-tetrazine conjugate (PINK) has previously been used to label cell nuclei of cultured cells. Here, we report tandem usage of VdU and PINK to induce cytotoxicity. Main methodsCell lines were subsequently treated with VdU and PINK, and cell viability was measured via well confluency and 3D tumor spheroid assays. DNA damage and apoptosis were evaluated using Western Blotting and cell cycle analysis by flow cytometry. Double stranded DNA break (DSB) formation was measured using the comet assay. Apoptosis was assessed by fluorescent detection of externalized phosphatidylserine residues. Key findingsWe report that the combination of VdU and PINK synergistically induces cytotoxicity in cultured human cells. The combination of VdU and PINK strongly reduced cell viability in 2D and 3D cultured cancer cells. Mechanistically, the compounds induced DNA damage through DSB formation, which leads to S-phase accumulation and apoptosis. SignificanceThe combination of VdU and PINK represents a novel and promising DNA-templated “click” approach for cancer treatment via selective induction of DNA damage.