Fast alkene functionalization in vivo by Photoclick chemistry: HOMO lifting of nitrile imine dipoles

Design and synthesis of highly reactive dienophiles for the tetrazine-trans-cyclooctene ligation

Computation was used to design a trans-cyclooctene derivative that displays enhanced reactivity in the tetrazine-trans-cycloctene ligation. The optimized derivative is an (E)-bicyclo[6.1.0]non-4-ene with a cis-ring fusion, in which the eight-membered ring is forced to adopt a highly strained 'half-chair' conformation. Toward 3,6-dipyridyl-s-tetrazine in MeOH at 25 °C, the strained derivative is 19 and 27 times more reactive than the parent trans-cyclooctene and 4E-cyclooct-4-enol, respectively. Toward 3,6-diphenyl-s-tetrazine in MeOH at 25 °C, the strained derivative is 160 times more reactive than the parent trans-cyclooctene.

Light-induced hetero-Diels-Alder cycloaddition: a facile and selective photoclick reaction

2-Napthoquinone-3-methides (oNQMs) generated by efficient photodehydration (Φ=0.2) of 3-(hydroxymethyl)-2-naphthol undergo facile hetero-Diels-Alder addition (k(D-A)∼ 4×10(4) M(-1) s(-1)) to electron-rich polarized olefins in an aqueous solution. The resulting photostable benzo[g]chromans are produced in high to quantitative yield. The unreacted oNQM is rapidly hydrated (k(H2O) ∼145 s(-1)) to regenerate the starting diol. This competition between hydration and cycloaddition makes oNQMs highly selective, since only vinyl ethers and enamines are reactive enough to form the Diels-Alder adduct in an aqueous solution; no cycloaddition was observed with other types of alkenes. To achieve photolabeling or photoligation of two substrates, one is derivatized with a vinyl ether moiety, while 3-(hydroxymethyl)-2-naphthol is attached to the other via an appropriate linker. The light-induced Diels-Alder "click" strategy permits the formation of either a permanent or hydrolytically labile linkage. Rapid kinetics of this photoclick reaction (k=4×10(4) M(-1) s(-1)) is useful for time-resolved applications. The short lifetime (τ ∼7 ms in H(2)O) of the active form of the photoclick reagent prevents its migration from the site of irradiation, thus, allowing for spatial control of the ligation or labeling.

Synthesis of macrocyclic tetrazoles for rapid photoinduced bioorthogonal 1,3-dipolar cycloaddition reactions

A series of conformationally constrained, macrocyclic tetrazoles were expediently prepared by double alkylation of a bis(o -phenolyl)tetrazole precursor. Several of them showed excellent reactivity toward norbornene in a photoinduced tetrazole-alkene cycloaddition reaction in organic solvent as well as toward a norbornene-modified protein in PBS buffer.

Azirine ligation: fast and selective protein conjugation via photoinduced azirine-alkene cycloaddition

We report a new bioorthogonal ligation reaction between p-nitrodiphenylazirine and dimethyl fumarate. This photoinduced azirine-alkene cycloaddition provides a rapid (~2 min) and highly selective route to protein conjugation at neutral pH and room temperature in biological medium.

A biosynthetic route to photoclick chemistry on proteins

Light-induced chemical reactions exist in nature, regulating many important cellular and organismal functions, e.g., photosensing in prokaryotes and vision formation in mammals. Here, we report the genetic incorporation of a photoreactive unnatural amino acid, p-(2-tetrazole)phenylalanine (p-Tpa), into myoglobin site-specifically in E. coli by evolving an orthogonal tRNA/aminoacyl-tRNA synthetase pair and the use of p-Tpa as a bioorthogonal chemical "handle" for fluorescent labeling of p-Tpa-encoded myoglobin via the photoclick reaction. Moreover, we elucidated the structural basis for the biosynthetic incorporation of p-Tpa into proteins by solving the X-ray structure of p-Tpa-specific aminoacyl-tRNA synthetase in complex with p-Tpa. The genetic encoding of this photoreactive amino acid should make it possible in the future to photoregulate protein function in living systems.

Azide: a unique dipole for metal-free bioorthogonal ligations

Covalently bound azide on a (small) organic molecule or a (large) biomolecular structure has proven an important handle for bioconjugation. Azides are readily introduced, small, and stable, yet undergo smooth ligation with a range of reactive probes under mild conditions. In particular, the potential of azides to undergo metal-free reactions with strained unsaturated systems has inspired the development of an increasing number of reactive probes, which are comprehensively summarized here. For each individual probe, the synthetic preparation is described, together with reaction kinetics and the full range of applications, from materials science to glycoprofiling. Finally, a qualitative and quantitative comparison of azido-reactive probes is provided.

A metabolic alkene reporter for spatiotemporally controlled imaging of newly synthesized proteins in Mammalian cells

The nonsymmetrical spatial distribution of newly synthesized proteins in animal cells plays a central role in many cellular processes. Here, we report that a simple alkene tag, homoallylglycine (HAG), was co-translationally incorporated into a recombinant protein as well as endogenous, newly synthesized proteins in mammalian cells with high efficiency. In conjunction with a photoinduced tetrazole-alkene cycloaddition reaction ("photoclick chemistry"), this alkene tag further served as a bioorthogonal chemical reporter both for the selective protein functionalization in vitro and for a spatiotemporally controlled imaging of the newly synthesized proteins in live mammalian cells. This two-step metabolic alkene tagging-photocontrolled chemical functionalization approach may offer a potentially useful tool to study the role of spatiotemporally regulated protein synthesis in mammalian cells.

High-density DNA functionalization by a combination of Cu-catalyzed and cu-free click chemistry

We report the regioselective Cu-free click modification of styrene functionalized DNA with nitrile oxides. A series of modified oligodeoxynucleotides (nine base pairs) was prepared with increasing styrene density. 1,3-Dipolar cycloaddition with nitrile oxides allows the high density functionalization of the styrene modified DNA directly on the DNA solid support and in solution. This click reaction proceeds smoothly even directly in the DNA synthesizer and gives exclusively 3,5-disubstituted isoxazolines. Additionally, PCR products (300 and 900 base pairs) were synthesized with a styrene triphosphate and KOD XL polymerase. The click reaction on the highly modified PCR fragments allows functionalization of hundreds of styrene units on these large DNA fragments simultaneously. Even sequential Cu-free and Cu-catalyzed click reaction of PCR amplicons containing styrene and alkyne carrying nucleobases was achieved. This new approach towards high-density functionalization of DNA is simple, modular, and efficient.

A bioorthogonal chemistry strategy for probing protein lipidation in live cells

We report a chemical lipidation model for the study of protein lipidations in vitro and in live mammalian cells based on a bioorthogonal, photoinduced tetrazole-alkene cycloaddition reaction.

Direct observation of a photoinduced nonstabilized nitrile imine structure in the solid state

We report the direct observation of a bent geometry for a nonstabilized nitrile imine in a metal-coordination crystal. The photoinduced tetrazole ring rupture to release N(2) appears to depend on the size of voids around the N(3)-N(4) bond in the crystal lattice. We further observed the selective formation of the 1,3-addition product when a reactive nitrile imine was photogenerated in water. Overall, the bent nitrile imine geometry agrees with the 1,3-dipolar structure, a transient reactive species that mediates the photoinduced 1,3-dipolar cycloaddition in the aqueous medium.

Bioorthogonal chemistry: recent progress and future directions

The ability to use covalent chemistry to label biomolecules selectively in their native habitats has greatly enhanced our understanding of biomolecular dynamics and function beyond what is possible with genetic tools alone. To attain the exquisite selectivity that is essential in this covalent approach a "bottom-up" two-step strategy has achieved many successes recently. In this approach, a bioorthogonal chemical functionality is built into life's basic building blocks-amino acids, nucleosides, lipids, and sugars-as well as coenzymes; after the incorporation, an array of biophysical probes are selectively appended to the tagged biomolecules via a suitable bioorthogonal reaction. While much has been accomplished in the expansion of non-natural building blocks carrying unique chemical moieties, the dearth of robust bioorthogonal reactions has limited both the scope and utility of this promising approach. Here, we summarize the recent progress in the development of bioorthogonal reactions and their applications in various biological systems. A major emphasis has been placed on the mechanistic and kinetic studies of these reactions with the hope that continuous improvements can be made with each reaction in the future. In view of the gap between the capabilities of the current repertoire of bioorthogonal reactions and the unmet needs of outstanding biological problems, we also strive to project the future directions of this rapidly developing field.

Facile synthesis of stapled, structurally reinforced peptide helices via a photoinduced intramolecular 1,3-dipolar cycloaddition reaction

We report the first use of a photoinduced 1,3-dipolar cycloaddition reaction in "stapling" peptide sidechains to reinforce a model peptide helical structure with moderate to excellent yields; the resulting pyrazoline "staplers" exhibit unique fluorescence useful in a cell permeability study.

Synthesis and evaluation of photoreactive tetrazole amino acids

Six photoreactive tetrazole amino acids were efficiently synthesized either by the de novo Kakehi tetrazole synthesis method or by alkylation of a glycine Schiff base with tetrazole-containing alkyl halides, and four of them showed excellent reactivity toward a simple alkene in the photoinduced 1,3-dipolar cycloaddition reaction in acetonitrile/PBS buffer (1:1) mixture.