Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions

Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.

Synthesis of Multisubstituted 1,2,3-Triazoles: Regioselective Formation and Reaction Mechanism

A synthetically useful approach to functionalized triazoles is described via the reaction of β-carbonyl phosphonates and azides. 1,4- and 1,5-disubstituted and 1,4,5-trisubstituted triazoles can be regio- and chemoselectively accessed under mild conditions in good to excellent yields (31 examples, up to 99%). A mechanism is proposed that rationalizes the avoidance of the 4-phosphonate byproducts, which is aligned with crystallographic and experimental evidence.

Site-Specific and Multiple Fluorogenic Metabolic Glycan Labeling and Glycoproteomic Profiling in Live Cells

Multicolor labeling for monitoring the intracellular localization of the same target type in the native environment using chemical fluorescent dyes is a challenging task. This approach requires both bioorthogonal and biocompatible ligations with an excellent fluorescence signal-to-noise ratio. Here, we present a metabolic glycan labeling technique that uses homemade fluorogenic dyes to investigate glycosylation patterns in live cells. These dyes allowed us to demonstrate rapid and efficient simultaneous multilabeling of glycoconjugates with minimum fluorescence noise. Our results demonstrate that this approach is capable of not only probing sialylation and GlcNAcylation in cells but also specifically labeling the cell-surface and intracellular sialylated glycoconjugates in live cells. In particular, we performed site-specific dual-channel fluorescence imaging of extra and intracellular sialylated glycans in HeLa and PC9 cancer cells as well as identified fluorescently labeled sialylated glycoproteins and glycans by a direct enrichment approach combined with an MS-based proteomic analysis in the same experiment. In conclusion, this study provides multilabeling tools in cellular systems for simultaneous site-specific glycan imaging and glycoproteomic analysis to study potential cancer- and disease-associated glycoconjugates.

Development of Fluorescent Isocoumarin-Fused Oxacyclononyne - 1,2,3-Triazole Pairs

Fluorescent isocoumarin-fused cycloalkynes, which are reactive in SPAAC and give fluorescent triazoles regardless of the azide nature, have been developed. The key structural feature that converts the non-fluorescent cycloalkyne/triazole pair to its fluorescent counterpart is the pi-acceptor group (COOMe, CN) at the C6 position of the isocoumarin ring. The design of the fluorescent cycloalkyne/triazole pairs is based on the theoretical study of the S1 state deactivation mechanism of the non-fluorescent isocoumarin-fused cycloalkyne IC9O using multi-configurational ab initio and DFT methodologies. The calculations revealed that deactivation proceeds through the electrocyclic ring opening of the α-pyrone cycle and is accompanied by a redistribution of electron density in the fused benzene ring. We proposed that the S1 excited state deactivation barrier could be increased by introducing a pi-acceptor group into a position that is in direct conjugation with the formed C=O group and has a reduced electron density in the transition state. As a proof of concept, we designed and synthesized two fluorescent isocoumarin-fused cycloalkynes IC9O-COOMe and IC9O-CN bearing pi-acceptors at the C6 position. The importance of the nature of a pi-acceptor group was shown by the example of much less fluorescent CF3 -substituted cycloalkyne IC9O-CF3 .

Bioorthogonal chemistry: Bridging chemistry, biology, and medicine

As chemical biologists sought methods to modify and study biomolecules in their native environments, the need for bioorthogonal chemical reactions emerged. These fast and selective reactions between otherwise inert, abiotic functional groups have enabled exploration of some of the most intriguing and challenging questions in chemical biology. Further, the ability to perform organic reactions in cells and organisms has led to important applications in clinical spaces, and one reaction is now an integral part of a phase 2 trial for treating solid tumors. Given that bioorthogonal chemistry was a recipient of the 2022 Nobel Prize, we expect this field to be even more energized. Here, we highlight some of the most recent studies in this sphere and how these set the stage for where bioorthogonal chemistry is headed.

To View Your Biomolecule, Click inside the Cell

The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.

Bioinspired tailoring of fluorogenic thiol responsive antioxidant precursors to protect cells against H2O2-induced DNA damage

Natural antioxidants, like phenolic acids, possess a unique chemical space that can protect cellular components from oxidative stress. However, their polar carboxylic acid chemotype reduces full intracellular antioxidant potential due to limited diffusion through biological membranes. Here, we have designed and developed a new generation of hydrophobic turn-on fluorescent antioxidant precursors that upon penetration of the cell membrane, reveal a more polar and more potent antioxidant core and simultaneously become fluorescent allowing their intracellular tracking. Their activation is stimulated by polarity alteration by sensing intracellular signals and specifically biothiols. In our design, the carboxylic group of phenolic acids that originally restricts cell entrance is derivatized and conjugated through Copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC) to a coumarin derivative that its fluorescence properties are quenched with a biothiol activatable element. This more hydrophobic precursor readily penetrates cell membrane and once inside the cell the antioxidant core is revealed upon sensing glutathione, its fluorescence is restored in a turn-on manner and the generation of a more polar character traps the molecule inside the cell. This turn-on fluorescent antioxidant precursor that can be applied to phenolic acids, was developed for rosmarinic acid and the conjugate was named as RCG. The selectivity and responsiveness of RCG towards the most abundant biothiols was monitored through a variety of biophysical techniques including UV-Vis, fluorescence and NMR spectroscopy. The electrochemical behavior and free radical scavenging capacity of the precursor RCG and the active compound (RC) was evaluated and compared with the parent compound (rosmarinic acid) through cyclic voltammetry and EPR spectroscopy, respectively. The stability of the newly synthesized bioactive conjugate RC was found significantly higher than the parent rosmarinic acid when exposed to oxygen. Cell uptake experiments were conducted and revealed the internalization of RCG. The degree of intracellular DNA protection offered by RCG and its active drug (RC) on exposure to H₂O₂ was also evaluated in Jurkat cells.

Enzyme- or light-triggered cyclopropenes for bioorthogonal ligation

Since first reported at the beginning of the 21st century, bioorthogonal reactions have become powerful tools for investigating biological systems. Here, we review several classic and current bioorthogonal reactions, including the Staudinger-Bertozzi ligation, strain-promoted azide-alkyne cycloaddition (SPAAC), 1,3-dipolar cycloaddition, and tetrazine-alkene ligation. We discuss the capabilities and limitations of the subset of current bioorthogonal reactions that can be "turned on" by exposure to light or an enzyme. Finally, we focus on our recently developed turn-on cyclopropenes, which can be activated for reaction with tetrazines by exposure to light or enzymes, like nitroreductase, depending on the modular reaction caging group appended to the cyclopropene. We discuss the caged cyclopropene's molecular design and synthesis, and we discuss experiments to evaluate and verify reactivity both in vitro and in vivo.

Facile Click-Mediated Cell Imaging Strategy of Liposomal Azido Mannosamine Lipids via Metabolic or Nonmetabolic Glycoengineering

Two Ac₄ManNAz (AAM) derivatives with octadecanoic ester (C18 ester) and octadecyl ether (C18 ether) attached to the anomeric hydroxyl groups were synthesized and used in preparation of liposomes. Both liposomes show strong cell-labeling efficiencies on MDA-MB-231 cancer cells. The cell surface-anchored azide group can react with DBCO-Cy5 via Cu-free click chemistry. The two liposomes exhibit different azide placement mechanisms; C18-ether-AAM-treated cells have azido placement through direct insertion, while C18-ester-AAM-treated cells express azido more through metabolic glycoengineering.

Synthesis of water-soluble fluorescent polymeric glycoconjugate for the detection of cholera toxin

Considering inherence optical properties of adjoint polyfluorenes and special functions of water-soluble conjugated glycopolymers, a triazole chain glycoconjugate via one-pot method were rapidly synthesized to prepare a lactate ligand polyfluorene with a clear fluorescent label by a nickel-catalyzed Yamamoto coupling polymerization. The water solubility and biocompatibility of the glycoconjugated polymer were ameliorated when the lactose group introduced as the side chain of the conjugated polymer. As a fluorescent multivalent system of glycoconjugates containing pyranogalactose groups, the interaction between pyranogalactose group and cholera toxin B subunit was studied by fluorescence spectrophotometric titration. PF-Lac has a broad application prospect in the check of cholera toxin and the study of glycoprotein interaction.

Bioorthogonal Fluorescence Turn-On Labeling Based on Bicyclononyne-Tetrazine Cycloaddition Reactions that Form Pyridazine Products

Fluorogenic bioorthogonal reactions enable visualization of biomolecules with excellent signal-to-noise ratio. A bicyclononyne-tetrazine ligation that produces fluorescent pyridazine products has been developed. In stark contrast to previous approaches, the formation of the dye is an inherent result of the chemical reaction and no additional fluorophores are needed in the reagents. The crucial structural elements that determine dye formation are electron-donating groups present in the starting tetrazine unit. The newly formed pyridazine fluorophores show interesting photophysical properties the fluorescence intensity increase in the reaction can reach an excellent 900-fold. Model imaging experiments demonstrate the application potential of this new fluorogenic bioorthogonal reaction.

A strained alkyne-containing bipyridine reagent; synthesis, reactivity and fluorescence properties

We report the synthesis of a bipyridyl reagent containing a strained alkyne, which significantly restricts its flexibility. Upon strain-promoted alkyne-azide cycloaddition (SPAAC) with an azide, which does not require a Cu catalyst, the structure becomes significantly more flexible and an increase in fluorescence is observed. Upon addition of Zn(ii), the fluorescence is enhanced further. The reagent has the potential to act as a fluorescent labelling agent with azide-containing substrates, including biological molecules.

A bipyridyl reagent containing a strained alkyne 7, reacts with benzyl azide to give a significantly more flexible product 10 and an increase in fluorescence is observed. Upon addition of Zn(ii), the fluorescence is enhanced further.

Fluorogenic Sydnone-Modified Coumarins Switched-On by Copper-Free Click Chemistry

The synthesis, photophysical characterization, and biochemical application of sydnone-modified coumarins, a novel class of fluorogenic clickable reagents, are reported. The sydnone moiety, a stable aromatic 1,3-dipole, efficiently quenched the fluorescence of coumarin, which could be restored, with a 132-fold enhancement, upon cycloadditions with cyclooctynes, thereby expanding the fluorogenic click toolbox. TD-DFT calculations suggest that the fluorescence quenching of the sydnone-modified coumarins is likely due to the presence of an energetically low-lying nonemissive charge-separated state.