Chemical modification of oligonucleotides has become an essential strategy to improve their properties and expand their functional utility in chemical biology, molecular imaging, and therapeutics. Among the various modification strategies, post-synthetic bioorthogonal click chemistry enables efficient, rapid, and biocompatible site-specific conjugation of functional moieties. Central to these advances is the development of clickable nucleoside phosphoramidites, namely nucleoside building blocks containing reactive bioorthogonal click handles that are compatible with the harsh conditions of solid-phase oligonucleotide synthesis (SPOS). This review provides a comprehensive overview of bioorthogonal cycloaddition-based nucleoside phosphoramidites reported to date that are compatible with SPOS. We highlight their synthetic accessibility and deviations from conventional SPOS protocols when required, as well as the stability and hybridization behavior of the resulting clickable oligonucleotides. Furthermore, we examine the performance of subsequent bioorthogonal reactions used for post-synthetic functionalization, with particular attention to their kinetics and efficiencies. Representative applications are also discussed, including the development of labeled probes, multifunctional assemblies, and targeted delivery systems.

Chemical biology tools for studying tissue development.

Diazirines and diazo compounds are widely employed as photoreactive precursors for generating carbenes, key intermediates in chemical biology and materials science. However, computationally modeling their reaction pathways remains challenging due to the need for large active spaces and the requirement to accurately capture excited-state surfaces along with transition states and conical intersections. In this work, we utilize a hybrid quantum-classical workflow for investigating carbene formation in representative diazirine-diazomethane systems. Our approach leverages Sample-based Quantum Diagonalization (SQD) and its extended variant, Extended Sample-based Quantum Diagonalization (Ext-SQD), for ground- and excited-state analysis, combined with classical tools for geometry optimization, active-space selection, and diagnostic evaluation. Quantum computations were carried out on superconducting quantum processors, and results for both aliphatic and aryl-substituted diazirine-diazomethane pairs were benchmarked against established classical methods, including density functional theory (DFT), coupled cluster with singles and doubles (CCSD), complete active space configuration interaction (CASCI), and selected configuration interaction (SCI). SQD achieves accuracy surpassing the chemical accuracy threshold for nearly all stationary points on the potential energy surface of parent diazirine relative to the CASCI(12,10) reference, and remains close to chemical accuracy for phenyl-substituted diazirine in a (30,30) active space, with an average deviation of 1.1 kcal/mol relative to the SCI benchmark. SQD closely follows CASCI and SCI trends, showing consistent agreement. The findings demonstrate the promise of quantum computing frameworks in modeling photochemical transformations of electronically complex and pharmacologically relevant molecules.

Coumarins are privileged scaffolds in medicinal chemistry, chemical biology, and functional materials, yet their synthesis remains dominated by classical condensations and metal-dependent methods that limit structural diversity and sustainability. This review reframes coumarin construction through energy-driven activation, highlighting photochemical, electrochemical, and biochemical strategies as sustainable alternatives. Visible-light processes enable access to three-dimensional, sp3-rich, and fused architectures that are inaccessible by conventional routes, while electrochemical methods replace stoichiometric oxidants with electrical input under metal-free conditions. Biocatalytic and biosynthetic platforms further extend coumarin synthesis into aqueous, selective, and renewable regimes. Collectively, these paradigms align molecular innovation with modern sustainability and design principles.

RNA polymerase III (Pol III) is specialized for the high-throughput synthesis of short RNAs, a capability linked to its unique TFIIE- and TFIIF-like subcomplexes that are stably associated through different stages of transcription. To date, the role of a winged helix domain (WH2) of Rpc34 subunit in the TFIIE-like subcomplex during elongation has remained a conundrum because its density is consistently absent in cryo-EM structures of Pol III elongation complexes (ECs), suggesting its high conformational mobility. In this study, we employed single-molecule Förster resonance energy transfer (smFRET) and nano-positioning triangulation to characterize the dynamics and determine the position of the Rpc34-WH2 domain within transcription-competent but nontranslocating Pol III ECs. To achieve the required site-specific labeling, we developed a chemical biology framework that utilizes azido-carrying unnatural amino acid incorporation and a thiol-capping strategy to eliminate off-target alkyne-thiol cross-reactivity. With the acceptor at Rpc34-WH2 and the donor at a defined position on the DNA template as the reference point, our smFRET results reveal that Rpc34-WH2 dynamically transitions among three discrete states, corresponding to preferred positional sites in downstream, middle, and upstream regions across the DNA-binding cleft. One of these sites coincides with Rpc34-WH2's position in the preinitiation complex, indicating positional similarity across transcriptional states. Together with prior Pol I and Pol II studies, these findings establish Rpc34-WH2 as a mobile regulatory element that engages the Pol III EC through transient, weak interactions. Additionally, the bio-orthogonal labeling strategy presented here provides a robust, generalizable route for smFRET studies of large, multisubunit protein assemblies.

Sulfur(vi) fluoride exchange (SuFEx) reactions were introduced as next-generation click transformations that form robust sulfur(vi)-based linkages under mild conditions. Their defining feature is the unusual behaviour of the S-F bond: it is thermodynamically stable, yet can be selectively substituted when a suitable nucleophile is properly positioned. This balance has made SuFEx a valuable platform in chemical biology, enabling novel covalent probes, inhibitors and conjugation strategies in complex aqueous environments. In contrast, SuFEx applications to nucleosides, nucleotides and nucleic acids remain comparatively scarce and are only now beginning to mature. Progress has been limited by scaffold-specific synthetic and workflow constraints, including the scarcity of broadly enabling methodological studies and limited compatibility with standard oligonucleotide workflows. Even so, recent reports show that these barriers can be overcome in selected settings and that SuFEx can be translated into functional nucleic-acid constructs. This review summarises current advances with a focus on concepts and practical design rules. The first part is chemistry-centered: it compares the most successful strategies for installing sulfur(vi)-fluoride electrophiles on nucleoside, nucleotide, and oligonucleotide frameworks, and discusses reagent choices, linker designs and warhead positioning. The second part focuses on applications, outlining how these synthetic advances are turned into chemical biology tools where proximity effects convert reversible recognition into durable capture. We conclude by highlighting key bottlenecks and the most promising opportunities for progress.

ConspectusImmune checkpoint blockade therapies have revolutionized cancer treatment. However, their clinical efficacy remains limited by dysfunctional T-cell states within the tumor microenvironment. These limitations are particularly evident in aged hosts, where metabolic and signaling impairments compromise immune fitness and reduce responsiveness to PD-1/PD-L1-directed therapies. Emerging evidence suggests that chemical modulation of immune cell function represents a promising strategy to overcome these barriers. Our work explores how small molecules can be leveraged to restore T-cell activity and potentiate antitumor immunity through complementary chemical mechanisms. By integrating cell-based screening with electrophile-focused chemoproteomics, we identified a covalent small-molecule activator, arvenin I, which engages a ligandable cysteine in MKK3, promoting signaling programs that revive exhausted T-cells and synergize with immune checkpoint blockade. In parallel, previous studies revealed that age-associated depletion of the endogenous polyamine spermidine contributes to impaired T-cell metabolism and diminished responses to checkpoint blockade. Using chemoproteomic tools, we profiled spermidine-interacting proteins and found that the majority were mitochondrial proteins, including lipid-metabolism factors. This chemoproteomic platform also enabled the identification of a biostable spermidine mimetic that restores mitochondrial fitness and enhances antitumor immune responses in vivo. Together, these studies establish a unified chemical biology framework in which covalent signaling activation and metabolite-inspired energy support converge to restore T-cell fitness. This Account highlights how chemoproteomic discovery can guide the development of immune-activating small molecules and underscores the potential of chemical approaches to complement and extend the impact of cancer immunotherapy.

Lysine methylation as a bidirectional switch.

The sulfo-click reaction, which relies on the chemoselective coupling of sulfonyl azides with thioacids to yield N-acylsulfonamides, has emerged as a powerful and versatile transformation in synthetic chemistry and bioconjugation. Its high efficiency, operational simplicity, and compatibility with mild conditions and diverse functional groups have enabled broad applications in both chemical biology and medicinal chemistry. Notably, this reaction supports site-selective bioconjugation in aqueous media and is well suited to complex biomolecular systems, facilitating the preparation of functionalized bioconjugates. In addition, the resulting N-acylsulfonamide motif has attracted significant interest in drug design as a metabolically stable bioisostere of carboxylic acids and phosphates. In this review, we summarize the development of the sulfo-click reaction, discuss its mechanistic features and reaction scope, and highlight recent advances and emerging applications, underscoring its value as a modular and reliable platform for both fundamental and applied research.

Dopamine receptors (DRs) have been implicated in numerous disorders and diseases (e.g., Alzheimer's disease, Parkinson's disease, schizophrenia, and substance use disorders) and have served as attractive drug targets for these ailments. Despite their potential clinical utility, the development of selective DR ligands has been challenging due to difficulties in selectivity among the DR subtypes as well as other biogenic amine receptors and poor pharmacokinetic properties. The realization of their full potential necessitates continued advancements in DR ligands as investigative tools. This review aims to highlight the recent developments made in the chemical biology of DR ligands (e.g., bivalent ligands, photoactivatable ligands, photoswitchable probes, and fluorescent probes).

Quinones are important oxidants in biology and synthetic chemistry. Herein, we study the kinetics of the oxidation of hydroquinones to quinones with redox-active guanidines and thioguanidines. In the first section, we report the synthesis and characterization of the first redox-active aromatic compounds with two, three, and four thioguanidino groups and compare their redox properties with the corresponding oligoguanidines. The stable salts obtained upon chemical two-electron oxidation of the tetra-thioguanidine were then applied in dehydrogenative P-P coupling reactions at room temperature, demonstrating their superior proton-coupled electron-transfer reactivity compared with previously used oligoguanidines. Oxidation of hydroquinones and halogenated derivatives to the 1,4-benzoquinones is also much faster with the new tetrathioguanidine than with oligoguanidines. Seemingly paradoxically, for tetraguanidines and tetrathioguanidines, oxidations to high-potential halogenated quinones are faster than those to low-potential quinones (due to proton-coupled electron transfer (PCET)), motivating the use of redox-active guanidines as redox mediators.

Bioorthogonal reactions have revolutionized our way of performing chemistry in a highly complex biological environment. In particular, strain-promoted 1,3-dipolar cycloadditions, employing cyclooctyne probes in conjunction with azido-reporters (strain-promoted alkyne-azide cycloaddition, SPAAC), have permitted the labeling and visualization of bio-macromolecules in vitro, in living cells, as well as in animals. However, SPAAC's slow kinetics (< 1 M-1s-1), in combination with the necessity to eliminate the excess of the used fluorescent probes, have hampered its widespread application, especially for the real-time imaging of low concentration targets. Here we describe two novel thiophene-based cycloalkynes that not only exhibit very high kinetics toward a variety of 1,3-dipoles (up to 1528 M-1s-1), but are also efficiently turned-on (up to 150-fold increase in brightness) upon reaction with their target. We demonstrated their fast and fluorogenic capabilities by monitoring the labeling overtime of a glycoprotein in physiological and no-wash conditions, using as little as 5 µM of the probes and reaching full labeling in less than 15min. These fluorogenic cycloalkynes significantly expand our chemical biology toolbox, and we anticipate them to open new avenues for the fast and real-time imaging of biomolecules in complex environments.

Translational activation: An unforeseen function of RNP biomolecular condensates.

Native chemical ligation (NCL) represents a powerful strategy for the chemical synthesis of tailor-made proteins that are difficult to obtain via biological expression approaches. Early desulfurization methods, particularly VA-044-based desulfurization, have profoundly advanced the field by enabling the post-ligation conversion of cysteine to alanine, thereby expanding the sequence space accessible for protein synthesis. In recent years, a variety of innovative desulfurization technologies have emerged that achieve superior reaction kinetics, broader functional group compatibility or elimination of harmful additives, significantly broadening the scope and practicality of desulfurization strategies. This review summarizes key enabling desulfurization methodologies developed in recent years, including boron reagent-based desulfurization, photochemically induced reactions, iron-catalyzed systems, and ultrasound-driven processes. We highlight their core mechanisms, technical advantages, and substrate tolerability, and showcase representative applications that have expanded the synthetic protein landscape. Finally, we provide an outlook on future directions, encompassing precise mechanistic elucidation, desulfurization-functionalization tandem strategies, and industrial scale-up, which are expected to further drive innovations in protein therapeutics, chemical biology, and novel biomaterials.

Photochemical reactions compatible with physiological conditions are powerful tools for chemical biology and medicinal chemistry. Herein, we report that 3,4-dimethoxy-o-nitrobenzyl (o-nitroveratril) amidoxime ethers generate amidinyl radicals upon photoirradiation, yielding 6-aminophenanthridines via the intramolecular cyclization of the corresponding biaryl precursors. This photoreaction proceeds under physiologically relevant conditions, specifically in the aqueous buffers, to yield a series of substituted amino-phenanthridines in moderate yields. Mechanistic studies demonstrated that the reaction proceeds through homolytic N-O bond cleavage triggered by the photoexcitation of the o-nitroveratril moiety. Detailed analysis also identified amino-azaspirolactam as a side product, highlighting the bilateral reaction modes of amidoxime-derived radical species. Finally, the photoinduced cyclization was demonstrated within HeLa cells, highlighting its potential for light-induced construction and control of bioactive compounds.

Glutarimide-containing Cereblon (CRBN) ligands are critical motifs for PROTACs, molecular glue degraders and next-generation Cereblon E3 ligase modulatory drugs (CELMoDs), which represent promising therapeutic modalities in targeted protein degradation. However, the multistep synthetic routes required to access glutarimide scaffolds continue to present formidable challenges for medicinal chemists, limiting rapid structure-activity relationship (SAR) exploration and late-stage diversification. To streamline access to these privileged motifs, modular and efficient methodologies are still highly desirable. Here, we report a unified organocatalytic synthesis platform for the rapid assembly of diverse glutarimide derivatives from readily available nitrogen heterocycles. Employing a sequence of phosphine-catalysed C-N bond formation, metal-free Giese addition and acid-mediated cyclisation, this approach provides high selectivity, broad functional group tolerance and operational simplicity under conditions amenable to both multigram synthesis and high-throughput parallel synthesis. Using this platform, we rapidly prepare CRBN binder libraries, access control analogues (for example, N‑alkylated glutarimides) and perform late‑stage functionalisation of bioactive molecules. This strategy could offer a transformative solution for the efficient and cost-effective synthesis of CRBN-targeted therapeutics and chemical biology probes, overcoming longstanding synthetic bottlenecks in the field.

In this study, we report the synthesis of an alkylene linker containing a terminal 2-cyanoethyl protected selenium functionality for coupling at the 5'-end of an oligonucleotide by solid phase synthesis for the preparation of oligonucleotide conjugates. Upon deprotection and cleavage from the solid support, quantitative formation of a 5'-diselenide cross-linked oligonucleotide dimer occurred, which was verified by denaturing polyacrylamide gel electrophoresis, ion-exchange (IEX) high performance liquid chromatography and mass spectrometry. Using dithiothreitol a reducing agent, the diselenide linkage can be converted into the corresponding monomeric selenol, which then reacts with an alkyl halide to form the desired conjugate. The efficient conjugation of various moieties demonstrates the adaptability of the platform to support oligonucleotide-based applications in chemical biology.

Mitochondria, central regulators of cellular bioenergetics, biosynthesis, and stress signaling, represent an attractive yet challenging target for cancer therapy. Although phototherapy offers a non-invasive approach with high spatiotemporal control, the development of small-molecule systems capable of precise mitochondrial targeting for combined chemo and phototherapeutic modalities remains limited. Here, we report a rationally engineered small-molecule platform that integrates a cationic heptamethine cyanine scaffold with non-steroidal anti-inflammatory drugs (NSAIDs) to enable multifunctional chemo-phototherapy. The heptamethine cyanine unit acts as a mitochondrial targeting vector, intrinsic fluorescent reporter, and phototherapeutic module, while the NSAID component provides chemotherapeutic activity through inhibition of mitochondrial cyclooxygenase-2 (Cox-2). Biological evaluation identified the indomethacin-conjugated derivative 7a as a lead candidate that self-assembles into nanoscale structures and selectively accumulates in the mitochondria of HCT-116 colon cancer cells. Near-infrared light activation induces photothermal heating and reactive oxygen species generation (ROS), causing mitochondrial membrane depolarization, structural disruption, and oxidative stress. This mitochondrial damage triggers apoptosis via inhibition of Bcl-2, Cas-3/9, PARP and Cox-2, as well as upregulation of BAX, alongside inducible autophagy that can be pharmacologically regulated. This heptamethine cyanine-NSAID conjugate establishes a versatile mitochondria-targeted chemo-phototherapeutic system and advances light-activated organelle-directed chemical biology as a promising strategy for minimally invasive cancer therapy.

The MYC oncoprotein is a master regulator of cell growth and transcriptional amplification and is aberrantly overexpressed in a broad spectrum of human cancers, including colorectal carcinoma. Despite its central role in tumorigenesis, MYC has remained pharmacologically intractable due to its intrinsically disordered architecture, which lacks persistent small-molecule binding pockets. Here, we report a chemical biology strategy that exploits MYC's structural disorder as a therapeutic vulnerability. By combining small-molecule disruption of the MYC-MAX protein-protein interaction with pharmacological activation of the 20S proteasome, we induce rapid and pronounced depletion of MYC in MYC-dependent colorectal cancer cell lines. MYC loss is proteasome-dependent and persists following knockdown of FBXW7, indicating a degradation mechanism distinct from canonical SCF-FBXW7-mediated turnover and consistent with direct 20S proteasomal degradation. Dual treatment also suppresses MYC-driven transcriptional programs and significantly enhances apoptotic cell death. Collectively, these findings establish a framework in which protein-protein interaction inhibition sensitizes intrinsically disordered oncoproteins to 20S proteasome-mediated degradation. This work expands the therapeutic landscape for MYC-driven malignancies and highlights proteasome activation as a complementary strategy for targeting structurally disordered cancer drivers.

Aryl C-glycosides are an important class of carbohydrate derivatives known for their exceptional stability and significant biological relevance; however, C-2 aryl glycosides remain rare and synthetically challenging targets. Herein, we report a mild and efficient palladium-catalyzed protocol for the stereoselective synthesis of 2-aryl-4-ketoglycosides from protected and unprotected 2,3-d-pseudoglycals using aryl diazonium salts. The transformation proceeds smoothly at room temperature under ligand and base-free conditions, affording the desired products in good to excellent yields with high stereocontrol. The methodology exhibits a broad substrate scope, tolerating aryl diazonium salts bearing electron-donating, electron-withdrawing, and halogen substituents, as well as a variety of benzyl-, alkyl-, silyl-protected and unprotected pseudoglycals. Notably, halogen substituents are retained, enabling further downstream functionalization. The protocol is also applicable to unprotected 2,3-pseudorhamnal and can be extended to a one-pot process from anilines via in situ diazonium formation. Gram-scale synthesis and postfunctionalization highlight the robustness and synthetic utility of the method. Overall, this operationally simple and practical strategy provides a general and stereoselective route to C-2 aryl glycosides, expanding access to valuable carbohydrate scaffolds for applications in medicinal chemistry and chemical biology.