Unsaturated valence-six reactive intermediates such as carbenes and nitrenes have long served as fundamental building blocks in organic synthesis. Our research group has focused on developing efficient strategies for generating organometallic species derived from these intermediates and exploiting their reactivities in catalytic organic synthesis. The present article exclusively summarizes our studies on nitrene-based transformations. We initiated our nitrene research by conceptualizing a mechanistic hypothesis in which the release of ring strain from nitrene surrogates could be combined with metal-mediated N-O bond cleavage followed by decarboxylation of isoxazol-5(4H)-ones (isoxazolone) as versatile nitrene precursors. These precursors have enabled a series of transition-metal-catalyzed transformations that lead to diverse nitrogen-containing molecules. By judicious choice of metal catalysts, we have established general and modular routes to a wide range of valuable N-heterocycles and functionalized nitrogen-based frameworks. This account emphasizes the power of rational precursor design in nitrene chemistry and demonstrates how transition-metal catalysts can precisely control pathways of reactive intermediates. We believe that the precursor strategy outlined here will continue to inspire new methodologies for the catalytic synthesis of nitrogen-containing compounds.

Endo-β-N-acetylglucosaminidases (ENGases) are endoglycosidases that hydrolyze the glycosidic bond between two N-acetylglucosamine residues in asparagine-linked glycans. ENGases are crucial tools for the structural analysis and glycan remodeling of glycoproteins. However, current ENGase activity assays are often complex and unsuitable for high-throughput analysis. To address this, we developed Förster resonance energy transfer (FRET)-based glycan molecular probes for the real-time detection of ENGase activity. We synthesized di-, tri-, and pentasaccharide probes bearing a fluorophore at the non-reducing end and a quencher at the reducing end, and evaluated their quenching efficiencies for activity detection. The pentasaccharide probe, MM3D, was efficiently cleaved by Endo-M, resulting in a significant increase in fluorescence. These results successfully demonstrate that our FRET-based glycan probes enable straightforward, real-time ENGase activity detection. Furthermore, we constructed a library of probes with diverse glycan structures. Using this library, we evaluated the activities of six commercially available ENGases and observed their distinct substrate specificities. This FRET probe library represents a valuable tool for detecting ENGase activity and will significantly contribute to advances in glycobiology research.

Artificial genes are engineered DNA sequences designed to express specific RNA or proteins, with broad applications in gene therapy, diagnostics, and synthetic biology. A major challenge in this field is developing technologies that enable precise, on-demand control of gene expression, which is essential for functional studies and safe therapeutic strategies. Conventional approaches, such as light-sensitive transcription factors or photo-responsive DNA modifications, are limited by poor tissue penetration of light, restricting their applicability. To address this limitation, we developed a novel system based on host-guest chemistry to reversibly regulate DNA duplex formation. Guest-modified adenosines were designed by attaching a guest molecule to the N⁶ position of adenosine via an alkyl linker. These modified nucleosides were incorporated into DNA strands using a post-synthetic approach and formed stable base pairs with complementary thymidine under normal conditions. Upon addition of cucurbit[7]uril (CB[7]), bulky host-guest complexes formed on DNA, destabilizing the duplex. Subsequent introduction of a competing guest molecule displaced CB[7], restoring duplex formation. By integrating this system into the transcription initiation region of artificial genes, we successfully demonstrated reversible control of gene expression in a cell-free expression system. This study highlights a new chemical strategy for dynamic gene regulation and its potential applications in synthetic biology and therapeutic design.

Anions are fundamental species in the environment and in living cells; therefore, the recognition of anions is important. We found that silanol derivatives, including silanediols, silanetriol, 1,3-disiloxane-1,3-diol, and 1,3-disiloxane-1,1,3,3-tetraol, form multiple hydrogen bonds with anions in organic solvents. The X-ray single crystal structure of di(1-naphthyl)silanediol and Cl⁻ revealed that the two hydroxy groups formed cooperatively hydrogen bonds to Cl⁻. The association constants of the silanol derivatives for anions were comparable to those of the corresponding urea derivatives. In addition, silanediols bearing pyrenyl and substituted naphthyl groups slowly react in the presence of a base to form the corresponding cyclotri- and cyclotetrasiloxanes, respectively under mild conditions without cleaving the Si-C bonds. The structures and the photophysical properties are also presented. Notably, silanol derivatives can be utilized as organocatalyst, similar to thiourea and squaramide derivatives. The addition of indole to β-nitrostyrene catalyzed by silanetriol was faster than that with silanediol indicating that three hydroxy groups cooperatively stabilize the transition state of the reaction.

This study describes the development of manufacturing processes for TAFIa inhibitor 1 and its prodrug 2. To establish an industrial-scale production process for 1, comprehensive screening of chiral catalysts was conducted. This investigation revealed that the Ru/BINAP catalyst system in fluorous alcohol solvents (2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP)) significantly enhanced both reactivity and selectivity. Consequently, a robust and efficient process was successfully developed, achieving an 85% overall yield from intermediate 12 over 5 steps. This represents a substantial improvement compared to the early-stage process (40% overall yield in 5 steps). Concurrently, a manufacturing process was developed for prodrug 2. A novel optically active prodrug fragment, (R)-32, utilizing HFIP as a leaving group, was designed to circumvent problematic chromatographic purification, and its synthetic route was established. Enzyme screening identified Chirazyme L-2, C4 as an effective catalyst, producing (R)-32 in 37% yield with 99.8% ee optical purity. Additionally, crystallization-induced asymmetric transformation (CIAT) of a diastereomeric mixture 2c from the (R,R)-form to the desired (R,S)-form was achieved, resulting in 97% yield with 94.8% de. Based on these methodologies, a manufacturing process was established for prodrug 2, achieving an overall yield of 66% from intermediate 12 through 6 steps.