Faculty Profiles - YAMAGUCHI, Shigehiro

Abstract

The inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red‐emissive IMM‐labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super‐resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling.

DOI： 10.1002/anie.202404328

Open Access

Web of Science

PubMed

In‐Silico Screening and Experimental Verification of Near‐Infrared‐Emissive Two‐Boron‐Doped Polycyclic Aromatic Hydrocarbons Reviewed Open Access

Izumi Hattori, Masaya Hagai, Masato Ito, Mika Sakai, Hiroki Narita, Kazuhiro J. Fujimoto, Takeshi Yanai, Shigehiro Yamaguchi

Angewandte Chemie International Edition Vol. 63 ( 22 ) page： e202403829 2024.5

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley

Embedding two boron atoms into a polycyclic aromatic hydrocarbon (PAH) leads to the formation of a neutral analogue that is isoelectronic to the corresponding dicationic PAH skeleton, which can significantly alter its electronic structure. Based on this concept, we explore herein the identification of near‐infrared (NIR)‐emissive PAHs with the aid of an in‐silico screening method. Using perylene as the PAH scaffold, we embedded two boron atoms and fused two thiophene rings to it. Based on this design concept, all possible structures (~2500 entities) were generated using a comprehensive structure generator. Time‐dependent DFT calculations were conducted on all these structures, and promising candidates were extracted based on the vertical excitation energy, transition dipole moment, and atomization energy per bond. One of the extracted dithieno‐diboraperylene candidates was synthesized and indeed exhibited emission at 724 nm with a quantum yield of 0.40 in toluene, demonstrating the validity of this screening method. This modification was further applied to other PAHs, and a series of thienobora‐modified PAHs was synthesized.

DOI： 10.1002/anie.202403829

Open Access

Web of Science

PubMed

Stereochemistry‐Dependent Labeling of Organelles with a Near‐Infrared‐Emissive Phosphorus‐Bridged Rhodamine Dye in Live‐Cell Imaging Reviewed

Qian Wu, Masayasu Taki, Yoshiki Tanaka, Manish Kesherwani, Quan Manh Phung, Sawako Enoki, Yasushi Okada, Florence Tama, Shigehiro Yamaguchi

Angewandte Chemie International Edition Vol. 63 ( 15 ) page： e202400711 2024.4

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley

The development of near‐infrared (NIR) fluorophores that have both excellent chemical stability and photostability, as well as efficient cell permeability, is highly demanded. In this study, we present phospha‐rhodamine (POR) dyes which display significantly improved performance for protein labeling. This is achieved by incorporating a 2‐carboxy‐3‐benzothiophenyl group at the 9‐position of the xanthene scaffold. The resulting cis and trans isomers were successfully isolated and structurally characterized using X‐ray diffraction. The HaloTag ligand conjugates of the two isomers exhibited different staining abilities in live cells. While the cis isomer showed non‐specific accumulation on the organelle membranes, the trans isomer selectively labeled the HaloTag‐fused proteins, enabling the long‐term imaging of cell division and the 5‐color imaging of cell organelles. Molecular dynamics simulations of the HaloTag ligand conjugates within the lipid membrane suggested that the cis isomer is more prone to forming oligomers in the membrane. In contrast, the oligomerization of the trans isomer is effectively suppressed by its interaction with the lipid molecules. By taking advantage of the superior labeling performance of the trans isomer and its NIR‐emissive properties, multi‐color time‐lapse super‐resolution 3D imaging, namely super‐resolution 5D‐imaging, of the interconnected network between the endoplasmic reticulum and microtubules was achieved in living cells.

DOI： 10.1002/anie.202400711

Web of Science

PubMed

Dithienoazepine-Based Near-Infrared Dyes: Janus-Faced Effects of a Thiophene-Fused Structure on Antiaromatic Azepines Reviewed

Murai, M; Enoki, T; Yamaguchi, S

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 62 ( 49 ) page： e202311445 2023.12

Theoretical Insight into the Effect of Phosphorus Oxygenation on Nonradiative Decays: Comparative Analysis of P-Bridged Stilbene Analogs Reviewed

Inai, N; Yamaguchi, S; Yanai, T

ACS PHYSICAL CHEMISTRY AU Vol. 3 ( 6 ) page： 540 - 552 2023.10

Biomimetic Design of a Robustly Stabilized Folded State Enabling Seed-Initiated Supramolecular Polymerization under Microfluidic Mixing Reviewed

Ogi, S; Takamatsu, A; Matsumoto, K; Hasegawa, S; Yamaguchi, S

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 62 ( 34 ) page： e202306428 2023.8

Amphiphile desymmetrisation-induced steric relief governs self-assembly pathways in aqueous media Reviewed International coauthorship

Bäumer, N; Ogi, S; Borsdorf, L; Yamaguchi, S; Fernández, G

CHEMICAL COMMUNICATIONS Vol. 59 ( 58 ) page： 8937 - 8940 2023.7

Germanium- and tin-bridged diazulenylmethyl cations: effects of group 14 elements on the structure and properties of π-extended cations Reviewed

Murai, M; Ito, M; Takahashi, S; Yamaguchi, S

DALTON TRANSACTIONS Vol. 52 ( 25 ) page： 8631 - 8635 2023.6

Photodissociative Modules that Control Dual-Emission Properties in Donor-pi-Acceptor Organoborane Fluorophores Reviewed

Midori Kawashiro, Tatsuya Mori, Masato Ito, Naoki Ando, Shigehiro Yamaguchi

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 62 ( 26 ) page： e202303725 2023.6

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：WILEY-V C H VERLAG GMBH

Donor-pi-acceptor fluorophores that consist of an electron-donating amino group and an electron-accepting triarylborane moiety generally exhibit substantial solvatochromism in their fluorescence while retaining high fluorescence quantum yields even in polar media. Herein, we report a new family of this compound class, which bears ortho-P(=X)R-2-substituted phenyl groups (X=O or S) as a photodissociative module. The P=X moiety that intramolecularly coordinates to the boron atom undergoes dissociation in the excited state, giving rise to dual emission from the corresponding tetra- and tricoordinate boron species. The susceptibility of the systems to photodissociation depends on the coordination ability of the P=O and P=S moieties, whereby the latter facilitates dissociation. The intensity ratios of the dual emission bands are sensitive to environmental parameters, including temperature, solution polarity, and the viscosity of the medium. Moreover, precise tuning of the P(=X)R-2 group and the electron-donating amino moiety led to single-molecule white emission in solution.

DOI： 10.1002/anie.202303725

Web of Science

PubMed

A Synthetic Strategy for Multi-Functionalized Phospharhodamines via Catalytic P-Arylation Reviewed

Yuichi Asada, Masayasu Taki, Shigehiro Yamaguchi

Bulletin of the Chemical Society of Japan Vol. 96 ( 6 ) page： 601 - 606 2023.6

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

The visualization of complex biological events in living cells is highly reliant on the development of sophisticated fluorescent probes with multiple functions. Herein, we report a general synthetic strategy for the synthesis of near-infraredemissive phospharhodamines (PORs) bearing various types of aryl groups on their bridging phosphorus atoms. This versatile approach utilizes a Ni-catalyzed P-arylation that allows for the design of POR-based multi-functionalized fluorescent probes. We found that PORs substituted with an aminophenyl group exhibited pH-responsive fluorescence intensity, where photo-induced electron transfer occurs to quench the fluorescence. The combination of our new approach with conventional modification at the 9-position of the xanthene skeleton facilitates the development of multi-functionalized fluorescent probes. As one demonstration of this method, we synthesized a fluorescence probe that can selectively visualize the lysosomes that result from endosomal maturation.

DOI： 10.1246/bcsj.20230082

Web of Science

Scopus

Impact of Hydrophobic/Hydrophilic Balance on Aggregation Pathways, Morphologies, and Excited-State Dynamics of Amphiphilic Diketopyrrolopyrrole Dyes in Aqueous Media. Reviewed International coauthorship International journal

Natsumi Fukaya, Soichiro Ogi, Hikaru Sotome, Kazuhiro J Fujimoto, Takeshi Yanai, Nils Bäumer, Gustavo Fernández, Hiroshi Miyasaka, Shigehiro Yamaguchi

Journal of the American Chemical Society Vol. 144 ( 49 ) page： 22479 - 22492 2022.12

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

We report the thermodynamic and kinetic aqueous self-assembly of a series of amide-functionalized dithienyldiketopyrrolopyrroles (TDPPs) that bear various hydrophilic oligoethylene glycol (OEG) and hydrophobic alkyl chains. Spectroscopic and microscopic studies showed that the TDPP-based amphiphiles with an octyl group form sheet-like aggregates with J-type exciton coupling. The effect of the alkyl chains on the aggregated structure and the internal molecular orientation was examined via computational studies combining MD simulations and TD-DFT calculations. Furthermore, solvent and thermal denaturation experiments provided a state diagram that indicates the formation of unexpected nanoparticles during the self-assembly into nanosheets when longer OEG side chains are introduced. A kinetic analysis revealed that the nanoparticles were obtained selectively as an on-pathway intermediate state toward the formation of thermodynamically controlled nanosheets. The metastable aggregates were used for seed-initiated supramolecular assembly, which allowed establishing control over the assembly kinetics and the aggregate size. The sheet-like aggregates prepared using the seeding method exhibited coherent vibration in the excited state, indicating a well-ordered orientation of the TDPP units. These results underline the significance of fine tuning of the hydrophobic/hydrophilic balance in the molecular design to kinetically control the assembly of amphiphilic π-conjugated molecules into two-dimensional nanostructures in aqueous media.

DOI： 10.1021/jacs.2c07299

Web of Science

PubMed

Diazulenylmethyl Cations with a Silicon Bridge: A π-Extended Cationic Motif to Form J-Aggregates with Near-Infrared Absorption and Emission Reviewed

Murai, M; Abe, M; Ogi, S; Yamaguchi, S

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 144 ( 44 ) page： 20385 - 20393 2022.10

Oxy-Borylenes as Photoreductants: Synthesis and Application in Dehalogenation and Detosylation Reactions Reviewed International coauthorship

Lenz, P; Oshimizu, R; Klabunde, S; Daniliuc, CG; Mück-Lichtenfeld, C; Tendyck, JC; Mori, T; Uhl, W; Hansen, MR; Eckert, H; Yamaguchi, S; Studer, A

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 61 ( 42 ) page： e202209391 2022.10

Olefin–Borane Interactions in Donor–π–Acceptor Fluorophores that Undergo Frustrated‐Lewis‐Pair‐Type Reactions Reviewed

Ryo Oshimizu, Naoki Ando, Shigehiro Yamaguchi

Angewandte Chemie International Edition Vol. 61 ( 41 ) page： e202209394 2022.10

Multiple resonance type thermally activated delayed fluorescence by dibenzo [1,4] azaborine derivatives Reviewed

Bae, J; Sakai, M; Tsuchiya, Y; Ando, N; Chen, XK; Nguyen, TB; Chan, CY; Lee, YT; Auffray, M; Nakanotani, H; Yamaguchi, S; Adachi, C

FRONTIERS IN CHEMISTRY Vol. 10 page： 990918 2022.9

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Papers - YAMAGUCHI, Shigehiro