Papers - Sasaki, Eita

Thermo-responsive targeting of polymeric micelles by controlling the cellular uptake based on the change of their surface arginine density

Sota Yamada, Eita Sasaki, Hisashi Ohno, Kenichi Nagase, Kenjiro Hanaoka

Communications Chemistry (Springer Nature)  8   325 2025.11

Research paper (scientific journal), Joint Work, Accepted

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Development of a silicon phthalocyanine analogue for near-infrared photoimmunotherapy and its application to HTLV-1-infected leukemic cells

Yoshikazu Fuse, Eita Sasaki, Masaharu Tamaki, Shunto Kawamura, Hisashi Ohno, Sota Yamada, Masahiro Yasunaga, Hideo Takakura, Hirofumi Hanaoka, Hisataka Kobayashi, Hideki Nakasone, Kenjiro Hanaoka

RSC Chemical Biology (Royal Society of Chemistry)  6   1576 - 1584 2025.08

Research paper (scientific journal), Joint Work, Accepted

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Development of a near-infrared fluorescence probe for hypochlorous acid based on the phenyl-induced twisted intramolecular charge transfer (p-TICT) mechanism

Hisashi Ohno, Shun Sumitani, Ariunbold Chuluun-Erdene, Takahiro Kuchimaru, Sota Yamada, Eita Sasaki, Kenjiro Hanaoka

Chemical Communications (Royal Society of Chemistry)  61 ( 57 ) 10522 - 10525 2025.06

Research paper (scientific journal), Joint Work, Accepted

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Trans-omics landscape of systemic vasculitis identified matrix metalloproteinase 12 as a novel signature molecule

Kotaro Matsumoto, Katsuya Suzuki, Mayu Magi, Shinichi Onishi, Hiroto Yoshida, Masaru Takeshita, Junko Kuramoto, Masaki Yazawa, Tatsuya Kato, Hideyuki Shimizu, Tsutomu Ito, Sota Yamada, Eita Sasaki, Kenjiro Hanaoka, Mariko Noguchi-Sasaki, Yoshihiro Matsumoto, Tsutomu Takeuchi, Yuko Kaneko

Rheumatology (Oxford University Press (OUP))   2025.03

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1462-0324

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Abstract

Objectives

To identify key molecules involved in the disease pathophysiology of systemic vasculitis through trans-omics analysis, with a specific focus on demonstrating matrix metalloproteinase (MMP) 12 as a potential biomarker in rheumatic entities.

Methods

Patients with newly diagnosed or relapsed rheumatic and musculoskeletal diseases from June 2013 until September 2022 were enrolled. We screened vasculitis-specific molecules by combining findings from serum proteome analysis and whole-blood RNA sequencing. We further validated the identified molecules using immunohistochemical staining and spatial transcriptome analysis.

Results

Serum proteome and RNA sequencing identified MMP12 as a significant molecule for systemic vasculitis; it distinguished vasculitis from other rheumatic and musculoskeletal diseases, reflected disease activity along with longitudinal change, and predicted relapse in patients with large-vessel vasculitis. MMP12 could also be used to detect insidious disease activity even under treatment with IL-6 inhibition. Immunohistochemical staining of the affected tissues demonstrated that MMP12 was specifically expressed in tissue-infiltrating CD206-positive macrophages. Spatial transcriptome analysis revealed the characteristic phenotype of MMP12-positive macrophages and its association with macrophage maturation and formation of multinucleated giant cells.

Conclusion

MMP12 is a disease-specific molecule that is associated with macrophage maturation and the formation of multinucleated giant cells and reflects disease activity independently of the IL-6 pathway in systemic vasculitis.

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In vitro selection of dye-fluorescence-enhancing peptide aptamer by cDNA display

Takashi Kubo, Tomoyuki Koike, Tomoki Ouchi, Nayab Khaliq, Eita Sasaki, Kouichi Kuroda, Mitsuyoshi Ueda, Kenjiro Hanaoka, Naoto Nemoto

Analytical Biochemistry (Elsevier)  698   115722 - 115722 2025.03

Research paper (scientific journal), Joint Work, Accepted,  ISSN  0003-2697

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Heat-guided drug delivery via thermally induced crosslinking of polymeric micelles

Sota Yamada, Eita Sasaki, Hisashi Ohno, Kenjiro Hanaoka

Communications Chemistry (Springer Nature)  7   287 2024.12

Research paper (scientific journal), Joint Work, Accepted

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A general fluorescence off/on strategy for fluorogenic probes: Steric repulsion-induced twisted intramolecular charge transfer (sr-TICT).

Kenjiro Hanaoka, Takayuki Ikeno, Shimpei Iwaki, Sayaka Deguchi, Kazuo Takayama, Hiroyuki Mizuguchi, Fumiya Tao, Nobuhiko Kojima, Hisashi Ohno, Eita Sasaki, Toru Komatsu, Tasuku Ueno, Kazuya Maeda, Hiroyuki Kusuhara, Yasuteru Urano

Science advances 10 ( 7 ) eadi8847 2024.02

Research paper (scientific journal), Joint Work, Accepted

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Various control strategies are available for building fluorogenic probes to visualize biological events in terms of a fluorescence change. Here, we performed the time-dependent density functional theory (TD-DFT) computational analysis of the twisted intramolecular charge transfer (TICT) process in rhodamine dyes. On the basis of the results, we designed and synthesized a series of rhodamine dyes and established a fluorescence quenching strategy that we call steric repulsion-induced TICT (sr-TICT), in which the fluorescence quenching process is greatly accelerated by simple intramolecular twisting. As proof of concept of this design strategy, we used it to develop a fluorogenic probe, 2-Me PeER (pentyloxyethylrhodamine), for the N-dealkylation activity of CYP3A4. We applied 2-Me PeER for CYP3A4 activity-based fluorescence-activated cell sorting (FACS), providing access to homogeneous, highly functional human-induced pluripotent stem cell (hiPSC)-derived hepatocytes and intestinal epithelial cells. Our results suggest that sr-TICT represents a general fluorescence control method for fluorogenic probes.

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Development of a Fluorescence Probe for Detecting Nitroreductase Activity Based on Steric Repulsion-Induced Twisted Intramolecular Charge Transfer (sr-TICT)

Mizuki Sugimoto, Eita Sasaki, Hisashi Ohno, Takayuki Ikeno, Sota Yamada, Kenjiro Hanaoka

Chemical and Pharmaceutical Bulletin 72 ( 9 ) 810 - 816 2024

Research paper (scientific journal), Joint Work, Accepted,  ISSN  0009-2363

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Recent advances in Si-rhodamine-based fluorescent probes for live-cell imaging

Hisashi Ohno, Eita Sasaki, Sota Yamada, Kenjiro Hanaoka

Organic & Biomolecular Chemistry (Royal Society of Chemistry (RSC))  22 ( 16 ) 3099 - 3108 2024

Accepted,  ISSN  1477-0520

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This review presents the recent advances in far-red to NIR fluorescent probes based on Si-rhodamines, focusing on live-cell imaging applications.

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Discovery of a Cystathionine γ-Lyase (CSE) Selective Inhibitor Targeting Active-site Pyridoxal 5’-Phosphate (PLP) via Schiff Base Formation

Honami Echizen, Kenjiro Hanaoka, Kazuhito Shimamoto, Ryota Hibi, Sachiko Toma-Fukai, Hisashi Ohno, Eita Sasaki, Toru Komatsu, Tasuku Ueno, Yukihiro Tsuchiya, Yasuo Watanabe, Takao Otsuka, Hiroaki Saito, Satoru Nagatoishi, Kouhei Tsumoto, Hirotatsu Kojima, Takayoshi Okabe, Toshiyuki Shimizu, Yasuteru Urano

Scientific Reports 13 ( 1 ) 16456 - 16456 2023.09

Research paper (scientific journal), Joint Work, Accepted

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D,L-Propargylglycine (PAG) has been widely used as a selective inhibitor to investigate the biological functions of cystathionine γ-lyase (CSE), which catalyzes the formation of reactive sulfur species (RSS). However, PAG also inhibits other PLP (pyridoxal-5'-phosphate)-dependent enzymes such as methionine γ-lyase (MGL) and L-alanine transaminase (ALT), so highly selective CSE inhibitors are still required. Here, we performed high-throughput screening (HTS) of a large chemical library and identified oxamic hydrazide 1 as a potent inhibitor of CSE (IC50 = 13 ± 1 μM (mean ± S.E.)) with high selectivity over other PLP-dependent enzymes and RSS-generating enzymes. Inhibitor 1 inhibited the enzymatic activity of human CSE in living cells, indicating that it is sufficiently membrane-permeable. X-Ray crystal structure analysis of the complex of rat CSE (rCSE) with 1 revealed that 1 forms a Schiff base linkage with the cofactor PLP in the active site of rCSE. PLP in the active site may be a promising target for development of selective inhibitors of PLP-dependent enzymes, including RSS-generating enzymes such as cystathionine β-synthase (CBS) and cysteinyl-tRNA synthetase 2 (CARS2), which have unique substrate binding pocket structures.

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Molecular design of near-infrared (NIR) fluorescent probes targeting exopeptidase and application for detection of dipeptidyl peptidase 4 (DPP-4) activity

Y Hoshino, K Hanaoka, K Sakamoto, M Yasunaga, T Kojima, D Kotani, A Nomoto, E Sasaki, T Komatsu, T Ueno, H Takamaru, Y Saito, Y Seto, Y Urano

RSC Chemical Biology (Royal Society of Chemistry (RSC))  3 ( 7 ) 859 - 867 2022.03

Research paper (scientific journal), Joint Work, Accepted

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We developed a new molecular design for NIR fluorescent probes that target exopeptidase by utilizing the >110 nm blueshift of unsymmetrical Si–rhodamines.

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General design strategy to precisely control the emission of fluorophores via a twisted intramolecular charge transfer (TICT) process

Kenjiro Hanaoka, Shimpei Iwaki, Kiyoshi Yagi, Takuya Myochin, Takayuki Ikeno, Hisashi Ohno, Eita Sasaki, Toru Komatsu, Tasuku Ueno, Motokazu Uchigashima, Takayasu Mikuni, Kazuki Tainaka, Shinya Tahara, Satoshi Takeuchi, Tahei Tahara, Masanobu Uchiyama, Tetsuo Nagano, Yasuteru Urano

Journal of the American Chemical Society (American Chemical Society (ACS))  144 ( 43 ) 19778 - 19790 2022

Research paper (scientific journal), Joint Work, Accepted,  ISSN  0002-7863

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Recent advances in detection, isolation, and imaging techniques for sulfane sulfur-containing biomolecules

Honami Echizen, Eita Sasaki, Kenjiro Hanaoka

Biomolecules 11   1553 2021

Accepted,  ISSN  2218-273X

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<jats:p>Hydrogen sulfide and its oxidation products are involved in many biological processes, and sulfane sulfur compounds, which contain sulfur atoms bonded to other sulfur atom(s), as found in hydropersulfides (R-S-SH), polysulfides (R-S-Sn-S-R), hydrogen polysulfides (H2Sn), etc., have attracted increasing interest. To characterize their physiological and pathophysiological roles, selective detection techniques are required. Classically, sulfane sulfur compounds can be detected by cyanolysis, involving nucleophilic attack by cyanide ion to cleave the sulfur–sulfur bonds. The generated thiocyanate reacts with ferric ion, and the resulting ferric thiocyanate complex can be easily detected by absorption spectroscopy. Recent exploration of the properties of sulfane sulfur compounds as both nucleophiles and electrophiles has led to the development of various chemical techniques for detection, isolation, and bioimaging of sulfane sulfur compounds in biological samples. These include tag-switch techniques, LC-MS/MS, Raman spectroscopy, and fluorescent probes. Herein, we present an overview of the techniques available for specific detection of sulfane sulfur species in biological contexts.</jats:p>

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Studies of lincosamide formation complete the biosynthetic pathway for lincomycin A

SA Wang, CI Lin, J Zhang, R Ushimaru, E Sasaki, H Liu

Proceedings of the National Academy of Sciences (Proceedings of the National Academy of Sciences)  117   24794 - 24801 2020.09

Research paper (scientific journal), Joint Work, Accepted,  ISSN  0027-8424

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The structure of lincomycin A consists of the unusual eight-carbon thiosugar core methyllincosamide (MTL) decorated with a pendent <italic>N</italic>-methylprolinyl moiety. Previous studies on MTL biosynthesis have suggested GDP-ᴅ-<italic>erythro</italic>-α-ᴅ-<italic>gluco</italic>-octose and GDP-ᴅ-α-ᴅ-lincosamide as key intermediates in the pathway. However, the enzyme-catalyzed reactions resulting in the conversion of GDP-ᴅ-<italic>erythro</italic>-α-ᴅ-<italic>gluco</italic>-octose to GDP-ᴅ-α-ᴅ-lincosamide have not yet been elucidated. Herein, a biosynthetic subpathway involving the activities of four enzymes—LmbM, LmbL, CcbZ, and CcbS (the LmbZ and LmbS equivalents in the closely related celesticetin pathway)—is reported. These enzymes catalyze the previously unknown biosynthetic steps including 6-epimerization, 6,8-dehydration, 4-epimerization, and 6-transamination that convert GDP-ᴅ-<italic>erythro</italic>-α-ᴅ-<italic>gluco</italic>-octose to GDP-ᴅ-α-ᴅ-lincosamide. Identification of these reactions completes the description of the entire lincomycin biosynthetic pathway. This work is significant since it not only resolves the missing link in octose core assembly of a thiosugar-containing natural product but also showcases the sophistication in catalytic logic of enzymes involved in carbohydrate transformations.

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Self‐Assembly of Proteinaceous Shells around Positively Charged Gold Nanomaterials Enhances Colloidal Stability in High‐Ionic‐Strength Buffers

E Sasaki, RM Dragoman, S Mantri, DN Dirin, MV Kovalenko, D Hilvert

ChemBioChem (Wiley)  21 ( 1-2 ) 74 - 79 2020.01

Research paper (scientific journal), Joint Work, Lead author, Accepted,  ISSN  1439-4227

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Expanding the structural analysis capabilities on an Orbitrap-based mass spectrometer for large macromolecular complexes

Kyle L. Fort, Michiel van de Waterbeemd, Dmitriy Boll, Maria Reinhardt-Szyba, Mikhail E. Belov, Eita Sasaki, Reinhard Zschoche, Donald Hilvert, Alexander A. Makarov, Albert J. R. Heck

Analyst (Royal Society of Chemistry (RSC))  143 ( 1 ) 100 - 105 2018

Research paper (scientific journal), Joint Work, Accepted,  ISSN  0003-2654

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<p>Native mass spectrometry can provide insight into the structure of macromolecular biological systems.</p>

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Structure and assembly of scalable porous protein cages

Eita Sasaki, Daniel Bohringer, Michiel van de Waterbeemd, Marc Leibundgut, Reinhard Zschoche, Albert J. R. Heck, Nenad Ban, Donald Hilvert

Nature Communications (NATURE PUBLISHING GROUP)  8   14663 2017.03

Research paper (scientific journal), Joint Work, Lead author, Accepted,  ISSN  2041-1723

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Proteins that self-assemble into regular shell-like polyhedra are useful, both in nature and in the laboratory, as molecular containers. Here we describe cryo-electron microscopy (EM) structures of two versatile encapsulation systems that exploit engineered electrostatic interactions for cargo loading. We show that increasing the number of negative charges on the lumenal surface of lumazine synthase, a protein that naturally assembles into a similar to 1-MDa dodecahedron composed of 12 pentamers, induces stepwise expansion of the native protein shell, giving rise to thermostable similar to 3-MDa and similar to 6-MDa assemblies containing 180 and 360 subunits, respectively. Remarkably, these expanded particles assume unprecedented tetrahedrally and icosahedrally symmetric structures constructed entirely from pentameric units. Large keyhole-shaped pores in the shell, not present in the wild-type capsid, enable diffusion-limited encapsulation of complementarily charged guests. The structures of these supercharged assemblies demonstrate how programmed electrostatic effects can be effectively harnessed to tailor the architecture and properties of protein cages.

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Self-Assembling Proteinaceous Molecular Sponges

Eita Sasaki, Donald Hilver

Cell Systems 4   368 - 368 2017

Lead author

Characterization of Enzymes Catalyzing Transformations of Cysteine S-Conjugated Intermediates in the Lincosamide Biosynthetic Pathway

Richiro Ushimaru, Chia-I Lin, Eita Sasaki, Hung-wen Liu

ChemBioChem (WILEY-V C H VERLAG GMBH)  17 ( 17 ) 1606 - 1611 2016.09

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1439-4227

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Lincosamides such as lincomycinA, celesticetin, and Bu-2545, constitute an important group of antibiotics. These natural products are characterized by a thiooctose linked to a l-proline residue, but they differ with regards to modifications of the thioacetal moiety, the pyrrolidine ring, and the octose core. Here we report that the pyridoxal 5-phosphate-dependent enzyme CcbF (celesticetin biosynthetic pathway) is a decarboxylating deaminase that converts a cysteine S-conjugated intermediate into an aldehyde. In contrast, the homologous enzyme LmbF (lincomycin biosynthetic pathway) catalyzes C-S bond cleavage of the same intermediate to afford a thioglycoside. We show that Ccb4 and LmbG (downstream methyltransferases) convert the aldehyde and thiol intermediates into a variety of methylated lincosamide compounds including Bu-2545. The substrates used in these studies are the -anomers of the natural substrates. The findings not only provide insight into how the biosynthetic pathway of lincosamide antibiotics can bifurcate to generate different lincosamides, but also reveal the promiscuity of the enzymes involved.

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Protein Nanocontainers from Nonviral Origin: Testing the Mechanics of Artificial and Natural Protein Cages by AFM

K Heinze, E Sasaki, NP King, D Baker, D Hilvert, GJL Wuite, WH Roos

The Journal of Physical Chemistry B (AMER CHEMICAL SOC)  120 ( 26 ) 5945 - 5952 2016.07

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1520-6106

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Self-assembling protein nanocontainers are promising candidates for an increasingly wide scope of purposes. Their applications range from drug delivery vehicles and imaging agents to nanocompartments for controlled enzymatic activity. In order to exploit their full potential in these different fields, characterization of their properties is vital. For example, their mechanical properties give insight into the stability of a particle as a function of their internal content. The mechanics can be probed by atomic force microscopy nanoindentation, and while this single particle method is increasingly used to probe material properties of viral nanocages, it has hardly been used to characterize nonviral nanocages. Here we report nanoindentation studies on two types of nonviral nanocontainers: (i) lumazine synthase from Aquifex aeolicus (AaLS), which naturally self-assembles into icosahedral cages, and (ii) the artificial protein cage O3-33 originating from a computational design approach. In addition, we tested particles that had been engineered toward improved cargo loading capacity and compared these nanocages in empty and loaded states. We found that the thermostable AaLS cages are stiffer and resist higher forces before breaking than the O3-33 particles, but that mutations affecting the size of AaLS particles have a dramatic effect on their structural stability. Furthermore, we show that cargo packaging can occur while maintaining the age's mechanical properties.

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