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330. Subcellular analysis of fatty acid metabolism using organelle-selective click chemistry
T. Kimura, S. Kawamoto, A. Fujisawa, M. Yoshida, Y. Shen, M. Tsuchiya, T. Tamura*, I. Hamachi*
Journal of the American Chemical Society, just accepted doi: 10.1021/jacs.5c02871
329. Recent advances in proximity labeling for chemical proteomics: paving the way for in vivo applications
F. Y. Tanimura Valor, T. Tamura, I. Hamachi*
Current Opinion in Chemical Biology, just accepted
328. Rapid and reversible fluorescent probe enables repeated snapshot imaging of AMPA receptors during synaptic plasticity
K. Soga, T. Fujiwara, M. Nakagawa, A. Shibata, H. Adriel, K. Yatsuzuka, W. Kakegawa, M. Yuzaki, I. Hamachi, E. Nango*, S. Kiyonaka*
Science Advances, 11, 23, 2375-2548 (2025) doi: 10.1126/sciadv.adt6683
327. In-brain synthesis of receptor-based protease sensors by coupling ligand-directed chemistry and click chemistry
S. Sakamoto, K. Shiraiwa, M. Wang, M. Ishikawa, H. Nonaka,* I. Hamachi*
Nature Synthesis (2025) doi: 10.1038/s44160-025-00815-6
326. Intratumour oxidative hotspots provide a niche for cancer cell dissemination
Y. Ueda, S. Kiyonaka*, L. M. Selfors, K. Inoue, H. Harada, T. Doura, K. Onuma, M. Uchiyama, R. Kurogi, Y. Yamada, J. H. Sun, R. Sakaguchi, Y. Tado, H. Omatsu, H. Suzuki, M. Aoun, T. Nakayama, T. Kajimoto, T. Yano, R. Holmdahl, I. Hamachi, M. Inoue, Y. Mori*, N. Takahashi*
Nature Cell Biology, 27, 530-543 (2025) doi: 10.1038/s41556-025-01617-w
325. Profiling proteins involved in peroxynitrite homeostasis using ROS/RNS conditional proteomics
H. Zhu*, H. Uno, K. Matsuba, I. Hamachi*
Journal of the American Chemical Society, 147, 9, 7305-7316 (2025) doi: 10.1021/jacs.4c14060
324. A Protein Cleavage Platform Based on Selective Formylation at Cysteine Residues
N. Zenmyo, Y. Matsumoto, A. Yasuda, S. Uchinomiya, N. Shindo, K. Sasaki-Tabata, E. Mishiro-Sato, T. Tamura, I. Hamachi, A. Ojida*
Journal of the American Chemical Society, 147, 4, 3080-3091(2025) doi: 10.1021/jacs.4c10991
323. Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure
K. Yamaura, N. Takemata*, M. Kariya, A. Osaka, S. Ishino, M. Yamauchi, T. Tamura, I. Hamachi, S. Takada, Y. Ishino, H. Atomi*
Nature Communications, 16: 1312 (2025) doi: 10.1038/s41467-025-56197-y
322. Conversion of silent synapses to AMPA receptor-mediated functional synapses in human cortical organoids
M. Nishimura, T. Kodera, S. Adachi, A. Y. Sato, R. F. Takeuchi, H. Nonaka, I. Hamachi, F. Osakada*
Neuroscience Research, 212, 20-30 (2025) doi: 10.1016/j.neures.2024.12.008
321. Thoughts for the future
L. M. Alkhalaf, C. Arrowsmith, E. P. Balskus, G. Bergamini, R. Bhandari, C. J. Chang, P. Chen, X. Chen, A. Ciulli, J. A. Cricco, B. G. Davis, M. Delbianco, N. Dudareva, E. Dueber, F. Ferguson, P. O. Giuseppe, I. Hamachi, M. C. Hammond, S. K. Hatzios, W. D. Heo, J. P. Janet, S. S. Kamat, S. Knapp, Y. Krishnan, K. Lang, L. Laraia, R. B. Leveson-Gower, X. D. Li, D. R. Liu, M. Liu, N. London, N. Mahanta, C. Mayor-Ruiz, T. Muir, M. T. Murakami, H. Rhee, M. Robers, A. Satz, B. A. Schulman, B. Shen, B. Shoichet, E. Strauss, T. Suzuki, P. Tiwary, H. Waldmann, T. R. Ward, A. Weeks, E. Weerapana, G. Winter
Nature Chemical Biology, 21, 6-15 (2025) doi:10.1038/s41589-024-01802-2
320. Selective Labeling of Phosphatidylcholine to Track Their Translocation Between Organelles in Living Cells
T. Tamura*, I. Hamachi*
Intracellular Lipid Transport, 1, 1-11 (2024) eBook ISBN 978-1-0716-4318-1
319. Targeted covalent modification strategies for drugging the undruggable targets
T. Tamura*, M. Kawano, I. Hamachi*
Chemical Reviews, 125, 2, 1191-1253 (2025) doi: 10.1021/acs.chemrev.4c00745
318. N-acyl-N-alkyl/aryl sulfonamide chemistry assisted by proximity for modification and covalent inhibition of endogenous proteins in living systems
T. Tamura*, I. Hamachi*
Accounts of Chemical Research, 58, 1, 87-100 (2025) doi: 10.1021/acs.accounts.4c00628
317. P2Y12 receptor ligands enable design of fluorescent imaging probes for microglia
H. Nonaka,* M. Wang, I. Hamachi*
Chemistry Letters, 53, 10, upae185 (2024) doi: 10.1093/chemle/upae185
316. Photoproximity labeling of endogenous receptors in the live mouse brain in minutes
M. Takato, S. Sakamoto, H. Nonaka, F. Y. Tanimura Valor, T. Tamura*, I. Hamachi*
Nature Chemical Biology, 21, 109-119 (2025) doi: 10.1038/s41589-024-01692-4
315. Molecular anchoring and fluorescent labeling in animals compatible with tissue clearing for 3D imaging
T. Mino, H. Nonaka, I. Hamachi*
Current Opinion in Chemical Biology, 81, 102474 (2024) doi: 10.1016/j.cbpa.2024.102474
314. Protein-labeling reagents selectively activated by copper(I)
R. Cheng, Y. Nishikawa, T. Wagatsuma, T. Kambe, Y. Tanaka, Y. Ogra, T. Tamura*, I. Hamachi*
ACS Chemical Biology, 19, 6, 1222-1228 (2024) doi: 10.1021/acschembio.4c00011
313. Post-click labeling enables highly accurate single cell analyses of glucose uptake ex vivo and in vivo
M. Tsuchiya*, N. Tachibana, I. Hamachi*
Communications Biology, 7: 459 (2024) doi: 10.1038/s42003-024-06164-y
312. Tyrosinase-based proximity labeling in living cells and in vivo
H. Zhu*, J. H. Oh, Y. Matsuda, T. Mino, M. Ishikawa, H. Nakamura, M. Tsujikawa, H. Nonaka, I. Hamachi*
Journal of the American Chemical Society, 146,11,7515-7523 (2024) doi: 10.1021/jacs.3c13183
311. Emergence of dynamic instability by hybridizing synthetic self-assembled dipeptide fibers with surfactant micelles
S. Torigoe, K. Nagao, R. Kubota*, I. Hamachi*
Journal of the American Chemical Society, 146, 9, 5799–5805 (2024) doi: 10.1021/jacs.3c14565
310. Bioorthogonal chemical labeling of endogenous neurotransmitter receptors in living mouse brains
H. Nonaka, S. Sakamoto, K. Shiraiwa, M. Ishikawa, T. Tamura, K. Okuno, T. Kondo, S. Kiyonaka, E. A. Susaki, C. Shimizu, H. R. Ueda, W. Kakegawa, I. Arai, M. Yuzaki, I. Hamachi*
Proceeding of National Academy of Science of USA, 121, 6: 2313887121 (2024) doi: 10.1073/pnas.2313887121
309. Naturally occurring quercetin and myricetin as potent inhibitors for Äb01 human ectonucleotide pyrophosphatase/phosphodiesterase 1
P. Duangiad, B. Nutho, T. Chaijarasphong, N. P. Morales, T. Pongtharangkul, I. Hamachi, A. Ojida, J. Wongkongkatep*
Scientific Reports, 14: 125 (2024) doi: 10.1038/s41598-023-50590-7
308. Lysine-reactive N-acyl-N-aryl sulfonamide warheads: Improved reaction properties and application in the covalent inhibition of an ibrutinib-resistant BTK mutant
M. Kawano, S. Murakawa, K. Higashiguchi, K. Matsuda, T. Tamura*, I. Hamachi*
Journal of the American Chemical Society, 145, 48, 26202–26212 (2023) doi: 10.1021/jacs.3c08740
307. Cell-Like Synthetic Supramolecular Soft Materials Realized in Multicomponent, Non-/Out-of-Equilibrium Dynamic Systems
R. Kubota*, I. Hamachi*
Advanced Science, 2806830 (2023) doi:10.1002/advs.202306830 open access
306. Protocol to visualize the distribution of exogenously administered small molecules in the mouse brain
T. Mino, H. Nonaka, S. Sakamoto, J. H. Oh, I. Hamachi*
STAR Protocols, 4,3,102555(2023) doi:10.1016/j.xpro.2023.102555
305. Visualizing formation and dynamics of a three-dimensional sponge-like network of a coacervate in real time
R. Kubota*, T. Hiroi, Y. Ikuta, Y. Liu, I. Hamachi*
Journal of the American Chemical Society, 145, 33, 18316-18328 (2023) doi:10.1021/jacs.3c03793
304. Flow cytometric analysis of phosphatidylcholine metabolism using organelle-selective click labeling
M. Tsuchiya*, N. Tachibana, I. Hamachi*
STAR Protocols, 4,3,102525(2023) doi:10.1016/j.xpro.2023.102525
303. Coronaridine congeners induce sedative and anxiolytic-like activity in naive and stressed/anxious mice by allosteric mechanisms involving increased GABAA receptor affinity for GABA
H. R. Arias, P. D. Deurwaerdère, P. Scholze, S. Sakamoto, I. Hamachi, G. D. Giovanni, A. Chagraoui
European Journal of Pharmacology, 953: 175854 (2023) doi: 10.1016/j.ejphar.2023.175854
302. Endogenous cell-surface receptor modification by metal chelation-assisted pyridinium oxime catalyst
V. Thimaradka, H. Utsunomiya, T. Tamura*, I. Hamachi*
Organic Letters, 25, 12, 2118-2122 (2023) doi:10.1021/acs.orglett.3c00541
301. Four distinct network patterns of supramolecular/polymer composite hydrogels controlled by formation kinetics and interfiber interactions
K. Nakamura, R. Kubota*, T. Aoyama, K. Urayama, I. Hamachi*
Nature Communications, 14: 1696 (2023) doi:10.1038/s41467-023-37412-0
300. Organelle-selective click labeling coupled with flow cytometry allows pooled CRISPR screening of genes involved in phosphatidylcholine metabolism
M. Tsuchiya, N. Tachibana, K. Nagao, T. Tamura*, I. Hamachi*
Cell Metabolism, 35, 6, 1072-1083 (2023) doi:10.1016/j.cmet.2023.02.014
299. Ligand-directed chemistry for protein labeling for affinity-based protein analysis
S. Sakamoto, I. Hamachi*
Israel Journal of Chemistry, e202200077 (2023) doi: 10.1002/ijch.202200077
298. Recent progress of subcellular-compartment-focused chemical proteomics
L. Wang, H. Nonaka, I. Hamachi
Advances in Chemical Proteomics, 217-247 (2022) doi: 10.1016/B978-0-12-821433-6.00006-4
297. Revisiting PFA-mediated tissue fixation chemistry: FixEL enables trapping of small molecules in the brain to visualize their distribution changes
H. Nonaka, T. Mino, S. Sakamoto, J. H. Oh, Y. Watanabe, M. Ishikawa, A. Tsushima, K. Amaike, S. Kiyonaka, T. Tamura, A. R. Aricescu, W. Kakegawa, E. Miura, M. Yuzaki, I. Hamachi*
Chem, 9, 2, 523-540 (2023) doi:10.1016/j.chempr.2022.11.005
296. Chemical, Pharmacological, and Structural Characterization of Novel Acrylamide-Derived Modulators of the GABAA Receptor
H. R. Arias*, S. R. Pierce, A. L. Germann, S. Q. Xu, M. O. Ortells, S. Sakamoto, D. Manetti, M. Novella R., I. Hamachi, G. Akk
Molecular Pharmacology, 104, 115(2023) doi: 10.1124/molpharm.123.000692
295. Fluorescence identification of arthropathic calcium pyrophosphate single crystals using alizarin red S and a xanthene dipicolylamine ZnII complex
W. Srinarawat, R. Hemstapat, T. Tawonsawatruk, N. Patikarnmonthon, I. Hamachi, A. Ojida and J. Wongkongkatep
Analyst, 147, 21, 4910-4918 (2022) doi:10.1039/D2AN01257J
294. Modulation of the mammalian GABAA receptor by type I and type II positive allosteric modulators of the α7 nicotinic acetylcholine receptor
H. R. Arias, A. L. Germann, S. R. Pierce, S. Sakamoto, M. O. Ortells, I. Hamachi, G. Akk
British Journal of Pharmacology, 179, 24, 5323-5337 (2022) doi:10.1111/bph.15948
293. Light-induced stabilization of microtubules by photo-crosslinking of Tau-derived peptide
S. Watari, H. Inaba, T. Tamura, A. Md. R. Kabir, A. Kakugo, K. Sada, I. Hamachi, K. Matsuura
Chemical Communications , 58, 9190 - 9193 (2022) doi:10.1039/D2CC01890J
292. Temporal stimulus patterns drive differentiation of a synthetic dipeptide-based coacervate
R. Kubota*, S. Torigoe, I. Hamachi*
Journal of the American Chemical Society , 144, 33, 15155-15164 (2022) doi:10.1021/jacs.2c05101
291. Chemical biology tools for imaging-based analysis of organelle membranes and lipids
T. Tamura, I. Hamachi
Current Opinion in Chemical Biology , 70: 102182 (2022) doi: 10.1016/j.cbpa.2022.102182
290. Coordination chemogenetics for activation of GPCR-type glutamate receptors in brain tissue
K. Ojima, W. Kakegawa, T. Yamasaki, Y. Miura, M. Itoh, Y. Michibata, R. Kubota, T. Doura, E. Miura, H. Nonaka, S. Mizuno, S. Takahashi, M. Yuzaki*, I. Hamachi*, S. Kiyonaka*
Nature Communications , 13, 3167 (2022) doi:10.1101/2021.10.01.462737
289. Orthogonal activation of metabotropic glutamate receptor using coordination chemogenetics
A. Senoo, Y. Yamada, K. Ojima, T. Doura, I. Hamachi, S. Kiyonaka
Frontiers in Chemistry , 9, 825669 (2022) doi:10.3389/fchem.2021.825669
288. Extracellular ATP limits homeostatic T cell migration within lymph nodes
D. Kobayashi, Y. Sugiura, E. Umemoto, A. Takeda, H. Ueta, H. Hayasaka, S. Matsuzaki, T. Katakai, M. Suematsu, I. Hamachi, G. G Yegutkin, M. Salmi, S. Jalkanen, M. Miyasaka
Frontiers in Immunology, 12 (2021) doi:10.3389/fimmu.2021.786595
287. Photo-triggered spatially controlled out-of-equilibrium patterns of peptide nanofibers in a self-sorting double network hydrogel
K. Nakamura, W. Tanaka, K. Sada, R. Kubota, T. Aoyama, K. Urayama, I. Hamachi
Journal of the American Chemical Society, 143, 46, 19532–19541(2021) doi:10.1021/jacs.1c09172
286. Organelle-selective labeling of choline-containing phospholipids(CPLs) and real-time imaging in living cells
M. Tsuchiya, T. Tamura, I. Hamachi*
Current Protocols , e105, Volume 1 (2021) doi: 10.1002/cpz1.105
285. Recent applications of N-acyl imidazole chemistry in chemical biology
T. Mino, S. Sakamoto, I. Hamachi*
Bioscience, Biotechnology, and Biochemistry , 85, 1, 53-60 (2021) doi:10.1093/bbb/zbaa026
284. Voices of chemical biology
B. Davis, K. Backus, G. Winter, R. Chica, D. Li, S. Lee, C. He, A. Weeks, C. Overall, S. Hagihara, B. Thuronyi, S. Kamat, L. Chen, R. HurtadoGuerrero, S. Yao, L. Mahal, C. Voigt, C. Woo, E. Strauss, K. Kikuchi, T. Dore, S. Radford, X. Li, W. Heo, G. S. Furga, T. Deans, V. Belousov, M. Matthews, C. Jackson, S. Malek, H. Waldmann, A. Rising, M. Jewett, D. Stamou, E. Parker, M. Murakami, K. Polizzi, I. Hamachi, T. Erb, C. Joo, M. Uesugi, R. Prinjha, G. Rechavi, R. Solano, B. Schulman, Y. David, R. Oslund
Nature Chemical Biology , 17, 1-4 (2021) doi:10.1038/s41589-020-00714-1
283. Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies
R. Kubota, W. Tanaka, I. Hamachi*
Chemical Reviews, 121, 22, 14281-14347 (2021) doi:10.1021/acs.chemrev.0c01334
282. Enhanced Suppression of a Protein–Protein Interaction in Cells Using Small-Molecule Covalent Inhibitors Based on an N-Acyl-N-alkyl Sulfonamide Warhead
T. Ueda, T. Tamura, M. Kawano, K. Shiono, F. Hobor, A. J. Wilson, and I. Hamachi*
Journal of the American Chemical Society , 143, 12, 4766–4774(2021) doi.org/10.1021/jacs.1c00703
281. Ligand-directed two-step labeling to quantify neuronal glutamate receptor trafficking
K. Ojima, K. Shiraiwa, T. Doura, M. Takato, K. Komatsu, M. Yuzaki, I. Hamachi*, S. Kiyonaka*
Nature Communications , 12:831 (2021) doi:10.1038/s41467-021-21082-x
280. Site-specific covalent labeling of His-tag fused proteins with N-acyl-N-alkyl sulfonamide reagent
V. Thimaradka, J. H. Oh, C. Heroven, A. R. Aricescu, M. Yuzaki, T. Tamura*, I. Hamachi*
Bioorganic & Medicinal Chemistry, , 30, 115947(2021) doi:10.1016/j.bmc.2020.115947
279. Fluorescence imaging of drug target proteins using chemical probes
H. Zhu, I. Hamachi*
Journal of Pharmaceutical Analysis , 10, 5, 426-433 (2020) doi:10.1016/j.jpha.2020.05.013
278. Chemical Tools for Endogenous Protein Labeling and Profiling
K. Shiraiwa, R. Cheng, H. Nonaka, T. Tamura, and I. Hamachi*
Cell Chemical Biology , 27, 8, 970-985(2020) doi:10.1016/j.chembio|.2020.06016
277. In Situ Real-time Confocal Imaging of a Self-assembling Peptide-grafted Polymer Showing pH-responsive Hydrogelation
R. Kubota, S. Torigoe, S. Liu, & I. Hamachi*
Chemistry Letters , 49, 11, 1319-1323(2020) doi:10.1246/cl.200513
276. Organelle membrane-specific chemical labeling and dynamic imaging in living cells
T. Tamura, A. Fujisawa, M. Tsuchiya, Y. Shen, K. Nagao, S. Kawano, Y. Tamura, T. Endo, M. Umeda & I. Hamachi*
Nature Chemical Biology , 16, 12, 1361-1367(2020) doi:10.1038/s41589-020-00651-z
275. Imaging and profiling of proteins under oxidative conditions in cells and tissues by hydrogen-peroxide-responsive labeling
H. Zhu, T. Tamura, A. Fujisawa, Y. Nishikawa, R. Cheng, M. Takato, and I. Hamachi*
Journal of the American Chemical Society , 142, 37, 15711–15721(2020) doi:10.1021/jacs.0c02547
274. Control of seed formation allows two distinct self-sorting patterns of supramolecular nanofibers
R. Kubota, K. Nagao, W. Tanaka, R. Matumura, T. Aoyama, K. Urayama and I. Hamachi*
Nature Communications , 11: 4100(2020) doi:10.1038/s41467-020-17984-x
273. Activity-Based Sensing with a Metal-Directed Acyl Imidazole Strategy Reveals Cell Type-Dependent Pools of Labile Brain Copper
S. Lee, Y. S. C. Chung, P. Liu, L. Craciun, Y. Nishikawa, K. Bruemmer, I. Hamachi, K. Saijo, E. Miller, C. Chang*
Journal of the American Chemical Society , 142, 35, 14993–15003(2020) doi:10.1021/jacs.0c05727
272. Protein-Responsive Protein-Release of Supramolecular/polymer Hydrogel Composite Integrating Enzyme Activation Systems
H. Shigemitsu, R. Kubota, K. Nakamura, T. Matsuzaki, S. Minami, T. Aoyama, K. Urayama and I. Hamachi*
Nature Communications , 11: 3859(2020) doi:10.1038/s41467-020-17698-0
271. Force generation by a propagating wave of supramolecular nanofibers
R. Kubota, M. Makuta, R. Suzuki, M. Ichikawa, M. Tanaka and I. Hamachi*
Nature Communications, 11: 3541(2020) doi:10.1038/s41467-020-17394-z
270. Fluorescence determination of soluble pyrophosphate levels in synovial fluid as a marker of pseudogout using middle point of quantification concept and molecular sensor
N. Yongwattana, N. Mekjinda, W. Thepsing, S. Ounsuk, P. Wongkongkatep, T. Tawonsawatruk, I. Hamachi, A. Ojida, J. Wongkongkatep*
Science Asia , 46, 36-42 (2020) doi:10.2306/scienceasia1513-1874.2020.S005
269. Fluorescence Differentiation of ATP-Related Multiple Enzymatic Activities in Synovial Fluid as a Marker of Calcium Pyrophosphate Deposition Disease Using Kyoto Green
N. Yongwattana, N. Mekjinda,T. Tawonsawatruk, I. Hamachi, A. Ojida and J. Wongkongkatep*
molecules, 25, 1116 (2020) doi:10.3390/molecules25051116
268. Screening of protein-ligand interactions under crude conditions by native mass spectrometry
K. Takano, S. Arai, S. Sakamoto, H. Ushijima, T. Ikegami, K. Saikusa, T. Konuma, I. Hamachi, S. Akashi
Analytical and Bioanalytical Chemistry , 412, 4037-4043 (2020) doi:10.1007/s00216-020-02649-x
267. Masking Phosphate with Rare-Earth Elements Enables Selective Detection of Arsenate by Dipycolylamine-ZnII Chemosensor
N. Mekjinda, S. Phunnarungsi, V. Ruangpornvisuti, R. Ritchie, I. Hamachi, A. Ojida, J. Wongkongkatep
Scientific Reports , 10:2656 (2020) doi:10.1038/s41598-020-59585-0
266. Development of a Photoactivatable Proximity Labeling Method for the Identification of Nuclear Proteins
T. Tamura*, M. Takato, K. Shiono, I. Hamachi*
Chemistry Letters , 49, 145-148 (2020) doi:10.1246/cl.190804
265. The Power of Confocal Laser Scanning Microscopy in Supramolecular Chemistry: In situ Real‐time Imaging of Stimuli‐Responsive Multicomponent Supramolecular Hydrogels
R. Kubota, K. Nakamura, S. Torigoe, I. Hamachi
ChemistryOPEN , 9,67-79 (2020) doi:10.1002/open.201900328
264. Development of a cell-based ligand-screening system for identifying Hsp90 inhibitors
T. Ueda, T. Tamura*, I. Hamachi*
Biochemistry , 59, 2, 179-182 (2020) doi:10.1021/acs.biochem.9b00781