Publication

- 研究業績 -

2025年度（2025.4-）

Asamitsu K, Hirokawa T, Okamoto T. Drug design for cyclin-dependent kinase 9 (CDK9) inhibitors in silico. Biochem Biophys Rep. 2025 Mar 28;42:101988. doi: 10.1016/j.bbrep.2025.101988. PMID: 40230495.
#SBDD #small molecule #in silico screening #docking simulation #MD simulation

Kitadokoro J, Hirokawa T, Kamo M, Furubayashi N, Okuno Y, Hikima T, Yamamoto M, Inaka K, Maenaka K, Kamitani S, Kitadokoro K. Structural analysis shows the mode of inhibition for Staphylococcus aureus lipase by antipsychotic penfluridol. Sci Rep. 2025 Apr 14;15(1):11876. doi: 10.1038/s41598-025-94981-4. PMID: 40229318
#docking simulation #small molecule #in silico screening #drug repositioning #infection

2024年度（2024.4-）

Kajino K, Sugai T, Kakumoto T, Kise R, Suzuki R, Tokuda A, Sekiya Y, Katamoto R, Kutsumura N, Nagumo Y, Hirokawa T, Inoue A, Saitoh T. Structure-Signal Relationships of the δ-Opioid-Receptor (DOR)-Selective Agonist KNT-127-Part II: Quinoline Ring Modifications for Enhanced G-Protein Signaling and Reduced β-Arrestin Recruitment. Chem Pharm Bull (Tokyo). 2025;73(4):336-348. doi: 10.1248/cpb.c24-00796. PMID: 40204491.
#GPCR #small molecule #docking simulation #MD simulation #SBDD

Horie F, Sanematsu K, Yasumatsu K, Hirokawa T, Shigemura N, Yamashita A, Kusakabe Y. Receptor mechanism producing a sweet taste from plant aroma compounds. Sci Rep. 2025 Mar 12;15(1):6795. doi: 10.1038/s41598-025-89711-9. PMID: 40075099.
#GPCR #small molecule #docking simulation #MD simulation

Ihara Y, Ijichi C, Nogi Y, Sugiki M, Kodama Y, Ihara S, Shirasu M, Hirokawa T, Touhara K. Predicting human olfactory perception by odorant structure and receptor activation profile. Chem Senses. 2025 Jan 31:bjaf002. doi: 10.1093/chemse/bjaf002. PMID: 39888390.
#small molecule #GPCR

Iwaki M, Sakamoto R, Tsutsumi R, Sawada T, Hirokawa T, Kato S, Nagasawa K. Development of an Environmentally Responsive Fluorescent Ligand for Vitamin D Receptor. Chembiochem. 2025 Jan 22:e202401038. doi: 10.1002/cbic.202401038. PMID: 39843389.
#small molecule #docking simulation

Michigami M, Kanata Y, Ven CI, Oshima A, Yamaguchi-Nomoto A, Kinoshita T, Hirokawa T, Fujii I. Deep mutational scanning-guided design of a high-affinity helix-loop-helix peptide targeting G-CSF receptor. Bioorg Med Chem Lett. 2025 Mar 1;117:130071. doi: 10.1016/j.bmcl.2024.130071. PMID: 39667506.
#peptide #modeling

Hama S, Watanabe-Takahashi M, Nishimura H, Omi J, Tamada M, Saitoh T, Maenaka K, Okuda Y, Ikegami A, Kitagawa A, Furuta K, Izumi K, Shimizu E, Nishizono T, Fujiwara M, Miyasaka T, Takamori S, Takayanagi H, Nishikawa K, Kobayashi T, Toyama-Sorimachi N, Yamashita M, Senda T, Hirokawa T, Bito H, Nishikawa K. CaMKII-dependent non-canonical RIG-I pathway promotes influenza virus propagation in the acute-phase of infection. mBio. 2025 Jan 8;16(1):e0008724. doi: 10.1128/mbio.00087-24. PMID: 39601535.
#peptide #modeling

Michigami M, Kira R, Kamo M, Hirokawa T, Kinoshita T, Inaka K, Nakase I, Fujii I. Structural Insights into Helix-Loop-Helix Peptides for "Ligand-Targeting" Intracellular Drug Delivery via VEGF Receptor-Mediated Endocytosis. Biochem Biophys Res Commun. 2024 Dec 31;741:150980. doi: 10.1016/j.bbrc.2024.150980. PMID: 39580956.
#peptide

Ishikawa R, Yanagita K, Shimada S, Sasaki S, Hirokawa T, Ma Y, Nagasawa K, Tera M. Topology-selective photo-crosslinking of G-quadruplexes via dual G-quartet and groove recognition. Chem Commun (Camb). 2024 Nov 14;60(92):13550-13553.doi: 10.1039/d4cc04804k. PMID: 39474792.
#docking simulation #modeling #nucleic acid

Iijima K, Sakamoto R, Tsutsumi R, Nakaya N, Hirokawa T, Odagi M, Sakaki T, Yasuda K, Nagasawa K. Discovery and Structural Analysis of Metabolites of Vitamin D3 Lactones. Chem Pharm Bull (Tokyo). 2024;72(10):899-908. doi: 10.1248/cpb.c24-00495. PMID: 39428509.
#docking simulation #metabolism

Sakamoto K, Fujimoto R, Kamiyama-Ando E, Hirokawa T. Anthricin-induced hyperactive proteasome and its molecular mechanism. Biochem Biophys Rep. 2024 Sep 23;40:101830. doi: 10.1016/j.bbrep.2024.101830. PMID: 39386079.
#MD simulation

Michigami M, Notsu K, Kamo M, Hirokawa T, Kinoshita T, Inaka K, Nakase I, Fujii I. Structural insights into molecular-targeting helix-loop-helix peptide against vascular endothelial growth factor-A. Biochem Biophys Res Commun. 2024 Nov 19;734:150749. doi: 10.1016/j.bbrc.2024.150749. PMID: 39357335.
#MD simulation

Sakamoto K, Iwata S, Jin Z, Chen L, Miyaoka T, Yamada M, Katahira K, Yokoyama R, Ono A, Asano S, Tanimoto K, Ishimura R, Nakagawa S, Hirokawa T, Ago Y, Miyako E. Cyclic Peptides KS-133 and KS-487 Multifunctionalized Nanoparticles Enable Efficient Brain Targeting for Treating Schizophrenia. JACS Au. 2024 Jun 20;4(8):2811-2817. doi: 10.1021/jacsau.4c00311. PMID: 39211592.
#MD simulation #modeling #peptide

Yuya M, Yusuke O, Takayuki S, Yuko Y, Kohsuke O, Hitoshi I, Akitoshi Y, Morimichi H, Yuji O, Wataru M, Kano N, Naho H, Maki M, Takahisa M, Tatsuya I, Kenta H, Mio H, Nobuko A, Takatsugu H, Taishin A. Pseudoirreversible inhibition elicits persistent efficacy of a sphingosine 1-phosphate receptor 1 antagonist. Nat. Comm. 2024 Jul 19;15:5743. doi: 10.1038/s41467-024-49893-8. PMID: 39030171.
#small molecule #docking simulation #MD simulation #modeling #GPCR

Genki K, Takumi H, Ryuhei H, Takatsugu H, Yasuteru S, Ryunosuke Y. Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation. Sci Rep. 2024 Jun 12;14(1):13508. doi: 10.1038/s41598-024-64236-9. PMID: 38866895.
#SBDD #small molecule #docking simulation #MD simulation #modeling

Zihan Z, Toru T, Sarah KF, Manabu I, Takatsugu H, Yukiko M, Koji Y, Chiho O, Masahiro N, Shuzo U, Allison G, Thomas S, Takeshi N. Hexestrol, an estrogen receptor agonist, inhibits Lassa virus entry. J. Virol. 2024 May 29:e0071424. doi: 10.1128/jvi.00714-24. PMID: 38809021.
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Genki K, Takumi H, Ryunosuke Y, Yasuteru S, Hirokawa T. Site Identification and Next Choice Protocol for Hit-to-Lead Optimization. J. Chem. Inf. Model. 2024 Jun 10;64(11):4475-4484. doi: 10.1021/acs.jcim.3c02036. PMID: 38768949.
#SBDD #software development #small molecule #docking simulation #MD simulation #modeling

Kitadokoro J, Kamitani S, Okuno Y, Hikima T, Yamamoto M, Hirokawa T, Kitadokoro K. Crystal Structure of Staphylococcus Aureus Lipase Complex with Unsaturated Petroselinic Acid. FEBS Open Bio. 2024 Jun;14(6):942-954. doi: 10.1002/2211-5463.13808. PMID: 38757397.
#modeling #small molecule #docking simulation

2023年度（2023.4-）

Sakamoto K, Hirokawa T. Lipid bilayer membrane permeability mechanism of the K-Ras(G12D)-inhibitory bicyclic peptide KS-58 elucidated by molecular dynamics simulations. Bioorg Med Chem Lett. 2024 Mar 1;100:129649. doi: 10.1016/j.bmcl.2024.129649. PMID: 38341162.
#MD simulation #peptide

Imamura K, Akagi K, Miyanoiri Y, Tsujimoto H, Hirokawa T, Ashida H, Murakami K, Inoue A, Suno R, Ikegami T, Sekiyama N, Iwata S, Kobayashi T, Tochio H. Interaction Modes of Human Orexin 2 Receptor with Selective and Nonselective Antagonists Studied by NMR Spectroscopy. Structure. 2024 Jan 1. doi: 10.1016/j.str.2023.12.008. PMID: 38194963.
#MD simulation #GPCR

Kudo G, Yanagisawa K, Yoshino R, Hirokawa T. AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics. J Chem Inf Model. 2023 Dec 25;63(24):7768-7777. doi: 10.1021/acs.jcim.3c01677. PMID: 38085669.
#MD simulation #peptide #MSMD

Fujiwara K, Nagasawa S, Maeyama R, Segawa R, Hirasawa N, Hirokawa T, Iwabuchi Y. Biological Evaluation of Isosteric Applicability of 1,3-Substituted Cuneanes as m-Substituted Benzenes Enabled by Selective Isomerization of 1,4-Substituted Cubanes. Chemistry. 2023 Nov 27:e202303548. doi: 10.1002/chem.202303548. PMID: 38012076.
#docking simulation #MD simulation #small molecule

Watanabe R, Tsuji D, Tanaka H, Uno MS, Ohnishi Y, Kitaguchi S, Matsugu T, Nakae R, Teramoto H, Yamamoto K, Shinohara Y, Hirokawa T, Okino N, Ito M, Itoh K. Lysoglycosphingolipids have the ability to induce cell death through direct PI3K inhibition. J Neurochem. 2023 Nov 17. doi: 10.1111/jnc.16012. PMID: 37975558.
#modeling #docking simulation #metabolism

Kawada Y, Hayashi E, Katsuragi Y, Imamura-Jinda A, Hirokawa T, Mizukami T, Hayashi M. Identification of Chemicals that Abrogate Folate-dependent Inhibition of Starch Accumulation in Non-photosynthetic Plastids of Arabidopsis. Plant Cell Physiol. 2023 Oct 6:pcad116. doi: 10.1093/pcp/pcad116. PMID: 37801291.
#in silico screening #small molecule

Nakagita T, Matsuya T, Narukawa M, Kobayashi T, Hirokawa T, Misaka T. Modeling the structure of the transmembrane domain of T1R3, a subunit of the sweet taste receptor, with neohesperidin dihydrochalcone using molecular dynamics simulation. Biosci Biotechnol Biochem. 2023 Sep 15:zbad133. doi: 10.1093/bbb/zbad133. PMID: 37715303.
#docking simulation #MD simulation #GPCR

Yoshino R, Yasuo N, Hagiwara Y, Ishida T, Inaoka DK, Amano Y, Tateishi Y, Ohno K, Namatame I, Niimi T, Orita M, Kita K, Akiyama Y, Sekijima M. Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography. ACS Omega. 2023 Jul 12;8(29):25850-25860. doi: 10.1021/acsomega.3c01314. PMID: 37521650.
#docking simulation #MD simulation #FMO

Mizumoto Y, Sakamoto R, Iijima K, Nakaya N, Odagi M, Tera M, Hirokawa T, Sakaki T, Yasuda K, Nagasawa K. Differential Metabolic Stability of 4α,25- and 4β,25-Dihydroxyvitamin D3 and Identification of Their Metabolites. Biomolecules. 2023 Jun 24;13(7):1036. doi: 10.3390/biom13071036. PMID: 37509072.
#docking simulation #modeling

Sasaki S, Ma Y, Hirokawa T, Ikebukuro K, Tera M, Nagasawa K. Regulation of thrombin activity by ligand-induced topological alteration in a thrombin-binding aptamer. Chem Commun (Camb). 2023 Jun 28. doi: 10.1039/d3cc02308g. Epub ahead of print. PMID: 37377065.
#RNA #docking simulation #modeling

Saito K, Sekiya M, Kainoh K, Yoshino R, Hayashi A, Han SI, Araki M, Ohno H, Takeuchi Y, Tsuyuzaki T, Yamazaki D, Wanpei C, Hada L, Watanabe S, Paramita Adi Putri PI, Murayama Y, Sugano Y, Osaki Y, Iwasaki H, Yahagi N, Suzuki H, Miyamoto T, Matsuzaka T, Shimano H. Obesity-induced metabolic imbalance allosterically modulates CtBP2 to inhibit PPAR-alpha transcriptional activity. J Biol Chem. 2023 Jun 5:104890. doi: 10.1016/j.jbc.2023.104890. Epub ahead of print. PMID: 37286039.
#docking simulation #modeling #small molecule

Uezono E, Mizobuchi Y, Miyano K, Ohbuchi K, Murata H, Komatsu A, Manabe S, Nonaka M, Hirokawa T, Yamaguchi K, Iseki M, Uezono Y, Hayashida M, Kawagoe I. Distinct Profiles of Desensitization of µ-Opioid Receptors Caused by Remifentanil or Fentanyl: In Vitro Assay with Cells and Three-Dimensional Structural Analyses. Int J Mol Sci. 2023 May 6;24(9):8369. doi: 10.3390/ijms24098369. PMID: 37176075; PMCID: PMC10179353.
#docking simulation #MD simulation #modeling #GPCR #small molecule

Igarashi M, Hirokawa T, Takada A. Structural and energetic basis for differential binding of Ebola and Marburg virus glycoproteins to a bat-derived Niemann-Pick C1 protein. J Infect Dis. 2023 Apr 29:jiad120. doi: 10.1093/infdis/jiad120. Epub ahead of print. PMID: 37119290.
#MD simulation #modeling #infection #small molecule

Kudo G, Hirao T, Yoshino R, Shigeta Y, Hirokawa T. Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres. Bioinformatics. 2023 Apr 3;39(4):btad212. doi: 10.1093/bioinformatics/btad212. PMID: 37086438; PMCID: PMC10148677.
#software development #SBDD #in silico screening #small molecule

- 研究業績 -

2025年度（2025.4-）

2024年度（2024.4-）

2023年度（2023.4-）

2022年度以前（-2023.3） PubMed

2022年度以前（-2023.3）
PubMed