Publication

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

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