T. Honma

发表

Crystallographic Approach to Identification of Cyclin-dependent Kinase 4 (CDK4)-specific Inhibitors by Using CDK4 Mimic CDK2 Protein*

T Honma, H. Hirai, K. Fukasawa, 2001, The Journal of Biological Chemistry.

Targeting Epigenetic and Posttranscriptional Gene Regulation by PSF Impairs Hormone Therapy–Refractory Cancer Growth

K. Takayama, S. Inoue, Yutaka Suzuki, 2021, Cancer Research.

Structure-based generation of a new class of potent Cdk4 inhibitors: new de novo design strategy and library design.

K. Fukasawa, T. Machida, Y. Iwasawa, 2001, Journal of medicinal chemistry.

Prediction of sites of metabolism in a substrate molecule, instanced by carbamazepine oxidation by CYP3A4.

T. Honma, Hitomi Yuki, M. Hata, 2012, Bioorganic & medicinal chemistry.

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target

Kun-Yi Hsin, Hiroaki Kitano, Y-h. Taguchi, 2015, Scientific Reports.

In silico functional profiling of small molecules and its applications.

Shigeyuki Yokoyama, Teruki Honma, Tomohiro Sato, 2008, Journal of medicinal chemistry.

A prospective compound screening contest identified broader inhibitors for Sirtuin 1

Shogo D. Suzuki, Hironori K. Nakamura, Kazuki Z. Yamamoto, 2019, Scientific Reports.

Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method

Kaori Fukuzawa, T. Maruyama, T. Honma, 2020, Journal of Molecular Graphics and Modelling.

New SIRT2 inhibitors: Histidine-based bleomycin spin-off.

Minoru Yoshida, T. Honma, A. Ito, 2019, Bioorganic & medicinal chemistry.

Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles.

T. Umehara, M. Shirouzu, T. Honma, 2022, ACS medicinal chemistry letters.

Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase

M. Shirouzu, T. Honma, H. Shimizu, 2019, PLoS neglected tropical diseases.

Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.

M. Shirouzu, T. Honma, Hitomi Yuki, 2017, Bioorganic & medicinal chemistry.

Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase

Kaori Fukuzawa, T. Honma, Shigenori Tanaka, 2018, Computational and structural biotechnology journal.

Structure of the trypanosome cyanide-insensitive alternative oxidase

T. Honma, H. Saimoto, T. Aoki, 2013, Proceedings of the National Academy of Sciences.

Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP

S. Yokoyama, Y. Yamaguchi, Takehiro Suzuki, 2018, Nature Chemical Biology.

Identification of novel drug-resistant EGFR mutant inhibitors by in silico screening using comprehensive assessments of protein structures.

S. Yokoyama, M. Shirouzu, T. Honma, 2012, Bioorganic & medicinal chemistry.

Quantitative prediction of hERG inhibitory activities using support vector regression and the integrated hERG dataset in AMED cardiotoxicity database

T. Honma, Tomohiro Sato, Hitomi Yuki, 2021, Chem-Bio Informatics Journal.

Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation

Kaori Fukuzawa, T. Honma, Koichiro Kato, 2020, Journal of Molecular Graphics and Modelling.

Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase of Trypanosoma brucei brucei

P. Michels, T. Honma, Tomohiro Sato, 2019, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors.

T. Umehara, M. Shirouzu, H. Seimiya, 2019, Journal of medicinal chemistry.

Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies.

Y. Urade, M. Shirouzu, K. Inaka, 2018, Bioorganic & medicinal chemistry.

Prediction of the site of CYP 3 A 4 metabolism of tolterodine by molecular dynamics simulation from multiple initial structures of the CYP 3 A 4-tolterodine complex

A. Konagaya, T. Honma, C. Watanabe, 2017 .

Prediction of the site of CYP3A4 metabolism of tolterodine by molecular dynamics simulation from multiple initial structures of the CYP3A4-tolterodine complex

A. Konagaya, T. Honma, C. Watanabe, 2017 .

Structure-activity relationship study of novel NR2B-selective antagonists with arylamides to avoid reactive metabolites formation.

Kazunari Hattori, T. Honma, K. Ando, 2007, Bioorganic & medicinal chemistry letters.

A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo

Satoshi Tanaka, Shigeyuki Yokoyama, Hiroshi Kajita, 2013, Science Translational Medicine.

Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments

T. Honma, Tomohiro Sato, N. Hashimoto, 2017, J. Chem. Inf. Model..

The ubiquinone synthesis pathway is a promising drug target for Chagas disease

M. Shirouzu, T. Honma, K. Kita, 2021, PloS one.

Crystallization and preliminary X-ray analysis of aspartate transcarbamoylase from the parasitic protist Trypanosoma cruzi.

T. Honma, T. Aoki, S. Matsuoka, 2009, Acta crystallographica. Section F, Structural biology and crystallization communications.

kGCN: a graph-based deep learning framework for chemical structures

R. Kojima, T. Honma, Yasushi Okuno, 2020, Journal of Cheminformatics.

Blockade of inflammatory responses by a small-molecule inhibitor of the Rac activator DOCK2.

S. Yokoyama, A. Suenaga, D. Kohda, 2012, Chemistry & biology.

Crystallization and preliminary crystallographic analysis of cyanide-insensitive alternative oxidase from Trypanosoma brucei brucei.

T. Honma, T. Aoki, A. Moore, 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.

Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Trypanosoma brucei gambiense glycerol kinase.

P. Michels, T. Honma, T. Aoki, 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.

N‐(3,4‐dimethoxyphenethyl)‐6‐methyl‐2,3,4,9‐tetrahydro‐1H‐carbazol‐1‐amine inhibits bladder cancer progression by suppressing YAP1/TAZ

M. Fujisawa, T. Maehama, T. Honma, 2022, Genes to cells : devoted to molecular & cellular mechanisms.

Utilizing public and private sector data to build better machine learning models for the prediction of pharmacokinetic parameters.

K. Mizuguchi, Tsuyoshi Esaki, T. Honma, 2022, Drug discovery today.

Establishment of a Monoclonal Antibody against Human NTCP That Blocks Hepatitis B Virus Infection

K. Chayama, M. Shirouzu, K. Shimotohno, 2022, Journal of virology.

Biochemical characterization of highly active Trypanosoma brucei gambiense glycerol kinase, a promising drug target.

P. Michels, T. Honma, T. Aoki, 2013, Journal of biochemistry.

Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules

Kaori Fukuzawa, T. Honma, Shigenori Tanaka, 2019, Chem-Bio Informatics Journal.

Pharmacological intervention of cholesterol sulfate-mediated T cell exclusion promotes antitumor immunity.

M. Kanai, T. Honma, Yoshihiro Izumi, 2022, Biochemical and biophysical research communications.

Intermolecular Interaction Analyses on SARS-CoV-2 Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/peptide Using Fragment Molecular Orbital Calculation

Kaori Fukuzawa, T. Honma, T. Takagi, 2021 .

Structure–Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2

T. Umehara, K. Matsuno, M. Shirouzu, 2022, ACS medicinal chemistry letters.

Supplemental Information Targeting Ras-Driven Cancer Cell Survival and Invasion through Selective Inhibition of DOCK 1

E. Oki, Y. Maehara, S. Yokoyama, 2022 .

Selective Inhibitor Design for Kinase Homologs Using Multiobjective Monte Carlo Tree Search

T. Honma, Tomohiro Sato, Kei Terayama, 2022, J. Chem. Inf. Model..

Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases

K. Shimuta, M. Ohnishi, K. Shinzawa-Itoh, 2022, Nature communications.

SYNTHESIS OF DISSYMMETRIC INDOLOCARBAZOLE GLYCOSIDES USING THE MITSUNOBU REACTION AT THE GLYCOSYLATION STEP

T. Honma, S. Ito, T. Nishimura, 1997 .

A novel approach for the development of selective Cdk4 inhibitors: library design based on locations of Cdk4 specific amino acid residues.

T Honma, K. Fukasawa, N. Kawanishi, 2001, Journal of medicinal chemistry.

Synthesis and structure-activity relationship of a new series of potent angiotensin II receptor antagonists: pyrazolo[1,5-a]pyrimidine derivatives.

T. Honma, T. Kawabata, M. Fujimoto, 1999, Chemical & pharmaceutical bulletin.

Practical synthesis of indolopyrrolocarbazoles

T. Honma, T. Nishimura, M. Ohkubo, 1996 .

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes

Daisuke Kihara, Takashi Ishida, Masakazu Sekijima, 2017, Scientific Reports.

Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor.

S. Yokoyama, M. Shirouzu, T. Honma, 2012, Acta crystallographica. Section F, Structural biology and crystallization communications.

A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors.

Masahiko Ito, Daisuke Takaya, Hideaki Umeyama, 2011, Bioorganic & Medicinal Chemistry.

Novel angiotensin II receptor antagonists. Design, synthesis, and in vitro evaluation of dibenzo[a,d]cycloheptene and dibenzo[b,f]oxepin derivatives. Searching for bioisosteres of biphenylyltetrazole using a three-dimensional search technique.

T Honma, T. Honma, T. Fujishita, 1995, Journal of medicinal chemistry.

Novel bicyclic pyrazoles as potent ALK2 (R206H) inhibitors for the treatment of fibrodysplasia ossificans progressiva.

K. Miyazono, M. Shirouzu, T. Honma, 2021, Bioorganic & medicinal chemistry letters.

Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches

K. Miyazono, S. Yokoyama, M. Shirouzu, 2020, ACS omega.

Bis-Heteroaryl Pyrazoles: Identification of Orally Bioavailable Inhibitors of Activin Receptor-Like Kinase-2 (R206H).

K. Miyazono, S. Yokoyama, M. Shirouzu, 2019, Chemical & pharmaceutical bulletin.

The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.

Shintaro Iwasaki, Kaori Fukuzawa, Nicholas T Ingolia, 2019, Molecular cell.

A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity

K. Matsuda, S. Yokoyama, M. Shirouzu, 2013, Nature.

Targeting Ras-Driven Cancer Cell Survival and Invasion through Selective Inhibition of DOCK1.

E. Oki, Y. Maehara, S. Yokoyama, 2017, Cell reports.

Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia

Jordan A. Ramilowski, Y. Okazaki, P. Vyas, 2021, Nature Cancer.

Crystal structures of the S6K1 kinase domain in complexes with inhibitors

S. Yokoyama, M. Shirouzu, T. Honma, 2014, Journal of Structural and Functional Genomics.

The Open Form Inducer Approach for Structure-Based Drug Design

T. Honma, S. Matsuoka, M. Inoue, 2016, PloS one.

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria

Masayuki Inoue, Teruki Honma, Dan Sato, 2015, International journal of molecular sciences.

Prediction of Ligand-Induced Structural Polymorphism of Receptor Interaction Sites Using Machine Learning

Hitomi Yuki, Teruki Honma, Daisuke Takaya, 2013, J. Chem. Inf. Model..

A novel Pim-1 kinase inhibitor targeting residues that bind the substrate peptide.

S. Yokoyama, T. Honma, T. Nagano, 2012, Journal of molecular biology.

Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening

Teruki Honma, Shigeyuki Yokoyama, Tomohiro Sato, 2010, J. Chem. Inf. Model..

Synthesis and biological activities of NB-506 analogues modified at the glucose group.

T. Honma, S. Nishimura, H. Suda, 2000, Bioorganic & medicinal chemistry letters.

Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti

Y. Fujikawa, Kaori Fukuzawa, T. Hirokawa, 2022, BMC Biology.

FMO Drug Design Consortium

Kaori Fukuzawa, K. Takaba, T. Honma, 2021 .

Design and Discovery of an Orally Efficacious Spiroindolinone-based Tankyrase Inhibitor for the Treatment of Colon Cancer.

T. Umehara, M. Shirouzu, H. Seimiya, 2020, Journal of medicinal chemistry.

Alantolactone is a natural product that potently inhibits YAP1/TAZ through promotion of reactive oxygen species accumulation

T. Mak, H. Nishina, A. Suzuki, 2021, Cancer science.

Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.

T. Umehara, M. Shirouzu, Minoru Yoshida, 2023, Journal of medicinal chemistry.

Synthesis and biological activities of NB-506 analogues: Effects of the positions of two hydroxyl groups at the indole rings.

T. Honma, S. Nishimura, H. Suda, 1999, Bioorganic & medicinal chemistry letters.

Recent advances in de novo design strategy for practical lead identification

Teruki Honma, T. Honma, 2003, Medicinal research reviews.

Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins

Kaori Fukuzawa, T. Honma, C. Watanabe, 2021, J. Chem. Inf. Model..

Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation

Kaori Fukuzawa, T. Honma, T. Takagi, 2021, The journal of physical chemistry letters.

Pharmacophore Modeling for Anti-Chagas Drug Design Using the Fragment Molecular Orbital Method

M. Sekijima, T. Honma, Yohsuke Hagiwara, 2015, PloS one.

Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method.

S. Yokoyama, T. Honma, D. Takaya, 2020, Journal of molecular graphics & modelling.

The domain of Epstein-Barr virus nuclear antigen 1 essential for binding to oriP region has a sequence fitted for the hypothetical basic-helix-loop-helix structure.

T. Honma, T. Kitamura, K. Yanagi, 1991, Virology.

Support Vector Machine model for hERG inhibitory activities based on the integrated hERG database using descriptor selection by NSGA-II

Keiji Ogura, Hitomi Yuki, Tomohiro Sato, 2019, Scientific Reports.

Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors

Hitomi Yuki, Teruki Honma, Daisuke Takaya, 2012, J. Chem. Inf. Model..

Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase

Masayuki Inoue, Teruki Honma, Akiko Tanaka, 2014, Molecular microbiology.

Design and synthesis of potent substrate-based inhibitors of the Trypanosoma cruzi dihydroorotate dehydrogenase.

T. Honma, M. Inoue, K. Kita, 2017, Bioorganic & medicinal chemistry.

Biogenetic intermediates, (3e and 3z,12z)-laurediols and (3e and 3z)-12,13- dihydrolaurediols, isolated from Laurencia nipponica

T. Honma, A. Murai, A. Fukuzawa, 1993 .

Predicting human liver microsomal stability with machine learning techniques.

Yojiro Sakiyama, Hitomi Yuki, Teruki Honma, 2008, Journal of molecular graphics & modelling.

A fluorescence correlation spectroscopy-based assay for fragment screening of slowly inhibiting protein-peptide interaction inhibitors.

S. Yokoyama, T. Honma, T. Nagano, 2010, Analytical biochemistry.

Population-based de novo molecule generation, using grammatical evolution

Koji Tsuda, Kenta Oono, Teruki Honma, 2018, 1804.02134.

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes

Shogo D. Suzuki, Kazuki Z. Yamamoto, D. Kihara, 2017, Scientific Reports.

FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method

Noriyuki Kurita, Kaori Fukuzawa, Tatsuya Takagi, 2021, J. Chem. Inf. Model..

Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach

Kaori Fukuzawa, Shigeyuki Yokoyama, Shigenori Tanaka, 2017, J. Chem. Inf. Model..

New antimalarials identified by a cell-based phenotypic approach: Structure-activity relationships of 2,3,4,9-tetrahydro-1H-β-carboline derivatives possessing a 2-((coumarin-5-yl)oxy)alkanoyl moiety.

T. Honma, Takeshi Shimizu, Y. Futamura, 2022, Bioorganic & medicinal chemistry.

A Fluorescent-Based High-Throughput Screening Assay for Small Molecules That Inhibit the Interaction of MdmX with p53

T. Kigawa, S. Yokoyama, T. Honma, 2013, Journal of biomolecular screening.

Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase.

T. Honma, H. Saimoto, A. Moore, 2019, Biochimica et biophysica acta. Bioenergetics.

High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning

Tomohide Masuda, Mitsunori Ikeguchi, Hiroshi Ueda, 2020, J. Chem. Inf. Model..

A public-private partnership to enrich the development of in silico predictive models for pharmacokinetic and cardiotoxic properties.

K. Mizuguchi, T. Honma, Tomohiro Sato, 2021, Drug discovery today.

Interruption of Vif/Elongin C interaction: In silico and experimental elucidation of the underlying molecular mechanism of benzimidazole-based APOBEC3G stabilizers.

T. Honma, M. Otsuka, A. Takaori-Kondo, 2020, Bioorganic & medicinal chemistry.

Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin.

S. Yokoyama, Yoshikazu Tanaka, M. Shirouzu, 2021, Phytochemistry.

Force‐field parametrization based on radial and energy distribution functions

Shuntaro Chiba, Mitsunori Ikeguchi, Yasushi Okuno, 2019, J. Comput. Chem..

Structural basis for chemical inhibition of human blood coagulation factor Xa.

Sung-Hou Kim, S. Kim, K. Kamata, 1998, Proceedings of the National Academy of Sciences of the United States of America.