A. Yoshimori

发表

Prediction of an MMP-1 inhibitor activity cliff using the SAR matrix approach and its experimental validation

J. Bajorath, Yasunobu Asawa, A. Yoshimori, 2020, Scientific Reports.

A combined bioinformatic approach oriented to the analysis and design of peptides with high affinity to MHC class I molecules

C. Del Carpio, A. Yoshimori, Tabea Hennig, 2002, Immunology and cell biology.

Structural insights into the active site of poly(ADP-ribose) glycohydrolase using docking modes of 6-hydroxy-3H-xanthen-3-one derivative inhibitors.

F. Uchiumi, S. Tanuma, A. Yoshimori, 2019, Bioorganic & medicinal chemistry.

A 3-styrylchromone converted from trimebutine 3D pharmacophore possesses dual suppressive effects on RAGE and TLR4 signaling pathways.

F. Uchiumi, H. Sakagami, S. Tanuma, 2021, Biochemical and biophysical research communications.

DeepAS - Chemical language model for the extension of active analogue series.

J. Bajorath, A. Yoshimori, 2022, Bioorganic & medicinal chemistry.

Computational analysis, alignment and extension of analogue series from medicinal chemistry

J. Bajorath, A. Yoshimori, 2022, Future science OA.

Papaverine identified as an inhibitor of high mobility group box 1/receptor for advanced glycation end-products interaction suppresses high mobility group box 1-mediated inflammatory responses.

S. Inoue, Yusuke Suzuki, T. Yokomizo, 2019, Biochemical and biophysical research communications.

Identification of Metal-Binding Peptides and Their Conjugation onto Nanoparticles of Superparamagnetic Iron Oxides and Liposomes.

B. Nilsson, K. Ekdahl, Y. Teramura, 2020, ACS applied materials & interfaces.

Design and synthesis of 14 and 15-membered macrocyclic scaffolds exhibiting inhibitory activities of hypoxia-inducible factor 1α.

V. Huber, H. Kouji, H. Seimiya, 2020, Bioorganic & medicinal chemistry.

Trimebutine attenuates high mobility group box 1-receptor for advanced glycation end-products inflammatory signaling pathways.

F. Uchiumi, S. Inoue, T. Yokomizo, 2020, Biochemical and biophysical research communications.

New Insights into the Roles of NAD+-Poly(ADP-ribose) Metabolism and Poly(ADP-ribose) Glycohydrolase.

F. Uchiumi, S. Tanuma, A. Yoshimori, 2016, Current protein & peptide science.

A novel inhibitor that protects apoptotic DNA fragmentation catalyzed by DNase gamma.

Takanobu Kobayashi, S. Tanuma, A. Yoshimori, 2004, Biochemical and biophysical research communications.

Enhancement of paclitaxel-induced apoptosis in HER2-overexpressing human breast cancer cells by a pertuzumab mimetic peptide, HRAP.

J. Magae, S. Tanuma, A. Yoshimori, 2010, Journal of bioscience and bioengineering.

Involvement of DNase gamma in the resected double-strand DNA breaks in immunoglobulin genes.

D. Kitamura, S. Tanuma, M. Okamoto, 2005, Biochemical and biophysical research communications.

Structural Basis of Beneficial Design for Effective Nicotinamide Phosphoribosyltransferase Inhibitors

N. Tanuma, F. Uchiumi, S. Tanuma, 2020, Molecules.

The structural differences between mushroom and human tyrosinase cleared by investigating the inhibitory activities of stilbenes

S. Tanuma, A. Yoshimori, T. Oyama, 2022, Journal of Molecular Structure.

Structure-based drug design of novel carborane-containing nicotinamide phosphoribosyltransferase inhibitors.

S. Tanuma, Yasunobu Asawa, A. Yoshimori, 2019, Bioorganic & medicinal chemistry.

Regulation of CD28 binding to SH2 domains of Grb2 and PI3K by trisubstituted carboranes for T-cell activation.

M. Oda, S. Ogawa, Yasunobu Asawa, 2022, Bioorganic & medicinal chemistry letters.

Design of MMP-1 inhibitors via SAR transfer and experimental validation

J. Bajorath, A. Yoshimori, Hiroyuki Nakamura, 2022, Scientific Reports.

Piceatannol, a natural trans-stilbene compound, inhibits human glyoxalase I.

S. Tanuma, A. Yoshimori, R. Takasawa, 2017, Bioorganic & medicinal chemistry letters.

TLSC702, a Novel Inhibitor of Human Glyoxalase I, Induces Apoptosis in Tumor Cells.

S. Tanuma, A. Yoshimori, R. Takasawa, 2016, Biological & pharmaceutical bulletin.

Discovery of a new type inhibitor of human glyoxalase I by myricetin-based 4-point pharmacophore.

S. Tanuma, A. Yoshimori, Kazunori Saeki, 2011, Bioorganic & medicinal chemistry letters.

Delphinidin, a dietary anthocyanidin in berry fruits, inhibits human glyoxalase I.

M. Fujiwara, S. Tanuma, A. Yoshimori, 2010, Bioorganic & medicinal chemistry.

Structure-activity relationship of human GLO I inhibitory natural flavonoids and their growth inhibitory effects.

S. Tanuma, A. Yoshimori, Kazunori Saeki, 2008, Bioorganic & medicinal chemistry.

Structure-based design of dipeptide derivatives for the human neutral endopeptidase.

S. Tanuma, A. Yoshimori, R. Takasawa, 2011, Bioorganic & medicinal chemistry.

Structural insight into the active site of mushroom tyrosinase using phenylbenzoic acid derivatives.

Tetsuya Yamamoto, S. Tanuma, A. Yoshimori, 2017, Bioorganic & medicinal chemistry letters.

Discovery of a new type of scaffold for the creation of novel tyrosinase inhibitors.

Tetsuya Yamamoto, S. Tanuma, A. Yoshimori, 2016, Bioorganic & medicinal chemistry.

Structure-activity relationships of the thujaplicins for inhibition of human tyrosinase.

S. Tanuma, A. Yoshimori, T. Oyama, 2014, Bioorganic & medicinal chemistry.

Structural insights into the hot spot amino acid residues of mushroom tyrosinase for the bindings of thujaplicins.

Satoshi Sunaga, Atsushi Yoshimori, Sei-ichi Tanuma, 2010, Bioorganic & medicinal chemistry.

A new small molecule that directly inhibits the DNA binding of NF-kappaB.

H. Miyazawa, K. Kino, Takanobu Kobayashi, 2009, Bioorganic & medicinal chemistry.

Effect of piceatannol-rich passion fruit seed extract on human glyoxalase I–mediated cancer cell growth

S. Tanuma, A. Yoshimori, Akira Sato, 2019, Biochemistry and biophysics reports.

Comprehensive exploration of chemical space using trisubstituted carboranes

H. Kouji, Yasunobu Asawa, A. Yoshimori, 2021, Scientific Reports.

Genomic drug discovery for apoptosis regulation using a new computer screening amino acid complement wave method.

S. Tanuma, A. Yoshimori, R. Takasawa, 2004, Biological & pharmaceutical bulletin.

Involvement of DNase γ in the resected double-strand DNA breaks in immunoglobulin genes

D. Kitamura, S. Tanuma, M. Okamoto, 2005 .

Structure basis for the inhibitory mechanism of a novel DNase γ-specific inhibitor, DR396

S. Tanuma, A. Yoshimori, D. Shiokawa, 2006 .

Molecular Designing of Small-Molecule Inhibitors for Apoptosis Regulation

S. Tanuma, A. Yoshimori, 2018 .

Identification of a novel gene family, paralogs of inhibitor of apoptosis proteins present in plants, fungi, and animals

K. Kuchitsu, A. Yoshimori, R. Takasawa, 2005, Apoptosis.

Correlation between c-Met and ALDH1 contributes to the survival and tumor-sphere formation of ALDH1 positive breast cancer stem cells and predicts poor clinical outcome in breast cancer

N. Shinomiya, R. Abe, K. Akimoto, 2017, Genes & cancer.

Discovery of Novel eEF2K Inhibitors Using HTS Fingerprint Generated from Predicted Profiling of Compound-Protein Interactions

A. Yoshimori, Ryuta Murakami, Chisato Kanai, 2021, Medicines.

A Unique Anti-Cancer 3-Styrylchromone Suppresses Inflammatory Response via HMGB1-RAGE Signaling

H. Sakagami, S. Tanuma, A. Yoshimori, 2021, Medicines.

Docking unbound proteins with MIAX: a novel algorithm for protein-protein soft docking.

Eiichiro Ichiishi, Atsushi Yoshimori, E. Ichiishi, 2003, Genome informatics. International Conference on Genome Informatics.

MIAX: A new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases

Eiichiro Ichiishi, Atsushi Yoshimori, Toshikazu Yoshikawa, 2002, Proteins.

MIAX: a system for assessment of macromolecular interaction. 3) A parallel hybrid GA for flexible protein docking.

A Yoshimori, C A Del Carpio, C. Del Carpio, 2000, Genome informatics. Workshop on Genome Informatics.

A Novel System for Assessment of Macromolecular Interaction in Condensed Phases. 2) Interaction Site Inference by Molecular Shape and Electrostatic Complementarity

A. Yoshimori, C. Munoz, 1999 .

Development of HER2-antagonistic peptides as novel anti-breast cancer drugs by in silico methods

S. Tanuma, A. Yoshimori, K. Sakaguchi, 2008, Breast cancer.

Structure-based design of an agonistic peptide targeting Fas

A. Yoshimori, A. Hayakawa, R. Takasawa, 2005, Apoptosis.

Automatic epitope recognition in proteins oriented to the system for macromolecular interaction assessment MIAX.

A Yoshimori, C A Del Carpio, C. Del Carpio, 2001, Genome informatics. International Conference on Genome Informatics.

Identification of a drug target motif: an anti-tumor drug NK109 interacts with a PNxxxxP.

Atsushi Yoshimori, Seiichi Saito, Kengo Morohashi, 2005, Biochemical pharmacology.

Glyoxalase 1 gene is highly expressed in basal-like human breast cancers and contributes to survival of ALDH1-positive breast cancer stem cells

R. Abe, K. Akimoto, T. Hanawa, 2018, Oncotarget.

Deep SAR matrix: SAR matrix expansion for advanced analog design using deep learning architectures

Jürgen Bajorath, Atsushi Yoshimori, J. Bajorath, 2020 .

Method for Systematic Analogue Search Using the Mega SAR Matrix Database

Jürgen Bajorath, Atsushi Yoshimori, Yuichi Horita, 2019, J. Chem. Inf. Model..

Effects of Thujaplicins on the Promoter Activities of the Human SIRT1 and Telomere Maintenance Factor Encoding Genes

F. Uchiumi, S. Larsen, S. Tanuma, 2012 .

Visualized and Quantitative Conformational Analysis of Peptidomimetics

S. Shuto, A. Yoshimori, Eiji Honda, 2021, ACS omega.

A mimetic of the mSin3-binding helix of NRSF/REST ameliorates abnormal pain behavior in chronic pain models.

H. Kouji, H. Ueda, H. Nakano, 2017, Bioorganic & medicinal chemistry letters.

Chemical language models for applications in medicinal chemistry.

J. Bajorath, A. Yoshimori, He-Gang Chen, 2023, Future medicinal chemistry.

Discovery of bicyclo[3,3,1]non-2-ene as a novel skeleton for HIF-1 inhibitors.

A. Yoshimori, Hiroyuki Nakamura, H. Ueda, 2018, Bioorganic & medicinal chemistry.

A novel method for evaluation and screening of caspase inhibitory peptides by the amino acid positional fitness score

Atsushi Yoshimori, Sei-ichi Tanuma, S. Tanuma, 2004, BMC pharmacology.

Design and Synthesis of DDR1 Inhibitors with a Desired Pharmacophore Using Deep Generative Models

M. Neya, Yasunobu Asawa, A. Yoshimori, 2020, ChemMedChem.

Prediction of Molecular Properties Using Molecular Topographic Map

A. Yoshimori, 2021, Molecules.

Motif2Mol: Prediction of New Active Compounds Based on Sequence Motifs of Ligand Binding Sites in Proteins Using a Biochemical Language Model

J. Bajorath, A. Yoshimori, 2023, Biomolecules.

Iterative DeepSARM Modeling for Compound Optimization

J. Bajorath, A. Yoshimori, 2021, Artificial Intelligence in the Life Sciences.

Adapting the DeepSARM approach for dual-target ligand design

Jürgen Bajorath, Huabin Hu, Atsushi Yoshimori, 2021, Journal of Computer-Aided Molecular Design.

Integrating the Structure–Activity Relationship Matrix Method with Molecular Grid Maps and Activity Landscape Models for Medicinal Chemistry Applications

Jürgen Bajorath, Atsushi Yoshimori, Toru Tanoue, 2019, ACS Omega.

Generalized–ensemble method study: A helix‐mimetic compound inhibits protein–protein interaction by long‐range and short‐range intermolecular interactions

Y. Fukunishi, J. Higo, A. Yoshimori, 2021, J. Comput. Chem..

Approach for the Design of Covalent Protein Kinase Inhibitors via Focused Deep Generative Modeling

J. Bajorath, A. Yoshimori, Filip Miljković, 2022, Molecules.

Structure-based discovery of a novel non-peptidic small molecular inhibitor of caspase-3.

S. Tanuma, A. Yoshimori, R. Takasawa, 2008, Bioorganic & medicinal chemistry.

Addition of hydrophobic side chains improve the apoptosis inducibility of the human glyoxalase I inhibitor, TLSC702.

S. Tanuma, A. Yoshimori, R. Takasawa, 2021, Bioorganic & medicinal chemistry letters.

Computational Prediction of Compound–Protein Interactions for Orphan Targets Using CGBVS

A. Yoshimori, Ryuta Murakami, Chisato Kanai, 2021, Molecules.

Structural and functional definition of the specificity of a novel caspase-3 inhibitor, Ac-DNLD-CHO

Takanobu Kobayashi, S. Tanuma, A. Yoshimori, 2007, BMC pharmacology.

The SAR Matrix Method and an Artificially Intelligent Variant for the Identification and Structural Organization of Analog Series, SAR Analysis, and Compound Design

Atsushi Yoshimori, Juergen Bajorath, J. Bajorath, 2020, Molecular informatics.

Strategies for Design of Molecular Structures with a Desired Pharmacophore Using Deep Reinforcement Learning.

Atsushi Yoshimori, Chisato Kanai, A. Yoshimori, 2020, Chemical & pharmaceutical bulletin.

Trimebutine suppresses Toll-like receptor 2/4/7/8/9 signaling pathways in macrophages.

F. Uchiumi, T. Yokomizo, S. Tanuma, 2021, Archives of biochemistry and biophysics.

Rational Strategy for Designing Peptidomimetic Small Molecules Based on Cyclic Peptides Targeting Protein–Protein Interaction between CTLA-4 and B7-1

K. Kojoh, A. Yoshimori, Eiji Honda, 2022, Pharmaceuticals.

Development of Low-Molecular-Weight Compounds Targeting the Cancer-Associated KLF5 Transcription Factor.

H. Kouji, Toru Suzuki, S. Dan, 2022, ACS medicinal chemistry letters.

Delphinidin, a dietary anthocyanidin in berry fruits, inhibits human glyoxalase I.

M. Fujiwara, S. Tanuma, A. Yoshimori, 2010, Bioorganic & medicinal chemistry.