Publications by authors named "Chiduru Watanabe"

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A Dual-Target-Based Screening Strategy for Anti-SARS-CoV-2 Active Compounds Enabling the Identification of Macrocyclic Peptide Natural Products: Chloropeptins.
Aoi Kimishima, Terumasa Ikeda, Otowa Takahashi, Kamrun Naher, Chiduru Watanabe

J Nat Prod· October 2025

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Quantitative Structure-Activity Relationships for Human Galectin-3 Inhibitors: Insights from Quantum Chemical Interaction Energy Terms.
Tomohide Masuda, Chiduru Watanabe, Koichiro Kato, Teruki Honma, Masateru Ohta

J Chem Inf Model· June 2025

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Discovery of a novel class NSD2 inhibitor for multiple myeloma with t(4;14).
Sae Matsuoka, Naoki Osada, Hirokazu Kubota, Ko Kikuzato, Hiroo Koyama, Chiduru Watanabe

Blood Neoplasia· May 2025

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Geometry Optimization Using the Frozen Domain and Partial Dimer Approaches in the Fragment Molecular Orbital Method: Implementation, Benchmark, and Applications to Protein Ligand-Binding Sites.
Koji Okuwaki, Naoki Watanabe, Koichiro Kato, Chiduru Watanabe, Naofumi Nakayama

J Chem Inf Model· December 2024

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Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method.
Daisuke Takaya, Shu Ohno, Toma Miyagishi, Sota Tanaka, Koji Okuwaki, Chiduru Watanabe

Sci Data· October 2024

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FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses.
Hirotomo Moriwaki, Yusuke Kawashima, Chiduru Watanabe, Kikuko Kamisaka, Yoshio Okiyama

J Chem Inf Model· September 2024

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Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir Compared with Its Initial Screening Hit.
Chiduru Watanabe, Shigenori Tanaka, Yoshio Okiyama, Hitomi Yuki, Tatsuya Ohyama

J Phys Chem Lett· April 2023

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Structural basis of transcription regulation by CNC family transcription factor, Nrf2.
Toru Sengoku, Masaaki Shiina, Kae Suzuki, Keisuke Hamada, Ko Sato, Chiduru Watanabe

Nucleic Acids Res· November 2022

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Structure-Activity Relationship and Evaluation of - and -PCPA-Derived Inhibitors of LSD1 and LSD2.
Hideaki Niwa, Chiduru Watanabe, Shin Sato, Toshiyuki Harada, Hisami Watanabe

ACS Med Chem Lett· September 2022

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Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy.
Kenichiro Takaba, Chiduru Watanabe, Atsushi Tokuhisa, Yoshinobu Akinaga, Biao Ma

J Comput Chem· July 2022

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Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles.
Yasuko Koda, Shin Sato, Hirofumi Yamamoto, Hideaki Niwa, Hisami Watanabe, Chiduru Watanabe

ACS Med Chem Lett· May 2022

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Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti.
Kazue Inaba, Kana Ebihara, Miki Senda, Ryunosuke Yoshino, Chisako Sakuma, Chiduru Watanabe, Akira Watanabe, Kodai Watanabe

BMC Biol· February 2022

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Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins.
Kaori Fukuzawa, Koichiro Kato, Chiduru Watanabe, Yusuke Kawashima, Yuma Handa, Kazuki Watanabe

J Chem Inf Model· September 2021

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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.
Kazuki Watanabe, Chiduru Watanabe, Teruki Honma, Yu-Shi Tian, Yusuke Kawashima

J Phys Chem Lett· April 2021

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Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses.
Chiduru Watanabe, Yoshio Okiyama, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma

Chem Sci· April 2021

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FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method.
Daisuke Takaya, Chiduru Watanabe, Shunpei Nagase, Kikuko Kamisaka, Yoshio Okiyama

J Chem Inf Model· February 2021

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Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method.
Shigenori Tanaka, Chiduru Watanabe, Teruki Honma, Kaori Fukuzawa, Kazue Ohishi

J Mol Graph Model· November 2020

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High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning.
Koichiro Kato, Tomohide Masuda, Chiduru Watanabe, Naoki Miyagawa, Hideo Mizouchi

J Chem Inf Model· July 2020

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Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies.
Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano

J Phys Chem B· February 2019

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The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.
Shintaro Iwasaki, Wakana Iwasaki, Mari Takahashi, Ayako Sakamoto, Chiduru Watanabe

Mol Cell· February 2019

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Towards good correlation between fragment molecular orbital interaction energies and experimental IC for ligand binding: A case study of p38 MAP kinase.
Yinglei Sheng, Hirofumi Watanabe, Keiya Maruyama, Chiduru Watanabe, Yoshio Okiyama

Comput Struct Biotechnol J· October 2018

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Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies.
Daisuke Takaya, Koji Inaka, Akifumi Omura, Kenji Takenuki, Masashi Kawanishi, Chiduru Watanabe

Bioorg Med Chem· September 2018

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Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP.
Toru Sengoku, Takehiro Suzuki, Naoshi Dohmae, Chiduru Watanabe, Teruki Honma

Nat Chem Biol· April 2018

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Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: Implementation and DNA Study.
Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki

J Phys Chem B· April 2018

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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.
Chiduru Watanabe, Hirofumi Watanabe, Kaori Fukuzawa, Lorien J Parker, Yoshio Okiyama

J Chem Inf Model· December 2017

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