Chiduru Watanabe
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View article: Quantitative Structure–Activity Relationships for Human Galectin-3 Inhibitors: Insights from Quantum Chemical Interaction Energy Terms
Quantitative Structure–Activity Relationships for Human Galectin-3 Inhibitors: Insights from Quantum Chemical Interaction Energy Terms Open
Human galectin-3 (hGal-3) is a target protein implicated in various diseases, including fibrosis, and several inhibitors have been identified. In this study, we investigated the quantitative structure-activity relationships (QSAR) t…
View article: Discovery of a novel class NSD2 inhibitor for multiple myeloma with t(4;14)+
Discovery of a novel class NSD2 inhibitor for multiple myeloma with t(4;14)+ Open
The prognosis for multiple myeloma (MM) has continued to improve with the development of a series of novel molecular targeted drugs over time. However, the prognosis remains poor for cases with high-risk chromosomal abnormalities. Of such …
View article: Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method
Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method Open
The function of a biomacromolecule is not only determined by its three-dimensional structure but also by its electronic state. Quantum chemical calculations are promising non-empirical methods available for determining the electronic state…
View article: FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses
FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses Open
The fragment molecular orbital (FMO) method is an efficient quantum chemical calculation technique for large biomolecules, dividing each into smaller fragments and providing interfragment interaction energies (IFIEs) that support our under…
View article: Geometry Optimization using the Frozen Domain and Partial Dimer Approach with the Fragment Molecular Orbital Method: Implementation, Benchmark, and Application for Ligand-Binding Site of Proteins
Geometry Optimization using the Frozen Domain and Partial Dimer Approach with the Fragment Molecular Orbital Method: Implementation, Benchmark, and Application for Ligand-Binding Site of Proteins Open
The frozen domain (FD) approximation with fragment molecular orbital (FMO) method is efficient for partial geometry optimization of large systems. We implemented the FD formulation (FD and frozen domain dimer [FDD] methods) already propose…
View article: FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses
FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses Open
The fragment molecular orbital (FMO) method is an efficient quantum chemical calculation technique for large biomolecules, dividing each into smaller fragments and providing inter-fragment interaction energies (IFIEs) that support our unde…
View article: Statistical analysis of interactions among amino acid residues in apo structures using fragment molecular orbital method
Statistical analysis of interactions among amino acid residues in apo structures using fragment molecular orbital method Open
In structure-based drug design, the fragment molecular orbital (FMO) method, which can quantitatively evaluate interaction energy with high accuracy, helps identify critical amino acid residues and types of inter- and intramolecular intera…
View article: Structural Stability and Binding Ability of SARS-CoV-2 Main Protease with GC376: A Stereoisomeric Covalent Ligand Analysis by FMO calculation
Structural Stability and Binding Ability of SARS-CoV-2 Main Protease with GC376: A Stereoisomeric Covalent Ligand Analysis by FMO calculation Open
In modeling structures with multiple conformers, the one with the higher occupancy is typically used under implicit understanding. Multiple conformers have rarely been studied to determine whether a structure with a higher ligand occupancy…
View article: FMOe: Preprocessing and visualizing package of the fragment molecular orbital method for Molecular Operating Environment and its applications in covalent ligand and metalloprotein analyses
FMOe: Preprocessing and visualizing package of the fragment molecular orbital method for Molecular Operating Environment and its applications in covalent ligand and metalloprotein analyses Open
The fragment molecular orbital (FMO) method is an efficient quantum chemical calculation technique for large biomolecules, dividing each into smaller fragments and providing inter-fragment interaction energies (IFIEs) that support our unde…
View article: Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method
Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method Open
The fragment molecular orbital (FMO) method enables quantum mechanical calculations for macromolecules by dividing the target into fragments. However, most calculations, even for metalloproteins, have been performed by removing metal ions …
View article: Structure and Mechanism Analysis of Proteins by Fragment Molecular Orbital Calculations
Structure and Mechanism Analysis of Proteins by Fragment Molecular Orbital Calculations Open
The fragment molecular orbital(FMO)method is a theoretical method that enables quantum chemical calculations of whole bio-macromolecules, such as proteins and nucleic acids, yielding the energies and electron densities of whole molecules a…
View article: Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir (Xocova) Compared with Its Initial Screening Hit
Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir (Xocova) Compared with Its Initial Screening Hit Open
A non-covalent oral drug targeting severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) main protease (Mpro), ensitrelvir (brand name Xocova), has been developed by Unoh et al. (J. Med. Chem. 2022, 65, 9, 6499–6512) using structure…
View article: Structural basis of transcription regulation by CNC family transcription factor, Nrf2
Structural basis of transcription regulation by CNC family transcription factor, Nrf2 Open
Several basic leucine zipper (bZIP) transcription factors have accessory motifs in their DNA-binding domains, such as the CNC motif of CNC family or the EHR motif of small Maf (sMaf) proteins. CNC family proteins heterodimerize with sMaf p…
View article: Fragment molecular orbital calculations containing Mg<sup>2+</sup> ions: PPlase domain of Cyclophilin G
Fragment molecular orbital calculations containing Mg<sup>2+</sup> ions: PPlase domain of Cyclophilin G Open
We investigated fragmentation methods around metals when performing fragment molecular orbital (FMO) calculations for metal-containing proteins, as well as appropriate structural preprocessing. The protein structure data was employed from …
View article: Structure–Activity Relationship and <i>In Silico</i> Evaluation of <i>cis</i>- and <i>trans</i>-PCPA-Derived Inhibitors of LSD1 and LSD2
Structure–Activity Relationship and <i>In Silico</i> Evaluation of <i>cis</i>- and <i>trans</i>-PCPA-Derived Inhibitors of LSD1 and LSD2 Open
trans-2-Phenylcycloproylamine (trans-PCPA) has been used as the scaffold to develop covalent-binding inhibitors against lysine-specific demethylase 1 (LSD1/KDM1A), a therapeutic target for several cancers. However, the effect…
View article: FMO calculations for zinc metalloprotease:Fragmentation of amino-acid residues coordinated to zinc ion
FMO calculations for zinc metalloprotease:Fragmentation of amino-acid residues coordinated to zinc ion Open
We investigated electronic states of a complex of zinc metalloprotease ubiquitin ligase 2(UBR2) with its peptide ligand using ab initio fragment molecular orbital (FMO) calculations. UBR2 possesses three Zn ions and several residues of UBR…
View article: Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles
Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles Open
Lysine-specific demethylase 1 (LSD1/KDM1A) is a promising therapeutic target for the treatment of cancers. Several derivatives of tranylcypromine (trans-2-phenylcyclopropylamine) have been developed as LSD1 inhibitors. One such deri…
View article: Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti
Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti Open
Background Mosquito control is a crucial global issue for protecting the human community from mosquito-borne diseases. There is an urgent need for the development of selective and safe reagents for mosquito control. Flavonoids, a group of …
View article: Importance of Hydrogen Atom Structure in Protein–Ligand Interaction Analysis
Importance of Hydrogen Atom Structure in Protein–Ligand Interaction Analysis Open
Protonation states of ionizable amino acid residues (e.g., Asp, Glu, Lys) on a ligand-binding pocket are critically important information for structure-based drug design. However, in general, hydrogen atoms including protons on the amino a…
View article: Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins
Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins Open
SARS-CoV-2 is the causative agent of coronavirus, globally known as COVID-19. There are ongoing researches to develop effective therapeutics and vaccines against COVID-19 using various methods. We currently conduct research based on the fr…
View article: Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins
Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins Open
SARS-CoV-2 is the causative agent of coronavirus, globally known as COVID-19. There are ongoing researches to develop effective therapeutics and vaccines against COVID-19 using various methods. We currently conduct research based on the fr…
View article: 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
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 Open
The spike glycoprotein (S-protein) mediates SARS-CoV-2 entry via intermolecular interaction with human angiotensin-converting enzyme 2 (hACE2). The receptor-binding domain (RBD) of the S-protein has been considered critical for this intera…
View article: 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
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 Open
The spike glycoprotein (S-protein) mediates SARS-CoV-2 entry via intermolecular interaction with human angiotensin-converting enzyme 2 (hACE2). The receptor-binding domain (RBD) of the S-protein has been considered critical for this intera…
View article: Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses
Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses Open
Quantum chemical calculations investigated molecular recognition of SARS-CoV-2 spike glycoproteins including its N501Y variant for ACE2 and antibody. Hot spot and epitope analyses revealed key residues to design drugs and antibodies agains…
View article: Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses
Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses Open
Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blo…
View article: Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses
Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses Open
Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blo…
View article: Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses
Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses Open
Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blo…
View article: Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses
Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses Open
Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blo…
View article: Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method
Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method Open
The calculation speed of the ab initio fragment molecular orbital (FMO) method can and must be increased by applying approximations to the environmental electrostatic potential (ESP) and the dimer electrostatic potential (dimer-es). These …
View article: Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method
Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method Open