Specific interactions between androgen receptor and its ligand: ab initio molecular orbital calculations in water

Kobayashi, Ittetsu; Takeda, Ryosuke; Suzuki, Rie; Shimamura, Kanako; Ishimura, Hiromi; Kadoya, Ryushi; Kawai, Kentaro; Takimoto‐Kamimura, Midori; Kurita, Noriyuki

doi:10.1016/j.jmgm.2017.06.003

Cited by 14 publications

(10 citation statements)

References 28 publications

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“…This fragmentation enabled us to analyze the interactions between each Mpro residue and the compound affected by the solvating water molecules. In our previous study [ 41 ], the binding properties between the androgen receptor (AR) protein and its ligands were investigated using the same FMO calculations. The evaluated total IFIEs between the AR residues and the ligands were confirmed to correlate well with the binding affinities of these ligands obtained through experiments.…”

Section: Details Of Molecular Simulationsmentioning

confidence: 99%

Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations

Shaji¹,

Yamamoto

Saito

et al. 2021

Biophysical Chemistry

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This paper proposes natural drug candidate compounds for the treatment of coronavirus disease 2019 (COVID-19). We investigated the binding properties between the compounds in the Moringa oleifera plant and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 using molecular docking and ab initio fragment molecular orbital calculations. Among the 12 compounds, niaziminin was found to bind the strongest to Mpro. We furthermore proposed novel compounds based on niaziminin and investigated their binding properties to Mpro. The results reveal that the introduction of a hydroxyl group into niaziminin enhances its binding affinity to Mpro. These niaziminin derivatives can be promising candidate drugs for the treatment of COVID-19.

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Section: Details Of Molecular Simulationsmentioning

confidence: 99%

Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations

Shaji¹,

Yamamoto

Saito

et al. 2021

Biophysical Chemistry

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“…We and newly calculated and collected more than 13 600 FMO calculation data sets ,,− including data sets for 1418 unique PDB entries in collaboration with the FMO Drug Design Consortium (FMODD), which was established for the application of computational science such as FMO calculation to drug discovery. Using these data, we constructed the FMODB, which is a treasure trove of quantitative inter- and intramolecular interaction energies in biomolecular systems that will be useful for a wide range of applications in many life science research fields related to drug discovery and structural biology, including the study of molecular recognition.…”

Section: Introductionmentioning

confidence: 99%

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

Takaya

Watanabe

Nagase

et al. 2021

J. Chem. Inf. Model.

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We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.

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“…Currently, FMO allows also to estimate the solvation contribution by interfacing with the polarizable continuum model (PCM) method [4]. The FMO methodology was successfully applied to various large biological systems, primarily in a retrospective analysis of binding sites [5][6][7][8][9][10][11][12][13][14][15][16], but also as a tool supporting drug design [17][18][19][20]. Among these, several studies [7,11,16,18] have focused on one of the most important groups of biological targets, a G protein-coupled receptors (GPCRs) family.…”

Section: Introductionmentioning

confidence: 99%

Recognition of repulsive and attractive regions of selected serotonin receptor binding site using FMO-EDA approach

et al. 2019

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The complexes of selected long-chain arylpiperazines with homology models of 5-HT 1A , 5-HT 2A , and 5-HT 7 receptors were investigated using quantum mechanical methods. The molecular geometries of the ligand-receptor complexes were firstly optimized with the Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) method. Next, the fragment molecular orbitals method with an energy decomposition analysis scheme (FMO-EDA) was employed to estimate the interaction energies in binding sites. The results clearly showed that orthosteric binding sites of studied serotonin receptors have both attractive and repulsive regions. In the case of 5-HT 1A and 5-HT 2A two repulsive areas, located in the lower part of the binding pocket, and one large area of attraction engaging many residues at the top of all helices were identified. Additionally, for the 5-HT 7 receptor, the third area of destabilization located at the extracellular end of the helix 6 was found.

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Specific interactions between androgen receptor and its ligand: ab initio molecular orbital calculations in water

Cited by 14 publications

References 28 publications

Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations

Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations

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

Recognition of repulsive and attractive regions of selected serotonin receptor binding site using FMO-EDA approach

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