Výsledky vyhledávání - "Hironori Kokubo"

Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations

Autor: Kai Liu, Hironori Kokubo

Publikováno v: Journal of Computer-Aided Molecular Design. 34:1195-1205

We propose a method to identify the correct binding mode of a ligand with a protein among multiple predicted docking poses. Our method consists of two steps. First, five independent MD simulations with different initial velocities are performed for e

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eef273387de1a974006c8af26e966574
https://doi.org/10.1007/s10822-020-00340-y

Zobrazit plný text záznamu

Plný text ve formátu HTML

Uncovering abnormal changes in logP after fluorination using molecular dynamics simulations

Autor: Kai Liu, Hironori Kokubo

Publikováno v: Journal of Computer-Aided Molecular Design. 33:345-356

The fluorination-induced changes in the logP (1-octanol/water partition coefficient) of ligands were examined by molecular dynamics simulations. The protocol and force field parameters were first evaluated by calculating the logP values for n-alkanes

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1ce4e2911578b44895172ea40556742b
https://doi.org/10.1007/s10822-018-0183-1

Zobrazit plný text záznamu

Plný text ve formátu HTML

Discovery of Clinical Candidate N-((1S)-1-(3-Fluoro-4-(trifluoromethoxy)phenyl)-2-methoxyethyl)-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915): A Highly Potent, Selective, and Brain-Penetrating Phosphodiesterase 2A Inhibitor for the Treatment of Cognitive Disorders

Autor: Hua Zou, Isaac Hoffman, Noriko Suzuki, Masanori Kawasaki, Shinji Nakamura, Kosuke Nakashima, Shigekazu Sasaki, Haruka Imada, Hiroki Iwashita, Hironori Kokubo, Satoshi Mikami, Takahiko Taniguchi, Naomi Kamiguchi, Hideyuki Oki, Noriko Uchiyama, Izumi Nomura, Tomoko Ashizawa

Publikováno v: Journal of Medicinal Chemistry. 60:7677-7702

Phosphodiesterase (PDE) 2A inhibitors have emerged as a novel mechanism with potential therapeutic option to ameliorate cognitive dysfunction in schizophrenia or Alzheimer’s disease through upregulation of cyclic nucleotides in the brain and thereb

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a88b3fef16a65867803a7feeb61c38f2
https://doi.org/10.1021/acs.jmedchem.7b00807

Zobrazit plný text záznamu

Discovery of a Novel Series of Pyrazolo[1,5-a]pyrimidine-Based Phosphodiesterase 2A Inhibitors Structurally Different from N-((1S)-1-(3-Fluoro-4-(trifluoromethoxy)phenyl)-2-methoxyethyl)-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915), for the Treatment of Cognitive Disorders

Autor: Shuhei Ikeda, Hironori Kokubo, Masato Nakashima, Shinji Nakamura, Hideyuki Oki, Noriko Uchiyama, Takahiko Taniguchi, Masanori Kawasaki, Hua Zou, Nobuyuki Negoro, Satoshi Mikami, Tomoko Ashizawa, Yuuki Itou, Yuuto Hiura, Hiroki Iwashita, Izumi Nomura, Maki Miyamoto, Isaac Hoffman

Publikováno v: CHEMICAL & PHARMACEUTICAL BULLETIN. 65:1058-1077

It has been hypothesized that selective inhibition of phosphodiesterase (PDE) 2A could potentially be a novel approach to treat cognitive impairment in neuropsychiatric and neurodegenerative disorders through augmentation of cyclic nucleotide signali

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::e31421eb699528cc923d333db0f7978b
https://doi.org/10.1248/cpb.c17-00564

Zobrazit plný text záznamu

Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion

Autor: Akinori Kidera, Hironori Kokubo, Satoshi Endo, Kei Moritsugu, Toshimasa Tanaka, Tohru Terada

Publikováno v: The Journal of chemical physics. 149(7)

Enhanced sampling yields a comprehensive structural ensemble or a free energy landscape, which is beyond the capability of a conventional molecular dynamics simulation. Our recently developed multiscale enhanced sampling (MSES) method employs a coars

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4857022aa86ae00e92d98784dfefd951
https://pubmed.ncbi.nlm.nih.gov/30134720

Zobrazit plný text záznamu

Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors

Autor: Hironori Kokubo, Gregg B. Morin, Noriko Uchiyama, Hironobu Maezaki, Nao Morishita, Tomohiro Kawamoto, Akinori Toita, Hua Zou, Satoshi Endo, Morio Murakami, Toshio Tanaka, Samuel Aparicio, Atsushi Nakanishi, Masahiro Ito, Tomoya Sameshima, Mitsuyo Kondo, Shinsuke Araki, Yasuhiro Imaeda, Michael G. Klein

Publikováno v: Journal of medicinal chemistry. 61(17)

Cyclin-dependent kinase 12 (CDK12) plays a key role in the coordination of transcription with elongation and mRNA processing. CDK12 mutations found in tumors and CDK12 inhibition sensitize cancer cells to DNA-damaging reagents and DNA-repair inhibito

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1fb8798139b709d0c707870b3238c7e0
https://pubmed.ncbi.nlm.nih.gov/30067358

Zobrazit plný text záznamu

Design and synthesis of a novel 2-oxindole scaffold as a highly potent and brain-penetrant phosphodiesterase 10A inhibitor

Autor: Takahiko Taniguchi, Kosuke Nakashima, Tomomi Ikemoto, Masato Yoshikawa, Jun Kunitomo, Haruhi Kamisaki, Naomi Kamiguchi, Hideyuki Oki, Hironori Kokubo, Akina Harada, Akihiro Suzuki, Haruhide Kimura

Publikováno v: Bioorganic & Medicinal Chemistry. 23:7138-7149

Highly potent and brain-penetrant phosphodiesterase 10A (PDE10A) inhibitors based on the 2-oxindole scaffold were designed and synthesized. (2-Oxo-1,3-oxazolidin-3-yl)phenyl derivative 1 showed the high P-glycoprotein (P-gp) efflux (efflux ratio (ER)

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::17c4b5ec73b4b477f29993952f043fc9
https://doi.org/10.1016/j.bmc.2015.10.002

Zobrazit plný text záznamu

Autor: Satoshi, Mikami, Masanori, Kawasaki, Shuhei, Ikeda, Nobuyuki, Negoro, Shinji, Nakamura, Izumi, Nomura, Tomoko, Ashizawa, Hironori, Kokubo, Isaac Dylan, Hoffman, Hua, Zou, Hideyuki, Oki, Noriko, Uchiyama, Yuuto, Hiura, Maki, Miyamoto, Yuuki, Itou, Masato, Nakashima, Hiroki, Iwashita, Takahiko, Taniguchi

Publikováno v: Chemicalpharmaceutical bulletin. 65(11)

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::af5b7eafd7fd2ea34dd12536bd8dfb62
https://pubmed.ncbi.nlm.nih.gov/29093293

Zobrazit plný text záznamu

Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study

Autor: Kai Liu, Hironori Kokubo

Publikováno v: Journal of chemical information and modeling. 57(10)

Docking has become an indispensable approach in drug discovery research to predict the binding mode of a ligand. One great challenge in docking is to efficiently refine the correct pose from various putative docking poses through scoring functions. W

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ea7d025fe15bbe66300e9e08f61da406
https://pubmed.ncbi.nlm.nih.gov/28902511

Zobrazit plný text záznamu

Vyhledávací nástroje:

Upřesnit hledání