Ryo Takano
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Research Subjects
Ryo Takano has a total of 5 co-authors. Here are the top co-authors by number of shared publications:
- Amzad Hossain
The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
1 shared publication - Mohammad Abdul Halim
Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
1 shared publication - Muhammad Shahinozzaman
Department of Nutrition and Food Sciences, University of Maryland, College Park, MD 20742, USA
1 shared publication - Shinkichi Tawata
PAK Research Center, University of the Ryukyus, Senbaru 1, Nishihara-cho, Okinawa 903-0213, Japan
1 shared publication - Takahiro Ishii
The United Graduate School of Agricultural Sciences Kagoshima University Kagoshima Japan
1 shared publication
Latest Publications
- Open Access
- 31 August 2018
- Published by MDPI AG in Scientia Pharmaceutica
- Vol. 86 (3) , 32
Cytotoxic Desulfated Saponin from Holothuria atra Predicted to Have High Binding Affinity to the Oncogenic Kinase PAK1: A Combined In Vitro and In Silico Study
Sea cucumbers have long been utilized in foods and Asiatic folk medicines for their nutritive and health benefits. Herein, three sea cucumber species were investigated and Holothuria atra showed the highest cytotoxicity among these. Next, a desulfated saponin, desulfated echinoside B (DEB), was purified from H. atra through bioassay-guided fractionation. LC-ESI-MS (Liquid chromatography-electrospray ionization mass spectrometry) analysis also showed H. atra to be a rich source of saponins. DEB showed cytotoxicity on cancer cells with IC50 values of 0.5–2.5 µM, and on brine shrimps with an IC50 value of 9.2 µM. In molecular docking studies, DEB was found to bind strongly with the catalytic domain of PAK1 (p21-activated kinase 1) and it showed binding energy of −8.2 kcal/mol compared to binding energy of −7.7 kcal/mol for frondoside A (FRA). Both of them bind to the novel allosteric site close to the ATP-binding cleft. Molecular dynamics (MD) simulation demonstrated that DEB can form a more stable complex with PAK1, remaining inside the allosteric binding pocket and forming the maximum number of hydrogen bonds with the surrounding residues. Moreover, important ligand binding residues were found to be less fluctuating in the DEB-PAK1 complex than in the FRA-PAK1 complex throughout MD simulation. Our experimental and computational studies showed that both DEB and FRA can act as natural allosteric PAK1 inhibitors and DEB appeared to be more promising than FRA.
- 31 August 2018
- Published by MDPI AG in Scientia Pharmaceutica
- Vol. 86 (3) , 32
Open AccessCytotoxic Desulfated Saponin from Holothuria atra Predicted to Have High Binding Affinity to the Oncogenic Kinase PAK1: A Combined In Vitro and In Silico Study
Sea cucumbers have long been utilized in foods and Asiatic folk medicines for their nutritive and health benefits. Herein, three sea cucumber species were investigated and Holothuria atra showed the highest cytotoxicity among these. Next, a desulfated saponin, desulfated echinoside B (DEB), was purified from H. atra through bioassay-guided fractionation. LC-ESI-MS (Liquid chromatography-electrospray ionization mass spectrometry) analysis also showed H. atra to be a rich source of saponins. DEB showed cytotoxicity on cancer cells with IC50 values of 0.5–2.5 µM, and on brine shrimps with an IC50 value of 9.2 µM. In molecular docking studies, DEB was found to bind strongly with the catalytic domain of PAK1 (p21-activated kinase 1) and it showed binding energy of −8.2 kcal/mol compared to binding energy of −7.7 kcal/mol for frondoside A (FRA). Both of them bind to the novel allosteric site close to the ATP-binding cleft. Molecular dynamics (MD) simulation demonstrated that DEB can form a more stable complex with PAK1, remaining inside the allosteric binding pocket and forming the maximum number of hydrogen bonds with the surrounding residues. Moreover, important ligand binding residues were found to be less fluctuating in the DEB-PAK1 complex than in the FRA-PAK1 complex throughout MD simulation. Our experimental and computational studies showed that both DEB and FRA can act as natural allosteric PAK1 inhibitors and DEB appeared to be more promising than FRA.