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Kawai R, Araki M, Yoshimura M, Kamiya N, Ono M, Saji H, Okuno Y. Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods. ACS Chem Neurosci 2018; 9:957-966. [PMID: 29381047 DOI: 10.1021/acschemneuro.7b00389] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Development of new diagnostic imaging probes for Alzheimer's disease, such as positron emission tomography (PET) and single photon emission computed tomography (SPECT) probes, has been strongly desired. In this study, we investigated the most accessible amyloid β (Aβ) binding site of [123I]IMPY, a Thioflavin-T-derived SPECT probe, using experimental and computational methods. First, we performed a competitive inhibition assay with Orange-G, which recognizes the KLVFFA region in Aβ fibrils, suggesting that IMPY and Orange-G bind to different sites in Aβ fibrils. Next, we precisely predicted the IMPY binding site on a multiple-protofilament Aβ fibril model using computational approaches, consisting of molecular dynamics and docking simulations. We generated possible IMPY-binding structures using docking simulations to identify candidates for probe-binding sites. The binding free energy of IMPY with the Aβ fibril was calculated by a free energy simulation method, MP-CAFEE. These computational results suggest that IMPY preferentially binds to an interfacial pocket located between two protofilaments and is stabilized mainly through hydrophobic interactions. Finally, our computational approach was validated by comparing it with the experimental results. The present study demonstrates the possibility of computational approaches to screen new PET/SPECT probes for Aβ imaging.
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Affiliation(s)
- Ryoko Kawai
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitsugu Araki
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, JAPAN
| | - Masashi Yoshimura
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Masahiro Ono
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hideo Saji
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasushi Okuno
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, JAPAN
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Ogata K, Hatakeyama M, Nakamura S. Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation. Molecules 2018; 23:E425. [PMID: 29462850 PMCID: PMC6017306 DOI: 10.3390/molecules23020425] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/11/2018] [Accepted: 02/14/2018] [Indexed: 11/17/2022] Open
Abstract
The octanol-water partition coefficient (logPow) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆Gwater values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of logPow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted logPow values.
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Affiliation(s)
- Koji Ogata
- RIKEN Innovation Center, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Makoto Hatakeyama
- RIKEN Innovation Center, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shinichiro Nakamura
- RIKEN Innovation Center, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Araki M, Kamiya N, Sato M, Nakatsui M, Hirokawa T, Okuno Y. The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors. J Chem Inf Model 2016; 56:2445-2456. [PMID: 28024406 DOI: 10.1021/acs.jcim.6b00398] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Accurate prediction of binding affinities of drug candidates to their targets remains challenging because of protein flexibility in solution. Conformational flexibility of the ATP-binding site in the CDK2 and ERK2 kinases was identified using molecular dynamics simulations. The binding free energy (ΔG) of twenty-four ATP-competitive inhibitors toward these kinases was assessed using an alchemical free energy perturbation method, MP-CAFEE. However, large calculation errors of 2-3 kcal/mol were observed using this method, where the free energy simulation starts from a single equilibrated conformation. Here, we developed a new ΔG computation method, where the starting structure was set to multiconformations to cover flexibility. The calculation accuracy was successfully improved, especially for larger molecular size compounds, leading to reliable prediction of a broader range of drug candidates. The present study demonstrates that conformational flexibility of interactions between a compound and the glycine-rich loop in the kinases is a key factor in ΔG estimation.
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Affiliation(s)
- Mitsugu Araki
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Narutoshi Kamiya
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Graduate School of Simulation Studies, University of Hyogo , 7-1-28 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Miwa Sato
- Mitsui Knowledge Industry Co., Ltd., 2-5-1 Atago, Minato-ku, Tokyo 105-6215, Japan
| | - Masahiko Nakatsui
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Graduate School of Medicine, Kyoto University , 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , 1-1-1 Tennodai, Tsukuba-shi, Ibaraki 305-8575, Japan
| | - Yasushi Okuno
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Graduate School of Medicine, Kyoto University , 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
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Yamashita T, Ueda A, Mitsui T, Tomonaga A, Matsumoto S, Kodama T, Fujitani H. The Feasibility of an Efficient Drug Design Method with High-Performance Computers. Chem Pharm Bull (Tokyo) 2015; 63:147-55. [DOI: 10.1248/cpb.c14-00596] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo
| | - Akihiko Ueda
- Bio-IT R&D Office, Next-Generation Healthcare Innovation Center, Fujitsu Limited
| | - Takashi Mitsui
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo
- Bio-IT R&D Office, Next-Generation Healthcare Innovation Center, Fujitsu Limited
| | - Atsushi Tomonaga
- Bio-IT R&D Office, Next-Generation Healthcare Innovation Center, Fujitsu Limited
| | - Shunji Matsumoto
- Bio-IT R&D Office, Next-Generation Healthcare Innovation Center, Fujitsu Limited
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo
| | - Hideaki Fujitani
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo
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