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Andoh Y, Ichikawa SI, Sakashita T, Fujimoto K, Yoshii N, Nagai T, Tang Z, Okazaki S. An exa-scale high-performance molecular dynamics simulation program: MODYLAS. J Chem Phys 2023; 158:2890480. [PMID: 37184018 DOI: 10.1063/5.0144361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023] Open
Abstract
A new version of the highly parallelized general-purpose molecular dynamics (MD) simulation program MODYLAS with high performance on the Fugaku computer was developed. A benchmark test using Fugaku indicated highly efficient communication, single instruction, multiple data (SIMD) processing, and on-cache arithmetic operations. The system's performance deteriorated only slightly, even under high parallelization. In particular, a newly developed minimum transferred data method, requiring a significantly lower amount of data transfer compared to conventional communications, showed significantly high performance. The coordinates and forces of 101 810 176 atoms and the multipole coefficients of the subcells could be distributed to the 32 768 nodes (1 572 864 cores) in 2.3 ms during one MD step calculation. The SIMD effective instruction rates for floating-point arithmetic operations in direct force and fast multipole method (FMM) calculations measured on Fugaku were 78.7% and 31.5%, respectively. The development of a data reuse algorithm enhanced the on-cache processing; the cache miss rate for direct force and FMM calculations was only 2.74% and 1.43%, respectively, on the L1 cache and 0.08% and 0.60%, respectively, on the L2 cache. The modified MODYLAS could complete one MD single time-step calculation within 8.5 ms for the aforementioned large system. Additionally, the program contains numerous functions for material research that enable free energy calculations, along with the generation of various ensembles and molecular constraints.
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Affiliation(s)
- Yoshimichi Andoh
- National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Shin-Ichi Ichikawa
- Computational Science Division, Technical Computing Business Unit, Fujitsu Limited, Chiba, Japan
| | - Tatsuya Sakashita
- Center for Quantum Information and Quantum Biology, Osaka University, 1-2, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kazushi Fujimoto
- Department of Materials Chemistry, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Noriyuki Yoshii
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Tetsuro Nagai
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1, Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Zhiye Tang
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, 38, Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Susumu Okazaki
- Department of Advanced Materials Science, The University of Tokyo, 5-1-5, Kashiwa-no-ha, Kashiwa, Chiba 277-0871, Japan
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Cytotoxic Fractions from Hechtia glomerata Extracts and p-Coumaric Acid as MAPK Inhibitors. Molecules 2021; 26:molecules26041096. [PMID: 33669666 PMCID: PMC7922350 DOI: 10.3390/molecules26041096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/06/2021] [Accepted: 02/13/2021] [Indexed: 12/24/2022] Open
Abstract
Preliminary bioassay-guided fractionation was performed to identify cytotoxic compounds from Hechtia glomerata, a plant that is used in Mexican ethnomedicine. Organic and aqueous extracts were prepared from H. glomerata’s leaves and evaluated against two cancer cell lines. The CHCl3/MeOH (1:1) active extract was fractionated, and the resulting fractions were assayed against prostate adenocarcinoma PC3 and breast adenocarcinoma MCF7 cell lines. Active fraction 4 was further analyzed by high-performance liquid chromatography–quadrupole time-of-flight–mass spectrometry analysis to identify its active constituents. Among the compounds that were responsible for the cytotoxic effects of this fraction were flavonoids, phenolic acids, and aromatic compounds, of which p-coumaric acid (p-CA) and its derivatives were abundant. To understand the mechanisms that underlie p-CA cytotoxicity, a microarray assay was performed on PC3 cells that were treated or not with this compound. The results showed that mitogen-activated protein kinases (MAPKs) that regulate many cancer-related pathways were targeted by p-CA, which could be related to the reported effects of reactive oxygen species (ROS). A molecular docking study of p-CA showed that this phenolic acid targeted these protein active sites (MAPK8 and Serine/Threonine protein kinase 3) at the same binding site as their inhibitors. Thus, we hypothesize that p-CA produces ROS, directly affects the MAPK signaling pathway, and consequently causes apoptosis, among other effects. Additionally, p-CA could be used as a platform for the design of new MAPK inhibitors and re-sensitizing agents for resistant cancers.
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Andoh Y, Hayakawa S, Okazaki S. Molecular dynamics study of lipid bilayers modeling outer and inner leaflets of plasma membranes of mouse hepatocytes. I. Differences in physicochemical properties between the two leaflets. J Chem Phys 2020; 153:035105. [PMID: 32716170 DOI: 10.1063/5.0012676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Outer and inner leaflets of plasma cell membranes have different lipid compositions, and the membrane properties of each leaflet can differ from each other significantly due to these composition differences. However, because of the experimental difficulty in measuring the membrane properties for each leaflet separately, the differences are not well understood at a molecular level. In this study, we constructed two lipid bilayer systems, modeling outer and inner leaflets of plasma membranes of mouse hepatocytes based on experimental composition data. The ion concentration in the interlamellar water phase was also set to match the concentration in extra- and intracellular fluids. The differences in physical properties between the outer and inner leaflets of mouse hepatocyte cell membrane models were investigated by performing 1.2 μs-long all-atomistic molecular dynamics calculations under physiological temperature and pressure conditions (310.15 K and 1 atm). The calculated electron density profiles along the bilayer normal for each model bilayer system captured well the asymmetric feature of the experimental electron density profile across actual cell plasma membranes, indicating that our procedure of modeling the outer and inner leaflets of the cell plasma membranes was satisfactory. We found that compared to the outer leaflet model, the inner leaflet model had a very bulky and soft structure in the lateral direction. To confirm the differences, membrane fluidity was measured from the lateral diffusivity and relaxation times. The fluidity was significantly higher in the inner leaflet model than in the outer leaflet model. We also discuss two topics that are of wide interest in biology, i.e., the interdigitation of acyl tails of lipid molecules between two monolayers and the lateral concentration fluctuation of lipid molecules in the bilayers.
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Affiliation(s)
- Yoshimichi Andoh
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Shiho Hayakawa
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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