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Nakamura S, Akaki T, Nishiwaki K, Nakatani M, Kawase Y, Takahashi Y, Nakanishi I. System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study. J Comput Chem 2023; 44:824-831. [PMID: 36444861 DOI: 10.1002/jcc.27044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022]
Abstract
The fragment molecular orbital (FMO) method is a fast quantum-mechanical method that divides systems into pieces of fragments and performs ab initio calculations. The system truncation enables further speed improvement. In this article, we systematically study the effects of system truncations on binding affinity calculations obtained with FMO in combination with either the polarizable continuum model (FMO/PCM) or in combination with the Møller-Plesset method (FMO-MP2). We have used five protein complexes with ligands of several charged states. The calculated binding energies of the size variants of the truncated system, including only a restricted number of atoms around the ligand, are compared to the energy obtained from a full system. The result shows that the systems could be truncated to a radius of 8 Å from neutral ligands within an error of 0.7 kcal/mol, and 12 Å from charged ligands within an error of 1.1 kcal/mol for calculating the binding energy in solution.
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Affiliation(s)
- Shinya Nakamura
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Tatsuo Akaki
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan.,Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
| | - Keiji Nishiwaki
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Midori Nakatani
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Yuji Kawase
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Yuki Takahashi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Isao Nakanishi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
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2
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Watanabe C, Okiyama Y, Tanaka S, Fukuzawa K, Honma T. Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Chem Sci 2021; 12:4722-4739. [PMID: 35355624 PMCID: PMC8892577 DOI: 10.1039/d0sc06528e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/21/2021] [Indexed: 12/18/2022] Open
Abstract
Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blocking antibody. However, the molecular recognition mechanism-critical information for drug and antibody design-has not been fully clarified at the amino acid residue level. Elucidating such a microscopic mechanism in detail requires a more accurate molecular interpretation that includes quantum mechanics to quantitatively evaluate hydrogen bonds, XH/π interactions (X = N, O, and C), and salt bridges. In this study, we applied the fragment molecular orbital (FMO) method to characterize the SARS-CoV-2 S-protein binding interactions with not only ACE2 but also the B38 Fab antibody involved in ACE2-inhibitory binding. By analyzing FMO-based interaction energies along a wide range of binding interfaces carefully, we identified amino acid residues critical for molecular recognition between S-protein and ACE2 or B38 Fab antibody. Importantly, hydrophobic residues that are involved in weak interactions such as CH-O hydrogen bond and XH/π interactions, as well as polar residues that construct conspicuous hydrogen bonds, play important roles in molecular recognition and binding ability. Moreover, through these FMO-based analyses, we also clarified novel hot spots and epitopes that had been overlooked in previous studies by structural and molecular mechanical approaches. Altogether, these hot spots/epitopes identified between S-protein and ACE2/B38 Fab antibody may provide useful information for future antibody design, evaluation of the binding property of the SARS-CoV-2 variants including its N501Y, and small or medium drug design against the SARS-CoV-2.
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Affiliation(s)
- Chiduru Watanabe
- Center for Biosystems Dynamics Research, RIKEN 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama Kanagawa 230-0045 Japan +81-45-503-9432 +81-45-503-9551
- JST, PRESTO 4-1-8, Honcho Kawaguchi Saitama 332-0012 Japan
| | - Yoshio Okiyama
- Division of Medicinal Safety Science, National Institute of Health Sciences 3-25-26 Tonomachi, Kawasaki-ku Kawasaki Kanagawa 210-9501 Japan
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University 1-1 Rokkodai, Nada-ku Kobe Hyogo 657-8501 Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University 2-4-41 Ebara, Shinagawa-ku Tokyo 142-8501 Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University 6-6-11 Aoba, Aramaki, Aoba-ku Sendai Miyagi 980-8579 Japan
| | - Teruki Honma
- Center for Biosystems Dynamics Research, RIKEN 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama Kanagawa 230-0045 Japan +81-45-503-9432 +81-45-503-9551
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3
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Kusumoto M, Ueno-Noto K, Takano K. Systematic Interaction Analysis of Anti-Human Immunodeficiency Virus Type-1 Neutralizing Antibodies with High Mannose Glycans Using Fragment Molecular Orbital and Molecular Dynamics Methods. J Comput Chem 2020; 41:31-42. [PMID: 31565801 DOI: 10.1002/jcc.26073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/18/2019] [Accepted: 09/01/2019] [Indexed: 11/10/2022]
Abstract
A series of broadly neutralizing antibodies called PGT have been shown to be bound directly to human immunodeficiency virus type-1 via high mannose glycans on glycoprotein gp120. Despite the sequence similarities of amino acids of the antibodies, their affinities to the glycan differ. Glycan-antibody interactions among these antibodies are systematically compared with quantum chemical fragment molecular orbital calculations and molecular dynamics simulations. The differences among structural stability of the glycan in the active site of the complexes and total interaction energies as well as binding free energies between the glycan and antibodies agree well with the experimentally shown affinities of the glycan to the antibodies. The terminal saccharide, Man D3, is structurally stable and responsible for the glycan-antibody binding through electrostatic and dispersion interactions. The structural stability of nonterminal saccharides such as Man 4 or Man C plays substantial roles in the interaction via direct hydrogen bonds. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Miyu Kusumoto
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Kaori Ueno-Noto
- Center for Natural Sciences, College of Liberal Arts and Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Keiko Takano
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
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4
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Yamanaka M. <b>Random matrix theory for an inter-fragment interaction energy matrix in fragment molecular orbital method </b>. CHEM-BIO INFORMATICS JOURNAL 2018. [DOI: 10.1273/cbij.18.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masanori Yamanaka
- Department of Physics, College of Science and Technology, Nihon University
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5
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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6
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Phipps MJS, Fox T, Tautermann CS, Skylaris CK. Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns. Chem Soc Rev 2015; 44:3177-211. [DOI: 10.1039/c4cs00375f] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The partitioning of the interaction energy into chemical components such as electrostatics, polarization, and charge transfer is possible with energy decomposition analysis approaches. We review and evaluate these for biomolecular applications.
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Affiliation(s)
| | - Thomas Fox
- Lead Identification and Optimization Support
- Boehringer Ingelheim Pharma GmbH & Co. KG
- 88397 Biberach
- Germany
| | - Christofer S. Tautermann
- Lead Identification and Optimization Support
- Boehringer Ingelheim Pharma GmbH & Co. KG
- 88397 Biberach
- Germany
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7
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Koyama Y, Ueno-Noto K, Takano K. Affinity of HIV-1 antibody 2G12 with monosaccharides: A theoretical study based on explicit and implicit water models. Comput Biol Chem 2014; 49:36-44. [DOI: 10.1016/j.compbiolchem.2014.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 01/14/2014] [Accepted: 01/14/2014] [Indexed: 11/25/2022]
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Hasegawa K, Mohri S, Yokoyama T. Comparison of the local structural stabilities of mammalian prion protein (PrP) by fragment molecular orbital calculations. Prion 2012; 7:185-91. [PMID: 23232497 PMCID: PMC3609128 DOI: 10.4161/pri.23122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE), a member of the prion diseases, is a fatal neurodegenerative disorder suspected to be caused by a malfunction of prion protein (PrP). Although BSE prions have been reported to be transmitted to a wide range of animal species, dogs and hamsters are known to be BSE-resistant animals. Analysis of canine and hamster PrP could elucidate the molecular mechanisms supporting the species barriers to BSE prion transmission. The structural stability of 6 mammalian PrPs, including human, cattle, mouse, hamster, dog and cat, was analyzed. We then evaluated intramolecular interactions in PrP by fragment molecular orbital (FMO) calculations. Despite similar backbone structures, the PrP side-chain orientations differed among the animal species examined. The pair interaction energies between secondary structural elements in the PrPs varied considerably, indicating that the local structural stabilities of PrP varied among the different animal species. Principal component analysis (PCA) demonstrated that different local structural stability exists in bovine PrP compared with the PrP of other animal species examined. The results of the present study suggest that differences in local structural stabilities between canine and bovine PrP link diversity in susceptibility to BSE prion infection.
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Asada N, Fedorov DG, Kitaura K, Nakanishi I, Merz KM. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method. J Phys Chem Lett 2012; 3:2604-2610. [PMID: 23050059 PMCID: PMC3462021 DOI: 10.1021/jz3010688] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4'-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies.
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Affiliation(s)
- Naoya Asada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Kazuo Kitaura
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kenneth M. Merz
- Quantum Theory Project, The University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
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10
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Fedorov DG, Nagata T, Kitaura K. Exploring chemistry with the fragment molecular orbital method. Phys Chem Chem Phys 2012; 14:7562-77. [DOI: 10.1039/c2cp23784a] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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11
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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12
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Okiyama Y, Fukuzawa K, Yamada H, Mochizuki Y, Nakano T, Tanaka S. Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.04.070] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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13
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Cao Y, Koh X, Dong L, Du X, Wu A, Ding X, Deng H, Shu Y, Chen J, Jiang T. Rapid estimation of binding activity of influenza virus hemagglutinin to human and avian receptors. PLoS One 2011; 6:e18664. [PMID: 21533248 PMCID: PMC3076431 DOI: 10.1371/journal.pone.0018664] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 03/09/2011] [Indexed: 11/19/2022] Open
Abstract
A critical step for avian influenza viruses to infect human hosts and cause epidemics or pandemics is acquisition of the ability of the viral hemagglutinin (HA) to bind to human receptors. However, current global influenza surveillance does not monitor HA binding specificity due to a lack of rapid and reliable assays. Here we report a computational method that uses an effective scoring function to quantify HA-receptor binding activities with high accuracy and speed. Application of this method reveals receptor specificity changes and its temporal relationship with antigenicity changes during the evolution of human H3N2 viruses. The method predicts that two amino acid differences at 222 and 225 between HAs of A/Fujian/411/02 and A/Panama/2007/99 viruses account for their differences in binding to both avian and human receptors; this prediction was verified experimentally. The new computational method could provide an urgently needed tool for rapid and large-scale analysis of HA receptor specificities for global influenza surveillance.
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Affiliation(s)
- Yang Cao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoying Koh
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Libo Dong
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangjun Du
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Aiping Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xilai Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Center for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hongyu Deng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Center for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuelong Shu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- * E-mail: (TJ); (JC); (YS)
| | - Jianzhu Chen
- Center for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (TJ); (JC); (YS)
| | - Taijiao Jiang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (TJ); (JC); (YS)
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Sawada T, Fedorov DG, Kitaura K. Role of the Key Mutation in the Selective Binding of Avian and Human Influenza Hemagglutinin to Sialosides Revealed by Quantum-Mechanical Calculations. J Am Chem Soc 2010; 132:16862-72. [DOI: 10.1021/ja105051e] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Toshihiko Sawada
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuo Kitaura
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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15
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Sawada T, Fedorov DG, Kitaura K. Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect. J Phys Chem B 2010; 114:15700-5. [DOI: 10.1021/jp1068895] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Toshihiko Sawada
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuo Kitaura
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Abstract
Outbreaks of influenza A viruses continue to cause morbidity and mortality worldwide. The global disease burden of influenza is substantial. While antiviral therapies are available, influenza vaccines are the mainstay of efforts to reduce the substantial health burden from seasonal influenza. Inactivated influenza vaccines have been available since the 1940s, with live attenuated, cold-adapted vaccines becoming available in the United States in 2003. In spite of the successes, more research is needed to develop more effective seasonal influenza vaccines that provide long-lasting immunity and broad protection against strains that differ antigenically from vaccine viruses. This review introduces the virus and its disease, the current state of seasonal and pandemic influenza vaccines, and the challenges we face in the future.
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17
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Ab initio fragment molecular orbital studies of influenza virus hemagglutinin–sialosaccharide complexes toward chemical clarification about the virus host range determination. Glycoconj J 2008; 25:805-15. [DOI: 10.1007/s10719-008-9141-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 04/28/2008] [Accepted: 04/29/2008] [Indexed: 10/21/2022]
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18
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Iwata T, Fukuzawa K, Nakajima K, Aida-Hyugaji S, Mochizuki Y, Watanabe H, Tanaka S. Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method. Comput Biol Chem 2008; 32:198-211. [DOI: 10.1016/j.compbiolchem.2008.03.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 11/26/2022]
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19
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Fedorov DG, Kitaura K. Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method. J Phys Chem A 2007; 111:6904-14. [PMID: 17511437 DOI: 10.1021/jp0716740] [Citation(s) in RCA: 437] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following the brief review of the modern fragment-based methods and other approaches to perform quantum-mechanical calculations of large systems, the theoretical development of the fragment molecular orbital method (FMO) is covered in detail, with the emphasis on the physical properties, which can be computed with FMO. The FMO-based polarizable continuum model (PCM) for treating the solvent effects in large systems and the pair interaction energy decomposition analysis (PIEDA) are described in some detail, and a range of applications of FMO to biological studies is introduced. The factors determining the relative stability of polypeptide conformers (alpha-helix, beta-turn, and extended form) are elucidated using FMO/PCM and PIEDA, and the interactions in the Trp-cage miniprotein construct (PDB: 1L2Y) are analyzed using PIEDA.
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Affiliation(s)
- Dmitri G Fedorov
- Research Institute for Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, Japan 305-8568.
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20
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FUKUZAWA K, NAKANO T, KATO A, MOCHIZUKI Y, TANAKA S. Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules. ACTA ACUST UNITED AC 2007. [DOI: 10.2477/jccj.6.185] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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