1
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Tang B, Luo S, Wang Q, Gao P, Duan L. Advanced molecular mechanisms of modified DRV compounds in targeting HIV-1 protease mutations and interrupting monomer dimerization. Phys Chem Chem Phys 2024; 26:4989-5001. [PMID: 38258432 DOI: 10.1039/d3cp05702j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
HIV-1 protease (PR) plays a crucial role in the treatment of HIV as a key target. The global issue of emerging drug resistance is escalating, and PR mutations pose a substantial challenge to the effectiveness of inhibitors. HIV-1 PR is an ideal model for studying drug resistance to inhibitors. The inhibitor, darunavir (DRV), exhibits a high genetic barrier to viral resistance, but with mutations of residues in the PR, there is also some resistance to DRV. Inhibitors can impede PR in two ways: one involves binding to the active site of the dimerization protease, and the other involves binding to the PR monomer, thereby preventing dimerization. In this study, we aimed to investigate the inhibitory effect of DRV with a modified inhibitor on PR, comparing the differences between wild-type and mutated PR, using molecular dynamics simulations. The inhibitory effect of the inhibitors on PR monomers was subsequently investigated. And molecular mechanics Poisson-Boltzmann surface area evaluated the binding free energy. The energy contribution of individual residues in the complex was accurately calculated by the alanine scanning binding interaction entropy method. The results showed that these inhibitors had strong inhibitory effects against PR mutations, with GRL-142 exhibiting potent inhibition of both the PR monomer and dimer. Improved inhibitors could strengthen hydrogen bonds and interactions with PR, thereby boosting inhibition efficacy. The binding of the inhibitor and mutation of the PR affected the distance between D25 and I50, preventing their dimerization and the development of drug resistance. This study could accelerate research targeting HIV-1 PR inhibitors and help to further facilitate drug design targeting both mechanisms.
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Affiliation(s)
- Bolin Tang
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
| | - Song Luo
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
| | - Qihang Wang
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
| | - Pengfei Gao
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
| | - Lili Duan
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
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2
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The electrostatic embedding contribution to DFT calculations of ligand-amino acid residues interaction. J Mol Model 2018; 24:211. [DOI: 10.1007/s00894-018-3743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
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3
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Sanusi ZK, Govender T, Maguire GEM, Maseko SB, Lin J, Kruger HG, Honarparvar B. An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant. J Comput Aided Mol Des 2018; 32:459-471. [PMID: 29397520 DOI: 10.1007/s10822-018-0099-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/16/2018] [Indexed: 01/12/2023]
Abstract
The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less activity towards the protease. A mutation and insertion designated L38L↑N↑L PR was recently reported from subtype of C-SA HIV-1. An integrated two-layered ONIOM (QM:MM) method was employed in this study to examine the binding affinities of the nine HIV PR inhibitors against this mutant. The computed binding free energies as well as experimental data revealed a reduced inhibitory activity towards the L38L↑N↑L PR in comparison with subtype C-SA HIV-1 PR. This observation suggests that the insertion and mutations significantly affect the binding affinities or characteristics of the HIV PIs and/or parent PR. The same trend for the computational binding free energies was observed for eight of the nine inhibitors with respect to the experimental binding free energies. The outcome of this study shows that ONIOM method can be used as a reliable computational approach to rationalize lead compounds against specific targets. The nature of the intermolecular interactions in terms of the host-guest hydrogen bond interactions is discussed using the atoms in molecules (AIM) analysis. Natural bond orbital analysis was also used to determine the extent of charge transfer between the QM region of the L38L↑N↑L PR enzyme and FDA approved drugs. AIM analysis showed that the interaction between the QM region of the L38L↑N↑L PR and FDA approved drugs are electrostatic dominant, the bond stability computed from the NBO analysis supports the results from the AIM application. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide information that will aid in the design of much improved HIV-1 PR antiviral drugs.
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Affiliation(s)
- Zainab K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Sibusiso B Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Johnson Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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4
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Sanusi ZK, Govender T, Maguire GEM, Maseko SB, Lin J, Kruger HG, Honarparvar B. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach. J Mol Graph Model 2017; 76:77-85. [PMID: 28711760 DOI: 10.1016/j.jmgm.2017.06.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 01/15/2023]
Abstract
Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B. In our hybrid ONIOM model, the HIV-1 PR inhibitors as well as the ASP 25/25' catalytic active residues were treated at high level quantum mechanics (QM) theory using B3LYP/6-31G(d), and the remaining HIV PR residues were considered using the AMBER force field. The experimental binding energies of the PR inhibitors were compared to the ONIOM calculated results. The theoretical binding free energies (?Gbind) for subtype B follow a similar trend to the experimental results, with one exemption. The computational model was less suitable for C-SA PR. Analysis of the results provided valuable information about the shortcomings of this approach. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide much improved binding energies for complex enzyme drug interactions.
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Affiliation(s)
- Z K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - T Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - G E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - S B Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - J Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - H G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - B Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
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5
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Nishimoto Y, Fedorov DG. Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding. J Comput Chem 2017; 38:406-418. [DOI: 10.1002/jcc.24693] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/14/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry, Kyoto University; 34-4 Takano Nishihiraki-cho Sakyo-ku Kyoto 606-8103 Japan
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat); National Institute of Advanced Industrial Science and Technology (AIST); 1-1-1 Umezono Tsukuba Ibaraki 305-8568 Japan
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6
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Nakata H, Nishimoto Y, Fedorov DG. Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method. J Chem Phys 2016; 145:044113. [DOI: 10.1063/1.4959231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Hiroya Nakata
- Department of Fundamental Technology Research, R and D Center Kagoshima, Kyocera, 1-4 Kokubu Yamashita-cho, Kirishima-shi, Kagoshima 899-4312, Japan
| | - Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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7
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Pruitt SR, Nakata H, Nagata T, Mayes M, Alexeev Y, Fletcher G, Fedorov DG, Kitaura K, Gordon MS. Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method. J Chem Theory Comput 2016; 12:1423-35. [DOI: 10.1021/acs.jctc.5b01208] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Spencer R. Pruitt
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Hiroya Nakata
- Department of Fundamental Technology Research, R&D Center Kagoshima, Kyocera Corporation, 1-4 Kokubu Yamashita-cho, Kirishima-shi, Kagoshima 899-4312, Japan
| | - Takeshi Nagata
- Nanosystem Research
Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umenzono, Tsukuba, Ibaraki 305-8568, Japan
| | - Maricris Mayes
- Department
of Chemistry and Biochemistry, University of Massachusetts Dartmouth, 285 Old Westport Road, Dartmouth, Massachusetts 02747-2300, United States
| | - Yuri Alexeev
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Graham Fletcher
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Dmitri G. Fedorov
- Nanosystem Research
Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umenzono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State University, 201 Spedding
Hall, Ames, Iowa 50011, United States
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8
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Nishimoto Y, Fedorov DG. The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model. Phys Chem Chem Phys 2016; 18:22047-61. [DOI: 10.1039/c6cp02186g] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electronic gap in proteins is analyzed in detail, and it is shown that FMO-DFTB/PCM is efficient and accurate in describing the molecular structure of proteins in solution.
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Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry
- Kyoto University
- Sakyo-ku, Kyoto 606-8103
- Japan
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat)
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tsukuba
- Japan
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9
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Nakata H, Fedorov DG, Nagata T, Kitaura K, Nakamura S. Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method. J Chem Theory Comput 2015; 11:3053-64. [DOI: 10.1021/acs.jctc.5b00277] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Research
Cluster for Innovation, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Takeshi Nagata
- Nanosystem
Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Shinichiro Nakamura
- Research
Cluster for Innovation, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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10
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Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method. J Chem Phys 2015; 142:124101. [DOI: 10.1063/1.4915068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Nishimoto Y, Fedorov DG, Irle S. Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:4801-12. [DOI: 10.1021/ct500489d] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan
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12
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Nakata H, Schmidt MW, Fedorov DG, Kitaura K, Nakamura S, Gordon MS. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method. J Phys Chem A 2014; 118:9762-71. [DOI: 10.1021/jp507726m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Research Cluster
for Innovation, Nakamura Lab, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Kojimachi Business
Center Building, Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Michael W. Schmidt
- Department
of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Shinichiro Nakamura
- Research Cluster
for Innovation, Nakamura Lab, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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13
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Nakata H, Fedorov DG, Yokojima S, Kitaura K, Nakamura S. Simulations of Raman Spectra Using the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:3689-98. [DOI: 10.1021/ct5003829] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Nakamura
Lab, Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi,
Chiyoda-ku, Tokyo 102-0083, Japan
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1
Umezono,Tsukuba, Ibaraki 305-8568, Japan
| | - Satoshi Yokojima
- Nakamura
Lab, Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachiouji-shi, Tokyo 192-0392, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 Japan
| | - Shinichiro Nakamura
- Nakamura
Lab, Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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14
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WU XUE, FU TING, XIU ZHILONG, YIN LIU, WANG JINGUANG, LI GUOHUI. COMPARING FOLDING MECHANISMS OF DIFFERENT PRION PROTEINS BY Gō MODEL. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prions are associated with neurodegenerative diseases induced by transmissible spongiform encephalopathies. The infectious scrapie form is referred to as PrP Sc , which has conformational change from normal prion with predominant α-helical conformation to the abnormal PrP Sc that is rich in β-sheet content. Neurodegenerative diseases have been found from both human and bovine sources, but there are no reports about infected by transmissible spongiform encephalopathies from rabbit, canine and horse sources. Here we used coarse-grained Gō model to compare the difference among human, bovine, rabbit, canine, and horse normal (cellular) prion proteins. The denatured state of normal prion has relation with the conversion from normal to abnormal prion protein, so we used all-atom Gō model to investigate the folding pathway and energy landscape for human prion protein. Through using coarse-grained Gō model, the cooperativity of the five prion proteins was characterized in terms of calorimetric criterion, sigmoidal transition, and free-energy profile. The rabbit and horse prion proteins have higher folding free-energy barrier and cooperativity, and canine prion protein has slightly higher folding free-energy barrier comparing with human and bovine prion proteins. The results from all-atom Gō model confirmed the validity of C α-Gō model. The correlations of our results with previous experimental and theoretical researches were discussed.
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Affiliation(s)
- XUE WU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - TING FU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - ZHI-LONG XIU
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, P. R. China
| | - LIU YIN
- Oncology Department in the 1st Affiliated Hospital of Dalian, Medical University, 222 Zhongshan Road, Liaoning Province, Dalian 116011, P. R. China
| | - JIN-GUANG WANG
- Thoracic Surgery Department in the 1st Affiliated Hospital of Dalian, Medical University, 222 Zhongshan Road, Liaoning Province, Dalian 116011, P. R. China
| | - GUO-HUI LI
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science 457, Zhongshan Road, Dalian, Liaoning, P. R. China
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15
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Liu J, He X, Zhang JZH. Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization. J Chem Inf Model 2013; 53:1306-14. [PMID: 23651068 DOI: 10.1021/ci400067c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Docking programs that use scoring functions to estimate binding affinities of small molecules to biological targets are widely applied in drug design and drug screening with partial success. But accurate and efficient scoring functions for protein-ligand binding affinity still present a grand challenge to computational chemists. In this study, the polarized protein-specific charge model (PPC) is incorporated into the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method to rescore the binding poses of some protein-ligand complexes, for which docking programs, such as Autodock, could not predict their binding modes correctly. Different sampling techniques (single minimized conformation and multiple molecular dynamics (MD) snapshots) are used to test the performance of MM/PBSA combined with the PPC model. Our results show the availability and effectiveness of this approach in correctly ranking the binding poses. More importantly, the bridging water molecules are found to play an important role in correctly determining the protein-ligand binding modes. Explicitly including these bridging water molecules in MM/PBSA calculations improves the prediction accuracy significantly. Our study sheds light on the importance of both bridging water molecules and the electronic polarization in the development of more reliable scoring functions for predicting molecular docking and protein-ligand binding affinity.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
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16
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Nakata H, Nagata T, Fedorov DG, Yokojima S, Kitaura K, Nakamura S. Analytic second derivatives of the energy in the fragment molecular orbital method. J Chem Phys 2013; 138:164103. [DOI: 10.1063/1.4800990] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Nagata T, Fedorov DG, Kitaura K. Analytic gradient for the embedding potential with approximations in the fragment molecular orbital method. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Nagata T, Fedorov DG, Kitaura K. Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1136-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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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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20
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Nagata T, Fedorov DG, Ishimura K, Kitaura K. Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method. J Chem Phys 2011; 135:044110. [DOI: 10.1063/1.3611020] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Brorsen K, Fedorov DG. Fully analytic energy gradient in the fragment molecular orbital method. J Chem Phys 2011; 134:124115. [DOI: 10.1063/1.3568010] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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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