1
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Nagura Y, Sabishiro H, Chimura N, Yuguchi M, Tada N, Takimoto D, Kurita N. Modification of MM force fields around heme-Fe in the CYP-ligand complex and ab initio FMO calculations for the complex. J Mol Graph Model 2024; 133:108875. [PMID: 39362061 DOI: 10.1016/j.jmgm.2024.108875] [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: 07/04/2024] [Revised: 08/30/2024] [Accepted: 09/24/2024] [Indexed: 10/05/2024]
Abstract
Cytochrome P450 (CYP) enzymes play essential roles in the synthesis and metabolic activation of physiologically active substances. CYP has a prosthetic heme (iron protoporphyrin IX) in its active center, where Fe ion (heme-Fe) is deeply involved in enzymatic reactions of CYP. To precisely describe the structure and electronic states around heme-Fe, we modified the force fields (FFs) around heme-Fe in molecular mechanics (MM) simulations and conducted ab initio fragment molecular orbital (FMO) calculations for the CYP-ligand complex. To describe the coordination bond between heme-Fe and its coordinated ligand (ketoconazole), we added FF between heme-Fe and the N atom of ketoconazole, and then the structure of the complex was optimized using the modified FF. Its adequacy was confirmed by comparing the MM-optimized structure with the X-ray crystal one of the CYP-ketoconazole complex. We also performed 100 ns molecular dynamics simulations and revealed that the coordination bonds around heme-Fe were maintained even at 310 K and that the CYP-ketoconazole structure was kept similar to the X-ray structure. Furthermore, we investigated the electronic states of the complex using the ab initio FMO method to identify the CYP residues and parts of ketoconazole that contribute to strong binding between CYP and ketoconazole. The present procedure of constructing FF between heme-Fe and ketoconazole can be applicable to other CYP-ligand complexes, and the modified FF can provide their accurate structures useful for predicting the specific interactions between CYP and its ligands.
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Affiliation(s)
- Yoshinobu Nagura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Haruna Sabishiro
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Nagomi Chimura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Masayuki Yuguchi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Narutoshi Tada
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Daichi Takimoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan.
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2
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Rutskoy B, Ozerov G, Bezrukov D. The Role of Bond Functions in Describing Intermolecular Electron Correlation for Van der Waals Dimers: A Study of (CH 4) 2 and Ne 2. Int J Mol Sci 2024; 25:1472. [PMID: 38338750 PMCID: PMC10855067 DOI: 10.3390/ijms25031472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
We present a study of the intermolecular interactions in van der Waals complexes of methane and neon dimers within the framework of the CCSD method. This approach was implemented and applied to calculate and examine the behavior of the contracted two-particle reduced density matrix (2-RDM). It was demonstrated that the region near the minimum of the two-particle density matrix correlation part, corresponding to the primary bulk of the Coulomb hole contribution, exerts a significant influence on the dispersion interaction energetics of the studied systems. As a result, the bond functions approach was applied to improve the convergence performance for the intermolecular correlation energy results with respect to the size of the atomic basis. For this, substantial acceleration was achieved by introducing an auxiliary basis of bond functions centered on the minima of the 2-RDM. For both methane and neon dimers, this general conclusion was confirmed with a series of CCSD calculations for the 2-RDM and the correlation energies.
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Affiliation(s)
- Bogdan Rutskoy
- National Research Centre “Kurchatov Institute”, Moscow 123182, Russia;
- Institute of Nuclear Physics and Technology, National Research Nuclear University “MEPhI” (Moscow Engineering Physics Institute), Moscow 115409, Russia
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Georgiy Ozerov
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Dmitry Bezrukov
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia;
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3
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Tanaka S. Protein-Protein Interaction Modelling with the Fragment Molecular Orbital Method. Methods Mol Biol 2023; 2552:295-305. [PMID: 36346599 DOI: 10.1007/978-1-0716-2609-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fragment molecular orbital (FMO) method enables ab initio quantum-chemical calculations for biomolecular systems with high accuracy and moderate computational cost. Through this analysis we can evaluate the inter-fragment interaction energies (IFIEs) that provide useful measures for effective interactions between the fragments representing amino-acid residues and ligand molecules. Here I describe how to prepare the input structures and perform the FMO calculations for protein-protein complex system. In addition to the pre-processing, some useful tools for the post-processing analysis are also illustrated.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, Kobe, Hyogo, Japan.
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4
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Phusi N, Hashimoto Y, Otsubo N, Imai K, Thongdee P, Sukchit D, Kamsri P, Punkvang A, Suttisintong K, Pungpo P, Kurita N. Structure-based drug design of novel M. tuberculosis InhA inhibitors based on fragment molecular orbital calculations. Comput Biol Med 2023; 152:106434. [PMID: 36543008 DOI: 10.1016/j.compbiomed.2022.106434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/24/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
2-trans enoyl-acyl carrier protein reductase (InhA) is a promising target for developing novel chemotherapy agents for tuberculosis, and their inhibitory effects on InhA activity were widely investigated by the physicochemical experiments. However, the reason for the wide range of their inhibitory effects induced by similar agents was not explained by only the difference in their chemical structures. In our previous molecular simulations, a series of heteroaryl benzamide derivatives were selected as candidate inhibitors against InhA, and their binding properties with InhA were investigated to propose novel derivatives with higher binding affinity to InhA. In the present study, we extended the simulations for a series of 4-hydroxy-2-pyridone derivatives to search widely for more potent inhibitors against InhA. Using ab initio fragment molecular orbital (FMO) calculations, we elucidated the specific interactions between InhA residues and the derivatives at an electronic level and highlighted key interactions between InhA and the derivatives. The FMO results clearly indicated that the most potent inhibitor has strong hydrogen bonds with the backbones of Tyr158, Thr196, and NADH of InhA. This finding may provide informative structural concepts for designing novel 4-hydroxy-2-pyridone derivatives with higher binding affinity to InhA. Our previous and present molecular simulations could provide important guidelines for the rational design of more potent InhA inhibitors.
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Affiliation(s)
- Naruedon Phusi
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Yuta Hashimoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Naoki Otsubo
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Kyohei Imai
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Paptawan Thongdee
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Darunee Sukchit
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center, NSTDA, 111 Thailand Science Park, Klong Luang, Pathum Thani, 12120, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand.
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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5
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Shaji D, Suzuki R, Yamamoto S, Orihashi D, Kurita N. Natural inhibitors for severe acute respiratory syndrome coronavirus 2 main protease from Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis: molecular docking and ab initio fragment molecular orbital calculations. Struct Chem 2022; 33:1771-1788. [PMID: 35938063 PMCID: PMC9340690 DOI: 10.1007/s11224-022-02021-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022]
Abstract
The novel coronavirus 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly worldwide, and new drug treatments for COVID-19 are urgently required. To find the potential inhibitors against the main protease (Mpro) of SARS-CoV-2, we investigated the inhibitory potential of naturally occurring compounds from the plants Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis, using molecular docking, classical molecular mechanics optimizations, and ab initio fragment molecular orbital (FMO) calculations. Of the 35 compounds that we simulated, feralolide from Aloe vera exhibited the highest binding affinity against Mpro. Therefore, we proposed novel compounds based on the feralolide and investigated their binding properties to Mpro. The FMO results indicated that the introduction of a hydroxyl group into feralolide significantly enhances its binding affinity to Mpro. These results provide useful information for developing potent Mpro inhibitors.
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Affiliation(s)
- Divya Shaji
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Ryo Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Daisuke Orihashi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
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6
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Saito R, Imai K, Takimoto D, Ezawa T, Sugiyama S, Takimoto-Kamimura M, Kurita N. Water molecule-mediated selective inhibition of bacterial zinc metalloproteinases by non-hydroxamate compounds: Ab initio molecular simulations. J Mol Graph Model 2022; 114:108200. [DOI: 10.1016/j.jmgm.2022.108200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
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7
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González-Olvera JC, Zamorano-Carrillo A, Arreola-Jardón G, Pless RC. Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods. J Mol Model 2022; 28:43. [DOI: 10.1007/s00894-022-05033-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/18/2022] [Indexed: 11/24/2022]
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8
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Saito R, Imai K, Yamamoto S, Ezawa T, Sugiyama S, Evenseth LSM, Sylte I, Kurita N. Specific interactions between the alkaline protease of P. aeruginosa and its natural peptide inhibitor: ab initio molecular simulations. J Mol Model 2021; 28:10. [PMID: 34914017 DOI: 10.1007/s00894-021-04991-y] [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: 05/14/2021] [Accepted: 11/21/2021] [Indexed: 11/30/2022]
Abstract
Alkaline protease aeruginolysin (APR) is an important virulence factor in the evasion of the immune system by Pseudomonas aeruginosa (P. aeruginosa). The P. aeruginosa genome also encodes the highly potent and specific APR peptide inhibitor (APRin). However, the structural reason for the significant inhibition has not been revealed. Using ab initio molecular simulations, we here investigated the specific interactions between APR and APRin to elucidate which amino acid residues of APRin and APR contribute strongest to the inhibition. Since APR has a Zn2+ ion at the ligand-binding site and histidine and glutamic acid residues are coordinated with Zn2+, it is essential to precisely describe these coordination bonds to elucidate the specific interactions between APR and APRin. Therefore, we employed the ab initio fragment molecular orbital method to investigate the specific interactions at an electronic level. The results revealed that Ser1 and Ser2 at the N-terminus of APRin significantly contribute to the binding between APRin and APR. In particular, Ser1 binds strongly to Zn2+ as well as to the sidechains of His176(Hid), His180(Hid), and His186(Hid) in APR. This is the main reason for the strong interaction between APR and APRin. The results also elucidated significant contributions of the positively charged Arg83 and Arg90 residues of APRin to the binding with APR. These findings may provide information useful for the design of novel small agents as potent APR inhibitors.
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Affiliation(s)
- Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Kyohei Imai
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Takuya Ezawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Satoshi Sugiyama
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Linn Samira Mari Evenseth
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan.
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9
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Imai K, Saito R, Ezawa T, Sugiyama S, Sylte I, Kurita N. Proposal of selective inhibitor for bacterial zinc metalloprotease: Molecular mechanics and ab initio molecular orbital calculations. J Mol Graph Model 2021; 110:108047. [PMID: 34655919 DOI: 10.1016/j.jmgm.2021.108047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022]
Abstract
The zinc metalloprotease pseudolysin (PLN) secreted from Pseudomonas aeruginosa degrades extracellular proteins to produce bacterial nutrition, and various types of PLN inhibitors have been developed to suppress the bacterial growth. However, as the structure of the ligand-binding pocket of PLN has large similarities to those of human matrix metalloproteinases (MMPs) and other human zinc metalloprotease, there is a risk that PLN inhibitors also inhibit human zinc proteases. In this study, we propose a novel agent that may bind stronger to PLN than to MMPs. The compound is proposed based on the specific molecular interactions between existing agents and PLN/MMP metalloproteases evaluated by the present molecular simulations. First, we confirmed that the binding energies of PLN agents evaluated using the ab initio fragment molecular orbital method were comparable to the IC50 values obtained through previous experiments. In addition, the specific molecular interactions between these agents and MMP-9 were investigated to elucidate the fact that some of the agents bind weaker to MMP than PLN. Based on the results, we proposed a novel agent having a succinimide group introduce by a hydroxamic acid group and investigated its binding properties with PLN and MMP. The results may provide useful information for the development of potent inhibitors for PLN with few potential side effects in human bodies.
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Affiliation(s)
- Kyohei Imai
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Takuya Ezawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Satoshi Sugiyama
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan.
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10
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Shaji D, Yamamoto S, Saito R, Suzuki R, Nakamura S, Kurita N. Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations. Biophys Chem 2021; 275:106608. [PMID: 33962341 PMCID: PMC8084281 DOI: 10.1016/j.bpc.2021.106608] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022]
Abstract
This paper proposes natural drug candidate compounds for the treatment of coronavirus disease 2019 (COVID-19). We investigated the binding properties between the compounds in the Moringa oleifera plant and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 using molecular docking and ab initio fragment molecular orbital calculations. Among the 12 compounds, niaziminin was found to bind the strongest to Mpro. We furthermore proposed novel compounds based on niaziminin and investigated their binding properties to Mpro. The results reveal that the introduction of a hydroxyl group into niaziminin enhances its binding affinity to Mpro. These niaziminin derivatives can be promising candidate drugs for the treatment of COVID-19.
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Affiliation(s)
- Divya Shaji
- Independent Researcher, Kerala 680642, India
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Ryo Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Shunya Nakamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan.
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11
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Nakamura S, Saito R, Yamamoto S, Terauchi Y, Kittaka A, Takimoto-Kamimura M, Kurita N. Proposal of novel inhibitors for vitamin-D receptor: Molecular docking, molecular mechanics and ab initio molecular orbital simulations. Biophys Chem 2021; 270:106540. [PMID: 33418104 DOI: 10.1016/j.bpc.2020.106540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022]
Abstract
The specific binding of active vitamin-D to the vitamin-D receptor (VDR) is closely related to the onset of immunological diseases. To inhibit the binding, various compounds have been developed as potent inhibitors against VDR. Among them, a compound NS-54c, which was developed based on the first VDR antagonist TEI-9647 (25-dehydro-1α-hydroxyvitamin D3-26,23-lactone), was revealed to posse almost 1000-fold improved antagonistic activity over the original TEI-9647. However, the reason for this significant improvement has not been elucidated. In the present study, we investigated the specific interactions between VDR and these inhibitors, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results simulated, we furthermore proposed novel inhibitors and investigated their binding properties to VDR. The results elucidate that the replacement of propyl group at the 24th site of NS-54c by a phenethyl group can enhance the binding affinity of the inhibitor to VDR. This finding provides useful information for developing novel potent inhibitors against VDR.
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Affiliation(s)
- Shunya Nakamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Yuta Terauchi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Bio-Medical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan.
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12
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Yamamoto S, Saito R, Nakamura S, Sogawa H, Karpov P, Shulga S, Blume Y, Kurita N. Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations. Antibiotics (Basel) 2020; 9:E846. [PMID: 33256135 PMCID: PMC7761175 DOI: 10.3390/antibiotics9120846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/21/2022] Open
Abstract
The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of Mycobacteria. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein-ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific interactions between FtsZ and the derivatives, as determined by FMO calculations, we proposed novel ligands, which can strongly bind to FtsZ and inhibit its aggregations. The introduction of a hydroxyl group into ZZ3 was found to enhance its binding affinity to FtsZ.
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Affiliation(s)
- Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Shunya Nakamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Haruki Sogawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Pavel Karpov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Sergey Shulga
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
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13
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Tanaka S, Watanabe C, Honma T, Fukuzawa K, Ohishi K, Maruyama T. Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method. J Mol Graph Model 2020; 100:107650. [PMID: 32707520 PMCID: PMC7346800 DOI: 10.1016/j.jmgm.2020.107650] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/11/2020] [Accepted: 05/17/2020] [Indexed: 12/23/2022]
Abstract
A theoretical scheme to systematically describe correlated (network-like) interactions between molecular fragments is proposed within the framework of the fragment molecular orbital (FMO) method. The method is mathematically based on the singular value decomposition (SVD) of the inter-fragment interaction energy (IFIE) matrix obtained by the FMO calculation, and can be applied to a comprehensive description of protein-protein interactions in the context of molecular recognition. In the present study we apply the proposed method to a complex of measles virus hemagglutinin and human SLAM receptor, thus finding a usefulness for efficiently eliciting the correlated interactions among the amino-acid residues involved in the two proteins. Additionally, collective interaction networks by amino-acid residues important for mutation experiments can be clearly visualized.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Chiduru Watanabe
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; JST PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Teruki Honma
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kaori Fukuzawa
- Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo, 142-8501, Japan
| | - Kazue Ohishi
- Faculty of Engineering, Tokyo Polytechnic University, 1583, Iiyama, Atsugi, Kanagawa, 243-0297, Japan
| | - Tadashi Maruyama
- Kitasato University, 1-15-1, Kitazato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
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14
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Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations. Comput Struct Biotechnol J 2020; 18:1676-1685. [PMID: 32670507 PMCID: PMC7338990 DOI: 10.1016/j.csbj.2020.06.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 11/22/2022] Open
Abstract
To elucidate structural changes in the retinoic acid receptor-related orphan receptor gamma (RORγt) induced by the binding of an agonist or an inverse agonist, we conducted molecular dynamics (MD) simulations in explicit water. In addition, ab initio fragment molecular orbital calculations were carried out for certain characteristic structures obtained from the MD simulations to reveal important interactions between the amino acid residues of RORγt, and to distinguish the different effects in the binding of an agonist and an inverse agonist on the structure of RORγt. The results elucidate that the hydrogen bond between His479 of helix11 (H11) and Tyr502 of helix12 (H12) is important to keep the H12 conformation in the agonist-bound RORγt. In contrast, in the inverse-agonist-bound RORγt, the side chain of His479 rotates, significantly weakening the interaction between His479 and Tyr502, leading to a conformational change in H12. Therefore, the present molecular simulations clearly indicate that the conformational change in the side chain of His479 in the inverse-agonist-bound RORγt is the main reason for the H12 destabilization induced by the binding of the inverse agonist. Such a conformational change does not occur on the binding of the agonist in RORγt, owing to the strong hydrogen bond between His479 and Tyr502.
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15
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Ezawa T, Saito R, Suzuki S, Sugiyama S, Sylte I, Kurita N. Protonation states of central amino acids in a zinc metalloprotease complexed with inhibitor: Molecular mechanics optimizations and ab initio molecular orbital calculations. Biophys Chem 2020; 261:106368. [PMID: 32272264 DOI: 10.1016/j.bpc.2020.106368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 12/16/2022]
Abstract
The zinc-metalloprotease pseudolysin (PLN) secreted from bacteria degrades extracellular proteins to produce bacterial nutrition. Since PLN has a Zn ion at the inhibitor-binding site, the interactions between Zn and PLN residues as well as inhibitor can be significantly changed depending on the protonation states of PLN residues at the inhibitor-binding site. To determine stable protonation states of these residues, we here considered different protonation states for Glu and His residues located around Zn and investigated the electronic states of the PLN + inhibitor complex, using ab initio molecular simulations. The protonation state of His223 was found to significantly affect the specific interactions between PLN and the inhibitor.
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Affiliation(s)
- Takuya Ezawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan
| | - Shusuke Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan
| | - Satoshi Sugiyama
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan.
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16
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Sato R, Vohra S, Yamamoto S, Suzuki K, Pavel K, Shulga S, Blume Y, Kurita N. Specific interactions between tau protein and curcumin derivatives: Molecular docking and ab initio molecular orbital simulations. J Mol Graph Model 2020; 98:107611. [PMID: 32276176 DOI: 10.1016/j.jmgm.2020.107611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder in the world, and there is currently no potent medicine for the treatment of ADs. Curcumin, a primary chemical contained in the ancient Indian herb known as turmeric, has been extensively studied and shown to be effective in inhibiting the aggregations of amyloid-β and tau proteins, both of which are observed in the brains of AD patients. In the present study, we focused on the tau protein and investigated its specific interactions with curcumin derivatives, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results, we attempted to propose novel potent inhibitors against the tau protein aggregation. Our molecular simulations provide useful information for developing novel medicines for the treatment of ADs.
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Affiliation(s)
- Riku Sato
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Shivani Vohra
- Chemical Engineering, Grove School of Engineering, The City College of New York, 160 Convent Avenue New York, NY, 10031, USA
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Katsumi Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Karpov Pavel
- Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a. Osypovskogo Str., Kyiv-123, 04123, Ukraine
| | - Sergiy Shulga
- Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a. Osypovskogo Str., Kyiv-123, 04123, Ukraine
| | - Yaroslav Blume
- Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a. Osypovskogo Str., Kyiv-123, 04123, Ukraine
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan.
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17
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Paciotti R, Agamennone M, Coletti C, Storchi L. Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach. J Comput Aided Mol Des 2020; 34:897-914. [PMID: 32185582 DOI: 10.1007/s10822-020-00306-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
The programmed cell death protein 1 (PD-1) and its ligand, PD-L1, constitute an important co-inhibitory immune checkpoint leading to downregulation of immune system. Tumor cells developed a strategy to trigger PD-1/PD-L1 pathway reducing the T cell anticancer activity. Anti-PD-L1 small drugs, generally with improved pharmacokinetic and technological profiles than monoclonal antibodies, became an attractive research topic. Nevertheless, still few works have been published on the chemical features of possible binding sites. In this work, we applied a novel computational protocol based on the combination of the ab initio Fragment Molecular Orbital (FMO) method and a newly developed GRID-DRY approach in order to characterize the PD-L1 binding sites, starting from PD-1/PD-L1 and PD-L1/BMS-ligands (Bristol-Mayers Squibb ligands) complexes. The FMO method allows the calculation of the pair-residues as well as the ligand-residues interactions with ab initio accuracy, whereas the GRID-DRY approach is an effective tool to investigate hydrophobic interactions, not easily detectable by ab initio methods. The present GRID-DRY protocol is able to determine the energy contributions of each ligand atoms to each hydrophobic interaction, both qualitatively and quantitatively. We were also able to identify the three specific hot regions involved in PD-1/PD-L1 protein-protein interaction and in PD-L1/BMS-ligand interactions, in agreement with preceding theoretical/experimental results, and to suggest a specific pharmacophore for PD-L1 inhibitors.
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Affiliation(s)
- Roberto Paciotti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy.
| | | | - Cecilia Coletti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| | - Loriano Storchi
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy. .,Molecular Discovery Limited, Middlesex, London, UK.
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18
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Sogawa H, Sato R, Suzuki K, Tomioka S, Shinzato T, Karpov P, Shulga S, Blume Y, Kurita N. Binding sites of Zantrin inhibitors to the bacterial cell division protein FtsZ: Molecular docking and ab initio molecular orbital calculations. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Shinzato T, Sato R, Suzuki K, Tomioka S, Sogawa H, Shulga S, Blume Y, Kurita N. Proposal of therapeutic curcumin derivatives for Alzheimer’s disease based on ab initio molecular simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Yoshida H, Sato K, Ishikawa T, Sakamoto T, Yamagishi K. Binding interaction analysis of RNA aptamer-Fc region of human immunoglobulin G using fragment molecular orbital calculation. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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González R, Mroginski MA. Fully Quantum Chemical Treatment of Chromophore–Protein Interactions in Phytochromes. J Phys Chem B 2019; 123:9819-9830. [DOI: 10.1021/acs.jpcb.9b08938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ronald González
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria A. Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
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22
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Ezawa T, Sugiyama S, Ara A, Sylte I, Kurita N. Design of galardine analogs as putative psudolysin inhibitors based on ab initio fragment molecular orbital calculations. J Biomol Struct Dyn 2019; 38:3307-3317. [PMID: 31422741 DOI: 10.1080/07391102.2019.1656672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Pseudolysin (PLN) is a metalloproteinase secreted from bacteria that degrades extracellular proteins to produce bacterial nutrition. It is thus expected that inhibitors against PLN can suppress the growth of bacteria and their pandemic spread. In addition, since these inhibitors do not attack to bacteria directly, there is a reduced risk for producing drug-resistant bacteria. On the other hand, as PLN has large structural similarity in the active sites with human matrix-metalloproteinases (MMPs), there is a possibility that the inhibitors for PLN also inhibit MMP activity, resulting in a loss of necessary nutrients to be produced by MMPs. Therefore, it is required the agents inhibiting the activity of only PLN not MMPs. In the present study, we employed a hydroxamate compound galardin, which has a significant inhibition effect against PLN and MMP, and investigated its specific interactions with PLN/MMP at atomic and electronic levels, by use of ab initio molecular simulations. Based on the results, we proposed several derivatives of galardin and elucidated which derivatives that can bind more strongly to PLN and be putative antimicrobial agents capable of inhibiting the PLN activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Takuya Ezawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | - Satoshi Sugiyama
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | - Ayami Ara
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromso, Norway
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan
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23
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Phusi N, Sato R, Ezawa T, Tomioka S, Hanwarinroj C, Khamsri B, Kamsri P, Punkvang A, Pungpo P, Kurita N. Specific interactions between 2-trans enoyl-acyl carrier protein reductase and its ligand: Protein-ligand docking and ab initio fragment molecular orbital calculations. J Mol Graph Model 2019; 88:299-308. [PMID: 30826710 DOI: 10.1016/j.jmgm.2019.02.011] [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: 12/07/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 11/28/2022]
Abstract
2-trans enoyl-acyl carrier protein reductase (InhA) has been identified as a promising target for the development of novel chemotherapy for tuberculosis. In the present study, a series of heteroaryl benzamide derivatives were selected as potent inhibitors against InhA, and their binding properties with InhA were investigated at atomic and electronic levels by ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics optimizations and ab initio fragment molecular orbital (FMO) calculations. The results evaluated by FMO highlight some key interactions between InhA and the derivatives, indicating that the most potent derivative has strong hydrogen bonds with the Met98 side chain of InhA and strong electrostatic interactions with the nicotinamide adenine dinucleotide cofactor. These findings provide informative structural concepts for designing novel heteroaryl benzamide derivatives with higher binding affinity to InhA.
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Affiliation(s)
- Naruedon Phusi
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Riku Sato
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Takuya Ezawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Shogo Tomioka
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Chayanin Hanwarinroj
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Bandit Khamsri
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Pharit Kamsri
- Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Auradee Punkvang
- Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand.
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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24
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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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25
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Komeiji Y, Okiyama Y, Mochizuki Y, Fukuzawa K. Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yuto Komeiji
- Biomedical Research Institute, National Institute of Industrial Science and Technology, AIST Tsukuba Central 6, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshio Okiyama
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kanagawa 210-9501, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
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26
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Fujimori M, Sogawa H, Ota S, Karpov P, Shulga S, Blume Y, Kurita N. Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.12.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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27
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Deciphering the catalytic amino acid residues of l -2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1: An in silico analysis. Comput Biol Chem 2017; 70:125-132. [DOI: 10.1016/j.compbiolchem.2017.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 11/22/2022]
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28
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Ara A, Kadoya R, Ishimura H, Shimamura K, Sylte I, Kurita N. Specific interactions between zinc metalloproteinase and its inhibitors: Ab initio fragment molecular orbital calculations. J Mol Graph Model 2017; 75:277-286. [PMID: 28618335 DOI: 10.1016/j.jmgm.2017.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/19/2017] [Accepted: 05/20/2017] [Indexed: 01/10/2023]
Abstract
Bacteria secrete the enzyme pseudolysin (PLN) to degrade exocellular proteins, and the produced peptides are used as a nutrient for the bacteria. It is thus expected that inhibition of PLN can suppress bacterial growth. Since such inhibitors do not attack to bacteria directly, the risk of producing drug-resistance bacteria is less. However, endogenous proteinases such as the matrix metalloproteinases (MMPs) have active site similar to that of PLN, and there is a possibility that PLN inhibitors also inhibit the activity of MMPs, resulting in a loss of substrate degradation by these proteinases. Therefore, agents that inhibit the activity of only PLN and not MMPs are required. In the present study, we select two compounds (ARP101 and LM2) and investigate their specific interactions with PLN and MMPs by use of ab initio molecular simulations. Based on the results, we propose several novel compounds as candidates for potent PLN inhibition and investigate their binding properties with PLN, elucidating that the compound, in which a toluene group is introduced into LM2, has larger binding energy with PLN compared with the pristine LM2. Therefore, this compound is suggested to be a potent PLN inhibitor.
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Affiliation(s)
- Ayami Ara
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Ryushi Kadoya
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Hiromi Ishimura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Kanako Shimamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan.
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29
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Yamada H, Mochizuki Y, Fukuzawa K, Okiyama Y, Komeiji Y. Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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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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31
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Storchi L, Paciotti R, Re N, Marrone A. Investigation of the molecular similarity in closely related protein systems: The PrP case study. Proteins 2015; 83:1751-65. [PMID: 26018750 DOI: 10.1002/prot.24836] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/04/2015] [Accepted: 05/19/2015] [Indexed: 12/24/2022]
Abstract
The amyloid conversion is a massive detrimental modification affecting several proteins upon specific physical or chemical stimuli characterizing a plethora of diseases. In many cases, the amyloidogenic stimuli induce specific structural features to the protein conferring the propensity to misfold and form amyloid deposits. The investigation of mutants, structurally similar to their native isoform but inherently prone to amyloid conversion, may be a viable strategy to elucidate the structural features connected with amyloidogenesis. In this article, we present a computational protocol based on the combination of molecular dynamics (MD) and grid-based approaches suited for the pairwise comparison of closely related protein structures. This method was applied on the cellular prion protein (PrP(C)) as a case study and, in particular, addressed to the quali/quantification of the structural features conferred by either E200K mutations and treatment with CaCl(2), both able to induce the scrapie conversion of PrP. Several schemes of comparison were developed and applied to this case study, and made up suitable of application to other protein systems. At this purpose an in-house python codes has been implemented that, together with the parallelization of the GRID force fields program, will spread the applicability of the proposed computational procedure.
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Affiliation(s)
- Loriano Storchi
- Department of Pharmacy, Università "G D'annunzio" Di Chieti-Pescara, 66100, Italy.,Molecular Discovery Limited, Pinner, Middlesex, UK-Ha5 5NE, London, United Kingdom
| | - Roberto Paciotti
- Department of Pharmacy, Università "G D'annunzio" Di Chieti-Pescara, 66100, Italy
| | - Nazzareno Re
- Department of Pharmacy, Università "G D'annunzio" Di Chieti-Pescara, 66100, Italy
| | - Alessandro Marrone
- Department of Pharmacy, Università "G D'annunzio" Di Chieti-Pescara, 66100, Italy
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32
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Ishimura H, Kadoya R, Suzuki T, Murakawa T, Shulga S, Kurita N. Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.05.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Kurauchi R, Watanabe C, Fukuzawa K, Tanaka S. Novel type of virtual ligand screening on the basis of quantum-chemical calculations for protein–ligand complexes and extended clustering techniques. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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34
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Matsushita Y, Murakawa T, Shimamura K, Ohyama T, Oishi M, Kurita N. Change in specific interactions between lactose repressor protein and DNA induced by ligand binding: molecular dynamics and molecular orbital calculations. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1036265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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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Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change. J Mol Graph Model 2014; 53:48-58. [DOI: 10.1016/j.jmgm.2014.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 11/19/2022]
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39
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Gonthier JF, Corminboeuf C. Exploration of zeroth-order wavefunctions and energies as a first step toward intramolecular symmetry-adapted perturbation theory. J Chem Phys 2014. [DOI: 10.1063/1.4871116] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Fukuzawa K, Watanabe C, Kurisaki I, Taguchi N, Mochizuki Y, Nakano T, Tanaka S, Komeiji Y. Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Kobori T, Sodeyama K, Otsuka T, Tateyama Y, Tsuneyuki S. Trimer effects in fragment molecular orbital-linear combination of molecular orbitals calculation of one-electron orbitals for biomolecules. J Chem Phys 2013; 139:094113. [DOI: 10.1063/1.4818599] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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42
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Qin T, Troisi A. Relation between Structure and Electronic Properties of Amorphous MEH-PPV Polymers. J Am Chem Soc 2013; 135:11247-56. [DOI: 10.1021/ja404385y] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ting Qin
- Department of Chemistry and Centre of Scientific Computing, University of Warwick, CV4 7AL Coventry, United Kingdom
| | - Alessandro Troisi
- Department of Chemistry and Centre of Scientific Computing, University of Warwick, CV4 7AL Coventry, United Kingdom
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43
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Ishikawa T, Burri RR, Kamatari YO, Sakuraba S, Matubayasi N, Kitao A, Kuwata K. A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method. Phys Chem Chem Phys 2013; 15:3646-54. [DOI: 10.1039/c3cp42761g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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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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46
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Lin PH, Tsai CW, Wu JW, Ruaan RC, Chen WY. Molecular dynamics simulation of the induced-fit binding process of DNA aptamer and L-argininamide. Biotechnol J 2012; 7:1367-75. [PMID: 22678933 DOI: 10.1002/biot.201200003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 05/21/2012] [Accepted: 06/06/2012] [Indexed: 11/11/2022]
Abstract
Aptamers are rare functional nucleic acids with binding affinity to and specificity for target ligands. Recent experiments have lead to the proposal of an induced-fit binding mechanism for L-argininamide (Arm) and its binding aptamer. However, at the molecular level, this mechanism between the aptamer and its coupled ligand is still poorly understood. The present study used explicit solvent molecular dynamics (MD) simulations to examine the critical bases involved in aptamer-Arm binding and the induced-fit binding process at atomic resolution. The simulation results revealed that the Watson-Crick pair (G10-C16), C9, A12, and C17 bases play important roles in aptamer-Arm binding, and that binding of Arm results in an aptamer conformation optimized through a general induced-fit process. In an aqueous solution, the mechanism has the following characteristic stages: (a) adsorption stage, the Arm anchors to the binding site of aptamer with strong electrostatic interaction; (b) binding stage, the Arm fits into the binding site of aptamer by hydrogen-bond formation; and (c) complex stabilization stage, the hydrogen bonding and electrostatic interactions cooperatively stabilize the complex structure. This study provides dynamics information on the aptamer-ligand induced-fit binding mechanism. The critical bases in aptamer-ligand binding may provide a guideline in aptamer design for molecular recognition engineering.
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Affiliation(s)
- Po-Hsun Lin
- Institute of Systems Biology and Bioinformatics, National Central University, Jhong-Li, Taiwan
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47
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Specific interactions and binding energies between thermolysin and potent inhibitors: Molecular simulations based on ab initio molecular orbital method. J Mol Graph Model 2012; 33:1-11. [DOI: 10.1016/j.jmgm.2011.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/18/2011] [Accepted: 10/18/2011] [Indexed: 11/19/2022]
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48
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Deshmukh MM, Sakaki S. Two-step evaluation of binding energy and potential energy surface of van der Waals complexes. J Comput Chem 2012; 33:617-28. [DOI: 10.1002/jcc.21993] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/17/2011] [Accepted: 10/17/2011] [Indexed: 11/07/2022]
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49
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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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50
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Yoshioka A, Takematsu K, Kurisaki I, Fukuzawa K, Mochizuki Y, Nakano T, Nobusawa E, Nakajima K, Tanaka S. Antigen–antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1048-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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