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Chuntakaruk H, Boonpalit K, Kinchagawat J, Nakarin F, Khotavivattana T, Aonbangkhen C, Shigeta Y, Hengphasatporn K, Nutanong S, Rungrotmongkol T, Hannongbua S. Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery. J Comput Chem 2024; 45:953-968. [PMID: 38174739 DOI: 10.1002/jcc.27298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Abstract
In the pursuit of novel antiretroviral therapies for human immunodeficiency virus type-1 (HIV-1) proteases (PRs), recent improvements in drug discovery have embraced machine learning (ML) techniques to guide the design process. This study employs ensemble learning models to identify crucial substructures as significant features for drug development. Using molecular docking techniques, a collection of 160 darunavir (DRV) analogs was designed based on these key substructures and subsequently screened using molecular docking techniques. Chemical structures with high fitness scores were selected, combined, and one-dimensional (1D) screening based on beyond Lipinski's rule of five (bRo5) and ADME (absorption, distribution, metabolism, and excretion) prediction implemented in the Combined Analog generator Tool (CAT) program. A total of 473 screened analogs were subjected to docking analysis through convolutional neural networks scoring function against both the wild-type (WT) and 12 major mutated PRs. DRV analogs with negative changes in binding free energy (ΔΔ G bind ) compared to DRV could be categorized into four attractive groups based on their interactions with the majority of vital PRs. The analysis of interaction profiles revealed that potent designed analogs, targeting both WT and mutant PRs, exhibited interactions with common key amino acid residues. This observation further confirms that the ML model-guided approach effectively identified the substructures that play a crucial role in potent analogs. It is expected to function as a powerful computational tool, offering valuable guidance in the identification of chemical substructures for synthesis and subsequent experimental testing.
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Affiliation(s)
- Hathaichanok Chuntakaruk
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
| | - Kajjana Boonpalit
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Jiramet Kinchagawat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Fahsai Nakarin
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | | | - Sarana Nutanong
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
| | - Supot Hannongbua
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Chemistry, Faculty of Science, Center of Excellence in Computational Chemistry (CECC), Chulalongkorn University, Bangkok, Thailand
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Chuntakaruk H, Hengphasatporn K, Shigeta Y, Aonbangkhen C, Lee VS, Khotavivattana T, Rungrotmongkol T, Hannongbua S. FMO-guided design of darunavir analogs as HIV-1 protease inhibitors. Sci Rep 2024; 14:3639. [PMID: 38351065 PMCID: PMC10864397 DOI: 10.1038/s41598-024-53940-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The prevalence of HIV-1 infection continues to pose a significant global public health issue, highlighting the need for antiretroviral drugs that target viral proteins to reduce viral replication. One such target is HIV-1 protease (PR), responsible for cleaving viral polyproteins, leading to the maturation of viral proteins. While darunavir (DRV) is a potent HIV-1 PR inhibitor, drug resistance can arise due to mutations in HIV-1 PR. To address this issue, we developed a novel approach using the fragment molecular orbital (FMO) method and structure-based drug design to create DRV analogs. Using combinatorial programming, we generated novel analogs freely accessible via an on-the-cloud mode implemented in Google Colab, Combined Analog generator Tool (CAT). The designed analogs underwent cascade screening through molecular docking with HIV-1 PR wild-type and major mutations at the active site. Molecular dynamics (MD) simulations confirmed the assess ligand binding and susceptibility of screened designed analogs. Our findings indicate that the three designed analogs guided by FMO, 19-0-14-3, 19-8-10-0, and 19-8-14-3, are superior to DRV and have the potential to serve as efficient PR inhibitors. These findings demonstrate the effectiveness of our approach and its potential to be used in further studies for developing new antiretroviral drugs.
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Affiliation(s)
- Hathaichanok Chuntakaruk
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Vannajan Sanghiran Lee
- Chemistry Department, Faculty of Science, University Malaya, Kuala Lumpur, 50603, Malaysia
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Ali S, Saokaew P, Aman A, Todsaporn D, Sanachai K, Krusong K, Hannongbua S, Wolschann P, Mahalapbutr P, Rungrotmongkol T. Enhancing solubility and stability of piperine using β-cyclodextrin derivatives: computational and experimental investigations. J Biomol Struct Dyn 2024:1-14. [PMID: 38260962 DOI: 10.1080/07391102.2024.2305696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/20/2023] [Indexed: 01/24/2024]
Abstract
Piperine (PP), a natural alkaloid found in black pepper, possesses significant bioactivities. However, its use in pharmaceutical applications is hindered by low water solubility and susceptibility to UV light degradation. To overcome these challenges, we investigated the potential of β-cyclodextrin (βCD) and its derivatives with dimethyl (DMβCD), hydroxy-propyl (HPβCD) and sulfobutyl-ether (SBEβCD) substitutions to enhance the solubility and stability of PP. This study employed computational and experimental approaches to examine the complexation between PP and βCDs. The results revealed the formation of two types of inclusion complexes: the P-form and M-form involving the insertion of piperidine moiety and the methylene-di-oxy-phenyl moiety, respectively. These complexes primarily rely on van der Waals interactions. Among the three derivatives, the PP/SBEβCD complex exhibited the highest stability followed by HPβCD, as attributed to maximum atom contacts and minimal solvent accessibility. Solubility studies confirmed the formation of inclusion complexes in a 1:1 ratio. Notably, the stability constant of the inclusion complex was approximately two-fold higher with SBEβCD and HPβCD compared to βCD. The DSC thermograms provided confirmation of the formation of the inclusion complex between the host and guest. These findings highlight the potential of βCD derivatives to effectively encapsulate PP, improving its solubility and presenting new opportunities for its pharmaceutical applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saba Ali
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Phattharapawn Saokaew
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Aamir Aman
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Duangjai Todsaporn
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Kuakarun Krusong
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
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Chokbunpiam T, Fritzsche S, Ploymeerusmee T, Chanajaree R, Thompho S, Janke W, Hannongbua S. Separation of the Chlorofluorocarbon (CFC) CCl 2F 2 from N 2 in NaY Zeolite, in MIL-127(Fe) and in the two Carbon Nanotubes CNT (9,9) and CNT (11,11). J Mol Graph Model 2023; 125:108597. [PMID: 37625172 DOI: 10.1016/j.jmgm.2023.108597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Four well-suited porous materials for the selective adsorption of the most prominent CFC, which is CCl2F2, from the air are carbon nanotubes CNT (9,9) and CNT (11,11), NaY zeolite, and the Metal Organic Framework MIL-125(Fe). The adsorption has been investigated through molecular simulations. Simulation results and theoretical considerations show that reasons for the extraordinarily high selectivity in all four cases were found to be the differences in the enthalpy of adsorption for the various adsorbed gases rather than steric reasons. The four adsorbate-adsorbent systems have been examined at different temperatures, pressures, and concentration ratios in the mixture. Among them, the carbon nanotube CNT (11,11) exhibited the highest selectivity, reaching up to 104.
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Affiliation(s)
- Tatiya Chokbunpiam
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, 10240, Bangkok, Thailand.
| | - Siegfried Fritzsche
- University of Leipzig, Faculty of Physics and Geosciences, Institute for Theoretical Physics, IPF 231101, 04081, Leipzig, Germany
| | - Tanawut Ploymeerusmee
- Computational Chemistry Unit Cell (CCUC), Department of Chemistry, Faculty of science, Chulalongkorn University, 10330, Bangkok, Thailand
| | - Rungroj Chanajaree
- Chulalongkorn University, Metallurgy and Materials Science Research Institute (MMRI), 10330, Bangkok, Thailand
| | - Somphob Thompho
- Pharmaceutical Research Instrument Center, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Pathum Wan, 10330, Bangkok, Thailand
| | - Wolfhard Janke
- University of Leipzig, Faculty of Physics and Geosciences, Institute for Theoretical Physics, IPF 231101, 04081, Leipzig, Germany
| | - Supot Hannongbua
- Computational Chemistry Unit Cell (CCUC), Department of Chemistry, Faculty of science, Chulalongkorn University, 10330, Bangkok, Thailand
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Pattaranggoon NC, Daduang S, Rungrotmongkol T, Teajaroen W, Tipmanee V, Hannongbua S. Computational model for lipid binding regions in phospholipase (Ves a 1) from Vespa venom. Sci Rep 2023; 13:10652. [PMID: 37391452 PMCID: PMC10313747 DOI: 10.1038/s41598-023-36742-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 06/08/2023] [Indexed: 07/02/2023] Open
Abstract
The Thai banded tiger wasp (Vespa affinis) is a dangerous vespid species found in Southeast Asia, and its stings often result in fatalities due to the presence of lethal phospholipase A[Formula: see text], known as Vespapase or Ves a 1. Developing anti-venoms for Ves a 1 using chemical drugs, such as chemical drug guide, remains a challenging task. In this study, we screened 2056 drugs against the opening conformation of the venom using the ZINC 15 and e-Drug 3D databases. The binding free energy of the top five drug candidates complexed with Ves a 1 was calculated using 300-ns-MD trajectories. Our results revealed that voxilaprevir had a higher binding free energy at the catalytic sites than other drug candidates. Furthermore, the MD simulation results indicated that voxilaprevir formed stable conformations within the catalytic pocket. Consequently, voxilaprevir could act as a potent inhibitor, opening up avenues for the development of more effective anti-venom therapeutics for Ves a 1.
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Affiliation(s)
- Nawanwat C Pattaranggoon
- Programme in Bioinformatics and Computational Biology, Graduate school, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sakda Daduang
- Division of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Thanyada Rungrotmongkol
- Programme in Bioinformatics and Computational Biology, Graduate school, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Withan Teajaroen
- Faculty of Associated Medical Sciences, Center for Innovation and Standard for Medical Technology and Physical Therapy, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
| | - Supot Hannongbua
- Department of Chemistry, Faculty of Science, Center of Excellence in Computational Chemistry (CECC), Chulalongkorn University, Bangkok, 10330, Thailand.
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Sangkhawasi M, Kerdpol K, Ismail A, Nutho B, Hanpiboon C, Wolschann P, Krusong K, Rungrotmongkol T, Hannongbua S. In Vitro and In Silico Study on the Molecular Encapsulation of α-Tocopherol in a Large-Ring Cyclodextrin. Int J Mol Sci 2023; 24:ijms24054425. [PMID: 36901859 PMCID: PMC10002136 DOI: 10.3390/ijms24054425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
α-tocopherol is the physiologically most active form of vitamin E, with numerous biological activities, such as significant antioxidant activity, anticancer capabilities, and anti-aging properties. However, its low water solubility has limited its potential use in the food, cosmetic, and pharmaceutical industries. One possible strategy for addressing this issue is the use of a supramolecular complex with large-ring cyclodextrins (LR-CDs). In this study, the phase solubility of the CD26/α-tocopherol complex was investigated to assess the possible ratios between host and guest in the solution phase. Next, the host-guest association of the CD26/α-tocopherol complex at different ratios of 1:2, 1:4, 1:6, 2:1, 4:1, and 6:1 was studied by all-atom molecular dynamics (MD) simulations. At 1:2 ratio, two α-tocopherol units interact spontaneously with CD26, forming an inclusion complex, as supported by the experimental data. In the 2:1 ratio, a single α-tocopherol unit was encapsulated by two CD26 molecules. In comparison, increasing the number of α-tocopherol or CD26 molecules above two led to self-aggregation and consequently limited the solubility of α-tocopherol. The computational and experimental results indicate that a 1:2 ratio could be the most suitable stoichiometry to use in the CD26/α-tocopherol complex to improve α-tocopherol solubility and stability in inclusion complex formation.
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Affiliation(s)
- Mattanun Sangkhawasi
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Khanittha Kerdpol
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Abbas Ismail
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Chonnikan Hanpiboon
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Kuakarun Krusong
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (T.R.); (S.H.); Tel.: +66-2218-5426 (T.R.); +66-8163-61957 (S.H.)
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (T.R.); (S.H.); Tel.: +66-2218-5426 (T.R.); +66-8163-61957 (S.H.)
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Chusuth P, Raksat P, Hannongbua S, Wangkanont K, Ounjai P, Rungrotmongkol T. Expression and purification of human alpha-7 nicotinic acetylcholine receptor extracellular domain in Pichia pastoris. ScienceAsia 2023. [DOI: 10.2306/scienceasia1513-1874.2022.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Chokbunpiam T, Ploymeerusmee T, Fritzsche S, Janke W, Hannongbua S. Exceptionally high selectivity in the separation of light hydrocarbons by adsorption on MIL-127(Fe) and on a (9,9) carbon nanotube. J Mol Graph Model 2022; 117:108293. [PMID: 35988438 DOI: 10.1016/j.jmgm.2022.108293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 01/14/2023]
Abstract
Porous solids with channel sizes that are not much above the size of small hydrocarbons can yield extremely large adsorption selectivity. Our Grand Canonical Monte-Carlo simulations indicate exceptionally high selectivity for the separation of methane, ethane and propane from natural gas. At 250 K the C3H8/CH4 separation on MIL-127 at low pressure has a selectivity of more than 1000 and the C3H8/CH4 separation on CNT (9,9) is even above 2000. This is due to the strong molecule lattice interaction in narrow channels which leads to large enthalpies of adsorption. The Arrhenius law for the Henry coefficients is analysed in order to show that the effect is due to this enthalpy rather than to steric reasons.
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Affiliation(s)
- Tatiya Chokbunpiam
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, 10240, Thailand.
| | - Tanawut Ploymeerusmee
- Petrochemistry and Polymer Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Siegfried Fritzsche
- University of Leipzig, Faculty of Physics and Geosciences, Institute for Theoretical Physics, IPF 231101, 04081, Leipzig, Germany
| | - Wolfhard Janke
- University of Leipzig, Faculty of Physics and Geosciences, Institute for Theoretical Physics, IPF 231101, 04081, Leipzig, Germany
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathum Wan, Bangkok, 10330, Thailand
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Sanachai K, Somboon T, Wilasluck P, Deetanya P, Wolschann P, Langer T, Lee VS, Wangkanont K, Rungrotmongkol T, Hannongbua S. Identification of repurposing therapeutics toward SARS-CoV-2 main protease by virtual screening. PLoS One 2022; 17:e0269563. [PMID: 35771802 PMCID: PMC9246117 DOI: 10.1371/journal.pone.0269563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/24/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 causes the current global pandemic coronavirus disease 2019. Widely-available effective drugs could be a critical factor in halting the pandemic. The main protease (3CLpro) plays a vital role in viral replication; therefore, it is of great interest to find inhibitors for this enzyme. We applied the combination of virtual screening based on molecular docking derived from the crystal structure of the peptidomimetic inhibitors (N3, 13b, and 11a), and experimental verification revealed FDA-approved drugs that could inhibit the 3CLpro of SARS-CoV-2. Three drugs were selected using the binding energy criteria and subsequently performed the 3CLpro inhibition by enzyme-based assay. In addition, six common drugs were also chosen to study the 3CLpro inhibition. Among these compounds, lapatinib showed high efficiency of 3CLpro inhibition (IC50 value of 35 ± 1 μM and Ki of 23 ± 1 μM). The binding behavior of lapatinib against 3CLpro was elucidated by molecular dynamics simulations. This drug could well bind with 3CLpro residues in the five subsites S1’, S1, S2, S3, and S4. Moreover, lapatinib’s key chemical pharmacophore features toward SAR-CoV-2 3CLpro shared important HBD and HBA with potent peptidomimetic inhibitors. The rational design of lapatinib was subsequently carried out using the obtained results. Our discovery provides an effective repurposed drug and its newly designed analogs to inhibit SARS-CoV-2 3CLpro.
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Affiliation(s)
- Kamonpan Sanachai
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
| | - Tuanjai Somboon
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Patcharin Wilasluck
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Peerapon Deetanya
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Peter Wolschann
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | | | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (KW); (TR); (SH)
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (KW); (TR); (SH)
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (KW); (TR); (SH)
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Hengphasatporn K, Wilasluck P, Deetanya P, Wangkanont K, Chavasiri W, Visitchanakun P, Leelahavanichkul A, Paunrat W, Boonyasuppayakorn S, Rungrotmongkol T, Hannongbua S, Shigeta Y. Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease. J Chem Inf Model 2022; 62:1498-1509. [PMID: 35245424 DOI: 10.1021/acs.jcim.1c01304] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The coronavirus disease pandemic is a constant reminder that global citizens are in imminent danger of exposure to emerging infectious diseases. Therefore, developing a technique for inhibitor discovery is essential for effective drug design. Herein, we proposed fragment molecular orbital (FMO)-based virtual screening to predict the molecular binding energy of potential severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease inhibitors. The integration of quantum mechanical approaches and trajectory analysis from a microsecond molecular dynamics simulation was used to identify potential inhibitors. We identified brominated baicalein as a potent inhibitor of the SARS-CoV-2 main protease and confirmed its inhibitory activity in an in vitro assay. Brominated baicalein did not demonstrate significant toxicity in either in vitro or in vivo studies. The pair interaction energy from FMO-RIMP2/PCM and inhibitory constants based on the protease enzyme assay suggested that the brominated baicalein could be further developed into novel SARS-CoV-2 protease inhibitors.
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Affiliation(s)
- Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Patcharin Wilasluck
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peerapon Deetanya
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peerapat Visitchanakun
- Translational Research in Inflammation and Immunology Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Asada Leelahavanichkul
- Translational Research in Inflammation and Immunology Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wattamon Paunrat
- Applied Medical Virology Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Siwaporn Boonyasuppayakorn
- Applied Medical Virology Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.,Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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11
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Ploymeerusmee T, Janke W, Remsungnen T, Hannongbua S, Chokbunpiam T. Porous material adsorbents ZIF-8, ZIF-67, Co/Zn-ZIF and MIL-127(Fe) for separation of H2S from an H2S/CH4 mixture. Molecular Simulation 2022. [DOI: 10.1080/08927022.2021.2025232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Tanawut Ploymeerusmee
- Petrochemistry and Polymer Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Wolfhard Janke
- Faculty of Physics and Geosciences, Institute of Theoretical Physics, University of Leipzig, Leipzig, Germany
| | - Tawun Remsungnen
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai, Thailand
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Tatiya Chokbunpiam
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok, Thailand
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12
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Sanachai K, Mahalapbutr P, Sanghiran Lee V, Rungrotmongkol T, Hannongbua S. In Silico Elucidation of Potent Inhibitors and Rational Drug Design against SARS-CoV-2 Papain-like Protease. J Phys Chem B 2021; 125:13644-13656. [PMID: 34904832 PMCID: PMC8691209 DOI: 10.1021/acs.jpcb.1c07060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/01/2021] [Indexed: 01/08/2023]
Abstract
Global public health has been a critical problem by the sudden increase of the COVID-19 outbreak. The papain-like protease (PLpro) of SARS-CoV-2 is a key promising target for antiviral drug development since it plays a pivotal role in viral replication and innate immunity. Here, we employed the all-atom molecular dynamics (MD) simulations and binding free energy calculations based on MM-PB(GB)SA and SIE methods to elucidate and compare the binding behaviors of five inhibitors derived from peptidomimetic inhibitors (VIR250 and VIR251) and naphthalene-based inhibitors (GRL-0617, compound 3, and compound Y96) against SARS-CoV-2 PLpro. The obtained results revealed that all inhibitors interacting within the PLpro active site are mostly driven by vdW interactions, and the hydrogen bond formation in residues G163 and G271 with peptidomimetics and the Q269 residue with naphthalene-based inhibitors was essential for stabilizing the protein-ligand complexes. Among the five studied inhibitors, VIR250 exhibited the most binding efficiency with SARS-CoV-2 PLpro, and thus, it was chosen for the rational drug design. Based on the computationally designed ligand-protein complexes, the replacement of aromatic rings including heteroatoms (e.g., thiazolopyridine) at the P2 and P4 sites could help to improve the inhibitor-binding efficiency. Furthermore, the hydrophobic interactions with residues at P1-P3 sites can be increased by enlarging the nonpolar moieties (e.g., ethene) at the N-terminal of VIR250. We expect that the structural data obtained will contribute to the development of new PLpro inhibitors with more inhibitory potency for COVID-19.
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Affiliation(s)
- Kamonpan Sanachai
- Center
of Excellence in Computational Chemistry (CECC), Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Biocatalyst
and Environmental Biotechnology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panupong Mahalapbutr
- Department
of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Vannajan Sanghiran Lee
- Department
of Chemistry, Faculty of Science, University
of Malaya, Kuala
Lumpur 50603, Malaysia
| | - Thanyada Rungrotmongkol
- Biocatalyst
and Environmental Biotechnology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Center
of Excellence in Computational Chemistry (CECC), Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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13
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Kerdpol K, Nutho B, Krusong K, Poo-arporn RP, Rungrotmongkol T, Hannongbua S. Encapsulation of α-tocopherol in large-ring cyclodextrin containing 26 α-D-glucopyranose units: A molecular dynamics study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Mahalapbutr P, Charoenwongpaiboon T, Phongern C, Kongtaworn N, Hannongbua S, Rungrotmongkol T. Molecular encapsulation of a key odor-active 2-acetyl-1-pyrroline in aromatic rice with β-cyclodextrin derivatives. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Thompho S, Fritzsche S, Chokbunpiam T, Remsungnen T, Janke W, Hannongbua S. Adsorption and the Chemical Reaction N 2O 4 ↔ 2NO 2 in the Presence of N 2 in a Gas Phase Connected with a Carbon Nanotube. ACS Omega 2021; 6:17342-17352. [PMID: 34278120 PMCID: PMC8280629 DOI: 10.1021/acsomega.1c01459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/16/2021] [Indexed: 05/17/2023]
Abstract
The paper shows, by molecular simulations, that a CNT (9,9) carbon nanotube allows very efficient separation of nitrogen oxides (NO x ) from N2, that has in good approximation properties of the complete air mixture. Gibbs ensemble Monte Carlo simulations are used to describe the adsorption. The permanent chemical reaction between N2O4 and NO2, which occurs simultaneously to adsorption, is treated by the reactive Monte Carlo simulation. A very high selectivity has been found. For a low pressure and at T = 298 K, an adsorption/reaction selectivity between NO x and N2 can reach values up to 3 × 103.
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Affiliation(s)
- Somphob Thompho
- Pharmaceutical
Research Instrument Center, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Pathum Wan, Bangkok 10330, Thailand
| | - Siegfried Fritzsche
- Institute
of Theoretical Physics, Leipzig University, 04081 Leipzig, Germany
| | - Tatiya Chokbunpiam
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry
Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
| | - Tawun Remsungnen
- Faculty
of Interdisciplinary Studies, Khon Kaen
University, Nong Khai 43000, Thailand
| | - Wolfhard Janke
- Institute
of Theoretical Physics, Faculty of Physics and Geosciences, Leipzig University, 04081 Leipzig, Germany
| | - Supot Hannongbua
- Computational
Chemistry Unit Cell (CCUC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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16
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Nutho B, Pengthaisong S, Tankrathok A, Lee VS, Ketudat Cairns JR, Rungrotmongkol T, Hannongbua S. Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7. Biomolecules 2020; 10:biom10060907. [PMID: 32549280 PMCID: PMC7356692 DOI: 10.3390/biom10060907] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/07/2023] Open
Abstract
β-Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B2,5 transition state (TS) conformation preferred for mannosides and glucosides via their preferred 4H3/4E TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the -1 subsite in a 4H3/4E conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the B2,5 conformation rapidly relaxed to a E3/4H3 conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the B2,5 conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant β-glycosidases.
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Affiliation(s)
- Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Salila Pengthaisong
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Anupong Tankrathok
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - James R. Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
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17
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Fritzsche S, Chokbunpiam T, Caro J, Hannongbua S, Janke W, Remsungnen T. Combined Adsorption and Reaction in the Ternary Mixture N 2, N 2O 4, NO 2 on MIL-127 Examined by Computer Simulations. ACS Omega 2020; 5:13023-13033. [PMID: 32548487 PMCID: PMC7288586 DOI: 10.1021/acsomega.9b04494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/13/2020] [Indexed: 05/28/2023]
Abstract
A high selectivity of NO x over N2 (simulating air) is found in silico when studying the adsorption of the ternary mixture N2O4/NO2/N2 on the metal-organic framework MIL-127(Fe) by molecular simulations under consideration of the recombination reaction N2O4 ↔ 2NO2. The number of N atoms in nitrogen oxides NO x and that in N2 is used to define a selectivity of the combined adsorption and chemical recombination that can reach values of about 1000.
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Affiliation(s)
- Siegfried Fritzsche
- Institute
of Theoretical Physics, Faculty of Physics and Geosciences, Leipzig University, Postfach 100920, D-04009 Leipzig, Germany
- Integrated
Research Group for Energy and Environment, Faculty of Applied Science
and Engineering, Khon Kaen University, Nong Khai Campus, Nong Khai 43000, Thailand
| | - Tatiya Chokbunpiam
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry
Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
| | - Jürgen Caro
- Institute
of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstr. 3-3A, D-30167 Hannover, Germany
| | - Supot Hannongbua
- Computational
Chemistry Unit Cell (CCUC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wolfhard Janke
- Institute
of Theoretical Physics, Faculty of Physics and Geosciences, Leipzig University, Postfach 100920, D-04009 Leipzig, Germany
| | - Tawun Remsungnen
- Integrated
Research Group for Energy and Environment, Faculty of Applied Science
and Engineering, Khon Kaen University, Nong Khai Campus, Nong Khai 43000, Thailand
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18
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Hotarat W, Nutho B, Wolschann P, Rungrotmongkol T, Hannongbua S. Delivery of Alpha-Mangostin Using Cyclodextrins through a Biological Membrane: Molecular Dynamics Simulation. Molecules 2020; 25:molecules25112532. [PMID: 32485931 PMCID: PMC7321106 DOI: 10.3390/molecules25112532] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
α-Mangostin (MGS) exhibits various pharmacological activities, including antioxidant, anticancer, antibacterial, and anti-inflammatory properties. However, its low water solubility is the major obstacle for its use in pharmaceutical applications. To increase the water solubility of MGS, complex formation with beta-cyclodextrins (βCDs), particularly with the native βCD and/or its derivative 2,6-dimethyl-β-CD (DMβCD) is a promising technique. Although there have been several reports on the adsorption of βCDs on the lipid bilayer, the release of the MGS/βCDs inclusion complex through the biological membrane remains unclear. In this present study, the release the MGS from the two different βCDs (βCD and DMβCD) across the lipid bilayer was investigated. Firstly, the adsorption of the free MGS, free βCDs, and inclusion complex formation was studied by conventional molecular dynamics simulation. The MGS in complex with those two βCDs was able to spontaneously release free MGS into the inner membrane. However, both MGS and DMβCD molecules potentially permeated into the deeper region of the interior membrane, whereas βCD only adsorbed at the outer membrane surface. The interaction between secondary rim of βCD and the 1-palmitoeyl-2-oleoyl-glycero-3-phosphocholine (POPC) phosphate groups showed the highest number of hydrogen bonds (up to 14) corresponding to the favorable location of βCD on the POPC membrane. Additionally, the findings suggested that electrostatic energy was the main driving force for βCD adsorption on the POPC membrane, while van der Waals interactions played a predominant role in DMβCD adsorption. The release profile of MGS from the βCDs pocket across the lipid bilayer exhibited two energy minima along the reaction coordinate associated with the permeation of the MGS molecule into the deeper region of the POPC membrane.
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Affiliation(s)
- Wiparat Hotarat
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (W.H.); (B.N.)
| | - Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (W.H.); (B.N.)
| | - Peter Wolschann
- Department of Pharmaceutical Chemistry, University of Vienna, 1090 Vienna, Austria;
- Institute of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Molecular Sensory Science Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (T.R.); (S.H.); Tel.: +66(0)2218-5418 (T.R.); +66(0)2218-7603 (S.H.)
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (W.H.); (B.N.)
- Correspondence: (T.R.); (S.H.); Tel.: +66(0)2218-5418 (T.R.); +66(0)2218-7603 (S.H.)
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19
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Nutho B, Mahalapbutr P, Hengphasatporn K, Pattaranggoon NC, Simanon N, Shigeta Y, Hannongbua S, Rungrotmongkol T. Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms. Biochemistry 2020; 59:1769-1779. [PMID: 32293875 PMCID: PMC7184878 DOI: 10.1021/acs.biochem.0c00160] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/08/2020] [Indexed: 12/12/2022]
Abstract
Since the emergence of a novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported from Wuhan, China, neither a specific vaccine nor an antiviral drug against SARS-CoV-2 has become available. However, a combination of two HIV-1 protease inhibitors, lopinavir and ritonavir, has been found to be effective against SARS-CoV, and both drugs could bind well to the SARS-CoV 3C-like protease (SARS-CoV 3CLpro). In this work, molecular complexation between each inhibitor and SARS-CoV-2 3CLpro was studied using all-atom molecular dynamics simulations, free energy calculations, and pair interaction energy analyses based on MM/PB(GB)SA and FMO-MP2/PCM/6-31G* methods. Both anti-HIV drugs interacted well with the residues at the active site of SARS-CoV-2 3CLpro. Ritonavir showed a somewhat higher number atomic contacts, a somewhat higher binding efficiency, and a somewhat higher number of key binding residues compared to lopinavir, which correspond with the slightly lower water accessibility at the 3CLpro active site. In addition, only ritonavir could interact with the oxyanion hole residues N142 and G143 via the formation of two hydrogen bonds. The interactions in terms of electrostatics, dispersion, and charge transfer played an important role in the drug binding. The obtained results demonstrated how repurposed anti-HIV drugs could be used to combat COVID-19.
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Affiliation(s)
- Bodee Nutho
- Center of Excellence in Computational Chemistry
(CECC), Department of Chemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Panupong Mahalapbutr
- Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences,
University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki
305-8577, Japan
| | | | - Nattapon Simanon
- Program in Bioinformatics and Computational Biology,
Graduate School, Chulalongkorn University, Bangkok 10330,
Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences,
University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki
305-8577, Japan
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry
(CECC), Department of Chemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology,
Graduate School, Chulalongkorn University, Bangkok 10330,
Thailand
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20
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Kamsri P, Punkvang A, Hannongbua S, Suttisintong K, Kittakoop P, Spencer J, Mulholland AJ, Pungpo P. In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR, CoMSIA and molecular dynamics simulations. SAR QSAR Environ Res 2019; 30:775-800. [PMID: 31607177 DOI: 10.1080/1062936x.2019.1658218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
Mycobacterium tuberculosis DNA gyrase subunit B (GyrB) has been identified as a promising target for rational drug design against fluoroquinolone drug-resistant tuberculosis. In this study, we attempted to identify the key structural feature for highly potent GyrB inhibitors through 2D-QSAR using HQSAR, 3D-QSAR using CoMSIA and molecular dynamics (MD) simulations approaches on a series of thiazole urea core derivatives. The best HQSAR and CoMSIA models based on IC50 and MIC displayed the structural basis required for good activity against both GyrB enzyme and mycobacterial cell. MD simulations and binding free energy analysis using MM-GBSA and waterswap calculations revealed that the urea core of inhibitors has the strongest interaction with Asp79 via hydrogen bond interactions. In addition, cation-pi interaction and hydrophobic interactions of the R2 substituent with Arg82 and Arg141 help to enhance the binding affinity in the GyrB ATPase binding site. Thus, the present study provides crucial structural features and a structural concept for rational design of novel DNA gyrase inhibitors with improved biological activities against both enzyme and mycobacterial cell, and with good pharmacokinetic properties and drug safety profiles.
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Affiliation(s)
- P Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University , Nakhon Phanon , Thailand
| | - A Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University , Nakhon Phanon , Thailand
| | - S Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University , Bangkok , Thailand
| | - K Suttisintong
- National Nanotechnology Center, NSTDA , Pathum Thani , Thailand
| | - P Kittakoop
- Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy , Bangkok , Thailand
- Chulabhorn Research Institute , Bangkok , Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education , Bangkok , Thailand
| | - J Spencer
- School of Cellular and Molecular Medicine, University of Bristol , Bristol , UK
| | - A J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol , UK
| | - P Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University , Ubon Ratchathani , Thailand
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21
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Ploymeerusmee T, Fritzsche S, Hannongbua S, Chokbunpiam T. CO2 induced swing effect at imidazolate of zeolitic imidazolate framework-90 using molecular simulations. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2501-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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22
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Kaburaki T, Nakahara H, Tanaka R, Okinaga K, Kawashima H, Hamasaki Y, Rungrotmongkol T, Hannongbua S, Noguchi H, Aihara M, Takeuchi F. Lymphocyte proliferation induced by high-affinity peptides for HLA-B*51:01 in Behçet's uveitis. PLoS One 2019; 14:e0222384. [PMID: 31513650 PMCID: PMC6742369 DOI: 10.1371/journal.pone.0222384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/28/2019] [Indexed: 01/12/2023] Open
Abstract
Several proteins have been proposed as candidate auto-antigens in the pathogenesis of Behçet’s disease (BD). In this study, we aimed to confirm the cellular responses to candidate peptide autoantigens with high affinity for the HLA-B*51:01 molecule using computerized binding predictions and molecular dynamics simulations. We identified two new candidate peptides (HSP65PD, derived from heat shock protein-65, and B51PD, derived from HLA-B*51:01) with high-affinity to the HLA-B*51:01 binding pocket using the Immune Epitope Database for Major Histocompatibility Complex-I Binding Prediction and molecular dynamics simulations. The peptide-induced proliferation of lymphocytes from patients with BD, sarcoidosis, Vogt–Koyanagi–Harada disease (VKH) with panuveitis, systemic scleroderma (SSc) without uveitis, and healthy controls (HC) was investigated using the bromodeoxyuridine assay. The proliferative response of leukocytes to HSP65PD was significantly higher in BD (SI 1.92 ± 0.65) than that in sarcoidosis (SI 1.38 ± 0.46), VKH (SI 1.40 ± 0.33), SSc (SI 1.32 ± 0.31), and HC (SI 1.27 ± 0.28) (P = 0.0004, P = 0.0007, P < 0.0001, P < 0.0001, respectively, Mann-Whitney’s U-test). The proliferative response of leukocytes to B51PD was also higher in BD than that in sarcoidosis, VKH, SSc without uveitis, and HC, whereas no significant differences were observed among the five groups in response to a control peptide derived from topoisomerase 1. A significantly higher response to HPS65PD and B51PD was observed in the HLA-B*51:01-positive patients with BD than in the HLA-B*51:01-negative patients. In conclusion, two peptides that had high affinity to HLA-B*51:01 in computerized binding prediction showed significantly higher response in HLA-B*51:01-positive patients with BD, indicating the usefulness of computerized simulations for identifying autoreactive peptides to HLAs.
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Affiliation(s)
- Toshikatsu Kaburaki
- Department of Ophthalmology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
- * E-mail:
| | - Hisae Nakahara
- Department of Ophthalmology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Rie Tanaka
- Department of Ophthalmology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kimiko Okinaga
- Department of Ophthalmology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | | | | | | | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Hiroshi Noguchi
- Department of Pharmacognosy, Nihon Pharmaceutical University, Saitama, Japan
- Department of Pharmacology, University of Shizuoka, Shizuoka, Japan
| | - Makoto Aihara
- Department of Ophthalmology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Fujio Takeuchi
- Department of Pharmacology, University of Shizuoka, Shizuoka, Japan
- Department of Health and Nutrition, Tokyo Seiei University, Tokyo, Japan
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Mahalapbutr P, Darai N, Panman W, Opasmahakul A, Kungwan N, Hannongbua S, Rungrotmongkol T. Atomistic mechanisms underlying the activation of the G protein-coupled sweet receptor heterodimer by sugar alcohol recognition. Sci Rep 2019; 9:10205. [PMID: 31308429 PMCID: PMC6629994 DOI: 10.1038/s41598-019-46668-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/03/2019] [Indexed: 12/03/2022] Open
Abstract
The human T1R2-T1R3 sweet taste receptor (STR) plays an important role in recognizing various low-molecular-weight sweet-tasting sugars and proteins, resulting in the release of intracellular heterotrimeric G protein that in turn leads to the sweet taste perception. Xylitol and sorbitol, which are naturally occurring sugar alcohols (polyols) found in many fruits and vegetables, exhibit the potential caries-reducing effect and are widely used for diabetic patients as low-calorie sweeteners. In the present study, computational tools were applied to investigate the structural details of binary complexes formed between these two polyols and the T1R2-T1R3 heterodimeric STR. Principal component analysis revealed that the Venus flytrap domain (VFD) of T1R2 monomer was adapted by the induced-fit mechanism to accommodate the focused polyols, in which α-helical residues 233-268 moved significantly closer to stabilize ligands. This finding likely suggested that these structural transformations might be the important mechanisms underlying polyols-STR recognitions. The calculated free energies also supported the VFD of T1R2 monomer as the preferential binding site for such polyols, rather than T1R3 region, in accord with the lower number of accessible water molecules in the T1R2 pocket. The E302 amino acid residue in T1R2 was found to be the important recognition residue for polyols binding through a strongly formed hydrogen bond. Additionally, the binding affinity of xylitol toward the T1R2 monomer was significantly higher than that of sorbitol, making it a sweeter tasting molecule.
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Affiliation(s)
- Panupong Mahalapbutr
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nitchakan Darai
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanwisa Panman
- Multidisciplinary Program of Petrochemistry and Polymer Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aunchan Opasmahakul
- Computational Chemistry Center of Excellent, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supot Hannongbua
- Computational Chemistry Center of Excellent, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Molecular Sensory Science Center, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Affiliation(s)
- C. Punwong
- Department of Physics, Faculty of Science, Prince of Songkla University, Songkhla 90112 Thailand
| | - S. Hannongbua
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - T. J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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25
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Kongkaew S, Rungrotmongkol T, Punwong C, Noguchi H, Takeuchi F, Kungwan N, Wolschann P, Hannongbua S. Interactions of HLA-DR and Topoisomerase I Epitope Modulated Genetic Risk for Systemic Sclerosis. Sci Rep 2019; 9:745. [PMID: 30679605 PMCID: PMC6345791 DOI: 10.1038/s41598-018-37038-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022] Open
Abstract
The association of systemic sclerosis with anti-Topoisomerase 1 antibody (ATASSc) with specific alleles of human leukocyte antigen (HLA)-DR has been observed among various ethnics. The anti-Topoisomerase 1 antibody is a common autoantibody in SSc with diffuse cutaneous scleroderma, which is one of the clinical subtypes of SSc. On the other hand, an immunodominant peptide of topoisomerase 1 (Top1) self-protein (residues 349-368) was reported to have strong association with ATASSc. In this study, molecular dynamics simulation was performed on the complexes of Top1 peptide with various HLA-DR subtypes divided into ATASSc-associated alleles (HLA-DRB1*08:02, HLA-DRB1*11:01 and HLA-DRB1*11:04), suspected allele (HLA-DRB5*01:02), and non-associated allele (HLA-DRB1*01:01). The unique interaction for each system was compared to the others in terms of dynamical behaviors, binding free energies and solvation effects. Our results showed that three HLA-DR/Top1 complexes of ATASSc association mostly exhibited high protein stability and increased binding efficiency without solvent interruption, in contrast to non-association. The suspected case (HLA-DRB5*01:02) binds Top1 as strongly as the ATASSc association case, which implied a highly possible risk for ATASSc development. This finding might support ATASSc development mechanism leading to a guideline for the treatment and avoidance of pathogens like Top1 self-peptide risk for ATASSc.
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Affiliation(s)
- Sirilak Kongkaew
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand. .,Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Chutintorn Punwong
- Department of Physics, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Hiroshi Noguchi
- School of Pharmacy, Nihon Pharmaceutical University, Saitama, 361-0806, Japan.,School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Fujio Takeuchi
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.,Faculty of Health and Nutrition, Tokyo Seiei University, Tokyo, 124-8530, Japan
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Peter Wolschann
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Department of Pharmaceutical Chemistry, University of Vienna, Vienna, 1090, Austria.,Institute of Theoretical Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Supot Hannongbua
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Chokbunpiam T, Thamyongkit P, Hannongbua S. Theoretical investigation of thiophene-linked porphyrin-perylene photosensitiser for bulk-heterojunction solar cells. Molecular Simulation 2018. [DOI: 10.1080/08927022.2018.1475734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Tatiya Chokbunpiam
- Department of Chemistry and Center of Excellence for Innovation in Chemistry Faculty of Science, Ramkhamhaeng University , Bangkok, Thailand
| | - Patchanita Thamyongkit
- Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok, Thailand
- Research Group on Materials for Clean Energy Production STAR, Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok, Thailand
| | - Supot Hannongbua
- Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok, Thailand
- Department of Chemistry, Computational Chemistry Unit Cell (CCUC), Faculty of Science, Chulalongkorn University , Bangkok, Thailand
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Kongsune P, Hannongbua S. The role of conserved QXG and binding affinity of S23G & S26G receptors on avian H5, swine H1 and human H1 of influenza A virus hemagglutinin. J Mol Graph Model 2018; 82:12-19. [PMID: 29625417 DOI: 10.1016/j.jmgm.2018.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/05/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
Outbreaks of avian, human and swine influenza are a serious concern for public health. In the reproductive cycle of the influenza virus, hemagglutinin (HA) is the primary protein responsible for binding to glycan receptor sites on the host cell surface. MD simulations of avian H5, swine H1 and human H1 complexed with S23G and S26G receptors were performed to study the role of key residues on the receptor conformational behaviors, hydrogen bond formation, binding free energy and residue-wise energy contribution. The obtained results indicated that the relative energies of swH1_S23G and swH1_S26G were found to be close to each other (3.1 kcal/mol) while the relative energies of AvH5 and HuH1 were found to be significantly different (11.1 ± 6.8 and 29.0 ± 8.2 kcal/mol for AvH5 and HuH1, respectively).
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Affiliation(s)
- Panita Kongsune
- Department of Chemistry, Faculty of Science, Thaksin University, Phattalung, 93210, Thailand.
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand
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28
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Meeprasert A, Hannongbua S, Kungwan N, Rungrotmongkol T. Effect of D168V mutation in NS3/4A HCV protease on susceptibilities of faldaprevir and danoprevir. Mol Biosyst 2017; 12:3666-3673. [PMID: 27731877 DOI: 10.1039/c6mb00610h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) is a serious cause of liver inflammation, cirrhosis and the development of hepatocellular carcinoma. Its NS3/4A serine protease functions to cleave a specific peptide bond, which is an important step in HCV replication. Thus the NS3/4A protease has become one of the main drug-targets in the design and development of anti-HCV agents. Unfortunately, high mutation rates in HCV have been reported due to the lack of RNA proofreading activity resulting in drug resistance. Herein, all-atom molecular dynamics simulations were employed to understand and illustrate the effects of the NS3/4A D168V mutation on faldaprevir (FDV) and danoprevir (DNV) binding efficiency. The D168V mutation was shown to interrupt the hydrogen bonding network of Q80R155D168R123 embedded in the extended S2 and partial S4 subsites of the NS3 protein and as a result the R123 side chain was displaced and moved out from the binding pocket. By means of MM/PBSA and MM/GBSA binding free energy calculations, the FDV and DNV binding affinities were shown to be significantly reduced by ∼10-15 kcal mol-1 and ∼4-9 kcal mol-1 relative to the wild-type complexes, respectively, which somewhat agrees with the experimental resistance folds.
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Affiliation(s)
- Arthitaya Meeprasert
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science Chulalongkorn University, 254, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science Chulalongkorn University, 254, Phayathai Road, Pathumwan, Bangkok 10330, Thailand and PhD Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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29
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Kruawan S, Ratanasak M, Chanajaree R, Rungrotmongkol T, Saengsawang O, Parasuk V, Kungwan N, Hannongbua S. Ethylene insertion in the presence of new alkoxysilane electron donors for Ziegler-Natta catalyzed polyethylene. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Khuntawee W, Kunaseth M, Rungnim C, Intagorn S, Wolschann P, Kungwan N, Rungrotmongkol T, Hannongbua S. Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics. J Chem Inf Model 2017; 57:778-786. [DOI: 10.1021/acs.jcim.6b00595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Manaschai Kunaseth
- National
Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chompoonut Rungnim
- National
Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Suradej Intagorn
- Department
of Mathematics, Statistics and Computer Science, Kasetsart University, Kamphaeng Saen
Campus, Nakhon Pathom 73140, Thailand
| | | | - Nawee Kungwan
- Department
of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay
Kaew Road, Muang District, Chiang Mai 50200, Thailand
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Jetsadawisut W, Nutho B, Meeprasert A, Rungrotmongkol T, Kungwan N, Wolschann P, Hannongbua S. Susceptibility of inhibitors against 3C protease of coxsackievirus A16 and enterovirus A71 causing hand, foot and mouth disease: A molecular dynamics study. Biophys Chem 2016; 219:9-16. [PMID: 27668727 DOI: 10.1016/j.bpc.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 10/21/2022]
Abstract
Hand foot and mouth disease (HFMD) epidemic has occurred in many countries. Coxsackievirus A16 (CV-A16) and Enterovirus A71 (EV-A71) are the main causes of HFMD. Up to now, there are no anti-HFMD drugs available. Rupintrivir, a broad-spectrum inhibitor, is a drug candidate for HFMD treatment, while other HFMD inhibitors designed from several studies have a relatively low efficiency. Therefore, in this work we aim to study the binding mechanisms of rupintrivir and a peptidic α,β-unsaturated ethyl ester (SG85) against both CV-A16 and EV-A71 3C proteases (3Cpro) using all-atoms molecular dynamics simulation. The obtained results indicate that SG85 shows a stronger binding affinity than rupintrivir against CV-A16. Both inhibitors exhibit a comparable affinity against EV-A71 3Cpro. The molecular information of the binding of the two inhibitors to the proteases will be elucidated. Thus, it is implied that these two compounds may be used as leads for further anti-HFMD drug design and development.
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Affiliation(s)
- W Jetsadawisut
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - B Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - A Meeprasert
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - T Rungrotmongkol
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand; Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| | - N Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai 50200, Thailand
| | - P Wolschann
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand; Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - S Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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Phanich J, Rungrotmongkol T, Kungwan N, Hannongbua S. Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study. J Comput Aided Mol Des 2016; 30:917-926. [PMID: 27714494 DOI: 10.1007/s10822-016-9981-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/27/2016] [Indexed: 12/12/2022]
Abstract
The H7N9 avian influenza virus is a novel re-assortment from at least four different strains of virus. Neuraminidase, which is a glycoprotein on the surface membrane, has been the target for drug treatment. However, some H7N9 strains that have been isolated from patient after drug treatment have a R292K mutation in neuraminidase. This substitution was found to facilitate drug resistance using protein- and virus- assays, in particular it gave a high resistance to the most commonly used drug, oseltamivir. The aim of this research is to understand the source of oseltamivir resistance using MD simulations and the MM/PB(GB)SA binding free energy approaches. Both methods can predict the reduced susceptibility of oseltamivir in good agreement to the IC 50 binding energy, although MM/GBSA underestimates this prediction compared to the MM/PBSA calculation. Electrostatic interaction is the main contribution for oseltamivir binding in terms of both interaction and solvation. We found that the source of the drug resistance is a decrease in the binding interaction combined with the reduction of the dehydration penalty. The smaller K292 mutated residue has a larger binding pocket cavity compared to the wild-type resulting in the loss of drug carboxylate-K292 hydrogen bonding and an increased accessibility for water molecules around the K292 mutated residue. In addition, oseltamivir does not bind well to the R292K mutant complex as shown by the high degree of fluctuation in ligand RMSD during the simulation and the change in angular distribution of bulky side chain groups.
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Affiliation(s)
- Jiraphorn Phanich
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Khuntawee W, Rungrotmongkol T, Wolschann P, Pongsawasdi P, Kungwan N, Okumura H, Hannongbua S. Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations. Carbohydr Polym 2016; 141:99-105. [DOI: 10.1016/j.carbpol.2015.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 09/04/2015] [Accepted: 10/08/2015] [Indexed: 11/27/2022]
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Rungnim C, Chanajaree R, Rungrotmongkol T, Hannongbua S, Kungwan N, Wolschann P, Karpfen A, Parasuk V. How strong is the edge effect in the adsorption of anticancer drugs on a graphene cluster? J Mol Model 2016; 22:85. [DOI: 10.1007/s00894-016-2937-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/22/2016] [Indexed: 10/22/2022]
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35
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Rungnim C, Rungrotmongkol T, Kungwan N, Hannongbua S. Protein-protein interactions between SWCNT/chitosan/EGF and EGF receptor: a model of drug delivery system. J Biomol Struct Dyn 2016; 34:1919-29. [PMID: 26381241 DOI: 10.1080/07391102.2015.1095114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Epidermal growth factor (EGF) was used as the targeting ligand to enhance the specificity of a cancer drug delivery system (DDS) via its specific interaction with the EGF receptor (EGFR) that is overexpressed on the surface of some cancer cells. To investigate the intermolecular interaction and binding affinity between the EGF-conjugated DDS and the EGFR, 50 ns molecular dynamics simulations were performed on the complex of tethered EGFR and EGF linked to single-wall carbon nanotube (SWCNT) through a biopolymer chitosan wrapping the tube outer surface (EGFR·EGF-CS-SWCNT-Drug complex), and compared to the EGFR·EGF complex and free EGFR. The binding pattern of the EGF-CS-SWCNT-Drug complex to the EGFR was broadly comparable to that for EGF, but the binding affinity of the EGF-CS-SWCNT-Drug complex was predicted to be somewhat better than that for EGF alone. Additionally, the chitosan chain could prevent undesired interactions of SWCNT at the binding pocket region. Therefore, EGF connected to SWCNT via a chitosan linker is a seemingly good formulation for developing a smart DDS served as part of an alternative cancer therapy.
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Affiliation(s)
- Chompoonut Rungnim
- a NANOTEC, National Science and Technology Development Agency (NSTDA) , Pathum Thani , 12120 , Thailand
| | - Thanyada Rungrotmongkol
- b Department of Biochemistry, Faculty of Science , Chulalongkorn University , Bangkok , Thailand.,c PhD Program in Bioinformatics and Computational Biology, Faculty of Science , Chulalongkorn University , Bangkok , Thailand
| | - Nawee Kungwan
- d Department of Chemistry, Faculty of Science , Chiang Mai University , Chiang Mai 50200 , Thailand
| | - Supot Hannongbua
- e Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
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Khuntawee W, Wolschann P, Rungrotmongkol T, Wong-ekkabut J, Hannongbua S. Molecular Dynamics Simulations of the Interaction of Beta Cyclodextrin with a Lipid Bilayer. J Chem Inf Model 2015; 55:1894-902. [DOI: 10.1021/acs.jcim.5b00152] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Peter Wolschann
- Department
of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, 14 Althan Straße 14, Vienna 1090, Austria
- Institute
of Theoretical Chemistry, University of Vienna, Währinger
Straße 17, Vienna 1090, Austria
| | | | - Jirasak Wong-ekkabut
- Department
of Physics, Faculty of Science, Kasetsart University, 50 Phahon
Yothin Road, Chatuchak, Bangkok 10900, Thailand
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Phanich J, Rungrotmongkol T, Sindhikara D, Phongphanphanee S, Yoshida N, Hirata F, Kungwan N, Hannongbua S. A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase. Protein Sci 2015; 25:147-58. [PMID: 26044768 DOI: 10.1002/pro.2718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 11/09/2022]
Abstract
The binding affinity of oseltamivir to the influenza B neuraminidase and to its variants with three single substitutions, E119G, R152K, and D198N, is investigated by the MM/3D-RISM method. The binding affinity or the binding free energy of ligand to receptor was found to be determined by a subtle balance of two major contributions that largely cancel out each other: the ligand-receptor interactions and the dehydration free energy. The theoretical results of the binding affinity of the drug to the mutants reproduced the observed trend in the resistivity, measured by IC50 ; the high-level resistance of E119G and R152K, and the low-level resistance of D198N. For E119G and R152K, reduction of the direct drug-target interaction, especially at the mutated residue, is the main source of high-level oseltamivir resistance. This phenomenon, however, is not found in the D198N strain, which is located in the framework of the active-site.
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Affiliation(s)
- Jiraphorn Phanich
- Department of Chemistry, Computational Chemistry Unit Cell, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Daniel Sindhikara
- Schrödinger, Inc, 120 West 45th Street, 17th Floor, New York, New York, 10036
| | - Saree Phongphanphanee
- Department of Materials Science, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Sciences, Kyushu University, Fukuoka, 812-8581, Japan
| | - Fumio Hirata
- College of Life Sciences, Ritsumeikan University, and Molecular Design Frontier Co. Ltd, Kusatsu, 525-8577, Japan
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supot Hannongbua
- Department of Chemistry, Computational Chemistry Unit Cell, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
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Yotmanee P, Rungrotmongkol T, Wichapong K, Choi SB, Wahab HA, Kungwan N, Hannongbua S. Binding specificity of polypeptide substrates in NS2B/NS3pro serine protease of dengue virus type 2: A molecular dynamics Study. J Mol Graph Model 2015; 60:24-33. [PMID: 26086900 DOI: 10.1016/j.jmgm.2015.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 02/05/2023]
Abstract
The pathogenic dengue virus (DV) is a growing global threat, particularly in South East Asia, for which there is no specific treatment available. The virus possesses a two-component (NS2B/NS3) serine protease that cleaves the viral precursor proteins. Here, we performed molecular dynamics simulations of the NS2B/NS3 protease complexes with six peptide substrates (capsid, intNS3, 2A/2B, 4B/5, 3/4A and 2B/3 containing the proteolytic site between P(1) and P(1)' subsites) of DV type 2 to compare the specificity of the protein-substrate binding recognition. Although all substrates were in the active conformation for cleavage reaction by NS2B/NS3 protease, their binding strength was somewhat different. The simulated results of intermolecular hydrogen bonds and decomposition energies suggested that among the ten substrate residues (P(5)-P(5)') the P(1) and P(2) subsites play a major role in the binding with the focused protease. The arginine residue at these two subsites was found to be specific preferential binding at the active site with a stabilization energy of <-10 kcal mol(-1). Besides, the P(3), P(1)', P(2)' and P(4)' subsites showed a less contribution in binding interaction (<-2 kcal mol(-1)). The catalytic water was detected nearby the carbonyl oxygen of the P(1) reacting center of the capsid, intNS3, 2A/2B and 4B/5 peptides. These results led to the order of absolute binding free energy (ΔGbind) between these substrates and the NS2B/NS3 protease ranked as capsid>intNS3>2A/2B>4B/5>3/4A>2B/3 in a relative correspondence with previous experimentally derived values.
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Affiliation(s)
- Pathumwadee Yotmanee
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand; Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanin Wichapong
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sy Bing Choi
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Pulau Pinang, Malaysia; Natural Product and Drug Discovery Centre, Malaysian Institutes of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Ministry of Science, Technology and Innovation, Block 5-A, Halaman Bukit Gambir, 11700, Penang, Malaysia
| | - Habibah A Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Pulau Pinang, Malaysia; Natural Product and Drug Discovery Centre, Malaysian Institutes of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Ministry of Science, Technology and Innovation, Block 5-A, Halaman Bukit Gambir, 11700, Penang, Malaysia.
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supot Hannongbua
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Kaiyawet N, Lonsdale R, Rungrotmongkol T, Mulholland AJ, Hannongbua S. High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase. J Chem Theory Comput 2015; 11:713-22. [PMID: 26579604 DOI: 10.1021/ct5005033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymidylate synthase (TS) is a promising cancer target, due to its crucial function in thymine synthesis. It performs the reductive methylation of 2'-deoxyuridine-5'-phosphate (dUMP) to thymidine-5'-phosphate (dTMP), using N-5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) as a cofactor. After the formation of the dUMP/mTHF/TS noncovalent complex, and subsequent conformational activation, this complex has been proposed to react via nucleophilic attack (Michael addition) by Cys146, followed by methylene-bridge formation to generate the ternary covalent intermediate. Herein, QM/MM (B3LYP-D/6-31+G(d)-CHARMM27) methods are used to model the formation of the ternary covalent intermediate. A two-dimensional potential energy surface reveals that the methylene-bridged intermediate is formed via a concerted mechanism, as indicated by a single transition state on the minimum energy pathway and the absence of a stable enolate intermediate. A range of different QM methods (B3LYP, MP2 and SCS-MP2, and different basis sets) are tested for the calculation of the activation energy barrier for the formation of the methylene-bridged intermediate. We test convergence of the QM/MM results with respect to size of the QM region. Inclusion of Arg166, which interacts with the nucleophilic thiolate, in the QM region is important for reliable results; the MM model apparently does not reproduce energies for distortion of the guanidinium side chain correctly. The spin component scaled-Møller-Plessett perturbation theory (SCS-MP2) approach was shown to be in best agreement (within 1.1 kcal/mol) while the results obtained with MP2 and B3LYP also yielded acceptable values (deviating by less than 3 kcal/mol) compared with the barrier derived from experiment. Our results indicate that using a dispersion-corrected DFT method, or a QM method with an accurate treatment of electron correlation, increases the agreement between the calculated and experimental activation energy barriers, compared with the semiempirical AM1 method. These calculations provide important insight into the reaction mechanism of TS and may be useful in the design of new TS inhibitors.
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Affiliation(s)
| | - Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TS, United Kingdom
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TS, United Kingdom
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Ratanasak M, Rungrotmongkol T, Saengsawang O, Hannongbua S, Parasuk V. Towards the design of new electron donors for Ziegler–Natta catalyzed propylene polymerization using QSPR modeling. POLYMER 2015. [DOI: 10.1016/j.polymer.2014.11.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Hannongbua S, Kokpol S, Gurskii Z, Heinzinger K. Cluster Formation in a Concentrated Lithium-Liquid Ammonia Solution. A Monte Carlo Study. ACTA ACUST UNITED AC 2014. [DOI: 10.1515/zna-1997-1111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Results of a Monte Carlo study of a lithium-liquid ammonia solution at 240 K are reported. The basic cube contained 135 Li+ and 1025 NH3 . With an experimental density of 0.554 g/cm3 a side-length of 37.89 Å resulted. The pseudopotential theory is employed, which permits the exclusion of the electrons from an explicit consideration. The structure of the solution is described by various site-site radial distribution functions. The six ammonia molecules in the first solvation shell of the lithium ion are arranged octahedrally. Clusters are formed which consist almost exclusively of two solvated Li+ which have simultaneously either one ammonia molecule or an octahedral edge or an octahedral plane in common. About one third of the ammonia molecules belong to the bulk phase.
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Affiliation(s)
- S. Hannongbua
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - S. Kokpol
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Z. Gurskii
- Institute for Condensed Matter Physics, Ukrainian Academy of Sciences, Lviv 290005, Ukraine
| | - K. Heinzinger
- Max-Planck-Institut für Chemie (Otto-Hahn-Institut), P.O.B. 3060, D-55020 Mainz
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Abstract
Abstract
Molecular dynamics simulations have been performed with and without three-body corrections at an average temperature of 240 K using a flexible ammonia model. The system consists of one calcium ion and 215 ammonia molecules. The calcium(II)-ammonia interactions were newly developed, based on ab initio calculations with a basis set of double zeta quality. The role of three-body interactions on the structural and dynamical properties of the solution has been investigated. The presence of three-body corrections leads to the reduction of the first shell coordination number of Ca(II) in liquid ammonia from 9 to 8, the increase of the size of the solvation shell by 0.33 A and the disappearance of the sec-ond solvation shell.
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Affiliation(s)
- Wiwat Sidhisoradej
- Department of Physics, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - David Ruffolo
- Department of Physics , Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Thuesombat P, Hannongbua S, Akasit S, Chadchawan S. Effect of silver nanoparticles on rice (Oryza sativa L. cv. KDML 105) seed germination and seedling growth. Ecotoxicol Environ Saf 2014; 104:302-9. [PMID: 24726943 DOI: 10.1016/j.ecoenv.2014.03.022] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 03/14/2014] [Accepted: 03/19/2014] [Indexed: 05/14/2023]
Abstract
With the advances in nanotechnology, silver nanoparticles (AgNPs) have been applied in many industries, increasing their potential exposure level in the environment, yet their environmental safety remains poorly evaluated. The possible effects of different sized AgNPs (20, 30-60, 70-120 and 150nm diameter) on jasmine rice, Oryza sativa L. cv. KDML 105, were investigated at different concentrations (0.1, 1, 10, 100 and 1000mg/L) upon seed germination and seedling growth. The results revealed that the level of seed germination and subsequent growth of those seedlings that germinated were both decreased with increasing sizes and concentrations of AgNPs. Based on the analysis of AgNPs accumulation in plant tissues, it implied that the higher uptake was found when the seeds were treated with the smaller AgNPs, 20nm diameter AgNPs, but it was trapped in the roots rather than transported to the leaves. These resulted in the less negative effects on seedling growth, when compared to the seed soaking with the larger AgNPs with 150nm diameter. The negative effects of AgNPs were supported by leaf cell deformation when rice seeds were treated with 150-nm-diameter AgNP at the concentration of 10 or 100mg/L during seed germination. These results further strengthen our understanding of environmental safety information with respect to nanomaterials.
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Affiliation(s)
- Pakvirun Thuesombat
- Nanoscience and Technology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supot Hannongbua
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sanong Akasit
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Meeprasert A, Rungrotmongkol T, Li M, Hannongbua S. In Silico Screening for Potent Inhibitors against the NS3/4A Protease of Hepatitis C Virus. Curr Pharm Des 2014; 20:3465-77. [DOI: 10.2174/13816128113199990632] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 08/27/2013] [Indexed: 11/22/2022]
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Kamsri P, Koohatammakun N, Srisupan A, Meewong P, Punkvang A, Saparpakorn P, Hannongbua S, Wolschann P, Prueksaaroon S, Leartsakulpanich U, Pungpo P. Rational design of InhA inhibitors in the class of diphenyl ether derivatives as potential anti-tubercular agents using molecular dynamics simulations. SAR QSAR Environ Res 2014; 25:473-488. [PMID: 24785640 DOI: 10.1080/1062936x.2014.898690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A series of diphenyl ether derivatives were developed and showed promising potency for inhibiting InhA, an essential enoyl acyl carrier protein reductase involved in mycolic acid biosynthesis, leading to the lysis of Mycobacterium tuberculosis. To understand the structural basis of diphenyl ether derivatives for designing more potent inhibitors, molecular dynamics (MD) simulations were performed. Based on the obtained results, the dynamic behaviour in terms of flexibility, binding free energy, binding energy decomposition, conformation, and the inhibitor-enzyme interaction of diphenyl ether inhibitors were elucidated. Phe149, Tyr158, Met161, Met199, Val203 and NAD+ are the key residues for binding of diphenyl ether inhibitors in the InhA binding pocket. Our results could provide the structural concept to design new diphenyl ether inhibitors with better enzyme inhibitory activity against M. tuberculosis InhA. The present work facilitates the design of new and potentially more effective anti-tuberculosis agents.
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Affiliation(s)
- P Kamsri
- a Department of Chemistry, Faculty of Science , Ubon Ratchathani University , Ubonratchathani , Thailand
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Meeprasert A, Hannongbua S, Rungrotmongkol T. Key binding and susceptibility of NS3/4A serine protease inhibitors against hepatitis C virus. J Chem Inf Model 2014; 54:1208-17. [PMID: 24689657 DOI: 10.1021/ci400605a] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Hepatitis C virus (HCV) causes an infectious disease that manifests itself as liver inflammation, cirrhosis, and can lead to the development of liver cancer. Its NS3/4A serine protease is a potent target for drug design and development since it is responsible for cleavage of the scissile peptide bonds in the polyprotein important for the HCV life cycle. Herein, the ligand-target interactions and the binding free energy of the four current NS3/4A inhibitors (boceprevir, telaprevir, danoprevir, and BI201335) were investigated by all-atom molecular dynamics simulations with three different initial atomic velocities. The per-residue free energy decomposition suggests that the key residues involved in inhibitor binding were residues 41-43, 57, 81, 136-139, 155-159, and 168 in the NS3 domain. The van der Waals interactions yielded the main driving force for inhibitor binding at the protease active site for the cleavage reaction. In addition, the highest number of hydrogen bonds was formed at the reactive P1 site of the four studied inhibitors. Although the hydrogen bond patterns of these inhibitors were different, their P3 site was most likely to be recognized by the A157 backbone. Both molecular mechanic (MM)/Poisson-Boltzmann surface area and MM/generalized Born surface area approaches predicted the relative binding affinities of the four inhibitors in a somewhat similar trend to their experimentally derived biological activities.
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Affiliation(s)
- Arthitaya Meeprasert
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University , 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
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Kaiyawet N, Rungrotmongkol T, Hannongbua S. Effect of halogen substitutions on dUMP to stability of thymidylate synthase/dUMP/mTHF ternary complex using molecular dynamics simulation. J Chem Inf Model 2013; 53:1315-23. [PMID: 23705822 DOI: 10.1021/ci400131y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stability of the thymidylate synthase (TS)/2-deoxyuridine-5-monophosphate (dUMP)/5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) ternary complex formation and Michael addition are considered as important steps that are involved in the inhibition mechanism of the anticancer prodrug 5-fluorouracil (5-FU). Here, the effect of three different halogen substitutions on the C-5 position of the dUMP (XdUMPs = FdUMP, CldUMP, and BrdUMP), the normal substrate, on the stability of the TS/dUMP and TS/dUMP/mTHF binary and ternary complexes, respectively, was investigated via molecular dynamics simulation. The simulated results revealed that the stability of all the systems was substantially increased by mTHF binding to the catalytic pocket. In the ternary complex, a much greater stabilization of the dUMP and XdUMPs through electrostatic interactions, including charge-charge and hydrogen bond interactions, was found compared to mTHF. An additional unique hydrogen bond between the substituted fluorine of FdUMP and the hydroxyl group of the TS Y94 residue was observed in both the binary and ternary complexes. The distance between the S(-) atom of the TS C146 residue and the C6 atom of dUMP, at <4 Å in all systems, suggested that a Michael addition with the formation of a S-C6 covalent bond potentially occurred, although the hydrogen atom on C6 of dUMP is substituted by a halogen atom. The MM/PBSA binding free energy revealed the significant role of the bridging waters around the ligands in the increased binding affinity (∼10 kcal/mol) of dUMP/XdUMP, either alone or together with mTHF, toward TS. The order of the averaged binding affinity in the ternary systems was found to be CldUMP ≈ FdUMP > dUMP > BrdUMP, suggesting that CldUMP could be a potent candidate TS inhibitor, the same as FdUMP (the metabolite form of 5-FU).
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Affiliation(s)
- Nopporn Kaiyawet
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand
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Nunthaboot N, Rungrotmongkol T, Aruksakunwong O, Hannongbua S. Effects of the Protonation State of the Catalytic Residues and Ligands Upon Binding and Recognition in Targeted Proteins of HIV-1 and Influenza Viruses. Curr Pharm Des 2013; 19:4276-90. [DOI: 10.2174/1381612811319230010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 11/19/2012] [Indexed: 11/22/2022]
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Saengsawang O, Vchirawongkwin V, Remsungnen T, Wiebcke M, Fritzsche S, Hannongbua S. Rotational flexibility of bridging ligands in paddle–wheel layer–pillar metal–organic frameworks studied by quantum calculations. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Rungnim C, Arsawang U, Rungrotmongkol T, Hannongbua S. Molecular dynamics properties of varying amounts of the anticancer drug gemcitabine inside an open-ended single-walled carbon nanotube. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.08.050] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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