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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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Panman W, Nutho B, Chamni S, Dokmaisrijan S, Kungwan N, Rungrotmongkol T. Computational screening of fatty acid synthase inhibitors against thioesterase domain. J Biomol Struct Dyn 2018; 36:4114-4125. [PMID: 29161996 DOI: 10.1080/07391102.2017.1408496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 07/11/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022]
Abstract
Thioesterase (TE) domain of fatty acid synthase (FAS) is an attractive therapeutic target for design and development of anticancer drugs. In this present work, we search for the potential FAS inhibitors of TE domain from the ZINC database based on similarity search using three natural compounds as templates, including flavonoids, terpenoids, and phenylpropanoids. Molecular docking was used to predict the interaction energy of each screened ligand compared to the reference compound, which is methyl γ-linolenylfluorophosphonate (MGLFP). Based on this computational technique, rosmarinic acid and its eight analogs were observed as a new series of potential FAS inhibitors, which showed a stronger binding affinity than MGLFP. Afterward, nine docked complexes were studied by molecular dynamics simulations for investigating protein-ligand interactions and binding free energies using MM-PB(GB)SA, MM-3DRISM-KH, and QM/MM-GBSA methods. The binding free energy calculation indicated that the ZINC85948835 (R34) displayed the strongest binding efficiency against the TE domain of FAS. There are eight residues (S2308, I2250, E2251, Y2347, Y2351, F2370, L2427, and E2431) mainly contributed for the R34 binding. Moreover, R34 could directly form hydrogen bonds with S2308, which is one of the catalytic triad of TE domain. Therefore, our finding suggested that R34 could be a potential candidate as a novel FAS-TE inhibitor for further drug design.
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Affiliation(s)
- Wanwisa Panman
- a Multidisciplinary Program of Petrochemistry and Polymer Science, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Bodee Nutho
- b Program in Biotechnology, Faculty of Science , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Supakarn Chamni
- c Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Supaporn Dokmaisrijan
- d Division of Chemistry, School of Science , Walailak University , Nakon Si Thammarat 80161 , Thailand
| | - Nawee Kungwan
- e Faculty of Science, Department of Chemistry , Chiang Mai University , 239 Huay Kaew Road, Muang District, Chiang Mai 50200 , Thailand
- f Research Center on Chemistry for Development of Health Promoting Products from Northern Resources , Chiang Mai University , Chiang Mai , 50200 , Thailand
| | - Thanyada Rungrotmongkol
- g Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry , Chulalongkorn University , Bangkok 10330 , Thailand
- h Faculty of Science, Program in Bioinformatics and Computational Biology , Chulalongkorn University , Bangkok 10330 , Thailand
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Wongpituk P, Nutho B, Panman W, Kungwan N, Wolschann P, Rungrotmongkol T, Nunthaboot N. Structural dynamics and binding free energy of neral-cyclodextrins inclusion complexes: molecular dynamics simulation. Molecular Simulation 2017. [DOI: 10.1080/08927022.2017.1356458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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)
- Peerapong Wongpituk
- Faculty of Science, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Mahasarakham University, Mahasarakham, Thailand
| | - Bodee Nutho
- Faculty of Science, Program in Biotechnology, Chulalongkorn University, Bangkok, Thailand
| | - Wanwisa Panman
- Faculty of Science, Multidisciplinary Program of Petrochemistry and Polymer Science, Chulalongkorn University, Bangkok, Thailand
| | - Nawee Kungwan
- Faculty of Science, Department of Chemistry, Chiang Mai University, Chiang Mai, Thailand
| | - Peter Wolschann
- Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Thanyada Rungrotmongkol
- Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Ph.D. Program in Bioinformatics and Computational Biology, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Molecular Sensory Science Center, Chulalongkorn University, Bangkok, Thailand
| | - Nadtanet Nunthaboot
- Faculty of Science, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Mahasarakham University, Mahasarakham, Thailand
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Panman W, Japrung D, Pongprayoon P. Exploring the interactions of a DNA aptamer with human serum albumins: simulation studies. J Biomol Struct Dyn 2016; 35:2328-2336. [PMID: 27600390 DOI: 10.1080/07391102.2016.1224733] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Wanwisa Panman
- a School of Science , Walailak University , Nakhon Si Thammarat 80161 , Thailand
| | - Deanpen Japrung
- b National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park , Pathumthani 12120 , Thailand
| | - Prapasiri Pongprayoon
- c Faculty of Science, Department of Chemistry , Kasetsart University , Chatuchak, Bangkok 10900 , Thailand.,d Center for Advanced Studies in Nanotechnology and Its Applications in Chemical , Food and Agricultural Industries, Kasetsart University , Bangkok 10900 , Thailand.,e Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST) , Kasetsart University , Bangkok 10900 , Thailand
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