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Zhou R, Zhu J, Niu Y, Zhang J, Xiao Z, Zhao L. Identification of characteristic compounds of sweet orange oil and their sweetening effects on the sucrose solution with sweetness meter, sensory analysis, electronic tongue, and molecular dynamics simulation. Food Chem 2024; 461:140815. [PMID: 39146686 DOI: 10.1016/j.foodchem.2024.140815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/21/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024]
Abstract
The characteristic aroma compounds of five-fold sweet orange oil were analyzed using gas chromatography-mass spectrometry combined with the odor aroma value (OAV) method. The results indicated that limonene, linalool, dodecanol, (E,E)-2,4-decadienal, (E)-citral, linalool, (E)-2-decenal, and geraniol are important contributors. The sweetening effects of key compounds on sucrose solutions were experimentally investigated. The results showed that the sweetness effects of five compounds (limonene, citronellal, geraniol, β-sinensal and β-caryophyllene) were better than those of (E)-citral, linalool and octanal. Molecular dynamics implied that the hydrogen bonding residues of the T1R2/T1R3-sucrose system were converted from LYS65, GLU302, ASP278, and SER144 to ASP278, SER144, ASP142, and ASP213 after the addition of limonene. Meanwhile, the hydrophobic interaction forces of the system are significantly enhanced. The total energy of the T1R2/T1R3-sucrose system decreased from -32.08 kcal/mol to -63.57 kcal/mol. The synergistic sweetening mechanism of characteristic aroma compounds of sweet orange oil on sucrose was revealed.
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Affiliation(s)
- Rujun Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China; School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jiancai Zhu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Yunwei Niu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jing Zhang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Zuobing Xiao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Liming Zhao
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
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2
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Zhang HX, Zhou HW, Liu SQ, Zheng ZF, Du ZZ. New Sweet-Tasting Gypenosides from "Jiaogulan" ( Gynostemma pentaphyllum) and Their Interactions with the Homology Model of Sweet Taste Receptors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18619-18629. [PMID: 39105697 DOI: 10.1021/acs.jafc.4c03566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Gynostemma pentaphyllum has been used as an herbal tea, vegetable, and dietary supplement for hundreds of years in East Asia. The sweet variety, grown in large areas in Fujian Province, China, is an essential source of "Jiaogulan" herbal tea. However, its sweet components are unknown. To investigate the sweet constituents of Fujian "Jiaogulan" and discover new natural high-potency sweeteners, phytochemical and sensory evaluations were combined to obtain 15 saponins, of which 11 (1-11) were sweet-tasting, including 2 new ones with sweetness intensities 20-200 times higher than that of sucrose, and four (12-15) were bitter-tasting. Their structures were elucidated using spectroscopic methods (NMR, MS, IR, UV), hydrolysis, and comparison with literature data. The contents of the 15 saponins were quantitatively analyzed using UPLC-MS/MS in multiple reaction monitoring mode. The contents of 1 and 2 sweet-tasting gypenosides were 9.913 ± 1.735 and 35.852 ± 1.739 mg/kg, respectively. The content of the sweetest compound (6) was 124.969 ± 0.961 mg/kg. Additionally, compound 4 was the most abundant sweet component (422.530 ± 3.702 mg/kg). Furthermore, molecular docking results suggested interactions of sweet saponins with sweet taste receptors. In general, this study revealed the material basis of the Fujian "Jiaogulan" taste.
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Affiliation(s)
- Hong-Xia Zhang
- National-Local Joint Engineering Research Center for Highly-Efficient Utilization Technology of Forest Biomass Resources; Key Laboratory for Highly-Efficient Utilization of Forest Biomass Resources in the Southwest China, National Forestry and Grassland Administration; College of Materials and Chemical Engineering, Southwest Forestry University, Kunming 650224, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hui-Wei Zhou
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Qing Liu
- National-Local Joint Engineering Research Center for Highly-Efficient Utilization Technology of Forest Biomass Resources; Key Laboratory for Highly-Efficient Utilization of Forest Biomass Resources in the Southwest China, National Forestry and Grassland Administration; College of Materials and Chemical Engineering, Southwest Forestry University, Kunming 650224, China
| | - Zhi-Feng Zheng
- National-Local Joint Engineering Research Center for Highly-Efficient Utilization Technology of Forest Biomass Resources; Key Laboratory for Highly-Efficient Utilization of Forest Biomass Resources in the Southwest China, National Forestry and Grassland Administration; College of Materials and Chemical Engineering, Southwest Forestry University, Kunming 650224, China
- Fujian Provincial Industry Technologies Development Based for New Energy; College of Energy, Xiamen University, Xiamen 361102, China
| | - Zhi-Zhi Du
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Maevskaya MV, Okovityi SV. Lactitol properties in the treatment of patients with lifestyle-related diseases. MEDITSINSKIY SOVET = MEDICAL COUNCIL 2024:162-169. [DOI: 10.21518/ms2024-184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
Russia and most countries of the world are currently facing pressures on their health services because of the growing number of diseases associated with unhealthy lifestyles: type 2 diabetes, obesity, non-alcoholic fatty liver disease, etc. Lifestyle modification is the first prerequisite in the treatment of non-alcoholic fatty liver disease and other diseases associated with unhealthy lifestyle. The use of lactitol provides the opportunity to make this process more effective, as it is able to increase the production of butyrate, reduce the damage to the intestine barrier structure, and interact with sweet-taste receptors. Lactitol has a low glycaemic index, it is not absorbed in the intestine and is fermented like dietary fibres. The results of the studies showed that the metabolic response to this drug corresponds to a lower increase in plasma glucose, insulin and C-peptide levels compared to the use of glucose in healthy, non-obese men. It has been shown through various experiments in animals and in humans that lactitol also reduces the plasma triglyceride levels, probably due to reduced triglyceride absorption as a result of accelerated transit of intestinal contents. An important property of the drug is its ability to increase the glucagon-like peptide-1 (GLP-1) and PYY levels, which is accompanied by delayed gastric emptying and reduced hunger, which is essential in the treatment of obesity, type 2 diabetes mellitus and non-alcoholic fatty liver disease. A 120-day randomized controlled trial was conducted to assess the efficacy, safety, and tolerability of lactitol in 139 patients with nonalcoholic fatty liver disease. Twice-daily administration of lactitol 6 g in addition to lifestyle modification events has been shown to increase their efficacy expressed as a significant decrease in ALT levels and an increase in the AST/ALT ratio compared to control subjects. Lactitol can be considered as a metabolic corrector and used in the treatment of diseases associated with an unhealthy lifestyle.
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Affiliation(s)
- M. V. Maevskaya
- Sechenov First Moscow State Medical University (Sechenov University)
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Mu Y, Meng Q, Fan X, Xi S, Xiong Z, Wang Y, Huang Y, Liu Z. Identification of the inhibition mechanism of carbonic anhydrase II by fructooligosaccharides. Front Mol Biosci 2024; 11:1398603. [PMID: 38863966 PMCID: PMC11165268 DOI: 10.3389/fmolb.2024.1398603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Polygonatum sibiricum (P. sibiricum), recognized as a precious nourishing Chinese traditional medicine, exhibits the pharmacological effect of anti-aging. In this work, we proposed a novel mechanism underlying this effect related to the less studied bioactive compounds fructooligosaccharides in P. sibiricum (PFOS) to identify the inhibition effect of the small glycosyl molecules on the age-related zinc metalloprotease carbonic anhydrase II (CA II). Molecular docking and molecular dynamics simulation were used to investigate the structural and energetic properties of the complex systems consisting of the CA II enzyme and two possible structures of PFOS molecules (PFOS-A and PFOS-B). The binding affinity of PFOS-A (-7.27 ± 1.02 kcal/mol) and PFOS-B (-8.09 ± 1.75 kcal/mol) shows the spontaneity of the binding process and the stability of the combination in the solvent. Based on the residue energy decomposition and nonbonded interactions analysis, the C-, D- and G-sheet fragments of the CA II were found to be crucial in binding process. Van der Waals interactions form on the hydrophobic surface of CAII mainly with 131PHE and 135VAL, while hydrogen bonds form on the hydrophilic surface mainly with 67ASN and 92GLN. The binding of PFOS results in the blocking of the zinc ions pocket and then inhibiting its catalytic activity, the stability of which has been further demonstrated by free energy landscape. These findings provide evidence of the effective inhibition of PFOS to CA II enzyme, which leads to a novel direction for exploring the mechanism of traditional Chinese medicine focused on small molecule fructooligosaccharides.
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Affiliation(s)
- Yue Mu
- School of Chemical Engineering, East China University of Science and Technology, Shanghai, China
| | - Qingyang Meng
- Shanghai Pechoin Biotechnology Co., Ltd., Shanghai, China
| | - Xinyi Fan
- Shanghai Pechoin Biotechnology Co., Ltd., Shanghai, China
| | - Shuyun Xi
- Shanghai Pechoin Biotechnology Co., Ltd., Shanghai, China
| | - Zhongli Xiong
- Shanghai Zhengxin Biotechnology Co., Ltd., Shanghai, China
| | - Yihua Wang
- Shanghai Zhengxin Biotechnology Co., Ltd., Shanghai, China
| | - Yanling Huang
- Shanghai Zhengxin Biotechnology Co., Ltd., Shanghai, China
| | - Zhen Liu
- School of Chemical Engineering, East China University of Science and Technology, Shanghai, China
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Zhu Z, Zhang W, Li Z, Zhao W, Liu C, Zhu B, He P, Tang S, Wu Y, Yang J, Yang Q. Rethinking Sweetener Discovering: Multiparameter Modeling of Molecular Docking Results between the T1R2-T1R3 Receptor and Compounds with Different Tastes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7336-7343. [PMID: 38508871 DOI: 10.1021/acs.jafc.4c00407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Molecular docking has been widely applied in the discovery of new sweeteners, yet the interpretation of computational results sometimes remains difficult. Here, the interaction between the T1R2-T1R3 sweet taste receptor and 66 tasting compounds, including 26 sweet, 19 bitter, and 21 sour substances was investigated by batch molecular docking processes. Statistical analysis of the docking results generated two novel methods of interpreting taste properties. Quantitative correlation between relative sweetness (RS) and docking results created a multiparameter model to predict sweetness intensity, whose correlation coefficient r = 0.74 is much higher than r = 0.17 for the linear correlation model between sweetness and binding energy. The improved correlation indicated that docking results besides binding energy contain undiscovered information about the ligand-protein interaction. Qualitative discriminant analysis of different tasting molecules generated an uncorrelated linear discriminant analysis (UDLA) model, which achieved an overall 93.1% accuracy in discriminating the taste of molecules, with specific accuracy for verifying sweet, bitter, and sour compounds reaching 88.0%, 92.1%, and 100%. These unprecedented models provide a unique perspective for interpreting computational results and may inspire future research on sweetener discovery.
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Affiliation(s)
- Zhiyang Zhu
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Wei Zhang
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Zhenjie Li
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Wei Zhao
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Chunbo Liu
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Baokun Zhu
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Pei He
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Shiyun Tang
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Yiqin Wu
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Ji Yang
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Qianxu Yang
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
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Dai MQ, Wang XC, Gao LY, Zhang LC, Lai B, Wang C, Yan JN, Wu HT. Effect of black wolfberry anthocyanin and maltitol on the gelation and microstructural properties of curdlan/gellan gum hybrid gels. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:3749-3756. [PMID: 38234140 DOI: 10.1002/jsfa.13259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/27/2023] [Accepted: 12/31/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Laboratory scale experiments have shown that curdlan and gellan gum gelled together as curdlan/gellan gum (CG) hybrid gels showed better gel properties than the individual curdlan and gellan gum. In this study, CG and black wolfberry anthocyanin (BWA), CG and maltitol (ML) hybrid gels were constructed using CG hybrid gel as matrix. The effects of BWA or ML on the gel properties and microstructure of CG hybrid gels were investigated and a confectionery gel was developed. RESULTS The presence of BWA increased the storage modulus (G') value of CG at 0.1 Hz, whereas ML had little effect on the G' value of CG. The addition of BWA (5 g L-1 ) and ML (0.3 mol L-1 ) increased the melting and gelling temperatures of CG hybrid gels to 42.4 °C and 34.1 °C and 44.2 °C and 33.2 °C, respectively. Meanwhile, the relaxation time T22 in CG-ML and CG-BWA hybrid gels was reduced to 91.96 and 410.27 ms, indicating the strong binding between BWA and CG, ML and CG. The hydrogen bond interaction between BWA or ML and CG was confirmed by the shift in the hydroxyl stretching vibration peak. Moreover, the microstructures of CG-ML and CG-BWA hybrid gels were denser than that of CG. In addition, confectionery gel containing CG-BWA-ML has good chewing properties. CONCLUSION These results indicated that the incorporation of BWA or ML could improve the structure of CG hybrid gels and assign a sustainability potential for the development of confectionery gels based on CG complex. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Meng-Qi Dai
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Xue-Chen Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Ling-Yi Gao
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Li-Chao Zhang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian, China
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Bin Lai
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian, China
| | - Ce Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian, China
| | - Jia-Nan Yan
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian, China
| | - Hai-Tao Wu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian, China
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7
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Cui Z, Meng H, Zhou T, Yu Y, Gu J, Zhang Z, Zhu Y, Zhang Y, Liu Y, Wang W. Noteworthy Consensus Effects of D/E Residues in Umami Peptides Used for Designing the Novel Umami Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2789-2800. [PMID: 38278623 DOI: 10.1021/acs.jafc.3c07026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Aspartic acid (D) and glutamic acid (E) play vital roles in the umami peptides. To understand their exact mechanism of action, umami peptides were collected and cut into 1/2/3/4 fragments. Connecting D/E to the N/C-termini of the fragments formed D/E consensus effect groups (DEEGs), and all fragments containing DEEG were summarized according to the ratio and ranking obtained in the above four situations. The interaction patterns between peptides in DEEG and T1R1/T1R3-VFD were compared by statistical analysis and molecular docking, and the most conservative contacts were found to be HdB_277_ARG and HdB_148_SER. The molecular docking score of the effector peptides significantly dropped compared to that of their original peptides (-1.076 ± 0.658 kcal/mol, p value < 0.05). Six types of consensus fingerprints were set according to the Top7 contacts. The exponential of relative umami was linearly correlated with ΔGbind (R2 = 0.961). Under the D/E consensus effect, the electrostatic effect of the umami peptide was improved, and the energy gap between the highest occupied molecular orbital-the least unoccupied molecular orbital (HOMO-LUMO) was decreased. The shortest path map showed that the peptides had similar T1R1-T1R3 recognition pathways. This study helps to reveal umami perception rules and provides support for the efficient screening of umami peptides based on the material richness in D/E sequences.
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Affiliation(s)
- Zhiyong Cui
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Hengli Meng
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Tianxing Zhou
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Department of Bioinformatics, Faculty of Science, The University of Melbourne, Victoria 3010, Australia
| | - Yanyang Yu
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jiaming Gu
- College of Humanities and Development Studies, China Agricultural University, Beijing 100083, P. R. China
| | - Zhiwei Zhang
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yiwen Zhu
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, P. R. China
| | - Yuan Liu
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Wenli Wang
- Department of Food Science & Technology, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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Posta E, Fekete I, Gyarmati E, Stündl L, Zold E, Barta Z. The Effects of Artificial Sweeteners on Intestinal Nutrient-Sensing Receptors: Dr. Jekyll or Mr. Hyde? Life (Basel) 2023; 14:10. [PMID: 38276259 PMCID: PMC10817473 DOI: 10.3390/life14010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
The consumption of artificial and low-calorie sweeteners (ASs, LCSs) is an important component of the Western diet. ASs play a role in the pathogenesis of metabolic syndrome, dysbiosis, inflammatory bowel diseases (IBDs), and various inflammatory conditions. Intestinal nutrient-sensing receptors act as a crosstalk between dietary components, the gut microbiota, and the regulation of immune, endocrinological, and neurological responses. This narrative review aimed to summarize the possible effects of ASs and LCSs on intestinal nutrient-sensing receptors and their related functions. Based on the findings of various studies, long-term AS consumption has effects on the gut microbiota and intestinal nutrient-sensing receptors in modulating incretin hormones, antimicrobial peptides, and cytokine secretion. These effects contribute to the regulation of glucose metabolism, ion transport, gut permeability, and inflammation and modulate the gut-brain, and gut-kidney axes. Based on the conflicting findings of several in vitro, in vivo, and randomized and controlled studies, artificial sweeteners may have a role in the pathogenesis of IBDs, functional bowel diseases, metabolic syndrome, and cancers via the modulation of nutrient-sensing receptors. Further studies are needed to explore the exact mechanisms underlying their effects to decide the risk/benefit ratio of sugar intake reduction via AS and LCS consumption.
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Affiliation(s)
- Edit Posta
- GI Unit, Department of Infectology, Faculty of Medicine, University of Debrecen, Bartok Bela Street 2-26, 4031 Debrecen, Hungary; (E.G.); (Z.B.)
| | - Istvan Fekete
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; (I.F.); (L.S.)
| | - Eva Gyarmati
- GI Unit, Department of Infectology, Faculty of Medicine, University of Debrecen, Bartok Bela Street 2-26, 4031 Debrecen, Hungary; (E.G.); (Z.B.)
- Doctoral School of Clinical Immunology and Allergology, Faculty of Medicine, University of Debrecen, Nagyerdei Blvd. 98, 4032 Debrecen, Hungary
| | - László Stündl
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; (I.F.); (L.S.)
| | - Eva Zold
- Department of Clinical Immunology, Institute of Internal Medicine, Faculty of Medicine, University of Debrecen, Móricz Zsigmond Str. 22, 4032 Debrecen, Hungary;
| | - Zsolt Barta
- GI Unit, Department of Infectology, Faculty of Medicine, University of Debrecen, Bartok Bela Street 2-26, 4031 Debrecen, Hungary; (E.G.); (Z.B.)
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9
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Leechaisit R, Mahalapbutr P, Boonsri P, Karnchanapandh K, Rungrotmongkol T, Prachayasittikul V, Prachayasittikul S, Ruchirawat S, Prachayasittikul V, Pingaew R. Discovery of Novel Naphthoquinone-Chalcone Hybrids as Potent FGFR1 Tyrosine Kinase Inhibitors: Synthesis, Biological Evaluation, and Molecular Modeling. ACS OMEGA 2023; 8:32593-32605. [PMID: 37720749 PMCID: PMC10500653 DOI: 10.1021/acsomega.3c03176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023]
Abstract
This work presents a flexible synthesis of 10 novel naphthoquinone-chalcone derivatives (1-10) by nucleophilic substitution of readily accessible aminochalcones and 2,3-dichloro-1,4-naphthoquinone. All compounds displayed broad-spectrum cytotoxic activities against all the tested cancer cell lines (i.e., HuCCA-1, HepG2, A549, MOLT-3, T47D, and MDA-MB-231) with IC50 values in the range of 0.81-62.06 μM, especially the four most potent compounds 1, 3, 8, and 9. The in vitro investigation on the fibroblast growth factor receptor 1 (FGFR1) inhibitory effect indicated that eight derivatives (1-2, 4-5, and 7-10) were active FGFR1 inhibitors (IC50 = 0.33-3.13 nM) with more potency than that of the known FGFR1 inhibitor, AZD4547 (IC50 = 12.17 nM). Promisingly, compounds 5 (IC50 = 0.33 ± 0.01 nM), 9 (IC50 = 0.50 ± 0.04 nM), and 7 (IC50 = 0.85 ± 0.08 nM) were the three most potent FGFR1 inhibitors. Molecular docking, molecular dynamics simulations, and MM/GBSA-based free energy calculation revealed that the key amino acid residues involved in the binding of the compounds 5, 7, and 9 and the target FGFR1 protein were similar with those of the AZD4547 (i.e., Val492, Lys514, Ile545, Val561, Ala640, and Asp641). These findings revealed that the newly synthesized naphthoquinone-chalcone scaffold is a promising structural feature for an efficient inhibition of FGFR1.
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Affiliation(s)
- Ronnakorn Leechaisit
- Department
of Chemistry, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
| | - Panupong Mahalapbutr
- Department
of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Pornthip Boonsri
- Department
of Chemistry, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
| | - Kun Karnchanapandh
- 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
| | - 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
| | - Veda Prachayasittikul
- Center
for Research Innovation and Biomedical Informatics, Faculty of Medical
Technology, Mahidol University, Bangkok 10700, Thailand
| | - Supaluk Prachayasittikul
- Center
for Research Innovation and Biomedical Informatics, Faculty of Medical
Technology, Mahidol University, Bangkok 10700, Thailand
| | - Somsak Ruchirawat
- Laboratory
of Medicinal Chemistry, Chulabhorn Research
Institute, Bangkok 10210, Thailand
- Program
in Chemical Sciences, Chulabhorn Graduate
Institute, Bangkok 10210, Thailand
- Center
of Excellence on Environmental Health and Toxicology (EHT), Commission
on Higher Education, Ministry of Education, Bangkok 10400, Thailand
| | - Virapong Prachayasittikul
- Department
of Clinical Microbiology and Applied Technology, Faculty of Medical
Technology, Mahidol University, Bangkok 10700, Thailand
| | - Ratchanok Pingaew
- Department
of Chemistry, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
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10
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Mahalapbutr P, Sabuakham S, Nasoontorn S, Rungrotmongkol T, Silsirivanit A, Suriya U. Discovery of amphotericin B, an antifungal drug as tyrosinase inhibitor with potent anti-melanogenic activity. Int J Biol Macromol 2023; 246:125587. [PMID: 37379954 DOI: 10.1016/j.ijbiomac.2023.125587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/05/2023] [Accepted: 06/25/2023] [Indexed: 06/30/2023]
Abstract
Tyrosinase, a rate-limiting enzyme for melanin production, has been the most efficient target for the development of depigmenting agents. Although hydroquinone, kojic acid, and arbutin are the most well-known tyrosinase inhibitors, their adverse effects are inevitable. In the present study, an in silico drug repositioning combined with experimental validation was performed to search for novel potent tyrosinase inhibitors. Docking-based virtual screening results revealed that, among the 3210 FDA-approved drugs available in the ZINC database, amphotericin B, an antifungal drug exhibited the highest binding efficiency against human tyrosinase. Results from tyrosinase inhibition assay demonstrated that amphotericin B could inhibit the activity of mushroom and cellular tyrosinases, especially from MNT-1 human melanoma cells. Molecular modeling results revealed that amphotericin B/human tyrosinase complex exhibited high stability in an aqueous environment. Melanin assay results demonstrated that amphotericin B significantly suppressed melanin production in α-MSH-induced B16F10 murine melanoma and MNT-1 human melanoma cell lines better than the known inhibitor, kojic acid. Mechanistically, amphotericin B treatment significantly activated ERK and Akt signaling pathways, resulting in the decreased expression of MITF and tyrosinase. The obtained results may pursue pre-clinical and clinical studies to examine the possibility of using amphotericin B as an alternative treatment for hyperpigmentation disorders.
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Affiliation(s)
- Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Sahachai Sabuakham
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sutita Nasoontorn
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, 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
| | - Atit Silsirivanit
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Utid Suriya
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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11
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Suntichaikamolkul N, Akashi T, Mahalapbutr P, Sanachai K, Rungrotmongkol T, Bassard JE, Schaller H, De-Eknamkul W, Vimolmangkang S, Yamazaki M, Sirikantaramas S. Daidzein Hydroxylation by CYP81E63 Is Involved in the Biosynthesis of Miroestrol in Pueraria mirifica. PLANT & CELL PHYSIOLOGY 2023; 64:64-79. [PMID: 36218384 DOI: 10.1093/pcp/pcac140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
White Kwao Krua (Pueraria candollei var. mirifica), a Thai medicinal plant, is a rich source of phytoestrogens, especially isoflavonoids and chromenes. These phytoestrogens are well known; however, their biosynthetic genes remain largely uncharacterized. Cytochrome P450 (P450) is a large protein family that plays a crucial role in the biosynthesis of various compounds in plants, including phytoestrogens. Thus, we focused on P450s involved in the isoflavone hydroxylation that potentially participates in the biosynthesis of miroestrol. Three candidate P450s were isolated from the transcriptome libraries by considering the phylogenetic and expression data of each tissue of P. mirifica. The candidate P450s were functionally characterized both in vitro and in planta. Accordingly, the yeast microsome harboring PmCYP81E63 regiospecifically exhibited either 2' or 3' daidzein hydroxylation and genistein hydroxylation. Based on in silico calculation, PmCYP81E63 had higher binding energy with daidzein than with genistein, which supported the in vitro result of the isoflavone specificity. To confirm in planta function, the candidate P450s were then transiently co-expressed with isoflavone-related genes in Nicotiana benthamiana. Despite no daidzein in the infiltrated N. benthamiana leaves, genistein and hydroxygenistein biosynthesis were detectable by liquid Chromatography with tandem mass spectrometry (LC-MS/MS). Additionally, we demonstrated that PmCYP81E63 interacted with several enzymes related to isoflavone biosynthesis using bimolecular fluorescence complementation studies and a yeast two-hybrid analysis, suggesting a scheme of metabolon formation in the pathway. Our findings provide compelling evidence regarding the involvement of PmCYP81E63 in the early step of the proposed miroestrol biosynthesis in P. mirifica.
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Affiliation(s)
- Nithiwat Suntichaikamolkul
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Tomoyoshi Akashi
- Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, 123 Muang District, Khon Kaen 40002, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, 123 Muang District, Khon Kaen 40002, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Jean-Etienne Bassard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, Strasbourg 67084, France
| | - Hubert Schaller
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, Strasbourg 67084, France
| | - Wanchai De-Eknamkul
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Mami Yamazaki
- Laboratory of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
- Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku Chiba 260-8675, Japan
| | - Supaart Sirikantaramas
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
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12
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Wu J, Zhao J, Zhou Y, Cui C, Xu J, Li L, Feng Y. Discovery of N-l-Lactoyl-l-Trp as a Bitterness Masker via Structure-Based Virtual Screening and a Sensory Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2082-2093. [PMID: 36689686 DOI: 10.1021/acs.jafc.2c07807] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
N-Lactoyl-amino acid derivatives (N-Lac-AAs) are of increasing interest as potential taste-active compounds. The complexity and diversity of N-Lac-AAs pose a significant challenge to the effective discovery of taste-active N-Lac-AAs. Therefore, a structure-based virtual screening was used to identify taste-active N-Lac-AAs. Virtual screening results showed that N-lactoyl-hydrophobic amino acids had a higher affinity for taste receptors, specifically N-l-Lac-l-Trp. And then, N-l-Lac-l-Trp was synthesized in yields of 22.3% by enzymatic synthesis in the presence of l-lactate and l-Trp, and its chemical structure was confirmed by MS/MS and one-dimensional (1D) and two-dimensional (2D) NMR. Sensory evaluation revealed that N-l-Lac-l-Trp had a significant taste-masking effect on quinine, d-salicin, caffeine, and l-Trp, particularly l-Trp and caffeine. N-l-Lac-l-Trp had a better masking effect on the higher concentration of bitter compounds. It reduced the bitterness of caffeine (500 mg/L) and l-Trp (1000 mg/L) by approximately 20 and 26%, respectively. The result of the ligand-receptor interaction and a quantum mechanical analysis showed that N-l-Lac-l-Trp increased the binding affinity to the bitter receptor mainly through hydrogen bonding and lowering the electrostatic potential.
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Affiliation(s)
- Jing Wu
- School of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Junpeng Zhao
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yubo Zhou
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chun Cui
- School of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
| | - Jucai Xu
- School of Biotechnology and Health Sciences & International Healthcare Innovation Institute (Jiangmen), Wuyi University, Jiangmen 529020, China
| | - Laihao Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Yunzi Feng
- School of Food Science and Technology, South China University of Technology, Guangzhou 510640, China
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13
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Ma Y, Li J, Liu Y, Dou N, Mu S, Wei X, Bilawal A, Hou J, Jiang Z. Lactitol and β-cyclodextrin alleviate the intensity of goaty flavor. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1588-1592. [PMID: 36318369 DOI: 10.1002/jsfa.12304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/06/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Goat milk has balanced nutritional composition, is conducive to digestion and absorption, and does not easily lead to allergic reactions. However, the special goaty flavor in milk has seriously affected consumer acceptance. It is imperative to alleviate the goaty flavor in a safe and efficient way. RESULTS This study indicated that the supplementation of 6 g kg-1 β-cyclodextrin or 8 g kg-1 lactitol in goat milk significantly alleviated goaty flavor and improved sensory characteristics. Furthermore, the supplementation of β-cyclodextrin and lactitol had a synergistic effect in reducing the content of free fatty acids that cause goaty flavor. The content of caproic acid (C6 H12 O2 ), octanoic acid (C8 H6 O2 ), and decanoic acid (C10 H20 O2 ) decreased by 42.46%, 39.45%, and 46.41%, respectively, after a combined group was supplemented with 6 g kg-1 β-cyclodextrin and 7 g kg-1 lactitol, which was significantly lower than in groups given β-cyclodextrin or lactitol individually. CONCLUSION This study provides a novel and effective approach to alleviate goaty flavor and promote the competitiveness of goat milk products. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Yue Ma
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
| | - Jinzhe Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
| | - Yue Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
| | - Nianxu Dou
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
| | - Sinan Mu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
| | - Xuan Wei
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
| | - Akhunzada Bilawal
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
| | - Juncai Hou
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
- Heilongjiang Green Food Science Research Institute, Harbin, People's Republic of China
| | - Zhanmei Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, People's Republic of China
- Heilongjiang Green Food Science Research Institute, Harbin, People's Republic of China
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14
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Mahalapbutr P, Nuramrum N, Rungrotmongkol T, Kongtaworn N, Sabuakham S. Structural dynamics and susceptibility of isobutylamido thiazolyl resorcinol (Thiamidol TM) against human and mushroom tyrosinases. J Biomol Struct Dyn 2023; 41:11810-11817. [PMID: 36644799 DOI: 10.1080/07391102.2023.2167001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/23/2022] [Indexed: 01/17/2023]
Abstract
Tyrosinase, a key enzyme catalyzing a rate-limiting step of the melanin production, has been the most promising target for suppressing hyperpigmentation. Although a number of tyrosinase inhibitors have been developed, most of those lack clinical efficacy as they were identified from using mushroom tyrosinase (mTyr) as the target. Previous study revealed that the inhibitory effect of isobutylamido thiazolyl resorcinol (ThiamidolTM) on human tyrosinase (hTyr) is ∼100 times higher than that on mTyr. In the present study, we aimed to investigate the structural dynamics and susceptibility of ThiamidolTM against hTyr and mTyr at the atomic level using molecular docking, molecular dynamics simulation, and free energy calculation based on the molecular mechanics/Poisson-Boltzmann surface area method. The obtained results revealed that the resorcinol moiety of ThiamidolTM was found to be embedded in the catalytic copper center, interacting with H180, H202, H211, F386, and H390 residues of hTyr as well as with F264 residue of mTyr, mostly through van der Waals interactions. However, the number of destabilizing residues was found to be more pronounced in the ThiamidolTM/mTyr complex than the ThiamidolTM/hTyr system, supported by the lower binding affinity of ThiamidolTM/mTyr complex as well as the higher water accessibility and the lower number of atomic contacts at the active site of mTyr. Altogether, the structural and energetic information from this work would be useful for further optimization of more potent human tyrosinase inhibitors based on ThiamidolTM scaffold.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Napat Nuramrum
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Napat Kongtaworn
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Sahachai Sabuakham
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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15
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Dandekar T, Kunz M. Design Principles of a Cell. Bioinformatics 2023. [DOI: 10.1007/978-3-662-65036-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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16
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Inclusion complexation of emodin with various β-cyclodextrin derivatives: Preparation, characterization, molecular docking, and anticancer activity. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Ponnusamy V, Subramanian G, Muthuswamy K, Shanmugamprema D, Krishnan V, Velusamy T, Subramaniam S. Genetic variation in sweet taste receptors and a mechanistic perspective on sweet and fat taste sensation in the context of obesity. Obes Rev 2022; 23:e13512. [PMID: 36282093 DOI: 10.1111/obr.13512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 10/05/2022] [Indexed: 11/30/2022]
Abstract
Taste sensation enables humans to make nutritionally important decisions such as food preference and consumption. It functions as deterministic factors for unpropitious eating behavior, leading to overweight and obesity. The hedonistic feeling on consumption of fat and sugar-rich meals, in particular, has a negative influence on health. In addition, impairment in the taste receptors alters the downstream signaling of taste transduction pathway. Hence, genetic polymorphism in typical taste receptors is a predictor of taste sensitivity variance across individuals. The present review summarizes the effect of a single nucleotide polymorphism (SNP) in sweet taste receptors (T1R2/T1R3) on taste perception among individuals of various body mass index (BMI). Furthermore, in the context of obesity, we discussed the possibility of crosstalk between fat and sweet receptors as well as taste dysfunction in diseased individuals. In overall, a greater understanding of the physiological relationship between taste receptors, altered taste sensitivity, and genetic polymorphisms should lead to more effective obesity prevention approaches.
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Affiliation(s)
- Vinithra Ponnusamy
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Gowtham Subramanian
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Karthi Muthuswamy
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Deepankumar Shanmugamprema
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Vasanth Krishnan
- Molecular Biology Laboratory, Department of Botany, School of Life Sciences, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Thirunavukkarasu Velusamy
- Department of Biotechnology, School of Biotechnology and Genetic Engineering, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
| | - Selvakumar Subramaniam
- Molecular Physiology Laboratory, Department of Biochemistry, Bharathiar University, Coimbatore, Tamilnadu, India, 641046
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18
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Sanachai K, Mahalapbutr P, Tabtimmai L, Seetaha S, Kittikool T, Yotphan S, Choowongkomon K, Rungrotmongkol T. Discovery of JAK2/3 Inhibitors from Quinoxalinone-Containing Compounds. ACS OMEGA 2022; 7:33587-33598. [PMID: 36157733 PMCID: PMC9494680 DOI: 10.1021/acsomega.2c04769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Janus kinases (JAKs) are involved in a wide variety of cell signaling associated with T-cell and B-cell mediated diseases. The pathogenesis of common lymphoid-derived diseases and leukemia cancer has been implicated in JAK2 and JAK3. Therefore, to decrease the risk of these diseases, targeting this pathway using JAK2/3 inhibitors could serve as a valuable research tool. Herein, we used a combination of the computational and biological approaches to identify the quinoxalinone-based dual inhibitors of JAK2/3. First, an in-house library of 49 quinoxalinones was screened by molecular docking. Then, the inhibitory activities of 17 screened compounds against both JAKs as well as against two human erythroleukemia cell lines, TF1 and HEL were examined. The obtained results revealed that several quinoxalinones could potentially inhibit JAK2/3, and among them, ST4j showed strong inhibition against JAKs with the IC50 values of 13.00 ± 1.31 nM for JAK2 and 14.86 ± 1.29 nM for JAK3, which are better than ruxolitinib and tofacitinib. In addition, ST4j potentially inhibited TF1 cells (IC50 of 15.53 ± 0.82 μM) and HEL cells (IC50 of 17.90 ± 1.36 μM), similar to both tofacitinib ruxolitinib. Mechanistically, ST4j inhibited JAK2 autophosphorylation and induced cell apoptosis in dose- and time-dependent manners. From molecular dynamics simulations, ST4j was mainly stabilized by van der Waals interactions, and its hydroxyl group could form hydrogen bonds in the hinge region at residues S936 and R938 of JAK2. This research highlights the potential of ST4j to be a novel therapeutic agent for the treatment of lymphoid-derived diseases and leukemia cancer.
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Affiliation(s)
- Kamonpan Sanachai
- Center
of Excellence in Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panupong Mahalapbutr
- Department
of Biochemistry, and Center for Translational Medicine, Faculty of
Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Lueacha Tabtimmai
- Department
of Biotechnology, Faculty of Applied Science, King Mongkut’s University of Technology of North Bangkok, Bangkok 10800, Thailand
| | - Supaphorn Seetaha
- Department
of Biochemistry, Faculty of Science, Kasetsart
University, Bangkok 10900, Thailand
| | - Tanakorn Kittikool
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Sirilata Yotphan
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Kiattawee Choowongkomon
- Department
of Biochemistry, Faculty of Science, Kasetsart
University, Bangkok 10900, Thailand
| | - Thanyada Rungrotmongkol
- Center
of Excellence in 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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19
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Sanachai K, Mahalapbutr P, Hengphasatporn K, Shigeta Y, Seetaha S, Tabtimmai L, Langer T, Wolschann P, Kittikool T, Yotphan S, Choowongkomon K, Rungrotmongkol T. Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus Kinases. ACS OMEGA 2022; 7:33548-33559. [PMID: 36157769 PMCID: PMC9494641 DOI: 10.1021/acsomega.2c04535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Janus kinases (JAKs) are nonreceptor protein tyrosine kinases that play a role in a broad range of cell signaling. JAK2 and JAK3 have been involved in the pathogenesis of common lymphoid-derived diseases and leukemia cancer. Thus, inhibition of both JAK2 and JAK3 can be a potent strategy to reduce the risk of these diseases. In the present study, the pharmacophore models built based on the commercial drug tofacitinib and the JAK2/3 proteins derived from molecular dynamics (MD) trajectories were employed to search for a dual potent JAK2/3 inhibitor by a pharmacophore-based virtual screening of 54 synthesized pyrazolone derivatives from an in-house data set. Twelve selected compounds from the virtual screening procedure were then tested for their inhibitory potency against both JAKs in the kinase assay. The in vitro kinase inhibition experiment indicated that compounds 3h, TK4g, and TK4b can inhibit both JAKs in the low nanomolar range. Among them, the compound TK4g showed the highest protein kinase inhibition with the half-maximal inhibitory concentration (IC50) value of 12.61 nM for JAK2 and 15.80 nM for JAK3. From the MD simulations study, it could be found that the sulfonamide group of TK4g can form hydrogen bonds in the hinge region at residues E930 and L932 of JAK2 and E903 and L905 of JAK3, while van der Waals interaction also plays a dominant role in ligand binding. Altogether, TK4g, found by virtual screening and biological tests, could serve as a novel therapeutical lead candidate.
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Affiliation(s)
- Kamonpan Sanachai
- Center
of Excellence in Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Panupong Mahalapbutr
- Department
of Biochemistry, Faculty of Medicine, Khon
Kaen University, Khon Kaen40002, Thailand
| | - Kowit Hengphasatporn
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba305-8577, Ibaraki, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba305-8577, Ibaraki, Japan
| | - Supaphorn Seetaha
- Department
of Biochemistry, Faculty of Science, Kasetsart
University, Bangkok10900, Thailand
| | - Lueacha Tabtimmai
- Department
of Biotechnology, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok10800, Thailand
| | - Thierry Langer
- Department
of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Althanstraße 14, ViennaA-1090, Austria
| | - Peter Wolschann
- Institute
of Theoretical Chemistry, University of
Vienna, Vienna1090, Austria
| | - Tanakorn Kittikool
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Rama VI Road, Bangkok10400, Thailand
| | - Sirilata Yotphan
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Rama VI Road, Bangkok10400, Thailand
| | - Kiattawee Choowongkomon
- Department
of Biochemistry, Faculty of Science, Kasetsart
University, Bangkok10900, Thailand
| | - Thanyada Rungrotmongkol
- Center
of Excellence in Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok10330, Thailand
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20
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Todsaporn D, Mahalapbutr P, Poo-Arporn RP, Choowongkomon K, Rungrotmongkol T. Structural dynamics and kinase inhibitory activity of three generations of tyrosine kinase inhibitors against wild-type, L858R/T790M, and L858R/T790M/C797S forms of EGFR. Comput Biol Med 2022; 147:105787. [PMID: 35803080 DOI: 10.1016/j.compbiomed.2022.105787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/25/2022] [Accepted: 06/26/2022] [Indexed: 11/19/2022]
Abstract
Mutations in the tyrosine kinase domain of epidermal growth factor receptor (EGFR), including L858R/T790M double and L858R/T790M/C797S triple mutations, are major causes of acquired resistance towards EGFR targeted drugs. In this work, a combination of comprehensive molecular modeling and in vitro kinase inhibition assay was used to unravel the mutational effects of EGFR on the susceptibility of three generations of EGFR tyrosine kinase inhibitors (erlotinib, gefitinib, afatinib, dacomitinib, and osimertinib) in comparison with the wild-type EGFR. The binding affinity of all studied inhibitors towards the double and triple EGFR mutations was in good agreement with the experimental data, ranked in the order of osimertinib > afatinib > dacomitinib > erlotinib > gefitinib. Three hot-spot residues at the hinge region (M790, M793, and C797) were involved in the binding of osimertinib and afatinib, enhancing their inhibitory activity towards mutated EGFRs. Both double and triple EGFR mutations causing erlotinib and gefitinib resistance are mainly caused by the low number of H-bond occupations, the low number of surrounding atoms, and the high number of water molecules accessible to the enzyme active site. According to principal component analysis, the molecular complexation of osimertinib against the two mutated EGFRs was in a closed conformation, whereas that against wild-type EGFR was in an open conformation, resulting in drug resistance. This work paves the way for further design of the novel EGFR inhibitors to overcome drug resistance mechanisms.
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Affiliation(s)
- Duangjai Todsaporn
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Rungtiva P Poo-Arporn
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, 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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21
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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] [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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22
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Mahalapbutr P, Leechaisit R, Thongnum A, Todsaporn D, Prachayasittikul V, Rungrotmongkol T, Prachayasittikul S, Ruchirawat S, Prachayasittikul V, Pingaew R. Discovery of Anilino-1,4-naphthoquinones as Potent EGFR Tyrosine Kinase Inhibitors: Synthesis, Biological Evaluation, and Comprehensive Molecular Modeling. ACS OMEGA 2022; 7:17881-17893. [PMID: 35664590 PMCID: PMC9161259 DOI: 10.1021/acsomega.2c01188] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/21/2022] [Indexed: 05/02/2023]
Abstract
Epidermal growth factor receptor (EGFR) has been recognized as one of the attractive targets for anticancer drug development. Herein, a set of anilino-1,4-naphthoquinone derivatives (3-18) was synthesized and investigated for their anticancer and EGFR inhibitory potentials. Among all tested compounds, three derivatives (3, 8, and 10) were selected for studying EGFR inhibitory activity (in vitro and in silico) due to their most potent cytotoxic activities against six tested cancer cell lines (i.e., HuCCA-1, HepG2, A549, MOLT-3, MDA-MB-231, and T47D; IC50 values = 1.75-27.91 μM), high selectivity index (>20), and good predicted drug-like properties. The experimental results showed that these three promising compounds are potent EGFR inhibitors with nanomolar IC50 values (3.96-18.64 nM). Interestingly, the most potent compound 3 bearing 4-methyl substituent on the phenyl ring displayed 4-fold higher potency than the known EGFR inhibitor, erlotinib. Molecular docking, molecular dynamics simulation, and MM/GBSA-based free energy calculation revealed that van der Waals force played a major role in the accommodations of compound 3 within the ATP-binding pocket of EGFR. Additionally, the 4-CH3 moiety of the compound was noted to be a key chemical feature contributing to the highly potent EGFR inhibitory activity via its formations of alkyl interactions with A743, K745, M766, and L788 residues as well as additional interactions with M766 and T790.
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Affiliation(s)
- Panupong Mahalapbutr
- Department
of Biochemistry, and Center for Translational Medicine, Faculty of
Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Ronnakorn Leechaisit
- Department
of Chemistry, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
| | - Anusit Thongnum
- Department
of Physics, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
| | - Duangjai Todsaporn
- Structural
and Computational Biology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Veda Prachayasittikul
- Center
of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, 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
| | - Supaluk Prachayasittikul
- Center
of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Somsak Ruchirawat
- Laboratory
of Medicinal Chemistry and Program in Chemical Sciences, Chulabhorn Research Institute, Chulabhorn Graduate
Institute, Bangkok 10210, Thailand
- Commission
on Higher Education, Ministry of Education, Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand
| | - Virapong Prachayasittikul
- Department
of Clinical Microbiology and Applied Technology, Faculty of Medical
Technology, Mahidol University, Bangkok 10700, Thailand
| | - Ratchanok Pingaew
- Department
of Chemistry, Faculty of Science, Srinakharinwirot
University, Bangkok 10110, Thailand
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23
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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: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [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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24
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Miao Y, Ni H, Zhang X, Zhi F, Long X, Yang X, He X, Zhang L. Investigating mechanism of sweetness intensity differences through dynamic analysis of sweetener-T1R2-membrane systems. Food Chem 2021; 374:131807. [PMID: 34915374 DOI: 10.1016/j.foodchem.2021.131807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 11/15/2022]
Abstract
Knowing the mechanism of action of sweet taste receptors is important for the design of new, healthy sweeteners. However, little is known about the structures and recognition mechanisms of these receptors. 28 sweeteners were assessed by molecular docking, and 8 typical sweeteners were chosen to construct sweetener-T1R2-membrane systems to analyze interactions between receptor and sweeteners. Natural sweeteners with low-intensity sweetness, such as fructose and xylitol, were released from the Venus flytrap domain at ∼30 ns, with displacements greater than 50 Å. In contrast, artificial neotame and advantame bound stably to the receptor, within 5 Å. Van der Waals interactions were significant in high-intensity sweetener systems, imparting an energy difference of over 15 kcal/mol between neotame (artificial sweetener) and fructose (natural). These results provide a deeper understanding of the mechanisms of sweetener function and offer a new direction for the design of sweeteners.
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Affiliation(s)
- Yulu Miao
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xingyi Zhang
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Fengdong Zhi
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiang Long
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xuepeng Yang
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
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25
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Jang J, Kim SK, Guthrie B, Goddard WA. Synergic Effects in the Activation of the Sweet Receptor GPCR Heterodimer for Various Sweeteners Predicted Using Molecular Metadynamics Simulations. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12250-12261. [PMID: 34613740 DOI: 10.1021/acs.jafc.1c03779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The sweet taste is elicited by activation of the TAS1R2/1R3 heterodimer G protein-coupled receptor. This is a therapeutic target for treatment of obesity and metabolic dysfunctions. Sweetener blends provide attractive strategies to lower the sugar level while preserving the attractive taste of food. To understand the synergic effect of various sweetener blend combinations of artificial and natural sweeteners, we carried out our molecular dynamics studies using predicted structures of the TAS1R2/1R3 heterodimer and predicted structures for the sweeteners. We used as a measure of activation the intracellular ionic lock distance between transmembrane helices 3 and 6 of TAS1R3. We find that full synergic combinations [rebaudioside A (Reb-A)/acesulfame K and Reb-A/sucralose] and partial synergic combinations (sucralose/acesulfame K) show significantly more negative changes in the free energy compared to single-ligand cases, while a pair known to be suppressive (saccharin and acesulfame K) shows significantly less changes than for the single-ligand case. This study provides an atomistic understanding of the mechanism for synergy and identifies new combinations of sweeteners to reduce the caloric content for treating diseases.
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Affiliation(s)
- Jaewan Jang
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Brian Guthrie
- Cargill Global Core Research, Wayzata, Minnesota 55391, United States
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
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26
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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: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Molecular basis of the new COVID-19 target neuropilin-1 in complex with SARS-CoV-2 S1 C-end rule peptide and small-molecule antagonists. J Mol Liq 2021; 335:116537. [PMID: 34031621 PMCID: PMC8133821 DOI: 10.1016/j.molliq.2021.116537] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for causing the current coronavirus 2019 (COVID-19) pandemic, uses its spike (S1) protein for host cell attachment and entry. Apart from angiotensin-converting enzyme 2, neuropilin-1 (NRP1) has been recently found to serve as another host factor for SARS-CoV-2 infection; thus, blocking S1-NRP1 interaction can be a potential treatment for COVID-19. Herein, molecular recognition between SARS-CoV-2 S1 C-end rule (CendR) heptapeptide including small-molecule antagonists (EG00229 and EG01377) and the NRP1 was investigated using molecular dynamics simulations and binding free energy calculations based on MM-PBSA method. The binding affinity and the number of hot-spot residues of EG01377/NRP1 complex were higher than those of CendR/NRP1 and EG00229/NRP1 systems, in line with the reported experimental data as well as with the lower water accessibility at the ligand-binding site. The (i) T316, P317, and D320 and (ii) S346, T349, and Y353 residues of NRP1 were confirmed to respectively form H-bonds with the positively charged guanidinium group and the negatively charged carboxyl moiety of all studied ligands. Moreover, Rosetta protein design was employed to improve the binding affinity between CendR peptide and NRP1. The newly designed peptides, especially R683G and A684M, exhibited higher binding efficiency than the native CendR heptapeptide as well as the small-molecule EG00229 by forming more H-bonds and hydrophobic interactions with NPR1, suggesting that these designed peptides could be promising NRP1 inhibitors to combat SARS-CoV-2 infection.
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28
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Substrate binding mechanism of glycerophosphodiesterase towards organophosphate pesticides. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Verma K, Mahalapbutr P, Auepattanapong A, Khaikate O, Kuhakarn C, Takahashi K, Rungrotmongkol T. Molecular dynamics simulations of sulfone derivatives in complex with DNA topoisomerase IIα ATPase domain. J Biomol Struct Dyn 2020; 40:1692-1701. [PMID: 33089727 DOI: 10.1080/07391102.2020.1831961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Human topoisomerase II alpha (TopoIIα) is a crucial enzyme involved in maintaining genomic integrity during the process of DNA replication and mitotic division. It is a vital therapeutic target for designing novel anticancer agents in targeted cancer therapy. Sulfones, members of organosulfur compounds, have been reported to possess various biological activities such as antimicrobial, anti-inflammatory, anti-HIV, anticancer, and antimalarial properties. In the present study, a series of sulfones was selected to evaluate their inhibitory activity against TopoIIα using computational approaches. Molecular docking results revealed that several sulfone analogs bind efficiently to the ATPase domain of TopoIIα. Among them, sulfones 18a, 60a, *4 b, *8 b, *3c, and 8c exhibit higher binding affinity than the known TopoII inhibitor, salvicine. Molecular dynamics simulations and free energy calculations based on MM/PB(GB)SA method demonstrated that sulfone *8 b strongly interacts with amino acid residues in the ATP-binding pocket (E87, N91, D94, I125, I141, F142, S149, G161, and A167), driven mainly by an electrostatic attraction and a strong H-bond formation at G161 residue. Altogether, the obtained results predicted that sulfones could have a high potential to be a lead molecule for targeting TopoIIα.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kanika Verma
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Atima Auepattanapong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Onnicha Khaikate
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chutima Kuhakarn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kaito Takahashi
- Institute of Atomic and Sciences, Academia Sinica, Taipei, Taiwan
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, 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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30
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Mahalapbutr P, Kongtaworn N, Rungrotmongkol T. Structural insight into the recognition of S-adenosyl-L-homocysteine and sinefungin in SARS-CoV-2 Nsp16/Nsp10 RNA cap 2'-O-Methyltransferase. Comput Struct Biotechnol J 2020; 18:2757-2765. [PMID: 33020707 PMCID: PMC7527316 DOI: 10.1016/j.csbj.2020.09.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 01/07/2023] Open
Abstract
The binding affinity towards SARS-CoV-2 nsp16 of SFG is higher than that of SAH. Asp99 is a key binding residue for SAH and SFG via charge-charge attraction. SFG could electrostatically interact with the 2′-OH and N3 groups of adenosine moiety of RNA substrate. The distance between 2′-OH of RNA and –NH3+ (at 6′ position) of SFG mimics the methyl transfer reaction.
The recent ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to rapidly spread across the world. To date, neither a specific antiviral drug nor a clinically effective vaccine is available. Among the 15 viral non-structural proteins (nsps), nsp16 methyltransferase has been considered as a potential target due to its crucial role in RNA cap 2′-O-methylation process, preventing the virus detection by cell innate immunity mechanisms. In the present study, molecular recognition between the two natural nucleoside analogs (S-adenosyl-l-homocysteine (SAH) and sinefungin (SFG)) and the SARS-CoV-2 nsp16/nsp10/m7GpppAC5 was studied using all-atom molecular dynamics simulations and free energy calculations based on MM/GBSA and WaterSwap approaches. The binding affinity and the number of hot-spot residues, atomic contacts, and H-bond formations of SFG/nsp16 complex were distinctly higher than those of SAH/nsp16 system, consistent with the lower water accessibility at the enzyme active site. Notably, only SFG could electrostatically interact with the 2′-OH and N3 of RNA’s adenosine moiety, mimicking the methyl transfer reaction of S-adenosyl-l-methionine substrate. The atomistic binding mechanism obtained from this work paves the way for further optimizations and designs of more specific SARS-CoV-2 nsp16 inhibitors in the fight against COVID-19.
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Affiliation(s)
- Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Napat Kongtaworn
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Corresponding author at: Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.
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