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Chen L, Yin S, Dong S, Xu P, Liu Y, Xiang X, Huang Q, Ye L. A new insight into the key matrix components for aftertaste in Ampelopsis grossedentata (vine tea) infusion: From the intensity and duration of taste profiles using non-targeted metabolomics and molecular simulation. Food Chem 2024; 450:139236. [PMID: 38640537 DOI: 10.1016/j.foodchem.2024.139236] [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: 11/17/2023] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/21/2024]
Abstract
The aftertaste with a prolonged duration in ampelopsis grossedentata infusion (AGTI) is easily perceived, however, its formation mechanism is unclear. Therefore, aftertaste-A and richness were confirmed as the characteristic aftertaste of AGTI through sensory evaluation and electronic tongue. Moreover, 5-KETE, theobromine, etc., metabolites were identified as the differential components between AGTI and green tea infusion. Among them, p-coumaroyl quinic acid, xanthine etc., and proline, dihydromyricetin, etc., components contributed more to the formation of aftertaste-A and richness, respectively. Further, the bonding between characteristic metabolites for aftertaste in AGTI with their receptors were shown to be more stable using molecular docking, compared to metabolites related to typical taste profiles. The aftertaste in AGTI was more easily perceived by saltiness components or in NaCl system by molecular simulation. This study offers novel insight into the interaction mechanism of aftertaste in tea infusion and will contribute to further study on aftertaste for other foods.
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Affiliation(s)
- Le Chen
- School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha, Hunan 410114, China
| | - Shengxin Yin
- School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha, Hunan 410114, China
| | - Shiqin Dong
- School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha, Hunan 410114, China
| | - Peng Xu
- School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha, Hunan 410114, China
| | - Yongle Liu
- School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha, Hunan 410114, China
| | - Xiaole Xiang
- School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha, Hunan 410114, China.
| | - Qun Huang
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550025, China
| | - Lin Ye
- College of Food Science and Engineering, Tarim University, Alar, Xinjiang 843300, China
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2
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Wang S, Chen Y, Lu Y, Jiang D, Lin H, Jiang Z, Tang J, Dong W, Zhao J. Interaction of pepper numbing substances with myofibrillar proteins and numbness perception under thermal conditions: A structural mechanism analysis. Food Chem 2024; 449:139203. [PMID: 38599105 DOI: 10.1016/j.foodchem.2024.139203] [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: 01/30/2024] [Revised: 03/18/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
This study examined the interaction between myofibrillar proteins (MPs) and the numbing substance hydroxy-α-sanshool (α-SOH) in a thermal environment, and provided an explanation of the numbness perception mechanism through muti-spectroscopic and molecular dynamics simulation methodology. Results showed that addition of α-SOH could reduce the particle size and molecular weight of MPs, accompanied by changes in the tertiary and secondary structure, causing the α-helix of MPs transitioned to β-sheet and β-turn due to the reorganization of hydrogen bonds. After a moderate heating (60 or 70 °C), MPs could form the stable complexes with α-SOH that were associated with attachment sites and protein wrapping. The thermal process might convert a portion of α-SOH' into hydroxy-β-sanshool' (β-SOH'). When docking with the sensory receptor TRPV1, the RMSD, RMSF and binding free energy all showed that β-SOH' demonstrated a low affinity, thereby reducing the numbing perception. These findings can provide a theoretical foundation for the advanced processing of numbing meat products.
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Affiliation(s)
- Shuaiqian Wang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yu Chen
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yan Lu
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Diandian Jiang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Hongbin Lin
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Zhenju Jiang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Jie Tang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Wei Dong
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; Beijing Laboratory of Food Quality and Safety/Key Laboratory of Alcoholic Beverages Quality and Safety of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Jie Zhao
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China.
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3
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Zhou J, Li J, Cheng C, Yao Y, Li Y, Liu H, Wu L. Unraveling the binding behavior of the antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one with human serum albumin: Multi-spectroscopic, atomic force microscope, computational simulation, and esterase activity. Int J Biol Macromol 2024; 274:133266. [PMID: 38906347 DOI: 10.1016/j.ijbiomac.2024.133266] [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: 04/02/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
As a marine antifouling biocide, 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT) exhibited high toxicity to marine organisms. This study investigated the interaction between DCOIT and human serum albumin (HSA) using several spectroscopic techniques combined with computer prediction methods. The UV-vis absorption spectra, Stern-Volmer constant (KSV) and fluorescence resonance energy transfer (FRET) results indicated that DCOIT caused static quenching of HSA fluorescence. The ΔG°, ΔH° and ΔS° values were -31.03 ± 0.17 kJ·mol-1, -133.54 ± 0.88 kJ·mol-1 and -348.46 ± 2.86 J.mol-1·K-1, respectively, suggesting that van der Waals forces and hydrogen bonds governed the spontaneous formation of the complex. Synchronous fluorescence and circular dichroism (CD) spectroscopy observed the burial of Trp residues within HSA and the unfolding of HSA secondary structure induced by DCOIT. Three-dimensional (3D) fluorescence and Atomic Force Microscopy (AFM) further detected DCOIT-induced loosening of HSA peptide chain structure. Site displacement experiments indicated that DCOIT binding at site I of HSA. Computational predictions indicated that hydrophobic interactions were also essential in the complex. The increased RMSD, Rg, SASA, and RMSF confirmed that DCOIT weakened the stability and compactness of HSA, rendering residues more flexible. Lastly, esterase activity assays demonstrated that DCOIT inhibited esterase activity and interfered with the human detoxification process.
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Affiliation(s)
- Junqiao Zhou
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Jiayin Li
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Cong Cheng
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - YuJuan Yao
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Yu Li
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Hao Liu
- Liyuan Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430077, PR China
| | - Laiyan Wu
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China.
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4
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Pang S, Wang M, Yuan J, Yang Z, Yu H, Zhang H, Dong T, Liu A. Sensitive Dual-Signal ELISA Based on Specific Phage-Displayed Double Peptide Probes with Internal Filtering Effect to Assay Monkeypox Virus Antigen. Anal Chem 2024; 96:10064-10073. [PMID: 38842443 DOI: 10.1021/acs.analchem.4c01802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The global spread of monkeypox has become a worldwide public healthcare issue. Therefore, there is an urgent need for accurate and sensitive detection methods to effectively control its spreading. Herein, we screened by phage display two peptides M4 (sequence: DPCGERICSIAL) and M6 (sequence: SCSSFLCSLKVG) with good affinity and specificity to monkeypox virus (MPXV) B21R protein. To simulate the state of the peptide in the phage and to avoid spatial obstacles of the peptide, GGGSK was added at the C terminus of M4 and named as M4a. Molecular docking shows that peptide M4a and peptide M6 are bound to different epitopes of B21R by hydrogen bonds and salt-bridge interactions, respectively. Then, peptide M4a was selected as the capture probe, phage M6 as the detection probe, and carbonized polymer dots (CPDs) as the fluorescent probe, and a colorimetric and fluorescent double-signal capture peptide/antigen/signal peptide-displayed phage sandwich ELISA triggered by horseradish peroxidase (HRP) through a simple internal filtration effect (IFE) was constructed. HRP catalyzes H2O2 to oxidize 3,3',5,5'-tetramethylbenzidine (TMB) to generate blue oxidized TMB, which can further quench the fluorescence of CPDs through IFE, enabling to detect MPXV B21R in colorimetric and fluorescent modes. The proposed simple immunoassay platform shows good sensitivity and reliability in MPXV B21R detection. The limit of detection for colorimetric and fluorescent modes was 27.8 and 9.14 pg/mL MPXV B21R, respectively. Thus, the established double-peptide sandwich-based dual-signal immunoassay provides guidance for the development of reliable and sensitive antigen detection capable of mutual confirmation, which also has great potential for exploring various analytical strategies for other respiratory virus surveillance.
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Affiliation(s)
- Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Jinlong Yuan
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Zhonghuang Yang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Haipeng Yu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Haohan Zhang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
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5
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M L SP, Kumari S, Martinek TA, M ES. De novo design of potential peptide analogs against the main protease of Omicron variant using in silico studies. Phys Chem Chem Phys 2024; 26:14006-14017. [PMID: 38683190 DOI: 10.1039/d4cp01199f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
SARS-CoV-2 and its variants are crossing the immunity barrier induced through vaccination. Recent Omicron sub-variants are highly transmissible and have a low mortality rate. Despite the low severity of Omicron variants, these new variants are known to cause acute post-infectious syndromes. Nowadays, novel strategies to develop new potential inhibitors for SARS-CoV-2 and other Omicron variants have gained prominence. For viral replication and survival the main protease of SARS-CoV-2 plays a vital role. Peptide-like inhibitors that mimic the substrate peptide have already proved to be effective in inhibiting the Mpro of SARS-CoV-2 variants. Our systematic canonical amino acid point mutation analysis on the native peptide has revealed various ways to improve the native peptide of the main protease. Multi mutation analysis has led us to identify and design potent peptide-analog inhibitors that act against the Mpro of the Omicron sub-variants. Our in-depth analysis of all-atom molecular dynamics studies has paved the way to characterize the atomistic behavior of Mpro in Omicron variants. Our goal is to develop potent peptide-analogs that could be therapeutically effective against Omicron and its sub-variants.
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Affiliation(s)
- Stanly Paul M L
- Institute of Pharmaceutical Analysis, University of Szeged, Eotvos u. 6, G-6720 Szeged, Hungary.
| | - Sonia Kumari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Mohali 160062, India.
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary.
| | - Elizabeth Sobhia M
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Mohali 160062, India.
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6
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Han M, Sun C, Bu Y, Zhu W, Li X, Zhang Y, Li J. Exploring the interaction mechanism of chlorogenic acid and myoglobin: Insights from structure and molecular dynamics simulation. Food Chem 2024; 438:138053. [PMID: 38007953 DOI: 10.1016/j.foodchem.2023.138053] [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: 08/18/2023] [Revised: 10/28/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
This study focused on non-covalent complex of myoglobin-chlorogenic acid (Mb-CA) and the changes in conformation, oxidation, and microstructure induced by varying concentrations of CA (10-40 μmol/g Mb). Employing molecular docking and dynamics simulations, further insights into the interaction between Mb and CA were obtained. The findings revealed that different CA concentrations enhanced Mb's thermal stability, while diminishing particle size, solubility, and relative content of metmyoglobin (MetMb%). The optimal interaction occurred at 40 μmol/g Mb. Furthermore, CA exhibited static quenching of Mb, with thermodynamic analysis confirming a 1:1 complex formation. These insights deepen our understanding of interaction between Mb and CA, providing valuable clarity.
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Affiliation(s)
- Menglin Han
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning, PR China; Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Chaonan Sun
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning, PR China
| | - Ying Bu
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning, PR China; College of Food Science, Fujian Agriculture and Forestry University, Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, Fujian, PR China.
| | - Wenhui Zhu
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning, PR China.
| | - Xuepeng Li
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning, PR China
| | - Yi Zhang
- College of Food Science, Fujian Agriculture and Forestry University, Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, Fujian, PR China
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning, PR China
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7
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Wu S, Sheng L, Kou G, Tian R, Ye Y, Wang W, Sun J, Ji J, Shao J, Zhang Y, Sun X. Double phage displayed peptides co-targeting-based biosensor with signal enhancement activity for colorimetric detection of Staphylococcus aureus. Biosens Bioelectron 2024; 249:116005. [PMID: 38199079 DOI: 10.1016/j.bios.2024.116005] [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: 11/21/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
The development of simple, fast, sensitive, and specific strategies for the detection of foodborne pathogenic bacteria is crucial for ensuring food safety and promoting human health. Currently, detection methods for Staphylococcus aureus still suffer from issues such as low specificity and low sensitivity. To address this problem, we proposed a sensitivity enhancement strategy based on double phage-displayed peptides (PDPs) co-targeting. Firstly, we screened two PDPs and analyzed their binding mechanisms through fluorescent localization, pull-down assay, and molecular docking. The two PDPs target S. aureus by binding to specific proteins on its outer membrane. Based on this phenomenon, a convenient and sensitive double PDPs colorimetric biosensor was developed. Double thiol-modified phage-displayed peptides (PDP-SH) enhance the aggregation of gold nanoparticles (AuNPs), whereas the specific interaction between the double PDPs and bacteria inhibits the aggregation of AuNPs, resulting in an increased visible color change before and after the addition of bacteria. This one-step colorimetric approach displayed a high sensitivity of 2.35 CFU/mL and a wide detection range from 10-2 × 108 CFU/mL. The combination with smartphone-based image analysis improved the portability of this method. This strategy achieves the straightforward, highly sensitive and portable detection of pathogenic bacteria.
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Affiliation(s)
- Shang Wu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Lina Sheng
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Guocheng Kou
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Run Tian
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Yongli Ye
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Weiya Wang
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Jiadi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Jian Ji
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Jingdong Shao
- Comprehensive Technology Center of Zhangjiagang Customs, Zhangjiagang, Jiangsu, 215600, China
| | - Yinzhi Zhang
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiulan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China.
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8
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Zhang W, Zhuang S, Guan H, Li F, Zou H, Li D. New insights into the anti-apoptotic mechanism of natural polyphenols in complex with Bax protein. J Biomol Struct Dyn 2024; 42:3081-3093. [PMID: 37184126 DOI: 10.1080/07391102.2023.2212066] [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: 10/28/2022] [Accepted: 05/01/2023] [Indexed: 05/16/2023]
Abstract
Excessive apoptosis can kill normal cells and lead to liver damage, heart failure and neurodegenerative diseases. Polyphenols are secondary metabolites of plants that can interact with proteins to inhibit toxins and disease-related apoptosis. Bax is the major pro-apoptotic protein that disrupts the outer mitochondrial membrane to induce apoptosis, but limited studies have focused on the interaction between polyphenols and Bax and the associated anti-apoptotic mechanisms, especially at the atomic level. In this article, we collected 69 common polyphenols for active ingredient screening targeting Bax. Polyphenols with better and worse molecular docking scores were selected, and their anti-apoptosis effects were compared using the H2O2-induced HepG2 cell model. The interactions between the selected polyphenols and Bax protein were analyzed using molecular dynamics simulation to explore the molecular mechanism underlying the anti-apoptosis effect. Secoisolariciresinol diglucoside (SDG) and Epigallocatechin-3-gallate (EGCG) with the best affinity for Bax (-6.76 and -6.52 kcal/mol) reduced the expression of cytochrome c and caspase 3, decreasing the apoptosis rate from 52 to 11% and 12%. Molecular dynamics simulation results showed that Bim unfolded the α1-α2 loop of Bax, and disrupted the non-bond interactions between the loop (Pro-43, Glu-44 and Leu-45) and surface (Ile-133, Arg-134 and Met-137) residues, with binding free energy changed from -15.0 to 0 kJ/mol. The hydrogen bonds and van der Waals interactions formed between polyphenols and Bax prevented the unfolding of the loop. Taken together, our results proved that polyphenols can inhibit apoptosis by maintaining the unactivated conformation of Bax to reduce outer mitochondrial membrane damage.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wenyuan Zhang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian, China
| | | | - Hui Guan
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian, China
| | - Feng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian, China
| | - Hui Zou
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian, China
| | - Dapeng Li
- Qingdao Institute for Food and Drug Control, Qingdao, China
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9
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Yu Z, Lv H, Zhou M, Fu P, Zhao W. Identification and molecular docking of tyrosinase inhibitory peptides from allophycocyanin in Spirulina platensis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:3648-3653. [PMID: 38224494 DOI: 10.1002/jsfa.13249] [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: 10/02/2023] [Revised: 12/22/2023] [Accepted: 01/15/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Tyrosinase, a copper-containing metalloenzyme with catalytic activity, is widely found in mammals. It is the key rate-limiting enzyme that catalyzes melanin synthesis. For humans, tyrosinase is beneficial to the darkening of eyes and hair. However, excessive deposition of melanin in the skin can lead to dull skin color and lead to pigmentation. Therefore, many skin-whitening compounds have been developed to decrease tyrosinase activity. This study aimed to identify a new tyrosinase inhibitory peptide through enzymatic hydrolysis, in vitro activity verification, molecular docking, and molecular dynamics (MD) simulation. RESULTS A tripeptide Asp-Glu-Arg (DER) was identified, with a '-CDOCKER_Energy' value of 121.26 Kcal mol-1 . DER has effective tyrosinase inhibitory activity. Research shows that its half maximal inhibitory concentration value is 1.04 ± 0.01 mmol L-1 . In addition, DER binds to tyrosinase residues His85, His244, His259, and Asn260, which are key residues that drive the interaction between the peptide and tyrosinase. Finally, through MD simulation, the conformational changes and structural stability of the complexes were further explored to verify and supplement the results of molecular docking. CONCLUSION This experiment shows that DER can effectively inhibit tyrosinase activity. His244, His259, His260, and Asn260 are the critical residues that drive the interaction between the peptide and tyrosinase, and hydrogen bonding is an important force. DER from Spirulina has the potential to develop functional products with tyrosinase inhibition. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Zhipeng Yu
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Hong Lv
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Mingjie Zhou
- School of Food Science and Engineering, Bohai University, Jinzhou, P. R. China
| | - Pengcheng Fu
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Wenzhu Zhao
- School of Food Science and Engineering, Hainan University, Haikou, P. R. China
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10
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Kong X, Wang W, Zhong Y, Wang N, Bai K, Wu Y, Qi Q, Zhang Y, Liu X, Xie J. Recent advances in the exploration and discovery of SARS-CoV-2 inhibitory peptides from edible animal proteins. Front Nutr 2024; 11:1346510. [PMID: 38389797 PMCID: PMC10883054 DOI: 10.3389/fnut.2024.1346510] [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: 12/01/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), is spreading worldwide. Although the COVID-19 epidemic has passed its peak of transmission, the harm it has caused deserves our attention. Scientists are striving to develop medications that can effectively treat COVID-19 symptoms without causing any adverse reactions. SARS-CoV-2 inhibitory peptides derived from animal proteins have a wide range of functional activities in addition to safety. Identifying animal protein sources is crucial to obtaining SARS-CoV-2 inhibitory peptides from animal sources. This review aims to reveal the mechanisms of action of these peptides on SARS-CoV-2 and the possibility of animal proteins as a material source of SARS-CoV-2 inhibitory peptides. Also, it introduces the utilization of computer-aided design methods, phage display, and drug delivery strategies in the research on SARS-CoV-2 inhibitor peptides from animal proteins. In order to identify new antiviral peptides and boost their efficiency, we recommend investigating the interaction between SARS-CoV-2 inhibitory peptides from animal protein sources and non-structural proteins (Nsps) using a variety of technologies, including computer-aided drug approaches, phage display techniques, and drug delivery techniques. This article provides useful information for the development of novel anti-COVID-19 drugs.
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Affiliation(s)
- Xiaoyue Kong
- College of Food and Health, Zhejiang Agriculture and Forestry University, Hangzhou, China
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Wei Wang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yizhi Zhong
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Nan Wang
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Kaiwen Bai
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yi Wu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Qianhui Qi
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yu Zhang
- Institute of Quality and Standard for Agriculture Products, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Xingquan Liu
- College of Food and Health, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Junran Xie
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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11
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Zhao S, Ma S, Zhang Y, Gao M, Luo Z, Cai S. Combining molecular docking and molecular dynamics simulation to discover four novel umami peptides from tuna skeletal myosin with sensory evaluation validation. Food Chem 2024; 433:137331. [PMID: 37678119 DOI: 10.1016/j.foodchem.2023.137331] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/28/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Umami peptides are an important component of food flavoring agents and have high nutritional value. This work aimed to identify umami peptides from tuna skeletal myosin using a new model method of computer simulation, explore their umami mechanism, and further validate the umami tastes with sensory evaluation. Umami peptides LADW, MEIDD, VAEQE, and EEAEGT were discovered, and all of them bound to taste type 1 receptor 1 and receptor 3 via hydrogen bonds and van der Waals forces to form stable complexes. LADW exhibited the best affinity energy and binding capability. Sensory evaluation and electronic tongue confirmed that all peptides possessed an umami taste, and LADW exhibited the strongest umami intensity. This study not only explored four novel umami peptides to improve the value of tuna skeletal myosin but also provided a new method for the rapid discovery of umami peptides.
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Affiliation(s)
- Shuai Zhao
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, People's Republic of China, 650500
| | - Shuang Ma
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, People's Republic of China, 650500
| | - Yuanyue Zhang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, People's Republic of China, 650500
| | - Ming Gao
- China National Research Institute of Food & Fermentation Industries CO., LTD, Beijing, People's Republic of China, 100048
| | - Zhenyu Luo
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, People's Republic of China, 650500
| | - Shengbao Cai
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, People's Republic of China, 650500.
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12
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Dinata R, Nisa N, Arati C, Rasmita B, Uditraj C, Siddhartha R, Bhanushree B, Saeed-Ahmed L, Manikandan B, Bidanchi RM, Abinash G, Pori B, Khushboo M, Roy VK, Gurusubramanian G. Repurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods. J Biomol Struct Dyn 2024; 42:43-81. [PMID: 37021347 DOI: 10.1080/07391102.2023.2192797] [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: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
The COVID-19 pandemic has caused adverse health (severe respiratory, enteric and systemic infections) and environmental impacts that have threatened public health and the economy worldwide. Drug repurposing and small molecule multi-target directed herbal medicine therapeutic approaches are the most appropriate exploration strategies for SARS-CoV-2 drug discovery. This study identified potential multi-target-directed Parkia bioactive entities against SARS-CoV-2 receptors (S-protein, ACE2, TMPRSS2, RBD/ACE2, RdRp, MPro, and PLPro) using ADMET, drug-likeness, molecular docking (AutoDock, FireDock and HDOCK), molecular dynamics simulation and MM-PBSA tools. One thousand Parkia bioactive entities were screened out by virtual screening and forty-five bioactive phytomolecules were selected based on favorable binding affinity and acceptable pharmacokinetic and pharmacodynamics properties. The binding affinity values of Parkia phyto-ligands (AutoDock: -6.00--10.40 kcal/mol; FireDock: -31.00--62.02 kcal/mol; and HDOCK: -150.0--294.93 kcal/mol) were observed to be higher than the reference antiviral drugs (AutoDock: -5.90--9.10 kcal/mol; FireDock: -35.64--59.35 kcal/mol; and HDOCK: -132.82--211.87 kcal/mol), suggesting a potent modulatory action of Parkia bioactive entities against the SARS-CoV-2. Didymin, rutin, epigallocatechin gallate, epicatechin-3-0-gallate, hyperin, ursolic acid, lupeol, stigmasta-5,24(28)-diene-3-ol, ellagic acid, apigenin, stigmasterol, and campesterol strongly bound with the multiple targets of the SARS-CoV-2 receptors, inhibiting viral entry, attachment, binding, replication, transcription, maturation, packaging and spread. Furthermore, ACE2, TMPRSS2, and MPro receptors possess significant molecular dynamic properties, including stability, compactness, flexibility and total binding energy. Residues GLU-589, and LEU-95 of ACE2, GLN-350, HIS-186, and ASP-257 of TMPRSS2, and GLU-14, MET-49, and GLN-189 of MPro receptors contributed to the formation of hydrogen bonds and binding interactions, playing vital roles in inhibiting the activity of the receptors. Promising results were achieved by developing multi-targeted antiviral Parkia bioactive entities as lead and prospective candidates under a small molecule strategy against SARS-CoV-2 pathogenesis. The antiviral activity of Parkia bioactive entities needs to be further validated by pre-clinical and clinical trials.
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Affiliation(s)
- Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Nisekhoto Nisa
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Chettri Arati
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Chetia Uditraj
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | | | | | - Bose Manikandan
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Giri Abinash
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Buragohain Pori
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Maurya Khushboo
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Vikas Kumar Roy
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
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13
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Zhao J, Wang S, Jiang D, Lu Y, Chen Y, Tang Y, Tang J, Jiang Z, Lin H, Dong W. Unravelling the interaction between α-SOH and myofibrillar protein based on spectroscopy and molecular dynamics simulation. Food Chem X 2023; 20:100986. [PMID: 38144868 PMCID: PMC10740131 DOI: 10.1016/j.fochx.2023.100986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/07/2023] [Accepted: 11/06/2023] [Indexed: 12/26/2023] Open
Abstract
This work systematically investigated the dose-response interaction between hydroxy-α-sanshool (α-SOH) and pork myofibrillar proteins (MPs) via spectroscopy, molecular docking, and molecular dynamics simulation methods. Results showed that MPs bound with low α-SOH can enhance the surface hydrophobicity and particle size of MPs, whereas high concentrations were exactly the opposite. The main interaction force in α-SOH/MPs complex changed from hydrophobic to hydrogen bonding with increased α-SOH. α-SOH causes tryptophan quenching and bring about a red shift at low concentration, as well as to promote α-helix conversion into β-sheet in MPs. Simultaneously, molecular docking and dynamics simulations verified that hydrogen bonding and hydrophobic forces were the main contributors to α-SOH/MPs complex, indicating that the binding of α-SOH with MPs proceeded spontaneously with high intensity, in which TYR286 contributed the most significant energy. Therefore, revealing the binding mechanism of α-SOH and MPs can contribute to the deep processing of numbing meat products.
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Affiliation(s)
- Jie Zhao
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Shuaiqian Wang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Diandian Jiang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yan Lu
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yu Chen
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yong Tang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Jie Tang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Zhenju Jiang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Hongbin Lin
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Wei Dong
- Beijing Laboratory of Food Quality and Safety/Key Laboratory of Alcoholic Beverages Quality and Safety of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
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14
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Liang R, Xu L, Fan C, Cao L, Guo X. Structural Characteristics and Antioxidant Mechanism of Donkey-Hide Gelatin Peptides by Molecular Dynamics Simulation. Molecules 2023; 28:7975. [PMID: 38138465 PMCID: PMC10745372 DOI: 10.3390/molecules28247975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
This study aimed to explore the structural characteristics and antioxidant mechanism of donkey-hide gelatin peptides. After hydrolysis and ultrafiltration treatment, five gelatin peptides with different molecular weights (MWs) were obtained. Amino acid analysis showed that gelatin peptides with different MWs contained a large number of amino acids, including G, P, E, N, A, and R, and differences were noted in the content of various amino acids. Fourier transform infrared spectroscopy and circular dichroism revealed that these gelatin peptides differed in terms of the peak strength of functional groups and number of secondary structures. Moreover, 26 pentapeptides/hexapeptides were identified. Among them, we investigated by molecular docking how PGPAP, which has the best antioxidant activity, may interact with the Keap1 protein. The results showed that the PGPAP-Keap1 complex had a stable conformation, and Arg415, Gly462, Phe478, and Tyr572 were the key residues involved in the binding of the peptide PGPAP to Keap1. Our results demonstrated that PGPAP could serve as a bioactive peptide with antioxidant activity.
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Affiliation(s)
| | | | | | | | - Xingfeng Guo
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng 252059, China; (R.L.); (L.X.); (C.F.); (L.C.)
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15
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Serseg T, Linani A, Benarous K, Goumri-Said S. Repurposing antibiotics as potent multi-drug candidates for SARS-CoV-2 delta and omicron variants: molecular docking and dynamics. J Biomol Struct Dyn 2023; 41:10377-10387. [PMID: 36541102 DOI: 10.1080/07391102.2022.2157876] [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: 06/22/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
There is a daunting public health emergency due to the emergence and rapid global spread of the new omicron variants of SARS-CoV-2. The variants differ in many characteristics, such as transmissibility, antigenicity and the immune system of the human hosts' shifting responses. This change in characteristics raises concern, as it leads to unknown consequences and also raises doubts about the efficacy of the currently available vaccines. As of March 2022, there are five variants of SARS-CoV-2 disseminating: the alpha, the beta, the gamma, the delta and the omicron variant. The omicron variant has more than 30 mutations on the spike protein, which is used by the virus to enter the host cell and is also used as a target for the vaccines. In this work, we studied the possible anti-COVID-19 effect of two molecules by molecular docking using Autodock Vina and molecular dynamic simulations using Gromacs 2020 software. We docked amoxicillin and clavulanate to the main protease (Mpro), the RNA-dependent RNA polymerase (RdRp) and the spike protein receptor-binding domain (SRBD) of the wild type with the two variants (delta and omicron) of SARS-CoV-2. The docking results show that the ligands bound tightly with the SRBD of the omicron variant, while the dynamic simulation revealed the ability of amoxicillin to bind to the SRBD of both variants' delta and omicron. The high number of mutations that occurred in both variants increases the affinity of amoxicillin towards them.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Talia Serseg
- Département des Sciences Naturelles, Ecole Normale Supérieure de Laghouat, Laghouat, Algeria
- Laboratoire des Sciences Appliquées et Didactiques, Ecole Normale Supérieure de Laghouat, Laghouat, Algeria
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Abderahmane Linani
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
- Biology Department, Amar Telidji University, Laghouat, Algeria
| | - Khedidja Benarous
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
- Biology Department, Amar Telidji University, Laghouat, Algeria
| | - Souraya Goumri-Said
- College of Science, Physics Department, Alfaisal University, Riyadh, Saudi Arabia
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16
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Li Z, Yang B, Ding Y, Meng J, Hu J, Zhou X, Liu L, Wu Z, Yang S. Insights into a class of natural eugenol and its optimized derivatives as potential tobacco mosaic virus helicase inhibitors by structure-based virtual screening. Int J Biol Macromol 2023; 248:125892. [PMID: 37473893 DOI: 10.1016/j.ijbiomac.2023.125892] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Plant diseases caused by malignant and refractory phytopathogenic viruses have considerably restricted crop yields and quality. To date, drug design targeting functional proteins or enzymes of viruses is an efficient and viable strategy to guide the development of new pesticides. Herein, a series of novel eugenol derivatives targeting the tobacco mosaic virus (TMV) helicase have been designed using structure-based virtual screening (SBVS). Structure-activity relationship indicated that 2 t displayed the most powerful bonding capability (Kd = 0.2 μM) along with brilliant TMV helicase ATPase inhibitory potency (IC50 = 141.9 μM) and applausive anti-TMV capability (EC50 = 315.7 μg/mL), ostentatiously outperforming that of commercial Acyclovir (Kd = 23.0 μM, IC50 = 183.7 μM) and Ribavirin (EC50 = 624.3 μg/mL). Molecular dynamics simulations and docking suggested ligand 2 t was stable and bound in the active pocket of the TMV helicase by multiple interactions. Given these superior properties, eugenol-based derivatives could be considered as the novel potential plant viral helicase inhibitors. Furthermore, this effective and feasible SBVS strategy established a valuable screening platform for helicase-targeted drug development.
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Affiliation(s)
- Zhenxing Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Binxin Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Yue Ding
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jiao Meng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jinhong Hu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Liwei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhibing Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China.
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17
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Zhang J, Li F, Shen S, Yang Z, Ji X, Wang X, Liao X, Zhang Y. More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review. Food Chem 2023; 416:135726. [PMID: 36893635 DOI: 10.1016/j.foodchem.2023.135726] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
The investigation of intermolecular interactions has become increasingly important in many studies, mainly by combining different analytical approaches to reveal the molecular mechanisms behind specific experimental phenomena. From spectroscopic analysis to sophisticated molecular simulation techniques like molecular docking, molecular dynamics (MD) simulation, and quantum chemical calculations (QCC), the mechanisms of intermolecular interactions are gradually being characterized more clearly and accurately, leading to revolutionary advances. This article aims to review the progression in the main techniques involving intermolecular interactions in food research and the corresponding experimental results. Finally, we discuss the significant impact that cutting-edge molecular simulation technologies may have on the future of conducting deeper exploration. Applications of molecular simulation technology may revolutionize the food research, making it possible to design new future foods with precise nutrition and desired properties.
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Affiliation(s)
- Jinghao Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Fangwei Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China; College of Food Science and Engineering, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Suxia Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Zhaotian Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xingyu Ji
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xiao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Yan Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China.
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18
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Prabakusuma AS, Wardono B, Fahlevi M, Zulham A, Djoko Sunarno MT, Syukur M, Aljuaid M, Saniuk S, Apriliani T, Pramoda R. A bibliometric approach to understanding the recent development of self-sufficient fish feed production utilizing agri-food wastes and by-products towards sustainable aquaculture. Heliyon 2023; 9:e17573. [PMID: 37449123 PMCID: PMC10336519 DOI: 10.1016/j.heliyon.2023.e17573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
The global agri-food industry generates a large volume of waste annually, which causes both environmental and economic problems. Recently, there has been a growing interest in the use of agri-food wastes and by-products to produce self-sufficient fish feed. This study aimed to analyze the intellectual structure of the recent research on the utilization of agri-food wastes and by-products as self-sufficient fish feed materials based on 922 Scopus-indexed core collection documents from 252 journals written by 4420 authors from 73 countries with an annual growth rate of 18.65% over the last four years (2019-2022). This bibliometric study implemented knowledge domain visualization (KDV) using VOSViewer and Biblioshiny in the Bibliometrix R-package to investigate the basic scientometric profile of the selected fields. The results showed that Dawood M.A.O., with PageRanks of 0.0732, 19 total publications, 695 global citations from 2019 to 2022, and closeness values of 0.25, was the most productive author within the field. Subsequently, China was determined to be the most productive country (93 valid documents) and have the strongest collaboration network. Major research hotspots in the field included aquaculture and sustainable aquaculture, fish feed with agri-food waste, rainbow trout species, the development of a circular economy, probiotic applications, and cell signaling cytokines and peptides. This bibliometric study provides comprehensive information on the intellectual domain and research landscape on self-sufficient fish feed and also shows how interest in this research topic and similar ones is growing.
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Affiliation(s)
- Adhita Sri Prabakusuma
- Vocational School of Foodservice Industry, Food Biotechnology Research Group, Universitas Ahmad Dahlan, Yogyakarta 55166, Indonesia
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Budi Wardono
- Research Center for Cooperative, Corporation, and People's Economy, National Research and Innovation Agency, Jakarta 12710, Indonesia
| | - Mochammad Fahlevi
- Management Department, BINUS Online Learning, Bina Nusantara University, Jakarta 11480, Indonesia
| | - Armen Zulham
- Research Center for Cooperative, Corporation, and People's Economy, National Research and Innovation Agency, Jakarta 12710, Indonesia
| | - Mas Tri Djoko Sunarno
- Research Center for Fishery, National Research and Innovation Agency, Cibinong 16912, Indonesia
| | - Mat Syukur
- Research Center for Cooperative, Corporation, and People's Economy, National Research and Innovation Agency, Jakarta 12710, Indonesia
| | - Mohammed Aljuaid
- Department of Health Administration, College of Business Administration, King Saud University, Riyadh 12372, Saudi Arabia
| | - Sebastian Saniuk
- Department of Engineering Management and Logistic Systems, Faculty of Economics and Management, University of Zielona Góra, Zielona Góra 65-417, Poland
| | - Tenny Apriliani
- Research Center for Behavioral and Circular Economics, National Research and Innovation Agency, Jakarta 12710, Indonesia
| | - Radityo Pramoda
- Research Center for Behavioral and Circular Economics, National Research and Innovation Agency, Jakarta 12710, Indonesia
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19
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Wu Z, Xu J, Ruan J, Chen J, Li X, Yu Y, Xie X, Tang J, Zhang D, Li H. Probing the mechanism of interaction between capsaicin and myofibrillar proteins through multispectral, molecular docking, and molecular dynamics simulation methods. Food Chem X 2023; 18:100734. [PMID: 37397215 PMCID: PMC10314199 DOI: 10.1016/j.fochx.2023.100734] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
The interaction between myofibrillar proteins (MPs) and capsaicin (CAP) was investigated using multispectral, molecular docking, and molecular dynamics simulation methods. The resulting complex increased the hydrophobicity of the tryptophan and tyrosine microenvironment as revealed by fluorescence spectral analysis. The fluorescence burst mechanism study indicated that the fluorescence burst of CAP on the MPs was a static one (Kq = 1.386 × 1012 m-1s-1) and that CAP could bind with MPs well (Ka = 3.31 × 104 L/mol, n = 1.09). The analysis of circular dichroism demonstrated that the interaction between CAP and MPs caused a decrease in the α-helical structure of MPs. The complexes formed exhibited lower particle size and higher absolute ζ potential. Furthermore, hydrogen bonding, van der Waals forces, and hydrophobic interactions were found to be the primary factors facilitating the interaction between CAP and MPs, as suggested by molecular docking models and molecular dynamics simulations.
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Affiliation(s)
- Zhicheng Wu
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Jingbing Xu
- Chongqing Institute for Food and Drug Control, Chongqing 401121, China
| | - Jinggang Ruan
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Jiaxin Chen
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Xue Li
- Agricultural Product Processing Institute, Chongqing Academy of Agricultural Science, Chongqing 401329, China
| | - Yiru Yu
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Xinrui Xie
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Jie Tang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Dong Zhang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
- Food Industry Collaborative Innovation Center, Xihua University, Chengdu 610039, China
| | - Hongjun Li
- College of Food Science, Southwest University, Chongqing 400715, China
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20
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Kan R, Yu Z, Zhao W. Identification and molecular action mechanism of novel TAS2R14 blocking peptides from egg white proteins. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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21
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Liu H, Zheng C, Li Z, Xia X, Jiang D, Wang W, Zhang R, Xiang X. Inhibitory mechanism of phenolic compounds in rapeseed oil on α-amylase and α-glucosidase: Spectroscopy, molecular docking, and molecular dynamic simulation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 289:122251. [PMID: 36542921 DOI: 10.1016/j.saa.2022.122251] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/24/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Developing naturally active components to control α-amylase/α-glucosidase activity is highly desired for preventing and managing type 2 diabetes. Rapeseed oil is rich in active phenolic compounds and seed oil is a major source of liposoluble inhibitors to these enzymes. However, it remains unclear about the interaction of phenolic compounds in rapeseed oil with α-amylase/α-glucosidase. This study found that the important phenolic compounds from rapeseed oil (Sinapic acid, SA; canolol, CAO; canolol dimer, CAO dimer) possessed effective inhibition performance against α-amylase and α-glucosidase. CAO showed the lowest and highest inhibitory effect, respectively. In the kinetics studies, the inhibition mechanism of SA/CAO/CAO dimer against α-glucosidase was non-competitive, exhibiting a different way from α-amylase. Fluorescence quenching spectra implied that the static processes were responsible for the spontaneous binding between the compounds and enzymes. Fourier-transform infrared spectroscopy (FT-IR) displayed these compounds-induced conformation alterations of α-amylase/α-glucosidase. Molecular docking revealed that SA/CAO/CAO dimer decreased the catalytic efficiency of α-amylase/α-glucosidase through hydrogen bonds, hydrophobic force, or π-π interaction. Molecular dynamics matched well with the experimental and docking results regarding the inhibitory behaviors and interactions toward α-amylase/α-glucosidase. These results demonstrated the potential benefits of phenolic compounds from rapeseed oil in antidiabetic-related activities.
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Affiliation(s)
- Huihui Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Key Laboratory of Oilseeds Processing, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Chang Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Key Laboratory of Oilseeds Processing, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Ziliang Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Key Laboratory of Oilseeds Processing, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Xiaoyang Xia
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Key Laboratory of Oilseeds Processing, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Dan Jiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Key Laboratory of Oilseeds Processing, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Wen Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Key Laboratory of Oilseeds Processing, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Ruiying Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Key Laboratory of Oilseeds Processing, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Xia Xiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Key Laboratory of Oilseeds Processing, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China.
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22
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Han J, Geng L, Lu C, Zhou J, Li Y, Ming T, Zhang Z, Su X. Analyzing the mechanism by which oyster peptides target IL-2 in melanoma cell apoptosis based on RNA-seq and m6A-seq. Food Funct 2023; 14:2362-2373. [PMID: 36779260 DOI: 10.1039/d2fo03672j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Melanoma is a kind of skin cancer with high malignancy and strong proliferation and invasion abilities. Chemotherapy drugs in the clinic have the disadvantages of high price and high toxicity. Peptides are natural active ingredients that have many functions and are safe and effective. Previous studies have shown that oysters are rich in protein and have antitumor effects. In this study, a high-throughput strategy combined with MALDI TOF/TOF-MS and molecular docking was developed to screen peptides with antitumor functions from oyster hydrolysate. Three dominant peptides were predicted to have similar functions to IL-2 via molecular docking. Then, the activity of the peptides was confirmed in B16 cells, and we found that the three peptides increased the apoptosis of B16 cells. Furthermore, via RNA-seq and m6A-seq of B16 cells treated with the peptides, we found that ILADSAPR downregulates the expression of Pcna, Tlr4, and Ncbp2 and upregulates the expression of Bax, Bad, Pak4, Rasa2, Cct6, and Gbp2. ILADSAPR inhibited B16 cell proliferation and promoted cell apoptosis by regulating the expression of these genes. In addition, the result of metabolic pathway analysis also proved this point. This study provides a preliminary reference for antitumor research on oyster peptides.
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Affiliation(s)
- Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China. .,School of Marine Science, Ningbo University, Ningbo, China
| | - Lingxin Geng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China. .,School of Marine Science, Ningbo University, Ningbo, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China. .,School of Marine Science, Ningbo University, Ningbo, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China. .,School of Marine Science, Ningbo University, Ningbo, China
| | - Ye Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China. .,School of Marine Science, Ningbo University, Ningbo, China
| | - Tinghong Ming
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China. .,School of Marine Science, Ningbo University, Ningbo, China
| | - Zhen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China. .,School of Marine Science, Ningbo University, Ningbo, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China. .,School of Marine Science, Ningbo University, Ningbo, China
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23
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Ye H, Xu Y, Sun Y, Liu B, Chen B, Liu G, Cao Y, Miao J. Purification, identification and hypolipidemic activities of three novel hypolipidemic peptides from tea protein. Food Res Int 2023; 165:112450. [PMID: 36869471 DOI: 10.1016/j.foodres.2022.112450] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
In this study, hypolipidemic peptides were obtained from tea protein by enzymatic hydrolysis, ultrafiltration and high-performance liquid chromatography. Subsequently, the hypolipidemic peptides were identified by mass spectrometry and screened through molecular docking technology, and the hypolipidemic activities and mechanisms of the active peptides were explored. The results showed that the hydrolysate of hypolipidemic peptides obtained by pepsin hydrolysis for 3 h had good bile salt binding ability. After purification, identification and molecular docking screening, three novel hypolipidemic peptides FLF, IYF and QIF were obtained. FLF, IYF and QIF can interact with the receptor proteins 1LPB and 1F6W through hydrogen bonds, π-π bonds, hydrophobic interactions and van der Waals forces, thus exerting hypolipidemic activities. Activity studies showed that, compared with the positive controls, FLF, IYF and QIF had excellent sodium taurocholate binding abilities, pancreatic lipase inhibitory activities and cholesterol esterase inhibitory activities. Moreover, FLF, IYF and QIF can effectively inhibit lipogenic differentiation of 3T3-L1 preadipocytes, reduce intracellular lipid and low-density lipoprotein content and increase high-density lipoprotein content. These results indicated that the three novel hypolipidemic peptides screened in this study had excellent hypolipidemic activities and were expected to be used as natural-derived hypolipidemic active ingredients for the development and application in functional foods.
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Affiliation(s)
- Haoduo Ye
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangzhou 510642, China
| | - Yan Xu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, China
| | - Yunnan Sun
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Laboratory of Tea Science, Menghai 666201, China
| | - Benying Liu
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Laboratory of Tea Science, Menghai 666201, China
| | - Bingbing Chen
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangzhou 510642, China
| | - Guo Liu
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangzhou 510642, China
| | - Yong Cao
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangzhou 510642, China
| | - Jianyin Miao
- College of Food Science, South China Agricultural University, Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang 438000, China.
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24
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Yu Y, Xu S, He R, Liang G. Application of Molecular Simulation Methods in Food Science: Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2684-2703. [PMID: 36719790 DOI: 10.1021/acs.jafc.2c06789] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.
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Affiliation(s)
- Yuandong Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Shiqi Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Ran He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
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25
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Yu Z, Wang Y, Shuian D, Liu J, Zhao W. Identification and Molecular Mechanism of Novel Immunomodulatory Peptides from Gelatin Hydrolysates: Molecular Docking, Dynamic Simulation, and Cell Experiments. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2924-2934. [PMID: 36748803 DOI: 10.1021/acs.jafc.2c06982] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The purpose of this study was to identify donkey-hide gelatin-derived immunomodulatory peptides targeting Toll-like receptor 4-myeloid differentiation 2 (TLR4-MD2) and elucidate their binding modes using physicochemical property prediction, molecular docking, molecular dynamics simulations, and in vitro cell experiments. After hydrolyzing gelatin, 519 peptides were identified by liquid chromatography-tandem mass spectrometry. Peptides VQLSGEEK and GFSGLDGAKG bound to TLR4-MD2 with high binding affinity. In TLR4-MD2, Arg90, Ser118, Phe126, Tyr131, and Arg264 were key residues involved in the binding of these peptides. The RMSD and Rg values demonstrated that VQLSGEEK-TLR4-MD2 and GFSGLDGAKG-TLR4-MD2 complexes had stable and compact conformations. VQLSGEEK and GFSGLDGAKG were found to increase the cell viability and phagocytic activity of RAW264.7 macrophages; significantly promote the production of cytokines TNF-α, IL-1β, and IL-6 in cells; and inhibit the overproduction of nitric oxide (NO) and cytokines in lipopolysaccharide (LPS)-induced RAW264.7 cells. Our results provided preliminary evidence that VQLSGEEK and GFSGLDGAKG could function as two-way immunomodulatory peptides with immunostimulatory and anti-inflammatory activities.
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Affiliation(s)
- Zhipeng Yu
- School of Food Science and Engineering, Hainan University, Haikou 570228, P. R. China
| | - Yingxue Wang
- College of Food Science and Engineering, Bohai University, Jinzhou 121013, P. R. China
| | - David Shuian
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, P. R. China
| | - Jingbo Liu
- Lab of Nutrition and Functional Food, Jilin University, Changchun 130062, P. R. China
| | - Wenzhu Zhao
- School of Food Science and Engineering, Hainan University, Haikou 570228, P. R. China
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26
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Pang C, Liu S, Zhang G, Zhou J, Du G, Li J. Improving the catalytic efficiency of Pseudomonas aeruginosa lipoxygenase by semi-rational design. Enzyme Microb Technol 2023; 162:110120. [DOI: 10.1016/j.enzmictec.2022.110120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
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27
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Lyu S, Yang Q, Duan X, Liu X, Du Z, Shang X, Xu M, Liu J, Pan F, Zhang T. Protective effects and potential mechanisms of fermented egg-milk peptides on the damaged intestinal barrier. Front Nutr 2022; 9:1068877. [PMID: 36570170 PMCID: PMC9767966 DOI: 10.3389/fnut.2022.1068877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Fermented egg-milk peptides (FEMPs) could enhance the colon-intestinal barrier and upgrade the expression of zonula occludens-1 and mucin 2. Besides, the underlying biological mechanism and the targets FEMPs could regulate were analyzed in our study. Methods Herein, the immunofluorescence technique and western blot were utilized to evaluate the repair of the intestinal barrier. Network pharmacology analysis and bioinformatics methods were performed to investigate the targets and pathways affected by FEMPs. Results and discussion Animal experiments showed that FEMPs could restore intestinal damage and enhance the expression of two key proteins. The pharmacological results revealed that FEMPs could regulate targets related to kinase activity, such as AKT, CASP, RAF, and GSK. The above targets could interact with each other. GO analysis indicated that the targets regulated by FEMPs could participate in the kinase activity of the metabolic process. KEGG enrichment revealed that the core targets were enriched in pathways related to cell apoptosis and other important procedures. Molecular docking demonstrated that FEMPs could bind to the key target AKT via hydrogen bond interactions. Our study combined the experiment in vivo with the method in silico and investigated the interaction between peptides and targets in a pattern of multi-targets and multi-pathways, which offered a new perspective on the functional validation and potential application of bioactive peptides.
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Affiliation(s)
- Siwen Lyu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Qi Yang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Xuehui Duan
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Xuanting Liu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Zhiyang Du
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Xiaomin Shang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Menglei Xu
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, China
| | - Jingbo Liu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Fengguang Pan
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China,Fengguang Pan
| | - Ting Zhang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, College of Food Science and Engineering, Jilin University, Changchun, China,*Correspondence: Ting Zhang
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28
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Yu Z, Cao Y, Kan R, Ji H, Zhao W, Wu S, Liu J, Shiuan D. Identification of egg protein-derived peptides as xanthine oxidase inhibitors: virtual hydrolysis, molecular docking, and in vitro activity evaluation. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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29
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Zhang W, Guan H, Huang D, Zou H, Li D. Effects of preheating temperatures on
β
‐lactoglobulin structure and binding interaction with dihydromyricetin. EFOOD 2022. [DOI: 10.1002/efd2.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Wenyuan Zhang
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
| | - Hui Guan
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
| | - Dongjie Huang
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
| | - Hui Zou
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
| | - Dapeng Li
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes Shandong Agricultural University Taian China
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30
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Xu J, Yang W, Pan Y, Xu H, He L, Zheng B, Xie Y, Wu X. Lucidenic acid A inhibits the binding of hACE2 receptor with spike protein to prevent SARS-CoV-2 invasion. Food Chem Toxicol 2022; 169:113438. [PMID: 36179993 PMCID: PMC9526994 DOI: 10.1016/j.fct.2022.113438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022]
Abstract
High infection caused by mutations of SARS-CoV-2 calls for new prevention strategy. Ganoderma lucidum known as a superior immunoenhancer exhibits various antiviral effects, whether it can resist SARS-CoV-2 remains unclear. Herein, virtual screening combined with in vitro hACE2 inhibition assays were used to investigate its anti SARS-CoV-2 effect. Potential 54 active components, 80 core targets and 20 crucial pathways were identified by the component-target-pathway network. The binding characters of these components to hACE2 and its complexes with spike protein including omicron variant was analyzed by molecular docking. Lucidenic acid A was selected as the top molecule with high affinity to all receptors by forming hydrogen bonds. Molecular dynamics simulation showed it had good binding stability with the receptor proteins. Finally, in vitro FRET test demonstrated it inhibited the hACE2 activity with IC50 2 μmol/mL. Therefore, lucidenic acid A can prevent the virus invasion by blocking hACE2 binding with SARS-CoV-2.
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Affiliation(s)
- Juan Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China
| | - WenTao Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China
| | - YiFeng Pan
- Hangzhou Xihu District Center for Disease Control and Prevention, Hangzhou, 310030, PR China
| | - HaiShun Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China
| | - Liang He
- Zhejiang Provincial Academy of Forestry, Hangzhou, 310000, Zhejiang, China
| | - BingSong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China
| | - YingQiu Xie
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - XueQian Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China; National Innovation Alliance of Lingzhi and Sanyeqing Industry, Lin'an, 311300, China.
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31
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Ji H, Yu Z, Zhao W. Colla corii asini–
derived peptides as tyrosinase inhibitors: Identification, inhibitory activity, and molecular mechanism. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.16095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Huizhuo Ji
- School of Food Science and Engineering Hainan University 570228 Haikou P.R. China
- School of Food and Health Beijing Technology and Business University, Bejing, 100048 China
| | - Zhipeng Yu
- School of Food Science and Engineering Hainan University 570228 Haikou P.R. China
| | - Wenzhu Zhao
- School of Food Science and Engineering Hainan University 570228 Haikou P.R. China
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32
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Chen H, Chen Y, Zheng H, Xiang X, Xu L. A novel angiotensin-I-converting enzyme inhibitory peptide from oyster: Simulated gastro-intestinal digestion, molecular docking, inhibition kinetics and antihypertensive effects in rats. Front Nutr 2022; 9:981163. [PMID: 36082025 PMCID: PMC9445672 DOI: 10.3389/fnut.2022.981163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, a novel peptide, AEYLCEAC with high angiotensin-I-converting enzyme inhibitory (ACEI) activity was screened from oyster (Crassostrea gigas) hydrolysates, which was obtained from simulated gastro-intestinal digestion. Candidate peptides were confirmed to have a higher binding to angiotensin-I-converting enzyme (ACE) than the positive drug phosphoinic tripeptide calculated by Discovery Studio, and AEYLCEAC showed the highest ACE inhibition rate in vitro with a IC50 of 4.287 mM. Lineweaver-Burk plots confirmed that the peptidic inhibitory type of ACE is competitive. The molecular docking showed that ACEI activity of the AEYLCEAC was mainly due to the hydrogen bonding interactions with the active pockets (S1 and S2) of ACE. In vivo, AEYLCEAC effectively reduced diastolic blood pressure (DBP) and Systolic blood pressure (SBP) in hypertensive rats. These results indicate that AEYLCEAC might act as a helpful ingredient in functional foods or pharmaceuticals for the prevention and treatment of hypertension.
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Affiliation(s)
- Hui Chen
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Hangzhou, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yu Chen
- Zhejiang Marine Fisheries Research Institute, Zhoushan, China
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhoushan, China
| | - Huizhen Zheng
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Xingwei Xiang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
- *Correspondence: Xingwei Xiang,
| | - Lu Xu
- Department of Animal Medicine, College of Agriculture and Forestry Science, Linyi University, Linyi, China
- Lu Xu,
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33
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Liu J, Ma P, Yu H, Wang M, Yin P, Pang S, Jiao Y, Dong T, Liu A. Discovery of a Phage Peptide Specifically Binding to the SARS-CoV-2 Spike S1 Protein for the Sensitive Phage-Based Enzyme-Linked Chemiluminescence Immunoassay of the SARS-CoV-2 Antigen. Anal Chem 2022; 94:11591-11599. [PMID: 35948070 PMCID: PMC9380820 DOI: 10.1021/acs.analchem.2c01988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic has led to a global crisis with devastating effects on public healthcare and the economy. Sensitive detection of SARS-CoV-2 is the key to diagnose and control its spread. The spike (S) protein is an abundant viral transmembrane protein and a suitable target protein for the selective recognition of SARS-CoV-2. Here, we report that with bovine serum albumin prescreening, a specific phage peptide targeting SARS-CoV-2 S1 protein was biopanned with the pIII phage display library. The identified phage #2 expressing the peptide (amino acid sequence: NFWISPKLAFAL) shows high affinity to the target with a dissociation constant of 3.45 ± 0.58 nM. Furthermore, the identified peptide shows good specificity with a binding site at the N-terminal domain of the S1 subunit through a hydrogen bond network and hydrophobic interaction, supported by molecular docking. Then, a sandwiched phage-based enzyme-linked chemiluminescence immunoassay (ELCLIA) was established by using phage #2 as a bifunctional probe capable of SARS-CoV-2 S1 antigen recognition and signal amplification. After optimizing the conditions, the proposed phage ELCLIA exhibited good sensitivity, and as low as 78 pg/mL SARS-CoV-2 S1 could be detected. This method can be applied to detect as low as 60 transducing units (TU)/mL SARS-CoV-2 pseudovirus in 50% saliva. Therefore, specific phage peptides have good prospects as powerful biological recognition probes for immunoassay detection and biomedical applications.
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Affiliation(s)
| | | | - Haipeng Yu
- Institute for Chemical Biology &
Biosensing, College of Life Sciences, Qingdao
University, 308 Ningxia Road, Qingdao 266071, China
| | - Mingyang Wang
- Institute for Chemical Biology &
Biosensing, College of Life Sciences, Qingdao
University, 308 Ningxia Road, Qingdao 266071, China
| | - Pengxue Yin
- Institute for Chemical Biology &
Biosensing, College of Life Sciences, Qingdao
University, 308 Ningxia Road, Qingdao 266071, China
| | - Shuang Pang
- Institute for Chemical Biology &
Biosensing, College of Life Sciences, Qingdao
University, 308 Ningxia Road, Qingdao 266071, China
| | - Yiming Jiao
- Institute for Chemical Biology &
Biosensing, College of Life Sciences, Qingdao
University, 308 Ningxia Road, Qingdao 266071, China
| | - Tao Dong
- Institute for Chemical Biology &
Biosensing, College of Life Sciences, Qingdao
University, 308 Ningxia Road, Qingdao 266071, China
| | - Aihua Liu
- Institute for Chemical Biology &
Biosensing, College of Life Sciences, Qingdao
University, 308 Ningxia Road, Qingdao 266071, China
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34
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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35
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Rathod NB, Elabed N, Özogul F, Regenstein JM, Galanakis CM, Aljaloud SO, Ibrahim SA. The Impact of COVID-19 Pandemic on Seafood Safety and Human Health. Front Microbiol 2022; 13:875164. [PMID: 35814679 PMCID: PMC9257084 DOI: 10.3389/fmicb.2022.875164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
The coronavirus disease (COVID-19) pandemic caused several negative impacts on global human health and the world’s economy. Food and seafood safety and security were among the principal challenges and causes of concern for the food industry and consumers during the spread of this global pandemic. This article focused on the effects of COVID-19 pandemic on potential safety issues with seafood products and their processing methods. Moreover, the potential impacts of coronavirus transmission through seafood on human health were evaluated. The role of authenticity, traceability, and antimicrobials from natural sources to preserve seafood and the possible interaction of functional foods on the human immune system are also discussed. Although seafood is not considered a principal vector of SARS-CoV-2 transmission, the possible infections through contaminated surfaces of such food products cannot be neglected. The positive effects of seafood consumption on possible immunity built up, and COVID-19 are also summarized.
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Affiliation(s)
- Nikheel Bhojraj Rathod
- Department of Post Harvest Management of Meat, Poultry and Fish, Post-graduate Institute of Post-harvest Management (Dr. Balasaheb Sawant Konkan Krishi Vidyapeeth), Raigad, India
| | - Nariman Elabed
- Laboratory of Protein Engineering and Bioactive Molecules (LIP-MB), National Institute of Applied Sciences and Technology (INSAT), University of Carthage, Carthage, Tunisia
| | - Fatih Özogul
- Department of Seafood Processing Technology, Faculty of Fisheries, Cukurova University, Adana, Turkey
- *Correspondence: Fatih Özogul,
| | - Joe M. Regenstein
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Charis M. Galanakis
- Research and Innovation Department, Galanakis Laboratories, Chania, Greece
- Food Waste Recovery Group, ISEKI Food Association, Vienna, Austria
| | - Sulaiman Omar Aljaloud
- College of Sports Science and Physical Activity, King Saud University, Riyadh, Saudi Arabia
| | - Salam A. Ibrahim
- Food Microbiology and Biotechnology Laboratory, 171 Carver Hall, College of Agriculture and Environmental Sciences, North Carolina A & T State University, Greensboro, NC, United States
- Salam A. Ibrahim,
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36
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Xue W, Liu X, Zhao W, Yu Z. Identification and molecular mechanism of novel tyrosinase inhibitory peptides from collagen. J Food Sci 2022; 87:2744-2756. [DOI: 10.1111/1750-3841.16160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/04/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Wenjun Xue
- College of Food Science and Engineering Bohai University Jinzhou P.R. China
| | - Xuan Liu
- College of Food Science and Engineering Bohai University Jinzhou P.R. China
| | - Wenzhu Zhao
- School of Food Science and Engineering Hainan University Haikou P.R. China
| | - Zhipeng Yu
- School of Food Science and Engineering Hainan University Haikou P.R. China
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37
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Molecular dynamics simulation of the interactions between sesamol and myosin combined with spectroscopy and molecular docking studies. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107801] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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38
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Chourasia R, Padhi S, Phukon LC, Abedin MM, Sirohi R, Singh SP, Rai AK. Peptide candidates for the development of therapeutics and vaccines against β-coronavirus infection. Bioengineered 2022; 13:9435-9454. [PMID: 35387556 PMCID: PMC9161909 DOI: 10.1080/21655979.2022.2060453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Betacoronaviruses (β-CoVs) have caused major viral outbreaks in the last two decades in the world. The mutation and recombination abilities in β-CoVs resulted in zoonotic diseases in humans. Proteins responsible for viral attachment and replication are highly conserved in β-CoVs. These conserved proteins have been extensively studied as targets for preventing infection and the spread of β-CoVs. Peptides are among the most promising candidates for developing vaccines and therapeutics against viral pathogens. The immunostimulatory and viral inhibitory potential of natural and synthetic peptides has been extensively studied since the SARS-CoV outbreak. Food-derived peptides demonstrating high antiviral activity can be used to develop effective therapeutics against β-CoVs. Specificity, tolerability, and customizability of peptides can be explored to develop potent drugs against β-CoVs. However, the proteolytic susceptibility and low bioavailability of peptides pose challenges for the development of therapeutics. This review illustrates the potential role of peptides in eliciting an adaptive immune response and inhibiting different stages of the β-CoV life cycle. Further, the challenges and future directions associated with developing peptide-based therapeutics and vaccines against existing and future β-CoV pathogens have been discussed.
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Affiliation(s)
- Rounak Chourasia
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India
| | - Ranjana Sirohi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, 02841, Republic of Korea
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing (DBT-CIAB), Sector-81, S.A.S. Nagar, Mohali- 140306, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong- 737102, India.,Institute of Bioresources and Sustainable Development (DBT-IBSD), Mizoram Node, Aizawl, India
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39
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Abstract
Over the past few months, numerous studies harnessed in silico methods such as molecular docking to evaluate food compounds for inhibitory activity against coronavirus infection and replication. These studies capitalize on the efficiency of computational methods to quickly guide subsequent research and examine diet-disease relationships, and their sudden widespread utility may signal new opportunities for future antiviral and bioactive food research. Using Coronavirus Disease 2019 (COVID-19) research as a case study, we herein provide an overview of findings from studies using molecular docking to study food compounds as potential inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), explore considerations for the critical interpretation of study findings, and discuss how these studies help shape larger conversations of diet and disease.
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40
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Vidal-Limon A, Aguilar-Toalá JE, Liceaga AM. Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:934-943. [PMID: 34990125 DOI: 10.1021/acs.jafc.1c06110] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In silico tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of in silico models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.
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Affiliation(s)
- Abraham Vidal-Limon
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - José E Aguilar-Toalá
- Departamento de Ciencias de la Alimentación, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Avenida de las Garzas 10, Colonia El Panteón, Lerma de Villada, Estado de México 52005, Mexico
| | - Andrea M Liceaga
- Protein Chemistry and Bioactive Peptides Laboratory. Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, Indiana 47907, United States
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41
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Linani A, Benarous K, Bou-Salah L, Yousfi M, Goumri-Said S. Exploring Structural Mechanism of COVID-19 Treatment with Glutathione as a Potential Peptide Inhibitor to the Main Protease: Molecular Dynamics Simulation and MM/PBSA Free Energy Calculations Study. Int J Pept Res Ther 2022; 28:55. [PMID: 35079241 PMCID: PMC8777181 DOI: 10.1007/s10989-022-10365-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2022] [Indexed: 01/08/2023]
Abstract
The 2019-novel coronavirus has unfolded everywhere in the world and obliged a billion human beings in open confinement, whereas many treatments, and vaccines have been proposed towards this pandemic. The main protease (Mpro) is an attractive drug target due to the fact that it is the essential protein for virus invasion. This research tests in silico the effect of five vitamins towards Mpro, by employing molecular docking (MD), molecular dynamics simulation (MDS) with molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) studies. To achieve this work, we have applied some software’s as Autodock Vina, Discovery Studio Visualizer, APBS, and GROMACS. The inhibitors used were decided entirely on the basis of their importance in the production of red blood cells that prevent anemia, in lymphocyte immune system responses, in the regulation of reactive oxygen species production, such as tocopherol (vitamin E), thiamine (vitamin B1), pantothenic acid (vitamin B5), pyridoxine (vitamin B6), biotin (vitamin B7), and glutathione (GSH). The best inhibitor pose established at the highest repetition ratio (RR) and the minimal affinity energy value (MEV), then the best selected inhibitor was considered to MDS. The results indicate that GSH is the leading inhibitor model among the other tested vitamins in the active site of Mpro with a RR value of 94% and MEV of − 5.5 kcal/mol, its RMSD, RMSF, Rg, and hydrogen bonds show stability with Mpro. Furthermore, thiamine, biotin, and tocopherol are viewed as satisfying inhibitors to Mpro, but pyridoxine was observed as the weakest inhibitor. Based on our result, we could recommend the usage of glutathione and vitamin B family as a supportive strategy for feasible remedy of COVID-19 virus.
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Affiliation(s)
- Abderahmane Linani
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Khedidja Benarous
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Leila Bou-Salah
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Mohamed Yousfi
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Souraya Goumri-Said
- Physics Department, College of Science, Alfaisal University, P.O. Box 50927, Riyadh, 11533 Saudi Arabia
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42
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Zhao W, Li X, Yu Z, Wu S, Ding L, Liu J. Identification of lactoferrin-derived peptides as potential inhibitors against the main protease of SARS-CoV-2. Lebensm Wiss Technol 2022; 154:112684. [PMID: 34720187 PMCID: PMC8537974 DOI: 10.1016/j.lwt.2021.112684] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/07/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022]
Abstract
COVID-19 is a global health emergency that causes serious concerns. A global effort is underway to identify drugs for the treatment of COVID-19. One possible solution to the present problem is to develop drugs that can inhibit SARS-CoV-2 main protease (Mpro), a coronavirus protein that been considered as one among many drug targets. In this work, lactoferrin from Bos taurus L. was in silico hydrolyzed. The bioactivity, water solubility, and ADMET properties of the generated peptides were predicted using various online tools. The molecular interactions between Mpro and the peptides were studied using molecular docking and molecular dynamic simulation. The results demonstrated that peptide GSRY was predicted to have better physicochemical properties, and the value of '-C DOCKER interaction energy' between peptide GSRY and Mpro was 80.8505 kcal/mol. The interaction between the peptide GSRY and the native ligand N3 co-crystallized with Mpro had overlapped amino acids, i.e., HIS163, GlY143, GLU166, GLN189 and MET165. Molecular dynamic simulation revealed that Mpro/GSRY complexes were stable. Collectively, the peptide GSRY may be a potential candidate drug against Mpro of SARS-CoV-2.
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Affiliation(s)
- Wenzhu Zhao
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
| | - Xin Li
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
- National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Bohai University, Jinzhou, 121013, PR China
| | - Zhipeng Yu
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
- National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Bohai University, Jinzhou, 121013, PR China
| | - Sijia Wu
- Lab of Nutrition and Functional Food, Jilin University, Changchun, 130062, PR China
| | - Long Ding
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, PR China
| | - Jingbo Liu
- Lab of Nutrition and Functional Food, Jilin University, Changchun, 130062, PR China
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Xu N, Lu Y, Yao X, Zhao R, Li Z, Li J, Zhang Y, Li B, Zhou Y, Shen H, Wang L, Chen K, Yang L, Lu S. NMCP-2 polysaccharide purified from Morchella conica effectively prevents doxorubicin-induced cardiotoxicity by decreasing cardiomyocyte apoptosis and myocardial oxidative stress. Food Sci Nutr 2021; 9:6262-6273. [PMID: 34760256 PMCID: PMC8565241 DOI: 10.1002/fsn3.2586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 11/18/2022] Open
Abstract
Doxorubicin (DOX) is an anthracycline antibiotic used in the clinical treatment of cancer, but its use is limited due to its cardiotoxic effects. Therefore, it is necessary to explore natural compounds that are effective in protecting against the cardiotoxicity caused by DOX. Neutral Morchella conica polysaccharides-2 (NMCP-2) is a natural polysaccharide with antioxidant activity that was isolated and purified from Morchella conica in our laboratory's previous study. This study aimed to investigate the possible protective effect of NMCP-2 on DOX-induced cardiotoxicity and the potential underlying mechanisms. The model of DOX-induced H9C2 cells and the model of DOX-induced mice were used in this study. In in vitro studies of H9C2 myocardial cells, NMCP-2 effectively increased the activity of H9C2 cells, reducing the levels of lactate dehydrogenase (LDH). In the mouse model of DOX-induced chronic cardiotoxicity, NMCP-2 significantly reduced the cardiac index, reduced the release of serum cardiac enzymes, and improved the pathology of murine myocardial tissues, thereby alleviating DOX-induced cardiotoxicity. Further mechanism studies showed that pretreatment with NMCP-2 counteracted the oxidative stress induced by DOX, as indicated by increasing superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) activities, and malondialdehyde (MDA) production decreased. In addition, we observed NMCP-2 inhibited the activation of the mitochondrial apoptosis pathway and regulated the disordered expression of Bcl-2 and Bax in the myocardial tissues of DOX-treated mice. These findings indicated that NMCP-2, a natural bioactive compound, could potentially be used as a food supplement to reduce the cardiotoxicity caused by DOX.
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Affiliation(s)
- Na Xu
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Yi Lu
- Key Laboratory of Zoonosis ResearchMinistry of EducationInstitute of ZoonosisCollege of Veterinary MedicineJilin UniversityChangchunChina
| | - Xinmiao Yao
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Rui Zhao
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Zhebin Li
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Jialei Li
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Yinglei Zhang
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Bo Li
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Ye Zhou
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Huifang Shen
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Liqun Wang
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Kaixin Chen
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
| | - Li Yang
- Key Laboratory of Zoonosis ResearchMinistry of EducationInstitute of ZoonosisCollege of Veterinary MedicineJilin UniversityChangchunChina
| | - Shuwen Lu
- Institute of Food ProcessingHeilongjiang Academy of Agricultural SciencesHarbinChina
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44
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Zhao W, Xu G, Yu Z, Li J, Liu J. Identification of nut protein-derived peptides against SARS-CoV-2 spike protein and main protease. Comput Biol Med 2021; 138:104937. [PMID: 34655899 PMCID: PMC8503973 DOI: 10.1016/j.compbiomed.2021.104937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/22/2022]
Abstract
Recently, an outbreak of a novel coronavirus disease (COVID-19) has reached pandemic proportions, and there is an urgent need to develop nutritional supplements to assist with prevention, treatment, and recovery. In this study, SARS-CoV-2 inhibitory peptides were screened from nut proteins in silico, and binding affinities of the peptides to the SARS-CoV-2 main protease (Mpro) and the spike protein receptor-binding domain (RBD) were evaluated. Peptide NDQF from peanuts and peptide ASGCGDC from almonds were found to have a strong binding affinity for both targets of the coronavirus. The binding sites of the NDQF and ASGCGDC peptides are highly consistent with the Mpro inhibitor N3. In addition, NDQF and ASGCGDC exhibited an effective binding affinity for amino acid residues Tyr453 and Gln493 of the spike RBD. Molecular dynamics simulation further confirmed that the NDQF and ASGCGDC peptides could bind stably to the SARS-COV-2 Mpro and spike RBD. In summary, nut protein may be helpful as nutritional supplements for COVID-19 patients, and the screened peptides could be considered a potential lead compound for designing entry inhibitors against SARS-CoV-2.
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Affiliation(s)
- Wenzhu Zhao
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
| | - Ge Xu
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
| | - Zhipeng Yu
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China.
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University, Jinzhou, 121013, PR China
| | - Jingbo Liu
- Lab of Nutrition and Functional Food, Jilin University, Changchun, 130062, PR China
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45
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Sahu S, Patil CR, Kumar S, Apparsundaram S, Goyal RK. Role of ACE2-Ang (1-7)-Mas axis in post-COVID-19 complications and its dietary modulation. Mol Cell Biochem 2021; 477:225-240. [PMID: 34655418 PMCID: PMC8520076 DOI: 10.1007/s11010-021-04275-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/07/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-2 (COVID-19) virus uses Angiotensin-Converting Enzyme 2 (ACE2) as a gateway for their entry into the human body. The ACE2 with cleaved products have emerged as major contributing factors to multiple physiological functions and pathogenic complications leading to the clinical consequences of the COVID-19 infection Decreased ACE2 expression restricts the viral entry into the human cells and reduces the viral load. COVID-19 infection reduces the ACE2 expression and induces post-COVID-19 complications like pneumonia and lung injury. The modulation of the ACE2-Ang (1–7)-Mas (AAM) axis is also being explored as a modality to treat post-COVID-19 complications. Evidence indicates that specific food components may modulate the AAM axis. The variations in the susceptibility to COVID-19 infection and the post-COVID its complications are being correlated with varied dietary habits. Some of the food substances have emerged to have supportive roles in treating post-COVID-19 complications and are being considered as adjuvants to the COVID-19 therapy. It is possible that some of their active ingredients may emerge as the direct treatment for the COVID-19.
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Affiliation(s)
- Santoshi Sahu
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), Delhi Pharmaceutical Sciences and Research University (DPDRU), PushpVihar Sector-3, New Delhi, 110017, India
| | - C R Patil
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), Delhi Pharmaceutical Sciences and Research University (DPDRU), PushpVihar Sector-3, New Delhi, 110017, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), Delhi Pharmaceutical Sciences and Research University (DPDRU), PushpVihar Sector-3, New Delhi, 110017, India
| | - Subbu Apparsundaram
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), Delhi Pharmaceutical Sciences and Research University (DPDRU), PushpVihar Sector-3, New Delhi, 110017, India
| | - Ramesh K Goyal
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), Delhi Pharmaceutical Sciences and Research University (DPDRU), PushpVihar Sector-3, New Delhi, 110017, India.
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Ruiz-Salmón I, Fernández-Ríos A, Campos C, Laso J, Margallo M, Aldaco R. The fishing and seafood sector in the time of COVID-19: Considerations for local and global opportunities and responses. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2021; 23:100286. [PMID: 34693103 PMCID: PMC8523167 DOI: 10.1016/j.coesh.2021.100286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
This article provides an overview of the impact of the COVID-19 pandemic on the fishing sector over the world, including several economic, social, environmental, and health challenges that the fisheries have had to face during the early days of the health crisis, and some of them still continue today. These problems, in short, are translated into a decrease in seafood demand, loss of jobs, changes in food consumption habits, economic losses, or increased vulnerability of the industry. As a consequence, governments have been forced to implement regulations and measures in support of this sector. However, a positive aspect of the pandemic also stands out, the opportunity to transform the food system to be greener, more inclusive, and resilient against future shocks.
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Affiliation(s)
- Israel Ruiz-Salmón
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. de Los Castros, s.n., Santander, 39005, Spain
| | - Ana Fernández-Ríos
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. de Los Castros, s.n., Santander, 39005, Spain
| | - Cristina Campos
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. de Los Castros, s.n., Santander, 39005, Spain
| | - Jara Laso
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. de Los Castros, s.n., Santander, 39005, Spain
| | - María Margallo
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. de Los Castros, s.n., Santander, 39005, Spain
| | - Rubén Aldaco
- Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. de Los Castros, s.n., Santander, 39005, Spain
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Mousavi SS, Karami A, Haghighi TM, Tumilaar SG, Fatimawali, Idroes R, Mahmud S, Celik I, Ağagündüz D, Tallei TE, Emran TB, Capasso R. In Silico Evaluation of Iranian Medicinal Plant Phytoconstituents as Inhibitors against Main Protease and the Receptor-Binding Domain of SARS-CoV-2. Molecules 2021; 26:5724. [PMID: 34577194 PMCID: PMC8470205 DOI: 10.3390/molecules26185724] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/22/2021] [Accepted: 09/01/2021] [Indexed: 12/22/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which initially appeared in Wuhan, China, in December 2019. Elderly individuals and those with comorbid conditions may be more vulnerable to this disease. Consequently, several research laboratories continue to focus on developing drugs to treat this infection because this disease has developed into a global pandemic with an extremely limited number of specific treatments available. Natural herbal remedies have long been used to treat illnesses in a variety of cultures. Modern medicine has achieved success due to the effectiveness of traditional medicines, which are derived from medicinal plants. The objective of this study was to determine whether components of natural origin from Iranian medicinal plants have an antiviral effect that can prevent humans from this coronavirus infection using the most reliable molecular docking method; in our case, we focused on the main protease (Mpro) and a receptor-binding domain (RBD). The results of molecular docking showed that among 169 molecules of natural origin from common Iranian medicinal plants, 20 molecules (chelidimerine, rutin, fumariline, catechin gallate, adlumidine, astragalin, somniferine, etc.) can be proposed as inhibitors against this coronavirus based on the binding free energy and type of interactions between these molecules and the studied proteins. Moreover, a molecular dynamics simulation study revealed that the chelidimerine-Mpro and somniferine-RBD complexes were stable for up to 50 ns below 0.5 nm. Our results provide valuable insights into this mechanism, which sheds light on future structure-based designs of high-potency inhibitors for SARS-CoV-2.
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Affiliation(s)
- Seyyed Sasan Mousavi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Akbar Karami
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Tahereh Movahhed Haghighi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Sefren Geiner Tumilaar
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia; (S.G.T.); (F.)
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia; (S.G.T.); (F.)
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado 95115, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Indonesia;
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Duygu Ağagündüz
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey;
| | - Trina Ekawati Tallei
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado 95115, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, Italy
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Padhi S, Sanjukta S, Chourasia R, Labala RK, Singh SP, Rai AK. A Multifunctional Peptide From Bacillus Fermented Soybean for Effective Inhibition of SARS-CoV-2 S1 Receptor Binding Domain and Modulation of Toll Like Receptor 4: A Molecular Docking Study. Front Mol Biosci 2021; 8:636647. [PMID: 33869283 PMCID: PMC8044374 DOI: 10.3389/fmolb.2021.636647] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
Fermented soybean products are traditionally consumed and popular in many Asian countries and the northeastern part of India. To search for potential agents for the interruption of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike glycoprotein 1 (S1) and human angiotensin-converting enzyme 2 (ACE2) receptor interactions, the in silico antiviral prospective of peptides identified from the proteome of kinema was investigated. Soybean was fermented using Bacillus licheniformis KN1G, Bacillus amyloliquefaciens KN2G and two different strains of Bacillus subtilis (KN2B and KN2M). The peptides were screened in silico for possible antiviral activity using two different web servers (AVPpred and meta-iAVP), and binding interactions of selected 44 peptides were further explored against the receptor-binding domain (RBD) of the S1 protein (PDB ID: 6M0J) by molecular docking using ZDOCK. The results showed that a peptide ALPEEVIQHTFNLKSQ (P13) belonging to B. licheniformis KN1G fermented kinema was able to make contacts with the binding motif of RBD by blocking specific residues designated as critical (GLN493, ASN501) in the binding of human angiotensin-converting enzyme 2 (ACE2) cell receptor. The selected peptide was also observed to have a significant affinity towards human toll like receptor 4 (TLR4)/Myeloid Differentiation factor 2 (MD2) (PDB ID: 3FXI) complex known for its essential role in cytokine storm. The energy properties of the docked complexes were analyzed through the Generalized Born model and Solvent Accessibility method (MM/GBSA) using HawkDock server. The results showed peptidyl amino acids GLU5, GLN8, PHE11, and LEU13 contributed most to P13-RBD binding. Similarly, ARG90, PHE121, LEU61, PHE126, and ILE94 were appeared to be significant in P13-TLR4/MD2 complex. The findings of the study suggest that the peptides from fermented soy prepared using B. licheniformis KN1G have better potential to be used as antiviral agents. The specific peptide ALPEEVIQHTFNLKSQ could be synthesized and used in combination with experimental studies to validate its effect on SARS-CoV-2-hACE2 interaction and modulation of TLR4 activity. Subsequently, the protein hydrolysate comprising these peptides could be used as prophylaxis against viral diseases, including COVID-19.
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Affiliation(s)
- Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | | | - Rounak Chourasia
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | | | - Sudhir P. Singh
- Centre of Innovative and Applied Bioprocessing, Mohali, India
| | - Amit K. Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
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49
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Schütz D, Ruiz-Blanco YB, Münch J, Kirchhoff F, Sanchez-Garcia E, Müller JA. Peptide and peptide-based inhibitors of SARS-CoV-2 entry. Adv Drug Deliv Rev 2020; 167:47-65. [PMID: 33189768 PMCID: PMC7665879 DOI: 10.1016/j.addr.2020.11.007] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/18/2022]
Abstract
To date, no effective vaccines or therapies are available against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pandemic agent of the coronavirus disease 2019 (COVID-19). Due to their safety, efficacy and specificity, peptide inhibitors hold great promise for the treatment of newly emerging viral pathogens. Based on the known structures of viral proteins and their cellular targets, antiviral peptides can be rationally designed and optimized. The resulting peptides may be highly specific for their respective targets and particular viral pathogens or exert broad antiviral activity. Here, we summarize the current status of peptides inhibiting SARS-CoV-2 entry and outline the strategies used to design peptides targeting the ACE2 receptor or the viral spike protein and its activating proteases furin, transmembrane serine protease 2 (TMPRSS2), or cathepsin L. In addition, we present approaches used against related viruses such as SARS-CoV-1 that might be implemented for inhibition of SARS-CoV-2 infection.
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Affiliation(s)
- Desiree Schütz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany.
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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