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Ariaeenejad S, Gharechahi J, Foroozandeh Shahraki M, Fallah Atanaki F, Han JL, Ding XZ, Hildebrand F, Bahram M, Kavousi K, Hosseini Salekdeh G. Precision enzyme discovery through targeted mining of metagenomic data. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:7. [PMID: 38200389 PMCID: PMC10781932 DOI: 10.1007/s13659-023-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehdi Foroozandeh Shahraki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Tang X, Chen X, Wang H, Yang J, Li L, Zhu J, Liu Y. Virtual Screening Technology for Two Novel Peptides in Soybean as Inhibitors of α-Amylase and α-Glucosidase. Foods 2023; 12:4387. [PMID: 38137191 PMCID: PMC10743026 DOI: 10.3390/foods12244387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Soybean peptides (SPs) have bioactivities of enzyme inhibition that are beneficial to human health, but their mechanism is not clear. This study aimed to identify peptide fragments in SPs that simultaneously inhibit α-amylase and α-glucosidase and to explore their enzyme inhibition mechanism. Firstly, the inhibitory activity of SPs against the enzymes was determined. And two octapeptides, LDQTPRVF and SRNPIYSN, were identified for the first time by using HPLC-QTOF-MS/MS and virtual screening. Molecular simulation results showed that hydrogen bonds and π-π bonds were the key factors, and the N-terminal (Leu and Ser) and C-terminal (Phe) of peptide were important inhibiting sites. Both octapeptides were synthesized, and their IC50 values were 3.08 and 5.58 mmol/L for α-amylase, and 2.52 and 4.57 mmol/L for α-glucosidase, respectively. This study provided evidence for SPs as a potential inhibitor of α-amylase and α-glucosidase in special dietary foods.
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Affiliation(s)
- Xiyao Tang
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China (Y.L.)
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Xu Chen
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China (Y.L.)
| | - Hong Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Jinyi Yang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Lin Li
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China (Y.L.)
| | - Jie Zhu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China (Y.L.)
| | - Yujia Liu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Life and Health Technology, Dongguan University of Technology, Dongguan 523808, China (Y.L.)
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Ansari MA, Chauhan W, Shoaib S, Alyahya SA, Ali M, Ashraf H, Alomary MN, Al-Suhaimi EA. Emerging therapeutic options in the management of diabetes: recent trends, challenges and future directions. Int J Obes (Lond) 2023; 47:1179-1199. [PMID: 37696926 DOI: 10.1038/s41366-023-01369-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 07/04/2023] [Accepted: 08/17/2023] [Indexed: 09/13/2023]
Abstract
Diabetes is a serious health issue that causes a progressive dysregulation of carbohydrate metabolism due to insufficient insulin hormone, leading to consistently high blood glucose levels. According to the epidemiological data, the prevalence of diabetes has been increasing globally, affecting millions of individuals. It is a long-term condition that increases the risk of various diseases caused by damage to small and large blood vessels. There are two main subtypes of diabetes: type 1 and type 2, with type 2 being the most prevalent. Genetic and molecular studies have identified several genetic variants and metabolic pathways that contribute to the development and progression of diabetes. Current treatments include gene therapy, stem cell therapy, statin therapy, and other drugs. Moreover, recent advancements in therapeutics have also focused on developing novel drugs targeting these pathways, including incretin mimetics, SGLT2 inhibitors, and GLP-1 receptor agonists, which have shown promising results in improving glycemic control and reducing the risk of complications. However, these treatments are often expensive, inaccessible to patients in underdeveloped countries, and can have severe side effects. Peptides, such as glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1), are being explored as a potential therapy for diabetes. These peptides are postprandial glucose-dependent pancreatic beta-cell insulin secretagogues and have received much attention as a possible treatment option. Despite these advances, diabetes remains a major health challenge, and further research is needed to develop effective treatments and prevent its complications. This review covers various aspects of diabetes, including epidemiology, genetic and molecular basis, and recent advancements in therapeutics including herbal and synthetic peptides.
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Affiliation(s)
- Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.
| | - Waseem Chauhan
- Department of Hematology, Duke University, Durham, NC, 27710, USA
| | - Shoaib Shoaib
- Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Sami A Alyahya
- Wellness and Preventive Medicine Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia
| | - Mubashshir Ali
- USF Health Byrd Alzheimer's Center and Neuroscience Institute, Department of Molecular Medicine, Tampa, FL, USA
| | - Hamid Ashraf
- Rajiv Gandhi Center for Diabetes and Endocrinology, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohammad N Alomary
- Advanced Diagnostic and Therapeutic Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia.
| | - Ebtesam A Al-Suhaimi
- King Abdulaziz & his Companions Foundation for Giftedness & Creativity, Riyadh, Saudi Arabia.
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Lan Y, Zhang W, Liu F, Wang L, Yang X, Ma S, Wang Y, Liu X. Recent advances in physiochemical changes, nutritional value, bioactivities, and food applications of germinated quinoa: A comprehensive review. Food Chem 2023; 426:136390. [PMID: 37307740 DOI: 10.1016/j.foodchem.2023.136390] [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: 11/16/2022] [Revised: 04/28/2023] [Accepted: 05/13/2023] [Indexed: 06/14/2023]
Abstract
The production and consumption of functional foods has become an essential food industry trend. Due to its high nutritional content, quinoa is regarded as a super pseudocereal for the development of nutritious foods. However, the presence of antinutritional factors and quinoa's distinctive grassy flavor limit its food applications. Due to its benefits in enhancing the nutritional bioavailability and organoleptic quality of quinoa, germination has garnered significant interest. To date, there is no systematic review of quinoa germination and the health benefits of germinated quinoa. This review details the nutritional components and bioactivities of germinated quinoa, as well as the potential mechanisms for the accumulation of bioactive compounds during the germination process. Additionally, evidence supporting the health benefits of germinated quinoa, the current status of related product development, and perspectives for future research are presented. Thus, our research is likely to provide theoretical support for the use of germinated quinoa resources.
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Affiliation(s)
- Yongli Lan
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Wengang Zhang
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China; Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining 810016, China; Academy of Agriculture and Forestry Sciences, Key Laboratory of Qinghai Province Tibetan Plateau Agric-Product Processing, Xining 810016, China
| | - Fuguo Liu
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Lei Wang
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Xijuan Yang
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining 810016, China; Academy of Agriculture and Forestry Sciences, Key Laboratory of Qinghai Province Tibetan Plateau Agric-Product Processing, Xining 810016, China
| | - Shaobo Ma
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Yutang Wang
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China.
| | - Xuebo Liu
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China.
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Enzymatically triggered delignification through a novel stable laccase: A mixed in-silico /in-vitro exploration of a complex environmental microbiota. Int J Biol Macromol 2022; 211:328-341. [PMID: 35551951 DOI: 10.1016/j.ijbiomac.2022.05.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 11/23/2022]
Abstract
Laccases have been broadly applied as a multitasking biocatalyst in various industries, but their applications tend to be limited by easy deactivation, lack of adequate stability, and susceptibility under complex conditions. Identifying stable laccase as a green-biocatalyst is crucial for developing cost-effective biorefining processes. In this direction, we attempted in-silico screening a stable metagenome-derived laccase (PersiLac1) from tannery wastewater in a complex environment. The laccase exhibited high thermostability, retaining 53.19% activity after 180 min at 70 °C, and it was stable in a wide range of pH (4.0-9.0). After 33 days of storage at 50°C, pH 6.0, the enzyme retained 71.65% of its activity. Various metal ions, inhibitors, and organic solvents showed that PersiLac1 has a stable structure. The stable PersiLac1 could successfully remove lignin and phenolic from quinoa husk and rice straw. In the separate hydrolysis and fermentation process (SHF) after 72 h, hydrolysis was obtained 100% and 73.4% for quinoa husk and rice straw, and fermentation by the S. cerevisiae was be produced 41.46 g/L and 27.75g/L ethanol, respectively. Results signified that the novel lignin-degrading enzyme was confirmed to have great potential for industrial application as a green-biocatalyst based on enzymatically triggered to delignification and detoxify lignocellulosic biomass.
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