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Eltaib L, Alzain AA. Targeting the omicron variant of SARS-CoV-2 with phytochemicals from Saudi medicinal plants: molecular docking combined with molecular dynamics investigations. J Biomol Struct Dyn 2023; 41:9732-9744. [PMID: 36369836 DOI: 10.1080/07391102.2022.2146203] [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: 09/14/2022] [Accepted: 11/05/2022] [Indexed: 11/14/2022]
Abstract
The new health crises caused by SARS-CoV-2 have resulted in millions of deaths worldwide. First discovered in November 2021, the omicron variant is more transmissible and is able to evade the immune system better than other previously identified SARS-CoV-2 variants, leading to a spike in cases. Great efforts have been made to discover inhibitors against SARS-CoV-2. Main protease (Mpro) inhibitors are considered promising anti-SARS-CoV-2 agents. The U.S. FDA has issued an Emergency Use Authorization for ritonavir-boosted nirmatrelvir. Nirmatrelvir is the first orally bioavailable inhibitor of SARS-CoV-2 Mpro. There is an urgent need to monitor the mutations and solve the problem of resistance, especially omicron Mpro, which contains one mutation - P132H. In the present study, 132,57 phytochemicals from 80 medicinal plants grown in Saudi Arabia were docked into the active site of Mpro omicron variant. Free binding energies were also calculated. This led to the discovery of five phytochemicals that showed better docking scores than the bound ligand nirmatrelvir. In addition, these molecules exhibited favorable free binding energies. The stability of compounds 1-5 with the protein was studied using molecular dynamics (MD) simulations. These compounds showed acceptable ADMET properties. The results were compared with the wild type. These candidates could be envisioned as new hits against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lina Eltaib
- Department of Pharmaceutics, Faculty of Pharmacy, Northern Border University, Arar, Saudi Arabia
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
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Arasu A, Prabha N, Devi D, Issac PK, Alarjani KM, Al Farraj DA, Aljeidi RA, Hussein DS, Mohan M, Tayyeb JZ, Guru A, Arockiaraj J. Antimicrobial Efficacy of Allium cepa and Zingiber officinale Against the Milk-Borne Pathogen Listeria monocytogenes. J Microbiol 2023; 61:993-1011. [PMID: 38048022 DOI: 10.1007/s12275-023-00086-w] [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: 07/19/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 12/05/2023]
Abstract
Listeria monocytogenes is an important food-borne pathogen that causes listeriosis and has a high case fatality rate despite its low incidence. Medicinal plants and their secondary metabolites have been identified as potential antibacterial substances, serving as replacements for synthetic chemical compounds. The present studies emphasize two significant medicinal plants, Allium cepa and Zingiber officinale, and their efficacy against L. monocytogenes. Firstly, a bacterial isolate was obtained from milk and identified through morphology and biochemical reactions. The species of the isolate were further confirmed through 16S rRNA analysis. Furthermore, polar solvents such as methanol and ethanol were used for the extraction of secondary metabolites from A. cepa and Z. officinale. Crude phytochemical components were identified using phytochemical tests, FTIR, and GC-MS. Moreover, the antibacterial activity of the crude extract and its various concentrations were tested against L. monocytogenes. Among all, A. cepa in methanolic extracts showed significant inhibitory activity. Since, the A. cepa for methanolic crude extract was used to perform autography to assess its bactericidal activity. Subsequently, molecular docking was performed to determine the specific compound inhibition. The docking results revealed that four compounds displayed strong binding affinity with the virulence factor Listeriolysin-O of L. monocytogenes. Based on the above results, it can be concluded that the medicinal plant A. cepa has potential antibacterial effects against L. monocytogenes, particularly targeting its virulence.
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Affiliation(s)
- Abirami Arasu
- Department of Microbiology, SRM Arts and Science College, Kattankulathur, Chennai, Tamil Nadu, 603203, India.
| | - Nagaram Prabha
- Department of Microbiology, SRM Arts and Science College, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Durga Devi
- Department of Microbiology, SRM Arts and Science College, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Praveen Kumar Issac
- Institute of Biotechnology, Department of Medical Biotechnology and Integrative Physiology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, 602105, India
| | - Khaloud Mohammed Alarjani
- Department of Botany and Microbiology, College of Science, King Saud University, P.O.2455, 11451, Riyadh, Saudi Arabia
| | - Dunia A Al Farraj
- Department of Botany and Microbiology, College of Science, King Saud University, P.O.2455, 11451, Riyadh, Saudi Arabia
| | - Reem A Aljeidi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O.2455, 11451, Riyadh, Saudi Arabia
| | - Dina S Hussein
- Department of Chemistry, College of Sciences and Health, Cleveland State University, Cleveland, 44115, USA
| | - Magesh Mohan
- Saveetha College of Pharmacy, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu, 602105, India
| | - Jehad Zuhair Tayyeb
- Department of Clinical Biochemistry, College of Medicine, University of Jeddah, 23890, Jeddah, Saudi Arabia.
| | - Ajay Guru
- Department of Cariology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 600077, India.
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamil Nadu, 603203, India.
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Olson KR, Derry PJ, Kent TA, Straub KD. The Effects of Antioxidant Nutraceuticals on Cellular Sulfur Metabolism and Signaling. Antioxid Redox Signal 2023; 38:68-94. [PMID: 35819295 PMCID: PMC9885552 DOI: 10.1089/ars.2022.0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 02/03/2023]
Abstract
Significance: Nutraceuticals are ingested for health benefits, in addition to their general nutritional value. These dietary supplements have become increasingly popular since the late 20th century and they are a rapidly expanding global industry approaching a half-trillion U.S. dollars annually. Many nutraceuticals are promulgated as potent antioxidants. Recent Advances: Experimental support for the efficacy of nutraceuticals has lagged behind anecdotal exuberance. However, accumulating epidemiological evidence and recent, well-controlled clinical trials are beginning to support earlier animal and in vitro studies. Although still somewhat limited, encouraging results have been suggested in essentially all organ systems and against a wide range of pathophysiological conditions. Critical Issues: Health benefits of "antioxidant" nutraceuticals are largely attributed to their ability to scavenge oxidants. This has been criticized based on several factors, including limited bioavailability, short tissue retention time, and the preponderance of endogenous antioxidants. Recent attention has turned to nutraceutical activation of downstream antioxidant systems, especially the Keap1/Nrf2 (Kelch like ECH associated protein 1/nuclear factor erythroid 2-related factor 2) axis. The question now becomes, how do nutraceuticals activate this axis? Future Directions: Reactive sulfur species (RSS), including hydrogen sulfide (H2S) and its metabolites, are potent activators of the Keap1/Nrf2 axis and avid scavengers of reactive oxygen species. Evidence is beginning to accumulate that a variety of nutraceuticals increase cellular RSS by directly providing RSS in the diet, or through a number of catalytic mechanisms that increase endogenous RSS production. We propose that nutraceutical-specific targeting of RSS metabolism will lead to the design and development of even more efficacious antioxidant therapeutic strategies. Antioxid. Redox Signal. 38, 68-94.
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Affiliation(s)
- Kenneth R. Olson
- Department of Physiology, Indiana University School of Medicine—South Bend, South Bend, Indiana, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Paul J. Derry
- Center for Genomics and Precision Medicine, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Thomas A. Kent
- Center for Genomics and Precision Medicine, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
- Department of Chemistry, Rice University, Houston, Texas, USA
- Stanley H. Appel Department of Neurology, Houston Methodist Hospital and Research Institute, Houston, Texas, USA
| | - Karl D. Straub
- Central Arkansas Veteran's Healthcare System, Little Rock, Arkansas, USA
- Department of Medicine and Biochemistry, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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Yan JK, Zhu J, Liu Y, Chen X, Wang W, Zhang H, Li L. Recent advances in research on Allium plants: functional ingredients, physiological activities, and applications in agricultural and food sciences. Crit Rev Food Sci Nutr 2022; 63:8107-8135. [PMID: 35343832 DOI: 10.1080/10408398.2022.2056132] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fruits and vegetables (FVs) have long been a major source of nutrients and dietary phytochemicals with outstanding physiological properties that are essential for protecting humans from chronic diseases. Moreover, the growing demand of consumers for nutritious and healthy foods is greatly promoting the increased intake of FVs. Allium (Alliaceae) is a perennial bulb plant genus of the Liliaceae family. They are customarily utilized as vegetable, medicinal, and ornamental plants and have an important role in agriculture, aquaculture, and the pharmaceutical industry. Allium plants produce abundant secondary metabolites, such as organosulfur compounds, flavonoids, phenols, saponins, alkaloids, and polysaccharides. Accordingly, Allium plants possess a variety of nutritional, biological, and health-promoting properties, including antimicrobial, antioxidant, antitumor, immunoregulatory, antidiabetic, and anti-inflammatory effects. This review aims to highlight the advances in the research on the bioactive components, physiological activities and clinical trials, toxicological assessment for safety, and applications of different Allium plants. It also aims to cover the direction of future research on the Allium genus. This review is expected to provide theoretical reference for the comprehensive development and utilization of Allium plants in the fields of functional foods, medicine, and cosmetics.
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Affiliation(s)
- Jing-Kun Yan
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, China
| | - Jie Zhu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, China
| | - Yujia Liu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, China
| | - Xu Chen
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, China
| | - Wenhan Wang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, China
| | - Henan Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, China
| | - Lin Li
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, China
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