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Senthil R, Archunan G, Vithya D, Saravanan KM. Hexadecanoic acid analogs as potential CviR-mediated quorum sensing inhibitors in Chromobacterium violaceum: an in silico study. J Biomol Struct Dyn 2025; 43:3635-3644. [PMID: 38165661 DOI: 10.1080/07391102.2023.2299945] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
Chromobacterium violaceum is a Gram-negative, rod-shaped and opportunistic human pathogen. C. violaceum is resistant to various antibiotics due to the production of quorum sensing (QS)-controlled virulence factor and biofilm formation. Hence, we need to find alternative strategies to overcome the antimicrobial resistance and biofilm formation in Gram-negative bacteria. QS is a mechanism in which bacteria's ability to regulate the virulence factors and biofilm formations leads to disease progression. Previously, hexadecanoic acid was identified as a CviR-mediated quorum-sensing inhibitor. In this study, we aimed to discover potential analogs of hexadecanoic acid as a CviR-mediated quorum-sensing inhibitor against C. violaceum by using ADME/T prediction, density functional theory, molecular docking, molecular dynamics and free energy binding calculations. ADME/T properties predicted for analogs were acceptable for human oral absorption and feasibility. The highest occupied molecular orbitals and lowest unoccupied molecular orbitals gap energies predicted and found oleic acid with -0.3748 energies. Docosatrienoic acid exhibited the highest binding affinity -8.15 Kcal/mol and strong and stable interactions with the amino acid residues on the active site of the CviR protein. These compounds on MD simulations for 100 ns show strong hydrogen-bonding interactions with the protein and remain stable inside the active site. Our results suggest hexadecanoic acid analogs could serve as anti-QS and anti-biofilm molecules for treating C. violaceum infections. However, further validation and investigation of these inhibitors against CviR are needed to claim their candidacy for clinical trials.
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Affiliation(s)
- Renganathan Senthil
- Department of Bioinformatics, School of Lifesciences, Vel's Institute of Science, Technology and Advanced Studies, Pallavaram, Chennai, Tamil Nadu, India
- Lysine Biotech Private Limited, Taramani, Chennai, Tamil Nadu, India
| | - Govindaraju Archunan
- Dean-Research, Maruthupandiyar College (Affiliated to Bharathidasan University), Thanjavur, Tamil Nadu, India
| | - Dharmaraj Vithya
- Department of Biotechnology, Dhanalakshmi Srinivasan College of Arts and Science for Women (Affiliated to Bharathidasan University), Perambalur, Tamil Nadu, India
| | - Konda Mani Saravanan
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
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Alshammari FA. Exploring the Antibacterial Potential of Artemisia judaica Compounds Targeting the Hydrolase/Antibiotic Protein in Klebsiella pneumoniae: In Vitro and In Silico Investigations. Pharmaceuticals (Basel) 2024; 17:667. [PMID: 38931335 PMCID: PMC11207000 DOI: 10.3390/ph17060667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Carbapenem antibiotic resistance is an emerging medical concern. Bacteria that possess the Klebsiella pneumoniae carbapenemase (KPC) protein, an enzyme that catalyzes the degradation of carbapenem antibiotics, have exhibited remarkable resistance to traditional and even modern therapeutic approaches. This study aimed to identify potential natural drug candidates sourced from the leaves of Artemisia judaica (A. judaica). The phytoconstituents present in A. judaica dried leaves were extracted using ethanol 80%. A reasonable amount of the extract was used to identify these phytochemicals via gas chromatography/mass spectrometry (GC/MS). One hundred twenty-two bioactive compounds from A. judaica were identified and subjected to docking analysis against the target bacterial protein. Four compounds (PubChem CID: 6917974, 159099, 628694, and 482788) were selected based on favorable docking scores (-9, -7.8, -7.7, and -7.5 kcal/mol). This computational investigation highlights the potential of these four compounds as promising antibacterial candidates against the specific KPC protein. Additionally, in vitro antibacterial assays using A. judaica extracts were conducted. The minimum inhibitory concentration (MIC) against the bacterium K. pneumonia was 125 μg/mL. Well-disk diffusion tests exhibited inhibition zones ranging from 10.3 ± 0.5 mm to 17 ± 0.5 mm at different concentrations, and time-kill kinetics at 12 h indicated effective inhibition of bacterial growth by A. judaica leaf extracts. Our findings have revealed the pharmaceutical potential of Artemisia judaica as a natural source for drug candidates against carbapenem-resistant pathogens.
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Affiliation(s)
- Fahdah Ayed Alshammari
- Department of Biology, College of Science, Northern Border University, Arar 76312, Saudi Arabia
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3
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Saha C, Naskar R, Chakraborty S. Antiviral Flavonoids: A Natural Scaffold with Prospects as Phytomedicines against SARS-CoV2. Mini Rev Med Chem 2024; 24:39-59. [PMID: 37138419 DOI: 10.2174/1389557523666230503105053] [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: 11/25/2022] [Revised: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023]
Abstract
Flavonoids are vital candidates to fight against a wide range of pathogenic microbial infections. Due to their therapeutic potential, many flavonoids from the herbs of traditional medicine systems are now being evaluated as lead compounds to develop potential antimicrobial hits. The emergence of SARS-CoV-2 caused one of the deadliest pandemics that has ever been known to mankind. To date, more than 600 million confirmed cases of SARS-CoV2 infection have been reported worldwide. Situations are worse due to the unavailability of therapeutics to combat the viral disease. Thus, there is an urgent need to develop drugs against SARS-CoV2 and its emerging variants. Here, we have carried out a detailed mechanistic analysis of the antiviral efficacy of flavonoids in terms of their potential targets and structural feature required for exerting their antiviral activity. A catalog of various promising flavonoid compounds has been shown to elicit inhibitory effects against SARS-CoV and MERS-CoV proteases. However, they act in the high-micromolar regime. Thus a proper leadoptimization against the various proteases of SARS-CoV2 can lead to high-affinity SARS-CoV2 protease inhibitors. To enable lead optimization, a quantitative structure-activity relationship (QSAR) analysis has been developed for the flavonoids that have shown antiviral activity against viral proteases of SARS-CoV and MERS-CoV. High sequence similarities between coronavirus proteases enable the applicability of the developed QSAR to SARS-CoV2 proteases inhibitor screening. The detailed mechanistic analysis of the antiviral flavonoids and the developed QSAR models is a step forward toward the development of flavonoid-based therapeutics or supplements to fight against COVID-19.
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Affiliation(s)
- Chiranjeet Saha
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, India
| | - Roumi Naskar
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, 500046, India
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Oselusi SO, Sibuyi NRS, Meyer M, Madiehe AM. Ehretia Species Phytoconstituents as Potential Lead Compounds against Klebsiella pneumoniae Carbapenemase: A Computational Approach. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8022356. [PMID: 37869630 PMCID: PMC10586912 DOI: 10.1155/2023/8022356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023]
Abstract
The evolution of antibiotic-resistant carbapenemase has negatively impacted the management of critical healthcare-associated infections. K. pneumoniae carbapenemase-2- (KPC-2-) expressing bacteria have developed resistance to conventional therapeutic options, including those used as a last resort for life-threatening diseases. In this study, Ehretia species phytoconstituents were screened for their potential to inhibit KPC-2 protein using in silico approaches. Molecular docking was used to identify strong KPC-2 protein binding phytoconstituents retrieved from the literature. The best-docked conformation of the ligands was selected based on their glide energy and binding interactions. To determine their binding free energies, these hit compounds were subjected to molecular mechanics with generalized born and surface area (MM-GBSA) in the PRIME module. Pharmacological assessments of the ligands were performed to evaluate their drug-likeness. Molecular dynamic (MD) simulations were used to analyze the conformational stability of the selected druglike compounds within the active site of the KPC-2 protein. Overall, a total of 69 phytoconstituents were compiled from the literature. Fourteen of these compounds exhibited a stronger binding affinity for the protein target than the reference drugs. Four of these top hit compounds, DB09, DB12, DB28, and DB66, revealed the highest efficacy in terms of drug-likeness properties. The MD simulation established that among the druglike compounds, DB66 attained stable conformations after 150 ns simulation in the active site of the protein. We concluded that DB66 from Ehretia species could play a significant role in therapeutic efforts against KPC-2-expressing bacteria.
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Affiliation(s)
- Samson O. Oselusi
- Nanobiotechnology Research Group, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Nicole R. S. Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Abram M. Madiehe
- Nanobiotechnology Research Group, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
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5
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Chen C, Liang H, Deng Y, Yang X, Li X, Hou C. Analysis and Identification of Bioactive Compounds of Cannabinoids in Silico for Inhibition of SARS-CoV-2 and SARS-CoV. Biomolecules 2022; 12:1729. [PMID: 36551156 PMCID: PMC9775500 DOI: 10.3390/biom12121729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the approval of multiple vaccinations in different countries, the majority of the world's population remains unvaccinated due to discrepancies in vaccine distribution and limited production capacity. The SARS-CoV-2 RBD-ACE2 complex (receptor binding domain that binds to ACE2) could be a suitable target for the development of a vaccine or an inhibitor. Various natural products have been used against SARS-CoV-2. Here, we docked 42 active cannabinoids to the active site of the SARS-CoV-2 and SARS-CoV complex of RBD-ACE2. To ensure the flexibility and stability of the complex produced after docking, the top three ligand molecules with the best overall binding energies were further analyzed through molecular dynamic simulation (MDS). Then, we used the webserver Swissadme program and binding free energy to calculate and estimate the MMPBSA and ADME characteristics. Our results showed that luteolin, CBGVA, and CBNA were the top three molecules that interact with the SARS-CoV-2 RBD-ACE2 complex, while luteolin, stigmasterol, and CBNA had the strongest contact with that SARS-CoV. Our findings show that luteolin may be a potential inhibitor of infections caused by coronavirus-like pathogens such as COVID-19, although further in vivo and in vitro research is required.
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Affiliation(s)
- Chenxiao Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Hao Liang
- National Engineering Research Center for Vegetables, Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing 100097, China
| | - Yanchun Deng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Xiushi Yang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Xiaoming Li
- Bioengineering Research Center, Institute of Advanced Technology, Guangzhou 510000, China
| | - Chunsheng Hou
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
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Arunachalam K, Sasidharan SP, Yang X. A concise review of mushrooms antiviral and immunomodulatory properties that may combat against COVID-19. FOOD CHEMISTRY ADVANCES 2022; 1:100023. [PMID: 36686330 PMCID: PMC8887958 DOI: 10.1016/j.focha.2022.100023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 01/25/2023]
Abstract
The World Health Organization (WHO) declared COVID-19 as a pandemic on March 11, 2020, because of its widespread transmission and infection rates. The unique severe disease was found in Wuhan, China, since December 2019, and swiftly spread throughout the world. Natural chemicals derived from herbal medicines and medicinal mushrooms provide a significant resource for the development of novel antiviral drugs. Many natural drugs have been proven to have antiviral properties against a variety of virus strains, such as the coronavirus and the herpes simplex virus (HSV).. In this research, successful dietary treatments for different COVID illnesses were compared to potential of mushroom products in its therapy. In Google Scholar, Science Direct, PubMed, and Scopus, search keywords like COVID, COVID-19, SARS, MERS, mushrooms, and their compounds were utilized. In this review of the literature we foucsed popular mushrooms such as Agaricus subrufescens Peck, Agaricus blazei Murill, Cordyceps sinensis (Berk.) Sacc., Ganoderma lucidum (Curtis.) P. Karst., Grifola frondosa (Dicks.) Gray, Hericium erinaceus (Bull.) Pers., Inonotus obliquus (Arch. Ex Pers.) Pilát., Lentinula edodes (Berk.) Pegler, Pleurotus ostreatus (Jacq.) P. Kumm., Poria cocos F.A. Wolf, and Trametes versicolor (L.) Lloyd.,. Changed forms of β-Glucan seem to have a good impact on viral replication suppression and might be used in future studies. However, the results seems terpenoids, lectins, glycoproteins, lentinan, galactomannan, and polysaccharides from mushrooms are promising prophylactic or therapeutic agents against COVID-19.
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Affiliation(s)
- Karuppusamy Arunachalam
- Key Laboratory of Economic Plants and Biotechnology, The Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China,University of Chinese Academy of Sciences, Beijing 100049, China,Corresponding authors at: Key Laboratory of Economic Plants and Biotechnology, The Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | | | - Xuefei Yang
- Key Laboratory of Economic Plants and Biotechnology, The Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China,University of Chinese Academy of Sciences, Beijing 100049, China,Corresponding authors at: Key Laboratory of Economic Plants and Biotechnology, The Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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7
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Ruchawapol C, Fu WW, Xu HX. A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 104:154324. [PMID: 35841663 PMCID: PMC9259013 DOI: 10.1016/j.phymed.2022.154324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/23/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND COVID-19 highly caused contagious infections and massive deaths worldwide as well as unprecedentedly disrupting global economies and societies, and the urgent development of new antiviral medications are required. Medicinal herbs are promising resources for the discovery of prophylactic candidate against COVID-19. Considerable amounts of experimental efforts have been made on vaccines and direct-acting antiviral agents (DAAs), but neither of them was fast and fully developed. PURPOSE This study examined the computational approaches that have played a significant role in drug discovery and development against COVID-19, and these computational methods and tools will be helpful for the discovery of lead compounds from phytochemicals and understanding the molecular mechanism of action of TCM in the prevention and control of the other diseases. METHODS A search conducting in scientific databases (PubMed, Science Direct, ResearchGate, Google Scholar, and Web of Science) found a total of 2172 articles, which were retrieved via web interface of the following websites. After applying some inclusion and exclusion criteria and full-text screening, only 292 articles were collected as eligible articles. RESULTS In this review, we highlight three main categories of computational approaches including structure-based, knowledge-mining (artificial intelligence) and network-based approaches. The most commonly used database, molecular docking tool, and MD simulation software include TCMSP, AutoDock Vina, and GROMACS, respectively. Network-based approaches were mainly provided to help readers understanding the complex mechanisms of multiple TCM ingredients, targets, diseases, and networks. CONCLUSION Computational approaches have been broadly applied to the research of phytochemicals and TCM against COVID-19, and played a significant role in drug discovery and development in terms of the financial and time saving.
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Affiliation(s)
- Chattarin Ruchawapol
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Cai Lun Lu 1200, Shanghai 201203, China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Cai Lun Lu 1200, Shanghai 201203, China
| | - Wen-Wei Fu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Cai Lun Lu 1200, Shanghai 201203, China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Cai Lun Lu 1200, Shanghai 201203, China.
| | - Hong-Xi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Cai Lun Lu 1200, Shanghai 201203, China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Cai Lun Lu 1200, Shanghai 201203, China.
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8
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Inhibition of Escherichia coli nitroreductase by the constituents in Syzygium aromaticum. Chin J Nat Med 2022; 20:506-517. [DOI: 10.1016/s1875-5364(22)60163-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Indexed: 11/23/2022]
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Patel K, Patel DK. Health Benefits of Avicularin in the Medicine Against Cancerous Disorders
and other Complications: Biological Importance, Therapeutic Benefit
and Analytical Aspects. CURRENT CANCER THERAPY REVIEWS 2022. [DOI: 10.2174/1573394717666210831163322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Herbal drugs and their derived phytochemicals have been used in
medicine for the preparation of different types of pharmaceutical products. Pure phytochemicals including
flavonoids, alkaloids and terpenoids have been used in medicine for the treatment of different
types of human disorders including cancerous disorders. Flavonoids have been well known in
medicine for their anti-viral, anti-bacterial, anti-inflammatory, anti-diabetic, anti-cancer, anti-aging
and cardioprotective potential. Avicularin, also called quercetin-3-α-l-arabino furanoside, is a pure
flavonoid, a class of phytochemicals, found to be present in Lindera erythrocarpa and Lespedeza
cuneata. Avicularin has been well known in medicine for its anti-cancer properties.
Methods:
In the present work, scientific data of avicularin have been collected from different
databases such as Google, PubMed, Science Direct, Google Scholar and Scopus and summarized
with reference to medicinal importance, pharmacological activities and analytical aspects of avicularin.
The present review summarized the health beneficial properties of avicularin in medicine
through data analysis of various scientific research works. Further analytical progress in medicine
for the qualitative and quantitative analysis of avicularin in medicine has been also discussed in the
present work.
Results:
Scientific data analysis of different literature work revealed the biological importance of
flavonoid class of phytochemical ‘avicularin’ in medicine. Scientific data analysis revealed that avicularin
was found to be present in the Lindera erythrocarpa, Lespedeza cuneata, Rhododendron
schlipenbachii and Psidium guajava. Avicularin has been well known in medicine for its anti-inflammatory,
anti-allergic, anti-oxidant, anti-tumor and hepatoprotective activities. Avicularin protects
cardiomyocytes and hepatocytes against oxidative stress-induced apoptosis and induces cytotoxicity
in cancer lines and tumor tissues. Avicularin has positive influence on human hepatocellular
carcinoma and inhibits intracellular lipid accumulation. The role of avicularin in rheumatoid
arthritis has been also established with its underlying molecular mechanisms in the scientific work.
Recent interest in avicularin has focused on pharmacological investigations for its anti-cancer activity
in the medicine.
Conclusion:
The present work signified the biological importance of avicularin in medicine
through its medicinal uses, pharmacological activities and analytical aspects in the biological system.
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Affiliation(s)
- Kanika Patel
- Department of Pharmaceutical Sciences, Faculty of Health Sciences, Sam Higginbottom University of Agriculture,
Technology and Sciences, Prayagraj, India
| | - Dinesh Kumar Patel
- Department of Pharmaceutical Sciences, Faculty of Health Sciences, Sam Higginbottom University of Agriculture,
Technology and Sciences, Prayagraj, India
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Senthil Kumar KJ, Gokila Vani M, Hsieh HW, Lin CC, Wang SY. Antcins from Antrodia cinnamomea and Antrodia salmonea Inhibit Angiotensin-Converting Enzyme 2 (ACE2) in Epithelial Cells: Can Be Potential Candidates for the Development of SARS-CoV-2 Prophylactic Agents. PLANTS (BASEL, SWITZERLAND) 2021; 10:1736. [PMID: 34451782 PMCID: PMC8399673 DOI: 10.3390/plants10081736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 12/24/2022]
Abstract
Antcins are newly identified steroid-like compounds from Taiwan's endemic medicinal mushrooms Antrodia cinnamomea and Antrodia salmonea. Scientific studies of the past two decades confirmed that antcins have various pharmacological activities, including potent anti-oxidant and anti-inflammatory effects. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease-2019 (COVID-19) pandemic and is characterized as a significant threat to global public health. It was recently identified that SARS-CoV-2 required angiotensin converting enzyme 2 (ACE2), a receptor which supports host cell entry and disease onset. Here, we report a novel function of antcins, in which antcins exhibit inhibitory effects on ACE2. Compared to the untreated control group, treatment with various antcins (antcin-A, antcin-B, antcin-C, antcin-H, antcin-I, and antcin-M) significantly inhibited ACE2 activity in cultured human epithelial cells. Indeed, among the investigated antcins, antcin-A, antcin-B, antcin-C, and antcin-I showed a pronounceable inhibition against ACE2. These findings suggest that antcins could be novel anti-ACE2 agents to prevent SARS-CoV-2 host cell entry and the following disease onset.
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Affiliation(s)
- K. J. Senthil Kumar
- Bachelor Program of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan;
| | - M. Gokila Vani
- Department of Forestry, National Chung Hsing University, Taichung 402, Taiwan;
| | - Han-Wen Hsieh
- Taiwan Leader Biotech Company, Taipei 103, Taiwan; (H.-W.H.); (C.-C.L.)
| | - Chin-Chung Lin
- Taiwan Leader Biotech Company, Taipei 103, Taiwan; (H.-W.H.); (C.-C.L.)
| | - Sheng-Yang Wang
- Bachelor Program of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan;
- Department of Forestry, National Chung Hsing University, Taichung 402, Taiwan;
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
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11
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Dutta M, Tareq AM, Rakib A, Mahmud S, Sami SA, Mallick J, Islam MN, Majumder M, Uddin MZ, Alsubaie A, Almalki ASA, Khandaker MU, Bradley D, Rana MS, Emran TB. Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations. BIOLOGY 2021; 10:789. [PMID: 34440024 PMCID: PMC8389631 DOI: 10.3390/biology10080789] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/05/2021] [Accepted: 08/15/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus's severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography-mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics-generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (-5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (-5.39 kcal/mol), and lorazepam, 2TMS derivative (-5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand-Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.
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Affiliation(s)
- Mycal Dutta
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (A.M.T.); (M.N.I.)
| | - Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.)
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.)
| | - Jewel Mallick
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Mohammad Nazmul Islam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (A.M.T.); (M.N.I.)
| | - Mohuya Majumder
- Drug Discovery, GUSTO A Research Group, Chittagong 4203, Bangladesh;
| | - Md. Zia Uddin
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Abdullah Alsubaie
- Department of Physics, College of Khurma, Taif University, Taif 21944, Saudi Arabia;
| | | | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (M.U.K.); (D.A.B.)
| | - D.A. Bradley
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (M.U.K.); (D.A.B.)
- Department of Physics, University of Surrey, Guilford GU2 7XH, UK
| | - Md. Sohel Rana
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
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