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Moneshwaran S, Macrin D, Kanagathara N. An unprecedented global challenge, emerging trends and innovations in the fight against COVID-19: A comprehensive review. Int J Biol Macromol 2024; 267:131324. [PMID: 38574936 DOI: 10.1016/j.ijbiomac.2024.131324] [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: 06/16/2023] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious and dangerous virus that caused the global COVID-19 pandemic in early 2020. It primarily affects the respiratory system, leading to severe illness and high rates of mortality worldwide. The virus enters the body by binding to a receptor called ACE2, which is present in specific cells of the lungs known as type 2 alveolar epithelial cells. Numerous studies have investigated the consequences of SARS-CoV-2 infection, revealing various impacts on the body. This review provides an overview of SARS-CoV-2, including its structure and how it infects cells. It also examines the different variants of concern, such as Alpha, Beta, Gamma, Delta, and the more recent Omicron variant, discussing their characteristics and the level of damage they cause. The usage of drugs to treat COVID-19 is another aspect that has been covered and compares the effectiveness and use of antiviral drugs in the treatment and its potential benefits in COVID-19 treatment. Furthermore, this review explores the consequences and abnormalities associated with SARS-CoV-2 infection, including its impact on various organs and systems in the body. And also discussing the different COVID-19 vaccines available and their effectiveness in preventing infection and reducing the severity of illness. The current review ensures the recent update of the COVID research with expert's knowledge, collection of numerous data from reliable sources and methodologies as well as update of findings based on reviews. This review also provided clear contextual explanations to aid the interpretation and application of the results. The main motto and limitation of this manuscript are to address the computational methods of drug discovery against the rapidly evolving SARS-CoV-2 virus, which has been discussed. Additionally, current computational approaches which are cost effective and can able to predict the therapeutic agents for the treatment against the virus have also been discussed.
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Affiliation(s)
- S Moneshwaran
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Thandalam, Chennai 602 105, India
| | - D Macrin
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Thandalam, Chennai 602 105, India
| | - N Kanagathara
- Department of Physics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Thandalam, Chennai 602 105, India.
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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 2024:1-10. [PMID: 38165661 DOI: 10.1080/07391102.2023.2299945] [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: 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.Communicated by Ramaswamy H. Sarma.
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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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Khazir J, Ahmed S, Thakur RK, Hussain M, Gandhi SG, Babbar S, Mir SA, Shafi N, Tonfack LB, Rajpal VR, Maqbool T, Mir BA, Peer LA. Repurposing of Plant-based Antiviral Molecules for the Treatment of COVID-19. Curr Top Med Chem 2024; 24:614-633. [PMID: 38477206 DOI: 10.2174/0115680266276749240206101847] [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: 09/28/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
COVID-19, stemming from SARS-CoV-2, poses a formidable threat to global healthcare, with a staggering 77 million confirmed cases and 690,067 deaths recorded till December 24, 2023. Given the absence of specific drugs for this viral infection, the exploration of novel antiviral compounds becomes imperative. High-throughput technologies are actively engaged in drug discovery, and there is a parallel effort to repurpose plant-based molecules with established antiviral properties. In this context, the review meticulously delves into the potential of plant-based folk remedies and existing molecules. These substances have showcased substantial viral inhibition in diverse in vivo, in silico, and in vitro studies, particularly against critical viral protein targets, including SARS-CoV-2. The findings position these plant-based molecules as promising antiviral drug candidates for the swift advancement of treatments for COVID-19. It is noteworthy that the inherent attributes of these plant-based molecules, such as their natural origin, potency, safety, and cost-effectiveness, contribute to their appeal as lead candidates. The review advocates for further exploration through comprehensive in vivo studies conducted on animal models, emphasizing the potential of plant-based compounds to help in the ongoing quest to develop effective antivirals against COVID-19.
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Affiliation(s)
- Jabeena Khazir
- Department of Chemistry, HKM Govt. Degree College Eidgah, Cluster University Srinagar, J&K, 190001, India
| | - Sajad Ahmed
- Indian Institute of Integrative Medicine, Canal Road Jammu, 180001, J&K, India
| | - Rakesh Kr Thakur
- Amity Institute of Biotechnology, Amity University, Noida, 201313, India
| | - Manzoor Hussain
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
- Department of Botany, North Campus, University of Kashmir, Delina, Baramulla, J&K, 193103, India
| | - Sumit G Gandhi
- Indian Institute of Integrative Medicine, Canal Road Jammu, 180001, J&K, India
| | - Sadhana Babbar
- Department of Botany, Swami Shradhanand College, University of Delhi, Delhi, 110036, India
| | - Shabir Ahmad Mir
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah, 11952, Saudi Arabia
| | - Nusrat Shafi
- Department of Chemistry, HKM Govt. Degree College Eidgah, Cluster University Srinagar, J&K, 190001, India
| | - Libert Brice Tonfack
- Laboratory of Biotechnology and Environment, Department of Plant Biology, Faculty of Science, University of Yaounde I, PO Box 812, Yaounde, Cameroon
| | - Vijay Rani Rajpal
- Department of Botany, Hans Raj College, University of Delhi, Delhi, 110007, India
| | - Tariq Maqbool
- Laboratory of Nanotherapeutics and Regenerative Medicine, University of Kashmir, Srinagar, 190006, India
| | - Bilal Ahmad Mir
- Department of Botany, North Campus, University of Kashmir, Delina, Baramulla, J&K, 193103, India
| | - Latif Ahmad Peer
- Department of Botany, University of Kashmir, Srinagar, J&K, 190006, India
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Boshah H, Samkari F, Valle-Pérez AU, Alsawaf SM, Aldoukhi AH, Bilalis P, Alshehri SA, Susapto HH, Hauser CAE. Evaluation of Potential Peptide-Based Inhibitors against SARS-CoV-2 and Variants of Concern. BIOMED RESEARCH INTERNATIONAL 2023; 2023:3892370. [PMID: 37869628 PMCID: PMC10589072 DOI: 10.1155/2023/3892370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/26/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has greatly affected all aspect of life. Although several vaccines and pharmaceuticals have been developed against SARS-CoV-2, the emergence of mutated variants has raised several concerns. The angiotensin-converting enzyme (ACE2) receptor cell entry mechanism of this virus has not changed despite the vast mutation in emerging variants. Inhibiting the spike protein by which the virus identifies the host ACE2 receptor is a promising therapeutic countermeasure to keep pace with rapidly emerging variants. Here, we synthesized two ACE2-derived peptides, P1 and P25, to target and potentially inhibit SARS-CoV-2 cell entry. These peptides were evaluated in vitro using pseudoviruses that contained the SARS-CoV-2 original spike protein, the Delta-mutated spike protein, or the Omicron spike protein. An in silico investigation was also done for these peptides to evaluate the interaction of the synthesized peptides and the SARS-CoV-2 variants. The P25 peptide showed a promising inhibition potency against the tested pseudoviruses and an even higher inhibition against the Omicron variant. The IC50 of the Omicron variant was 60.8 μM, while the IC50s of the SARS-CoV-2 original strain and the Delta variant were 455.2 μM and 546.4 μM, respectively. The in silico experiments also showed that the amino acid composition design and structure of P25 boosted the interaction with the spike protein. These findings suggest that ACE2-derived peptides, such as P25, have the potential to inhibit SARS-CoV-2 cell entry in vitro. However, further in vivo studies are needed to confirm their therapeutic efficacy against emerging variants.
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Affiliation(s)
- Hattan Boshah
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Faris Samkari
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Alexander U. Valle-Pérez
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Sarah M. Alsawaf
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Ali H. Aldoukhi
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Panayiotis Bilalis
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Salwa A. Alshehri
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Department of Biochemistry, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hepi H. Susapto
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Charlotte A. E. Hauser
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Smart Health Initiative (KSHI), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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Wu JJ, Zhang J, Xia CY, Ding K, Li XX, Pan XG, Xu JK, He J, Zhang WK. Hypericin: A natural anthraquinone as promising therapeutic agent. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 111:154654. [PMID: 36689857 DOI: 10.1016/j.phymed.2023.154654] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/31/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Hypericin is a prominent secondary metabolite mainly existing in genus Hypericum. It has become a research focus for a quiet long time owing to its extensively pharmacological activities especially the anti-cancer, anti-bacterial, anti-viral and neuroprotective effects. This review concentrated on summarizing and analyzing the existing studies of hypericin in a comprehensive perspective. METHODS The literature with desired information about hypericin published after 2010 was gained from electronic databases including PubMed, SciFinder, Science Direct, Web of Science, China National Knowledge Infrastructure databases and Wan Fang DATA. RESULTS According to extensive preclinical and clinical studies conducted on the hypericin, an organized and comprehensive summary of the natural and artificial sources, strategies for improving the bioactivities, pharmacological activities, drug combination of hypericin was presented to explore the future therapeutic potential of this active compound. CONCLUSIONS Overall, this review offered a theoretical guidance for the follow-up research of hypericin. However, the pharmacological mechanisms, pharmacokinetics and structure activity relationship of hypericin should be further studied in future research.
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Affiliation(s)
- Jing-Jing Wu
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100029, China; Institute of Clinical Medical Sciences & Department of Pharmacy, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jia Zhang
- School of Life Sciences & School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Cong-Yuan Xia
- Institute of Clinical Medical Sciences & Department of Pharmacy, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Kang Ding
- School of Life Sciences & School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xin-Xin Li
- School of Life Sciences & School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xue-Ge Pan
- School of Life Sciences & School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jie-Kun Xu
- School of Life Sciences & School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Jun He
- Institute of Clinical Medical Sciences & Department of Pharmacy, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Wei-Ku Zhang
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100029, China; Institute of Clinical Medical Sciences & Department of Pharmacy, China-Japan Friendship Hospital, Beijing, 100029, China.
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Shanmugam V, Muthukrishnan S. Investigation of novel ligand targeting bromodomain-containing protein 4 (BRD4) for cancer drug discovery: complete pharmacophore approach. J Biomol Struct Dyn 2023; 41:14524-14539. [PMID: 36841551 DOI: 10.1080/07391102.2023.2183034] [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: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023]
Abstract
The Bromodomain (BRD4) and extra-terminal (BET) protein family are reversible; lysine-acetylated epigenetic readers identified as key important epigenetic regulators for protein recognition in posttranslational modifications for targeting cancer for its role in super-enhancers and transcription of oncogene expression in cancer and other forms of cancer and various diseases. Firstly, JQ-1a small potent BET inhibitors, targeting BET proteins were currently in clinical trials to ablate cancer. The identified compounds were taken from the library of preexisting therapeutically potent molecules. The objective of the present study is to identify the potential small molecule inhibitors against BRD4 through in-silico approach for the treatment of cancer. In present study, designed an in-silico screening of small molecules through ligand-based pharmacophore studies against bromodomain-containing protein 4 (BRD-4) protein and used for virtual screening through Database and their binding affinity and interaction of identified molecules were predicted through molecular docking, molecular dynamics simulations for 12 fixed time period, Molecular mechanics (MMGBSA) binding free energy calculations, ADME with drug-likeness properties including violations of lipinski's rule of 5, Jorgensens rule of 3 and other parameters were studied. The docking results indicate from the reported database screened molecules were validated with docking score -7.92 to -4.27Kcal/mol for BRD4-BD1 and the best model identified 21 hits. Among these two drugs were filtered and scrutinized for their ability based on binding modes and common interaction, MMGBSA of the highest affinity -54.53 Kcal/mol of BRD4-BD1 and ADME properties of selected molecules were predicted for its various parameters, dynamics studies evaluating its binding stability using Maestro software. In Conclusion, two BRD4 inhibitors were found to bind strongly in the similar binding sites as JQ-1, highlighting the role of BRD4-BD1. These compounds were identified as promising new options for regulating epigenetics and understanding the structural needs of BRD4 protein, further research in these areas could lead to the development of more effective and targeted cancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vaishnavi Shanmugam
- Department of Pharmacology, PSG College of Pharmacy, Peelamedu, Coimbatore, India
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Structural Insights into Plasticity and Discovery of Flavonoid Allosteric Inhibitors of Flavivirus NS2B–NS3 Protease. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Flaviviruses are among the most critical pathogens in tropical regions; they cause various severe diseases in developing countries but are not restricted to these countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Ten proteins are encoded in the flavivirus RNA. The N2B–NS3pro protein complex plays a fundamental role in flavivirus replication and is a promising drug target; however, no flavivirus protease inhibitors have progressed to the preclinical stage. This study analyzed the structural models and plasticity of the NS2B–NS3pro protein complex of five medically important non-dengue flaviviruses (West Nile, Rocio, Ilhéus, yellow fever, and Saint Louis encephalitis). The flavonoids amentoflavone, tetrahydrorobustaflavone, and quercetin were selected for their exceptional binding energies as potential inhibitors of the NS2B–NS3pro protein complex. AutoDock Vina results ranged from −7.0 kcal/mol to −11.5 kcal/mol and the compounds preferentially acted non-competitively. Additionally, the first structural model for the NS2B–NS3pro protein complex was proposed for Ilhéus and Rocio viruses. The NS2B–NS3pro protease is an attractive molecular target for drug development. The three identified natural flavonoids showed great inhibitory potential against the viral species. Nevertheless, further in silico and in vitro studies are required to obtain more information regarding NS2B–NS3pro inhibition by these flavonoids and their therapeutic potential.
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Shoaib S, Ansari MA, Kandasamy G, Vasudevan R, Hani U, Chauhan W, Alhumaidi MS, Altammar KA, Azmi S, Ahmad W, Wahab S, Islam N. An Attention towards the Prophylactic and Therapeutic Options of Phytochemicals for SARS-CoV-2: A Molecular Insight. Molecules 2023; 28:molecules28020795. [PMID: 36677853 PMCID: PMC9864057 DOI: 10.3390/molecules28020795] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
The novel pathogenic virus was discovered in Wuhan, China (December 2019), and quickly spread throughout the world. Further analysis revealed that the pathogenic strain of virus was corona but it was distinct from other coronavirus strains, and thus it was renamed 2019-nCoV or SARS-CoV-2. This coronavirus shares many characteristics with other coronaviruses, including SARS-CoV and MERS-CoV. The clinical manifestations raised in the form of a cytokine storm trigger a complicated spectrum of pathophysiological changes that include cardiovascular, kidney, and liver problems. The lack of an effective treatment strategy has imposed a health and socio-economic burden. Even though the mortality rate of patients with this disease is lower, since it is judged to be the most contagious, it is considered more lethal. Globally, the researchers are continuously engaged to develop and identify possible preventive and therapeutic regimens for the management of disease. Notably, to combat SARS-CoV-2, various vaccine types have been developed and are currently being tested in clinical trials; these have also been used as a health emergency during a pandemic. Despite this, many old antiviral and other drugs (such as chloroquine/hydroxychloroquine, corticosteroids, and so on) are still used in various countries as emergency medicine. Plant-based products have been reported to be safe as alternative options for several infectious and non-infectious diseases, as many of them showed chemopreventive and chemotherapeutic effects in the case of tuberculosis, cancer, malaria, diabetes, cardiac problems, and others. Therefore, plant-derived products may play crucial roles in improving health for a variety of ailments by providing a variety of effective cures. Due to current therapeutic repurposing efforts against this newly discovered virus, we attempted to outline many plant-based compounds in this review to aid in the fight against SARS-CoV-2.
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Affiliation(s)
- Shoaib Shoaib
- Department Biochemistry, Faculty of Medicine, J. N. Medical College, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
- Correspondence: (M.A.A.); (N.I.)
| | - Geetha Kandasamy
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University (KKU), Abha 62529, Saudi Arabia
| | - Rajalakshimi Vasudevan
- Department of Pharmacology, College of Pharmacy, King Khalid University (KKU), Abha 62529, Saudi Arabia
| | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University (KKU), Abha 62529, Saudi Arabia
| | - Waseem Chauhan
- Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Maryam S. Alhumaidi
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Khadijah A. Altammar
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Sarfuddin Azmi
- Molecular Microbiology Biology Division, Scientific Research Centre (SRC), Prince Sultan Military Medical City (PSMMC), Riyadh 11159, Saudi Arabia
| | - Wasim Ahmad
- Department of Pharmacy, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Shadma Wahab
- Deparment of Pharmacognosy, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | - Najmul Islam
- Department Biochemistry, Faculty of Medicine, J. N. Medical College, Aligarh Muslim University, Aligarh 202002, India
- Correspondence: (M.A.A.); (N.I.)
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Rao SS, Parthasarathy K, Sounderrajan V, Neelagandan K, Anbazhagan P, Chandramouli V. Susceptibility of SARS Coronavirus-2 infection in domestic and wild animals: a systematic review. 3 Biotech 2023; 13:5. [PMID: 36514483 PMCID: PMC9741861 DOI: 10.1007/s13205-022-03416-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/26/2022] [Indexed: 12/14/2022] Open
Abstract
Animals and viruses have constantly been co-evolving under natural circumstances and pandemic like situations. They harbour harmful viruses which can spread easily. In the recent times we have seen pandemic like situations being created as a result of the spread of deadly and fatal viruses. Coronaviruses (CoVs) are one of the wellrecognized groups of viruses. There are four known genera of Coronavirus family namely, alpha (α), beta (β), gamma (γ), and delta (δ). Animals have been infected with CoVs belonging to all four genera. In the last few decades the world has witnessed an emergence of severe acute respiratory syndromes which had created a pandemic like situation such as SARS CoV, MERS-CoV. We are currently in another pandemic like situation created due to the uncontrolled spread of a similar coronavirus namely SARSCoV-2. These findings are based on a small number of animals and do not indicate whether animals can transmit disease to humans. Several mammals, including cats, dogs, bank voles, ferrets, fruit bats, hamsters, mink, pigs, rabbits, racoon dogs, and white-tailed deer, have been found to be infected naturally by the virus. Certain laboratory discoveries revealed that animals such as cats, ferrets, fruit bats, hamsters, racoon dogs, and white-tailed deer can spread the illness to other animals of the same species. This review article gives insights on the current knowledge about SARS-CoV-2 infection and development in animals on the farm and in domestic community and their impact on society.
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Affiliation(s)
- Sudhanarayani S. Rao
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119 India
| | - Krupakar Parthasarathy
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119 India
| | - Vignesh Sounderrajan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119 India
| | - K. Neelagandan
- Centre for Chemical Biology and Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, India
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10
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Danova K, Motyka V, Trendafilova A, Dobrev PI, Ivanova V, Aneva I. Evolutionary Aspects of Hypericin Productivity and Endogenous Phytohormone Pools Evidenced in Hypericum Species In Vitro Culture Model. PLANTS (BASEL, SWITZERLAND) 2022; 11:2753. [PMID: 36297777 PMCID: PMC9609395 DOI: 10.3390/plants11202753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Shoot cultures of hypericin non-producing H. calycinum L. (primitive Ascyreia section), hypericin-producing H. perforatum L., H. tetrapterum Fries (section Hypericum) and H. richeri Vill. (the evolutionarily most advanced section Drosocarpium in our study) were developed and investigated for their growth, development, hypericin content and endogenous phytohormone levels. Hypericins in wild-growing H. richeri significantly exceeded those in H. perforatum and H. tetrapterum. H. richeri also had the highest hypericin productivity in vitro in medium supplemented with 0.2 mg/L N6-benzyladenine and 0.1 mg/L indole-3-butyric acid and H. tetrapterum-the lowest one in all media modifications. In shoot culture conditions, the evolutionarily oldest H. calycinum had the highest content of salicylic acid and total jasmonates in some of its treatments, as well as dominance of the storage form of abscisic acid (ABA-glucose ester) and lowest cytokinin ribosides and cytokinin O-glucosides as compared with the other three species. In addition, the evolutionarily youngest H. richeri was characterized by the highest total amount of cytokinin ribosides. Thus, both evolutionary development and the hypericin production capacity seemed to interact closely with the physiological parameters of the plant organism, such as endogenous phytohormones, leading to the possible hypothesis that hypericin productivity may have arisen in the evolution of Hypericum as a means to adapt to environmental changes.
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Affiliation(s)
- Kalina Danova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., bl.9, 1113 Sofia, Bulgaria
| | - Vaclav Motyka
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague, Czech Republic
| | - Antoaneta Trendafilova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., bl.9, 1113 Sofia, Bulgaria
| | - Petre I. Dobrev
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague, Czech Republic
| | - Viktorya Ivanova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., bl.9, 1113 Sofia, Bulgaria
| | - Ina Aneva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Str., 1113 Sofia, Bulgaria
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11
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Tuan NA, Khanh PN, Ha NX, Binh TC, Khanh ND, Oanh TT. Compounds Isolated from Lawsonia inermis L. Collected in Vietnam and Evaluation of Their Potential Activity Against the Main Protease of SARS-CoV-2 Using In silico Molecular Docking and Molecular Dynamic Simulation. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221125161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since late 2019 to early 2020, an outbreak caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has become a worldwide health emergency due to its rapid infection and mortality of millions of people around the world. As the main protease Mpro or 3CLpro produced by the virus plays an important role in coronavirus survival and proliferation, it becomes an excellent drug target to identify COVID-19 inhibitors. Lawsonia inermis L. (henna) is a medicinal plant that has been used for a long time for the treatment of many fungal and bacterial infections. In the search for new anti-COVID agents from medicinal plants, we report the results of our study into the potential inhibition of Mpro by the compounds isolated from the extracts of L. inermis roots and leaves using molecular docking and molecular dynamics simulation. The molecular modeling results showed that all isolated compounds bonded spontaneously into the catalytic pockets of Mpro with binding energies <0. The docking and calculated pharmacokinetic results of the compounds (1-3, 6-8) were similar to and even better than those of the commercial COVID-19 inhibitor remdesivir. In particular, the triterpenoid glycoside suavissimoside R1 (8) showed the best binding to SARS-CoV Mpro, with the lowest binding energy ΔG and IC50,calc. values of −8.19 kcal/mol and 0.98 μM, respectively. Furthermore, the calculations of ADMET (absorption, distribution, metabolism, excretion, and toxicity) showed that it had the lowest toxicity, with a predicted LD50 value of 3320 mg/kg. These triterpenoids are worthy of further study to evaluate their actual bioactivity against SARS-CoV-2 in vitro and in vivo in the hope of contributing valuable scientific data for natural resources for the development novel drug formulations for either the prevention or treatment of COVID-19.
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Affiliation(s)
- Nguyen Anh Tuan
- Institute for Research and Development of Organic Products (IRDOP), Hanoi, Vietnam
| | - Pham Ngoc Khanh
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- College of Pharmacy, Peace University, Hanoi, Vietnam
| | - Nguyen Xuan Ha
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ta Chi Binh
- Institute for Research and Development of Organic Products (IRDOP), Hanoi, Vietnam
| | - Nguyen Duy Khanh
- Institute for Research and Development of Organic Products (IRDOP), Hanoi, Vietnam
| | - Tran Thị Oanh
- Institute for Research and Development of Organic Products (IRDOP), Hanoi, Vietnam
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12
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The Main Protease of SARS-CoV-2 as a Target for Phytochemicals against Coronavirus. PLANTS 2022; 11:plants11141862. [PMID: 35890496 PMCID: PMC9319234 DOI: 10.3390/plants11141862] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 11/23/2022]
Abstract
In late December 2019, the first cases of COVID-19 emerged as an outbreak in Wuhan, China that later spread vastly around the world, evolving into a pandemic and one of the worst global health crises in modern history. The causative agent was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although several vaccines were authorized for emergency use, constantly emerging new viral mutants and limited treatment options for COVID-19 drastically highlighted the need for developing an efficient treatment for this disease. One of the most important viral components to target for this purpose is the main protease of the coronavirus (Mpro). This enzyme is an excellent target for a potential drug, as it is essential for viral replication and has no closely related homologues in humans, making its inhibitors unlikely to be toxic. Our review describes a variety of approaches that could be applied in search of potential inhibitors among plant-derived compounds, including virtual in silico screening (a data-driven approach), which could be structure-based or fragment-guided, the classical approach of high-throughput screening, and antiviral activity cell-based assays. We will focus on several classes of compounds reported to be potential inhibitors of Mpro, including phenols and polyphenols, alkaloids, and terpenoids.
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13
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Feng Y, Cheng X, Wu S, Mani Saravanan K, Liu W. Hybrid drug-screening strategy identifies potential SARS-CoV-2 cell-entry inhibitors targeting human transmembrane serine protease. Struct Chem 2022; 33:1503-1515. [PMID: 35571866 PMCID: PMC9091140 DOI: 10.1007/s11224-022-01960-w] [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: 02/28/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022]
Abstract
The spread of coronavirus infectious disease (COVID-19) is associated with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has risked public health more than any other infectious disease. Researchers around the globe use multiple approaches to identify an effective approved drug (drug repurposing) that treats viral infections. Most of the drug repurposing approaches target spike protein or main protease. Here we use transmembrane serine protease 2 (TMPRSS2) as a target that can prevent the virus entry into the cell by interacting with the surface receptors. By hypothesizing that the TMPRSS2 binders may help prevent the virus entry into the cell, we performed a systematic drug screening over the current approved drug database. Furthermore, we screened the Enamine REAL fragments dataset against the TMPRSS2 and presented nine potential drug-like compounds that give us clues about which kinds of groups the pocket prefers to bind, aiding future structure-based drug design for COVID-19. Also, we employ molecular dynamics simulations, binding free energy calculations, and well-tempered metadynamics to validate the obtained candidate drug and fragment list. Our results suggested three potential FDA-approved drugs against human TMPRSS2 as a target. These findings may pave the way for more drugs to be exposed to TMPRSS2, and testing the efficacy of these drugs with biochemical experiments will help improve COVID-19 treatment.
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14
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Fatima SW, Alam S, Khare SK. Molecular and structural insights of β-boswellic acid and glycyrrhizic acid as potent SARS-CoV-2 Envelope protein inhibitors. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 2:100241. [PMID: 35403092 PMCID: PMC8840829 DOI: 10.1016/j.phyplu.2022.100241] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
BACKGROUND Over million people have been infected with SARS-CoV-2 virus worldwide, with around 3% reported deaths till date. A few conventional antiviral treatments have been tried to mitigate the coronavirus. However, many alternative therapeutics are being evaluated worldwide. In the present study, we investigated traditional Indian medicinal compounds antiviral potencies as an effective drug for targeting SARS-CoV-2E. SARS-CoV-2 E protein plays a key role in coronavirus life cycle and is an interesting target for the development of anti-SARS-CoV-2 E drugs. METHODS Molecular docking studies of medicinal compounds possessing wide range of pharmacological and antiviral activities against enveloped viruses were evaluated with the computer-aided drug design screening software; PyRx. Twelve medicinal compounds isolated from plants were screened and visualized on Biovia Discovery-Studio. Moreover, SARS-CoV-2 E protein's secondary structural insights were deciphered using Swiss Model and ProFunc web server. RESULTS Glycyrrhizic acid, triterpene glycoside isolated from plants of Glycyrrhiza (licorice) showed interactions with envelope protein at chain A: Arg 61, chain B: Phe 23, chain B: Tyr 57, and chain C: Val 25. β- boswellic acid, an ayurvedic herb (pentacyclic terpenoid are produced by Boswellia) represented direct interactions and indirect binding with chain C. Their pharmacological aspects and drug-likeness properties were deduced by DruLiTo. Toxicological assessment, along with their ADME profiling, was validated using vNNADMET. The findings showed that ligands, β-boswellic acid, and glycyrrhizic acid possessed the best bindings, with the target having binding affinity (-9.1 kcal/mol) amongst compounds tested against SARS-CoV-2 E. In-vitro studies reveals the promising effect as potent SARS-CoV-2 E inhibitors. Functionality loss and structural disruptions with ∼90% were observed by UV-spectra and fluorescent based analyses. CONCLUSION The study demonstrated that β-boswellic acid, and glycyrrhizic acid are strong SARS-CoV-2 E protein inhibitors. In addition, the work linked GA antiviral activity to its effect on SARS-CoV- 2 E protein that can pave the way for designing antiviral therapeutics.
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Affiliation(s)
- Syeda Warisul Fatima
- Enzyme and Microbial Biochemistry Laboratory,Department of Chemistry,Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shahenvaz Alam
- Enzyme and Microbial Biochemistry Laboratory,Department of Chemistry,Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Sunil K Khare
- Enzyme and Microbial Biochemistry Laboratory,Department of Chemistry,Indian Institute of Technology Delhi, New Delhi 110016, India
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15
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Xiong X, Tang N, Lai X, Zhang J, Wen W, Li X, Li A, Wu Y, Liu Z. Insights Into Amentoflavone: A Natural Multifunctional Biflavonoid. Front Pharmacol 2022; 12:768708. [PMID: 35002708 PMCID: PMC8727548 DOI: 10.3389/fphar.2021.768708] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Amentoflavone is an active phenolic compound isolated from Selaginella tamariscina over 40 years. Amentoflavone has been extensively recorded as a molecule which displays multifunctional biological activities. Especially, amentoflavone involves in anti-cancer activity by mediating various signaling pathways such as extracellular signal-regulated kinase (ERK), nuclear factor kappa-B (NF-κB) and phosphoinositide 3-kinase/protein kinase B (PI3K/Akt), and emerges anti-SARS-CoV-2 effect via binding towards the main protease (Mpro/3CLpro), spike protein receptor binding domain (RBD) and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Therefore, amentoflavone is considered to be a promising therapeutic agent for clinical research. Considering the multifunction of amentoflavone, the current review comprehensively discuss the chemistry, the progress in its diverse biological activities, including anti-inflammatory, anti-oxidation, anti-microorganism, metabolism regulation, neuroprotection, radioprotection, musculoskeletal protection and antidepressant, specially the fascinating role against various types of cancers. In addition, the bioavailability and drug delivery of amentoflavone, the molecular mechanisms underlying the activities of amentoflavone, the molecular docking simulation of amentoflavone through in silico approach and anti-SARS-CoV-2 effect of amentoflavone are discussed.
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Affiliation(s)
- Xifeng Xiong
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Nan Tang
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Xudong Lai
- Department of Infectious Disease, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Jinli Zhang
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Weilun Wen
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Xiaojian Li
- Department of Burn and Plastic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Aiguo Li
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Yanhua Wu
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Zhihe Liu
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
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16
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Verma D, Mitra D, Paul M, Chaudhary P, Kamboj A, Thatoi H, Janmeda P, Jain D, Panneerselvam P, Shrivastav R, Pant K, Das Mohapatra PK. Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL pro and M pro/ 3CL pro: molecular docking and simulation studies of three pertinent medicinal plant natural components. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100038. [PMID: 34870149 PMCID: PMC8178537 DOI: 10.1016/j.crphar.2021.100038] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - coronavirus disease 2019 (COVID-19) has raised a severe global public health issue and creates a pandemic situation. The present work aims to study the molecular -docking and dynamic of three pertinent medicinal plants i.e. Eurycoma harmandiana, Sophora flavescens and Andrographis paniculata phyto-compounds against SARS-COV-2 papain-like protease (PLpro) and main protease (Mpro)/3-chymotrypsin-like protease (3CLpro). The interaction of protein targets and ligands was performed through AutoDock-Vina visualized using PyMOL and BIOVIA-Discovery Studio 2020. Molecular docking with canthin-6-one 9-O-beta-glucopyranoside showed highest binding affinity and less binding energy with both PLpro and Mpro/3CLpro proteases and was subjected to molecular dynamic (MD) simulations for a period of 100ns. Stability of the protein-ligand complexes was evaluated by different analyses. The binding free energy calculated using MM-PBSA and the results showed that the molecule must have stable interactions with the protein binding site. ADMET analysis of the compounds suggested that it is having drug-like properties like high gastrointestinal (GI) absorption, no blood-brain barrier permeability and high lipophilicity. The outcome revealed that canthin-6-one 9-O-beta-glucopyranoside can be used as a potential natural drug against COVID-19 protease.
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Affiliation(s)
- Devvret Verma
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, 248 002, Uttarakhand, India
| | - Debasis Mitra
- Department of Microbiology, Raiganj University, Raiganj, 733 134, Uttar Dinajpur, West Bengal, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, 757003, Odisha, India
| | - Priya Chaudhary
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, 304022, Rajasthan, India
| | - Anshul Kamboj
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, 248 002, Uttarakhand, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, 757003, Odisha, India
| | - Pracheta Janmeda
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, 304022, Rajasthan, India
| | - Divya Jain
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, 304022, Rajasthan, India
| | - Periyasamy Panneerselvam
- Microbiology, Crop Production Division, ICAR- National Rice Research Institute, Cuttack, 753 006, Odisha, India
| | - Rakesh Shrivastav
- Department of Applied Sciences, NGF College of Engineering and Technology, Palwal, Haryana, India
| | - Kumud Pant
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, 248 002, Uttarakhand, India
| | - Pradeep K Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj, 733 134, Uttar Dinajpur, West Bengal, India.,PAKB Environment Conservation Centre, Raiganj University, Raiganj, 733 134, Uttar Dinajpur, West Bengal, India
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17
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Zhang Y, Chen H, Zou M, Oerlemans R, Shao C, Ren Y, Zhang R, Huang X, Li G, Cong Y. Hypericin Inhibit Alpha-Coronavirus Replication by Targeting 3CL Protease. Viruses 2021; 13:v13091825. [PMID: 34578406 PMCID: PMC8473218 DOI: 10.3390/v13091825] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
The porcine epidemic diarrhea virus (PEDV) is an Alphacoronavirus (α-CoV) that causes high mortality in infected piglets, resulting in serious economic losses in the farming industry. Hypericin is a dianthrone compound that has been shown as an antiviral activity on several viruses. Here, we first evaluated the antiviral effect of hypericin in PEDV and found the viral replication and egression were significantly reduced with hypericin post-treatment. As hypericin has been shown in SARS-CoV-2 that it is bound to viral 3CLpro, we thus established a molecular docking between hypericin and PEDV 3CLpro using different software and found hypericin bound to 3CLpro through two pockets. These binding pockets were further verified by another docking between hypericin and PEDV 3CLpro pocket mutants, and the fluorescence resonance energy transfer (FRET) assay confirmed that hypericin inhibits the PEDV 3CLpro activity. Moreover, the alignments of α-CoV 3CLpro sequences or crystal structure revealed that the pockets mediating hypericin and PEDV 3CLpro binding were highly conserved, especially in transmissible gastroenteritis virus (TGEV). We then validated the anti-TGEV effect of hypericin through viral replication and egression. Overall, our results push forward that hypericin was for the first time shown to have an inhibitory effect on PEDV and TGEV by targeting 3CLpro, and it deserves further attention as not only a pan-anti-α-CoV compound but potentially also as a compound of other coronaviral infections.
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Affiliation(s)
- Yue Zhang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Huijie Chen
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- College of Pharmaceutical Engineering, Jilin Agriculture Science and Technology University, Jilin 132101, China
| | - Mengmeng Zou
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Rick Oerlemans
- Department of Drug Design, University of Groningen, 9713 AV Groningen, The Netherlands;
| | - Changhao Shao
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Yudong Ren
- Department of Computer Science and Technology, College of Electrical and Information Technology, Northeast Agricultural University, Harbin 150030, China;
| | - Ruili Zhang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Xiaodan Huang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Guangxing Li
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- Correspondence: (G.L.); (Y.C.)
| | - Yingying Cong
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
- Correspondence: (G.L.); (Y.C.)
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18
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Fouedjou RT, Chtita S, Bakhouch M, Belaidi S, Ouassaf M, Djoumbissie LA, Tapondjou LA, Abul Qais F. Cameroonian medicinal plants as potential candidates of SARS-CoV-2 inhibitors. J Biomol Struct Dyn 2021; 40:8615-8629. [PMID: 33908318 DOI: 10.1080/07391102.2021.1914170] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an ongoing pandemic instigated by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) which changed the daily train of the world's population and cause several dead. Despite the significant efforts made in developing vaccines and therapeutic drugs, there is currently no available effective treatment against this new coronavirus infection, hence the need to continue research which is aimed at limiting the progression of this virus. The present study which has as objective to carry out in silico studies on the metabolites of some Cameroonian medicinal plants of the Asteraceae family with a view to propose potential molecules to fight against COVID-19. The selected plants are commonly used to treat respiratory infectious diseases, and for this reason they may contain some constituents which could exhibit an antiviral activity against SARS-CoV-2. In this work, a set of 74 naturally occurring compounds are computed with SARS-CoV-2 main protease protein (PDB ID: 6lu7) and spike protein (PDB ID: 6m0j) for their affinity and stability using binding energy analysis and molecular docking. Chrysoeriol-7-O-β-D-glucuronopyranoside (compound 16) has showed promising results including excellent Absorption, Distribution, Metabolism and Excretion (ADME) parameters as well as insignificant toxicity. Finally, the stability of this compound is complex with the two proteins validated through molecular dynamics (MD) simulation, they displayed stable trajectory and molecular properties with consistent interaction profile in molecular dynamics simulations. These findings call for further in vitro and in vivo challenges of phytoconstituents against the COVID-19 as a potential agent to fight the spread of this dramatic pandemic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Romuald Tematio Fouedjou
- Research Unit of Environmental and Applied Chemistry, Department of Chemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Samir Chtita
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohamed Bakhouch
- Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - Salah Belaidi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria.,Centre de Recherche en Sciences Pharmaceutiques - CRSP-la nouvelle ville Ali Mendjeli, Constantine, Algérie
| | - Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Loris Alvine Djoumbissie
- Research Unit of Noxious Chemistry and Environmental Engineering, Department of Chemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Léon Azefack Tapondjou
- Research Unit of Environmental and Applied Chemistry, Department of Chemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
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19
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Miroshnychenko KV, Shestopalova AV. Combined use of the hepatitis C drugs and amentoflavone could interfere with binding of the spike glycoprotein of SARS-CoV-2 to ACE2: the results of a molecular simulation study. J Biomol Struct Dyn 2021; 40:8672-8686. [PMID: 33896392 PMCID: PMC8074653 DOI: 10.1080/07391102.2021.1914168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
The worldwide rapid spread of the COVID-19 disease necessitates the search for fast and effective treatments. The repurposing of existing drugs seems to be the best solution in this situation. In this study, the molecular docking method was used to test 248 drugs against the receptor-binding domain (RBD) of spike glycoprotein of SARS-CoV-2, which is responsible for viral entry into the host cell. Among the top-ranked ligands are drugs that are used for hepatitis C virus (HCV) treatments (paritaprevir, ledipasvir, simeprevir) and a natural biflavonoid amentoflavone. The binding sites of the HCV drugs and amentoflavone are different. Therefore, the ternary complexes of the HCV drug, amentoflavone, and RBD can be created. For the 5 top-ranked ligands, the validating molecular dynamics simulations of binary and ternary complexes with RBD were performed. According to the MMPBSA-binding free energies, the HCV drugs ledipasvir and paritaprevir (in a neutral form) are the most efficient binders of the RBD when used in combination with amentoflavone.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Anna V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics of NAS of Ukraine, Kharkiv, Ukraine
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
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20
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Maddah M, Bahramsoltani R, Yekta NH, Rahimi R, Aliabadi R, Pourfath M. Proposing high-affinity inhibitors from Glycyrrhiza glabra L. against SARS-CoV-2 infection: virtual screening and computational analysis. NEW J CHEM 2021. [DOI: 10.1039/d1nj02031e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Licorice as a traditional medicine introduces promising antiviral phytochemicals against SARS-CoV-2.
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Affiliation(s)
- Mina Maddah
- School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Iran
- Super Computing Institute, University of Tehran, Tehran, Iran
| | - Roodabeh Bahramsoltani
- Department of Traditional Pharmacy, School of Persian Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Nafiseh Hoseini Yekta
- Department of Persian Medicine, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Roja Rahimi
- Department of Traditional Pharmacy, School of Persian Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Phytopharmacology Interest Group (PPIG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Rasoul Aliabadi
- School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Iran
| | - Mahdi Pourfath
- School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Iran
- Super Computing Institute, University of Tehran, Tehran, Iran
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