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Saravanan K, Elavarasi S, Revathi G, Karuppannan P, Ashokkumar M, Muthusamy C, Ram Kumar A. Targeting SARS-CoV2 spike glycoprotein: molecular insights into phytocompounds binding interactions - in-silico molecular docking. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2024:1-18. [PMID: 39225011 DOI: 10.1080/09205063.2024.2399395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
This study utilized small molecular characterization and docking study to evaluate the binding affinity of seven antiviral phytocompounds with the SARS CoV-2 variants (SARS-CoV-2 Spike Glycoprotein, SARS-CoV-2 Spike Protein Variant in 1-RBD, Alpha Variant SARS-CoV2- Spike Protein). The results revealed that five of seven compounds, possesses excellent drug lead property reveled through in-silico ADMET analysis. In addition, six of seven except D-Glucosamine, exhibited excellent binding affinity. Six ligands possess significant binding affinity towards SARS-CoV-2 variants 6VXX, 7LWV and 7R13, which is certainly greater than Remdesivir. Fagaronine found to be the best drug candidate against SARS-CoV-2 variants, It was found that -7.4, -5.6 and -6.3 is the docking score respectively. Aranotin, Beta aescin, Gliotoxin, and Fagaronine formed hydrogen bonds with specific amino acids and exhibited significant binding interactions. These findings suggest that these phytocompounds could be promising candidates for developing antiviral therapies against SARS-CoV-2. Moreover, the study underscores the importance of molecular docking in understanding protein-ligand interactions and its role in drug discovery. The documented pharmacological properties of these compounds in the literature further support their potential therapeutic relevance in various diseases.
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Affiliation(s)
- K Saravanan
- PG and Research Dept. of Zoology, Nehru Memorial College (Autonomous), Puthanampatti, Thiruchirappalli, Tamilnadu, India
| | - S Elavarasi
- PG and Research Dept. of Zoology, Holy Cross College (Autonomous), Thiruchirappalli, Tamilnadu, India
| | - G Revathi
- PG and Research Dept. of Zoology, Nehru Memorial College (Autonomous), Puthanampatti, Thiruchirappalli, Tamilnadu, India
| | - P Karuppannan
- PG and Research Dept. of Zoology, Vivekananda College of Arts and Science for women (Autonomous), Tiruchengode, Tamilnadu, India
| | - M Ashokkumar
- Department of Physics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, India
| | - C Muthusamy
- Department of Food Technology, School of Liberal Arts and Applied Sciences, Hindustan Institute of Technology and Science, Padur, OMR, Chennai, Tamilnadu, India
| | - A Ram Kumar
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, Tamil Nadu, India
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2
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Menacer R, Bouchekioua S, Meliani S, Belattar N. New combined Inverse-QSAR and molecular docking method for scaffold-based drug discovery. Comput Biol Med 2024; 180:108992. [PMID: 39128176 DOI: 10.1016/j.compbiomed.2024.108992] [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: 03/25/2024] [Revised: 07/14/2024] [Accepted: 08/02/2024] [Indexed: 08/13/2024]
Abstract
Computer-aided drug discovery plays a vital role in developing novel medications for various diseases. The COVID-19 pandemic has heightened the need for innovative approaches to design lead compounds with the potential to become effective drugs. Specifically, designing promising inhibitors of the SARS-CoV-2 main protease (Mpro) is crucial, as it plays a key role in viral replication. Phytochemicals, primarily flavonoids and flavonols from medicinal plants, were screened. Fifty small molecules were selected for molecular docking analysis against SARS-CoV-2 Mpro (PDB ID: 6LU7). Binding energies and interactions were analyzed and compared to those of the anti-SARS-CoV-2 inhibitor Nirmatrelvir. Using these 50 structures as a training set, a QSAR model was built employing simple, reversible topological descriptors. An inverse-QSAR analysis was then performed on 2⁹ = 512 hydroxyl combinations at nine possible positions on the flavone and flavonol scaffold. The model predicted three novel, promising compounds exhibiting the most favorable binding energies (-8.5 kcal/mol) among the 512 possible hydroxyl combinations: 3,6,7,2',4'-pentahydroxyflavone (PF9), 6,7,2',4'-tetrahydroxyflavone (PF11), and 3,6,7,4'-tetrahydroxyflavone (PF15). Molecular dynamics (MD) simulations demonstrated the stability of the PF9/Mpro complex over 300 ns of simulation. These predicted structures, reported here for the first time, warrant synthesis and further evaluation of their biological activity through in vitro and in vivo studies.
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Affiliation(s)
- Rafik Menacer
- Centre de Recherche en Sciences Pharmaceutiques, Constantine, 25000, Algeria; Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques CRAPC, BP 384, Zone Industrielle, Bou-ismail, Tipaza, RP, 42004, Algeria.
| | - Saad Bouchekioua
- Centre de Recherche en Sciences Pharmaceutiques, Constantine, 25000, Algeria
| | - Saida Meliani
- Centre de Recherche en Sciences Pharmaceutiques, Constantine, 25000, Algeria
| | - Nadjah Belattar
- Centre de Recherche en Sciences Pharmaceutiques, Constantine, 25000, Algeria
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3
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Ma H, Wang Y, Li YX, Xie BK, Hu ZL, Yu RJ, Long YT, Ying YL. Label-Free Mapping of Multivalent Binding Pathways with Ligand-Receptor-Anchored Nanopores. J Am Chem Soc 2024. [PMID: 39180483 DOI: 10.1021/jacs.4c04934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
Understanding single-molecule multivalent ligand-receptor interactions is crucial for comprehending molecular recognition at biological interfaces. However, label-free identifications of these transient interactions during multistep binding processes remains challenging. Herein, we introduce a ligand-receptor-anchored nanopore that allows the protein to maintain structural flexibility and favorable orientations in native states, mapping dynamic multivalent interactions. Using a four-state Markov chain model, we clarify two concentration-dependent binding pathways for the Omicron spike protein (Omicron S) and soluble angiotensin-converting enzyme 2 (sACE2): sequential and concurrent. Real-time kinetic analysis at the single-monomeric subunit level reveals that three S1 monomers of Omicron S exhibit a consistent and robust binding affinity toward sACE2 (-13.1 ± 0.2 kcal/mol). These results highlight the enhanced infectivity of Omicron S compared to other homologous spike proteins (WT S and Delta S). Notably, the preceding binding of sACE2 to Omicron S facilitates the subsequent binding steps, which was previously obscured in bulk measurements. Our single-molecule studies resolve the controversy over the disparity between the measured spike protein binding affinity with sACE2 and the viral infectivity, offering valuable insights for drug design and therapies.
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Affiliation(s)
- Hui Ma
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yongyong Wang
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Ya-Xue Li
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Bao-Kang Xie
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Zheng-Li Hu
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Ru-Jia Yu
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China
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4
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Tatsing Foka FE, Tumelo Mufhandu H. Predictive Assessment of the Antiviral Properties of Imperata cylindrica against SARS-CoV-2. Adv Virol 2024; 2024:8598708. [PMID: 39135917 PMCID: PMC11317227 DOI: 10.1155/2024/8598708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 06/26/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024] Open
Abstract
The omicron variant and its sublineages are highly contagious, and they still constitute a global source of concern despite vaccinations. Hospitalizations and mortality rates resulting from infections by these variants of concern are still common. The existing therapeutic alternatives have presented various setbacks such as low potency, poor pharmacokinetic profiles, and drug resistance. The need for alternative therapeutic options cannot be overemphasized. Plants and their phytochemicals present interesting characteristics that make them suitable candidates for the development of antiviral therapeutic agents. This study aimed to investigate the antiviral potential of Imperata cylindrica (I. cylindrica). Specifically, the objective of this study was to identify I. cylindrica phytochemicals that display inhibitory effects against SARS-CoV-2 main protease (Mpro), a highly conserved protein among coronaviruses. Molecular docking and in silico pharmacokinetic assays were used to assess 72 phytocompounds that are found in I. cylindrica as ligands and Mpro (6LU7) as the target. Only eight phytochemicals (bifendate, cylindrene, tabanone, siderin, 5-hydroxy-2-[2-(2-hydroxyphenyl)ethyl]-4H-1-benzopyran-4-one, maritimin, 5-methoxyflavone, and flavone) displayed high binding affinities with Mpro with docking scores ranging from -5.6 kcal/mol to -9.1 kcal/mol. The in silico pharmacokinetic and toxicological assays revealed that tabanone was the best and safest phytochemical for the development of an inhibitory agent against coronavirus main protease. Thus, the study served as a baseline for further in vitro and in vivo assessment of this phytochemical against Mpro of SARS-CoV-2 variants of concern to validate these in silico findings.
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Affiliation(s)
- Frank Eric Tatsing Foka
- Department of Microbiology Virology Laboratory School of Biological Sciences Faculty of Natural and Agricultural Sciences North West University, Mafikeng, Private Bag X2046, Mmabatho, South Africa
| | - Hazel Tumelo Mufhandu
- Department of Microbiology Virology Laboratory School of Biological Sciences Faculty of Natural and Agricultural Sciences North West University, Mafikeng, Private Bag X2046, Mmabatho, South Africa
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5
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Bugnon M, Röhrig UF, Goullieux M, Perez MS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res 2024; 52:W324-W332. [PMID: 38686803 PMCID: PMC11223881 DOI: 10.1093/nar/gkae300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions between small molecules and macromolecular targets and potentially accelerating screening campaigns. SwissDock is a computational tool released in 2011 as part of the SwissDrugDesign project, providing a free web-based service for small-molecule docking after automatized preparation of ligands and targets. Here, we present the latest version of SwissDock, in which EADock DSS has been replaced by two state-of-the-art docking programs, i.e. Attracting Cavities and AutoDock Vina. AutoDock Vina provides faster docking predictions, while Attracting Cavities offers more accurate results. Ligands can be imported in various ways, including as files, SMILES notation or molecular sketches. Targets can be imported as PDB files or identified by their PDB ID. In addition, advanced search options are available both for ligands and targets, giving users automatized access to widely-used databases. The web interface has been completely redesigned for interactive submission and analysis of docking results. Moreover, we developed a user-friendly command-line access which, in addition to all options of the web site, also enables covalent ligand docking with Attracting Cavities. The new version of SwissDock is freely available at https://www.swissdock.ch/.
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Affiliation(s)
- Marine Bugnon
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Mathilde Goullieux
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Marta A S Perez
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Antoine Daina
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology, Geneva University Hospital (HUG), CH-1205 Geneva, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology UNIL-CHUV, Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, CH-1015 Lausanne, Switzerland
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6
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Kowalczyk A. Hesperidin, a Potential Antiviral Agent against SARS-CoV-2: The Influence of Citrus Consumption on COVID-19 Incidence and Severity in China. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:892. [PMID: 38929512 PMCID: PMC11206107 DOI: 10.3390/medicina60060892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024]
Abstract
This review examines hesperidin, a citrus bioflavonoid, as a potential antiviral agent against SARS-CoV-2. The COVID-19 pandemic has demanded an urgent need to search for effective antiviral compounds, including those of natural origin, such as hesperidin. The review provides a comprehensive analysis of the chemical properties, bioavailability and antiviral mechanisms of hesperidin, particularly its potential efficacy against SARS-CoV-2. A review of databases, including PubMedPico, Scopus and Web of Science, was conducted using specific keywords and search criteria in accordance with PRISMA (Re-porting Items for Systematic Reviews and Meta-Analysis) guidelines between 2020 and 2024. Of the 207 articles, 37 were selected for the review. A key aspect is the correlation of in vitro, in silico and clinical studies on the antiviral effects of hesperidin with epidemiological data on citrus consumption in China during 2020-2024. The importance of integrating laboratory findings with actual consumption patterns to better understand the role of hesperidin in mitigating COVID-19 was highlighted, and an attempt was made to analyze epidemiological studies to examine the association between citrus juice consumption as a source of hesperidin and the incidence and severity of COVID-19 using China as an example. The review identifies consistencies and discrepancies between experimental and epidemiological data, highlighting the need to correlate the two fields to better understand the potential of hesperidin as an agent against SARS-CoV-2. Challenges and limitations in interpreting the results and future research perspectives in this area are discussed. The aim of this comprehensive review is to bridge the gap between experimental studies and epidemiological evidence and to contribute to the understanding of their correlation.
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Affiliation(s)
- Adam Kowalczyk
- Department of Pharmacognosy and Herbal Medicines, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wrocław, Poland
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7
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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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8
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Shang W, Hu X, Lin X, Li S, Xiong S, Huang B, Wang X. Iterative In Silico Screening for Optimizing Stable Conformation of Anti-SARS-CoV-2 Nanobodies. Pharmaceuticals (Basel) 2024; 17:424. [PMID: 38675386 PMCID: PMC11054880 DOI: 10.3390/ph17040424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Nanobodies (Nbs or VHHs) are single-domain antibodies (sdAbs) derived from camelid heavy-chain antibodies. Nbs have special and unique characteristics, such as small size, good tissue penetration, and cost-effective production, making Nbs a good candidate for the diagnosis and treatment of viruses and other pathologies. Identifying effective Nbs against COVID-19 would help us control this dangerous virus or other unknown variants in the future. Herein, we introduce an in silico screening strategy for optimizing stable conformation of anti-SARS-CoV-2 Nbs. Firstly, various complexes containing nanobodies were downloaded from the RCSB database, which were identified from immunized llamas. The primary docking between Nbs and the SARS-CoV-2 spike protein receptor-binding domain was performed through the ClusPro program, with the manual screening leaving the reasonable conformation to the next step. Then, the binding distances of atoms between the antigen-antibody interfaces were measured through the NeighborSearch algorithm. Finally, filtered nanobodies were acquired according to HADDOCK scores through HADDOCK docking the COVID-19 spike protein with nanobodies under restrictions of calculated molecular distance between active residues and antigenic epitopes less than 4.5 Å. In this way, those nanobodies with more reasonable conformation and stronger neutralizing efficacy were acquired. To validate the efficacy ranking of the nanobodies we obtained, we calculated the binding affinities (∆G) and dissociation constants (Kd) of all screened nanobodies using the PRODIGY web tool and predicted the stability changes induced by all possible point mutations in nanobodies using the MAESTROWeb server. Furthermore, we examined the performance of the relationship between nanobodies' ranking and their number of mutation-sensitive sites (Spearman correlation > 0.68); the results revealed a robust correlation, indicating that the superior nanobodies identified through our screening process exhibited fewer mutation hotspots and higher stability. This correlation analysis demonstrates the validity of our screening criteria, underscoring the suitability of these nanobodies for future development and practical implementation. In conclusion, this three-step screening strategy iteratively in silico greatly improved the accuracy of screening desired nanobodies compared to using only ClusPro docking or default HADDOCK docking settings. It provides new ideas for the screening of novel antibodies and computer-aided screening methods.
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Affiliation(s)
| | | | | | | | | | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
| | - Xin Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
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9
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Ji Z, Deng W, Chen D, Liu Z, Shen Y, Dai J, Zhou H, Zhang M, Xu H, Dai B. Recent understanding of the mechanisms of the biological activities of hesperidin and hesperetin and their therapeutic effects on diseases. Heliyon 2024; 10:e26862. [PMID: 38486739 PMCID: PMC10937595 DOI: 10.1016/j.heliyon.2024.e26862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
Flavonoids are natural phytochemicals that have therapeutic effects and act in the prevention of several pathologies. These phytochemicals can be found in lemon, sweet orange, bitter orange, clementine. Hesperidin and hesperetin are citrus flavonoids from the flavanones subclass that have anti-inflammatory, antioxidant, antitumor and antibacterial potential. Preclinical studies and clinical trials demonstrated therapeutical effects of hesperidin and its aglycone hesperetin in various diseases, such as bone diseases, cardiovascular diseases, neurological diseases, respiratory diseases, digestive diseases, urinary tract diseases. This review provides a comprehensive overview of the biological activities of hesperidin and hesperetin, their therapeutic potential in various diseases and their associated molecular mechanisms. This article also discusses future considerations for the clinical applications of hesperidin and hesperetin.
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Affiliation(s)
| | | | - Dong Chen
- Binhai County People's Hospital, No.148, Middle Fudong Road, Dongkan Town, Binhai County, Yancheng City, 224500, China
| | - Zhidong Liu
- Binhai County People's Hospital, No.148, Middle Fudong Road, Dongkan Town, Binhai County, Yancheng City, 224500, China
| | - Yucheng Shen
- Binhai County People's Hospital, No.148, Middle Fudong Road, Dongkan Town, Binhai County, Yancheng City, 224500, China
| | - Jiuming Dai
- Binhai County People's Hospital, No.148, Middle Fudong Road, Dongkan Town, Binhai County, Yancheng City, 224500, China
| | - Hai Zhou
- Binhai County People's Hospital, No.148, Middle Fudong Road, Dongkan Town, Binhai County, Yancheng City, 224500, China
| | - Miao Zhang
- Binhai County People's Hospital, No.148, Middle Fudong Road, Dongkan Town, Binhai County, Yancheng City, 224500, China
| | - Hucheng Xu
- Binhai County People's Hospital, No.148, Middle Fudong Road, Dongkan Town, Binhai County, Yancheng City, 224500, China
| | - Bin Dai
- Binhai County People's Hospital, No.148, Middle Fudong Road, Dongkan Town, Binhai County, Yancheng City, 224500, China
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10
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Musini A, Singh HN, Vulise J, Pammi SSS, Archana Giri. Quercetin's antibiofilm effectiveness against drug resistant Staphylococcus aureus and its validation by in silico modeling. Res Microbiol 2024; 175:104091. [PMID: 37331493 DOI: 10.1016/j.resmic.2023.104091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 06/20/2023]
Abstract
Staphylococcus aureus is typically treated with antibiotics, however, due to its widespread and unselective usage, resistant strains of S. aureus have increased to a great extent. Treatment failure and recurring staphylococcal infections are also brought on by biofilm development, which boosts an organism's ability to withstand antibiotics and is thought to be a virulence factor in patients. The present study investigates the antibiofilm activity of naturally available polyphenol Quercetin against drug-resistant S. aureus. Micro dilution plating and tube adhesion methods were performed to evaluate the antibiofilm activity of quercetin against S. aureus. Quercetin treatment resulted in remarkably reduction of biofilm in S. aureus cells. Further we performed a study to investigate binding efficacies of quercetin with genes icaB and icaC from ica locus involved in biofilm formation. 3D structure of icaB, icaC and quercetin were retrieved from Protein data bank and PubChem chemical compound database, respectively. All computational simulation were carried out using AutoDock Vina and AutoDockTools (ADT) v 1.5.4. In silico study demonstrated a strong complex formation, large binding constants (Kb) and low free binding energy (ΔG) between quercetin and icaB (Kb = 1.63 × 10-5, ΔG = -7.2 k cal/mol) and icaC (Kb = 1.98 × 10-6, ΔG = -8.7 kcal/mol). This in silico analysis indicates that quercetin is capable of targeting icaB and icaC proteins which are essential for biofilm formation in S. aureus. Our study highlighted the antibiofilm activity of quercetin against drug resistant pathogen S.aureus.
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Affiliation(s)
- Anjaneyulu Musini
- Centre for Biotechnology, University College of Engineering, Science and Technology Hyderabad, Jawaharlal Nehru Technological University Hyderabad, 500085, India.
| | | | - Jhansi Vulise
- Centre for Biotechnology, University College of Engineering, Science and Technology Hyderabad, Jawaharlal Nehru Technological University Hyderabad, 500085, India
| | - S S Sravanthi Pammi
- Centre for Biotechnology, University College of Engineering, Science and Technology Hyderabad, Jawaharlal Nehru Technological University Hyderabad, 500085, India
| | - Archana Giri
- Centre for Biotechnology, University College of Engineering, Science and Technology Hyderabad, Jawaharlal Nehru Technological University Hyderabad, 500085, India
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11
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Pillai U J, Cherian L, Taunk K, Iype E, Dutta M. Identification of antiviral phytochemicals from cranberry as potential inhibitors of SARS-CoV-2 main protease (M pro). Int J Biol Macromol 2024; 261:129655. [PMID: 38266830 DOI: 10.1016/j.ijbiomac.2024.129655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Cranberry phytochemicals are known to possess antiviral activities. In the current study, we explored the therapeutic potential of cranberry against SARS-CoV-2 by targeting its main protease (Mpro) enzyme. Firstly, phytochemicals of cranberry origin were identified from three independent databases. Subsequently, virtual screening, using molecular docking and molecular dynamics simulation approaches, led to the identification of three lead phytochemicals namely, cyanidin 3-O-galactoside, β-carotene and epicatechin. Furthermore, in vitro enzymatic assays revealed that cyanidin 3-O-galactoside had the highest inhibitory potential with IC50 of 9.98 μM compared to the other two phytochemicals. Cyanidin 3-O-galactoside belongs to the class of anthocyanins. Anthocyanins extracted from frozen cranberry also exhibited the highest inhibitory potential with IC50 of 23.58 μg/ml compared to the extracts of carotenoids and flavanols, the class for β-carotene and epicatechin, respectively. Finally, we confirm the presence of the phytochemicals in the cranberry extracts using targeted LC-MS/MS analysis. Our results, therefore, indicate that the identified cranberry-derived bioactive compounds as well as cranberry could be used for therapeutic interventions against SARS-CoV-2.
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Affiliation(s)
- Jisha Pillai U
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates
| | - Lucy Cherian
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates
| | - Khushman Taunk
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Eldhose Iype
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Mainak Dutta
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates.
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12
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Xiao M, Dhungel S, Azad R, Favaro DC, Rajesh RP, Gardner KH, Kikani CK. Signal-regulated Unmasking of Nuclear Localization Motif in the PAS Domain Regulates the Nuclear Translocation of PASK. J Mol Biol 2024; 436:168433. [PMID: 38182104 PMCID: PMC10922792 DOI: 10.1016/j.jmb.2023.168433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The ligand-regulated PAS domains are one of the most diverse signal-integrating domains found in proteins from prokaryotes to humans. By biochemically connecting cellular processes with their environment, PAS domains facilitate an appropriate cellular response. PAS domain-containing Kinase (PASK) is an evolutionarily conserved protein kinase that plays important signaling roles in mammalian stem cells to establish stem cell fate. We have shown that the nuclear translocation of PASK is stimulated by differentiation signaling cues in muscle stem cells. However, the mechanistic basis of the regulation of PASK nucleo-cytoplasmic translocation remains unknown. Here, we show that the PAS-A domain of PASK contains a putative monopartite nuclear localization sequence (NLS) motif. This NLS is inhibited in cells through intramolecular association with a short linear motif, termed the PAS Interacting Motif (PIM), found upstream of the kinase domain. This interaction serves to retain PASK in the cytosol in the absence of signaling cues. Consistent with that, we show that metabolic inputs induce PASK nuclear import, likely by disrupting this association. We suggest that a route for such linkage may occur through the PAS-A ligand binding cavity. We show that PIM recruitment and artificial ligand binding to the PAS-A domain occur at neighboring locations that could facilitate metabolic control of the PAS-PIM interaction. Thus, the intramolecular interaction in PASK integrates metabolic signaling cues for nuclear translocation and could be targeted to control the balance between self-renewal and differentiation in stem cells.
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Affiliation(s)
- Michael Xiao
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Sajina Dhungel
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Roksana Azad
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Ph.D. Program in Biochemistry, Graduate Center, City University of New York, NY 10016, USA
| | - Denize C Favaro
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | | | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Department of Chemistry and Biochemistry, City College of New York, NY 10031, USA; Ph.D. Programs in Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, NY 10016, USA.
| | - Chintan K Kikani
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA.
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13
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Sharma V, Singh A, Chauhan S, Sharma PK, Chaudhary S, Sharma A, Porwal O, Fuloria NK. Role of Artificial Intelligence in Drug Discovery and Target Identification in Cancer. Curr Drug Deliv 2024; 21:870-886. [PMID: 37670704 DOI: 10.2174/1567201821666230905090621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/08/2023] [Accepted: 03/24/2023] [Indexed: 09/07/2023]
Abstract
Drug discovery and development (DDD) is a highly complex process that necessitates precise monitoring and extensive data analysis at each stage. Furthermore, the DDD process is both timeconsuming and costly. To tackle these concerns, artificial intelligence (AI) technology can be used, which facilitates rapid and precise analysis of extensive datasets within a limited timeframe. The pathophysiology of cancer disease is complicated and requires extensive research for novel drug discovery and development. The first stage in the process of drug discovery and development involves identifying targets. Cell structure and molecular functioning are complex due to the vast number of molecules that function constantly, performing various roles. Furthermore, scientists are continually discovering novel cellular mechanisms and molecules, expanding the range of potential targets. Accurately identifying the correct target is a crucial step in the preparation of a treatment strategy. Various forms of AI, such as machine learning, neural-based learning, deep learning, and network-based learning, are currently being utilised in applications, online services, and databases. These technologies facilitate the identification and validation of targets, ultimately contributing to the success of projects. This review focuses on the different types and subcategories of AI databases utilised in the field of drug discovery and target identification for cancer.
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Affiliation(s)
- Vishal Sharma
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Amit Singh
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Sanjana Chauhan
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Pramod Kumar Sharma
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Shubham Chaudhary
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Astha Sharma
- Department of Pharmacy, Galgotias University, Greater Noida, Uttar Pradesh, 201310, India
| | - Omji Porwal
- Department of Pharmacognosy, Faculty of Pharmacy, Tishk International University, Erbil 44001, Iraq
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14
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Ghosh S, Singha PS, Das LK, Ghosh D. Systematic Review on Major Antiviral Phytocompounds from Common Medicinal Plants against SARS-CoV-2. Med Chem 2024; 20:613-629. [PMID: 38317467 DOI: 10.2174/0115734064262843231120051452] [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: 05/17/2023] [Revised: 08/02/2023] [Accepted: 09/14/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Viral infections are rising around the globe and with evolving virus types and increasing varieties of viral invasions; the human body is developing antimicrobial resistance continuously. This is making the fight of mankind against viruses weak and unsecured. On the other hand, changing lifestyle, globalization and human activities adversely affecting the environment are opening up risks for new viral predominance on human race. In this context the world has witnessed the pandemic of the human Coronavirus disease (COVID-19) recently. The disease is caused by the Coronavirus namely Severe Acute Respiratory Syndrome Coronavirus 2 (SARSCoV- 2). METHODS AND MATERIALS Developing potential and effective vaccine is also time consuming and challenging. The huge resource of plants around us has rich source of potent antiviral compounds. Some of these molecules may serve as tremendously potent lead molecules whose slight structural modifications may give us highly bioactive antiviral derivatives of phytocompounds. Every geographical region is rich in unique plant biodiversity and hence every corner of the world with rich plant biodiversity can serve as abode for potential magical phytocompounds most of which have not been extensively explored for development of antiviral drug formulations against various viruses like the HIV, HPV etc., and the Coronavirus, also known as SARS-CoV-2 which causes the disease COVID-19. RESULTS Several phytocompounds from various medicinal plants have already been screened using in silico tools and some of them have yielded promising results establishing themselves as potent lead molecules for development of drugs against the highly mutating SARS-CoV-2 virus and thus these phytocompounds may be beneficial in treating COVID-19 and help human to win the life threatening battle against the deadly virus. CONCLUSION The best advantage is that these phytocompounds being derived from nature in most of the cases, come with minimum or no side effects compared to that of chemically synthesized conventional bioactive compounds and are indigenously available hence are the source of cost effective drug formulations with strong therapeutic potentials.
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Affiliation(s)
- Suvendu Ghosh
- Department of Physiology, Hooghly Mohsin College, Chinsura, Hooghly 712 101, West Bengal, India
| | - Partha Sarathi Singha
- Department of Chemistry, Government General Degree College, Kharagpur II, P.O Madpur, Dist, Paschim Medinipur, Pin: 721149, West Bengal, India
| | - Lakshmi Kanta Das
- Department of Chemistry, Government General Degree College, Kharagpur II, P.O Madpur, Dist, Paschim Medinipur, Pin: 721149, West Bengal, India
| | - Debosree Ghosh
- Department of Physiology, Government General Degree College, Kharagpur II, P.O Madpur, Dist, Paschim Medinipur, Pin: 721149, West Bengal, India
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15
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Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [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: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
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16
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Fauquet J, Carette J, Duez P, Zhang J, Nachtergael A. Microfluidic Diffusion Sizing Applied to the Study of Natural Products and Extracts That Modulate the SARS-CoV-2 Spike RBD/ACE2 Interaction. Molecules 2023; 28:8072. [PMID: 38138562 PMCID: PMC10745392 DOI: 10.3390/molecules28248072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The interaction between SARS-CoV-2 spike RBD and ACE2 proteins is a crucial step for host cell infection by the virus. Without it, the entire virion entrance mechanism is compromised. The aim of this study was to evaluate the capacity of various natural product classes, including flavonoids, anthraquinones, saponins, ivermectin, chloroquine, and erythromycin, to modulate this interaction. To accomplish this, we applied a recently developed a microfluidic diffusional sizing (MDS) technique that allows us to probe protein-protein interactions via measurements of the hydrodynamic radius (Rh) and dissociation constant (KD); the evolution of Rh is monitored in the presence of increasing concentrations of the partner protein (ACE2); and the KD is determined through a binding curve experimental design. In a second time, with the protein partners present in equimolar amounts, the Rh of the protein complex was measured in the presence of different natural products. Five of the nine natural products/extracts tested were found to modulate the formation of the protein complex. A methanol extract of Chenopodium quinoa Willd bitter seed husks (50 µg/mL; bisdesmoside saponins) and the flavonoid naringenin (1 µM) were particularly effective. This rapid selection of effective modulators will allow us to better understand agents that may prevent SARS-CoV-2 infection.
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Affiliation(s)
- Jason Fauquet
- Unit of Therapeutic Chemistry and Pharmacognosy, University of Mons (UMONS), 7000 Mons, Belgium; (J.F.); (P.D.); (A.N.)
| | - Julie Carette
- Unit of Therapeutic Chemistry and Pharmacognosy, University of Mons (UMONS), 7000 Mons, Belgium; (J.F.); (P.D.); (A.N.)
| | - Pierre Duez
- Unit of Therapeutic Chemistry and Pharmacognosy, University of Mons (UMONS), 7000 Mons, Belgium; (J.F.); (P.D.); (A.N.)
| | - Jiuliang Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Amandine Nachtergael
- Unit of Therapeutic Chemistry and Pharmacognosy, University of Mons (UMONS), 7000 Mons, Belgium; (J.F.); (P.D.); (A.N.)
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17
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Patar AK, Borah SM, Barman J, Bora A, Baruah TJ. Dronabinol as an answer to flavivirus infections: an in-silico investigation. J Biomol Struct Dyn 2023; 41:11219-11230. [PMID: 36576139 DOI: 10.1080/07391102.2022.2160817] [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: 09/23/2021] [Accepted: 12/15/2022] [Indexed: 12/29/2022]
Abstract
Flavivirus infections are common in several parts of the world. Two major types of flaviviruses are dengue and zika viruses. Both these two viral infections have caused many fatalities around the world. There is an absence of a vaccine and an effective medication against these viruses. In this study, we analyzed the ability of dronabinol to act as a potential cure against these viral infections. We performed the docking of dronabinol with several viral proteins followed by molecular dynamics simulation, MM/PBSA and PCA analysis. We checked the ability of the polyphenol dronabinol to interfere with the binding of viral helicases to their cellular targets. We performed 2 D-QSAR studies, drug likeliness, ADMET and target prediction studies. From our study, we observed that dronabinol had the best docking ability against the helicase proteins of dengue and zika. Molecular dynamics simulation and MM/PBSA investigation confirmed the stability of the binding while PCA investigation showed a lowering of molecular motions in response to dronabinol docking to the helicases. Dronabinol interfered in the binding of the helicases to RNA. 2 D QSAR studies revealed a low IC50 value for dronabinol. Dronabinol showed favorable drug-likeness, ADMET properties and target prediction results. Thus we propose dronabinol be further investigated in-vitro as a cure against dengue and zika virus infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abani Kumar Patar
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Sapna Mayuri Borah
- Department of Plant Pathology, Assam Agricultural University, Jorhat, Assam, India
| | - Jitul Barman
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Anupam Bora
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Taranga Jyoti Baruah
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
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18
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Dawoody Nejad L, Julian LM. Stem cell-derived organoid models for SARS-CoV-2 and its molecular interaction with host cells. Mol Biol Rep 2023; 50:10627-10635. [PMID: 37740859 DOI: 10.1007/s11033-023-08785-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/25/2023]
Abstract
Modeling severe acute respiratory syndrome, Coronavirus 2 (SARS-CoV-2) infection in stem cell-derived organoids has helped in our understanding of the molecular pathogenesis of COVID-19 disease due to their resemblance to actual human tissues or organs. Over the past decade, organoid 3-dimensional (3D) cultures have represented a new perspective and considerable advancement over traditional in vitro 2-dimensional (2D) cell cultures. COVID-19 disease causes lung injury and multi-organ failure leading to death, especially in older patients. There is an urgent need for physiological models to study SARS-CoV-2 infection during the pandemic. Human stem cell-derived organoids can provide insight into understanding the SARS-CoV-2 cell entry molecular mechanism. Identifying such complexities will help to develop the best preventive drug targets.
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Affiliation(s)
- Ladan Dawoody Nejad
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada.
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.
- Department of Medical Genetics, Life Science Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Lisa Marie Julian
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, Canada
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19
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He Z, Yuan J, Zhang Y, Li R, Mo M, Wang Y, Ti H. Recent advances towards natural plants as potential inhibitors of SARS-Cov-2 targets. PHARMACEUTICAL BIOLOGY 2023; 61:1186-1210. [PMID: 37605622 PMCID: PMC10446791 DOI: 10.1080/13880209.2023.2241518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/29/2023] [Accepted: 07/23/2023] [Indexed: 08/23/2023]
Abstract
CONTEXT Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still ongoing and currently the most striking epidemic disease. With the rapid global spread of SARS-CoV-2 variants, new antivirals are urgently needed to avert a more serious crisis. Inhibitors from traditional medicines or natural plants have shown promising results to fight COVID-19 with different mechanisms of action. OBJECTIVES To provide comprehensive and promising approaches to the medical community in the fight against this epidemic by reviewing potential plant-derived anti-SARS-CoV-2 inhibitors. METHODS Structural databases such as TCMSP (http://lsp.nwu.edu.cn/tcmsp.php), TCM Database @ Taiwan (http://tcm.cmu.edu.tw/), BATMAN-TCM (http://bionet.ncpsb.org/batman-tcm/) and TCMID (http://www.megabionet.org/tcmid/), as well as PubMed, Sci Finder, Research Gate, Science Direct, CNKI, Web of Science and Google Scholar were searched for relevant articles on TCMs and natural products against SARS-CoV-2. RESULTS Seven traditional Chinese medicines formulas have unique advantages in regulating the immune system for treating COVID-19. The plant-derived natural compounds as anti-SARS-CoV-2 inhibitors were identified based on 5 SARS-CoV-2 key proteins, namely, angiotensin-converting enzyme 2 (ACE2), 3 C-like protease (3CLpro), papain-like protease (PLpro), spike (S) protein, and nucleocapsid (N) protein. CONCLUSIONS A variety of natural products, such as flavonoids, terpenoids, phenols, and alkaloids, were identified, which could be used as potential SASR-Cov-2 inhibitors. These shed new light on the efficient discovery of SASR-Cov-2 inhibitors from natural products.
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Affiliation(s)
- Zhouman He
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Jia Yuan
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Yuanwen Zhang
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Runfeng Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, P. R. China
| | - Meilan Mo
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Yutao Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, P. R. China
| | - Huihui Ti
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
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20
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de Oliveira DF. In silico identification of five binding sites on the SARS-CoV-2 spike protein and selection of seven ligands for such sites. J Biomol Struct Dyn 2023:1-19. [PMID: 37921757 DOI: 10.1080/07391102.2023.2278077] [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: 01/27/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
To contribute to the development of products capable of complexing with the SARS-CoV-2 spike protein, and thus preventing the virus from entering the host cell, this work aimed at discovering binding sites in the whole protein structure, as well as selecting substances capable of binding efficiently to such sites. Initially, the three-dimensional structure of the protein, with all receptor binding domains in the closed state, underwent blind docking with 38 substances potentially capable of binding to this protein according to the literature. This allowed the identification of five binding sites. Then, those substances with more affinities for these sites underwent pharmacophoric search in the ZINC15 database. The 14,329 substances selected from ZINC15 were subjected to docking to the five selected sites of the spike protein. The ligands with more affinities for the protein sites, as well as the selected sites themselves, were used in the de novo design of new ligands that were also docked to the binding sites of the protein. The best ligands, regardless of their origins, were used to form complexes with the spike protein, which were subsequently used in molecular dynamics simulations and calculations of ligands affinities to the protein through the molecular mechanics/Poisson-Boltzmann surface area method (MMPBSA). Seven substances with good affinities to the spike protein (-12.9 to -20.6 kcal/mol), satisfactory druggability (Bioavailability score: 0.17 to 0.55), and low acute toxicity to mice (LD50: 751 to 1421 mg/kg) were selected as potentially useful for the future development of new products to manage COVID-19 infections.Communicated by Ramaswamy H. Sarma.
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21
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Xiao M, Dhungel S, Azad R, Favaro DC, Rajesh RP, Gardner KH, Kikani CK. Signal-regulated unmasking of the nuclear localization motif in the PAS domain regulates the nuclear translocation of PASK. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556462. [PMID: 37732199 PMCID: PMC10508781 DOI: 10.1101/2023.09.06.556462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The ligand-regulated PAS domains are one of the most diverse signal-integrating domains found in proteins from prokaryotes to humans. By biochemically connecting cellular processes with their environment, PAS domains facilitate an appropriate cellular response. PAS domain-containing Kinase (PASK) is an evolutionarily conserved protein kinase that plays important signaling roles in mammalian stem cells to establish stem cell fate. We have shown that the nuclear translocation of PASK is stimulated by differentiation signaling cues in muscle stem cells. However, the mechanistic basis of the regulation of PASK nucleo-cytoplasmic translocation remains unknown. Here, we show that the PAS-A domain of PASK contains a putative monopartite nuclear localization sequence (NLS) motif. This NLS is inhibited in cells via intramolecular association with a short linear motif, termed the PAS Interacting Motif (PIM), found upstream of the kinase domain. The interaction between the PAS-A domain and PIM is evolutionarily conserved and serves to retain PASK in the cytosol in the absence of signaling cues. Consistent with that, we show that metabolic inputs induce PASK nuclear import, likely by disrupting the PAS-A: PIM association. We suggest that a route for such linkage may occur through the PAS-A ligand binding cavity. We show that PIM recruitment and artificial ligand binding to the PAS-A domain occur at neighboring locations that could facilitate metabolic control of the PAS-PIM interaction. Thus, the PAS-A domain of PASK integrates metabolic signaling cues for nuclear translocation and could be targeted to control the balance between self-renewal and differentiation in stem cells.
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Affiliation(s)
- Michael Xiao
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Sajina Dhungel
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Roksana Azad
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Ph.D. Program in Biochemistry, Graduate Center, City University of New York, NY 10016, USA
| | - Denize C. Favaro
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | | | - Kevin H. Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York, NY 10031, USA
- Ph.D. Programs in Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, NY 10016, USA
| | - Chintan K. Kikani
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
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22
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Murali M, Nair B, Vishnu VR, Aneesh TP, Nath LR. 2,4-Dihydroxycinnamic acid as spike ACE2 inhibitor and apigenin as RdRp inhibitor in Nimbamritadi Panchatiktam Kashayam against COVID-19: an in silico and in vitro approach. Mol Divers 2023; 27:2353-2363. [PMID: 36357813 PMCID: PMC9648999 DOI: 10.1007/s11030-022-10552-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
Nimbamritadi Panchatiktam Kashayam (NPK) is an ayurvedic formulation composed of ingredients with potent anti-viral activities. We studied the interaction energy of 144 phytoconstituents present in NPK against spike receptor-binding domain (RBD) complexed with ACE2 protein (PDB ID: 6LZG) and RNA-dependent RNA polymerase protein (PDB ID: 7BTF) using Biovia Drug Discovery studio. The result indicated that 2,4-hydroxycinnamic acid exerts more significant binding affinities (28.43 kcal/mol) than Umifenovir (21.24 kcal/mol) against spike ACE2. Apigenin exhibited the highest binding affinities (54.63 kcal/mol) compared with Remdesivir (24.52 kcal/mol) against RdRp. An in vitro analysis showed a reduction in the number of lentiviral particles on transfected HEK293T-hACE2 cells as assessed by pseudovirus inhibition assay. At the same time, the tested compounds showed non-toxic up to 100 µg/ml in normal cells by MTT assay. The study highlights the plausible clinical utility of this traditional medicine against SARS CoV2.
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Affiliation(s)
- Maneesha Murali
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - Bhagyalakshmi Nair
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - V R Vishnu
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - T P Aneesh
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India.
| | - Lekshmi R Nath
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India.
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23
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Sahu PP, Sarma G, Das S, Borkakoty B. Rapid diagnosis of COVID-19 using disposal paper capacitive sensor. Anal Chim Acta 2023; 1273:341500. [PMID: 37423659 DOI: 10.1016/j.aca.2023.341500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023]
Abstract
Accurate and rapid detection and isolation become indispensable to restrict the spread of COVID-19. Since the start of COVID-19 pandemic in December 2019, many indisposal diagnostic tools are being developed incessantly. Out of all presently used tools, the gold standard rRT- PCR tool having very high sensitivity and specificity is a time consuming complicated molecular technique having requirements of special expensive equipment. Here, the main focus of this work is to develop rapid disposal paper capacitance sensor having simple and easy detection. We discovered a strong interaction between limonin and Spike-glycoprotein of SARS-COV-2 in comparison to its interaction with other similar viruses such as HCOV-OC43, HCOV-NL63, HCOV-HKU1, Influenza B and A viruses. The antibody free capacitive sensor having comb electrode structure was fabricated on whatman paper with drop coating of limonin (extracted using green method from pomelo seeds) and calibrated with known swab samples. The Blind test with unknown swab samples shows high sensitivity of 91.5% and high specificity of 88.37%. Requiring low sample volume and detection time and using biodegradable materials in the sensor fabrication assure the potential application as a point of care disposal diagnostic tool.
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Affiliation(s)
- Partha P Sahu
- Department of Electronics and Communication Engineering, Tezpur University, Napaam, Tezpur, 784028, Assam, India
| | - Geetartha Sarma
- Department of Electronics and Communication Engineering, Tezpur University, Napaam, Tezpur, 784028, Assam, India.
| | - Satyajit Das
- Department of Electronics and Communication Engineering, Tezpur University, Napaam, Tezpur, 784028, Assam, India
| | - Biswajyoti Borkakoty
- Regional VRDL, Regional Medical Research Centre, ICMR, N.E. Region, Dibrugarh, 786001, Assam, India
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24
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Rajamanickam K, Rathinavel T, Periyannan V, Ammashi S, Marimuthu S, Nasir Iqbal M. Molecular insight of phytocompounds from Indian spices and its hyaluronic acid conjugates to block SARS-CoV-2 viral entry. J Biomol Struct Dyn 2023; 41:7386-7405. [PMID: 36093954 DOI: 10.1080/07391102.2022.2121757] [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: 01/08/2022] [Accepted: 08/31/2022] [Indexed: 10/14/2022]
Abstract
Human corona viral infection leads to acute breathing disease and death if not diagnosed and treated properly in time. The disease can be treated with the help of simple natural compounds, which we use in day-to-day life. These natural compounds act against several diseases but their drug targeting mechanism needs to be improved for more efficient and promising applications. In the present study five compounds (gingerol, thymol, thymohydroquinone, cyclocurcumin, hydrazinocurcumin) from three Indian medicinal plants (ginger, black cumin, turmeric) and its hyaluronic acid (HA) conjugates were docked against initially deposited spike structural proteins (PDB ID 6WPT) and its mutant variant D-614G (PDB ID 6XS6). Docking study result reveals that all the HA conjugates showed the most effective inhibitor of S-protein of initially deposited and D-614G variant forms of SARS-CoV-2. The compounds like Gingerol, Thymol, Thymohydroquinone, Cyclocurcumin, Hydrazinocurcumin, Hydroxychloroquinone, and hyaluronic acid conjugates inhibit the viral protein of both wild-type and mutated S-protein of SARS-CoV-2. The molecular docking studies of phytocompounds with initial deposited and variant spike protein targets show superior binding affinity than with the commercial repurposed viral entry inhibitor hydroxychloroquine. Further, the docking result was modeled using MD simulation study shows excellent simulation trajectories between spike proteins and HA conjugates spices constituents than its free form. DFT analysis was carried out to affirm the reason behind the highest binding affinity of HA conjugates over its free form towards SARS-CoV-2 spike protein targets. Further HA conjugates synthesis and its evaluation against SARS-CoV-2 in vitro studies are needed to prove our novel idea for an anti-viral drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karthika Rajamanickam
- Department of Biotechnology, Mahendra Arts and Science College, Namakkal, Tamil Nadu, India
| | | | - Velu Periyannan
- Department of Biotechnology and Biochemistry, Annamalai University, Chidambaram, Tamil Nadu, India
| | - Subramanian Ammashi
- PG and Research Department of Biochemistry, Rajah Serfoji Government College (Autonomous), Thanjavur, Tamil Nadu, India
| | | | - Muhammad Nasir Iqbal
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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25
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Muralitharan I, Sahoo AK, Augusthian PD, Samal A. Computational prediction of phytochemical inhibitors against the cap-binding domain of Rift Valley fever virus. Mol Divers 2023:10.1007/s11030-023-10702-x. [PMID: 37481749 DOI: 10.1007/s11030-023-10702-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/16/2023] [Indexed: 07/25/2023]
Abstract
Rift Valley fever is a zoonotic disease that can spread through livestock and mosquitoes, and its symptoms include retinitis, photophobia, hemorrhagic fever and neurological effects. The World Health Organization has identified Rift Valley fever as one of the viral infections that has potential to cause a future epidemic. Hence, efforts are urgently needed toward development of therapeutics and vaccine against this infectious disease. Notably, the causative virus namely, the Rift Valley fever virus (RVFV), utilizes the cap-snatching mechanism for viral transcription, rendering its cap-binding domain (CBD) as an effective antiviral target. To date, there are no published studies towards identification of potential small molecule inhibitors for the CBD of RVFV. Here, we employ a virtual screening workflow comprising of molecular docking and molecular dynamics (MD) simulation, to identify 5 potential phytochemical inhibitors of the CBD of RVFV. These 5 phytochemical inhibitors can be sourced from Indian medicinal plants, Ferula assa-foetida, Glycyrrhiza glabra and Leucas cephalotes, used in traditional medicine. In sum, the 5 phytochemical inhibitors of the CBD of RVFV identified by this purely computational study are promising drug lead molecules which can be considered for detailed experimental validation against RVFV infection.
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Affiliation(s)
- Ishwarya Muralitharan
- Computational Biology Group, The Institute of Mathematical Sciences (IMSc), CIT Campus, Taramani, Chennai, 600113, India
| | - Ajaya Kumar Sahoo
- Computational Biology Group, The Institute of Mathematical Sciences (IMSc), CIT Campus, Taramani, Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | - Priya Dharshini Augusthian
- Computational Biology Group, The Institute of Mathematical Sciences (IMSc), CIT Campus, Taramani, Chennai, 600113, India
| | - Areejit Samal
- Computational Biology Group, The Institute of Mathematical Sciences (IMSc), CIT Campus, Taramani, Chennai, 600113, India.
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India.
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26
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Mohanty M, Mohanty PS. Molecular docking in organic, inorganic, and hybrid systems: a tutorial review. MONATSHEFTE FUR CHEMIE 2023; 154:1-25. [PMID: 37361694 PMCID: PMC10243279 DOI: 10.1007/s00706-023-03076-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023]
Abstract
Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular interactions between a natural organic molecule (ideally taken as a receptor) such as an enzyme, protein, DNA, RNA and a natural or synthetic organic/inorganic molecule (considered as a ligand). But the implementation of docking ideas to synthetic organic, inorganic, or hybrid systems is very limited with respect to their use as a receptor despite their huge popularity in different experimental systems. In this context, molecular docking can be an efficient computational tool for understanding the role of intermolecular interactions in hybrid systems that can help in designing materials on mesoscale for different applications. The current review focuses on the implementation of the docking method in organic, inorganic, and hybrid systems along with examples from different case studies. We describe different resources, including databases and tools required in the docking study and applications. The concept of docking techniques, types of docking models, and the role of different intermolecular interactions involved in the docking process to understand the binding mechanisms are explained. Finally, the challenges and limitations of dockings are also discussed in this review. Graphical abstract
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Affiliation(s)
- Madhuchhanda Mohanty
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024 India
| | - Priti S. Mohanty
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024 India
- School of Chemical Technology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024 India
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27
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Tiwari A, Tiwari V, Sharma A, Singh D, Singh Rawat M, Virmani T, Virmani R, Kumar G, Kumar M, Alhalmi A, Noman OM, Mothana RA, Alali M. Tanshinone-I for the treatment of uterine fibroids: Molecular docking, simulation, and density functional theory investigations. Saudi Pharm J 2023; 31:1061-1076. [PMID: 37250358 PMCID: PMC10209546 DOI: 10.1016/j.jsps.2023.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/01/2023] [Indexed: 05/31/2023] Open
Abstract
Uterine fibroids (UF), most prevalent gynecological disorder, require surgery when symptomatic. It is estimated that between 25 and 35 percent of women wait until the symptoms have worsened like extended heavy menstrual bleeding and severe pelvic pain. These UF may be reduced in size through various methods such as medical or surgical intervention. Progesterone (prog) is a crucial hormone that restores the endometrium and controls uterine function. In the current study, 28 plant-based molecules are identified from previous literature and docked onto the prog receptors with 1E3K and 2OVH. Tanshinone-I has shown the best docking score against both proteins. The synthetic prog inhibitor Norethindrone Acetate is used as a standard to evaluate the docking outcomes. The best compound, tanshinone-I, was analyzed using molecular modeling and DFT. The RMSD for the 1E3K protein-ligand complex ranged from 0.10 to 0.42 Å, with an average of 0.21 Å and a standard deviation (SD) of 0.06, while the RMSD for the 2OVH protein-ligand complex ranged from 0.08 to 0.42 Å, with an average of 0.20 Å and a SD of 0.06 showing stable interaction. In principal component analysis, the observed eigen values of HPR-Tanshinone-I fluctuate between -1.11 to 1.48 and -1.07 to 1.25 for PC1 and PC2, respectively (1E3K), and the prog-tanshinone-I complex shows eigen values of -38.88 to -31.32 and -31.32 to 35.87 for PC1 and PC2, respectively (2OVH), which shows Tanshinone-I forms a stable protein-ligand complex with 1E3K in comparison to 2OVH. The Free Energy Landscape (FEL) analysis shows the Gibbs free energy in the range of 0 to 8 kJ/mol for Tanshinone-I with 1E3K and 0 to 14 kJ/mol for Tanshinone-I with the 2OVH complex. The DFT calculation reveals ΔE value of 2.8070 eV shows tanshinone-I as a stable compound. 1E3K modulates the prog pathway, it may have either an agonistic or antagonistic effect on hPRs. Tanshinone-I can cause ROS, apoptosis, autophagy (p62 accumulation), up-regulation of inositol requiring protein-1, enhancer-binding protein homologous protein, p-c-Jun N-terminal kinase (p-JNK), and suppression of MMPs. Bcl-2 expression can change LC3I to LC3II and cause apoptosis through Beclin-1 expression.
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Affiliation(s)
- Abhishek Tiwari
- Department of Pharmacy, Pharmacy Academy, IFTM University, Lodhipur-Rajpur, Moradabad 244102, India
| | - Varsha Tiwari
- Department of Pharmacy, Pharmacy Academy, IFTM University, Lodhipur-Rajpur, Moradabad 244102, India
| | - Ajay Sharma
- Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, New Delhi 110017, India
| | - Deependra Singh
- University Institute of Pharmacy, Pt. Ravi Shankar Shukla University, Raipur, Chhattisgarh, India
| | - Manju Singh Rawat
- University Institute of Pharmacy, Pt. Ravi Shankar Shukla University, Raipur, Chhattisgarh, India
| | - Tarun Virmani
- School of Pharmaceutical Sciences, MVN University, Palwal, Haryana 121105, India
| | - Reshu Virmani
- School of Pharmaceutical Sciences, MVN University, Palwal, Haryana 121105, India
| | - Girish Kumar
- School of Pharmaceutical Sciences, MVN University, Palwal, Haryana 121105, India
| | - Manish Kumar
- School of Pharmaceutical Sciences, CT University, Ludhiana- 142024 Punjab, India
| | - Abdulsalam Alhalmi
- Department of Pharmaceutical Sciences, College of Pharmacy, Aden University, Aden, Yemen
| | - Omar M. Noman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ramzi A. Mothana
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Alali
- Institute of Pharmacy, Clinical Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489 Greifswald, Germany
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28
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Panja A, Roy J, Mazumder A, Choudhury SM. Divergent mutations of Delta and Omicron variants: key players behind differential viral attributes across the COVID-19 waves. Virusdisease 2023:1-14. [PMID: 37363365 PMCID: PMC10171727 DOI: 10.1007/s13337-023-00823-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/17/2023] [Indexed: 06/28/2023] Open
Abstract
The third SARS-CoV-2 pandemic wave causing Omicron variant has comparatively higher replication rate and transmissibility than the second wave-causing Delta variant. The exact mechanism behind the differential properties of Delta and Omicron in respect to infectivity and virulence is not properly understood yet. This study reports the analysis of different mutations within the receptor binding domain (RBD) of spike glycoprotein and non-structural protein (nsp) of Delta and Omicron strains. We have used computational studies to evaluate the properties of Delta and Omicron variants in this work. Q498R, Q493R and S375F mutations of RBD showed better docking scores for Omicron compared to Delta variant of SARS-CoV-2, whereas nsp3_L1266I with PARP15 (7OUX), nsp3_L1266I with PARP15 (7OUX), and nsp6_G107 with ISG15 (1Z2M) showed significantly higher docking score. The findings of the present study might be helpful to reveal the probable cause of relatively milder form of COVID-19 disease manifested by Omicron in comparison to Delta variant of SARS-CoV-2 virus. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00823-0.
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Affiliation(s)
- Amrita Panja
- Biochemistry, Molecular Endocrinology, and Reproductive Physiology Laboratory, Department of Human Physiology, Vidyasagar University, Paschim Medinipore, Midnapore, West Bengal 721102 India
| | - Jayita Roy
- National Institute of Biomedical Genomics (NIBMG), Nadia, Kalyani, West Bengal 741251 India
| | - Anup Mazumder
- National Institute of Biomedical Genomics (NIBMG), Nadia, Kalyani, West Bengal 741251 India
| | - Sujata Maiti Choudhury
- Biochemistry, Molecular Endocrinology, and Reproductive Physiology Laboratory, Department of Human Physiology, Vidyasagar University, Paschim Medinipore, Midnapore, West Bengal 721102 India
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29
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Rahmani F, Imani Fooladi AA, Ajoudanifar H, Soleimani NA. In silico and experimental methods for designing a potent anticancer arazyme-herceptin fusion protein in HER2-positive breast cancer. J Mol Model 2023; 29:160. [PMID: 37103612 DOI: 10.1007/s00894-023-05562-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023]
Abstract
CONTEXT Breast cancer is the most prevalent type of malignancies among women worldwide and is associated with serious physical and mental consequences. Current chemotherapies may lack successful outcomes; thus, the development of targeted recombinant immunotoxins is plausible. The predicted B cell and T cell epitopes of arazyme of the fusion protein are able to elicit immune response. The results of codon adaptation tool of herceptin-arazyme have improved from 0.4 to 1. The in silico immune simulation results showed significant response for immune cells. In conclusion, our findings show that the known multi-epitope fusion protein may activate humoral and cellular immune responses and maybe a possible candidate for breast cancer treatment. METHODS In this study, the selected monoclonal antibody constituting herceptin and the bacterial metalloprotease, arazyme, was used with different peptide linkers to design a novel fusion protein to predict different B cell and T cell epitopes by the means of the relevant databases. Modeler 10.1 and I-TASSER online server were used to predict and validate the 3D structure and then docked to HER2-receptor using HADDOCK2.4 web server. The molecular dynamics (MD) simulations of the arazyme-linker-herceptin-HER2 complex were performed by GROMACS 2019.6 software. The sequence of arazyme-herceptin was optimized for the expression in prokaryotic host using online servers and cloned into pET-28a plasmid. The recombinant pET28a was transferred into the Escherichia coli BL21DE3. Expression and binding affinity of arazyme-herceptin and arazyme to human breast cancer cell lines (SK-BR-3/HER2 + and MDA-MB-468/HER2 -) were validated by the SDS-PAGE and cell‑ELISA, respectively.
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Affiliation(s)
- Farideh Rahmani
- Department of Microbiology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Hatef Ajoudanifar
- Department of Microbiology, Damghan Branch, Islamic Azad University, Damghan, Iran
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30
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Aldahish A, Balaji P, Vasudevan R, Kandasamy G, James JP, Prabahar K. Elucidating the Potential Inhibitor against Type 2 Diabetes Mellitus Associated Gene of GLUT4. J Pers Med 2023; 13:jpm13040660. [PMID: 37109046 PMCID: PMC10146764 DOI: 10.3390/jpm13040660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/02/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Diabetes is a chronic hyperglycemic disorder that leads to a group of metabolic diseases. This condition of chronic hyperglycemia is caused by abnormal insulin levels. The impact of hyperglycemia on the human vascular tree is the leading cause of disease and death in type 1 and type 2 diabetes. People with type 2 diabetes mellitus (T2DM) have abnormal secretion as well as the action of insulin. Type 2 (non-insulin-dependent) diabetes is caused by a combination of genetic factors associated with decreased insulin production, insulin resistance, and environmental conditions. These conditions include overeating, lack of exercise, obesity, and aging. Glucose transport limits the rate of dietary glucose used by fat and muscle. The glucose transporter GLUT4 is kept intracellular and sorted dynamically, and GLUT4 translocation or insulin-regulated vesicular traffic distributes it to the plasma membrane. Different chemical compounds have antidiabetic properties. The complexity, metabolism, digestion, and interaction of these chemical compounds make it difficult to understand and apply them to reduce chronic inflammation and thus prevent chronic disease. In this study, we have applied a virtual screening approach to screen the most suitable and drug-able chemical compounds to be used as potential drug targets against T2DM. We have found that out of 5000 chemical compounds that we have analyzed, only two are known to be more effective as per our experiments based upon molecular docking studies and virtual screening through Lipinski's rule and ADMET properties.
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Affiliation(s)
- Afaf Aldahish
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | | | - Rajalakshimi Vasudevan
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | - Geetha Kandasamy
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | - Jainey P James
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Deralakatte, Mangaluru 575018, Karnataka, India
| | - Kousalya Prabahar
- Department of Pharmacy Practice, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
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31
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Mahnam K, Rajaee SM. A theoretical survey to find potential natural compound for inhibition of binding the RBD domain to ACE2 receptor based on plant antivirals. J Biomol Struct Dyn 2023; 41:14540-14565. [PMID: 36974837 DOI: 10.1080/07391102.2023.2183033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/16/2023] [Indexed: 03/29/2023]
Abstract
The spike protein of coronavirus is crucial in binding and arrival of the virus to the human cell via binding to the human ACE2 receptor. In this study, at first 25 antiviral phytochemicals were docked into the RBD domain of spike protein, and then all complexes and free RBD domains were separately subjected to molecular dynamics simulation for 100 ns and MM/PBSA binding free energy calculation. In this phase, four ligands were chosen as hit compounds and a natural compound database (NPASS) was screened based on high similarity with these ligands, and 367 ligands were found. Then the same previous procedure was repeated for these ligands and ADME properties were investigated. Finally, virtual screening and 4400 ns MD simulation and MM/PBSA calculation revealed that new ligands including NPC67959, NPC157855, NPC248793, and NPC216361 can inhibit the RBD domain of spike protein and we propose them as potential drugs for experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karim Mahnam
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
- Nanotechnology Research Center, Shahrekord University, Shahrekord, Iran
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32
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Vivek-Ananth R, Mohanraj K, Sahoo AK, Samal A. IMPPAT 2.0: An Enhanced and Expanded Phytochemical Atlas of Indian Medicinal Plants. ACS OMEGA 2023; 8:8827-8845. [PMID: 36910986 PMCID: PMC9996785 DOI: 10.1021/acsomega.3c00156] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Compilation, curation, digitization, and exploration of the phytochemical space of Indian medicinal plants can expedite ongoing efforts toward natural product and traditional knowledge based drug discovery. To this end, we present IMPPAT 2.0, an enhanced and expanded database compiling manually curated information on 4010 Indian medicinal plants, 17,967 phytochemicals, and 1095 therapeutic uses. Notably, IMPPAT 2.0 compiles associations at the level of plant parts and provides a FAIR-compliant nonredundant in silico stereo-aware library of 17,967 phytochemicals from Indian medicinal plants. The phytochemical library has been annotated with several useful properties to enable easier exploration of the chemical space. We have also filtered a subset of 1335 drug-like phytochemicals of which majority have no similarity to existing approved drugs. Using cheminformatics, we have characterized the molecular complexity and molecular scaffold based structural diversity of the phytochemical space of Indian medicinal plants and performed a comparative analysis with other chemical libraries. Altogether, IMPPAT 2.0 is a manually curated extensive phytochemical atlas of Indian medicinal plants that is accessible at https://cb.imsc.res.in/imppat/.
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Affiliation(s)
- R.P. Vivek-Ananth
- The
Institute of Mathematical Sciences (IMSc), Chennai 600113, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
| | | | - Ajaya Kumar Sahoo
- The
Institute of Mathematical Sciences (IMSc), Chennai 600113, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Areejit Samal
- The
Institute of Mathematical Sciences (IMSc), Chennai 600113, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
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33
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Avelar M, Pedraza-González L, Sinicropi A, Flores-Morales V. Triterpene Derivatives as Potential Inhibitors of the RBD Spike Protein from SARS-CoV-2: An In Silico Approach. Molecules 2023; 28:molecules28052333. [PMID: 36903578 PMCID: PMC10005606 DOI: 10.3390/molecules28052333] [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: 01/30/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The appearance of a new coronavirus, SARS-CoV-2, in 2019 kicked off an international public health emergency. Although rapid progress in vaccination has reduced the number of deaths, the development of alternative treatments to overcome the disease is still necessary. It is known that the infection begins with the interaction of the spike glycoprotein (at the virus surface) and the angiotensin-converting enzyme 2 cell receptor (ACE2). Therefore, a straightforward solution for promoting virus inhibition seems to be the search for molecules capable of abolishing such attachment. In this work, we tested 18 triterpene derivatives as potential inhibitors of SARS-CoV-2 against the receptor-binding domain (RBD) of the spike protein by means of molecular docking and molecular dynamics simulations, modeling the RBD S1 subunit from the X-ray structure of the RBD-ACE2 complex (PDB ID: 6M0J). Molecular docking revealed that at least three triterpene derivatives of each type (i.e., oleanolic, moronic and ursolic) present similar interaction energies as the reference molecule, i.e., glycyrrhizic acid. Molecular dynamics suggest that two compounds from oleanolic and ursolic acid, OA5 and UA2, can induce conformational changes capable of disrupting the RBD-ACE2 interaction. Finally, physicochemical and pharmacokinetic properties simulations revealed favorable biological activity as antivirals.
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Affiliation(s)
- Mayra Avelar
- Laboratorio de Síntesis Asimétrica y Bio-Quimioinformática (LSAyB), Ingeniería Química (UACQ), Universidad Autónoma de Zacatecas, Campus XXI Km 6 Carr. Zac-Gdl, Zacatecas 98160, Mexico
- Correspondence: (M.A.); (V.F.-M.)
| | - Laura Pedraza-González
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, 56124 Pisa, Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Virginia Flores-Morales
- Laboratorio de Síntesis Asimétrica y Bio-Quimioinformática (LSAyB), Ingeniería Química (UACQ), Universidad Autónoma de Zacatecas, Campus XXI Km 6 Carr. Zac-Gdl, Zacatecas 98160, Mexico
- Correspondence: (M.A.); (V.F.-M.)
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Jantan I, Arshad L, Septama AW, Haque MA, Mohamed-Hussein ZA, Govender NT. Antiviral effects of phytochemicals against severe acute respiratory syndrome coronavirus 2 and their mechanisms of action: A review. Phytother Res 2023; 37:1036-1056. [PMID: 36343627 PMCID: PMC9878073 DOI: 10.1002/ptr.7671] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022]
Abstract
The worldwide spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to health, economic, environmental, and social aspects of human lives. Currently, there are no approved treatments that can effectively block the virus although several existing antimalarial and antiviral agents have been repurposed and allowed use during the pandemic under the emergency use authorization (EUA) status. This review gives an updated overview of the antiviral effects of phytochemicals including alkaloids, flavonoids, and terpenoids against the COVID-19 virus and their mechanisms of action. Search for natural lead molecules against SARS-CoV-2 has been focusing on virtual screening and in vitro studies on phytochemicals that have shown great promise against other coronaviruses such as SARS-CoV. Until now, there is limited data on in vivo investigations to examine the antiviral activity of plants in SARS-CoV-2-infected animal models and the studies were performed using crude extracts. Further experimental and preclinical investigations on the in vivo effects of phytochemicals have to be performed to provide sufficient efficacy and safety data before clinical studies can be performed to develop them into COVID-19 drugs. Phytochemicals are potential sources of new chemical leads for the development of safe and potent anti-SARS-CoV-2 agents.
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Affiliation(s)
- Ibrahim Jantan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Laiba Arshad
- Department of Pharmacy, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Abdi Wira Septama
- Research Center for Pharmaceutical Ingredient and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong Science Center, West Java, Indonesia
| | - Md Areeful Haque
- Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia.,Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Nisha T Govender
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
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Paul A, Chakraborty N, Sarkar A, Acharya K, Ranjan A, Chauhan A, Srivastava S, Singh AK, Rai AK, Mubeen I, Prasad R. Ethnopharmacological Potential of Phytochemicals and Phytogenic Products against Human RNA Viral Diseases as Preventive Therapeutics. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1977602. [PMID: 36860811 PMCID: PMC9970710 DOI: 10.1155/2023/1977602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 02/22/2023]
Abstract
RNA viruses have been the most destructive due to their transmissibility and lack of control measures. Developments of vaccines for RNA viruses are very tough or almost impossible as viruses are highly mutable. For the last few decades, most of the epidemic and pandemic viral diseases have wreaked huge devastation with innumerable fatalities. To combat this threat to mankind, plant-derived novel antiviral products may contribute as reliable alternatives. They are assumed to be nontoxic, less hazardous, and safe compounds that have been in uses in the beginning of human civilization. In this growing COVID-19 pandemic, the present review amalgamates and depicts the role of various plant products in curing viral diseases in humans.
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Affiliation(s)
- Anamika Paul
- Department of Botany, Scottish Church College, Kolkata 700006, India
| | | | - Anik Sarkar
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, Kolkata 700019, India
| | - Krishnendu Acharya
- Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, Kolkata 700019, India
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, 344090 Rostov-on-Don, Russia
| | - Abhishek Chauhan
- Amity Institute of Environment Toxicology and Safety Management, Amity University, Noida, U.P., India
| | - Shilpi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Akhilesh Kumar Singh
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, 845401 Bihar, India
| | - Ashutosh Kumar Rai
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Iqra Mubeen
- State Key Laboratory of Rice Biology, and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari, 845401 Bihar, India
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Bellavite P, Ferraresi A, Isidoro C. Immune Response and Molecular Mechanisms of Cardiovascular Adverse Effects of Spike Proteins from SARS-CoV-2 and mRNA Vaccines. Biomedicines 2023; 11:451. [PMID: 36830987 PMCID: PMC9953067 DOI: 10.3390/biomedicines11020451] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
The SARS-CoV-2 (severe acute respiratory syndrome coronavirus responsible for the COVID-19 disease) uses the Spike proteins of its envelope for infecting target cells expressing on the membrane the angiotensin converting enzyme 2 (ACE2) enzyme that acts as a receptor. To control the pandemic, genetically engineered vaccines have been designed for inducing neutralizing antibodies against the Spike proteins. These vaccines do not act like traditional protein-based vaccines, as they deliver the message in the form of mRNA or DNA to host cells that then produce and expose the Spike protein on the membrane (from which it can be shed in soluble form) to alert the immune system. Mass vaccination has brought to light various adverse effects associated with these genetically based vaccines, mainly affecting the circulatory and cardiovascular system. ACE2 is present as membrane-bound on several cell types, including the mucosa of the upper respiratory and of the gastrointestinal tracts, the endothelium, the platelets, and in soluble form in the plasma. The ACE2 enzyme converts the vasoconstrictor angiotensin II into peptides with vasodilator properties. Here we review the pathways for immunization and the molecular mechanisms through which the Spike protein, either from SARS-CoV-2 or encoded by the mRNA-based vaccines, interferes with the Renin-Angiotensin-System governed by ACE2, thus altering the homeostasis of the circulation and of the cardiovascular system. Understanding the molecular interactions of the Spike protein with ACE2 and the consequent impact on cardiovascular system homeostasis will direct the diagnosis and therapy of the vaccine-related adverse effects and provide information for development of a personalized vaccination that considers pathophysiological conditions predisposing to such adverse events.
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Affiliation(s)
| | - Alessandra Ferraresi
- Laboratory of Molecular Pathology, Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Ciro Isidoro
- Laboratory of Molecular Pathology, Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
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Zorzi G, Gambini S, Negri S, Guzzo F, Commisso M. Untargeted Metabolomics Analysis of the Orchid Species Oncidium sotoanum Reveals the Presence of Rare Bioactive C-Diglycosylated Chrysin Derivatives. PLANTS (BASEL, SWITZERLAND) 2023; 12:655. [PMID: 36771739 PMCID: PMC9920315 DOI: 10.3390/plants12030655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Plants are valuable sources of secondary metabolites with pharmaceutical properties, but only a small proportion of plant life has been actively exploited for medicinal purposes to date. Underexplored plant species are therefore likely to contain novel bioactive compounds. In this study, we investigated the content of secondary metabolites in the flowers, leaves and pseudobulbs of the orchid Oncidium sotoanum using an untargeted metabolomics approach. We observed the strong accumulation of C-diglycosylated chrysin derivatives, which are rarely found in nature. Further characterization revealed evidence of antioxidant activity (FRAP and DPPH assays) and potential activity against neurodegenerative disorders (MAO-B inhibition assay) depending on the specific molecular structure of the metabolites. Natural product bioprospecting in underexplored plant species based on untargeted metabolomics can therefore help to identify novel chemical structures with diverse pharmaceutical properties.
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Affiliation(s)
- Gianluca Zorzi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Sofia Gambini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Stefano Negri
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Flavia Guzzo
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Mauro Commisso
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
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Fatouros PR, Roy U, Sur S. Implications of SARS-CoV-2 spike protein interactions with Zn-bound form of ACE2: a computational structural study. Biometals 2023:10.1007/s10534-023-00491-z. [PMID: 36725769 PMCID: PMC9891659 DOI: 10.1007/s10534-023-00491-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023]
Abstract
The COVID-19 pandemic has generated a major interest in designing inhibitors to prevent SARS-CoV-2 binding on host cells to protect against infection. One promising approach to such research utilizes molecular dynamics simulation to identify potential inhibitors that can prevent the interaction between spike (S) protein on the virus and angiotensin converting enzyme 2 (ACE2) receptor on the host cells. In these studies, many groups have chosen to exclude the ACE2-bound zinc (Zn) ion, which is critical for its enzymatic activity. While the relatively distant location of Zn ion from the S protein binding site (S1 domain), combined with the difficulties in modeling this ion has motivated the decision of exclusion, Zn can potentially contribute to the structural stability of the entire protein, and thus, may have implications on S protein-ACE2 interaction. In this study, the authors model both the ACE2-S1 and ACE2-inhibitor (mAb) system to investigate if there are variations in structure and the readouts due to the presence of Zn ion. Although distant from the S1 or inhibitor binding region, inclusion/exclusion of Zn has statistically significant effects on the structural stability and binding free energy in these systems. In particular, the binding free energy of the ACE2-S1 and ACE2-inhibitor structures is - 3.26 and - 14.8 kcal/mol stronger, respectively, in the Zn-bound structure than in the Zn-free structures. This finding suggests that including Zn may be important in screening potentially inhibitors and may be particularly important in modeling monoclonal antibodies, which may be more sensitive to changes in antigen structure.
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Affiliation(s)
- Peter R. Fatouros
- Department of Chemical and Biomolecular Engineering, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
| | - Shantanu Sur
- Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
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Wang Y, Guo Y, Zhang L, Yuan M, Zhao L, Bai C, McClements DJ. Impacts of hesperidin on whey protein functionality: Interacting mechanism, antioxidant capacity, and emulsion stabilizing effects. Front Nutr 2023; 9:1043095. [PMID: 36687727 PMCID: PMC9846557 DOI: 10.3389/fnut.2022.1043095] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
The objective of this work was to explore the possibility of improving the antioxidant capacity and application of whey protein (WP) through non-covalent interactions with hesperidin (HES), a citrus polyphenol with nutraceutical activity. The interaction mechanism was elucidated using several spectroscopic methods and molecular docking analysis. The antioxidant capacity of the WP-HES complexes was analyzed and compared to that of the proteins alone. Moreover, the resistance of oil-in-water emulsions formulated using the WP-HES complexes as antioxidant emulsifiers to changes in environmental conditions (pH, ion strength, and oxidant) was evaluated. Our results showed that HES was incorporated into a single hydrophobic cavity in the WP molecule, where it was mainly held by hydrophobic attractive forces. As a result, the microenvironments of the non-polar tyrosine and tryptophan residues in the protein molecules were altered after complexation. Moreover, the α-helix and β-sheet regions in the protein decreased after complexation, while the β-turn and random regions increased. The antioxidant capacity of the WP-HES complexes was greater than that of the proteins alone. Non-radiative energy transfer from WP to HES was detected during complex formation. Compared to WP alone, the WP-HES complexes produced emulsions with smaller mean droplet diameters, exhibited higher pH and salt stability, and had better oxidative stability. The magnitude of these effects increased as the HES concentration was increased. This research would supply valuable information on the nature of the interactions between WP and HES. Moreover, it may lead to the creation of dual-function antioxidant emulsifiers for application in emulsified food products.
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Affiliation(s)
- Yin Wang
- National R&D Branch Center for Freshwater Fish Processing, College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yangkai Guo
- National R&D Branch Center for Freshwater Fish Processing, College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Longtao Zhang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Meilan Yuan
- National R&D Branch Center for Freshwater Fish Processing, College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Li Zhao
- National R&D Branch Center for Freshwater Fish Processing, College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Chunqing Bai
- National R&D Branch Center for Freshwater Fish Processing, College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China,*Correspondence: Chunqing Bai,
| | - David Julian McClements
- Department of Food Science, University of Massachusetts, Amherst, MA, United States,David Julian McClements,
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Supianto AA, Nurdiansyah R, Weng CW, Zilvan V, Yuwana RS, Arisal A, Pardede HF, Lee MM, Huang CH, Ng KL. Cluster-based text mining for extracting drug candidates for the prevention of COVID-19 from the biomedical literature. J Taibah Univ Med Sci 2023; 18:787-801. [PMID: 36618881 PMCID: PMC9810500 DOI: 10.1016/j.jtumed.2022.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/14/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Objective The coronavirus disease 2019 (COVID-19) health crisis that began at the end of 2019 made researchers around the world quickly race to find effective solutions. Related literature exploded and it was inevitable that an automated approach was needed to find useful information, namely text mining, to overcome COVID-19, especially in terms of drug candidate discovery. While text mining methods for finding drug candidates mostly try to extract bioentity associations from PubMed, very few of them mine with a clustering approach. The purpose of this study was to demonstrate the effectiveness of our approach to identify drugs for the prevention of COVID-19 through literature review, cluster analysis, drug docking calculations, and clinical trial data. Methods This research was conducted in four main stages. First, the text mining stage was carried out by involving Bidirectional Encoder Representations from Transformers for Biomedical to obtain vector representation of each word in the sentence from texts. The next stage generated the disease-drug associations, which were obtained from the correlation between disease and drug. Next, the clustering stage grouped the rules through the similarity of diseases by utilizing Term Frequency-Inverse Document Frequency as its feature. Finally, the drug candidate extraction stage was processed through leveraging PubChem and DrugBank databases. We further used the drug docking package AUTODOCK VINA in PyRx software to verify the results. Results Comparative analyses showed that the percentage of findings using mining with clustering outperformed mining without clustering in all experimental settings. In addition, we suggest that the top three drugs/phytochemicals by drug docking analysis may be effective in preventing COVID-19. Conclusions The proposed method for text mining utilizing the clustering method is quite promising in the discovery of drug candidates for the prevention of COVID-19 through the biomedical literature.
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Affiliation(s)
- Ahmad Afif Supianto
- Research Center for Data and Information Sciences, National Research and Innovation Agency, Indonesia
| | - Rizky Nurdiansyah
- Department of Bioinformatics, Indonesia International Institute for Life Sciences, Indonesia
| | - Chia-Wei Weng
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Vicky Zilvan
- Research Center for Data and Information Sciences, National Research and Innovation Agency, Indonesia
| | - Raden Sandra Yuwana
- Research Center for Data and Information Sciences, National Research and Innovation Agency, Indonesia
| | - Andria Arisal
- Research Center for Data and Information Sciences, National Research and Innovation Agency, Indonesia
| | | | - Min-Min Lee
- Department of Food Nutrition and Health Biotechnology, Asia University, Taiwan
| | - Chien-Hung Huang
- Department of Computer Science and Information Engineering, National Formosa University, Taiwan
| | - Ka-Lok Ng
- Department of Bioinformatics and Medical Engineering, Asia University, Taiwan,Department of Medical Research, China Medical University Hospital, China Medical University, Taiwan,Center for Artificial Intelligence and Precision Medicine Research, Asia University, Taiwan,Corresponding address: Department of Bioinformatics and Medical Engineering, No. 500, LiuFeng Rd., WuFeng Dist., Taichung City, 41354, Taiwan.
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Krishnamurthy N, Ananda A, Nagendra Prasad H, Prabhuprasad P, Manju N, Karthik C, Jayanth H, Logaraj T, Savitha K. HR-LCMS assisted phytochemical screening of antioxidant, antibacterial activity of Priva cordifolia (L.f) Druce plant and molecular docking approach. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Maschietto F, Qiu T, Wang J, Shi Y, Allen B, Lisi GP, Lolis E, Batista VS. Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism. Comput Struct Biotechnol J 2023; 21:1066-1076. [PMID: 36688026 PMCID: PMC9841741 DOI: 10.1016/j.csbj.2023.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The receptor-binding domains (RBDs) of the SARS-CoV-2 spike trimer exhibit "up" and "down" conformations often targeted by neutralizing antibodies. Only in the "up" configuration can RBDs bind to the ACE2 receptor of the host cell and initiate the process of viral multiplication. Here, we identify a lead compound (3-oxo-valproate-coenzyme A conjugate or Val-CoA) that stabilizes the spike trimer with RBDs in the down conformation. Val-CoA interacts with three R408 residues, one from each RBD, which significantly reduces the inter-subunit R408-R408 distance by ∼ 13 Å and closes the central pore formed by the three RBDs. Experimental evidence is presented that R408 is part of a triggering mechanism that controls the prefusion to postfusion state transition of the spike trimer. By stabilizing the RBDs in the down configuration, this and other related compounds can likely attenuate viral transmission. The reported findings for binding of Val-CoA to the spike trimer suggest a new approach for the design of allosteric antiviral drugs that do not have to compete for specific virus-receptor interactions but instead hinder the conformational motion of viral membrane proteins essential for interaction with the host cell. Here, we introduce an approach to target the spike protein by identifying lead compounds that stabilize the RBDs in the trimeric "down" configuration. When these compounds trimerize monomeric RBD immunogens as co-immunogens, they could also induce new types of non-ACE2 blocking antibodies that prevent local cell-to-cell transmission of the virus, providing a novel approach for inhibition of SARS-CoV-2.
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Affiliation(s)
| | - Tianyin Qiu
- Department of Chemistry, Yale University, New Haven, CT 06520-8449, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- Corresponding authors.
| | - Yuanjun Shi
- Department of Chemistry, Yale University, New Haven, CT 06520-8449, USA
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT 06520-8449, USA
| | - George P. Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Elias Lolis
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06520-8449, USA
- Corresponding authors.
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Chugh A, Sehgal I, Khurana N, Verma K, Rolta R, Vats P, Salaria D, Fadare OA, Awofisayo O, Verma A, Phartyal R, Verma M. Comparative docking studies of drugs and phytocompounds for emerging variants of SARS-CoV-2. 3 Biotech 2023; 13:36. [PMID: 36619821 PMCID: PMC9815891 DOI: 10.1007/s13205-022-03450-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
In the last three years, COVID-19 has impacted the world with back-to-back waves leading to devastating consequences. SARS-CoV-2, the causative agent of COVID-19, was first detected in 2019 and since then has spread to 228 countries. Even though the primary focus of research groups was diverted to fight against COVID-19, yet no dedicated drug has been developed to combat the emergent life-threatening medical conditions. In this study, 35 phytocompounds and 43 drugs were investigated for comparative docking analysis. Molecular docking and virtual screening were performed against SARS-CoV-2 spike glycoprotein of 13 variants using AutoDock Vina tool 1.5.6 and Discovery Studio, respectively, to identify the most efficient drugs. Selection of the most suitable compounds with the best binding affinity was done after screening for toxicity, ADME (absorption, distribution, metabolism and excretion) properties and drug-likeliness. The potential candidates were discovered to be Liquiritin (binding affinities ranging between -7.0 and -8.1 kcal/mol for the 13 variants) and Apigenin (binding affinities ranging between -6.8 and -7.3 kcal/mol for the 13 variants) based on their toxicity and consistent binding affinity with the Spike protein of all variants. The stability of the protein-ligand complex was determined using Molecular dynamics (MD) simulation of Apigenin with the Delta plus variant of SARS-CoV-2. Furthermore, Liquiritin and Apigenin were also found to be less toxic than the presently used drugs and showed promising results based on in silico studies, though, confirmation using in vitro studies is required. This in-depth comparative investigation suggests potential drug candidates to fight against SARS-CoV-2 variants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03450-6.
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Affiliation(s)
- Ananya Chugh
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Ishita Sehgal
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Nimisha Khurana
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Kangna Verma
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Rajan Rolta
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Pranjal Vats
- School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Deeksha Salaria
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Olatomide A. Fadare
- Organic Chemistry Research Lab, Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Osun 220282 Nigeria
| | - Oladoja Awofisayo
- Department of Pharmaceutical and Medical Chemistry, University of Uyo, Uyo, 520003 Nigeria
| | - Anita Verma
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Rajendra Phartyal
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Delhi, 110007 India
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Ożarowski M, Karpiński TM. The Effects of Propolis on Viral Respiratory Diseases. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010359. [PMID: 36615554 PMCID: PMC9824023 DOI: 10.3390/molecules28010359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/18/2022] [Accepted: 12/24/2022] [Indexed: 01/04/2023]
Abstract
Propolis remains an interesting source of natural chemical compounds that show, among others, antibacterial, antifungal, antiviral, antioxidative and anti-inflammatory activities. Due to the growing incidence of respiratory tract infections caused by various pathogenic viruses, complementary methods of prevention and therapy supporting pharmacotherapy are constantly being sought out. The properties of propolis may be important in the prevention and treatment of respiratory tract diseases caused by viruses such as severe acute respiratory syndrome coronavirus 2, influenza viruses, the parainfluenza virus and rhinoviruses. One of the main challenges in recent years has been severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing COVID-19. Recently, an increasing number of studies are focusing on the activity of various propolis preparations against SARS-CoV-2 as an adjuvant treatment for this infection. Propolis has shown a few key mechanisms of anti-SARS-CoV-2 action such as: the inhibition of the interaction of the S1 spike protein and ACE-2 protein; decreasing the replication of viruses by diminishing the synthesis of RNA transcripts in cells; decreasing the particles of coronaviruses. The anti-viral effect is observed not only with extracts but also with the single biologically active compounds found in propolis (e.g., apigenin, caffeic acid, chrysin, kaempferol, quercetin). Moreover, propolis is effective in the treatment of hyperglycemia, which increases the risk of SARS-CoV-2 infections. The aim of the literature review was to summarize recent studies from the PubMed database evaluating the antiviral activity of propolis extracts in terms of prevention and the therapy of respiratory tract diseases (in vitro, in vivo, clinical trials). Based upon this review, it was found that in recent years studies have focused mainly on the assessment of the effectiveness of propolis and its chemical components against COVID-19. Propolis exerts wide-spectrum antimicrobial activities; thus, propolis extracts can be an effective option in the prevention and treatment of co-infections associated with diseases of the respiratory tract.
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Affiliation(s)
- Marcin Ożarowski
- Department of Biotechnology, Institute of Natural Fibres and Medicinal Plants—National Research Institute, Wojska Polskiego 71b, 60-630 Poznań, Poland
| | - Tomasz M. Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Rokietnicka 10, 60-806 Poznań, Poland
- Correspondence:
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Alavi M, Mozafari MR, Ghaemi S, Ashengroph M, Hasanzadeh Davarani F, Mohammadabadi M. Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study. Biomedicines 2022; 10:biomedicines10123074. [PMID: 36551830 PMCID: PMC9775955 DOI: 10.3390/biomedicines10123074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 12/03/2022] Open
Abstract
Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of -9.9 and -8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.
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Affiliation(s)
- Mehran Alavi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Kurdistan 6617715175, Iran
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah 6714414971, Iran
- Correspondence: (M.A.); (M.R.M.)
| | - M. R. Mozafari
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia
- Correspondence: (M.A.); (M.R.M.)
| | - Saba Ghaemi
- Research Committee of Medical School, Alborz University of Medical Science, Karaj 3149779453, Iran
| | - Morahem Ashengroph
- Department of Biological Science, Faculty of Science, University of Kurdistan, Kurdistan 6617715175, Iran
| | | | - Mohammadreza Mohammadabadi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616913439, Iran
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46
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Vaseghi G, Golestaneh A, Jafari L, Ghasemi F. Drug Repurposing Against Angiotensin-Converting Enzyme-Related Carboxypeptidase (ACE2) Through Computational Approach. JOURNAL OF MEDICAL SIGNALS & SENSORS 2022; 12:341-346. [PMID: 36726422 PMCID: PMC9885507 DOI: 10.4103/jmss.jmss_66_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/29/2021] [Accepted: 02/03/2022] [Indexed: 02/03/2023]
Abstract
Ongoing novel coronavirus (COVID-19) with high mortality is an infectious disease in the world which epidemic in 2019 with human-human transmission. According to the literature, S-protein is one of the main proteins of COVID-19 that bind to the human cell receptor angiotensin-converting enzyme 2 (ACE2). In this study, it was attempted to identify the main effective drugs approved that may be repurposed to the binding site of ACE2. High throughput virtual screening based on the docking study was performed to know which one of the small-molecules had a potential interaction with ACE2 structure. Forasmuch as investigating and identifying the best ACE2 inhibitors among more than 3,500 small-molecules is time-consuming, supercomputer was utilized to apply docking-based virtual screening. Outputs of the proposed computational model revealed that vincristine, vinbelastin and bisoctrizole can significantly bind to ACE2 and may interface with its normal activity.
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Affiliation(s)
- Golnaz Vaseghi
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Golestaneh
- Applied Physiology Research Center, Cardiovascular Research Institute, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Leila Jafari
- Department of Bioinformatics and Systems Biology, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fahimeh Ghasemi
- Medical Image and Signal Processing Research Center, Isfahan University of Medical Sciences, Isfahan, Iran,Address for correspondence: Dr. Fahimeh Ghasemi, Department of Bioinformatics and Systems Biology, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran. E-mail:
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Zaccaria M, Genovese L, Dawson W, Cristiglio V, Nakajima T, Johnson W, Farzan M, Momeni B. Probing the mutational landscape of the SARS-CoV-2 spike protein via quantum mechanical modeling of crystallographic structures. PNAS NEXUS 2022; 1:pgac180. [PMID: 36712320 PMCID: PMC9802038 DOI: 10.1093/pnasnexus/pgac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/29/2022] [Indexed: 02/01/2023]
Abstract
We employ a recently developed complexity-reduction quantum mechanical (QM-CR) approach, based on complexity reduction of density functional theory calculations, to characterize the interactions of the SARS-CoV-2 spike receptor binding domain (RBD) with ACE2 host receptors and antibodies. QM-CR operates via ab initio identification of individual amino acid residue's contributions to chemical binding and leads to the identification of the impact of point mutations. Here, we especially focus on the E484K mutation of the viral spike protein. We find that spike residue 484 hinders the spike's binding to the human ACE2 receptor (hACE2). In contrast, the same residue is beneficial in binding to the bat receptor Rhinolophus macrotis ACE2 (macACE2). In agreement with empirical evidence, QM-CR shows that the E484K mutation allows the spike to evade categories of neutralizing antibodies like C121 and C144. The simulation also shows how the Delta variant spike binds more strongly to hACE2 compared to the original Wuhan strain, and predicts that a E484K mutation can further improve its binding. Broad agreement between the QM-CR predictions and experimental evidence supports the notion that ab initio modeling has now reached the maturity required to handle large intermolecular interactions central to biological processes.
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Affiliation(s)
- Marco Zaccaria
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Luigi Genovese
- Université Grenoble Alpes, CEA, INAC-MEM, L_Sim, 38000 Grenoble, France
| | - William Dawson
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minamimi-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | | | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minamimi-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Welkin Johnson
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458,
USA
| | - Babak Momeni
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
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Basu A, Sarkar A, Bandyopadhyay S, Maulik U. In silico strategies to identify protein-protein interaction modulator in cell-to-cell transmission of SARS CoV2. Transbound Emerg Dis 2022; 69:3896-3905. [PMID: 36379049 DOI: 10.1111/tbed.14760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/08/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022]
Abstract
RNA sequence data from SARS CoV2 patients helps to construct a gene network related to this disease. A detailed analysis of the human host response to SARS CoV2 with expression profiling by high-throughput sequencing has been accomplished with primary human lung epithelial cell lines. Using this data, the clustered gene annotation and gene network construction are performed with the help of the String database. Among the four clusters identified, only 1 with 44 genes could be annotated. Interestingly, this corresponded to basal cells with p = 1.37e - 05, which is relevant for respiratory tract infection. Functional enrichment analysis of genes present in the gene network has been completed using the String database and the Network Analyst tool. Among three types of cell-cell communication, only the anchoring junction between the basal cell membrane and the basal lamina in the host cell is involved in the virus transmission. In this junction point, a hemidesmosome structure plays a vital role in virus spread from one cell to basal lamina in the respiratory tract. In this protein complex structure, different integrin protein molecules of the host cell are used to promote the spread of virus infection into the extracellular matrix. So, small molecular blockers of different anchoring junction proteins, such as integrin alpha 3, integrin beta 1, can provide efficient protection against this deadly viral disease. ORF8 from SARS CoV2 virus can interact with both integrin proteins of human host. By using molecular docking technique, a ternary complex of these three proteins is modelled. Several oligopeptides are predicted as modulators for this ternary complex. In silico analysis of these modulators is very important to develop novel therapeutics for the treatment of SARS CoV2.
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Affiliation(s)
- Anamika Basu
- Department of Biochemistry, Gurudas College, Kolkata, India
| | - Anasua Sarkar
- Computer Science and Engineering Department, Jadavpur University, Kolkata, India
| | | | - Ujjwal Maulik
- Computer Science and Engineering Department, Jadavpur University, Kolkata, India
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Dey R, Samadder A, Nandi S. Exploring the Targets of Novel Corona Virus and Docking-based Screening of Potential Natural Inhibitors to Combat COVID-19. Curr Top Med Chem 2022; 22:2410-2434. [PMID: 36281864 DOI: 10.2174/1568026623666221020163831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 01/20/2023]
Abstract
There is a need to explore natural compounds against COVID-19 due to their multitargeted actions against various targets of nCoV. They act on multiple sites rather than single targets against several diseases. Thus, there is a possibility that natural resources can be repurposed to combat COVID-19. However, the biochemical mechanisms of these inhibitors were not known. To reveal the mode of anti-nCoV action, structure-based docking plays a major role. The present study is an attempt to explore various potential targets of SARS-CoV-2 and the structure-based screening of various potential natural inhibitors to combat the novel coronavirus.
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Affiliation(s)
- Rishita Dey
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India.,Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
| | - Asmita Samadder
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
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Kim YS, Kwon EB, Kim B, Chung HS, Choi G, Kim YH, Choi JG. Mulberry Component Kuwanon C Exerts Potent Therapeutic Efficacy In Vitro against COVID-19 by Blocking the SARS-CoV-2 Spike S1 RBD:ACE2 Receptor Interaction. Int J Mol Sci 2022; 23:12516. [PMID: 36293371 PMCID: PMC9604257 DOI: 10.3390/ijms232012516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 11/24/2022] Open
Abstract
There has been an immense effort by global pharmaceutical companies to develop anti-COVID-19 drugs, including small molecule-based RNA replication inhibitors via drug repositioning and antibody-based spike protein blockers related to cell entry by SARS-CoV-2. However, several limitations to their clinical use have emerged in addition to a lack of progress in the development of small molecule-based cell entry inhibitors from natural products. In this study, we tested the effectiveness of kuwanon C (KC), which has mainly been researched using in silico docking simulation and can serve as an effective building block for developing anti-COVID-19 drugs, in blocking the spike S1 RBD:ACE2 receptor interaction. KC is a natural product derived from Morus alba L., commonly known as mulberry, which has known antiviral efficacy. Molecular interaction studies using competitive ELISA and the BLItz system revealed that KC targets both the spike S1 RBD and the ACE2 receptor, successfully disrupting their interaction, as supported by the in silico docking simulation. Furthermore, we established a mechanism of action by observing how KC prevents the infection of SARS-CoV-2 spike pseudotyped virus in ACE2/TPRSS2-overexpressing HEK293T cells. Finally, we demonstrated that KC inhibits clinical isolates of SARS-CoV-2 in Vero cells. Future combinations of small molecule-based cell entry inhibitors, such as KC, with the currently prescribed RNA replication inhibitors are anticipated to significantly enhance the efficacy of COVID-19 therapies.
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Affiliation(s)
- Young Soo Kim
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
| | - Eun-Bin Kwon
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
| | - Buyun Kim
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
| | - Hwan-Suck Chung
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
| | - Garam Choi
- R&D Center, Etnova Therapeutics Corp., 198 Saneop-ro, Gwonseon-gu, Suwon 13207, Korea
| | - Yeoun-Hee Kim
- R&D Center, Etnova Therapeutics Corp., 198 Saneop-ro, Gwonseon-gu, Suwon 13207, Korea
| | - Jang-Gi Choi
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
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