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Xu J, Zhu Q, Li W, Yin X, Li J. Structural basis for the inhibition of the HCoV-NL63 main protease M pro by X77. Biochem Biophys Res Commun 2024; 724:150231. [PMID: 38852502 DOI: 10.1016/j.bbrc.2024.150231] [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: 05/24/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Human coronaviruses are a group of pathogens that primarily cause respiratory and intestinal diseases. Infection can easily cause respiratory symptoms, as well as a variety of serious complications. There are several types of human coronaviruses, such as SARS-CoV, MERS-CoV, HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, and SARS-CoV-2. The prevalence of COVID-19 has led to a growing focus on drug research against human coronaviruses. The main protease (Mpro) from human coronaviruses is a relatively conserved that controls viral replication. X77 was discovered to have extremely high inhibitory activity against SARS-CoV-2 Mpro through the use of computer-simulated docking. In this paper, we have resolved the crystal structure of the HCoV-NL63 Mpro complexed with X77 and analyzed their interaction in detail. This data provides essential information for solving their binding modes and their structural determinants. Then, we compared the binding modes of X77 with SARS-CoV-2 Mpro and HCoV-NL63 Mpro in detail. This study illustrates the structural basis of HCoV-NL63 Mpro binding to the inhibitor X77. The structural insights derived from this study will inform the development of new drugs with broad-spectrum resistance to human coronaviruses.
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Affiliation(s)
- Jie Xu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Qinyao Zhu
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, 110142, China
| | - Wenwen Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Xiushan Yin
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, 110142, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
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2
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Molaakbari E, Aallae MR, Golestanifar F, Garakani-Nejad Z, Khosravi A, Rezapour M, Eshaghi Malekshah R, Ghomi M, Ren G. In silico assessment of hesperidin on SARS-CoV-2 main protease and RNA polymerase: Molecular docking and dynamics simulation approach. Biochem Biophys Rep 2024; 39:101804. [PMID: 39193225 PMCID: PMC11347860 DOI: 10.1016/j.bbrep.2024.101804] [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: 05/06/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/29/2024] Open
Abstract
The present study uses molecular docking and dynamic simulations to evaluate the inhibitory effect of flavonoid glycosides-based compounds on coronavirus Main protease (Mpro) and RNA polymerase. The Molegro Virtual Docker (MVD) software is utilized to simulate and calculate the binding parameters of compounds with coronavirus. The docking results show that the selected herbal compounds are more effective than those of chemical compounds. It is also revealed that five herbal ligands and two chemical ligands have the best docking scores. Furthermore, a Molecular Dynamics (MD) simulation was conducted for Hesperidin, confirming docking results. Analysis based on different parameters such as Root-mean-square deviation (RMSD), Root mean square fluctuation (RMSF), Radius of gyration (Rg), Solvent accessibility surface area (SASA), and the total number of hydrogen bonds suggests that Hesperidin formed a stable complex with Mpro. Absorption, Distribution, Metabolism, Excretion, And Toxicity (ADMET) analysis was performed to compare Hesperidin and Grazoprevir as potential antiviral medicines, evaluating both herbal and chemical ligand results. According to the study, herbal compounds could be effective on coronavirus and are admissible candidates for developing potential operative anti-viral medicines. Hesperidin was found to be the most acceptable interaction. Grazoprevir is an encouraging candidate for drug development and clinical trials, with the potential to become a highly effective Mpro inhibitor. Compared to RNA polymerase, Mpro showed a greater affinity for bonding with Hesperidin. van der Waals and electrostatic energies dominated, creating a stable Hesperidin-Mpro and Hesperidin-RNA polymerase complex.
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Affiliation(s)
- Elaheh Molaakbari
- Leishmaniasis Research Center, Kerman University of Medical Science, Kerman, Iran
| | | | | | | | - Ahmad Khosravi
- Leishmaniasis Research Center, Kerman University of Medical Science, Kerman, Iran
| | - Mohsen Rezapour
- Department of Biostatics and Data Science, University of Texas, Health Science Center at Houston, Texas, USA
| | | | - Mahsa Ghomi
- Students Research Committee, Faculty of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Guogang Ren
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, AL10 9AB, UK
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Cherigo L, Liao-Luo J, Fernández J, Martínez-Luis S. Isolation of Alpha-Glucosidase Inhibitors from the Panamanian Mangrove Plant Mora oleifera (Triana ex Hemsl.) Ducke. Pharmaceuticals (Basel) 2024; 17:890. [PMID: 39065741 PMCID: PMC11279897 DOI: 10.3390/ph17070890] [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: 05/13/2024] [Revised: 06/24/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Panama boasts an expansive mangrove area and stands as one of the most biodiverse countries in America. While mangrove plants have long been utilized in traditional medicine, there are still unstudied species whose potential medicinal applications remain unknown. This study aimed to extract bioactive compounds from Mora oleifera (Triana ex Hemsl.) Ducke, an understudied mangrove species. Through bioassay-guided fractionation of the crude extract, we isolated seven active compounds identified as lupenone (1), lupeol (2), α-amyrin (3), β-amyrin (4), palmitic acid (5), sitosterol (6), and stigmasterol (7). Compound structures were determined using spectroscopic analyses, including APCI-HR-MS and NMR. Compounds 1-7 displayed concentration-dependent inhibition of the alpha-glucosidase enzyme, with IC50 values of 0.72, 1.05, 2.13, 1.22, 240.20, 18.70, and 163.10 µM, respectively. Their inhibitory activity surpassed acarbose, the positive control (IC50 241.6 µM). Kinetic analysis revealed that all compounds acted as competitive inhibitors. Docking analysis predicted that all triterpenes bonded to the same site as acarbose in human intestinal alpha-glucosidase (PDB: 3TOP). A complementary metabolomic analysis of M. oleifera active fractions revealed the presence of 64 compounds, shedding new light on the plant's chemical composition. These findings suggest that M. oleifera holds promise as a valuable botanical source for developing compounds for managing blood sugar levels in individuals with diabetes.
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Affiliation(s)
- Lilia Cherigo
- Departamento de Química Orgánica, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá P.O. Box 3366, Panama; (L.C.); (J.L.-L.)
| | - Javier Liao-Luo
- Departamento de Química Orgánica, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá P.O. Box 3366, Panama; (L.C.); (J.L.-L.)
| | - Juan Fernández
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Edificio 208, Ciudad del Saber, Apartado 0843-01103, Panama;
| | - Sergio Martínez-Luis
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Edificio 208, Ciudad del Saber, Apartado 0843-01103, Panama;
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Akermi S, Smaoui S, Chaari M, Elhadef K, Gentile R, Hait M, Roymahapatra G, Mellouli L. Combined in vitro/in silico approaches, molecular dynamics simulations and safety assessment of the multifunctional properties of thymol and carvacrol: A comparative insight. Chem Biodivers 2024; 21:e202301575. [PMID: 38116885 DOI: 10.1002/cbdv.202301575] [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: 10/07/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
Bioactive compounds derived from medicinal plants have acquired immense attentiveness in drug discovery and development. The present study investigated in vitro and predicted in silico the antibacterial, antifungal, and antiviral properties of thymol and carvacrol, and assessed their safety. The performed microbiological assays against Pseudomonas aeruginosa, Escherichia coli, Salmonella enterica Typhimurium revealed that the minimal inhibitory concentration values ranged from (0.078 to 0.312 mg/mL) and the minimal fungicidal concentration against Candida albicans was 0.625 mg/mL. Molecular docking simulations, stipulated that these compounds could inhibit bacterial replication and transcription functions by targeting DNA and RNA polymerases receptors with docking scores varying between (-5.1 to -6.9 kcal/mol). Studied hydroxylated monoterpenes could hinder C. albicans growth by impeding lanosterol 14α-demethylase enzyme and showed a (ΔG=-6.2 and -6.3 kcal/mol). Computational studies revealed that thymol and carvacrol could target the SARS-Cov-2 spike protein of the Omicron variant RBD domain. Molecular dynamics simulations disclosed that these compounds have a stable dynamic behavior over 100 ns as compared to remdesivir. Chemo-computational toxicity prediction using Protox II webserver indicated that thymol and carvacrol could be safely and effectively used as drug candidates to tackle bacterial, fungal, and viral infections as compared to chemical medication.
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Affiliation(s)
- Sarra Akermi
- Laboratory of Microbial and Enzymatic Biotechnologies and Biomolecules. Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax, 3018, Sfax-, Tunisia
| | - Slim Smaoui
- Laboratory of Microbial and Enzymatic Biotechnologies and Biomolecules. Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax, 3018, Sfax-, Tunisia
| | - Moufida Chaari
- Laboratory of Microbial and Enzymatic Biotechnologies and Biomolecules. Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax, 3018, Sfax-, Tunisia
| | - Khaoula Elhadef
- Laboratory of Microbial and Enzymatic Biotechnologies and Biomolecules. Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax, 3018, Sfax-, Tunisia
| | - Rocco Gentile
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Milan Hait
- Department of Chemistry, Dr. C. V. Raman University, Kota, 495113, Bilaspur, India
| | | | - Lotfi Mellouli
- Laboratory of Microbial and Enzymatic Biotechnologies and Biomolecules. Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax, 3018, Sfax-, Tunisia
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Cui J, Fan Y, Lian D, Wang S, Wang M, Du Y, Li Y, Li L. Interaction of narcissoside with α-amylase from Bacillus subtilis and Porcine pancreatic by multi-spectral analysis and molecular dynamics simulation. LUMINESCENCE 2023. [PMID: 38038156 DOI: 10.1002/bio.4637] [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: 08/26/2023] [Revised: 09/23/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
In this work, interaction mechanism of narcissoside with two α-amylase from Bacillus subtilis (BSA) and Porcine pancreatic (PPA) are comparatively studied by multi-spectral analysis, molecular docking and molecular dynamics simulation. The results prove that narcissoside can statically quench fluorescence of BSA/PPA. Two complexes are mainly formed by hydrogen bond and van der Waals force. With the increase of temperature, the two complexes formed by narcissoside and two enzymes become unstable. At the same experimental temperature, the binding force of narcissoside to PPA is higher than that of BSA. The binding of narcissoside to PPA/BSA increases the hydrophobicity of microenvironment. Moreover, the secondary structure of PPA/BSA is mainly changed by decreasing the α-helix. The optimal binding modes of narcissoside with BSA/PPA are predicted by molecular docking, and the stability of the two complexes is evaluated by molecular dynamics simulations.
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Affiliation(s)
- Jingjing Cui
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yangyang Fan
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Di Lian
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Suqing Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Meizi Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yutong Du
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yuan Li
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Li Li
- The College of Chemistry, Changchun Normal University, Changchun, China
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Alkafaas SS, Abdallah AM, Hussien AM, Bedair H, Abdo M, Ghosh S, Elkafas SS, Apollon W, Saki M, Loutfy SA, Onyeaka H, Hessien M. A study on the effect of natural products against the transmission of B.1.1.529 Omicron. Virol J 2023; 20:191. [PMID: 37626376 PMCID: PMC10464336 DOI: 10.1186/s12985-023-02160-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The recent outbreak of the Coronavirus pandemic resulted in a successful vaccination program launched by the World Health Organization. However, a large population is still unvaccinated, leading to the emergence of mutated strains like alpha, beta, delta, and B.1.1.529 (Omicron). Recent reports from the World Health Organization raised concerns about the Omicron variant, which emerged in South Africa during a surge in COVID-19 cases in November 2021. Vaccines are not proven completely effective or safe against Omicron, leading to clinical trials for combating infection by the mutated virus. The absence of suitable pharmaceuticals has led scientists and clinicians to search for alternative and supplementary therapies, including dietary patterns, to reduce the effect of mutated strains. MAIN BODY This review analyzed Coronavirus aetiology, epidemiology, and natural products for combating Omicron. Although the literature search did not include keywords related to in silico or computational research, in silico investigations were emphasized in this study. Molecular docking was implemented to compare the interaction between natural products and Chloroquine with the ACE2 receptor protein amino acid residues of Omicron. The global Omicron infection proceeding SARS-CoV-2 vaccination was also elucidated. The docking results suggest that DGCG may bind to the ACE2 receptor three times more effectively than standard chloroquine. CONCLUSION The emergence of the Omicron variant has highlighted the need for alternative therapies to reduce the impact of mutated strains. The current review suggests that natural products such as DGCG may be effective in binding to the ACE2 receptor and combating the Omicron variant, however, further research is required to validate the results of this study and explore the potential of natural products to mitigate COVID-19.
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Affiliation(s)
- Samar Sami Alkafaas
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Abanoub Mosaad Abdallah
- Narcotic Research Department, National Center for Social and Criminological Research (NCSCR), Giza, 11561, Egypt
| | - Aya Misbah Hussien
- Biotechnology Department at Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Heba Bedair
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Mahmoud Abdo
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa.
| | - Sara Samy Elkafas
- Production Engineering and Mechanical Design Department, Faculty of Engineering, Menofia University, Menofia, Egypt
| | - Wilgince Apollon
- Department of Agricultural and Food Engineering, Faculty of Agronomy, Universidad Autónoma de Nuevo León, Francisco Villa S/N, Ex-Hacienda El Canadá, 66050, General Escobedo, Nuevo León, Mexico
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Nanotechnology Research Center, British University, Cairo, Egypt
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Mohamed Hessien
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
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Toigo L, Dos Santos Teodoro EI, Guidi AC, Gancedo NC, Petruco MV, Melo EB, Tonin FS, Fernandez-Llimos F, Chierrito D, de Mello JCP, de Medeiros Araújo DC, Sanches ACC. Flavonoid as possible therapeutic targets against COVID-19: a scoping review of in silico studies. Daru 2023; 31:51-68. [PMID: 37195402 PMCID: PMC10191091 DOI: 10.1007/s40199-023-00461-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/25/2023] [Indexed: 05/18/2023] Open
Abstract
OBJECTIVES This scoping review aims to present flavonoid compounds' promising effects and possible mechanisms of action on potential therapeutic targets in the SARS-CoV-2 infection process. METHODS A search of electronic databases such as PubMed and Scopus was carried out to evaluate the performance of substances from the flavonoid class at different stages of SARS-CoV-2 infection. RESULTS The search strategy yielded 382 articles after the exclusion of duplicates. During the screening process, 265 records were deemed as irrelevant. At the end of the full-text appraisal, 37 studies were considered eligible for data extraction and qualitative synthesis. All the studies used virtual molecular docking models to verify the affinity of compounds from the flavonoid class with crucial proteins in the replication cycle of the SARS-CoV-2 virus (Spike protein, PLpro, 3CLpro/ MPro, RdRP, and inhibition of the host's ACE II receptor). The flavonoids with more targets and lowest binding energies were: orientin, quercetin, epigallocatechin, narcissoside, silymarin, neohesperidin, delphinidin-3,5-diglucoside, and delphinidin-3-sambubioside-5-glucoside. CONCLUSION These studies allow us to provide a basis for in vitro and in vivo assays to assist in developing drugs for the treatment and prevention of COVID-19.
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Affiliation(s)
- Larissa Toigo
- Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | | | - Ana Carolina Guidi
- Laboratório de Biologia Farmacêutica, Departamento de Farmácia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Naiara Cássia Gancedo
- Laboratório de Biologia Farmacêutica, Departamento de Farmácia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Marcus Vinícius Petruco
- Clínica de Reumatologia-Pneumologia Laboratório do Sono de Maringá e Hospital Bom Samaritano de Maringá, Maringá, Brazil
| | - Eduardo Borges Melo
- Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Fernanda Stumpf Tonin
- Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Federal do Paraná, Curitiba, Brazil
- H&TRC- Health & Technology Research Center, ESTeSLEscola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | | | - Danielly Chierrito
- Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
- Centro Universitário Ingá - UNINGÁ, Maringá, Brazil
| | - João Carlos Palazzo de Mello
- Laboratório de Biologia Farmacêutica, Departamento de Farmácia, Universidade Estadual de Maringá, Maringá, Brazil
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Liu T, Cao L, Zhang T, Fu H. Molecular docking studies, anti-Alzheimer's disease, antidiabetic, and anti-acute myeloid leukemia potentials of narcissoside. Arch Physiol Biochem 2023; 129:405-415. [PMID: 33075241 DOI: 10.1080/13813455.2020.1828483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this research, we explored their capacity for Narcissoside antioxidant and anticholinergic, antidiabetic, and anti-acute myeloid leukaemia. Narcissoside's antioxidant activities were elucidated by the use of various bioanalytical assays. Narcissoside's radical scavenging activities were evaluated by DPPH• and ABTS•+ scavenging activities. On the other hand, IC50 values were calculated for DPPH•, and ABTS•+ scavenging, acetylcholinesterase, and α-glucosidase inhibition effects of narcissoside. IC50 values narcissoside, as 11.54 nM for AChE and 65.58 nM for α-glucosidase were calculated with % Activity-[Inhibitory] graphs. Then, ADME/T analysis of narcissoside molecule was performed to calculate the drug becoming parameters.
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Affiliation(s)
- Tingting Liu
- Department of Hematology, People's Hospital of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Hematology, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China
- Key Biologic Laboratory of Blood Tumor Cell of Jiangxi Province, Nanchang, Jiangxi, China
| | - Lixia Cao
- Department of Hematology, People's Hospital of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Hematology, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China
- Key Biologic Laboratory of Blood Tumor Cell of Jiangxi Province, Nanchang, Jiangxi, China
| | - Tingting Zhang
- Department of Hematology, People's Hospital of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Hematology, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China
- Key Biologic Laboratory of Blood Tumor Cell of Jiangxi Province, Nanchang, Jiangxi, China
| | - Huan Fu
- Department of Hematology, People's Hospital of Jiangxi Province, Nanchang, Jiangxi, China
- Department of Hematology, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China
- Key Biologic Laboratory of Blood Tumor Cell of Jiangxi Province, Nanchang, Jiangxi, China
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Computational studies of potential antiviral compounds from some selected Nigerian medicinal plants against SARS-CoV-2 proteins. INFORMATICS IN MEDICINE UNLOCKED 2023; 38:101230. [PMID: 36974159 PMCID: PMC10030444 DOI: 10.1016/j.imu.2023.101230] [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: 02/17/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/24/2023] Open
Abstract
The challenges posed by COVID-19's emergence have led to a search for its therapies. There is no cure for COVID-19 infection yet, but there is significant progress in vaccine formulation for prophylaxis and drug development (such as paxlovid) for high-risk patients. As a contribution to the ongoing quest for solutions, this study shows potent phytocompounds identification as inhibitors of SARS-CoV-2 targets using in silico methods. We used virtual screening, molecular docking, and molecular dynamics (MD) simulations to investigate the interaction of some phytochemicals with 3CLpro, ACE2, and PLpro proteins crucial to the SARS-CoV-2 viral cycle. The predicted docking scores range from −5.5 to −9.4 kcal/mol, denoting appreciable binding of these compounds to the SARS-CoV-2 proteins and presenting a multitarget inhibition for COVID-19. Some phytocompounds interact favorably at non-active sites of the enzymes. For instance, MD simulation shows that an identified site on PLpro is stable and likely an allosteric region for inhibitor binding and modulation. These phytocompounds could be developed into effective therapy against COVID-19 and probed as potential multitarget-directed ligands and drug candidates against the SARS-CoV-2 virus. The study unveils drug repurposing, selectivity, allosteric site targeting, and multitarget-directed ligand in one piece. These concepts are three distinct approaches in the drug design and discovery pipeline.
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Yan J, Zeng H, Chen W, Zheng S, Luo J, Jiang H, Yang B, Farag MA, Lou H, Song L, Wu J. Effects of tree age on flavonoids and antioxidant activity in
Torreya grandis
nuts via integrated metabolome and transcriptome analyses. FOOD FRONTIERS 2023. [DOI: 10.1002/fft2.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Jingwei Yan
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou Zhejiang China
| | - Hao Zeng
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou Zhejiang China
| | - Weijie Chen
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou Zhejiang China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou Zhejiang China
| | - Jiali Luo
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou Zhejiang China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin China
- National Center of Technology Innovation for Synthetic Biology Tianjin China
| | - Baoru Yang
- Food Sciences, Department of Life Technologies University of Turku Turku Finland
| | - Mohamed A. Farag
- Pharmacognosy Department, College of Pharmacy Cairo University Cairo P.B Egypt
| | - Heqiang Lou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou Zhejiang China
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou Zhejiang China
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou Zhejiang China
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11
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Srivastava S, He F, Huang Y, Niu M, Adholeya A, Peng WK. A Brief Review on Medicinal Plants-At-Arms against COVID-19. Interdiscip Perspect Infect Dis 2023; 2023:7598307. [PMID: 37139479 PMCID: PMC10151152 DOI: 10.1155/2023/7598307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/09/2023] [Accepted: 03/22/2023] [Indexed: 05/05/2023] Open
Abstract
COVID-19 pandemic caused by the novel SARS-CoV-2 has impacted human livelihood globally. Strenuous efforts have been employed for its control and prevention; however, with recent reports on mutated strains with much higher infectivity, transmissibility, and ability to evade immunity developed from previous SARS-CoV-2 infections, prevention alternatives must be prepared beforehand in case. We have perused over 128 recent works (found on Google Scholar, PubMed, and ScienceDirect as of February 2023) on medicinal plants and their compounds for anti-SARS-CoV-2 activity and eventually reviewed 102 of them. The clinical application and the curative effect were reported high in China and in India. Accordingly, this review highlights the unprecedented opportunities offered by medicinal plants and their compounds, candidates as the therapeutic agent, against COVID-19 by acting as viral protein inhibitors and immunomodulator in (32 clinical trials and hundreds of in silico experiments) conjecture with modern science. Moreover, the associated foreseeable challenges for their viral outbreak management were discussed in comparison to synthetic drugs.
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Affiliation(s)
- Shivani Srivastava
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gwal Pahari, Gurugram 122001, India
| | - Fangzhou He
- Songshan Lake Materials Laboratory, University Innovation Park, Dongguan 523-808, China
| | - Yuanding Huang
- Songshan Lake Materials Laboratory, University Innovation Park, Dongguan 523-808, China
| | - Meng Niu
- China Medical University, Shenyang, China
| | - Alok Adholeya
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gwal Pahari, Gurugram 122001, India
| | - Weng Kung Peng
- Songshan Lake Materials Laboratory, University Innovation Park, Dongguan 523-808, China
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12
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Singh MP, Singh N, Mishra D, Ehsan S, Chaturvedi VK, Chaudhary A, Singh V, Vamanu E. Computational Approaches to Designing Antiviral Drugs against COVID-19: A Comprehensive Review. Curr Pharm Des 2023; 29:2601-2617. [PMID: 37916490 DOI: 10.2174/0113816128259795231023193419] [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: 09/21/2023] [Indexed: 11/03/2023]
Abstract
The global impact of the COVID-19 pandemic caused by SARS-CoV-2 necessitates innovative strategies for the rapid development of effective treatments. Computational methodologies, such as molecular modelling, molecular dynamics simulations, and artificial intelligence, have emerged as indispensable tools in the drug discovery process. This review aimed to provide a comprehensive overview of these computational approaches and their application in the design of antiviral agents for COVID-19. Starting with an examination of ligand-based and structure-based drug discovery, the review has delved into the intricate ways through which molecular modelling can accelerate the identification of potential therapies. Additionally, the investigation extends to phytochemicals sourced from nature, which have shown promise as potential antiviral agents. Noteworthy compounds, including gallic acid, naringin, hesperidin, Tinospora cordifolia, curcumin, nimbin, azadironic acid, nimbionone, nimbionol, and nimocinol, have exhibited high affinity for COVID-19 Mpro and favourable binding energy profiles compared to current drugs. Although these compounds hold potential, their further validation through in vitro and in vivo experimentation is imperative. Throughout this exploration, the review has emphasized the pivotal role of computational biologists, bioinformaticians, and biotechnologists in driving rapid advancements in clinical research and therapeutic development. By combining state-of-the-art computational techniques with insights from structural and molecular biology, the search for potent antiviral agents has been accelerated. The collaboration between these disciplines holds immense promise in addressing the transmissibility and virulence of SARS-CoV-2.
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Affiliation(s)
- Mohan P Singh
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Nidhi Singh
- Centre of Bioinformatics, University of Allahabad, Prayagraj 211002, India
| | - Divya Mishra
- Centre of Bioinformatics, University of Allahabad, Prayagraj 211002, India
| | - Saba Ehsan
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Vivek K Chaturvedi
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anupriya Chaudhary
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Veer Singh
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Emanuel Vamanu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine of Bucharest, Bucharest 011464, Romania
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13
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Citric Acid Changes the Fingerprint of Flavonoids and Promotes Their Accumulation in Phellinus igniarius (L.) Quél. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010068. [PMID: 36676017 PMCID: PMC9861953 DOI: 10.3390/life13010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
Phellinus igniarius is a valuable medicinal fungus. P. igniarius is rich in a variety of chemical compounds with medicinal value, among which are flavonoids. Therefore, increasing the content of flavonoids in P. igniarius is beneficial for its potential use in medicinal applications. This study demonstrated that exogenous treatment with citric acid (CA) could significantly increase flavonoid accumulation in P. igniarius. Additionally, we found that CA induced the biosynthesis of flavonoids in a concentration- and time-dependent manner. The flavonoid content could be increased up to 60.96 mg/g when using the treatment with 2.77 mM citric acid for 69.74 h, which was determined by using the response surface method. The changes in the fingerprint profiles of P. igniarius flavonoids with the treatment of CA as an exogenous inducer were also analyzed. In this study, the effect of citric acid as the exogenous inducer on the flavonoid content of P. igniarius was studied, and the processing conditions were optimized through the surface response curve. This approach provides novel insights and a theoretical basis for the production of high-quality P. igniarius.
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14
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Sadeghi M, Sheikhi M, Miroliaei M. Control of eriocitrin release from pH-sensitive gelatin-based microgels to inhibit α-glucosidase: an experimental and computational study. Food Funct 2022; 13:10055-10068. [PMID: 36093798 DOI: 10.1039/d2fo00824f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Glucosidase is among the intestinal epithelial enzymes that produce absorbable glucose in the final stage of glycan catabolism. It leads to an increase in blood glucose levels as a result of high glucose uptake in diabetic patients. However, inhibition of this essential biochemical process can be a useful therapeutic approach to diabetes mellitus (DM). Eriocitrin (ER) is an abundant "flavanone glycoside" in citrus fruits with rich antioxidant properties whose effects on α-Glu inhibition in the small intestine remain to be determined. Herein, pH-sensitive microgels (MGs) were designed based on cross-linked methacrylate with acrylamide (AM) and acrylic acid (AAc) (molar ratio 70 : 30 of AAc : AM) as a controlled release system for sustained delivery of ER into the small intestine. The presence of amide and acrylate in MGs and the mechanical resistance were determined using FT-IR spectroscopy, rheology, and viscoelastometry. In vitro experiments showed that MGs could protect ER against diffusion in the gastric location and adjust its release in the intestinal milieu. The intestinal α-Glu activity was inhibited by ER (IC50 value of 12.50 ± 0.73 μM) in an uncompetitive dose-dependent manner. The presence of ER altered the structure of α-Glu and reduced the hydrophobic pockets of the enzyme. Molecular docking analysis along with molecular dynamics simulation displayed that ER-α-Glu formation is directed by hydrogen binding with Asp69, Asp215, Glu411, Asp307, and Tyr347 residues. Moreover, in vivo assessment showed that rat blood glucose concentration decreased after ER administration compared with the control group. The results highlight that ER-loaded-MGs can be considered as a useful releasing strategy in treating DM via α-Glu inhibition.
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Affiliation(s)
- Morteza Sadeghi
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran.
| | - Mehdi Sheikhi
- Polymer Chemistry Research Laboratory, Department of Chemistry, University of Isfahan, Isfahan, Iran
| | - Mehran Miroliaei
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran.
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15
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León-Gutiérrez G, Elste JE, Cabello-Gutiérrez C, Millán-Pacheco C, Martínez-Gómez MH, Mejía-Alvarez R, Tiwari V, Mejía A. A potent virucidal activity of functionalized TiO 2 nanoparticles adsorbed with flavonoids against SARS-CoV-2. Appl Microbiol Biotechnol 2022; 106:5987-6002. [PMID: 35951081 PMCID: PMC9366830 DOI: 10.1007/s00253-022-12112-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022]
Abstract
Abstract The coronavirus SARS-CoV-2 has caused a pandemic with > 550 millions of cases and > 6 millions of deaths worldwide. Medical management of COVID-19 relies on supportive care as no specific targeted therapies are available yet. Given its devastating effects on the economy and mental health, it is imperative to develop novel antivirals. An ideal candidate will be an agent that blocks the early events of viral attachment and cell entry, thereby preventing viral infection and spread. This work reports functionalized titanium dioxide (TiO2)-based nanoparticles adsorbed with flavonoids that block SARS-CoV-2 entry and fusion. Using molecular docking analysis, two flavonoids were chosen for their specific binding to critical regions of the SARS-CoV-2 spike glycoprotein that interacts with the host cell angiotensin-converting enzyme-2 (ACE-2) receptor. These flavonoids were adsorbed onto TiO2 functionalized nanoparticles (FTNP). This new nanoparticulate compound was assayed in vitro against two different coronaviruses; HCoV 229E and SARS-CoV-2, in both cases a clear antiviral effect was observed. Furthermore, using a reporter-based cell culture model, a potent antiviral activity is demonstrated. The adsorption of flavonoids to functionalized TiO2 nanoparticles induces a ~ threefold increase of that activity. These studies also indicate that FTNP interferes with the SARS-CoV-2 spike, impairing the cell fusion mechanism. Key points/Highlights • Unique TiO2nanoparticles displaying flavonoid showed potent anti-SARS-CoV-2 activity. • The nanoparticles precisely targeting SARS-CoV-2 were quantitatively verified by cell infectivity in vitro. • Flavonoids on nanoparticles impair the interactions between the spike glycoprotein and ACE-2 receptor. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12112-9.
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Affiliation(s)
- Gabriela León-Gutiérrez
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico, Mexico
| | - James Edward Elste
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL, USA
| | - Carlos Cabello-Gutiérrez
- Departamento de Virología e Investigación en Micología, Instituto Nacional de Enfermedades Respiratorias, Ciudad de Mexico, Mexico
| | - Cesar Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Mario H Martínez-Gómez
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico, Mexico
| | - Rafael Mejía-Alvarez
- Department of Physiology, College of Graduate Studies, Midwestern University, Downers Grove, IL, USA
| | - Vaibhav Tiwari
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL, USA
| | - Armando Mejía
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico, Mexico.
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16
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Owona BA, Njayou FN, Mkounga P, Moundipa PF. Khaya grandifoliola active fraction as a source of therapeutic compounds for Alzheimer’s disease treatment: In silico validation of identified compounds. In Silico Pharmacol 2022; 10:11. [DOI: 10.1007/s40203-022-00126-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 05/24/2022] [Indexed: 10/17/2022] Open
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17
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Molecular docking and molecular dynamic simulation approaches for drug development and repurposing of drugs for severe acute respiratory syndrome-Coronavirus-2. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300476 DOI: 10.1016/b978-0-323-91172-6.00007-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Lochab A, Thareja R, Gadre SD, Saxena R. Potential Protein and Enzyme Targets for In‐silico Development and Repurposing of Drug Against Coronaviruses. ChemistrySelect 2021. [DOI: 10.1002/slct.202103350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amit Lochab
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
| | - Rakhi Thareja
- Department of Chemistry St. Stephens College University of Delhi Delhi India
| | - Sangeeta D. Gadre
- Department of Physics Kirori Mal College University of Delhi Delhi India
| | - Reena Saxena
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
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19
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Singla RK, He X, Chopra H, Tsagkaris C, Shen L, Kamal MA, Shen B. Natural Products for the Prevention and Control of the COVID-19 Pandemic: Sustainable Bioresources. Front Pharmacol 2021; 12:758159. [PMID: 34925017 PMCID: PMC8671886 DOI: 10.3389/fphar.2021.758159] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/27/2021] [Indexed: 02/05/2023] Open
Abstract
Background: The world has been unprecedentedly hit by a global pandemic which broke the record of deadly pandemics that faced humanity ever since its existence. Even kids are well-versed in the terminologies and basics of the SARS-CoV-2 virus and COVID-19 now. The vaccination program has been successfully launched in various countries, given that the huge global population of concern is still far behind to be vaccinated. Furthermore, the scarcity of any potential drug against the COVID-19-causing virus forces scientists and clinicians to search for alternative and complementary medicines on a war-footing basis. Aims and Objectives: The present review aims to cover and analyze the etiology and epidemiology of COVID-19, the role of intestinal microbiota and pro-inflammatory markers, and most importantly, the natural products to combat this deadly SARS-CoV-2 virus. Methods: A primary literature search was conducted through PubMed and Google Scholar using relevant keywords. Natural products were searched from January 2020 to November 2020. No timeline limit has been imposed on the search for the biological sources of those phytochemicals. Interactive mapping has been done to analyze the multi-modal and multi-target sources. Results and Discussion: The intestinal microbiota and the pro-inflammatory markers that can serve the prognosis, diagnosis, and treatment of COVID-19 were discussed. The literature search resulted in yielding 70 phytochemicals and ten polyherbal formulations which were scientifically analyzed against the SARS-CoV-2 virus and its targets and found significant. Retrospective analyses led to provide information about 165 biological sources that can also be screened if not done earlier. Conclusion: The interactive analysis mapping of biological sources with phytochemicals and targets as well as that of phytochemical class with phytochemicals and COVID-19 targets yielded insights into the multitarget and multimodal evidence-based complementary medicines.
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Affiliation(s)
- Rajeev K. Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Xuefei He
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura, India
| | | | - Li Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Enzymoics; Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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20
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Liao Q, Chen Z, Tao Y, Zhang B, Wu X, Yang L, Wang Q, Wang Z. An integrated method for optimized identification of effective natural inhibitors against SARS-CoV-2 3CLpro. Sci Rep 2021; 11:22796. [PMID: 34815498 PMCID: PMC8611036 DOI: 10.1038/s41598-021-02266-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/12/2021] [Indexed: 02/06/2023] Open
Abstract
The current severe situation of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has not been reversed and posed great threats to global health. Therefore, there is an urgent need to find out effective antiviral drugs. The 3-chymotrypsin-like protease (3CLpro) in SARS-CoV-2 serve as a promising anti-virus target due to its essential role in the regulation of virus reproduction. Here, we report an improved integrated approach to identify effective 3CLpro inhibitors from effective Chinese herbal formulas. With this approach, we identified the 5 natural products (NPs) including narcissoside, kaempferol-3-O-gentiobioside, rutin, vicenin-2 and isoschaftoside as potential anti-SARS-CoV-2 candidates. Subsequent molecular dynamics simulation additionally revealed that these molecules can be tightly bound to 3CLpro and confirmed effectiveness against COVID-19. Moreover, kaempferol-3-o-gentiobioside, vicenin-2 and isoschaftoside were first reported to have SARS-CoV-2 3CLpro inhibitory activity. In summary, this optimized integrated strategy for drug screening can be utilized in the discovery of antiviral drugs to achieve rapid acquisition of drugs with specific effects on antiviral targets.
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Affiliation(s)
- Qi Liao
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ziyu Chen
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yanlin Tao
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Beibei Zhang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaojun Wu
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li Yang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Qingzhong Wang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Zhengtao Wang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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21
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In Silico Modeling as a Perspective in Developing Potential Vaccine Candidates and Therapeutics for COVID-19. COATINGS 2021. [DOI: 10.3390/coatings11111273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The potential of computational models to identify new therapeutics and repurpose existing drugs has gained significance in recent times. The current ‘COVID-19’ pandemic caused by the new SARS CoV2 virus has affected over 200 million people and caused over 4 million deaths. The enormity and the consequences of this viral infection have fueled the research community to identify drugs or vaccines through a relatively expeditious process. The availability of high-throughput datasets has cultivated new strategies for drug development and can provide the foundation towards effective therapy options. Molecular modeling methods using structure-based or computer-aided virtual screening can potentially be employed as research guides to identify novel antiviral agents. This review focuses on in-silico modeling of the potential therapeutic candidates against SARS CoVs, in addition to strategies for vaccine design. Here, we particularly focus on the recently published SARS CoV main protease (Mpro) active site, the RNA-dependent RNA polymerase (RdRp) of SARS CoV2, and the spike S-protein as potential targets for vaccine development. This review can offer future perspectives for further research and the development of COVID-19 therapies via the design of new drug candidates and multi-epitopic vaccines and through the repurposing of either approved drugs or drugs under clinical trial.
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22
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Panigrahi D. Molecular Docking Analysis of the Phytochemicals from Tinospora Cordifolia as Potential Inhibitor Against Multi Targeted SARS-CoV-2 & Cytokine Storm. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2, a novel coronavirus, is a member of the Coronoviridae family that has spread worldwide. Developing efficacious therapeutics for the treatment of SARS-CoV-2 is of high priority. Therefore, in this study, the chemical constituents obtained from Tinospora cordifolia are investigated for their in-silico interaction with protein targets crucial for SARSCoV-2 infection and cytokine storm. The five important targets chosen for SARSCoV-2 were the main protease (Mpro), Spike receptor binding domain (Spike-RBD), RNA-dependent RNA polymerase (RdRp or Nsp12), nonstructural protein 15 (Nsp15) of SARS-CoV-2 and the host angiotensin converting enzyme-2 (ACE-2) spike-RBD binding domain and cytokine receptors TNF-[Formula: see text] (Tumor Necrosis Factor-[Formula: see text]) and IL-6 (Interleukine-6). This was accomplished using Maestro 12.4 (Schrodinger Suite) to obtain docking scores. Also, the absorption, distribution, metabolism, elimination, and toxicity parameters (ADMET) were determined using Maestro QikProp modules. The results of computational study revealed that four constituents Cordifolioside-A, Palmatoside-E, Tinocordioside and Tinosporaside significantly antagonize the five targets of SARS-CoV-2 by binding in the binding pocket with docking score ranging from −9.664 to −6.488 kcal/mol and shows drug-like property and also effectively inhibit cytokine storm by antagonizing the TNF-[Formula: see text] and IL-6 receptors. Promising drug-like properties, excellent docking scores, and binding pose against each target makes the screened compounds as possible lead candidate which can be further evaluated in future studies to assess their in vitro and in vivo efficacy against SARS-CoV-2. The structure of these compounds can be used further for optimization and design of drugs against COVID-19.
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Affiliation(s)
- Debadash Panigrahi
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri-Konark Marine Drive Road, Puri, Odisha 752002, India
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23
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Mishra GP, Bhadane RN, Panigrahi D, Amawi HA, Asbhy CR, Tiwari AK. The interaction of the bioflavonoids with five SARS-CoV-2 proteins targets: An in silico study. Comput Biol Med 2021; 134:104464. [PMID: 34020130 PMCID: PMC8108478 DOI: 10.1016/j.compbiomed.2021.104464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
Flavonoids have been shown to have antioxidant, anti-inflammatory, anti-proliferative, antibacterial and antiviral efficacy. Therefore, in this study, we choose 85 flavonoid compounds and screened them to determine their in-silico interaction with protein targets crucial for SARS-CoV-2 infection. The five important targets chosen were the main protease (Mpro), Spike receptor binding domain (Spike-RBD), RNA - dependent RNA polymerase (RdRp or Nsp12), non-structural protein 15 (Nsp15) of SARS-CoV-2 and the host angiotensin converting enzyme-2 (ACE-2) spike-RBD binding domain. The compounds were initially docked at the selected sites and further evaluated for binding free energy, using the molecular mechanics/generalized Born surface area (MMGBSA) method. The three compounds with the best binding scores were subjected to molecular dynamics (MD) simulations. The compound, tribuloside, had a high average binding free energy of -86.99 and -88.98 kcal/mol for Mpro and Nsp12, respectively. The compound, legalon, had an average binding free energy of -59.02 kcal/mol at the ACE2 spike-RBD binding site. The compound, isosilybin, had an average free binding energy of -63.06 kcal/mol for the Spike-RBD protein. Overall, our results suggest that tribuloside, legalon and isosilybin should be evaluated in future studies to determine their efficacy to inhibit SARS-CoV-2 infectivity.
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Affiliation(s)
- Ganesh Prasad Mishra
- Kharvel Subharti College of Pharmacy, Swami VivekanandSubharti University, Subhartipuram, NH-58, Delhi-Haridwar Bypass Road, Meerut, U.P, 250005, India,Corresponding author
| | - Rajendra N. Bhadane
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI, 20520, Turku, Finland,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI, 20520, Turku, Finland
| | - Debadash Panigrahi
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri- Konark Marine Drive Road, Puri, Odisha, 752002, India
| | - Haneen A. Amawi
- Department of Clinical Pharmacy and Pharmacy Practice, College of Pharmacy, Yarmouk University, Shafiq Irshidat St, Irbid, Jordan
| | - Charles R. Asbhy
- Department of Pharmaceutical Sciences, College of Pharmacy & Pharmaceutical Sciences, St. John's University, Queens, NY, USA, 10049
| | - Amit K. Tiwari
- Department of Pharmacology & Experimental Therapeutics, College of Pharmacy & Pharmaceutical Sciences, The University of Toledo, Toledo, OH, 43614, USA,Department of Cancer Biology, College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, 43614, USA,Corresponding author. Department of Pharmacology & Experimental Therapeutics, College of Pharmacy & Pharmaceutical Sciences, The University of Toledo, Toledo, OH, 43614, USA
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24
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Abiri R, Abdul-Hamid H, Sytar O, Abiri R, Bezerra de Almeida E, Sharma SK, Bulgakov VP, Arroo RRJ, Malik S. A Brief Overview of Potential Treatments for Viral Diseases Using Natural Plant Compounds: The Case of SARS-Cov. Molecules 2021; 26:molecules26133868. [PMID: 34202844 PMCID: PMC8270261 DOI: 10.3390/molecules26133868] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, as well as the more general global increase in viral diseases, has led researchers to look to the plant kingdom as a potential source for antiviral compounds. Since ancient times, herbal medicines have been extensively applied in the treatment and prevention of various infectious diseases in different traditional systems. The purpose of this review is to highlight the potential antiviral activity of plant compounds as effective and reliable agents against viral infections, especially by viruses from the coronavirus group. Various antiviral mechanisms shown by crude plant extracts and plant-derived bioactive compounds are discussed. The understanding of the action mechanisms of complex plant extract and isolated plant-derived compounds will help pave the way towards the combat of this life-threatening disease. Further, molecular docking studies, in silico analyses of extracted compounds, and future prospects are included. The in vitro production of antiviral chemical compounds from plants using molecular pharming is also considered. Notably, hairy root cultures represent a promising and sustainable way to obtain a range of biologically active compounds that may be applied in the development of novel antiviral agents.
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Affiliation(s)
- Rambod Abiri
- Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang 43400, Malaysia; or
| | - Hazandy Abdul-Hamid
- Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang 43400, Malaysia; or
- Laboratory of Bioresource Management, Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: (H.A.-H.); (V.P.B.); or (S.M.)
| | - Oksana Sytar
- Educational and Scientific Center “Institute of Biology and Medicine”, Department of Plant Biology, Taras Shevchenko National University of Kyiv, Volodymyrska 60, 01033 Kyiv, Ukraine;
- Department of Plant Physiology, Slovak University of Agriculture Nitra, A. Hlinku 2, 94976 Nitra, Slovakia
| | - Ramin Abiri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah 6718773654, Iran;
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6718773654, Iran
| | - Eduardo Bezerra de Almeida
- Biological and Health Sciences Centre, Laboratory of Botanical Studies, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil;
| | - Surender K. Sharma
- Department of Physics, Central University of Punjab, Bathinda 151401, India;
| | - Victor P. Bulgakov
- Department of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity (Institute of Biology and Soil Science), Far Eastern Branch of the Russian Academy of Sciences, 159 Stoletija Str., 690022 Vladivostok, Russia
- Correspondence: (H.A.-H.); (V.P.B.); or (S.M.)
| | - Randolph R. J. Arroo
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK;
| | - Sonia Malik
- Health Sciences Graduate Program, Biological & Health Sciences Centre, Federal University of Maranhão, São Luís 65080-805, MA, Brazil
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), University of Orléans, 1 Rue de Chartres-BP 6759, 45067 Orleans, France
- Correspondence: (H.A.-H.); (V.P.B.); or (S.M.)
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25
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Godinho PIC, Soengas RG, Silva VLM. Therapeutic Potential of Glycosyl Flavonoids as Anti-Coronaviral Agents. Pharmaceuticals (Basel) 2021; 14:546. [PMID: 34200456 PMCID: PMC8227519 DOI: 10.3390/ph14060546] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/26/2022] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread all over the world, creating a devastating socio-economic impact. Even though protective vaccines are starting to be administered, an effective antiviral agent for the prevention and treatment of COVID-19 is not available yet. Moreover, since new and deadly CoVs can emerge at any time with the potential of becoming pandemics, the development of therapeutic agents against potentially deadly CoVs is a research area of much current interest. In the search for anti-coronaviral drugs, researchers soon turned their heads towards glycosylated flavonoids. Glycosyl flavonoids, widespread in the plant kingdom, have received a lot of attention due to their widely recognized antioxidant, anti-inflammatory, neuroprotective, anticarcinogenic, antidiabetic, antimicrobial, and antiviral properties together with their capacity to modulate key cellular functions. The wide range of biological activities displayed by glycosyl flavonoids, along with their low toxicity, make them ideal candidates for drug development. In this review, we examine and discuss the up-to-date developments on glycosyl flavonoids as evidence-based natural sources of antivirals against coronaviruses and their potential role in the management of COVID-19.
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Affiliation(s)
- Patrícia I. C. Godinho
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Raquel G. Soengas
- Department of Organic and Inorganic Chemistry, University of Oviedo, Julián Clavería 7, 33006 Oviedo, Spain
| | - Vera L. M. Silva
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
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26
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Dutta M, Nezam M, Chowdhury S, Rakib A, Paul A, Sami SA, Uddin MZ, Rana MS, Hossain S, Effendi Y, Idroes R, Tallei T, Alqahtani AM, Emran TB. Appraisals of the Bangladeshi Medicinal Plant Calotropis gigantea Used by Folk Medicine Practitioners in the Management of COVID-19: A Biochemical and Computational Approach. Front Mol Biosci 2021; 8:625391. [PMID: 34124140 PMCID: PMC8187851 DOI: 10.3389/fmolb.2021.625391] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 05/11/2021] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first recognized in Wuhan in late 2019 and, since then, had spread globally, eventually culminating in the ongoing pandemic. As there is a lack of targeted therapeutics, there is certain opportunity for the scientific community to develop new drugs or vaccines against COVID-19 and so many synthetic bioactive compounds are undergoing clinical trials. In most of the countries, due to the broad therapeutic spectrum and minimal side effects, medicinal plants have been used widely throughout history as traditional healing remedy. Because of the unavailability of synthetic bioactive antiviral drugs, hence all possible efforts have been focused on the search for new drugs and alternative medicines from different herbal formulations. In recent times, it has been assured that the Mpro, also called 3CLpro, is the SARS-CoV-2 main protease enzyme responsible for viral reproduction and thereby impeding the host's immune response. As such, Mpro represents a highly specified target for drugs capable of inhibitory action against coronavirus disease 2019 (COVID-19). As there continue to be no clear options for the treatment of COVID-19, the identification of potential candidates has become a necessity. The present investigation focuses on the in silico pharmacological activity of Calotropis gigantea, a large shrub, as a potential option for COVID-19 Mpro inhibition and includes an ADME/T profile analysis of that ligand. For this study, with the help of gas chromatography-mass spectrometry analysis of C. gigantea methanolic leaf extract, a total of 30 bioactive compounds were selected. Our analyses unveiled the top four options that might turn out to be prospective anti-SARS-CoV-2 lead molecules; these warrant further exploration as well as possible application in processes of drug development to combat COVID-19.
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Affiliation(s)
- Mycal Dutta
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh
| | - Mohammad Nezam
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Subrata Chowdhury
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Arkajyoti Paul
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Md. Zia Uddin
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh
| | - Md. Sohel Rana
- Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh
| | | | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Banda Aceh, Indonesia
| | - Trina Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, Indonesia
| | - Ali M. Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
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27
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Wahab S, Ahmad I, Irfan S, Baig MH, Farouk AE, Dong JJ. Use of Natural Compounds as a Potential Therapeutic Agent Against COVID-19. Curr Pharm Des 2021; 27:1144-1152. [PMID: 33388014 DOI: 10.2174/1381612826666210101154118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022]
Abstract
The current 2019-nCoV outbreak is becoming extremely harmful and has affected the whole world. Its control is challenging because there is no effective vaccine or drug available for coronavirus disease. The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), previously named as 2019 novel coronavirus (2019-nCoV), primarily targets the human respiratory system to lung lesions and lethal pneumonia. Natural products have always shown a crucial role in the process of drug development against various diseases. They may serve as leads for further drug development to combat emergent mutants of the coronavirus. In this review, the current status of natural compounds and their derivatives acting against different species of CoV are discussed.
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Affiliation(s)
- Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Safia Irfan
- Department of Biotechnology, Faculty of Biosciences, Integral University, Lucknow, UP, India
| | - Mohammad H Baig
- Department of Family Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 120-752, Korea
| | - Abd-ElAziem Farouk
- Department of Biotechnology, Faculty of Science, Taif University, Al-Hawiya 888, Saudi Arabia
| | - Jae-June Dong
- Department of Family Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 120-752, Korea
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28
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Sytwu HK. Expeditious responses to COVID-19 crisis: From governmental management to laboratory approach. Biomed J 2020; 43:311-313. [PMID: 33046218 PMCID: PMC7501831 DOI: 10.1016/j.bj.2020.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 11/10/2022] Open
Affiliation(s)
- Huey-Kang Sytwu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan; National Defense Medical Center, Neihu, Taipei, Taiwan.
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29
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Häfner SJ. Don't sugar coat the COVID (only the vasculature). Biomed J 2020; 43:393-398. [PMID: 33115641 PMCID: PMC7547304 DOI: 10.1016/j.bj.2020.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 11/24/2022] Open
Abstract
This issue of the Biomedical Journal acquaints us with the compelling hypothesis that the vascular glycocalyx lies at the intersection of severe COVID-19 risk factors and damages, and the ways used by artificial intelligence to predict interactions between SARS-CoV-2 and human proteins. Furthermore, we explore the antiviral potential of valinomycin and the long list of COVID-19-related clinical trials, and learn how (not) to fix a broken femoral head. Last but not least, we get to enjoy the tale of the cellular oxygen-sensing system as well as the role of the host complement system during Leptospira infection, and learn that SARS-CoV-2 can sometimes come with a pathogenic plus one.
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Affiliation(s)
- Sophia Julia Häfner
- University of Copenhagen, BRIC Biotech Research & Innovation Centre, Anders Lund Group, Copenhagen, Denmark.
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30
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Russo M, Moccia S, Spagnuolo C, Tedesco I, Russo GL. Roles of flavonoids against coronavirus infection. Chem Biol Interact 2020; 328:109211. [PMID: 32735799 PMCID: PMC7385538 DOI: 10.1016/j.cbi.2020.109211] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/13/2020] [Accepted: 07/23/2020] [Indexed: 01/18/2023]
Abstract
In terms of public health, the 21st century has been characterized by coronavirus pandemics: in 2002-03 the virus SARS-CoV caused SARS; in 2012 MERS-CoV emerged and in 2019 a new human betacoronavirus strain, called SARS-CoV-2, caused the unprecedented COVID-19 outbreak. During the course of the current epidemic, medical challenges to save lives and scientific research aimed to reveal the genetic evolution and the biochemistry of the vital cycle of the new pathogen could lead to new preventive and therapeutic strategies against SARS-CoV-2. Up to now, there is no cure for COVID-19 and waiting for an efficacious vaccine, the development of "savage" protocols, based on "old" anti-inflammatory and anti-viral drugs represents a valid and alternative therapeutic approach. As an alternative or additional therapeutic/preventive option, different in silico and in vitro studies demonstrated that small natural molecules, belonging to polyphenol family, can interfere with various stages of coronavirus entry and replication cycle. Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PLpro, 3CLpro, NTPase/helicase. Due to their pleiotropic activities and lack of systemic toxicity, flavonoids and their derivative may represent target compounds to be tested in future clinical trials to enrich the drug arsenal against coronavirus infections.
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Affiliation(s)
- Maria Russo
- National Research Council, Institute of Food Sciences, 83100, Avellino, Italy
| | - Stefania Moccia
- National Research Council, Institute of Food Sciences, 83100, Avellino, Italy
| | - Carmela Spagnuolo
- National Research Council, Institute of Food Sciences, 83100, Avellino, Italy
| | - Idolo Tedesco
- National Research Council, Institute of Food Sciences, 83100, Avellino, Italy
| | - Gian Luigi Russo
- National Research Council, Institute of Food Sciences, 83100, Avellino, Italy.
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31
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Al-Zaqri N, Pooventhiran T, Alsalme A, Warad I, John AM, Thomas R. Structural and physico-chemical evaluation of melatonin and its solution-state excited properties, with emphasis on its binding with novel coronavirus proteins. J Mol Liq 2020; 318:114082. [PMID: 32863490 PMCID: PMC7443329 DOI: 10.1016/j.molliq.2020.114082] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/03/2020] [Accepted: 08/16/2020] [Indexed: 12/20/2022]
Abstract
Melatonin is a natural hormone from the pineal gland that regulates the sleep-wake cycle. We examined the structure and physico-chemical properties of melatonin using electronic structure methods and molecular-mechanics tools. Density functional theory (DFT) was used to optimise the ground-state geometry of the molecule from frontier molecular orbitals, which were analysed using the B3LYP functional. As its electrons interacted with electromagnetic radiation, electronic excitations between different energy levels were analysed in detail using time-dependent DFT with CAM-B3LYP orbitals. The results provide a wealth of information about melatonin's electronic properties, which will enable the prediction of its bioactivity. Molecular docking studies predict the biological activity of the molecules against the coronavirus2 protein. Excellent docking scores of −7.28, −7.20, and −7.06 kcal/mol indicate that melatonin can help to defend against the viral load in vulnerable populations. Hence it can be investigated as a candidate drug for the management of COVID. Detailed quantum mechanical studies of the sleep regulating hormone melatonin Analysed the intramolecular stabilisation and nonlinear properties Excited state properties using TD-DFT formalism Compound active binds to three known novel coronavirus 2019 proteins.
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Affiliation(s)
- Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.,Department of Chemistry, College of Science, Ibb University, P.O. Box 70270, Ibb, Yemen
| | - T Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Ali Alsalme
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ismail Warad
- Department of Chemistry, Science College, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Athira M John
- Department of Chemistry, CHRIST (Deemed to be University), Bangalore, Karnataka, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
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32
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Häfner SJ. Pandemic number five - Latest insights into the COVID-19 crisis. Biomed J 2020; 43:305-310. [PMID: 32967801 PMCID: PMC7451056 DOI: 10.1016/j.bj.2020.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 11/20/2022] Open
Abstract
About nine months after the emergence of SARS-CoV-2, this special issue of the Biomedical Journal takes stock of its evolution into a pandemic. We acquire an elaborate overview of the history and virology of SARS-CoV-2, the epidemiology of COVID-19, and the development of therapies and vaccines, based on useful tools such as a pseudovirus system, artificial intelligence, and repurposing of existing drugs. Moreover, we learn about a potential link between COVID-19 and oral health, and some of the strategies that allowed Taiwan to handle the outbreak exceptionally well, including a COVID-19 biobank establishment, online tools for contact tracing, and the efficient management of emergency departments.
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Affiliation(s)
- Sophia Julia Häfner
- University of Copenhagen, BRIC Biotech Research & Innovation Centre, Anders Lund Group, Copenhagen, Denmark.
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