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Liu M, Yao C, Liu S, Xiu J, Li X, Yang H, Zhang J, Zhao X. Intelligent response micelles with high andrographolide loading for the effective treatment of atherosclerosis. Int J Pharm 2024; 665:124705. [PMID: 39307442 DOI: 10.1016/j.ijpharm.2024.124705] [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: 05/27/2024] [Revised: 08/26/2024] [Accepted: 09/10/2024] [Indexed: 10/01/2024]
Abstract
Atherosclerosis (AS) is a chronic inflammatory disease which associated with a maladaptive immune response driven by macrophages. In the development of AS, macrophages have gradually become new therapeutic targets due to their involvement in numerous inflammatory-related pathological processes in AS. However, despite significant breakthroughs in the development of macrophages targeting nanocarriers, unsatisfactory drug loading, and inexact drug release limited the development of nano-therapy. Therefore, developing a high drug-loading nanocarrier that can accurately release drugs at AS lesions is quite essential. Herein, we optimized double moieties coupled mPEG-PLA copolymer micelles via phenylboronic acid (PBA)-terminated on the hydrophobic chain and cRGD coupled in hydrophilic chain to enhance AS therapy. The micelles loaded with andrographolide (AND) exhibited advanced drug loading capacity, as PBA could form a reversible boronic ester with AND at physiological pH. The cRGD-modified AND-loaded micelles (RPPPA) could be efficaciously internalized by macrophages and efficiently prevent macrophages from differentiating to foam cells. After intravenous administration, RPPPA could accumulate in plaques and exert therapeutic effects. The optimistic therapeutic results of atherosclerosis were shown in RPPPA, included the fewer plaques, a smaller necrotic core, a more stabilized fibrous cap, and lower macrophages and MMP-9, compared with the control group. To sum up, the proposed encouraging therapy can contribute to high drug loading, exact target, and precise drug release as well as reduce inflammation for AS treatment.
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Affiliation(s)
- Min Liu
- College of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Chen Yao
- College of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Siyi Liu
- College of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Jingya Xiu
- College of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Xiaofang Li
- College of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Han Yang
- College of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Jiulong Zhang
- College of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China.
| | - Xiuli Zhao
- College of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China.
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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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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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In silico study of novel niclosamide derivatives, SARS-CoV-2 nonstructural proteins catalytic residue-targeting small molecules drug candidates. ARAB J CHEM 2023; 16:104654. [PMID: 36777994 PMCID: PMC9904858 DOI: 10.1016/j.arabjc.2023.104654] [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: 07/26/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-mediated coronavirus disease 2019 (COVID-19) infection remains a global pandemic and health emergency with overwhelming social and economic impacts throughout the world. Therapeutics for COVID-19 are limited to only remdesivir; therefore, there is a need for combined, multidisciplinary efforts to develop new therapeutic molecules and explore the effectiveness of existing drugs against SARS-CoV-2. In the present study, we reported eight (SCOV-L-02, SCOV-L-09, SCOV-L-10, SCOV-L-11, SCOV-L-15, SCOV-L-18, SCOV-L-22, and SCOV-L-23) novel structurally related small-molecule derivatives of niclosamide (SCOV-L series) for their targeting potential against angiotensin-converting enzyme-2 (ACE2), type II transmembrane serine protease (TMPRSS2), and SARS-COV-2 nonstructural proteins (NSPs) including NSP5 (3CLpro), NSP3 (PLpro), and RdRp. Our correlation analysis suggested that ACE2 and TMPRSS2 modulate host immune response via regulation of immune-infiltrating cells at the site of tissue/organs entries. In addition, we identified some TMPRSS2 and ACE2 microRNAs target regulatory networks in SARS-CoV-2 infection and thus open up a new window for microRNAs-based therapy for the treatment of SARS-CoV-2 infection. Our in vitro study revealed that with the exception of SCOV-L-11 and SCOV-L-23 which were non-active, the SCOV-L series exhibited strict antiproliferative activities and non-cytotoxic effects against ACE2- and TMPRSS2-expressing cells. Our molecular docking for the analysis of receptor-ligand interactions revealed that SCOV-L series demonstrated high ligand binding efficacies (at higher levels than clinical drugs) against the ACE2, TMPRSS2, and SARS-COV-2 NSPs. SCOV-L-18, SCOV-L-15, and SCOV-L-09 were particularly found to exhibit strong binding affinities with three key SARS-CoV-2's proteins: 3CLpro, PLpro, and RdRp. These compounds bind to the several catalytic residues of the proteins, and satisfied the criteria of drug-like candidates, having good adsorption, distribution, metabolism, excretion, and toxicity (ADMET) pharmacokinetic profile. Altogether, the present study suggests the therapeutic potential of SCOV-L series for preventing and managing SARs-COV-2 infection and are currently under detailed investigation in our lab.
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Mokhtari T, Azizi M, Sheikhbahaei F, Sharifi H, Sadr M. Plant-Derived Antioxidants for Management of COVID-19: A Comprehensive Review of Molecular Mechanisms. TANAFFOS 2023; 22:27-39. [PMID: 37920320 PMCID: PMC10618592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/09/2022] [Indexed: 11/04/2023]
Abstract
We aimed to review the literature to introduce some effective plant-derived antioxidants to prevent and treat COVID-19. Natural products from plants are excellent sources to be used for such discoveries. Among different plant-derived bioactive substances, components including luteolin, quercetin, glycyrrhizin, andrographolide, patchouli alcohol, baicalin, and baicalein were investigated for several viral infections as well as SARS-COV-2. The mechanisms of effects detected for these agents were related to their antiviral activity through inhibition of viral entry and/or suppuration of virus function. Also, the majority of components exert anti-inflammatory effects and reduce the cytokine storm induced by virus infection. The data from different studies confirmed that these agents may play a critical role against SARS-COVID-2 via direct (antiviral activity) and indirect (antioxidant and anti-inflammatory) mechanisms, suggesting that natural products are a potential option for management of patients with COVID-19 due to the lower side effects and high efficiency.
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Affiliation(s)
- Tahmineh Mokhtari
- Hubei Key Laboratory of Embryonic Stem Cell Research, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, People’s Republic of China
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, People’s Republic of China
| | - Maryam Azizi
- Department of Anatomy, School of Medicine, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Sheikhbahaei
- Department of Anatomy, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hooman Sharifi
- Tobacco Prevention and Control Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Makan Sadr
- Virology Research Center, NRITLD, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Mun CS, Hui LY, Sing LC, Karunakaran R, Ravichandran V. Multi-targeted molecular docking, pharmacokinetics, and drug-likeness evaluation of coumarin based compounds targeting proteins involved in development of COVID-19. Saudi J Biol Sci 2022; 29:103458. [PMID: 36187455 PMCID: PMC9512525 DOI: 10.1016/j.sjbs.2022.103458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
COVID-19 is a progressing pandemic of coronavirus disease-2019, which had drowned the whole world in a deep sorrow sea. Uncountable deaths were extending the list of deaths every single day. The present research was aimed to study the multi-target interaction of coumarins against COVID-19 using molecular docking analysis. The structure of coumarin compounds was checked for ADME and Lipinski rule of five by using SwissADME, an online tool. SARS-CoV-2 proteins such as RdRp, PLpro, Mpro and spike protein were collected from the Protein Data Bank. The molecular docking study was performed in the PyRx tool, and the molecular interactions were visualised by Discovery Studio Visualizer. All the coumarin compounds used in the study were obeyed Lipinski’s rule of 5 without any violations. All the three designed derivatives of phenprocoumon, hymecromone, and psoralen were showed high binding affinity and prominent interactions with the drug target. The presence of –OH groups in the compound, His41, a catalytic dyad in Mpro, number of and the distance of hydrogen bond interactions with SARS-CoV-2 targets was accountable for the high binding attractions. The modified drug structures possess better binding efficacy towards at least three targets compared to their parent compounds. Further, molecular dynamic studies can be suggested to find the ligand–protein complex stability. The present study outcome reveals that the designed coumarins can be synthesised and examined as a potent inhibitory drug of SARS-CoV-2.
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Affiliation(s)
- Chan Sook Mun
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Lok Yong Hui
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Lai Cong Sing
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Semeling 08100, Kedah, Malaysia.,Centre of Excellence for Biomaterial Science, AIMST University, Semeling 08100, Kedah, Malaysia
| | - Veerasamy Ravichandran
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia.,Centre of Excellence for Biomaterial Science, AIMST University, Semeling 08100, Kedah, Malaysia.,Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
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7
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Singh R, Bhardwaj VK, Purohit R. Inhibition of nonstructural protein 15 of SARS-CoV-2 by golden spice: A computational insight. Cell Biochem Funct 2022; 40:926-934. [PMID: 36203381 PMCID: PMC9874790 DOI: 10.1002/cbf.3753] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/16/2022] [Accepted: 09/15/2022] [Indexed: 01/27/2023]
Abstract
The quick widespread of the coronavirus and speedy upsurge in the tally of cases demand the fast development of effective drugs. The uridine-directed endoribonuclease activity of nonstructural protein 15 (Nsp15) of the coronavirus is responsible for the invasion of the host immune system. Therefore, developing potential inhibitors against Nsp15 is a promising strategy. In this concern, the in silico approach can play a significant role, as it is fast and cost-effective in comparison to the trial and error approaches of experimental investigations. In this study, six turmeric derivatives (curcuminoids) were chosen for in silico analysis. The molecular interactions, pharmacokinetics, and drug-likeness of all the curcuminoids were measured. Further, the stability of Nsp15-curcuminoids complexes was appraised by employing molecular dynamics (MD) simulations and MM-PBSA approaches. All the molecules were affirmed to have strong interactions and pharmacokinetic profile. The MD simulations data stated that the Nsp15-curcuminoids complexes were stable during simulations. All the curcuminoids showed stable and high binding affinity, and these curcuminoids could be admitted as potential modulators for Nsp15 inhibition.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
| | - Vijay K. Bhardwaj
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
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Negru PA, Miculas DC, Behl T, Bungau AF, Marin RC, Bungau SG. Virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses. Biomed Pharmacother 2022; 153:113432. [PMID: 36076487 PMCID: PMC9289048 DOI: 10.1016/j.biopha.2022.113432] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/07/2022] [Accepted: 07/15/2022] [Indexed: 12/12/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is considered the etiological agent of the disease that caused the COVID-19 pandemic, and for which there is currently no effective treatment. This pandemic has shown that the rapid identification of therapeutic compounds is critical (when a new virus with high transmissibility occurs) to prevent or reduce as much as possible the loss of human lives. To meet the urgent need for drugs, many strategies were applied for the discovery, respectively the identification of potential therapies / drugs for SARS-CoV-2. Molecular docking and virtual screening are two of the in silico tools/techniques that provided the identification of few SARS-CoV-2 inhibitors, removing ineffective or less effective drugs and thus preventing the loss of resources such as time and additional costs. The main target of this review is to provide a comprehensive overview of how in-silico tools have been used in the crisis management of anti-SARS-CoV-2 drugs, especially in virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses; also, completions were added to the way in which these methods came to meet the requirements of biomedical research in the field. Moreover, the importance and impact of the topic approached for researchers was highlighted by conducting an extensive bibliometric analysis.
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Affiliation(s)
- Paul Andrei Negru
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | - Denisa Claudia Miculas
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania.
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Alexa Florina Bungau
- Medicine Programm of Study, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Ruxandra-Cristina Marin
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | - Simona Gabriela Bungau
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania.
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The Main Protease of SARS-CoV-2 as a Target for Phytochemicals against Coronavirus. PLANTS 2022; 11:plants11141862. [PMID: 35890496 PMCID: PMC9319234 DOI: 10.3390/plants11141862] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 11/23/2022]
Abstract
In late December 2019, the first cases of COVID-19 emerged as an outbreak in Wuhan, China that later spread vastly around the world, evolving into a pandemic and one of the worst global health crises in modern history. The causative agent was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although several vaccines were authorized for emergency use, constantly emerging new viral mutants and limited treatment options for COVID-19 drastically highlighted the need for developing an efficient treatment for this disease. One of the most important viral components to target for this purpose is the main protease of the coronavirus (Mpro). This enzyme is an excellent target for a potential drug, as it is essential for viral replication and has no closely related homologues in humans, making its inhibitors unlikely to be toxic. Our review describes a variety of approaches that could be applied in search of potential inhibitors among plant-derived compounds, including virtual in silico screening (a data-driven approach), which could be structure-based or fragment-guided, the classical approach of high-throughput screening, and antiviral activity cell-based assays. We will focus on several classes of compounds reported to be potential inhibitors of Mpro, including phenols and polyphenols, alkaloids, and terpenoids.
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