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Sopjani M, Falco F, Impellitteri F, Guarrasi V, Nguyen Thi X, Dërmaku-Sopjani M, Faggio C. Flavonoids derived from medicinal plants as a COVID-19 treatment. Phytother Res 2024; 38:1589-1609. [PMID: 38284138 DOI: 10.1002/ptr.8123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/30/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease. Through its viral spike (S) protein, the virus enters and infects epithelial cells by utilizing angiotensin-converting enzyme 2 as a host cell's receptor protein. The COVID-19 pandemic had a profound impact on global public health and economies. Although various effective vaccinations and medications are now available to prevent and treat COVID-19, natural compounds derived from medicinal plants, particularly flavonoids, demonstrated therapeutic potential to treat COVID-19 disease. Flavonoids exhibit dual antiviral mechanisms: direct interference with viral invasion and inhibition of replication. Specifically, they target key viral molecules, particularly viral proteases, involved in infection. These compounds showcase significant immunomodulatory and anti-inflammatory properties, effectively inhibiting various inflammatory cytokines. Additionally, emerging evidence supports the potential of flavonoids to mitigate the progression of COVID-19 in individuals with obesity by positively influencing lipid metabolism. This review aims to elucidate the molecular structure of SARS-CoV-2 and the underlying mechanism of action of flavonoids on the virus. This study evaluates the potential anti-SARS-CoV-2 properties exhibited by flavonoid compounds, with a specific interest in their structure and mechanisms of action, as therapeutic applications for the prevention and treatment of COVID-19. Nevertheless, a significant portion of existing knowledge is based on theoretical frameworks and findings derived from in vitro investigations. Further research is required to better assess the effectiveness of flavonoids in combating SARS-CoV-2, with a particular emphasis on in vivo and clinical investigations.
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Affiliation(s)
- Mentor Sopjani
- Faculty of Medicine, University of Prishtina, Prishtina, Kosova
| | - Francesca Falco
- Institute for Marine Biological Resources and Biotechnology (IRBIM)-CNR, Mazara del Vallo, Italy
| | | | - Valeria Guarrasi
- Institute of Biophysics, National Research Council (CNR), Palermo, Italy
| | - Xuan Nguyen Thi
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Messina, Italy
- Department of Eco sustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Naples, Italy
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2
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Herzog AM, Göbel K, Marongiu L, Ruetalo N, Alonso MC, Leischner C, Busch C, Burkard M, Lauer UM, Geurink PP, Knobeloch KP, Schindler M, Fritz G, Venturelli S. Compounds derived from Humulus lupulus inhibit SARS-CoV-2 papain-like protease and virus replication. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 123:155176. [PMID: 37976697 DOI: 10.1016/j.phymed.2023.155176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Selected natural compounds exhibit very good antiviral properties. Especially, the medicinal plant Humulus lupulus (hop) contains several secondary plant metabolites some of which have previously shown antiviral activities. Among them, the prenylated chalcone xanthohumol (XN) demonstrated to be a potent inhibitor of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). HYPOTHESIS/PURPOSE Following the finding that xanthohumol (XN) is a potent inhibitor of SARS-CoV-2 Mpro, the effect of XN and its major derivatives isoxanthohumol (IXN), 6-prenylnaringenin (6-PN), and 8-prenylnaringenin (8-PN) from hops on SARS-CoV-2 papain-like protease (PLpro) were investigated. STUDY DESIGN The modulatory effect of the hop compounds on PLpro were studied first in silico and then in vitro. In addition, the actual effect of hop compounds on the replication of SARS-CoV-2 in host cells was investigated. METHODS In silico docking analysis was used to predict the binding affinity of hop compounds to the active site of PLpro. A recombinant PLpro was cloned, purified, characterized, and analyzed by small-angle X-ray scattering (SAXS), deISGylation assays, and kinetic analyses. Antiviral activity of hop compounds was assessed using the fluorescently labeled wildtype SARS-CoV-2 (icSARS-CoV-2-mNG) in Caco-2 host cells. RESULTS Our in silico docking suggests that the purified hop compounds bind to the active site of SARS-CoV-2 PLpro blocking the access of its natural substrates. The hop-derived compounds inhibit SARS-CoV-2 PLpro with half maximal inhibitory concentration (IC50) values in the range of 59-162 µM. Furthermore, we demonstrate that XN and 6-PN, in particular, impede viral replication with IC50 values of 3.3 µM and 7.3 µM, respectively. CONCLUSION In addition to the already known inhibition of Mpro by XN, our results show, for the first time, that hop-derived compounds target also SARS-CoV-2 PLpro which is a promising therapeutic target as it contributes to both viral replication and modulation of the immune system. These findings support the possibility to develop new hop-derived antiviral drugs targeting human coronaviruses.
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Affiliation(s)
- Anna-Maria Herzog
- Department of Cellular Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Katharina Göbel
- Department of Cellular Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Luigi Marongiu
- Department of Internal Medicine VIII, University Hospital Tuebingen, 72076 Tuebingen, Germany; Department of Nutritional Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany
| | - Marta Campos Alonso
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Christian Leischner
- Department of Nutritional Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany
| | | | - Markus Burkard
- Department of Nutritional Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine VIII, University Hospital Tuebingen, 72076 Tuebingen, Germany
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Günter Fritz
- Department of Cellular Microbiology, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Sascha Venturelli
- Department of Nutritional Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany; Institute of Physiology, Department of Vegetative and Clinical Physiology, University Hospital Tuebingen, 72076 Tuebingen, Germany.
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3
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Chan LC, Mat Yassim AS, Ahmad Fuaad AAH, Leow TC, Sabri S, Radin Yahaya RS, Abu Bakar AMS. Inhibition of SARS-CoV-2 3CL protease by the anti-viral chimeric protein RetroMAD1. Sci Rep 2023; 13:20178. [PMID: 37978223 PMCID: PMC10656507 DOI: 10.1038/s41598-023-47511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
COVID-19 results from SARS-CoV-2, which mutates frequently, challenging current treatments. Therefore, it is critical to develop new therapeutic drugs against this disease. This study explores the interaction between SARS-CoV-2 3CLpro and RetroMAD1, a well-characterized coronavirus protein and potential drug target, using in-silico methods. The analysis through the HDOCK server showed stable complex formation with a binding energy of -12.3, the lowest among reference drugs. The RetroMAD1-3CLpro complex underwent a 100 ns molecular dynamics simulation (MDS) in an explicit solvation system, generating various trajectories, including RMSD, RMSF, hydrogen bonding, radius of gyration, and ligand binding energy. MDS results confirmed intact interactions within the RetroMAD1-3CLpro complex during simulations. In vitro experiments validated RetroMAD1's ability to inhibit 3CLpro enzyme activity and prevent SARS-CoV-2 infection in human bronchial cells. RetroMAD1 exhibited antiviral efficacy comparable to Remdesivir without cytotoxicity at effective concentrations. These results suggest RetroMAD1 as a potential drug candidate against SARS-CoV-2, warranting further in vivo and clinical studies to assess its efficiency.
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Affiliation(s)
- Lee-Chin Chan
- Biovalence Sdn. Bhd., 22, Jalan SS 25/34, Taman Mayang, 47301, Petaling Jaya, Selangor, Malaysia
- Biovalence Technologies Pte. Ltd., #06-307 The Plaza, 7500A Beach Road, Singapore, 199591, Singapore
| | - Aini Syahida Mat Yassim
- Biovalence Sdn. Bhd., 22, Jalan SS 25/34, Taman Mayang, 47301, Petaling Jaya, Selangor, Malaysia.
- Biovalence Technologies Pte. Ltd., #06-307 The Plaza, 7500A Beach Road, Singapore, 199591, Singapore.
- School of Health Science, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
| | - Abdullah Al Hadi Ahmad Fuaad
- Centre of Fundamental and Frontier Sciences in Self-Assembly (FSSA), Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Thean Chor Leow
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Radin Shafierul Radin Yahaya
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Awang Muhammad Sagaf Abu Bakar
- Jabatan Perkhidmatan Veterinar Sabah, Aras 3, Blok B, Wisma Pertanian Sabah, Jalan Tasik, Luyang (Off Jln Maktab Gaya), Beg Berkunci 2051, 88999, Kota Kinabalu, Sabah, Malaysia.
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Aboul-Fotouh S, Mahmoud AN, Elnahas EM, Habib MZ, Abdelraouf SM. What are the current anti-COVID-19 drugs? From traditional to smart molecular mechanisms. Virol J 2023; 20:241. [PMID: 37875904 PMCID: PMC10594888 DOI: 10.1186/s12985-023-02210-z] [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: 11/05/2022] [Accepted: 10/13/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Coronavirus disease 19 (COVID-19) is the disease caused by SARS-CoV-2, a highly infectious member of the coronavirus family, which emerged in December 2019 in "Wuhan, China". It induces respiratory illness ranging from mild symptoms to severe disease. It was declared a "pandemic" by the World Health Organization (WHO) in March 2020. Since then, a vast number of clinical and experimental studies have been conducted to identify effective approaches for its prevention and treatment. MAIN BODY The pathophysiology of COVID-19 represents an unprecedented challenge; it triggers a strong immune response, which may be exacerbated by "a cytokine storm syndrome". It also induces thrombogenesis and may trigger multi-organ injury. Therefore, different drug classes have been proposed for its treatment and prevention, such as antivirals, anti-SARS-CoV-2 antibody agents (monoclonal antibodies, convalescent plasma, and immunoglobulins), anti-inflammatory drugs, immunomodulators, and anticoagulant drugs. To the best of our knowledge, this review is the first to present, discuss, and summarize the current knowledge about the different drug classes used for the treatment of COVID-19, with special emphasis on their targets, mechanisms of action, and important adverse effects and drug interactions. Additionally, we spotlight the latest "October 2023" important guidelines (NIH, IDSA, and NICE) and FDA approval or authorization regarding the use of these agents in the management of COVID-19. CONCLUSION Despite the wide array of therapeutic strategies introduced for the treatment of COVID-19, one of the most prominent therapeutic challenges is SARS-CoV-2 mutations and emerging new variants and subvariants. Currently, the anti-COVID-19 drug pipeline is continuously affording novel treatments to face this growing challenge.
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Affiliation(s)
- Sawsan Aboul-Fotouh
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Clinical Pharmacology Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Ahmed Nageh Mahmoud
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Esraa M Elnahas
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mohamed Z Habib
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Sahar M Abdelraouf
- Department of Biochemistry, Faculty of Pharmacy, Misr International University, Cairo, Egypt
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Dakpa G, Kumar KJS, Nelen J, Pérez-Sánchez H, Wang SY. Antcin-B, a phytosterol-like compound from Taiwanofungus camphoratus inhibits SARS-CoV-2 3-chymotrypsin-like protease (3CL Pro) activity in silico and in vitro. Sci Rep 2023; 13:17106. [PMID: 37816832 PMCID: PMC10564890 DOI: 10.1038/s41598-023-44476-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/09/2023] [Indexed: 10/12/2023] Open
Abstract
Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CLPro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CLPro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CLPro. Further, these compounds were subjected to study their inhibitory effects on 3CLPro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets.
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Affiliation(s)
- Gyaltsen Dakpa
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 108, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - K J Senthil Kumar
- Bachelor Program of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Jochem Nelen
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica de Murcia (UCAM), 30107, Murcia, Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica de Murcia (UCAM), 30107, Murcia, Spain
| | - Sheng-Yang Wang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 108, Taiwan.
- Department of Forestry, National Chung Hsing University, Taichung, 402, Taiwan.
- Special Crop and Metabolome Discipline Cluster, Academy of Circle Economy, National Chung Hsing University, Taichung, 402, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 108, Taiwan.
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Gurushankar K, Jeyaseelan SC, Grishina M, Siswanto I, Tiwari R, Puspaningsih NNT. Density Functional Theory, Molecular Dynamics and AlteQ Studies Approaches of Baimantuoluoamide A and Baimantuoluoamide B to Identify Potential Inhibitors of M pro Proteins: a Novel Target for the Treatment of SARS COVID-19. JETP LETTERS 2023; 117:1-10. [PMID: 37360903 PMCID: PMC10184967 DOI: 10.1134/s0021364023600039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/28/2023]
Abstract
COVID-19 has resulted in epidemi conditions over the world. Despite efforts by scientists from all over the world to develop an effective va ine against this virus, there is presently no recognized cure for COVID-19. The most succeed treatments for various ailments come from natural components found in medicinal plants, which are also rucial for the development of new medications. This study intends to understand the role of the baimantuoluoamide A and baimantuoluoamide B molecules in the treatment of Covid19. Initially, density functional theory (DFT) used to explore their electronic potentials along with the Becke3-Lee-Yang-Parr (B3LYP) 6-311 + G(d, p) basis set. A number of characteristics, including the energy gap, hardness, local softness, electronegativity, and electrophilicity, have also been calculated to discuss the reactivity of mole ules. Using natural bond orbital, the title compound's bioactive nature and stability were investigated. Further, both compounds potential inhibitors with main protease (Mpro) proteins, molecular dynamics simulations and AlteQ investigations also studied. Supplementary Information The online version contains supplementary material available at 10.1134/S0021364023600039.
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Affiliation(s)
- K. Gurushankar
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
- Department of Physics, Kalasalingam Academy of Research and Education, 626126 Krishnankoil, Tamilnadu India
| | - S. Ch. Jeyaseelan
- Post Graduate & Research Department of Physics, N.M.S.S.V.N. College, 625019 Madurai, Tamilnadu India
- Post Graduate Department of Physics, Mannar Thirumalai Naciker College, 625004 Madurai, Tamilnadu India
| | - M. Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
| | - I. Siswanto
- Bioinformati Laboratory, UCoE Research Center for Bio-Molecule Engineering Universitas Airlangga, 60115 Surabaya, Indonesia
| | - R. Tiwari
- Department of Physics, Coordinator Research and Development Cell, Dr CV Raman University, 495113 Kargi Kota, Bilaspur CG India
| | - N. N. T. Puspaningsih
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, 60115 Surabaya, Indonesia
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Ashraf H, Dilshad E, Afsar T, Almajwal A, Shafique H, Razak S. Molecular Screening of Bioactive Compounds of Garlic for Therapeutic Effects against COVID-19. Biomedicines 2023; 11:biomedicines11020643. [PMID: 36831179 PMCID: PMC9953069 DOI: 10.3390/biomedicines11020643] [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: 01/30/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
An outbreak of pneumonia occurred on December 2019 in Wuhan, China, which caused a serious public health emergency by spreading around the globe. Globally, natural products are being focused on more than synthetic ones. So, keeping that in view, the current study was conducted to discover potential antiviral compounds from Allium sativum. Twenty-five phytocompounds of this plant were selected from the literature and databases including 3-(Allylsulphinyl)-L-alanine, Allicin, Diallyl sulfide, Diallyl disulfide, Diallyl trisulfide, Glutathione, L-Cysteine, S-allyl-mercapto-glutathione, Quercetin, Myricetin, Thiocysteine, Gamma-glutamyl-Lcysteine, Gamma-glutamylallyl-cysteine, Fructan, Lauricacid, Linoleicacid, Allixin, Ajoene, Diazinon Kaempferol, Levamisole, Caffeicacid, Ethyl linoleate, Scutellarein, and S-allylcysteine methyl-ester. Virtual screening of these selected ligands was carried out against drug target 3CL protease by CB-dock. Pharmacokinetic and pharmacodynamic properties defined the final destiny of compounds as drug or non-drug molecules. The best five compounds screened were Allicin, Diallyl Sulfide, Diallyl Disulfide, Diallyl Trisulfide, Ajoene, and Levamisole, which showed themselves as hit compounds. Further refining by screening filters represented Levamisole as a lead compound. All the interaction visualization analysis studies were performed using the PyMol molecular visualization tool and LigPlot+. Conclusively, Levamisole was screened as a likely antiviral compound which might be a drug candidate to treat SARS-CoV-2 in the future. Nevertheless, further research needs to be carried out to study their potential medicinal use.
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Affiliation(s)
- Huma Ashraf
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST), Islamabad 44000, Pakistan
| | - Erum Dilshad
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST), Islamabad 44000, Pakistan
- Correspondence: (E.D.); (S.R.)
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
| | - Huma Shafique
- Institute of Cellular Medicine, Newcastle University Medical School, Newcastle University, Newcastle NE1 7RU, UK
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
- Correspondence: (E.D.); (S.R.)
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Cheohen CFDAR, Esteves MEA, da Fonseca TS, Leal CM, Assis FDLF, Campos MF, Rebelo RS, Allonso D, Leitão GG, da Silva ML, Leitão SG. In silico screening of phenylethanoid glycosides, a class of pharmacologically active compounds as natural inhibitors of SARS-CoV-2 proteases. Comput Struct Biotechnol J 2023; 21:1461-1472. [PMID: 36817956 PMCID: PMC9920770 DOI: 10.1016/j.csbj.2023.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023] Open
Abstract
Since the advent of Covid-19, several natural products have been investigated regarding their in silico interactions with SARS-CoV-2 proteases - 3CLpro and PLpro, two of the most important pharmacological targets for antiviral development. Phenylethanoid glycosides (PG) are a class of natural products present in important medicinal plants and a drug containing this group of active ingredients has been successfully used in the treatment of Covid-19 in China. Thus, a dataset with 567 derivatives of this class was built from reviews published between 1994 and 2020, and their interaction against both SARS-CoV-2 proteases was investigated. The virtual screening was performed by filtering the PGs through the evaluation of scores based on the AutoDock Vina, GOLD/ChemPLP, and GOLD/GoldScore evaluation functions. The bRO5 pharmacokinetic parameters of the PGs ranked in the previous step were analyzed and their interaction with key amino acid residues of the 3CLpro and PLpro enzymes was evaluated. Ninety-eight compounds were identified by computational approaches against PLpro and 80 PGs against 3CLpro. Of these, four interacted with key catalytic residues of PLpro, which is an indicative of inhibitory activity, and three compounds interacted with catalytic key residues of 3CLpro. Of these, five PGs occur in plants of the Traditional Chinese Medicine (TCM), while two are components of plants/formulations currently used in the Covid-19 protocols in China. The data presented here show the potential of PGs as selective inhibitors of SARS-CoV-2 3CLpro and PLpro.
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Affiliation(s)
- Caio Felipe de Araujo Ribas Cheohen
- Programa de Pós-graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé, RJ 27965045, Brazil
| | - Maria Eduarda Alves Esteves
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, RJ 21041361, Brazil
| | - Thamirys Silva da Fonseca
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil,Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Carla Monteiro Leal
- Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Fernanda de Lemos Fernandes Assis
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Mariana Freire Campos
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil,Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Raianne Soares Rebelo
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Diego Allonso
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais, Centro de Ciências da Saúde, Bl. H, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Manuela Leal da Silva
- Programa de Pós-graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé, RJ 27965045, Brazil,Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, RJ 21041361, Brazil,Corresponding author at: Programa de Pós-graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé, RJ 27965045, Brazil.
| | - Suzana Guimarães Leitão
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil,Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil,Corresponding author at: Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil.
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HIV and SARS-CoV-2 Co-Infection: From Population Study Evidence to In Vitro Studies. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122089. [PMID: 36556453 PMCID: PMC9781275 DOI: 10.3390/life12122089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have caused two major viral outbreaks during the last century. Two major aspects of HIV-1 and SARS-CoV-2 co-infection have been extensively investigated and deserve attention. First, the impact of the co-infection on the progression of disease caused by HIV-1 or SARS-CoV-2. Second, the impact of the HIV-1 anti-retroviral treatment on SARS-CoV-2 infection. In this review, we aim to summarize and discuss the works produced since the beginning of the SARS-CoV-2 pandemic ranging from clinical studies to in vitro experiments in the context of co-infection and drug development.
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Akinosoglou K, Schinas G, Gogos C. Oral Antiviral Treatment for COVID-19: A Comprehensive Review on Nirmatrelvir/Ritonavir. Viruses 2022; 14:2540. [PMID: 36423149 PMCID: PMC9696049 DOI: 10.3390/v14112540] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Despite the rapid development of efficient and safe vaccines against COVID-19, the need to confine the pandemic and treat infected individuals on an outpatient basis has led to the approval of oral antiviral agents. Taking into account the viral kinetic pattern of SARS-CoV-2, it is of high importance to intervene at the early stages of the disease. A protease inhibitor called nirmatrelvir coupled with ritonavir (NMV/r), which acts as a CYP3A inhibitor, delivered as an oral formulation, has shown much promise in preventing disease progression in high-risk patients with no need for supplemental oxygen administration. Real-world data seem to confirm the drug combination's efficacy and safety against all viral variants of concern in adult populations. Although, not fully clarified, viral rebound and recurrence of COVID-19 symptoms have been described following treatment; however, more data on potential resistance issues concerning the Mpro gene, which acts as the drug's therapeutic target, are needed. NMV/r has been a gamechanger in the fight against the pandemic by preventing hospitalizations and halting disease severity; therefore, more research on future development and greater awareness on its use are warranted.
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Affiliation(s)
- Karolina Akinosoglou
- Department of Internal Medicine, Medical School, University of Patras, 26504 Rio, Greece
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11
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Razali R, Fahrudin FA, Subbiah VK, Takano K, Budiman C. Heterologous Expression and Catalytic Properties of Codon-Optimized Small-Sized Bromelain from MD2 Pineapple. Molecules 2022; 27:molecules27186031. [PMID: 36144767 PMCID: PMC9502857 DOI: 10.3390/molecules27186031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Bromelain is a unique enzyme-based bioactive complex containing a mixture of cysteine proteases specifically found in the stems and fruits of pineapple (Ananas comosus) with a wide range of applications. MD2 pineapple harbors a gene encoding a small bromelain cysteine protease with the size of about 19 kDa, which might possess unique properties compared to the other cysteine protease bromelain. This study aims to determine the expressibility and catalytic properties of small-sized (19 kDa) bromelain from MD2 pineapple (MD2-SBro). Accordingly, the gene encoding MD2-SBro was firstly optimized in its codon profile, synthesized, and inserted into the pGS-21a vector. The insolubly expressed MD2-SBro was then resolubilized and refolded using urea treatment, followed by purification by glutathione S-transferase (GST) affinity chromatography, yielding 14 mg of pure MD2-SBro from 1 L of culture. The specific activity and catalytic efficiency (kcat/Km) of MD2-SBro were 3.56 ± 0.08 U mg−1 and 4.75 ± 0.23 × 10−3 µM−1 s−1, respectively, where optimally active at 50 °C and pH 8.0, and modulated by divalent ions. The MD2-SBro also exhibited the ability to scavenge the 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) with an IC50 of 0.022 mg mL−1. Altogether, this study provides the production feasibility of active and functional MD2-Bro as a bioactive compound.
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Affiliation(s)
- Rafida Razali
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Fikran Aranda Fahrudin
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
- Correspondence:
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12
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Halimi M, Bararpour P. Natural inhibitors of SARS-CoV-2 main protease: structure based pharmacophore modeling, molecular docking and molecular dynamic simulation studies. J Mol Model 2022; 28:279. [PMID: 36031629 PMCID: PMC9420677 DOI: 10.1007/s00894-022-05286-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022]
Abstract
Main protease (Mpro) plays a key role in replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study was designed for finding natural inhibitors of SARS-CoV-2 Mpro by in silico methods. To this end, the co-crystal structure of Mpro with telaprevir was explored and receptor-ligand pharmacophore models were developed and validated using pharmit. The database of “ZINC Natural Products” was screened, and 288 compounds were filtered according to pharmacophore features. In the next step, Lipinski’s rule of five was applied and absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the filtered compounds were calculated using in silico methods. The resulted 15 compounds were docked into the active site of Mpro and those with the highest binding scores and better interaction including ZINC61991204, ZINC67910260, ZINC61991203, and ZINC08790293 were selected. Further analysis by molecular dynamic simulation studies showed that ZINC61991203 and ZINC08790293 dissociated from Mpro active site, while ZINC426421106 and ZINC5481346 were stable. Root mean square deviation (RMSD), radius of gyration (Rg), number of hydrogen bonds between ligand and protein during the time of simulation, and root mean square fluctuations (RMSF) of protein and ligands were calculated, and components of binding free energy were calculated using the molecular mechanic/Poisson-Boltzmann surface area (MM/PBSA) method. The result of all the analysis indicated that ZINC61991204 and ZINC67910260 are drug-like and nontoxic and have a high potential for inhibiting Mpro.
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Affiliation(s)
- Mohammad Halimi
- Department of Biology, Babol Branch, Islamic Azad University, Babol, Iran.
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13
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Alzyoud L, Ghattas MA, Atatreh N. Allosteric Binding Sites of the SARS-CoV-2 Main Protease: Potential Targets for Broad-Spectrum Anti-Coronavirus Agents. Drug Des Devel Ther 2022; 16:2463-2478. [PMID: 35941927 PMCID: PMC9356625 DOI: 10.2147/dddt.s370574] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/23/2022] [Indexed: 12/23/2022] Open
Abstract
The current pandemic caused by the COVID-19 disease has reached everywhere in the world and has affected every aspect of our lives. As of the current data, the World Health Organization (WHO) has reported more than 300 million confirmed COVID-19 cases worldwide and more than 5 million deaths. Mpro is an enzyme that plays a key role in the life cycle of the SARS-CoV-2 virus, and it is vital for the disease progression. The Mpro enzyme seems to have several allosteric sites that can hinder the enzyme catalytic activity. Furthermore, some of these allosteric sites are located at or nearby the dimerization interface which is essential for the overall Mpro activity. In this review paper, we investigate the potential of the Mpro allosteric site to act as a drug target, especially since they interestingly appear to be resistant to mutation. The work is illustrated through three subsequent sections: First, the two main categories of Mpro allosteric sites have been explained and discussed. Second, a total of six pockets have been studied and evaluated for their druggability and cavity characteristics. Third, the experimental and computational attempts for the discovery of new allosteric inhibitors have been illustrated and discussed. To sum up, this review paper gives a detailed insight into the feasibility of developing new Mpro inhibitors to act as a potential treatment for the COVID-19 disease.
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Affiliation(s)
- Lara Alzyoud
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- Correspondence: Mohammad A Ghattas; Noor Atatreh, Email ;
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
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Nocentini A, Capasso C, Supuran CT. Perspectives on the design and discovery of α-ketoamide inhibitors for the treatment of novel coronavirus: where do we stand and where do we go? Expert Opin Drug Discov 2022; 17:547-557. [DOI: 10.1080/17460441.2022.2052847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
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