151
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Yang Z, Twidale RM, Gervasoni S, Suardíaz R, Colenso CK, Lang EJM, Spencer J, Mulholland AJ. Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins. J Chem Inf Model 2021; 61:5658-5672. [PMID: 34748329 DOI: 10.1021/acs.jcim.1c01109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zinc metalloproteins are ubiquitous, with protein zinc centers of structural and functional importance, involved in interactions with ligands and substrates and often of pharmacological interest. Biomolecular simulations are increasingly prominent in investigations of protein structure, dynamics, ligand interactions, and catalysis, but zinc poses a particular challenge, in part because of its versatile, flexible coordination. A computational workflow generating reliable models of ligand complexes of biological zinc centers would find broad application. Here, we evaluate the ability of alternative treatments, using (nonbonded) molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) at semiempirical (DFTB3) and density functional theory (DFT) levels of theory, to describe the zinc centers of ligand complexes of six metalloenzyme systems differing in coordination geometries, zinc stoichiometries (mono- and dinuclear), and the nature of interacting groups (specifically the presence of zinc-sulfur interactions). MM molecular dynamics (MD) simulations can overfavor octahedral geometries, introducing additional water molecules to the zinc coordination shell, but this can be rectified by subsequent semiempirical (DFTB3) QM/MM MD simulations. B3LYP/MM geometry optimization further improved the accuracy of the description of coordination distances, with the overall effectiveness of the approach depending upon factors, including the presence of zinc-sulfur interactions that are less well described by semiempirical methods. We describe a workflow comprising QM/MM MD using DFTB3 followed by QM/MM geometry optimization using DFT (e.g., B3LYP) that well describes our set of zinc metalloenzyme complexes and is likely to be suitable for creating accurate models of zinc protein complexes when structural information is more limited.
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Affiliation(s)
- Zongfan Yang
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - Silvia Gervasoni
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli, 25, I-20133 Milano, Italy
| | - Reynier Suardíaz
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - Charlotte K Colenso
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Eric J M Lang
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
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152
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Villa A, Brunialti E, Dellavedova J, Meda C, Rebecchi M, Conti M, Donnici L, De Francesco R, Reggiani A, Lionetti V, Ciana P. DNA aptamers masking angiotensin converting enzyme 2 as an innovative way to treat SARS-CoV-2 pandemic. Pharmacol Res 2021; 175:105982. [PMID: 34798263 PMCID: PMC8594078 DOI: 10.1016/j.phrs.2021.105982] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
Abstract
All the different coronavirus SARS-CoV-2 variants isolated so far share the same mechanism of infection mediated by the interaction of their spike (S) glycoprotein with specific residues on their cellular receptor: the angiotensin converting enzyme 2 (ACE2). Therefore, the steric hindrance on this cellular receptor created by a bulk macromolecule may represent an effective strategy for the prevention of the viral spreading and the onset of severe forms of Corona Virus disease 19 (COVID-19). Here, we applied a systematic evolution of ligands by exponential enrichment (SELEX) procedure to identify two single strand DNA molecules (aptamers) binding specifically to the region surrounding the K353, the key residue in human ACE2 interacting with the N501 amino acid of the SARS-CoV-2 S. 3D docking in silico experiments and biochemical assays demonstrated that these aptamers bind to this region, efficiently prevent the SARS-CoV-2 S/human ACE2 interaction and the viral infection in the nanomolar range, regardless of the viral variant, thus suggesting the possible clinical development of these aptamers as SARS-CoV-2 infection inhibitors. Our approach brings a significant innovation to the therapeutic paradigm of the SARS-CoV-2 pandemic by protecting the target cell instead of focusing on the virus; this is particularly attractive in light of the increasing number of viral mutants that may potentially escape the currently developed immune-mediated neutralization strategies.
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Affiliation(s)
- Alessandro Villa
- Department of Health Sciences, University of Milan, Milan 20146, Italy
| | - Electra Brunialti
- Department of Health Sciences, University of Milan, Milan 20146, Italy
| | | | - Clara Meda
- Department of Health Sciences, University of Milan, Milan 20146, Italy
| | - Monica Rebecchi
- Department of Health Sciences, University of Milan, Milan 20146, Italy
| | - Matteo Conti
- INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan 20122, Italy
| | - Lorena Donnici
- INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan 20122, Italy
| | - Raffaele De Francesco
- INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan 20122, Italy; Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Angelo Reggiani
- D3 Validation Research Line, Italian Institute of Technology, Genoa 16163, Italy
| | - Vincenzo Lionetti
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Paolo Ciana
- D3 Validation Research Line, Italian Institute of Technology, Genoa 16163, Italy.
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153
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Feng H, Chen G, Zhang Y, Guo M. Exploring Multifunctional Bioactive Components from Podophyllum sinense Using Multi-Target Ultrafiltration. Front Pharmacol 2021; 12:749189. [PMID: 34759823 PMCID: PMC8573357 DOI: 10.3389/fphar.2021.749189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 12/18/2022] Open
Abstract
Podophyllum sinense (P. sinense) has been used as a traditional herbal medicine for ages due to its extensive pharmaceutical activities, including antiproliferative, anti-inflammatory, antiviral, insecticidal effects, etc. Nevertheless, the specific bioactive constituents responsible for its antiproliferative, anti-inflammatory, and antiviral activities remain elusive, owing to its complicated and diversified chemical components. In order to explore these specific bioactive components and their potential interaction targets, affinity ultrafiltration with multiple drug targets coupled with high performance liquid chromatography/mass spectrometry (UF–HPLC/MS) strategy was developed to rapidly screen out and identify bioactive compounds against four well-known drug targets that are correlated to the application of P. sinense as a traditional medicine, namely, Topo I, Topo II, COX-2, and ACE2. As a result, 7, 10, 6, and 7 phytochemicals were screened out as the potential Topo I, Topo II, COX-2, and ACE2 ligands, respectively. Further confirmation of these potential bioactive components with antiproliferative and COX-2 inhibitory assays in vitro was also implemented. Herein, diphyllin and podophyllotoxin with higher EF values demonstrated higher inhibitory rates against A549 and HT-29 cells as compared with those of 5-FU and etoposide. The IC50 values of diphyllin were calculated at 6.46 ± 1.79 and 30.73 ± 0.56 μM on A549 and HT-29 cells, respectively. Moreover, diphyllin exhibited good COX-2 inhibitory activity with the IC50 value at 1.29 ± 0.14 μM, whereas indomethacin was 1.22 ± 0.08 μM. In addition, those representative constituents with good affinity on Topo I, Topo II, COX-2, or ACE2, such as diphyllin, podophyllotoxin, and diphyllin O-glucoside, were further validated with molecular docking analysis. Above all, the integrated method of UF–HPLC/MS with multiple drug targets rapidly singled out multi-target bioactive components and partly elucidated their action mechanisms regarding its multiple pharmacological effects from P. sinense, which could provide valuable information about its further development for the new multi-target drug discovery from natural medicines.
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Affiliation(s)
- Huixia Feng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai, China
| | - Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai, China
| | - Yongli Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai, China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai, China
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154
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Feng F, Chen J, Zhao J, Li Y, Li M, Sun C. Killing Two Birds with One Stone by Administration of Soluble ACE2: A Promising Strategy to Treat Both Cardiovascular Diseases and SARS-CoV-2 Infection. Viruses 2021; 13:2243. [PMID: 34835049 PMCID: PMC8622942 DOI: 10.3390/v13112243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/19/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells mainly by the angiotensin converting enzyme 2 (ACE2) receptor, which can recognize the spike (S) protein by its extracellular domain. Previously, recombinant soluble ACE2 (sACE2) has been clinically used as a therapeutic treatment for cardiovascular diseases. Recent data demonstrated that sACE2 can also be exploited as a decoy to effectively inhibit the cell entry of SARS-CoV-2, through blocking SARS-CoV-2 binding to membrane-anchored ACE2. In this study, we summarized the current findings on the optimized sACE2-based strategies as a therapeutic agent, including Fc fusion to prolong the half-life of sACE2, deep mutagenesis to create high-affinity decoys for SARS-CoV-2, or designing the truncated functional fragments to enhance its safety, among others. Considering that COVID-19 patients are often accompanied by manifestations of cardiovascular complications, we think that administration of sACE2 in COVID-19 patients may be a promising therapeutic strategy to simultaneously treat both cardiovascular diseases and SARS-CoV-2 infection. This review would provide insights for the development of novel therapeutic agents against the COVID-19 pandemic.
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Affiliation(s)
- Fengling Feng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Jiaoshan Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Jin Zhao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Yanjun Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Minchao Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
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155
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Khelfaoui H, Harkati D, Saleh BA. Molecular docking, molecular dynamics simulations and reactivity, studies on approved drugs library targeting ACE2 and SARS-CoV-2 binding with ACE2. J Biomol Struct Dyn 2021; 39:7246-7262. [PMID: 32752951 PMCID: PMC7484571 DOI: 10.1080/07391102.2020.1803967] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023]
Abstract
The recent new contagion coronavirus 2019 (COVID-19) disease is a new generation of severe acute respiratory syndrome coronavirus-2 SARS-CoV-2 which infected millions confirmed cases and hundreds of thousands death cases around the world so far. Molecular docking combined with molecular dynamics is one of the most important tools of drug discovery and drug design, which it used to examine the type of binding between the ligand and its protein enzyme. Global reactivity has important properties, which enable chemists to understand the chemical reactivity and kinetic stability of compounds. In this study, molecular docking and reactivity were applied for eighteen drugs, which are similar in structure to chloroquine and hydroxychloroquine, the potential inhibitors to angiotensin-converting enzyme (ACE2). Those drugs were selected from DrugBank. The reactivity, molecular docking and molecular dynamics were performed for two receptors ACE2 and [SARS-CoV-2/ACE2] complex receptor in two active sites to find a ligand, which may inhibit COVID-19. The results obtained from this study showed that Ramipril, Delapril and Lisinopril could bind with ACE2 receptor and [SARS-CoV-2/ACE2] complex better than chloroquine and hydroxychloroquine. This new understanding should help to improve predictions of the impact of such alternatives on COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hadjer Khelfaoui
- Group of Computational Pharmaceutical
Chemistry, LMCE Laboratory, Faculty of Exact and Natural Sciences, Department of Matter
Sciences, University of Biskra, Biskra,
Algeria
| | - Dalal Harkati
- Group of Computational Pharmaceutical
Chemistry, LMCE Laboratory, Faculty of Exact and Natural Sciences, Department of Matter
Sciences, University of Biskra, Biskra,
Algeria
| | - Basil A. Saleh
- Department of Chemistry, College of Science,
University of Basrah, Basrah, Iraq
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156
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Jayaraman S, Kocot J, Esfahani SH, Wangler NJ, Uyar A, Mechref Y, Trippier PC, Abbruscato TJ, Dickson A, Aihara H, Ostrov DA, Karamyan VT. Identification and Characterization of Two Structurally Related Dipeptides that Enhance Catalytic Efficiency of Neurolysin. J Pharmacol Exp Ther 2021; 379:191-202. [PMID: 34389655 PMCID: PMC8626779 DOI: 10.1124/jpet.121.000840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/10/2021] [Indexed: 11/22/2022] Open
Abstract
Neurolysin (Nln) is a recently recognized endogenous mechanism functioning to preserve the brain from ischemic injury. To further understand the pathophysiological function of this peptidase in stroke and other neurologic disorders, the present study was designed to identify small molecule activators of Nln. Using a computational approach, the structure of Nln was explored, which was followed by docking and in silico screening of ∼140,000 molecules from the National Cancer Institute Developmental Therapeutics Program database. Top ranking compounds were evaluated in an Nln enzymatic assay, and two hit histidine-dipeptides were further studied in detail. The identified dipeptides enhanced the rate of synthetic substrate hydrolysis by recombinant (human and rat) and mouse brain-purified Nln in a concentration-dependent manner (micromolar A50 and Amax ≥ 300%) but had negligible effect on activity of closely related peptidases. Both dipeptides also enhanced hydrolysis of Nln endogenous substrates neurotensin, angiotensin I, and bradykinin and increased efficiency of the synthetic substrate hydrolysis (Vmax/Km ratio) in a concentration-dependent manner. The dipeptides and competitive inhibitor dynorphin A (1-13) did not affect each other's affinity for Nln, suggesting differing nature of their respective binding sites. Lastly, drug affinity responsive target stability (DARTS) and differential scanning fluorimetry (DSF) assays confirmed concentration-dependent interaction of Nln with the activator molecule. This is the first study demonstrating that Nln activity can be enhanced by small molecules, although the peptidic nature and low potency of the activators limit their application. The identified dipeptides provide a chemical scaffold to develop high-potency, drug-like molecules as research tools and potential drug leads. SIGNIFICANCE STATEMENT: This study describes discovery of two molecules that selectively enhance activity of peptidase Nln-a newly recognized cerebroprotective mechanism in the poststroke brain. The identified molecules will serve as a chemical scaffold for development of drug-like molecules to further study Nln and may become lead structures for a new class of drugs. In addition, our conceptual and methodological framework and research findings might be used for other peptidases and enzymes, the activation of which bears therapeutic potential.
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Affiliation(s)
- Srinidhi Jayaraman
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Joanna Kocot
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Shiva Hadi Esfahani
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Naomi J Wangler
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Arzu Uyar
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Yehia Mechref
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Paul C Trippier
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Thomas J Abbruscato
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Alex Dickson
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Hideki Aihara
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - David A Ostrov
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
| | - Vardan T Karamyan
- Department of Pharmaceutical Sciences (S.J., J.K., S.H.E., N.J.W., T.J.A., V.T.K.) and Center for Blood Brain Barrier Research (T.J.A., V.T.K.), School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan (A.U., A.D.); Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas (Y.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska (P.C.T.); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (H.A.); and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida (D.A.O.)
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157
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Singh S, Pandey R, Tomar S, Varshney R, Sharma D, Gangenahalli G. A brief molecular insight of COVID-19: epidemiology, clinical manifestation, molecular mechanism, cellular tropism and immuno-pathogenesis. Mol Cell Biochem 2021; 476:3987-4002. [PMID: 34195882 PMCID: PMC8244678 DOI: 10.1007/s11010-021-04217-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
In December 2019, the emergence and expansion of novel and infectious respiratory virus SARS-CoV-2 originated from Wuhan, China caused an unprecedented threat to the public health and became a global pandemic. SARS-CoV-2 is an enveloped, positive sense and single stranded RNA virus belonging to genera betacoronavirus, of Coronaviridae family. The viral genome sequencing studies revealed 75-80% similarity with SARS-CoV. SARS-CoV-2 mainly affects the lower respiratory system and may progress to pneumonia and Acute Respiratory Distress Syndrome (ARDS). Apart from life-threatening situations and burden on the global healthcare system, the COVID-19 pandemic has imposed several challenges on the worldwide economics and livelihood. The novel pathogen is highly virulent, rapidly mutating and has a tendency to cross the species boundaries such as from bats to humans through the evolution and natural selection from intermediate host. In this review we tried to summarize the overall picture of SARS-CoV-2 including origin/ emergence, epidemiology, pathogenesis, genome organization, comparative analysis with other CoVs, infection and replication mechanism along with cellular tropism and immunopathogenesis which will provide a brief panoramic view about the virus and disease.
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Affiliation(s)
- Sweta Singh
- Division of Stem Cell and Gene Therapy, Institute of Nuclear Medicine and Allied Sciences, Brig. S. K. Mazumdar Road, Delhi, 110054, India
| | - Rakesh Pandey
- Division of Stem Cell and Gene Therapy, Institute of Nuclear Medicine and Allied Sciences, Brig. S. K. Mazumdar Road, Delhi, 110054, India
| | - Sarika Tomar
- Division of Stem Cell and Gene Therapy, Institute of Nuclear Medicine and Allied Sciences, Brig. S. K. Mazumdar Road, Delhi, 110054, India
| | - Raunak Varshney
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Brig. S. K. Mazumdar Road, Delhi, 110054, India
| | - Darshika Sharma
- Division of Stem Cell and Gene Therapy, Institute of Nuclear Medicine and Allied Sciences, Brig. S. K. Mazumdar Road, Delhi, 110054, India
- Meerut Institute of Engineering and Technology, Meerut, India
| | - Gurudutta Gangenahalli
- Division of Stem Cell and Gene Therapy, Institute of Nuclear Medicine and Allied Sciences, Brig. S. K. Mazumdar Road, Delhi, 110054, India.
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158
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Machado TR, Ribeiro MMJ, Sodero ACR, Domingos TFS, Rapozo R, de Paula DC, Domingos AS, Rodrigues CR, Cabral LM, de Souza AMT, Abrahim-Vieira BDA. Evaluation of chloroquine and hydroxychloroquine as ACE-2 Inhibitors By In Silico Approaches: Cardiac Arrhythmia Cause? J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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159
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Faisal HMN, Katti KS, Katti DR. Binding of SARS-COV-2 (COVID-19) and SARS-COV to human ACE2: Identifying binding sites and consequences on ACE2 stiffness. Chem Phys 2021; 551:111353. [PMID: 34511698 PMCID: PMC8420131 DOI: 10.1016/j.chemphys.2021.111353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/20/2021] [Accepted: 09/02/2021] [Indexed: 01/08/2023]
Abstract
The SARS-CoV-2 coronavirus (COVID-19) that is causing the massive global pandemic exhibits similar human cell invasion mechanism as the coronavirus SARS-CoV, which had significantly lower fatalities. The cell membrane protein Angiotensin-converting enzyme 2 (ACE2) is the initiation point for both the coronavirus infections in humans. Here, we model the molecular interactions and mechanical properties of ACE2 with both SARS-CoV and COVID-19 spike protein receptor-binding domains (RBD). We report that the COVID-19 spike RBD interacts with ACE2 more strongly and at only two protein residues, as compared to multi-residue interaction of the SARS-CoV. Although both coronaviruses stiffen the ACE2, the impact of COVID-19 is six times larger, which points towards differences in the severity of the reported respiratory distress. The recognition of specific residues of ACE2 attachments to coronaviruses is important as the residues suggest potential sites of intervention to inhibit attachment and subsequent entry of the COVID-19 into human host cells
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Affiliation(s)
- H M Nasrullah Faisal
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58108, United States
| | - Kalpana S Katti
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58108, United States.,Center for Engineered Cancer Testbeds, North Dakota State University, Fargo, ND 58108, United States
| | - Dinesh R Katti
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58108, United States.,Center for Engineered Cancer Testbeds, North Dakota State University, Fargo, ND 58108, United States
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160
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Chamata Y, Jackson KG, Watson KA, Jauregi P. Whey-Derived Peptides at the Heart of the COVID-19 Pandemic. Int J Mol Sci 2021; 22:11662. [PMID: 34769093 PMCID: PMC8584039 DOI: 10.3390/ijms222111662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022] Open
Abstract
The renin-angiotensin system (RAS) is a key regulator of blood pressure and hypertension. Angiotensin-converting enzyme 2 (ACE2) and angiotensin-converting enzyme I (ACE) are two main components of the RAS that play a major role in blood pressure homeostasis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses ACE2 as a receptor to enter cells. Despite some controversies, numerous studies have reported a significant association between the use of ACE inhibitors and reduced risk of COVID-19. In our previous studies, we produced and identified peptide sequences present in whey hydrolysates exhibiting high ACE inhibitory activity. Therefore, the aim of this work is to obtain an improved understanding of the function of these natural peptides as RAS inhibitors and investigate their potential therapeutic role in the COVID-19 pandemic. The molecular interactions between peptides IPP, LIVTQ, IIAE, LVYPFP, and human ACE2 were assessed by employing a molecular docking approach. The results show that natural whey-derived peptides have a dual inhibitory action against both ACE and ACE2. This dual activity distinguishes these ACE inhibitory peptides from synthetic drugs, such as Captopril and Lisinopril which were not shown to inhibit ACE2 activity, and may represent a potential strategy in the treatment of COVID-19.
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Affiliation(s)
- Yara Chamata
- Harry Nursten Building, Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6DZ, UK; (K.G.J.); (P.J.)
| | - Kim G. Jackson
- Harry Nursten Building, Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6DZ, UK; (K.G.J.); (P.J.)
| | - Kimberly A. Watson
- Health and Life Sciences Building, School of Biological Sciences, University of Reading, Reading RG6 6EX, UK;
| | - Paula Jauregi
- Harry Nursten Building, Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6DZ, UK; (K.G.J.); (P.J.)
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161
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Song F, Yang N, Khalil ZG, Salim AA, Han J, Bernhardt PV, Lin R, Xu X, Capon RJ. Bhimamycin J, a Rare Benzo[f]isoindole-dione Alkaloid from the Marine-Derived Actinomycete Streptomyces sp. MS180069. Chem Biodivers 2021; 18:e2100674. [PMID: 34609053 DOI: 10.1002/cbdv.202100674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022]
Abstract
Chemical investigation on a Streptomyces sp. strain MS180069 isolated from a sediment sample collected from the South China Sea, yielded the new benzo[f]isoindole-dione alkaloid, bhimamycin J (1). The structure was determined by extensive spectroscopic analysis, including HRMS, 1D, 2D NMR, and X-ray diffraction techniques. A molecular docking study revealed 1 as a new molecular motif that binds with human angiotensin converting enzyme2 (ACE2), recently described as the cell surface receptor responsible for uptake of 2019-CoV-2. Using enzyme assays we confirm that 1 inhibits human ACE2 79.7 % at 25 μg/mL.
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Affiliation(s)
- Fuhang Song
- School of Light Industry, Beijing Technology and Business University, Beijing, 100048, P. R. China
| | - Na Yang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, P. R. China
| | - Zeinab G Khalil
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Angela A Salim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jiahui Han
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, P. R. China
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rui Lin
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, P. R. China
| | - Xiuli Xu
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, P. R. China
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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162
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Verschelden G, Noeparast M, Noparast M, Goossens MC, Lauwers M, Cotton F, Michel C, Goyvaerts C, Hites M. Plasma zinc status and hyperinflammatory syndrome in hospitalized COVID-19 patients: An observational study. Int Immunopharmacol 2021; 100:108163. [PMID: 34583122 PMCID: PMC8450071 DOI: 10.1016/j.intimp.2021.108163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022]
Abstract
Zinc deficiency is associated with impaired antiviral response, cytokine releasing syndrome (CRS), and acute respiratory distress syndrome. Notably, similar complications are being observed during severe SARS-CoV-2 infection. We conducted a prospective, single-center, observational study in a tertiary university hospital (CUB-Hôpital Erasme, Brussels) to address the zinc status, the association between the plasma zinc concentration, development of CRS, and the clinical outcomes in PCR-confirmed and hospitalized COVID-19 patients. One hundred and thirty-nine eligible patients were included between May 2020 and November 2020 (median age of 65 years [IQR = 54, 77]). Our cohort's median plasma zinc concentration was 57 µg/dL (interquartile range [IQR] = 45, 67) compared to 74 µg/dL (IQR = 64, 84) in the retrospective non-COVID-19 control group (N = 1513; p < 0.001). Markedly, the absolute majority of COVID-19 patients (96%) were zinc deficient (<80 µg/dL). The median zinc concentration was lower in patients with CRS compared to those without CRS (-5 µg/dL; 95% CI = -10.5, 0.051; p = 0.048). Among the tested outcomes, zinc concentration is significantly correlated with only the length of hospital stay (rho = -0.19; p = 0.022), but not with mortality or morbidity. As such, our findings do not support the role of zinc as a robust prognostic marker among hospitalized COVID-19 patients who in our cohort presented a high prevalence of zinc deficiency. It might be more beneficial to explore the role of zinc as a biomarker for assessing the risk of developing a tissue-damaging CRS and predicting outcomes in patients diagnosed with COVID-19 at the early stage of the disease.
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Affiliation(s)
- Gil Verschelden
- Clinic of Infectious Diseases, Cliniques Universitaires de Bruxelles (CUB), Erasme Hospital, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium.
| | - Maxim Noeparast
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University, 35043 Marburg, Germany; Fonds Wetenschappelijk Onderzoek (FWO) - Vlaanderen, Belgium.
| | - Maryam Noparast
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Maïlis Lauwers
- Department of Clinical Chemistry, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Frédéric Cotton
- Department of Clinical Chemistry, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Brussels, Belgium
| | - Cleo Goyvaerts
- Laboratory for Molecular and Cellular Therapy (LMCT), Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Maya Hites
- Clinic of Infectious Diseases, Cliniques Universitaires de Bruxelles (CUB), Erasme Hospital, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
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163
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Zamir A, Ben-Zeev T, Hoffman JR. Manipulation of Dietary Intake on Changes in Circulating Testosterone Concentrations. Nutrients 2021; 13:3375. [PMID: 34684376 PMCID: PMC8538516 DOI: 10.3390/nu13103375] [Citation(s) in RCA: 4] [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: 09/04/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/22/2022] Open
Abstract
Elevations in the circulating concentration of androgens are thought to have a positive effect on the anabolic processes leading to improved athletic performance. Anabolic-androgenic steroids have often been used by competitive athletes to augment this effect. Although there has been concerted effort on examining how manipulating training variables (e.g., intensity and volume of training) can influence the androgen response to exercise, there has been much less effort directed at understanding how changes in both macronutrient and micronutrient intake can impact the androgen response. Thus, the focus of this review is to examine the effect that manipulating energy and nutrient intake has on circulating concentrations of testosterone and what the potential mechanism is governing these changes.
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Affiliation(s)
| | | | - Jay R. Hoffman
- Department of Physical Therapy, Faculty of Health Sciences, Ariel University, 40700 Ariel, Israel; (A.Z.); (T.B.-Z.)
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164
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Andújar SA, Gutiérrez LJ, Enriz RD, Baldoni HA. Structure, interface stability and hot-spots identification for RBD(SARS-CoV-2):hACE2 complex formation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1979229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sebastián A. Andújar
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Lucas J. Gutiérrez
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Ricardo D. Enriz
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Héctor A. Baldoni
- Faculty of Chemistry, Biochemistry and Pharmacy, Institute of Applied Mathematics of San Luis (IMASL. CONICET), National University of San Luis, San Luis, Argentina
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165
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Tateyama-Makino R, Abe-Yutori M, Iwamoto T, Tsutsumi K, Tsuji M, Morishita S, Kurita K, Yamamoto Y, Nishinaga E, Tsukinoki K. The inhibitory effects of toothpaste and mouthwash ingredients on the interaction between the SARS-CoV-2 spike protein and ACE2, and the protease activity of TMPRSS2 in vitro. PLoS One 2021; 16:e0257705. [PMID: 34534255 PMCID: PMC8448299 DOI: 10.1371/journal.pone.0257705] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/03/2021] [Indexed: 12/27/2022] Open
Abstract
SARS-CoV-2 enters host cells when the viral spike protein is cleaved by transmembrane protease serine 2 (TMPRSS2) after binding to the host angiotensin-converting enzyme 2 (ACE2). Since ACE2 and TMPRSS2 are expressed in the tongue and gingival mucosa, the oral cavity is a potential entry point for SARS-CoV-2. This study evaluated the inhibitory effects of general ingredients of toothpastes and mouthwashes on the spike protein-ACE2 interaction and the TMPRSS2 protease activity using an in vitro assay. Both assays detected inhibitory effects of sodium tetradecene sulfonate, sodium N-lauroyl-N-methyltaurate, sodium N-lauroylsarcosinate, sodium dodecyl sulfate, and copper gluconate. Molecular docking simulations suggested that these ingredients could bind to inhibitor-binding site of ACE2. Furthermore, tranexamic acid exerted inhibitory effects on TMPRSS2 protease activity. Our findings suggest that these toothpaste and mouthwash ingredients could help prevent SARS-CoV-2 infection.
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Affiliation(s)
- Riho Tateyama-Makino
- Research & Development Headquarters, Lion Corporation, Edogawa-ku, Tokyo, Japan
- * E-mail:
| | - Mari Abe-Yutori
- Research & Development Headquarters, Lion Corporation, Edogawa-ku, Tokyo, Japan
| | - Taku Iwamoto
- Research & Development Headquarters, Lion Corporation, Edogawa-ku, Tokyo, Japan
| | - Kota Tsutsumi
- Research & Development Headquarters, Lion Corporation, Edogawa-ku, Tokyo, Japan
| | - Motonori Tsuji
- Institute of Molecular Function, Misato-shi, Saitama, Japan
| | - Satoru Morishita
- Research & Development Headquarters, Lion Corporation, Edogawa-ku, Tokyo, Japan
| | - Kei Kurita
- Research & Development Headquarters, Lion Corporation, Edogawa-ku, Tokyo, Japan
| | - Yukio Yamamoto
- Research & Development Headquarters, Lion Corporation, Edogawa-ku, Tokyo, Japan
| | - Eiji Nishinaga
- Research & Development Headquarters, Lion Corporation, Edogawa-ku, Tokyo, Japan
| | - Keiichi Tsukinoki
- Division of Environmental Pathology, Department of Oral Science, Kanagawa Dental University, Yokosuka, Kanagawa, Japan
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166
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Ye F, Lin X, Chen Z, Yang F, Lin S, Yang J, Chen H, Sun H, Wang L, Wen A, Zhang X, Dai Y, Cao Y, Yang J, Shen G, Yang L, Li J, Wang Z, Wang W, Wei X, Lu G. S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis. Signal Transduct Target Ther 2021; 6:343. [PMID: 34531369 PMCID: PMC8444507 DOI: 10.1038/s41392-021-00756-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 recognizes, via its spike receptor-binding domain (S-RBD), human angiotensin-converting enzyme 2 (ACE2) to initiate infection. Ecto-domain protein of ACE2 can therefore function as a decoy. Here we show that mutations of S19W, T27W, and N330Y in ACE2 could individually enhance SARS-CoV-2 S-RBD binding. Y330 could be synergistically combined with either W19 or W27, whereas W19 and W27 are mutually unbeneficial. The structures of SARS-CoV-2 S-RBD bound to the ACE2 mutants reveal that the enhanced binding is mainly contributed by the van der Waals interactions mediated by the aromatic side-chains from W19, W27, and Y330. While Y330 and W19/W27 are distantly located and devoid of any steric interference, W19 and W27 are shown to orient their side-chains toward each other and to cause steric conflicts, explaining their incompatibility. Finally, using pseudotyped SARS-CoV-2 viruses, we demonstrate that these residue substitutions are associated with dramatically improved entry-inhibition efficacy toward both wild-type and antibody-resistant viruses. Taken together, our biochemical and structural data have delineated the basis for the elevated S-RBD binding associated with S19W, T27W, and N330Y mutations in ACE2, paving the way for potential application of these mutants in clinical treatment of COVID-19.
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Affiliation(s)
- Fei Ye
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xi Lin
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zimin Chen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fanli Yang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sheng Lin
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Yang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hua Chen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Honglu Sun
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Wang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ao Wen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xindan Zhang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yushan Dai
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Cao
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingyun Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guobo Shen
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiong Li
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhenling Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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167
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Choudhary V, Gupta A, Sharma R, Parmar HS. Therapeutically effective covalent spike protein inhibitors in treatment of SARS-CoV-2. JOURNAL OF PROTEINS AND PROTEOMICS 2021; 12:257-270. [PMID: 34539131 PMCID: PMC8440732 DOI: 10.1007/s42485-021-00074-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 02/08/2023]
Abstract
COVID-19 [coronavirus disease 2019] has resulted in over 204,644,849 confirmed cases and over 4,323,139 deaths throughout the world as of 12 August 2021, a total of 4,428,168,759 vaccine doses have been administered. The lack of potentially effective drugs against the virus is making the situation worse and dangerous. Numerous forces are working on finding an effective treatment against the virus but it is believed that a de novo drug would take several months even if huge financial support is provided. The only solution left with is drug repurposing that would not only provide effective therapy with the already used clinical drugs, but also save time and cost of the de novo drug discovery. The initiation of the COVID-19 infection starts with the attachment of spike glycoprotein of SARS-CoV-2 to the host receptor. Hence, the inhibition of the binding of the virus to the host membrane and the entry of the viral particle into the host cell are one of the main therapeutic targets. This paper not only summarizes the structure and the mechanism of spike protein, but the main focus is on the potential covalent spike protein inhibitors.
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Affiliation(s)
- Vikram Choudhary
- School of Pharmacy, Devi Ahilya Vishwavidyalaya, Takshila Campus, Khandwa Road (Ring Road), Indore, 452001 Madhya Pradesh India
| | - Amisha Gupta
- School of Pharmacy, Devi Ahilya Vishwavidyalaya, Takshila Campus, Khandwa Road (Ring Road), Indore, 452001 Madhya Pradesh India
| | - Rajesh Sharma
- School of Pharmacy, Devi Ahilya Vishwavidyalaya, Takshila Campus, Khandwa Road (Ring Road), Indore, 452001 Madhya Pradesh India
| | - Hamendra Singh Parmar
- School of Biotechnology, Devi Ahilya Vishwavidyalaya, Takshila Campus, Khandwa Road, Indore, 452001 Madhya Pradesh India
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168
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Uyar A, Dickson A. Perturbation of ACE2 Structural Ensembles by SARS-CoV-2 Spike Protein Binding. J Chem Theory Comput 2021; 17:5896-5906. [PMID: 34383488 PMCID: PMC8370119 DOI: 10.1021/acs.jctc.1c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Indexed: 01/23/2023]
Abstract
The human ACE2 enzyme serves as a critical first recognition point of coronaviruses, including SARS-CoV-2. In particular, the extracellular domain of ACE2 interacts directly with the S1 tailspike protein of the SARS-CoV-2 virion through a broad protein-protein interface. Although this interaction has been characterized by X-ray crystallography, these structures do not reveal significant differences in the ACE2 structure upon S1 protein binding. In this work, using several all-atom molecular dynamics simulations, we show persistent differences in the ACE2 structure upon binding. These differences are determined with the linear discriminant analysis (LDA) machine learning method and validated using independent training and testing datasets, including long trajectories generated by D. E. Shaw Research on the Anton 2 supercomputer. In addition, long trajectories for 78 potent ACE2-binding compounds, also generated by D. E. Shaw Research, were projected onto the LDA classification vector in order to determine whether the ligand-bound ACE2 structures were compatible with S1 protein binding. This allows us to predict which compounds are "apo-like" versus "complex-like" and to pinpoint long-range ligand-induced allosteric changes in the ACE2 structure.
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Affiliation(s)
- Arzu Uyar
- Department
of Biochemistry & Molecular Biology, Michigan State University, East Lansing Michigan 48824, United States
| | - Alex Dickson
- Department
of Biochemistry & Molecular Biology, Michigan State University, East Lansing Michigan 48824, United States
- Department
of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing Michigan 48824, United States
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169
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Wang J, Maschietto F, Guberman-Pfeffer MJ, Reiss K, Allen B, Xiong Y, Lolis E, Batista VS. Computational insights into the membrane fusion mechanism of SARS-CoV-2 at the cellular level. Comput Struct Biotechnol J 2021; 19:5019-5028. [PMID: 34540146 PMCID: PMC8442599 DOI: 10.1016/j.csbj.2021.08.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/14/2021] [Accepted: 08/31/2021] [Indexed: 12/25/2022] Open
Abstract
The membrane fusion mechanism of SARS-CoV-2 offers an attractive target for the development of small molecule antiviral inhibitors. Fusion involves an initial binding of the crown-like trimeric spike glycoproteins of SARS-CoV-2 to the receptor angiotensin II-converting enzyme 2 (ACE2) on the permissive host cellular membrane and a prefusion to post-fusion conversion of the spike trimer. During this conversion, the fusion peptides of the spike trimer are inserted into the host membrane to bring together the host and viral membranes for membrane fusion in highly choreographic events. However, geometric constraints due to interactions with the membranes remain poorly understood. In this study, we build structural models of super-complexes of spike trimer/ACE2 dimers based on the molecular structures of the ACE2/neutral amino acid transporter B(0)AT heterodimer. We determine the conformational constraints due to the membrane geometry on the enzymatic activity of ACE2 and on the viral fusion process. Furthermore, we find that binding three ACE2 dimers per spike trimer is essential to open the central pore as necessary for triggering productive membrane fusion through an elongation of the central stalk. The reported findings thus provide valuable insights for targeting the membrane fusion mechanism for drug design at the molecular level.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, United States
| | - Federica Maschietto
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | | | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, United States
| | - Elias Lolis
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
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170
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Pach S, Nguyen TN, Trimpert J, Kunec D, Osterrieder N, Wolber G. ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: A Molecular Dynamics Study. Mol Inform 2021; 40:e2100031. [PMID: 34378348 PMCID: PMC8420607 DOI: 10.1002/minf.202100031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to be a global threat, causing millions of deaths worldwide. SARS-CoV-2 is an enveloped virus with spike (S) glycoproteins conferring binding to the host cell's angiotensin-converting enzyme 2 (ACE2), which is critical for cellular entry. The host range of the virus extends well beyond humans and non-human primates. Natural and experimental infections have confirmed the high susceptibility of cats, ferrets, and Syrian hamsters, whereas dogs, mice, rats, pigs, and chickens are refractory to SARS-CoV-2 infection. To investigate the underlying reason for the variable susceptibility observed in different species, we have developed molecular descriptors to efficiently analyse dynamic simulation models of complexes between SARS-CoV-2 S and ACE2. Our extensive analyses represent the first systematic structure-based approach that allows predictions of species susceptibility to SARS-CoV-2 infection.
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Affiliation(s)
- Szymon Pach
- Pharmaceutical and Medicinal ChemistryInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Str. 2–414195BerlinGermany
| | - Trung Ngoc Nguyen
- Pharmaceutical and Medicinal ChemistryInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Str. 2–414195BerlinGermany
| | - Jakob Trimpert
- Institut für VirologieFreie Universität BerlinRobert-Von-Ostertag-Str. 7–1314163BerlinGermany
| | - Dusan Kunec
- Institut für VirologieFreie Universität BerlinRobert-Von-Ostertag-Str. 7–1314163BerlinGermany
| | - Nikolaus Osterrieder
- Institut für VirologieFreie Universität BerlinRobert-Von-Ostertag-Str. 7–1314163BerlinGermany
- Department of Infectious Diseases and Public HealthJocky Club College of Veterinary Medicine and Life SciencesCity University of Hong Kong
| | - Gerhard Wolber
- Pharmaceutical and Medicinal ChemistryInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Str. 2–414195BerlinGermany
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171
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Synthesis and Biological Evaluation of Honokiol Derivatives Bearing 3-((5-phenyl-1,3,4-oxadiazol-2-yl)methyl)oxazol-2(3H)-ones as Potential Viral Entry Inhibitors against SARS-CoV-2. Pharmaceuticals (Basel) 2021; 14:ph14090885. [PMID: 34577585 PMCID: PMC8471451 DOI: 10.3390/ph14090885] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 01/18/2023] Open
Abstract
The 2019 coronavirus disease (COVID-19) caused by SARS-CoV-2 virus infection has posed a serious danger to global health and the economy. However, SARS-CoV-2 medications that are specific and effective are still being developed. Honokiol is a bioactive component from Magnoliae officinalis Cortex with damp-drying effect. To develop new potent antiviral molecules, a series of novel honokiol analogues were synthesized by introducing various 3-((5-phenyl-1,3,4-oxadiazol-2-yl)methyl)oxazol-2(3H)-ones to its molecule. In a SARS-CoV-2 pseudovirus model, all honokiol derivatives were examined for their antiviral entry activities. As a result, 6a and 6p demonstrated antiviral entry effect with IC50 values of 29.23 and 9.82 µM, respectively. However, the parental honokiol had a very weak antiviral activity with an IC50 value more than 50 µM. A biolayer interfero-metry (BLI) binding assay and molecular docking study revealed that 6p binds to human ACE2 protein with higher binding affinity and lower binding energy than the parental honokiol. A competitive ELISA assay confirmed the inhibitory effect of 6p on SARS-CoV-2 spike RBD’s binding with ACE2. Importantly, 6a and 6p (TC50 > 100 μM) also had higher biological safety for host cells than honokiol (TC50 of 48.23 μM). This research may contribute to the discovery of potential viral entrance inhibitors for the SARS-CoV-2 virus, although 6p’s antiviral efficacy needs to be validated on SARS-CoV-2 viral strains in a biosafety level 3 facility.
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172
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Chen Y, Zhang YN, Yan R, Wang G, Zhang Y, Zhang ZR, Li Y, Ou J, Chu W, Liang Z, Wang Y, Chen YL, Chen G, Wang Q, Zhou Q, Zhang B, Wang C. ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. Signal Transduct Target Ther 2021; 6:315. [PMID: 34433803 PMCID: PMC8385704 DOI: 10.1038/s41392-021-00740-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/16/2022] Open
Abstract
The evolution of coronaviruses, such as SARS-CoV-2, makes broad-spectrum coronavirus preventional or therapeutical strategies highly sought after. Here we report a human angiotensin-converting enzyme 2 (ACE2)-targeting monoclonal antibody, 3E8, blocked the S1-subunits and pseudo-typed virus constructs from multiple coronaviruses including SARS-CoV-2, SARS-CoV-2 mutant variants (SARS-CoV-2-D614G, B.1.1.7, B.1.351, B.1.617.1, and P.1), SARS-CoV and HCoV-NL63, without markedly affecting the physiological activities of ACE2 or causing severe toxicity in ACE2 “knock-in” mice. 3E8 also blocked live SARS-CoV-2 infection in vitro and in a prophylactic mouse model of COVID-19. Cryo-EM and “alanine walk” studies revealed the key binding residues on ACE2 interacting with the CDR3 domain of 3E8 heavy chain. Although full evaluation of safety in non-human primates is necessary before clinical development of 3E8, we provided a potentially potent and “broad-spectrum” management strategy against all coronaviruses that utilize ACE2 as entry receptors and disclosed an anti-coronavirus epitope on human ACE2.
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Affiliation(s)
- Yuning Chen
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Nan Zhang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-ScienceChinese Academy of Sciences, Wuhan, Hubei, China
| | - Renhong Yan
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Guifeng Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yuanyuan Zhang
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Zhe-Rui Zhang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-ScienceChinese Academy of Sciences, Wuhan, Hubei, China
| | - Yaning Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jianxia Ou
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Wendi Chu
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhijuan Liang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongmei Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi-Li Chen
- Dartsbio Pharmaceuticals, Zhongshan, Guangdong, China.,Fudan University, School of Pharmacy, Shanghai, China
| | - Ganjun Chen
- Dartsbio Pharmaceuticals, Zhongshan, Guangdong, China
| | - Qi Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Zhou
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, and Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-ScienceChinese Academy of Sciences, Wuhan, Hubei, China. .,Drug Discovery Center for Infectious Disease, Nankai University, Tianjin, China.
| | - Chunhe Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. .,University of Chinese Academy of Sciences, Beijing, China. .,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China. .,Dartsbio Pharmaceuticals, Zhongshan, Guangdong, China. .,Fudan University, School of Pharmacy, Shanghai, China.
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173
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Al-Zaidan L, Mestiri S, Raza A, Merhi M, Inchakalody VP, Fernandes Q, Taib N, Uddin S, Dermime S. The expression of hACE2 receptor protein and its involvement in SARS-CoV-2 entry, pathogenesis, and its application as potential therapeutic target. Tumour Biol 2021; 43:177-196. [PMID: 34420993 DOI: 10.3233/tub-200084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Pneumonia cases of unknown etiology in Wuhan, Hubei province, China were reported to the World Health Organization on 31st of December 2019. Later the pathogen was reported to be a novel coronavirus designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Corona virus disease 2019 (COVID-19). The disease outspread was followed by WHO declaration of COVID-19 pandemic as a "Public Health Emergency of International Concern". SARS-CoV-2 is a novel pathogenic beta coronavirus that infects humans causing severe respiratory illness. However, multifarious factors can contribute to the susceptibility to COVID-19 related morbidity and mortality such as age, gender, and underlying comorbidities. Infection initiates when viral particles bind to the host cell surface receptors where SARS-CoV-2 spike glycoprotein subunit 1 binds to the Angiotensin Converting Enzyme 2 (ACE2). It is of importance to mention that SARS-CoV and SARS-CoV-2 viruses' mediate entry into the host cells via ACE2 receptor which might be correlated with the structural similarity of spike glycoprotein subunit 1 of both SARS viruses. However, the structural binding differs, whereas ACE2 receptor binding affinity with SARS-CoV-2 is 4 folds higher than that with SARS-CoV. Moreover, amino acids sequence divergence between the two S glycoproteins might be responsible for differential modulations of the specific immune response to both viruses. Identification of different aspects such as binding affinity, differential antigenic profiles of S-glycoproteins, and ACE2 mutations might influence the investigation of potential therapeutic strategies targeting SARS-CoV-2/ACE2 binding interface. In this review, we aim to elaborate on the expression of hACE2 receptor protein and its binding with SARS-CoV-2 S1 subunit, the possible immunogenic sequences of spike protein, effect of ACE 2 polymorphism on viral binding, and infectivity/susceptibility to disease. Furthermore, targeting of hACE2 receptor binding with SARS-CoV-2 S1 subunit via various mechanisms will be discussed to understand its role in therapeutics.
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Affiliation(s)
- Lobna Al-Zaidan
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Translational Cancer Research Facility and Clinical Trial Unit, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Translational Cancer Research Facility and Clinical Trial Unit, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Translational Cancer Research Facility and Clinical Trial Unit, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Translational Cancer Research Facility and Clinical Trial Unit, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Philipose Inchakalody
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Translational Cancer Research Facility and Clinical Trial Unit, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Queenie Fernandes
- Translational Cancer Research Facility and Clinical Trial Unit, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,Qatar University Biomedical Research Center, Qatar University, Doha, Qatar
| | - Nassiba Taib
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Translational Cancer Research Facility and Clinical Trial Unit, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Translational Cancer Research Facility and Clinical Trial Unit, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
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174
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Drugs repurposing against SARS-CoV2 and the new variant B.1.1.7 (alpha strain) targeting the spike protein: molecular docking and simulation studies. Heliyon 2021; 7:e07803. [PMID: 34423145 PMCID: PMC8367657 DOI: 10.1016/j.heliyon.2021.e07803] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/20/2021] [Accepted: 08/12/2021] [Indexed: 12/23/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) is responsible for the global COVID-19 pandemic and millions of deaths worldwide. In December 2020, a new alpha strain of SARS-CoV2 was identified in the United Kingdom. It was referred to as VUI 202012/01 (Alpha strain modelled under investigation, 2020, month 12, number 01). The interaction between spike protein and ACE2 receptor is a prerequisite for entering virion into the host cell. The present study is focussed on the spike protein of the SARS-COV 2, involving the comparison of binding affinity of new alpha strain modelled spike with previous strain spike (PDB ID:7DDN) using in silico molecular docking, dynamics and simulation studies. The molecular docking studies of the alpha strain modelled spike protein confirmed its higher affinity for the ACE2 receptor than the spike protein of the dominant strain. Similar computational approaches have also been used to investigate the potency of FDA approved drugs from the ZINC Database against the spike protein of new alpha strain modelled and old ones. The drug molecules which showed strong affinity for both the spike proteins are then subjected to ADME analysis. The overall binding energy of Conivaptan (-107.503 kJ/mol) and Trosec (-94.029 kJ/mol) is indicative of their strong binding affinities, well supported by interactions with critical residues. We investigated the potential FDA drugs for repurposing against the spike protein of alpha strain modelled of SARS-CoV-2. Spike protein of alpha strain modelled of SARS-CoV-2 has more affinity for the ACE2 receptor of host cell than previous strains and, therefore, is more contagious. Conivaptan, Ecamsule and Trosec are common drugs that bind strongly with spike protein of both the strains . Molecular Docking and simulation studies show that Conivaptan and Trosec emerged as potential inhibitors of the alpha strain modelled spike protein.
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175
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Nejati M, Dehghan* P, Hashempour- Baltork* F, Alizadeh AM, Farshi P, Khosravi- Darani K. Potential Dietary Interventions for COVID-19 Infection Based on the Gut-Immune Axis: An Update Review on Bioactive Component of Macronutrients. Int J Prev Med 2021; 12:105. [PMID: 34729139 PMCID: PMC8505687 DOI: 10.4103/ijpvm.ijpvm_493_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/19/2020] [Indexed: 01/08/2023] Open
Abstract
Recently emerged coronavirus, known as SARS-CoV-2 or Covid-19 is considered as a serious threat for human health. Due to unavailable specific drugs for this virus, there is an urgent need for supportive cares. Epigenetic immune boosting approaches and developing anti-inflammatory agents by gut-associated bioactive macronutrients can be plausible protective cares for COVID-19. Suitable intake of bioactive macronutrients including prebiotics, fatty acids, proteins and branched-chain amino acids may result in anti-viral responses through modulating macrophages and dendritic cells via Toll-like receptors, decreasing viral load, inactivating the enveloped viruses, increasing the anti-inflammatory metabolites and inhibiting the proliferation of microbial organisms. Bioactive macronutrients may help in promotion of immunological responses and recovery acceleration against Covid-19. This review focuses on the mechanisms of bioactive macronutrients and related clinical trials on enveloped viruses with emphasis on gut-microbiome-immune axis. Macronutrients and this axis may be conducive strategies to protect host against the viral infection.
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Affiliation(s)
- Marzieh Nejati
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parvin Dehghan*
- Department of Biochemistry and Diet Therapy, Faculty of Nutrition and Food Sciences, Tabriz, University of Medical Sciences, Tabriz, Iran
| | - Fataneh Hashempour- Baltork*
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Adel Mirza Alizadeh
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parastou Farshi
- Food Science Institute, Kansas State University, Manhattan, KS, USA
| | - Kianoush Khosravi- Darani
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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176
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Which ones, when and why should renin-angiotensin system inhibitors work against COVID-19? Adv Biol Regul 2021; 81:100820. [PMID: 34419773 PMCID: PMC8359569 DOI: 10.1016/j.jbior.2021.100820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022]
Abstract
The article describes the possible pathophysiological origin of COVID-19 and the crucial role of renin-angiotensin system (RAS), providing several “converging” evidence in support of this hypothesis. SARS-CoV-2 has been shown to initially upregulate ACE2 systemic activity (early phase), which can subsequently induce compensatory responses leading to upregulation of both arms of the RAS (late phase) and consequently to critical, advanced and untreatable stages of COVID-19 disease. The main and initial actors of the process are ACE2 and ADAM17 zinc-metalloproteases, which, initially triggered by SARS-CoV-2 spike proteins, work together in increasing circulating Ang 1–7 and Ang 1–9 peptides and downstream (Mas and Angiotensin type 2 receptors) pathways with anti-inflammatory, hypotensive and antithrombotic activities. During the late phase of severe COVID-19, compensatory secretion of renin and ACE enzymes are subsequently upregulated, leading to inflammation, hypertension and thrombosis, which further sustain ACE2 and ADAM17 upregulation. Based on this hypothesis, COVID-19-phase-specific inhibition of different RAS enzymes is proposed as a pharmacological strategy against COVID-19 and vaccine-induced adverse effects. The aim is to prevent the establishment of positive feedback-loops, which can sustain hyperactivity of both arms of the RAS independently of viral trigger and, in some cases, may lead to Long-COVID syndrome.
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177
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Navya VB, Hosur MV. A computational study on hydroxychloroquine binding to target proteins related to SARS-COV-2 infection. INFORMATICS IN MEDICINE UNLOCKED 2021; 26:100714. [PMID: 34458558 PMCID: PMC8381687 DOI: 10.1016/j.imu.2021.100714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has posed a global health emergency. Repurposing of existing drugs can be a rapid and effective strategy to fight the infection. Clinical trials have reported reduction or elimination of viral load when patients were treated with the anti-malarial drug Hydroxychloroquine (HCQ). To understand the molecular mechanism of action for effective repurposing of this drug we have carried out in silico docking and dynamics studies on complexes between HCQ and target proteins, which were identified through both literature survey and structural similarity searches in databases of small molecule - protein complexes. The proteins identified as binding HCQ are: Angiotensin Converting Enzyme 2 (ACE2), α7 nicotinic AcetylCholine Receptor (α7 nAChR), α1D-adrenergic receptor (α1D-AR), Histamine N- Methyl Transferase (HNMT) and DNA gyrase/Topoisomerase III β (Top3β). The majority of these proteins are novel and have not been used before, in docking studies. Our docking and simulation results support action of HCQ both at the entry and post-entry stages of SARS-CoV2 infection. The mechanism of action at the entry stage is through blocking the virus-binding sites on the two receptors, ACE2 & α7 nAChR, by binding directly at those sites. Our computational studies also show that the action of HCQ at the post-entry stage is to prevent both viral replication and generation of 'cytokine storm' by inhibiting host Top3β enzyme and α1D-AR, respectively. Binding of HCQ to HNMT is not a desired binding, and therefore this should be reduced during repurposing of HCQ.
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Affiliation(s)
- V B Navya
- National Institute of Advanced Studies, IISc. Campus, Bangalore, 560012, India
| | - M V Hosur
- National Institute of Advanced Studies, IISc. Campus, Bangalore, 560012, India
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178
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Shukla SP, Cho KB, Rustagi V, Gao X, Fu X, Zhang SX, Guo B, Udugamasooriya DG. "Molecular Masks" for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. Int J Mol Sci 2021; 22:ijms22168963. [PMID: 34445669 PMCID: PMC8396575 DOI: 10.3390/ijms22168963] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 01/14/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19) remains a global health crisis, despite the development and success of vaccines in certain countries. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, uses its spike protein to bind to the human cell surface receptor angiotensin-converting enzyme 2 (ACE2), which allows the virus to enter the human body. Using our unique cell screening technology, we identified two ACE2-binding peptoid compounds and developed dimeric derivatives (ACE2P1D1 and ACE2P2D1) that effectively blocked spike protein-ACE2 interaction, resulting in the inhibition of SARS-CoV-2 pseudovirus entry into human cells. ACE2P1D1 and ACE2P2D1 also blocked infection by a D614G mutant pseudovirus. More importantly, these compounds do not decrease ACE2 expression nor its enzyme activity (which is important in normal blood pressure regulation), suggesting safe applicability in humans
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Affiliation(s)
- Satya Prakash Shukla
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Kwang Bog Cho
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Vineeta Rustagi
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Xiang Gao
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Xinping Fu
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5037, USA; (X.F.); (S.X.Z.)
| | - Shaun Xiaoliu Zhang
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5037, USA; (X.F.); (S.X.Z.)
| | - Bin Guo
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
- Correspondence: (B.G.); (D.G.U.)
| | - D. Gomika Udugamasooriya
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
- MD Anderson Cancer Center, Department of Cancer Systems Imaging, 1881 East Road, Houston, TX 77030-4009, USA
- Correspondence: (B.G.); (D.G.U.)
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Giordano D, De Masi L, Argenio MA, Facchiano A. Structural Dissection of Viral Spike-Protein Binding of SARS-CoV-2 and SARS-CoV-1 to the Human Angiotensin-Converting Enzyme 2 (ACE2) as Cellular Receptor. Biomedicines 2021; 9:biomedicines9081038. [PMID: 34440241 PMCID: PMC8394803 DOI: 10.3390/biomedicines9081038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 12/17/2022] Open
Abstract
An outbreak by a new severe acute respiratory syndrome betacoronavirus (SARS-CoV-2) has spread CoronaVirus Disease 2019 (COVID-19) all over the world. Immediately, following studies have confirmed the human Angiotensin-Converting Enzyme 2 (ACE2) as a cellular receptor of viral Spike-Protein (Sp) that mediates the CoV-2 invasion into the pulmonary host cells. Here, we compared the molecular interactions of the viral Sp from previous SARS-CoV-1 of 2002 and SARS-CoV-2 with the host ACE2 protein by in silico analysis of the available experimental structures of Sp-ACE2 complexes. The K417 amino acid residue, located in the region of Sp Receptor-Binding Domain (RBD) of the new coronavirus SARS-CoV-2, showed to have a key role for the binding to the ACE2 N-terminal region. The R426 residue of SARS-CoV-1 Sp-RBD also plays a key role, although by interacting with the central region of the ACE2 sequence. Therefore, our study evidenced peculiarities in the interactions of the two Sp-ACE2 complexes. Our outcomes were consistent with previously reported mutagenesis studies on SARS-CoV-1 and support the idea that a new and different RBD was acquired by SARS-CoV-2. These results have interesting implications and suggest further investigations.
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Affiliation(s)
- Deborah Giordano
- National Research Council (CNR), Institute of Food Sciences (ISA), via Roma 64, 83100 Avellino, Italy; (D.G.), (M.A.A.)
| | - Luigi De Masi
- National Research Council (CNR), Institute of Biosciences and BioResources (IBBR), via Università 133, 80055 Portici, Italy
- Correspondence: (L.D.M.); (A.F.)
| | - Maria Antonia Argenio
- National Research Council (CNR), Institute of Food Sciences (ISA), via Roma 64, 83100 Avellino, Italy; (D.G.), (M.A.A.)
| | - Angelo Facchiano
- National Research Council (CNR), Institute of Food Sciences (ISA), via Roma 64, 83100 Avellino, Italy; (D.G.), (M.A.A.)
- Correspondence: (L.D.M.); (A.F.)
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180
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Gyebi GA, Ogunyemi OM, Ibrahim IM, Ogunro OB, Adegunloye AP, Afolabi SO. SARS-CoV-2 host cell entry: an in silico investigation of potential inhibitory roles of terpenoids. J Genet Eng Biotechnol 2021; 19:113. [PMID: 34351542 PMCID: PMC8339396 DOI: 10.1186/s43141-021-00209-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/16/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Targeting viral cell entry proteins is an emerging therapeutic strategy for inhibiting the first stage of SARS-CoV-2 infection. In this study, 106 bioactive terpenoids from African medicinal plants were screened through molecular docking analysis against human angiotensin-converting enzyme 2 (hACE2), human transmembrane protease serine 2 (TMPRSS2), and the spike (S) proteins of SARS-CoV-2, SARS-CoV, and MERS-CoV. In silico absorption-distribution-metabolism-excretion-toxicity (ADMET) and drug-likeness prediction, molecular dynamics (MD) simulation, binding free energy calculations, and clustering analysis of MD simulation trajectories were performed on the top docked terpenoids to respective protein targets. RESULTS The results revealed eight terpenoids with high binding tendencies to the catalytic residues of different targets. Two pentacyclic terpenoids (24-methylene cycloartenol and isoiguesteri) interacted with the hACE2 binding hotspots for the SARS-CoV-2 spike protein, while the abietane diterpenes were found accommodated within the S1-specificity pocket, interacting strongly with the active site residues TMPRSS2. 3-benzoylhosloppone and cucurbitacin interacted with the RBD and S2 subunit of SARS-CoV-2 spike protein respectively. These interactions were preserved in a simulated dynamic environment, thereby, demonstrating high structural stability. The MM-GBSA binding free energy calculations corroborated the docking interactions. The top docked terpenoids showed favorable drug-likeness and ADMET properties over a wide range of molecular descriptors. CONCLUSION The identified terpenoids from this study provides core structure that can be exploited for further lead optimization to design drugs against SARS-CoV-2 cell-mediated entry proteins. They are therefore recommended for further in vitro and in vivo studies towards developing entry inhibitors against the ongoing COVID-19 pandemic.
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Affiliation(s)
- Gideon A Gyebi
- Department of Biochemistry, Faculty of Sciences and Technology, Bingham University, P.M.B 005, Karu, Nasarawa State, Nigeria.
| | - Oludare M Ogunyemi
- Human Nutraceuticals and Bioinformatics Research Unit, Department of Biochemistry, Salem University, Lokoja, Nigeria
| | - Ibrahim M Ibrahim
- Faculty of Sciences, Department of Biophysics Cairo University, Giza, Egypt
| | - Olalekan B Ogunro
- Department of Biological Sciences, KolaDaisi University, Ibadan, Nigeria
| | - Adegbenro P Adegunloye
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria
| | - Saheed O Afolabi
- Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences, University of Ilorin, Ilorin, Nigeria
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181
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Zarezade V, Rezaei H, Shakerinezhad G, Safavi A, Nazeri Z, Veisi A, Azadbakht O, Hatami M, Sabaghan M, Shajirat Z. The identification of novel inhibitors of human angiotensin-converting enzyme 2 and main protease of Sars-Cov-2: A combination of in silico methods for treatment of COVID-19. J Mol Struct 2021; 1237:130409. [PMID: 33840836 PMCID: PMC8023563 DOI: 10.1016/j.molstruc.2021.130409] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/23/2022]
Abstract
The angiotensin-converting enzyme 2 (ACE2) and main protease (MPro), are the putative drug candidates for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, we performed 3D-QSAR pharmacophore modeling and screened 1,264,479 ligands gathered from Pubchem and Zinc databases. Following the calculation of the ADMET properties, molecular docking was carried out. Moreover, the de novo ligand design was performed. MD simulation was then applied to survey the behavior of the ligand-protein complexes. Furthermore, MMPBSA has utilized to re-estimate the binding affinities. Then, a free energy landscape was used to find the most stable conformation of the complexes. Finally, the hybrid QM-MM method was carried out for the precise calculation of the energies. The Hypo1 pharmacophore model was selected as the best model. Our docking results indicate that the compounds ZINC12562757 and 112,260,215 were the best potential inhibitors of the ACE2 and MPro, respectively. Furthermore, the Evo_1 compound enjoys the highest docking energy among the designed de novo ligands. Results of RMSD, RMSF, H-bond, and DSSP analyses have demonstrated that the lead compounds preserve the stability of the complexes' conformation during the MD simulation. MMPBSA data confirmed the molecular docking results. The results of QM-MM showed that Evo_1 has a stronger potential for specific inhibition of MPro, as compared to the 112,260,215 compound.
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Affiliation(s)
- Vahid Zarezade
- Behbahan Faculty of Medical Sciences, Behbahan, Iran
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hamzeh Rezaei
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Arman Safavi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Zahra Nazeri
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Veisi
- Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | | | - Mahdi Hatami
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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182
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Sansoè G, Aragno M, Wong F. COVID-19 and Liver Cirrhosis: Focus on the Nonclassical Renin-Angiotensin System and Implications for Therapy. Hepatology 2021; 74:1074-1080. [PMID: 33524188 PMCID: PMC8013494 DOI: 10.1002/hep.31728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/28/2020] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Giovanni Sansoè
- Division of GastroenterologyHumanitas InstituteGradenigo HospitalTorinoItaly
| | - Manuela Aragno
- Department of Clinical and Biological SciencesUniversity of TorinoTorinoItaly
| | - Florence Wong
- Department of MedicineUniversity of TorontoToronto General HospitalTorontoOntarioCanada
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183
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Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY. Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. PHARMACIA 2021. [DOI: 10.3897/pharmacia.68.e68432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
With the uncontrolled spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), development and distribution of antiviral drugs and vaccines have gained tremendous importance. This study focused on two viral proteases namely main protease (Mpro) and papain-like protease (PLpro) and human angiotensin-converting enzyme (ACE-2) to identify which of these are essential for viral replication. We screened 102 secondary metabolites against SARS-CoV-2 isolated from 36 terrestrial plants and 36 marine organisms from Indonesian biodiversity. These organisms are typically presumed to have antiviral effects, and some of them have been used as an immunomodulatory activity in traditional medicine. For the molecular docking procedure to obtain Gibbs free energy value (∆G), toxicity, ADME and Lipinski, AutoDock Vina was used. In this study, five secondary metabolites, namely corilagin, dieckol, phlorofucofuroeckol A, proanthocyanidins, and isovitexin, were found to inhibit ACE-2, Mpro, and PLpro receptors in SARS-CoV-2, with a high affinity to the same sites of ptilidepsin, remdesivir, and chloroquine as the control molecules. This study was delimited to molecular docking without any validation by simulations concerned with molecular dynamics. The interactions with two viral proteases and human ACE-2 may play a key role in developing antiviral drugs for five active compounds. In future, we intend to investigate antiviral drugs and the mechanisms of action by in vitro study.
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184
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Salih AEM, Thissera B, Yaseen M, Hassane ASI, El-Seedi HR, Sayed AM, Rateb ME. Marine Sulfated Polysaccharides as Promising Antiviral Agents: A Comprehensive Report and Modeling Study Focusing on SARS CoV-2. Mar Drugs 2021; 19:406. [PMID: 34436245 PMCID: PMC8401819 DOI: 10.3390/md19080406] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) is a novel coronavirus strain that emerged at the end of 2019, causing millions of deaths so far. Despite enormous efforts being made through various drug discovery campaigns, there is still a desperate need for treatments with high efficacy and selectivity. Recently, marine sulfated polysaccharides (MSPs) have earned significant attention and are widely examined against many viral infections. This article attempted to produce a comprehensive report about MSPs from different marine sources alongside their antiviral effects against various viral species covering the last 25 years of research articles. Additionally, these reported MSPs were subjected to molecular docking and dynamic simulation experiments to ascertain potential interactions with both the receptor-binding domain (RBD) of SARS CoV-2's spike protein (S-protein) and human angiotensin-converting enzyme-2 (ACE2). The possible binding sites on both S-protein's RBD and ACE2 were determined based on how they bind to heparin, which has been reported to exhibit significant antiviral activity against SARS CoV-2 through binding to RBD, preventing the virus from affecting ACE2. Moreover, our modeling results illustrate that heparin can also bind to and block ACE2, acting as a competitor and protective agent against SARS CoV-2 infection. Nine of the investigated MSPs candidates exhibited promising results, taking into consideration the newly emerged SARS CoV-2 variants, of which five were not previously reported to exert antiviral activity against SARS CoV-2, including sulfated galactofucan (1), sulfated polymannuroguluronate (SPMG) (2), sulfated mannan (3), sulfated heterorhamnan (8), and chondroitin sulfate E (CS-E) (9). These results shed light on the importance of sulfated polysaccharides as potential SARS-CoV-2 inhibitors.
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Affiliation(s)
- Abdalla E. M. Salih
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (A.E.M.S.); (B.T.); (M.Y.); (A.S.I.H.)
| | - Bathini Thissera
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (A.E.M.S.); (B.T.); (M.Y.); (A.S.I.H.)
| | - Mohammed Yaseen
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (A.E.M.S.); (B.T.); (M.Y.); (A.S.I.H.)
| | - Ahmed S. I. Hassane
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (A.E.M.S.); (B.T.); (M.Y.); (A.S.I.H.)
- Aberdeen Royal Infirmary, Foresterhill Health Campus, Aberdeen AB25 2ZN, UK
| | - Hesham R. El-Seedi
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, BMC, Uppsala University, Uppsala, Box 591, SE 751 24 Uppsala, Sweden;
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Mostafa E. Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (A.E.M.S.); (B.T.); (M.Y.); (A.S.I.H.)
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185
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Aljindan RY, Al-Subaie AM, Al-Ohali AI, Kumar D T, Doss C GP, Kamaraj B. Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Comput Biol Med 2021; 135:104654. [PMID: 34346317 PMCID: PMC8282961 DOI: 10.1016/j.compbiomed.2021.104654] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
COVID-19 is an infectious and pathogenic viral disease caused by SARS-CoV-2 that leads to septic shock, coagulation dysfunction, and acute respiratory distress syndrome. The spreading rate of SARS-CoV-2 is higher than MERS-CoV and SARS-CoV. The receptor-binding domain (RBD) of the Spike-protein (S-protein) interacts with the human cells through the host angiotensin-converting enzyme 2 (ACE2) receptor. However, the molecular mechanism of pathological mutations of S-protein is still unclear. In this perspective, we investigated the impact of mutations in the S-protein and their interaction with the ACE2 receptor for SAR-CoV-2 viral infection. We examined the stability of pathological nonsynonymous mutations in the S-protein, and the binding behavior of the ACE2 receptor with the S-protein upon nonsynonymous mutations using the molecular docking and MM_GBSA approaches. Using the extensive bioinformatics pipeline, we screened the destabilizing (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) and stabilizing (H49Y, S50L, N501Y, D614G, A845V, and P1143L) nonsynonymous mutations in the S-protein. The docking and binding free energy (ddG) scores revealed that the stabilizing nonsynonymous mutations show increased interaction between the S-protein and the ACE2 receptor compared to native and destabilizing S-proteins and that they may have been responsible for the virulent high level. Further, the molecular dynamics simulation (MDS) approach reveals the structural transition of mutants (N501Y and D614G) S-protein. These insights might help researchers to understand the pathological mechanisms of the S-protein and provide clues regarding mutations in viral infection and disease propagation. Further, it helps researchers to develop an efficient treatment approach against this SARS-CoV-2 pandemic.
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Affiliation(s)
- Reem Y Aljindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Abeer M Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Ahoud I Al-Ohali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Thirumal Kumar D
- Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, 600078, India.
| | - George Priya Doss C
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia.
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186
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Pulakuntla S, Lokhande KB, Padmavathi P, Pal M, Swamy KV, Sadasivam J, Singh SA, Aramgam SL, Reddy VD. Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Virusdisease 2021; 32:690-702. [PMID: 34307771 PMCID: PMC8282177 DOI: 10.1007/s13337-021-00720-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/23/2021] [Indexed: 01/11/2023] Open
Abstract
The novel SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) is spreading, as the causative pathogen of coronavirus disease-19 (COVID-19). It has infected more than 1.65 billion people all over the world since it was discovered and reported 3.43 million deaths by mid of May 2021. SARS-CoV-2 enters the host cell by binding to viral surface glycoprotein (S protein) with human ACE2 (angiotensin-converting enzyme2). Spike protein (contains S1 and S2 sub-domains) molecular interaction with the host cells is considered as a major step in the viral entry and disease initiation and progression and this identifies spike protein as a promising therapeutic target against antiviral drugs. Currently, there are no efficient antiviral drugs for the prevention of COVID-19 infection. In this study, we have analyzed global 8719 spike protein sequences from patients infected with SAR-CoV-2. These SAR-CoV-2 genome sequences were downloaded from the GISAID database. By using an open reading frame (ORF) tool we have identified the spike protein sequence. With these, all spike protein amino acid sequences are subjected to multiple sequence alignment (MSA) with Wuhan strain spike protein sequence as a query sequence, and it shows all SAR-CoV strain spike proteins are 99.8% identical. In the mutational analysis, we found 639 mutations in the spike protein sequence of SARS-CoV-2 and identified/highlighted 20 common mutations L5F, T22I, T29I, H49Y, L54F, V90F, S98F, S221L, S254F, V367F, A520S, T572I, D614G, H655Y, P809S, A879S, D936Y, A1020S, A1078S, and H1101Y. Further, we have analyzed the crystal structure of the 2019-nCoV chimeric receptor-binding complex with ACE2 (PDB ID: 6VW1) as a major target protein. The spike receptor binding protein (RBD) used as target region for our studies with FDA-approved drugs for repurposing, and identified few anti-SARS-CoV2 potential drugs (Silmitasertib, AC-55541, Merimepodib, XL413, AZ3451) based on their docking score and binding mode calculations expected to strongly bind to motifs of ACE2 receptor and may show impart relief in COVID-19 patients.
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Affiliation(s)
- Swetha Pulakuntla
- Department of Biochemistry, REVA University, Bangalore, Karnataka 560064 India
| | - Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra 411033 India
| | - Pannuru Padmavathi
- DR Biosciences, Research & Development Unit, Bettahalasur, Bangalore, 562157 India
| | - Meena Pal
- Department of Molecular Biology, National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh 20130 India
| | - Kakumani Venkateswara Swamy
- MIT School of Bioengineering Science and Research, MIT Art Design and Technology University, Pune, Maharashtra 412202 India
| | - Jayashree Sadasivam
- Department of Biochemistry, REVA University, Bangalore, Karnataka 560064 India
| | - Shri Abhiav Singh
- Department of ISRM, Indian Council of Medical Research, New Delhi, 110029 India
| | - Sree Latha Aramgam
- Department of Biochemistry, REVA University, Bangalore, Karnataka 560064 India
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30329 USA
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187
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The interaction of the severe acute respiratory syndrome coronavirus 2 spike protein with drug-inhibited angiotensin converting enzyme 2 studied by molecular dynamics simulation. J Hypertens 2021; 39:1705-1716. [PMID: 34188005 DOI: 10.1097/hjh.0000000000002829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Hypertension has been identified as the most common comorbidity in coronavirus disease 2019 (COVID-19) patients, and has been suggested as a risk factor for COVID-19 disease outcomes. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host human cells via binding to host cell angiotensin-converting enzyme 2 (ACE2) receptors. Inhibition of ACE2 has been proposed as a potential therapeutic approach to block SARS-CoV-2 contagion. However, some experts suggest that ACE2 inhibition could worsen the infection. Here, we aimed to study the effect of ACE2 inhibition on the SARS-CoV-2 spike protein binding to ACE2. METHOD Crystallographic structures of the SARS-CoV-2 spike protein, the spike receptor-binding domain, native ACE2, and the ACE2 complexed with MLN-4760 were used as the study model structures. The spike proteins were docked to the ACE2 structures and the dynamics of the complexes, ligand-protein, and protein-protein interactions were studied by molecular dynamics simulation for 100 ns. RESULTS Our result showed that inhibition of ACE2 by MLN-4760 increased the affinity of the SARS-CoV-2 spike protein binding to ACE2. Results also revealed that spike protein binding to the ACE2 inhibited by MLN-4760 restored the enzymatic active conformation of the ACE2 from closed/inactive to open/active conformation by removing MLN-4760 binding from the ligand-binding pocket of ACE2. CONCLUSION We conclude that using ACE2 inhibitors can increase the risk of SARS-CoV-2 infection and worsen COVID-19 disease outcome. We also found that the SARS-CoV-2 can abrogate the function of ACE2 inhibitors and rescue the enzymatic activity of ACE2. Therefore, ACE2 inhibition is not a useful treatment against COVID-19 infection.
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188
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Zhang Z, Zhang Y, Liu K, Li Y, Lu Q, Wang Q, Zhang Y, Wang L, Liao H, Zheng A, Ma S, Fan Z, Li H, Huang W, Bi Y, Zhao X, Wang Q, Gao GF, Xiao H, Tong Z, Qi J, Sun Y. The molecular basis for SARS-CoV-2 binding to dog ACE2. Nat Commun 2021; 12:4195. [PMID: 34234119 PMCID: PMC8263772 DOI: 10.1038/s41467-021-24326-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 can infect many domestic animals, including dogs. Herein, we show that dog angiotensin-converting enzyme 2 (dACE2) can bind to the SARS-CoV-2 spike (S) protein receptor binding domain (RBD), and that both pseudotyped and authentic SARS-CoV-2 can infect dACE2-expressing cells. We solved the crystal structure of RBD in complex with dACE2 and found that the total number of contact residues, contact atoms, hydrogen bonds and salt bridges at the binding interface in this complex are slightly fewer than those in the complex of the RBD and human ACE2 (hACE2). This result is consistent with the fact that the binding affinity of RBD to dACE2 is lower than that of hACE2. We further show that a few important mutations in the RBD binding interface play a pivotal role in the binding affinity of RBD to both dACE2 and hACE2. Our work reveals a molecular basis for cross-species transmission and potential animal spread of SARS-CoV-2, and provides new clues to block the potential transmission chains of this virus.
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Affiliation(s)
- Zengyuan Zhang
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Yanfang Zhang
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China ,grid.458513.e0000 0004 1763 3963Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Kefang Liu
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qiong Lu
- grid.410749.f0000 0004 0577 6238Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Qingling Wang
- grid.412262.10000 0004 1761 5538Shanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi’an, China
| | - Yuqin Zhang
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Liang Wang
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hanyi Liao
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Anqi Zheng
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Sufang Ma
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zheng Fan
- grid.458488.d0000 0004 0627 1442Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huifang Li
- grid.414252.40000 0004 1761 8894The Northern Medical District of the PLA General Hospital, Beijing, China
| | - Weijin Huang
- grid.410749.f0000 0004 0577 6238Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Yuhai Bi
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qihui Wang
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F. Gao
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haixia Xiao
- grid.458513.e0000 0004 1763 3963Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhou Tong
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yeping Sun
- grid.458488.d0000 0004 0627 1442CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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189
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Narang D, James DA, Balmer MT, Wilson DJ. Protein Footprinting, Conformational Dynamics, and Core Interface-Adjacent Neutralization "Hotspots" in the SARS-CoV-2 Spike Protein Receptor Binding Domain/Human ACE2 Interaction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1593-1600. [PMID: 33794092 PMCID: PMC8029444 DOI: 10.1021/jasms.0c00465] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/22/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
The novel severe respiratory syndrome-like coronavirus (SARS-CoV-2) causes COVID-19 in humans and is responsible for one of the most destructive pandemics of the last century. At the root of SARS-CoV infection is the interaction between the viral spike protein and the human angiotensin converting enzyme 2 protein, which allows the virus to gain entry into host cells through endocytosis. In this work, we apply hydrogen-deuterium exchange mass spectrometry (HDX-MS) to provide a detailed view of the functional footprint and conformational dynamics associated with this interaction. Our results broadly agree with the binding interface derived from high resolution X-ray crystal structure data but also provide insights into shifts in structure and dynamics that accompany complexation, including some that occur immediately outside of the core binding interface. We propose that dampening of these "binding-site adjacent" dynamic shifts could represent a mechanism for neutralizing activity in a multitude of spike protein-targeted mAbs that have been found to specifically bind these "peripheral" sites. Our results highlight the unique capacity of HDX-MS to detect potential neutralization "hotspots" outside of the core binding interfaces defined by high resolution structural data.
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Affiliation(s)
- Dominic Narang
- Department of Chemistry, York
University, Toronto M3J 1P3, Ontario, Canada
| | - D. Andrew James
- Sanofi Pasteur Limited,
1755 Steeles Avenue West, Toronto M2R 3T4, Ontario, Canada
| | - Matthew T. Balmer
- Sanofi Pasteur Limited,
1755 Steeles Avenue West, Toronto M2R 3T4, Ontario, Canada
| | - Derek J. Wilson
- Department of Chemistry, York
University, Toronto M3J 1P3, Ontario, Canada
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190
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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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191
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Ahmad S, Waheed Y, Abro A, Abbasi SW, Ismail S. Molecular screening of glycyrrhizin-based inhibitors against ACE2 host receptor of SARS-CoV-2. J Mol Model 2021; 27:206. [PMID: 34169390 PMCID: PMC8225399 DOI: 10.1007/s00894-021-04816-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023]
Abstract
The interaction between SARS-CoV-2 Spike protein and angiotensin-converting enzyme 2 (ACE2) is essential to viral attachment and the subsequent fusion process. Interfering with this event represents an attractive avenue for the development of therapeutics and vaccine development. Here, a hybrid approach of ligand- and structure-based virtual screening techniques were employed to disclose similar analogues of a reported antiviral phytochemical, glycyrrhizin, targeting the blockade of ACE2 interaction with the SARS-CoV-2 Spike. A ligand-based similarity search using a stringent cut-off revealed 40 FDA-approved compounds in DrugBank. These filtered hits were screened against ACE2 using a blind docking approach to determine the natural binding tendency of the compounds with ACE2. Three compounds, deslanoside, digitoxin, and digoxin, were reported to show strong binding with ACE2. These compounds bind at the H1-H2 binding pocket, in a manner similar to that of glycyrrhizin which was used as a control. To achieve consistency in the docking results, docking calculations were performed via two sets of docking software that predicted binding energy as ACE2-Deslanoside (AutoDock, -10.3 kcal/mol and DockThor, -9.53 kcal/mol), ACE2-Digitoxin (AutoDock, -10.6 kcal/mol and DockThor, -8.84 kcal/mol), and ACE2-Digoxin (AutoDock, -10.6 kcal/mol and DockThor, -8.81 kcal/mol). The docking results were validated by running molecular simulations in aqueous solution that demonstrated the stability of ACE2 with no major conformational changes in the ligand original binding mode (~ 2 Å average RMSD). Binding interactions remained quite stable with an increased potential for getting stronger as the simulation proceeded. MMGB/PBSA binding free energies were also estimated and these supported the high stability of the complexes compared to the control (~ -50 kcal/mol net MMGB/PBSA binding energy versus ~ -30 kcal/mol). Collectively, the data demonstrated that the compounds shortlisted in this study might be subjected to experimental evaluation to uncover their real blockade capacity of SARS-CoV-2 host ACE2 receptor.
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Affiliation(s)
- Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000 Pakistan
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad, 44000 Pakistan
| | - Asma Abro
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology Engineering and Management Sciences, Quetta, Pakistan
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, The Mall, Rawalpindi, Pakistan
| | - Saba Ismail
- NUMS Department of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, The Mall, Rawalpindi, Pakistan
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192
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Rey F. Structure-function relations of the SARS-CoV-2 spike protein and impact of mutations in the variants of concern. C R Biol 2021; 344:77-110. [PMID: 34213849 DOI: 10.5802/crbiol.53] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review covers the main features of the severe acquired respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, its interaction with the main entry receptor, the human angiotensin converting enzyme 2 (ACE2), and the subsequent membrane fusion step. The focus is on the structural organization of these proteins and mechanistic aspects of their interactions that lead to cytoplasmic release of the viral genome. The most potently neutralizing antibodies against SARS-CoV-2 were shown to interfere with the spike/ACE2 interaction. I thus also review the location and the potential impact of mutations in the spike protein observed in the variants of concern that emerged concomitantly with acquired immunity in the population after one year of virus circulation. Understanding how these interactions affect the spike/ACE2 interactions and the subsequent spike-protein-induced membrane fusion reaction is important to stay one step ahead of the virus evolution and develop efficient countermeasures.
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Affiliation(s)
- Félix Rey
- Unité de Virologie Structurale, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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193
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Nesci S. SARS-CoV-2 first contact: Spike-ACE2 interactions in COVID-19. Chem Biol Drug Des 2021; 98:207-211. [PMID: 34047452 PMCID: PMC8239675 DOI: 10.1111/cbdd.13898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/08/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022]
Abstract
The full-length human ACE2 in complex with B0 AT1 is anchored to two S in open pre-fusion state which allows establishing pre-invasion interactions with the ACE2 N-terminal domain.
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Affiliation(s)
- Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
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194
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Higuchi Y, Suzuki T, Arimori T, Ikemura N, Mihara E, Kirita Y, Ohgitani E, Mazda O, Motooka D, Nakamura S, Sakai Y, Itoh Y, Sugihara F, Matsuura Y, Matoba S, Okamoto T, Takagi J, Hoshino A. Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2. Nat Commun 2021; 12:3802. [PMID: 34155214 PMCID: PMC8217473 DOI: 10.1038/s41467-021-24013-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/28/2021] [Indexed: 01/06/2023] Open
Abstract
SARS-CoV-2 has mutated during the global pandemic leading to viral adaptation to medications and vaccinations. Here we describe an engineered human virus receptor, ACE2, by mutagenesis and screening for binding to the receptor binding domain (RBD). Three cycles of random mutagenesis and cell sorting achieved sub-nanomolar affinity to RBD. Our structural data show that the enhanced affinity comes from better hydrophobic packing and hydrogen-bonding geometry at the interface. Additional disulfide mutations caused the fixing of a closed ACE2 conformation to avoid off-target effects of protease activity, and also improved structural stability. Our engineered ACE2 neutralized SARS-CoV-2 at a 100-fold lower concentration than wild type; we also report that no escape mutants emerged in the co-incubation after 15 passages. Therapeutic administration of engineered ACE2 protected hamsters from SARS-CoV-2 infection, decreased lung virus titers and pathology. Our results provide evidence of a therapeutic potential of engineered ACE2.
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Affiliation(s)
- Yusuke Higuchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takao Arimori
- Laboratory for Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Nariko Ikemura
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Emiko Mihara
- Laboratory for Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yusuke Sakai
- Department of Veterinary Pathology, Yamaguchi University, Yamaguchi, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Fuminori Sugihara
- The Core Instrumentation Facility, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
| | - Junichi Takagi
- Laboratory for Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan.
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.
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195
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Zang Y, Li X, Zhao Y, Wang H, Hao D, Zhang L, Yang Z, Yuan X, Zhang S. Molecular insights into the binding variance of the SARS-CoV-2 spike with human, cat and dog ACE2 proteins. Phys Chem Chem Phys 2021; 23:13752-13759. [PMID: 34132301 DOI: 10.1039/d1cp01611c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 has recently caused an epidemic in humans and poses a huge threat to global public health. As a primary receptor of SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2) exists in different hosts that are in close contact with humans, especially cats and dogs. However, the underlying mechanism of how the spike receptor binding domain (RBD) of SARS-CoV-2 cooperates with human ACE2 (hACE2), cat ACE2 (cACE2) and dog ACE2 (dACE2) and the variation in binding remains largely unsolved. Therefore, we explored the binding behavior of the spike RBD with cACE2, dACE2 and hACE2 via all-atom molecular dynamics simulations. In accordance with the binding free energies and residue interactions, the spike RBD has respective binding specificities with cACE2, dACE2 and hACE2, and the binding affinities decrease in the order of hACE2, cACE2, dACE2, mainly due to changes in the amino acids Q24L, H34Y, and M82T in cACE2 or dACE2. Furthermore, alanine scanning analysis results validated some key residues of the spike RBD interact with ACE2 and provided clues to the variation of amino acid that could influence the transmissibility or immune responses of SARS-CoV-2. Decreasing dynamic correlations strengths of ACE2 with the RBD were found in all hACE2-RBD, cACE2-RBD and dACE2-RBD systems. The ACE2 protein shows variable motion modes across the zinc metallopeptidase domain, which induces different interactions between ACE2 and the RBD. Our studies reveal that the motion pattern of the zinc metallopeptidase domain is critical to the binding behavior of RBD with ACE2. These findings could aid our understanding of selective recognition involving various ACE2 with the SARS-CoV-2 spike and shed further light on the binding mechanisms.
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Affiliation(s)
- Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
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196
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Virtual screenings of the bioactive constituents of tea, prickly chaff, catechu, lemon, black pepper, and synthetic compounds with the main protease (Mpro) and human angiotensin-converting enzyme 2 (ACE 2) of SARS-CoV-2. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:121. [PMID: 34150913 PMCID: PMC8204119 DOI: 10.1186/s43094-021-00275-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/07/2021] [Indexed: 12/24/2022] Open
Abstract
Background COVID-19 has mutation capability, and there are no specific drug therapies that are available to fight or inhibit the proteins of this virus. The present study aims to investigate the binding affinity of the bioactive and synthetic compounds with the main protease (Mpro) enzymes and angiotensin-converting enzyme 2 (ACE 2) by computational approach. PASS prediction, pharmacokinetics, and toxicological properties prediction studies were performed through the Google PASS prediction and Swiss ADME/T website. Besides, molecular docking studies were accomplished by BIOVIA Discovery Studio 2020, UCSF Chimera, and PyRx autodock vina. Results The docking scores were inferred and the selected compounds showed results varying from −3.2 to −9.8 (kcal/mol). Theaflavin scored the highest docking score to the 5REB, 6VW1, and 1R42 enzymes and showed the binding affinity as −6.3 kcal/mol, −9.8 kcal/mol, and −8.6 kcal/mol, respectively. Again, kaempferol showed the best binding affinity to the 7BQY (−7.1 kcal/mol) and 6Y2FB (−6.6 kcal/mol) enzymes. All the chemical constituents showed better probability in action in pass prediction analysis. Besides, no ligands (except theaflavin) have any conflict with Lipinski’s rules of five, which authorized the drug probability of these ligands. Conclusion Therefore, the selected compounds could be considered a potential herbal treatment source against SARS-CoV-2.
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197
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Zeng MS, Yu WD, Wang HX, Liu JY, Xu PP. A potential antiviral activity of Esculentoside A against binding interactions of SARS-COV-2 spike protein and angiotensin converting enzyme 2 (ACE2). Int J Biol Macromol 2021; 183:2248-2261. [PMID: 34111482 PMCID: PMC8183004 DOI: 10.1016/j.ijbiomac.2021.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022]
Abstract
The recent emergence of the novel coronavirus (SARS-CoV-2) has resulted in a devastating pandemic with global concern. However, to date, there are no regimens to prevent and treat SARS-CoV-2 virus. There is an urgent need to identify novel leads with anti-viral properties that impede viral pathogenesis in the host system. Esculentoside A (EsA), a saponin isolated from the root of Phytolacca esculenta, is known to exhibit diverse pharmacological properties, especially anti-inflammatory activity. To our knowledge, SARS-CoV-2 uses angiotensin converting enzyme 2 (ACE2) to enter host cells. This is mediated through the proteins of SARS-CoV-2, especially the spike glycoprotein receptor binding domain. Thus, our primary goal is to prevent virus replication and binding to the host, which allows us to explore the efficiency of EsA on key surface drug target proteins using the computational biology paradigm approach. Here, the anti-coronavirus activity of EsA in vitro and its potential mode of inhibitory action on the S-protein of SARS-CoV-2 were investigated. We found that EsA inhibited the HCoV-OC43 coronavirus during the attachment and penetration stage. Molecular docking results showed that EsA had a strong binding affinity with the spike glycoprotein from SARS-CoV-2. The results of the molecular dynamics simulation revealed that EsA had higher stable binding with the spike protein. These results demonstrated that Esculentoside A can act as a spike protein blocker to inhibit SARS-CoV-2. Considering the poor bioavailability and low toxicity of EsA, it is suitable as novel lead for the inhibitor against binding interactions of SARS-CoV-2 of S-protein and ACE2.
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Affiliation(s)
- Mao-Sen Zeng
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Wen-Di Yu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Hui-Xian Wang
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Jin-Yuan Liu
- Basic Medical College, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Pei-Ping Xu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, PR China.
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198
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Praissman JL, Wells L. Proteomics-Based Insights Into the SARS-CoV-2-Mediated COVID-19 Pandemic: A Review of the First Year of Research. Mol Cell Proteomics 2021; 20:100103. [PMID: 34089862 PMCID: PMC8176883 DOI: 10.1016/j.mcpro.2021.100103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 02/08/2023] Open
Abstract
In late 2019, a virus subsequently named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China and led to a worldwide pandemic of the disease termed coronavirus disease 2019. The global health threat posed by this pandemic led to an extremely rapid and robust mobilization of the scientific and medical communities as evidenced by the publication of more than 10,000 peer-reviewed articles and thousands of preprints in the first year of the pandemic alone. With the publication of the initial genome sequence of SARS-CoV-2, the proteomics community immediately joined this effort publishing, to date, more than 100 peer-reviewed proteomics studies and submitting many more preprints to preprint servers. In this review, we focus on peer-reviewed articles published on the proteome, glycoproteome, and glycome of SARS-CoV-2. At a basic level, proteomic studies provide valuable information on quantitative aspects of viral infection course; information on the identities, sites, and microheterogeneity of post-translational modifications; and, information on protein-protein interactions. At a biological systems level, these studies elucidate host cell and tissue responses, characterize antibodies and other immune system factors in infection, suggest biomarkers that may be useful for diagnosis and disease-course monitoring, and help in the development or repurposing of potential therapeutics. Here, we summarize results from selected early studies to provide a perspective on the current rapidly evolving literature.
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Affiliation(s)
- Jeremy L Praissman
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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199
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Shadrack DM, Deogratias G, Kiruri LW, Swai HS, Vianney JM, Nyandoro SS. Ensemble-based screening of natural products and FDA-approved drugs identified potent inhibitors of SARS-CoV-2 that work with two distinct mechanisms. J Mol Graph Model 2021; 105:107871. [PMID: 33684603 PMCID: PMC7901283 DOI: 10.1016/j.jmgm.2021.107871] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 12/27/2022]
Abstract
The recent outbreak of SARS-CoV-2 is responsible for high morbidity and mortality rate across the globe. This requires an urgent identification of drugs and other interventions to overcome this pandemic. Computational drug repurposing represents an alternative approach to provide a more effective approach in search for COVID-19 drugs. Selected natural product known to have antiviral activities were screened, and based on their hits; a similarity search with FDA approved drugs was performed using computational methods. Obtained drugs from similarity search were assessed for their stability and inhibition against SARS-CoV-2 targets. Diosmin (DB08995) was found to be a promising drug that works with two distinct mechanisms, preventing viral replication and viral fusion into the host cell. Isoquercetin (DB12665) and rutin (DB01698) work by inhibiting viral replication and preventing cell entry, respectively. Our analysis based on molecular dynamics simulation and MM-PBSA binding free energy calculation suggests that diosmin, isoquercetin, rutin and other similar flavone glycosides could serve as SARS-CoV-2 inhibitor, hence an alternative solution to treat COVID-19 upon further clinical validation.
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Affiliation(s)
- Daniel M Shadrack
- Department of Health and Biomedical Sciences, School of Life Science and Bioengineering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania; Department of Chemistry, Faculty of Natural and Applied Sciences, St John's University of Tanzania, P.O.Box 47, Dodoma, Tanzania.
| | - Geradius Deogratias
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania; Department of Materials and Energy Science and Engineering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - Lucy W Kiruri
- Department of Chemistry, P.O.Box 43844-00100, Kenyatta University, Nairobi, Kenya
| | - Hulda S Swai
- Department of Health and Biomedical Sciences, School of Life Science and Bioengineering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - John-Mary Vianney
- Department of Health and Biomedical Sciences, School of Life Science and Bioengineering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - Stephen S Nyandoro
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania.
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Pirolli D, Righino B, De Rosa MC. Targeting SARS-CoV-2 Spike Protein/ACE2 Protein-Protein Interactions: a Computational Study. Mol Inform 2021; 40:e2060080. [PMID: 33904240 PMCID: PMC8206717 DOI: 10.1002/minf.202060080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/28/2022]
Abstract
The spike glycoprotein (S) of the SARS-CoV-2 virus surface plays a key role in receptor binding and virus entry. The S protein uses the angiotensin converting enzyme (ACE2) for entry into the host cell and binding to ACE2 occurs at the receptor binding domain (RBD) of the S protein. Therefore, the protein-protein interactions (PPIs) between the SARS-CoV-2 RBD and human ACE2, could be attractive therapeutic targets for drug discovery approaches designed to inhibit the entry of SARS-CoV-2 into the host cells. Herein, with the support of machine learning approaches, we report structure-based virtual screening as an effective strategy to discover PPIs inhibitors from ZINC database. The proposed computational protocol led to the identification of a promising scaffold which was selected for subsequent binding mode analysis and that can represent a useful starting point for the development of new treatments of the SARS-CoV-2 infection.
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Affiliation(s)
- Davide Pirolli
- Institute of Chemical Sciences and Technologies “Giulio Natta” (SCITEC) – CNRRome00168Italy
| | - Benedetta Righino
- Institute of Chemical Sciences and Technologies “Giulio Natta” (SCITEC) – CNRRome00168Italy
| | - Maria Cristina De Rosa
- Institute of Chemical Sciences and Technologies “Giulio Natta” (SCITEC) – CNRRome00168Italy
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