365
Views
59
CrossRef citations to date
0
Altmetric
Original Research

Withanone from Withania somnifera Attenuates SARS-CoV-2 RBD and Host ACE2 Interactions to Rescue Spike Protein Induced Pathologies in Humanized Zebrafish Model

, , , , , & ORCID Icon show all
Pages 1111-1133 | Published online: 11 Mar 2021

References

  • LuH, StrattonCW, TangYW. Outbreak of pneumonia of unknown etiology in Wuhan, China: the mystery and the miracle. J Med Virol. 2020;92(4):401–402. doi:10.1002/jmv.2567831950516
  • GorbalenyaAE, BakerSC, BaricRS, et al. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020;5(4):536–544. doi:10.1038/s41564-020-0695-z32123347
  • NiW, YangX, YangD, et al. Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19. Crit Care. 2020;24(1):1–10. doi:10.1186/s13054-020-03120-031898531
  • WHO. Solidarity trial consortium. Repurposed antiviral drugs for COVID-19 – interim WHO SOLIDARITY trial results. medRxiv. 2020;(October 15). doi:10.1101/2020.10.15.20209817
  • BuppK, RothMJ. Alteration and analyses of viral entry with library-derived peptides. Adv Virus Res. 2005;65(5):147–172. doi:10.1016/S0065-3527(05)65005-116387196
  • DauB, HolodniyM. Novel targets for antiretroviral therapy: clinical progress to date. Drugs. 2009;69(1):31–50. doi:10.2165/00003495-200969010-0000319192935
  • AnandK, ZiebuhrJ, WadhwaniP, MestersJR, HilgenfeldR. Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science. 2003;300(5626):1763–1767. doi:10.1126/science.108565812746549
  • SangwanRS, ChaurasiyaND, MisraLN, et al. Phytochemical variability in commercial herbal products and preparations of Withania somnifera (Ashwagandha). Curr Sci. 2004;86(3):461–465.
  • ZamanW, SaqibS, UllahF, AyazA, YeJ. COVID-19: phylogenetic approaches may help in finding resources for natural cure. Phytother Res. 2020;34(11):2783–2785. doi:10.1002/ptr.678732648294
  • KambiziL, GoosenBM, TaylorMB, AfolayanAJ. Anti-viral effects of aqueous extracts of Aloe ferox and Withania somnifera on herpes simplex virus type 1 in cell culture. S Afr J Sci. 2007;103:(October):359–362.
  • CaiZ, ZhangG, TangB, LiuY, FuX, ZhangX. Promising anti-influenza properties of active constituent of Withania somnifera ayurvedic herb in targeting neuraminidase of H1N1 influenza: computational study. Cell Biochem Biophys. 2015;72(3):727–739. doi:10.1007/s12013-015-0524-925627548
  • BalkrishnaA, PokhrelS, SinghJ, VarshneyA. Withanone from Withania somnifera may inhibit novel coronavirus (COVID-19) entry by disrupting interactions between viral s-protein receptor binding domain and host ACE2 receptor. Res Sq. 2020. doi:10.21203/rs.3.rs-17806/v1
  • KumarV, DhanjalJK, KaulSC, WadhwaR, SundarD. Withanone and caffeic acid phenethyl ester are predicted to interact with main protease (Mpro) of SARS-CoV-2 and inhibit its activity. J Biomol Struct Dyn. 2020. doi:10.1080/07391102.2020.1772108
  • KumarV, DhanjalJK, BhargavaP, et al. Withanone and withaferin-A are predicted to interact with transmembrane protease serine 2 (TMPRSS2) and block entry of SARS-CoV-2 into cells. J Biomol Struct Dyn. 2020. doi:10.1080/07391102.2020.1775704
  • SudeepH. Molecular docking analysis of Withaferin A from Withania somnifera with the glucose regulated protein 78 (GRP78) in comparison with the COVID-19 main protease. Bioinformation. 2020;16(5):411–417. doi:10.6026/9732063001641132831523
  • CaseJB, RothlaufPW, ChenRE, et al. Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. SSRN Electron J. 2020. doi:10.2139/ssrn.3606354
  • BatlleD, WysockiJ, SatchellK. Soluble angiotensin-converting enzyme 2: a potential approach for coronavirus infection therapy? Clin Sci. 2020;134(5):543–545. doi:10.1042/CS20200163
  • InalJM. Decoy ACE2-expressing extracellular vesicles that competitively bind SARS-CoV-2 as a possible COVID-19 therapy. Clin Sci. 2020;134(12):1301–1304. doi:10.1042/CS20200623
  • WalterJD, HutterCAJ, ZimmermannI, et al. Sybodies targeting the SARS-CoV-2 receptor-binding domain. bioRxiv. 2020. doi:10.1101/2020.04.16.045419
  • KaulSC, IshidaY, TamuraK, et al. Novel methods to generate active ingredients-enriched Ashwagandha leaves and extracts. PLoS One. 2016;11(12):1–15. doi:10.1371/journal.pone.0166945
  • DuttaR, KhalilR, GreenR, MohapatraSS, MohapatraS. Withania somnifera (Ashwagandha) and withaferin a: potential in integrative oncology. Int J Mol Sci. 2019;20(21):21. doi:10.3390/ijms20215310
  • PiresN, GotaV, GuliaA, HingoraniL, AgarwalM, PuriA. Safety and pharmacokinetics of Withaferin-A in advanced stage high grade osteosarcoma: a Phase I trial. J Ayurveda Integr Med. 2020;11(1):68–72. doi:10.1016/j.jaim.2018.12.00830904387
  • BurgosJS, Ripoll-gomezJ, AlfaroJM, SastreI, ValdiviesoF. Zebrafish as a new model for herpes simplex virus type 1 infection. Zebrafish. 2008;5(4):323–333. doi:10.1089/zeb.2008.055219133831
  • CrimMJ, RileyLK. Viral diseases in zebrafish: what is known and unknown. ILAR J. 2012;53(2):135–143. doi:10.1093/ilar.53.2.13523382345
  • PressleyME, PhelanPE, WittenPE, MellonMT, KimCH. Pathogenesis and inflammatory response to Edwardsiella tarda infection in the zebrafish. Dev Comp Immunol. 2005;29(6):501–513. doi:10.1016/j.dci.2004.10.00715752547
  • DasCN, UniyalGC, LalP, et al. Analysis of withanolides in root and leaf of Withania somnifera by HPLC with photodiode array and evaporative light scattering detection. Phytochem Anal. 2008;19(2):148–154. doi:10.1002/pca.102917879227
  • PettersenEF, GoddardTD, HuangCC, et al. UCSF chimera - a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612. doi:10.1002/jcc.2008415264254
  • LuthyR, BowieJU, EisenbergD. Assessment of protein models with three-dimensional profiles. Nature. 1992;356(6364):83–85. doi:10.1038/356083a01538787
  • ColovosC, YeatesTO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 1993;2(9):1511–1519. doi:10.1002/pro.55600209168401235
  • LaskowskiRA, MacArthurMW, MossDS, ThorntonJM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993;26(2):283–291. doi:10.1107/s0021889892009944
  • LovellSC, DavisIW, AdrendallWB, et al. Structure validation by C alpha geom basic local alignment search tool. J Mol Biol. 2003;50(August2002):437–450. doi:10.1002/prot.10286
  • O’BoyleNM, BanckM, JamesCA, MorleyC, VandermeerschT, HutchisonGR. Open babel: an open chemical toolbox - 1758-2946-3-33.pdf. J Cheminform. 2011;3(33):1–14. doi:10.1186/1758-2946-3-3321214931
  • FukunishiY, NakamuraH. Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library. Protein Sci. 2011;20(1):95–106. doi:10.1002/pro.54021064162
  • GhersiD, SanchezR. Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites. Proteins. 2009;74(2):417–424. doi:10.1002/prot.2215418636505
  • DallakyanS, OlsonAJ. Small-molecule library screening by docking with PyRx. In: HempelJE, AlE, editors. Chemical Biology. Methods in Molecular Biology. Vol. 1263. New York, NY: Humana Press; 2015: 243–250. doi:10.1007/978-1-4939-2269-7_19.
  • Dassault. Dassault Systèmes BIOVIA, Discovery Studio 2017 R2 Client, Release 2017. San Diego: Dassault Systèmes; 2017.
  • DeLanoWL. Pymol: an open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr. 2002;40:82–92.
  • HumphreyW, DalkeA, TheoreticalKS. VMD: visual molecular dynamics. J Mol Graph. 1996;14(1):33–38. doi:10.1016/j.carbon.2017.07.0128744570
  • JoS, KimT, IyerVG, ImW. CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem. 2008;29(11):1859–1865. doi:10.1002/jcc18351591
  • PhillipsJC, BraunR, WangW, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26(16):1781–1802. doi:10.1002/jcc.2028916222654
  • HendschZS, TidorB. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 1994;3(2):211–226. doi:10.1002/pro.55600302068003958
  • LiL, LiC, SarkarS, et al. DelPhi: a comprehensive suite for DelPhi software and associated resources. BMC Biophys. 2012;5(1):9. doi:10.1186/2046-1682-5-922583952
  • SitkoffD, SharpKA, HonigB. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem. 1994;98(7):1978–1988. doi:10.1021/j100058a043
  • FogolariF, BrigoA, MolinariH. The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recognit. 2002;15(6):377–392. doi:10.1002/jmr.57712501158
  • AltmannSM, MellonMT, DistelDL, KimCH. Molecular and functional analysis of an interferon gene from the zebrafish, danio rerio. J Virol. 2003;77(3):1992–2002. doi:10.1128/JVI.77.3.199212525633
  • IgawaD, SakaiM, SavanR. An unexpected discovery of two interferon gamma-like genes along with interleukin (IL) −22 and −26 from teleost: IL-22 and −26 genes have been described for the first time outside mammals. Mol Immunol. 2006;43(7):999–1009. doi:10.1016/j.molimm.2005.05.00916005068
  • PraveenK, EvansDL, Jaso-friedmannL. Constitutive expression of tumor necrosis factor-alpha in cytotoxic cells of teleosts and its role in regulation of cell-mediated cytotoxicity. Mol Endocrinol. 2006;43:279–291. doi:10.1016/j.molimm.2005.01.012
  • SullivanC, KimCH. Zebrafish as a model for infectious disease and immune function. Fish Shellfish Immunol. 2008;25(4):341–350. doi:10.1016/j.fsi.2008.05.00518640057
  • VinayagamS, SattuK. SARS-CoV-2 and coagulation disorders in different organs. Life Sci. 2020;260:118431. doi:10.1016/j.lfs.2020.11843132946915
  • GiannisD, ZiogasIA, GianniP. Coagulation disorders in coronavirus infected patients: COVID-19, SARS- CoV-1, MERS-CoV and lessons from the past. J Clin Virol. 2020;127:104362. doi:10.1016/j.jcv.2020.10436232305883
  • CatanzaroM, FagianiF, RacchiM, CorsiniE, GovoniS, LanniC. Immune response in COVID-19: addressing a pharmacological challenge by targeting pathways triggered by SARS-CoV-2. Signal Transduct Target Ther. 2020;5(84):1–10. doi:10.1038/s41392-020-0191-132296011
  • SoleimaniM. Acute kidney injury in SARS-CoV-2 infection: direct effect of virus on kidney proximal tubule cells. Int J Mol Sci. 2020;21(3275):2–6. doi:10.3390/ijms21093275
  • PrabakaranP, GanJ, FengY, et al. Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody. J Biol Chem. 2006;281(23):15829–15836. doi:10.1074/jbc.M60069720016597622
  • LiF, LiW, FarzanM, HarrisonSC. Structural biology: structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science. 2005;309(5742):1864–1868. doi:10.1126/science.111648016166518
  • BarlowDJ, ThorntonJM. The distribution of charged groups in proteins. Biopolymers. 1986;25(9):1717–1733. doi:10.1002/bip.3602509133768483
  • XuD, LinSL, NussinovR. Protein binding versus protein folding: the role of hydrophilic bridges in protein associations. J Mol Biol. 1997;265(1):68–84. doi:10.1006/jmbi.1996.07128995525
  • NorelR, WolfsonHJ, NussinovR. Small molecule recognition: solid angles surface representation and molecular shape complementarity. Comb Chem High Throughput Screen. 1999;2(4):223–236.10469882
  • JinZ, DuX, XuY, et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020;582(7811):289–293. doi:10.1038/s41586-020-2223-y32272481
  • YangH, XieW, XueX, et al. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol. 2005;3:10. doi:10.1371/journal.pbio.0030324
  • Castro-AlvarezA, CostaAM, VilarrasaJ. The performance of several docking programs at reproducing protein-macrolide-like crystal structures. Molecules. 2017;22(1):1. doi:10.3390/molecules22010136
  • HamzaM, AliA, KhanS, et al. nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of Moringa oleifera and hydroxychloroquine. J Biomol Struct Dyn. 2020:1–11. doi:10.1080/07391102.2020.1778534.
  • HubbardS, DarmaniNA, ThrushGR, DeyD, BurnhamL. Zebrafish-encoded 3-O-sulfotransferase-3 isoform mediates herpes simplex virus type 1 entry and spread. Zebrafish. 2010;7(2):181–187. doi:10.1089/zeb.2009.062120441522
  • WuC, LiuY, YangY, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. 2020;10(5):766–788. doi:10.1016/j.apsb.2020.02.00832292689
  • GautretP, LagierJ-C, ParolaP, et al. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int J Antimicrob Agents. 2020;56(1):105949. doi:10.1016/j.ijantimicag.2020.10594932205204