Cs-GRP78 Recognition Site on Dengue Virus Envelope Protein: in silico perspective

References

• Badawi A , VelummailumR , RyooSGet al. Prevalence of chronic comorbidities in dengue fever and West Nile virus: a systematic review and meta-analysis. PLOS One13(7), e0200200 (2018).
   PubMed Web of Science ®Google Scholar
• Pierson TC , DiamondMS. The continued threat of emerging flaviviruses. Nat. Microbiol.5(6), 796–812 (2020).
   PubMed Web of Science ®Google Scholar
• Salles TS , daEncarnação Sá-Guimarães T , de AlvarengaESLet al. History, epidemiology and diagnostics of dengue in the American and Brazilian contexts: a review. Parasites & vectors11(1), 264 (2018).
   PubMedGoogle Scholar
• Colón-González FJ , SeweMO , TompkinsAMet al. Projecting the risk of mosquito-borne diseases in a warmer and more populated world: a multi-model, multi-scenario intercomparison modelling study. Lancet Plan. Health5(7), e404–e414 (2021).
   PubMedGoogle Scholar
• Guo C , ZhouZ , WenZet al. Global epidemiology of Dengue outbreaks in 1990–2015: a systematic review and meta-analysis. Frontiers in Cellular and Infection Microbiology7, 317 (2017).
   PubMed Web of Science ®Google Scholar
• Khan NU , DanishL , KhanHUet al. Prevalence of dengue virus serotypes in the 2017 outbreak in Peshawar, KP, Pakistan. J. Clin. Lab. Anal.34(9), e23371 (2020).
   PubMed Web of Science ®Google Scholar
• Senaratne UTN , MurugananthanK , SirisenaP , CarrJM , NoordeenF. Dengue virus co-infections with multiple serotypes do not result in a different clinical outcome compared to mono-infections. Epidemiol. Infect.148, e119 (2020).
   PubMed Web of Science ®Google Scholar
• Shrivastava S , TirakiD , DiwanAet al. Co-circulation of all the four dengue virus serotypes and detection of a novel clade of DENV-4 (genotype I) virus in Pune, India during 2016 season. PLOS One13(2), e0192672 (2018).
   PubMed Web of Science ®Google Scholar
• Sharmila PF , VanathyK , RajamaniB , KaliaperumalV , DhodapkarR. Emergence of dengue virus 4 as the predominant serotype during the outbreak of 2017 in South India. Indian Journal of Medical Microbiology37(3), 393–400 (2019).
   PubMed Web of Science ®Google Scholar
• Douglas KO , DuttaSK , MartinaB , AnfasaF , SamuelsTA , HilaireMG. Dengue fever and severe Dengue in Barbados, 2008-2016. Trop. Med. Infect. Dis.5(2), 68 (2020).
   PubMedGoogle Scholar
• Mwanyika GO , MboeraLEG , RugarabamuSet al. Circulation of dengue serotype 1 viruses during the 2019 outbreak in Dar es Salaam, Tanzania. Pathog. Glob. Health115(7–8), 467–475 (2021).
   PubMed Web of Science ®Google Scholar
• Nicholls CMR , SevvanaM , KuhnRJ. Structure-guided paradigm shifts in flavivirus assembly and maturation mechanisms. Adv. Virus Res.108, 33–83 (2020).
   PubMed Web of Science ®Google Scholar
• Norazharuddin H , LaiNS. Roles and prospects of Dengue virus non-structural proteins as antiviral targets: an easy digest. Malays J Med Sci25(5), 6–15 (2018).
   PubMedGoogle Scholar
• Sotcheff S , RouthA. Understanding Flavivirus capsid protein functions: the tip of the iceberg. Pathogens (Basel, Switzerland)9(1), 42 (2020).
   PubMed Web of Science ®Google Scholar
• Kellermann M , ScharteF , HenselM. Manipulation of host cell organelles by intracellular pathogens. Int. J. Mol. Sci.22(12), 6484 (2021).
   PubMed Web of Science ®Google Scholar
• Lescar J , SohS , LeeLT , VasudevanSG , KangC , LimSP. The Dengue virus replication complex: from RNA replication to protein–protein interactions to evasion of innate immunity. Adv. Exp. Med. Biol.1062, 115–129 (2018).
   PubMed Web of Science ®Google Scholar
• Plaszczyca A , ScaturroP , NeufeldtCJet al. A novel interaction between dengue virus nonstructural protein 1 and the NS4A-2K-4B precursor is required for viral RNA replication but not for formation of the membranous replication organelle. PLOS Pathog15(5), e1007736 (2019).
   PubMed Web of Science ®Google Scholar
• Zeidler JD , Fernandes-SiqueiraLO , BarbosaGM , DaPoian AT. Non-canonical roles of Dengue Virus non-structural proteins. Viruses9(3), 42 (2017).
   PubMed Web of Science ®Google Scholar
• Chen HR , LaiYC , YehTM. Dengue virus non-structural protein 1: a pathogenic factor, therapeutic target, and vaccine candidate. Journal of Biomedical Science25(1), 58 (2018).
   PubMedGoogle Scholar
• Glasner DR , Puerta-GuardoH , BeattyPR , HarrisE. The good, the bad, and the shocking: The multiple roles of Dengue virus nonstructural protein 1 in protection and pathogenesis. Annu. Rev. Virol.5(1), 227–253 (2018).
   PubMed Web of Science ®Google Scholar
• Slon Campos JL , MongkolsapayaJ , ScreatonGR. The immune response against flaviviruses. Nature immunology19(11), 1189–1198 (2018).
   PubMed Web of Science ®Google Scholar
• Uno N , RossTM. Dengue virus and the host innate immune response. Emerg. Microbes Infect.7(1), 167 (2018).
   PubMedGoogle Scholar
• Akiyama BM , GrahamME , ODonoghue Z , BeckhamJD , KieftJS. Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res.49(12), 7122–7138 (2021).
   PubMed Web of Science ®Google Scholar
• da Silva-Junior EF , de Araujo-JuniorJX. Peptide derivatives as inhibitors of NS2B-NS3 protease from Dengue, West Nile, and Zika flaviviruses. Bioorg. Med. Chem.27(18), 3963–3978 (2019).
   PubMed Web of Science ®Google Scholar
• Tay MYF , VasudevanSG. The transactions of NS3 and NS5 in flaviviral RNA replication. Adv. Exp. Med. Biol.1062, 147–163 (2018).
   PubMed Web of Science ®Google Scholar
• Wahaab A , MustafaBE , HameedMet al. Potential role of flavivirus NS2B-NS3 proteases in viral pathogenesis and anti-flavivirus drug discovery employing animal cells and models: a review. Viruses14(1), 44 (2022).
   Web of Science ®Google Scholar
• Tay MYF , VasudevanSG (Ed.) . The transactions of NS3 and NS5 in flaviviral RNA replication. In: Dengue and Zika: Control and Antiviral Treatment Strategies.HilgenfeldR ( Ed.). Springer, Singapore, 147–163 (2018).
   Google Scholar
• Wang S , ChanKWK , NaripoguKB , SwarbrickCMD , AaskovJ , VasudevanSG. Subgenomic RNA from Dengue virus Type 2 suppresses replication of Dengue virus genomes and interacts with virus-encoded NS3 and NS5 proteins. ACS Infect. Dis.6(3), 436–446 (2020).
   PubMed Web of Science ®Google Scholar
• Anasir MI , RamanathanB , PohCL. Structure-based design of antivirals against envelope glycoprotein of Dengue virus. Viruses12(4), 367 (2020).
   PubMed Web of Science ®Google Scholar
• Ngono AE , ShrestaS. Immune response to Dengue and Zika. Annu. Rev. Immunol.36, 279–308 (2018).
   PubMed Web of Science ®Google Scholar
• Newton ND , HardyJM , ModhiranNet al. The structure of an infectious immature flavivirus redefines viral architecture and maturation. Sci Adv7(20), eabe4507 (2021).
   PubMed Web of Science ®Google Scholar
• Nicholls CMR , SevvanaM , KuhnRJ. Chapter Two - Structure-guided paradigm shifts in flavivirus assembly and maturation mechanisms. In: Advances in virus research.KielianM, MettenleiterTC, RoossinckMJ ( Eds). Academic Press, 33–83 (2020).
   Google Scholar
• Bhardwaj T , SaumyaKU , KumarPet al. Japanese encephalitis virus – exploring the dark proteome and disorder-function paradigm. FEBS J.287(17), 3751–3776 (2020).
   PubMed Web of Science ®Google Scholar
• van Leur SW , HeunisT , MunnurD , SanyalS. Pathogenesis and virulence of flavivirus infections. Virulence12(1), 2814–2838 (2021).
   PubMed Web of Science ®Google Scholar
• Ibrahim IM , AbdelmalekDH , ElfikyAA. GRP78: a cell's response to stress. Life Sci.226, 156–163 (2019).
   PubMed Web of Science ®Google Scholar
• Gonzalez-Gronow M , GopalU , AustinRC , PizzoSV. Glucose-regulated protein (GRP78) is an important cell surface receptor for viral invasion, cancers, and neurological disorders. IUBMB Life73(6), 843–854 (2021).
   PubMed Web of Science ®Google Scholar
• Gurusinghe K , MishraA , MishraS. Glucose-regulated protein 78 substrate-binding domain alters its conformation upon EGCG inhibitor binding to nucleotide-binding domain: molecular dynamics studies. Sci. Rep.8(1), 5487 (2018).
   PubMedGoogle Scholar
• Elfiky AA , BaghdadyAM , AliSA , AhmedMI. GRP78 targeting: hitting two birds with a stone. Life Sci.260, DOI:10.1016/j.lfs.2020.118317 (2020).
   PubMed Web of Science ®Google Scholar
• da Silva DC , ValentaoP , AndradePB , PereiraDM. Endoplasmic reticulum stress signaling in cancer and neurodegenerative disorders: tools and strategies to understand its complexity. Pharmacol. Res.155, DOI:10.1016/j.phrs.2020.104702 (2020).
   PubMed Web of Science ®Google Scholar
• Farshbaf M , KhosroushahiAY , Mojarad-JabaliS , ZarebkohanA , ValizadehH , WalkerPR. Cell surface GRP78: an emerging imaging marker and therapeutic target for cancer. J. Control Release328, 932–941 (2020).
   PubMed Web of Science ®Google Scholar
• Hernandez I , CohenM. Linking cell-surface GRP78 to cancer: from basic research to clinical value of GRP78 antibodies. Cancer Lett.524, 1–14 (2022).
   PubMed Web of Science ®Google Scholar
• Mustapha S , MohammedM , AzemiAKet al. Potential roles of endoplasmic reticulum stress and cellular proteins implicated in diabesity. Oxid. Med. Cell. Longev.2021, DOI:10.1155/2021/8830880 (2021).
   PubMed Web of Science ®Google Scholar
• Zhang LH , ZhangX. Roles of GRP78 in physiology and cancer. J. Cell. Biochem.110(6), 1299–1305 (2010).
   PubMed Web of Science ®Google Scholar
• Elfiky AA , IbrahimIM. Zika virus envelope - heat shock protein A5 (GRP78) binding site prediction. J. Biomol. Struct. Dyn.39(14), 5248–5260 (2021).
   PubMed Web of Science ®Google Scholar
• Nassar A , IbrahimIM , AminFGet al. A review of human coronaviruses' receptors: the host-cell targets for the crown bearing viruses. Molecules26(21), 6455 (2021).
   PubMed Web of Science ®Google Scholar
• Ibrahim IM , ElfikyAA , ElgoharyAM. Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. Biochem. Biophys. Res. Commun.562, 89–93 (2021).
   PubMed Web of Science ®Google Scholar
• Elgohary AM , ElfikyAA , BarakatK. GRP78: a possible relationship of COVID-19 and the mucormycosis; in silico perspective. Comput. Biol. Med.139, DOI:10.1016/j.compbiomed.2021.104956 (2021).
   PubMed Web of Science ®Google Scholar
• Elshemey WM , ElfikyAA , IbrahimIM , ElgoharyAM. Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective. Comput. Biol. Med.145, DOI:10.1016/j.compbiomed.2022.105478 (2022).
   PubMed Web of Science ®Google Scholar
• Elfiky AA , IbrahimIM , ElgoharyAM. SARS-CoV-2 Delta variant is recognized through GRP78 host-cell surface receptor, in silico perspective. Int. J. Peptide Res. Ther.28(5), 146 (2022).
   PubMed Web of Science ®Google Scholar
• Sussman JL , LinD , JiangJet al. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr. D. Biol. Crystallogr.54(Pt 6 Pt 1), 1078–1084 (1998).
   PubMedGoogle Scholar
• Rauf MA , ZubairS , AzharA. Ligand docking and binding site analysis with pymol and autodock/vina. International Journal of Basic and Applied Sciences4(2), 168 (2015).
   Google Scholar
• Robert X , GouetP. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res.42(Web Server issue), W320–324 (2014).
   PubMed Web of Science ®Google Scholar
• Sievers F , WilmA , DineenDet al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol.7(1), 539 (2011).
   PubMed Web of Science ®Google Scholar
• Gasteiger E , HooglandC , GattikerAet al. Protein identification and analysis tools on the ExPASy server. In: The Proteomics Protocols Handbook.WalkerJM ( Ed.). Humana Press, Totowa, NJ, 571–607 (2005).
   Google Scholar
• Kyte J , DoolittleRF. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol.157(1), 105–132 (1982).
   PubMed Web of Science ®Google Scholar
• van Zundert GCP , RodriguesJ , TrelletMet al. The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J. Mol. Biol.428(4), 720–725 (2016).
   PubMed Web of Science ®Google Scholar
• de Vries SJ , van DijkM , BonvinAMJJ. The HADDOCK web server for data-driven biomolecular docking. Nature Protocols5(5), 883–897 (2010).
   PubMed Web of Science ®Google Scholar
• Xue LC , RodriguesJP , KastritisPL , BonvinAM , VangoneA. PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics32(23), 3676–3678 (2016).
   PubMed Web of Science ®Google Scholar
• Adasme MF , LinnemannKL , BolzSNet al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucleic Acids Res.49(W1), W530–W534 (2021).
   PubMed Web of Science ®Google Scholar
• Salentin S , SchreiberS , HauptVJ , AdasmeMF , SchroederM. PLIP: fully automated protein–ligand interaction profiler. Nucleic Acids Res.43(W1), W443–W447 (2015).
   PubMed Web of Science ®Google Scholar
• Yoneda Y , SteinigerSC , CapkovaKet al. A cell-penetrating peptidic GRP78 ligand for tumor cell-specific prodrug therapy. Bioorg. Med. Chem. Lett.18(5), 1632–1636 (2008).
   PubMed Web of Science ®Google Scholar
• Liu Y , SteinigerSC , KimY , KaufmannGF , Felding-HabermannB , JandaKD. Mechanistic studies of a peptidic GRP78 ligand for cancer cell-specific drug delivery. Mol. Pharm.4(3), 435–447 (2007).
   PubMed Web of Science ®Google Scholar