Acta Scientific Microbiology (ISSN: 2581-3226)

Research Article Volume 6 Issue 6

Molecular Docking - Study of Potential Cyclophilin-Dependent Mechanism of SARS-CoV-2 Viral Entry

Aneta Maria Molenda*

Department of Molecular Genetics, UK

*Corresponding Author: Aneta Maria Molenda, Department of Molecular Genetics, UK.

Received: April 27, 2023; Published: May 30, 2023

Abstract

Objectives: The aim of this article is to analyse interaction of the SARS-CoV2 fragments with cyclophilins and to validate the mechanism of the viral entry involving spike glycoprotein or membrane proteins.

Coronavirus Disease: COVID-19 is a disease caused by RNA virus that got potential to cause respiratory and intestinal illness in humans as well as animals. There are 7 different type of Coronavirus diseases (229E, NL63, OC43, HKU1, MERS-CoV, SARS-CoV, SARS-CoV-2) reported in humans that are known to cause illness ranging from common cold to more severe forms [1]. The epicentre of the COVID-19 disease was Wuhan city, Huban province of China where a cluster of unexplained pneumonia cases of unknown aetiology were officially reported on Dec 31 2019 [2]. Though Covid-19 has a lower mortality rate (2.3%) than SARS (9.5%) or MERS (34.4%) it is highly transmissible and has rapidly progressed from epidemic to pandemic scale [3].

 Keywords: SARS-CoV-2; Covid-19; Docking

References

    1. “Centers for Disease Control and Prevention”. Coronavirus (2020).
    2. World Health Organisation. “Pneumonia of unknown cause - China” (2020).
    3. Petrosillo., et al. “COVID-19, SARS and MERS: are they closely related?” Clinical Microbiology and Infection 26.6 (2020): 729-734.
    4. Li., et al. “Structure, function, and evolution of coronavirus spike proteins”. Annual Review of Virology 3 (2016): 237-261.
    5. Almehdi., et al. “SARS-CoV-2 spike protein: pathogenesis, vaccines, and potential therapies”. Infection 49.5 (2021): 855-876. 
    6. Fani M., et al. “Comparison of the COVID-2019 (SARS-CoV-2) pathogenesis with SARS-CoV and MERS-CoV infections”. Future Medicine Ltd Future Virology 15.5 (2020): 317-323.
    7. Huang., et al. “Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19”. Acta Pharmacologica Sinica 41 (2020): 1141-1149.
    8. Bianchi., et al. “Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics?” Hindawi BioMed Research International (2020): 6.
    9. Mahtarin., et al. “Structure and dynamics of membrane protein in SARS-CoV-2”. Journal of Biomolecular Structure and Dynamics (2020): 4725-4738.
    10. Neuman BW., et al. “A structural analysis of M protein in coronavirus assembly and morphology”. The Journal of Structural Biology 174 (2011): 11-22.
    11. Radzikowska., et al. “Distribution of ACE2, CD147, CD26, and other SARS‐CoV‐2 associated molecules in tissues and immune cells in health and in asthma, COPD, obesity, hypertension, and COVID‐19 risk factors”. Allergy 75.11 (2020): 2829-2845.
    12. Gur., et al. “Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states”. The Journal of Chemical Physics 153.7 (2020): 075101.
    13. Lan., et al. “Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor”. Nature 581.7807 (2020): 215-220.
    14. Kumari., et al. “Cyclophilins Proteins in search of function”. Plant Signaling and Behavior 8.1 (2013): e22734.
    15. Qu., et al. “The Roles of CD147 and/or Cyclophilin A in Kidney Diseases Review Article”. Hindawi Publishing Corporation Mediators of Inflammation (2014): 10.
    16. Chen., et al. “Function of HAb18G/CD147 in Invasion of Host Cells by Severe Acute Respiratory Syndrome Coronavirus”. The Journal of Infectious Diseases 191.5 (2005): 755-760.
    17. Parkinson., et al. “Dynamic data-driven meta-analysis for prioritisation of host genes implicated in COVID-19”. Scientific Report 10.1 (2020): 22303.
    18. Allain., et al. “Cyclophilin B Binding to Platelets Supports Calcium-Dependent Adhesion to Collagen”. Blood 94.3 (1999): 976-983.
    19. Allain., et al. “Interaction with glycosaminoglycans is required for cyclophilin B to trigger integrin-mediated adhesion of peripheral blood T lymphocytes to extracellular matrix”. Proceedings of the National Academy of Sciences (PNAS) of the United States of America 99.5 (2002): 2714-2719.
    20. Bukrinsky., et al. “Extracellular cyclophilins in health and disease”. Biochimica et Biophysica Acta General Subjects 1850.10 (2015): 2087-2095. 
    21. Hopkins., et al. “The role of immunophilins in viral infection”. Biochimica et Biophysica Acta General Subjects 1850.10 (2015): 2103-2110.
    22. Dawar., et al. “Cyclophilin A: A Key Factor in Virus Replication and Potential Target for Anti-viral Therapy”. Current Issues in Molecular Biology 21 (2017): 1-20.
    23. Wilde., et al. “Cyclophilins and cyclophilin inhibitors in nidovirus replication”. Virology 522 (2018): 46-55.
    24. Jean-Michel Pawlotsky. “COVID-19 Pandemic: Time to Revive the Cyclophilin Inhibitor Alisporivir”. Clinical Infectious Diseases® 71.16 (2020): 2191-2194.
    25. Ma., et al. “NIM811, a Cyclophilin Inhibitor, Exhibits Potent In Vitro Activity against Hepatitis C Virus Alone or in Combination with Alpha Interferon”. Antimicrobial Agents and Chemotherapy 50.9 (2006): 2976-2982.
    26. Pushkarsky., et al. “CD147 facilitates HIV‐1 infection by interacting with virus‐associated cyclophilin A”. Proceedings of the National Academy of Sciences (PNAS) of the United States of America 98 (2001): 6360-6365.
    27. Braaten., et al. “Cyclophilin A regulates HIV-1 infectivity, as demonstrated by gene targeting in human T cells”. The European Molecular Biology Organization (EMBO) Journal 20.6 (2001): 1300-1309.
    28. Watashi., et al. “Cyclophilin B is a functional regulator of hepatitis C virus RNA polymerase”. Molecular Cell 19.1 (2005): 111-122.
    29. Elfikya., et al. “Novel guanosine derivatives against MERS CoV polymerase: An in silico perspective”. Journal of Biomolecular Structure and Dynamics (2020): 1-9.
    30. Pfefferle., et al. “The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors”. The Public Library of Science (PLOS) Pathogens 7.10 (2011): e1002331.
    31. Sauerhering., et al. “Cyclophilin inhibitors restrict Middle East respiratory syndrome coronavirus via interferon-λ in vitro and in mice”. European Respiratory Journal 56 (2020): 1901826.
    32. Clausen., et al. “SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2”. Cell 183.4 (2020): 1043-1057.e15.
    33. Hao., et al. “Binding of the SARS-CoVCoV-2 Spike Protein to Glycans”. Science Bulletin (Beijing) 66.12 (2021): 1205-1214.
    34. Mycroft-West., et al. “The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 Receptor Binding Domain undergoes conformational change upon heparin binding”. Pre-print version posted April 29, (2020).
    35. Helal., et al. “Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia”. Journal of Biomolecular Structure and Dynamics (2020): 1-11.
    36. Wang., et al. “The cyclophilins”. Genome Biology 6.7 (2005): 226.
    37. Sekhon., et al. “Cyclophilin A-mediated mitigation of coronavirus SARS-CoV-2”. Bioengineering and Translational Medicine 8 (2023): e10436.
    38. Saphire., et al. “Host cyclophilin A mediates HIV-1 attachment to target cells via heparans”. The European Molecular Biology Organization (EMBO) Journal 18.23 (1991): 6771-6785.
    39. Pakula., et al. “Syndecan-1/CD147 association is essential for cyclophilin B-induced activation of p44/42 mitogen-activated protein kinases and promotion of cell adhesion and chemotaxis”. Glycobiology 17.5 (2007): 492-503.
    40. Prakash., et al. “Human Cyclophilin B forms part of a multi-protein complex during erythrocyte invasion by Plasmodium falciparum”. Nature Communications 8 (2017): 1548.
    41. Walls., et al. “Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein”. Cell 180 (2020): 281-292.
    42. Fehr., et al. “Coronaviruses: an overview of their replication and pathogenesis”. Methods in Molecular Biology 1282 (2015): 1-23.
    43. Vajda., et al. “New additions to the ClusPro server motivated by CAPRI”. Proteins: Structure, Function, and Bioinformatics 85.3 (2017): 435-444.  
    44. Kozakov., et al. “The ClusPro web server for protein-protein docking”. Nature Protocols 12.2 (2017): 255-278.
    45. Kozakov., et al. “How good is automated protein docking?” Proteins: Structure, Function, and Bioinformatics 81.12 (2013): 2159-2166.  
    46. Kong., et al. “COVID-19 Docking Server: An interactive server for docking small molecules, peptides and antibodies against potential targets of COVID-19”. Bioinformatics (2020): btaa645. 
    47. Kong., et al. “CoDockPP: a multistage approach for global and site-specific protein-protein docking”. Journal of Chemical Information and Modeling 59.8 (2019): 3556-3564. 
    48. Kong., et al. “Template‐based modeling and ab‐initio docking using CoDock in CAPRI”. Proteins-Structure Function and Bioinformatics 88.8 (2020): 1100-1109.
    49. Trott., et al. “AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading”. The Journal of Computational Chemistry 31 (2010): 455-461. 
    50. Li., et al. “Correcting the impact of docking pose generation error on binding affinity prediction”. BMC Bioinformatics 17 (2016): 308.
    51. Seizer., et al. “Extracellular cyclophilin A activates platelets via EMMPRIN (CD147) and PI3K/Akt signaling, which promotes platelet adhesion and thrombus formation in vitro and in vivo”. Arteriosclerosis, Thrombosis, and Vascular Biology 35 (2015): 655-663.
    52. Cao., et al. “Probing the formation, structure and free energy relationships of M protein dimers of SARS-CoV-2”. Computational and Structural Biotechnology Journal 20 (2022): 573-582.
    53. Neuman., et al. “A structural analysis of M protein in coronavirus assembly and morphology”. The Journal of Structural Biology 174.1 (2011): 11-22.

     

     

     

    Citation

    Citation: Aneta Maria Molenda. “Molecular Docking - Study of Potential Cyclophilin-Dependent Mechanism of SARS-CoV-2 Viral Entry". Acta Scientific Microbiology 6.6 (2023): 81-101.

    Copyright

    Copyright: © 2023 Aneta Maria Molenda. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.




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