DOI: https://doi.org/10.14710/jbtr.v6i2.7590

In silico Identification of Characteristics Spike Glycoprotein of SARS-CoV-2 in the Development Novel Candidates for COVID-19 Infectious Diseases

Universitas Islam Bandung, Indonesia

Received: 19 Mar 2020; Revised: 21 Jul 2020; Accepted: 14 Aug 2020; Available online: 31 Aug 2020; Published: 31 Aug 2020.
Open Access Copyright (c) 2020 Journal of Biomedicine and Translational Research

Citation Format:
Abstract

Background: The emergence of infectious diseases caused by SARS-CoV-2 has resulted in more than 90,000 infections and 3,000 deaths. The coronavirus spike glycoprotein encourages the entry of SARS-CoV-2 into cells and is the main target of antivirals. SARS-CoV-2 uses ACE2 to enter cells with an affinity similar to SARS-CoV, correlated with the efficient spread of SARS-CoV-2 among humans.

Objective: In the research, identification, evaluation, and exploration of the structure of SARS-CoV and SARS-CoV-2 spike glycoprotein macromolecules and their effects on Angiotensin-Converting Enzyme 2 (ACE-2) using in silico studies.

Methods: The spike glycoproteins of the two coronaviruses were prepared using the BIOVIA Discovery Studio 2020. Further identification of the three-dimensional structure and sequencing of the macromolecular spike glycoprotein structure using Chimera 1.14 and Notepad++. To ensure the affinity and molecular interactions between the SARS-CoV and SARS-CoV-2 spike glycoproteins against ACE-2 protein-protein docking simulations using PatchDock was accomplished. The results of the simulations were verified using the BIOVIA Discovery Studio 2020.

Results: Based on the results of the identification of the macromolecular structure of the spike glycoprotein, it was found that there are some similarities in characteristics between SARS-CoV and SARS-CoV-2. Protein-protein docking simulations resulted that SARS-COV-2 spike glycoprotein has the strongest bond with ACE-2, with an ACE score of −1509.13 kJ/mol.

Conclusion: Therefore, some information obtained from the results of this research can be used as a reference in the development of SARS-CoV-2 spike glycoprotein inhibitor candidates for the treatment of infectious diseases of COVID-19.

Note: This article has supplementary file(s).

Fulltext View|Download |  Research Instrument
Letter to the Editor
Subject
Type Research Instrument
  Download (49KB)    Indexing metadata
 Copyright Transfer Agreement
Copyright Transfer Agreement
Subject Copyright Transfer Agreement
Type Copyright Transfer Agreement
  Download (68KB)    Indexing metadata
Keywords: COVID-19; SARS-CoV-2; spike glycoprotein; ACE-2; in silico study

Article Metrics:

Article Info
Section: Original Research Articles
Language : EN
Recent articles
In silico Identification of Characteristics Spike Glycoprotein of SARS-CoV-2 in the Development Novel Candidates for COVID-19 Infectious Diseases Optimizing Real-Time PCR methods for detection of ssaN gene Salmonella enterica subsp.enterica in the blood specimen Effect of Metformin on Bcl-2/Bax Expression Ratio and Endometrial Implants: A Mouse Model in Endometriosis Study A Rare Case of 18-year-old female with Primary Sclerosing Cholangitis, Mixed Connective Tissue Disease, Short Stature Knowing When and How to Fight: COVID-19 Between Viral Clearance and Immune Tolerance More recent articles
  1. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA, 2012. Isolation of a novel coronavirus from a man with pneumonia in
  2. Saudi Arabia, The New England Journal of Medicine, 367, (19), 1814-1820
  3. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al, 2020. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China, Lancet, 395, (10223), 497-506
  4. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al, 2020. A Novel Coronavirus from Patients with Pneumonia in China, 2019, The New England Journal of Medicine, 382, (8), 727-733
  5. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al, 2020. A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, 579, 270-273
  6. Haagmans BL, Al Dhahiry SH, Reusken CB, Raj VS, Galiano M, Myers R, et al, 2014. Middle-East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation, Lancet Infectious Disease, 14, (2), 140-145
  7. Memish ZA, Mishra N, Olival KJ, Fagbo SF, Kapoor V, Epstein JH, et al, 2013. Middle-East respiratory syndrome coronavirus in bats, Saudi Arabia, Emerging Infectious Diseases, 19, (11), 1819-1823
  8. Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, et al, 2013. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor, Nature, 503, (7477), 535-538
  9. Hu B, Zeng LP, Yang XL, Ge XY, Zhang W, Li B, et al, 2017. Discovery of a rich gene pool of bat SARSrelated coronaviruses provides new insights into the origin of SARS coronavirus, PLOS Pathogens, 13, (11), e1006698
  10. Xiong X, Tortorici MA, Snijder J, Yoshioka C, Walls AC, Li W, et al, 2018. Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections, Journal of Virology, 92, (4), e01628-17
  11. Yang Y, Du L, Liu C, Wang L, Ma C, Tang J, et al, 2014. Receptor usage and cell entry of bat coronavirus HKU4 provide insight into bat-to-human transmission of MERS coronavirus, Proceedings of the National Academy of Sciences of the United States of America, 111, (34), 12516-12521
  12. Yang XL, Hu B, Wang B, Wang MN, Zhang Q, Zhang W, et al, 2015. Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus, Journal of Virology, 90, (6), 3253-3256
  13. Yang Y, Liu C, Du L, Jiang S, Shi Z, Baric RS, et al, 2015. Two Mutations Were Critical for Bat-to-Human Transmission of Middle East Respiratory Syndrome Coronavirus, Journal of Virology, 89, (17), 9119-9123
  14. Graham RL, Becker MM, Eckerle LD, Bolles M, Denison MR, Baric RS, 2020. A live, impaired-fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal disease, Nature Medicine, 18, (12), 1820-1826
  15. Ng OW, Chia A, Tan AT, Jadi RS, Leong HN, Bertoletti A, et al, 2016. Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection, Vaccine, 34, (17), 2008-2014
  16. Liu WJ, Zhao M, Liu K, Xu K, Wong G, Tan W, et al, 2017. T-cell immunity of SARS-CoV: Implications for vaccine development against MERS-CoV, Antiviral Research, 137, 82-92
  17. Kumar S, Maurya VK, Prasad AK, Bhatt MLB, Saxena SK, 2020. Structural, glycosylation and antigenic variation between 2019 novel coronavirus (2019-nCoV) and SARS coronavirus (SARS-CoV), Virusdisease, 31, (3), 13-21
  18. Hwang WC, Lin Y, Santelli E, Sui J, Jaroszewski L, Stec B, et al, 2006. Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R, The Journal of Biological Chemistry, 281, (45), 34610-34616
  19. Shang J, Ye G, Shi K, Wan Y, Luo C, Aihara H, et al, 2020. Structural basis of receptor recognition by SARS-CoV-2, Nature
  20. Dassault Systemes BIOVIA, Discovery Studio Modeling Environment, Release 2020, Dassault Systemes: San Diego, CA, USA
  21. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE, 2006. Tools for Integrated Sequence-Structure Analysis with UCSF Chimera, BMC Bioinformatics, 7, 339
  22. Li F, Li W, Farzan M, Harrison SC, 2005. Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor, Science, 309, (5742), 1864-1868
  23. Prabhu DS, Rajeswari VD, 2016. In silico docking analysis of bioactive compounds from Chinese medicine Jinqi Jiangtang Tablet (JQJTT) using Patch Dock, Journal of Chemical and Pharmaceutical Research, 5, (8), 15-21

Last update:

No citation recorded.

Last update:

No citation recorded.