eISSN: 1896-9151
ISSN: 1734-1922
Archives of Medical Science
Current issue Archive Manuscripts accepted About the journal Special issues Editorial board Abstracting and indexing Subscription Contact Instructions for authors Ethical standards and procedures
SCImago Journal & Country Rank
3/2020
vol. 16
 
Share:
Share:
more
 
 
COVID-19/SARS-CoV-2
abstract:
Research paper

State-of-the-art tools to identify druggable protein ligand of SARS-CoV-2

Sayed Abdul Azeez
1
,
Zahra Ghalib Alhashim
1, 2
,
Waad Mohammed Al Otaibi
1
,
Hind Saleh Alsuwat
1
,
Abdallah M. Ibrahim
1, 3
,
Noor B. Almandil
4
,
J. Francis Borgio
1, 5

1.
Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
2.
College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
3.
Department of Fundamentals of Nursing, College of Nursing, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
4.
Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
5.
Department of Epidemic Diseases Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
Arch Med Sci 2020; 16 (3): 497–507
Online publish date: 2020/03/27
View full text
Get citation
ENW
EndNote
BIB
JabRef, Mendeley
RIS
Papers, Reference Manager, RefWorks, Zotero
AMA
APA
Chicago
Harvard
MLA
Vancouver
 
Introduction
The SARS-CoV-2 (previously 2019-nCoV) outbreak in Wuhan, China and other parts of the world affects people and spreads coronavirus disease 2019 (COVID-19) through human-to-human contact, with a mortality rate of > 2%. There are no approved drugs or vaccines yet available against SARS-CoV-2.

Material and methods
State-of-the-art tools based on in-silico methods are a cost-effective initial approach for identifying appropriate ligands against SARS-CoV-2. The present study developed the 3D structure of the envelope and nucleocapsid phosphoprotein of SARS-CoV-2, and molecular docking analysis was done against various ligands.

Results
The highest log octanol/water partition coefficient, high number of hydrogen bond donors and acceptors, lowest non-bonded interaction energy between the receptor and the ligand, and high binding affinity were considered for the best ligand for the envelope (mycophenolic acid: log P = 3.00; ΔG = –10.2567 kcal/mol; pKi = 7.713 µM) and nucleocapsid phosphoprotein (1-[(2,4-dichlorophenyl)methyl]pyrazole-3,5-dicarboxylic acid: log P = 2.901; ΔG = –12.2112 kcal/mol; pKi = 7.885 µM) of SARS-CoV-2.

Conclusions
The study identifies the most potent compounds against the SARS-CoV-2 envelope and nucleocapsid phosphoprotein through state-of-the-art tools based on an in-silico approach. A combination of these two ligands could be the best option to consider for further detailed studies to develop a drug for treating patients infected with SARS-CoV-2, COVID-19.

keywords:

COVID-19, SARS-CoV-2, druggable protein, ligand, nucleocapsid phosphoprotein, molecular docking, envelope protein, phylogenetic tree

Quick links
© 2020 Termedia Sp. z o.o. All rights reserved.
Developed by Bentus.
PayU - płatności internetowe