The effect of temperature on interaction and dynamical study of protease inhibitors as a SARS-CoV-2 potential drug

The development of drugs and vaccines to resolve the Coronavirus Disease (Covid-19) pandemic is still growing globally even the pandemic has been happening for more than a year. The easily spread nature of the virus makes antiviral drugs for Covid-19 challenging to develop. Therefore, the study abou...

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Bibliographic Details
Main Authors: Damayanti, Ayu Octa, Asy'ari, Mukhammad, Prasasty, Vivitri Dewi, Siahaan, Parsaoran
Format: Conference Proceeding
Language:English
Subjects:
Binding sites
Chymotrypsin
Coronaviruses
COVID-19
Drugs
Molecular docking
Molecular dynamics
Pandemics
Protease
Protease inhibitors
Proteins
Severe acute respiratory syndrome coronavirus 2
Temperature effects
Viral diseases
Viruses
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Summary:The development of drugs and vaccines to resolve the Coronavirus Disease (Covid-19) pandemic is still growing globally even the pandemic has been happening for more than a year. The easily spread nature of the virus makes antiviral drugs for Covid-19 challenging to develop. Therefore, the study about potential drugs for diseases at the molecular level is needed. From all potential protein targets in SARS-CoV-2, 3-Chymotrypsin like protease (3CLpro) is the most potential developed gene because it has 96% similarity identity with SARS-CoV. 3CLpro is the key to the viral polyprotein process that is synthesized by RNA after the virus is infected and makes the virus protein active, also has functions in the replication process. One of the suitable inhibitors is the HIV inhibitor, namely lopinavir, ritonavir, nelfinavir, and saquinavir. In this study, the binding sites and bond energies between SARS-CoV-2 and the 3CLpro inhibitor for drug potential are determined. In addition, a molecular dynamic simulation complex for drug potential in various temperature was also determined. The method is computational molecular mechanics that is divided into two steps, molecular docking and molecular dynamics. The analysis results show that all ligand complexes have the potential to be used as 3CLpro inhibitor compounds with saquinavir having the best value -9.38 kcal/mol for binding site energy and 0.1336 µm inhibition constant. The MD simulation results showed that the stability of the lopinavir, ritonavir, nelfinavir, and saquinavir complexes were different and sensitive to temperature changes.
ISSN:0094-243X
1551-7616
DOI:10.1063/5.0103742