TY - JOUR
T1 - In silico antivirus repurposing and its modification to organoselenium compounds as sars-cov-2 spike inhibitors
AU - Huang, Manaman
AU - Saragih, Mutiara
AU - Tambunan, Usman Sumo Friend
N1 - Funding Information:
The authors are grateful to Directorate Research and Community Service, Universitas Indonesia through Hibah Publikasi Artikel di Jurnal Internasional Kuartil Q1 NKB-1376/UN2.RST/HKP.05.00/2020 for funding this research.
Publisher Copyright:
© 2023 Manaman Huang et al.
PY - 2023
Y1 - 2023
N2 - Background and Objective: The COVID-19, which has been circulating since late 2019, is caused by SARS-CoV-2. Because of its high infectivity, this virus has spread widely throughout the world. Spike glycoprotein is one of the proteins found in SARS-CoV-2. Spike glycoproteins directly affect infection by forming ACE-2 receptors on host cells. Inhibiting glycoprotein spikes could be one method of treating COVID-19. In this study, the antivirus marketed as a database will be repurposed into an antiviral SARS-CoV-2 and the selected compounds will be modified to become organoselenium compounds. Materials and Methods: The research was carried out using in silico methods, such as rigid docking and flexible docking. To obtain information about the interaction between spike glycoprotein and ligands, MOE 2014.09 was used to perform the molecular docking simulation. Results: The analysis of binding energy values was used to select the ten best ligands from the first stage of the molecular docking simulation, which was then modified according to the previous QSAR study to produce 96 new molecules. The second stage of molecular docking simulation was performed with modified molecules. The best-modified ligand was chosen by analyzing the ADME-Tox property, RMSD value and binding energy value. Conclusion: The best three unmodified ligands, Ombitasvir, Elbasvir and Ledipasvir, have a binding energy value of -15.8065, -15.3842 and -15.1255 kcal mol-1, respectively and the best three modified ligands ModL1, ModL2 and ModL3 has a binding value of -15.6716, -13.9489 and -13.2951 kcal mol-1, respectively with an RMSD value of 1.7109 Å, 2.3179 Å and 1.7836 Å.
AB - Background and Objective: The COVID-19, which has been circulating since late 2019, is caused by SARS-CoV-2. Because of its high infectivity, this virus has spread widely throughout the world. Spike glycoprotein is one of the proteins found in SARS-CoV-2. Spike glycoproteins directly affect infection by forming ACE-2 receptors on host cells. Inhibiting glycoprotein spikes could be one method of treating COVID-19. In this study, the antivirus marketed as a database will be repurposed into an antiviral SARS-CoV-2 and the selected compounds will be modified to become organoselenium compounds. Materials and Methods: The research was carried out using in silico methods, such as rigid docking and flexible docking. To obtain information about the interaction between spike glycoprotein and ligands, MOE 2014.09 was used to perform the molecular docking simulation. Results: The analysis of binding energy values was used to select the ten best ligands from the first stage of the molecular docking simulation, which was then modified according to the previous QSAR study to produce 96 new molecules. The second stage of molecular docking simulation was performed with modified molecules. The best-modified ligand was chosen by analyzing the ADME-Tox property, RMSD value and binding energy value. Conclusion: The best three unmodified ligands, Ombitasvir, Elbasvir and Ledipasvir, have a binding energy value of -15.8065, -15.3842 and -15.1255 kcal mol-1, respectively and the best three modified ligands ModL1, ModL2 and ModL3 has a binding value of -15.6716, -13.9489 and -13.2951 kcal mol-1, respectively with an RMSD value of 1.7109 Å, 2.3179 Å and 1.7836 Å.
KW - Antivirus
KW - Binding energy
KW - In silico
KW - Modification
KW - QSAR
KW - Repurposed
KW - Spike glycoprotein
UR - http://www.scopus.com/inward/record.url?scp=85160968824&partnerID=8YFLogxK
U2 - 10.3923/pjbs.2023.81.90
DO - 10.3923/pjbs.2023.81.90
M3 - Article
C2 - 37265039
AN - SCOPUS:85160968824
SN - 1028-8880
VL - 26
SP - 81
EP - 90
JO - Pakistan Journal of Biological Sciences
JF - Pakistan Journal of Biological Sciences
IS - 2
ER -