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Title: | Molecular Docking of Bicycloproline Derivative Synthetic Compounds on Envelope Protein: Anti-SARS-CoV-2 Drug Discovery |
Authors: | Prayogi, Syaiful Asrining Dhiani, Binar Djaliasrin Djalil, Asmiyenti |
Keywords: | COVID-19, homology modeling, envelope protein, bicycloproline, molecular docking |
Issue Date: | 30-Apr-2023 |
Publisher: | Faculty of Pharmacy Univesrsitas Airlangga |
Abstract: | Abstract Background: Although a SARS-CoV-2 vaccine is readily available, new cases of COVID-19 are still occurring. New drug discovery is needed to treat COVID-19. Protein E is one of the potential targets. Two synthetic compounds of bicycloproline derivatives have the potential to be developed. Objective: This study aimed to estimate the interaction of bicycloproline compounds to protein E in-silico. Methods: There were two bicycloproline-derived compounds, MI-09 and MI-30, used in docking. Remdesivir was used as a reference ligand. The crystal structure of the E protein was created using homology modeling, while the test compound was drawn using the Marvin Sketch. MOE 2022.02 and BDS 2021 were used for docking and visualization processes. Results: The pentamer of the SARS-CoV-2 E protein obtained a clash score (1.06); poor rotatomer (0.00%); favored rotamers (98.11%); Ramachandran favored (96.43%); Ramachandran outlier (1.78%); Rama Z-score (-1.08); and mol probity (1.04). Research shows promising inhibition potential of the MI-09 and MI-30. The MI-30 has the best binding energy of -10.3326 kcal/mol. Conclusion: The docking results show that MI-30 has potency as an inhibitor of protein E and can be developed in treating COVID-19. Further research is needed to confirm the result by in vitro and in vivo studies. Keywords: Abstract Background: Although a SARS-CoV-2 vaccine is readily available, new cases of COVID-19 are still occurring. New drug discovery is needed to treat COVID-19. Protein E is one of the potential targets. Two synthetic compounds of bicycloproline derivatives have the potential to be developed. Objective: This study aimed to estimate the interaction of bicycloproline compounds to protein E in-silico. Methods: There were two bicycloproline-derived compounds, MI-09 and MI-30, used in docking. Remdesivir was used as a reference ligand. The crystal structure of the E protein was created using homology modeling, while the test compound was drawn using the Marvin Sketch. MOE 2022.02 and BDS 2021 were used for docking and visualization processes. Results: The pentamer of the SARS-CoV-2 E protein obtained a clash score (1.06); poor rotatomer (0.00%); favored rotamers (98.11%); Ramachandran favored (96.43%); Ramachandran outlier (1.78%); Rama Z-score (-1.08); and mol probity (1.04). Research shows promising inhibition potential of the MI-09 and MI-30. The MI-30 has the best binding energy of -10.3326 kcal/mol. Conclusion: The docking results show that MI-30 has potency as an inhibitor of protein E and can be developed in treating COVID-19. Further research is needed to confirm the result by in vitro and in vivo studies. Keywords: COVID-19, homology modeling, envelope protein, bicycloproline, molecular docking |
URI: | http://localhost:8080/xmlui/handle/123456789/7541 |
ISSN: | 25808303 |
Appears in Collections: | VOL 10 NO 1 2023 |
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