How to cite this paper
Salah, M., Abdallaoui, O., Zeroual, A., Acharjee, N & idrissi, M. (2024). Insight into a new discovery of SARS-CoV-2 inhibitor activated through Chloroquine derivatives.Current Chemistry Letters, 13(1), 49-60.
Refrences
1. Achan, J., Talisuna, A. O., Erhart, A., Yeka, A., Tibenderana, J. K., Baliraine, F. N., et al. (2011) Quinine, an old anti-malarial drug in a modern world: role in the treatment of malaria. Malar J. 10, 144. DOI: 10.1186/1475-2875-10-144.
2. Magdalini A., Julija M., Enrico P., John H. (2022) The Coronavirus pandemic – 2022: Viruses, variants and vaccines. Cytokine Growth Factor Rev., 36, 1-9. DOI: 10.1016/j.cytogfr.2022.02.002.
3. Erikstrup, C., Hother, C. E., Pedersen, O. B. V., Mølbak, K., Skov, R. L., Holm, D. K., et al. (2020). Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors. Clin. Infect. Dis, 27, 249-253. DOI: 10.1093/cid/ciaa849.
4. Chen, Y., Shen, T., Zhong, L., Liu, Z., Dong, X., Huang, T., ... & Xiao, H. (2020). Research progress of chloroquine and hydroxychloroquine on the COVID-19 and their potential risks in clinic use. Front. Pharmacol, 11, 1167.
5. ul Qamar, M. T., Alqahtani, S. M., Alamri, M. A., & Chen, L. L. (2020). Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J. Pharm. Anal., 10(4), 313-319.
6. Anand K., Ziebuhr J., Wadhwani P., & Mesters JR. (2014) Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs. Hilgenfeld. Science (New York, N.Y.), 300 (5626), 1763–1767. DOI: 10.1126/science.1085658.
7. Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., ... & Rao, Z. (2003) The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proceedings of the National Academy of Sciences, 100(23), 13190-13195.
8. Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., ... & Bolton, E. E. (2019) PubChem 2019 update: improved access to chemical data. Nucleic Acids Res., 47(D1), D1102-D1109. DOI: 10.1093/nar/gky1033.
9. Duan, J., Dixon, S. L., Lowrie, J. F., & Sherman, W. (2010). Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods. J. Mol. Graph Model, 29(2), 157-170.
10. Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., ... & Yang, H. (2020) Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289-293.
11. DOI: 10.1038/s41586-020-2223-y.
12. Yuan M., Wu NC., Zhu X., et al., (2020) A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. Science, 368, 630–633. DOI: 10.1126/science.abb7269.
13. Osipiuk J., Jedrzejczak R., Tesar C., Endres M., Stols L., Babnigg G., Kim Y., Michalska K., Joachimiak A., (2020) The crystal structure of papain-like protease of SARS CoV-2. Worldwide PDB Protein Data Bank, 01, 1–14. DOI: 10.2210/pdb6w9c/pdb.
14. Burley SK., Berman HM., Christie C., Duarte JM., Feng Z., Westbrook J. (2018) RCSB Protein Data Bank: sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. Protein Sci, 27(1), 316–330. DOI :10.1002/pro.3331
15. MJ. Vincent, E. Bergeron, S. Benjannet, et al., (2005) Chloroquine is a potent inhibitor of SARS coronavirus infection and spread.Virol. J, 2, 69. DOI: 10.1186/1743-422X-2-69.
16. He, Z., Chen, L., You, J., Qin, L., & Chen, X. (2009). Antiretroviral protease inhibitors potentiate chloroquine antimalarial activity in malaria parasites by regulating intracellular glutathione metabolism. Exp. Par., 123(2), 122-127. DOI: 10.1016/j.exppara.2009.06.008.
17. Sastry GM., Adzhigirey M., Sherman W., (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of computer-aidedmolecular design, 27 (3), 221–234. DOI: 10.1007/s10822-013-9644-8.
18. Zhang L., Lin D., Sun X., et al. (2020) Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors Science (New York, N.Y.) 368, 6489, 409–412. https://doi. org/10.1126/science.abb3405.
19. Arya R., Das A., Prashar V., Kumar M., (2020) Potential inhibitors against papain-like protease of novel coronavirus (SARS-CoV-2) from FDA approved drugs. J. Biological and Medicinal Chemistry. DOI: 10.26434/chemrxiv.11860011.v1.
20. Shang J., Ye G., Shi K., et al, (2020) Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221–224. DOI: 10.1038/s41586-020-2179-y.
21. Kim S., Thiessen PA., Bolton EE., et al, (2016) PubChem Substance and Compound databases Nucleicacids research, 44, D1202-13. DOI: 10.1093/nar/gkv951.
22. Genheden S., Ryde U., (2015) The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery 10(5), 449–461. DOI: 10.1517/17460441.2015.1032936.
23. Wang J., Morin P., Wang W., Kollman PA., (2001) Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA. J Am Chem Soc, 123(22), 5221–5230. DOI: 10.1021/ja003834q.
24. Hou T., Wang J., Li Y., Wang W., (2011) Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations, J. Chem Inf Model, 51(1), 69–82. DOI: 10.1021/ci100275a.
25. Sitkoff D., Sharp KA., Honig B., (1994) Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys Chem, 98(7), 1978–1988. DOI: 10.1021/j100058a043.
26. Wang J., Hou T., (2012) Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations, J. Chem Inf Model, 52(5), 1199–1212 (2012). DOI: 10.1021/ci300064d.
27. Turner P. J. C. f. C., (2005) Land-Margin Research, and Technology, B., OR. XMGRACE, Version 5.1. 19.
28. Lipinski CA., Lombardo F., Dominy BW., Feeney PJ., (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Advanced Drug Delivery Reviews, 23, 3–25. DOI: 10.1016/S0169-409X(96)00423-1.
29. Ibrahim IM., Abdelmalek DH., Elshahat ME., Elfiky AA., (2020) COVID-19 spike-host cell receptor GRP78 binding site prediction, Journal of infection, 80(5),554–562. DOI: 10.1016/j.jinf.2020.02.026.
30. Mcclain CB., Vabret N., (2020) SARS-CoV-2: the many pros of targeting PLpro, Signal Transduction and Targeted Therapy, 5(1), 223. DOI: 10.1038/s41392-020-00335-z.
31. Rut W., Lv Z., Zmudzinski M., et al., (2020) Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design, Science Advances, 6(42). DOI: 10.1126/sciadv.abd4596.
32. V. Gramany, FI. Khan, A. Govender, et al. (2016) Cloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus, J. Biomolecular Structure and Dynamics, 34(8), 1681–1692. DOI: 10.1080/07391102.2015.1089186.
33. Beg A., Khan FI., Lobb KA. , et al., (2019) High throughput screening, docking, and molecular dynamics studies to identify potential inhibitors of human calcium/calmodulin-dependent protein kinase IV, J. Biomolecular Structure and Dynamics, 37(8), 2179–2192. DOI: 10.1080/07391102.2018.1479310.
34. Shubham S., Pakhuri M., Omprakash S., et al., (2019) Computationally guided identification of Akt-3, a serine/threonine kinase inhibitors: Insights from homology modelling, structure-based screening, molecular dynamics and quantum mechanical calculations, J. biomolecular structure and dynamics, 38(14), 4179–4188. DOI: 10.1080/07391102.2019.1675536.
35. Islam R., Parves R., Paul AS., et al., (2020) A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2, J. biomolecular structure and dynamics, 39(9), 3213–3224. DOI: 10.1080/07391102.2020.1761883.
36. Cruz Jorddy N., Costa F. S., José Khayat S., Kuca A., Barros A. L. , Carlos Neto A. M. J. C, (2019) Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13, J. Biomol. Struct. Dyn., 37(6), 1616–1627. DOI: 10.1080/07391102.2018.1462734.
2. Magdalini A., Julija M., Enrico P., John H. (2022) The Coronavirus pandemic – 2022: Viruses, variants and vaccines. Cytokine Growth Factor Rev., 36, 1-9. DOI: 10.1016/j.cytogfr.2022.02.002.
3. Erikstrup, C., Hother, C. E., Pedersen, O. B. V., Mølbak, K., Skov, R. L., Holm, D. K., et al. (2020). Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors. Clin. Infect. Dis, 27, 249-253. DOI: 10.1093/cid/ciaa849.
4. Chen, Y., Shen, T., Zhong, L., Liu, Z., Dong, X., Huang, T., ... & Xiao, H. (2020). Research progress of chloroquine and hydroxychloroquine on the COVID-19 and their potential risks in clinic use. Front. Pharmacol, 11, 1167.
5. ul Qamar, M. T., Alqahtani, S. M., Alamri, M. A., & Chen, L. L. (2020). Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J. Pharm. Anal., 10(4), 313-319.
6. Anand K., Ziebuhr J., Wadhwani P., & Mesters JR. (2014) Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs. Hilgenfeld. Science (New York, N.Y.), 300 (5626), 1763–1767. DOI: 10.1126/science.1085658.
7. Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., ... & Rao, Z. (2003) The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proceedings of the National Academy of Sciences, 100(23), 13190-13195.
8. Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., ... & Bolton, E. E. (2019) PubChem 2019 update: improved access to chemical data. Nucleic Acids Res., 47(D1), D1102-D1109. DOI: 10.1093/nar/gky1033.
9. Duan, J., Dixon, S. L., Lowrie, J. F., & Sherman, W. (2010). Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods. J. Mol. Graph Model, 29(2), 157-170.
10. Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., ... & Yang, H. (2020) Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289-293.
11. DOI: 10.1038/s41586-020-2223-y.
12. Yuan M., Wu NC., Zhu X., et al., (2020) A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. Science, 368, 630–633. DOI: 10.1126/science.abb7269.
13. Osipiuk J., Jedrzejczak R., Tesar C., Endres M., Stols L., Babnigg G., Kim Y., Michalska K., Joachimiak A., (2020) The crystal structure of papain-like protease of SARS CoV-2. Worldwide PDB Protein Data Bank, 01, 1–14. DOI: 10.2210/pdb6w9c/pdb.
14. Burley SK., Berman HM., Christie C., Duarte JM., Feng Z., Westbrook J. (2018) RCSB Protein Data Bank: sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. Protein Sci, 27(1), 316–330. DOI :10.1002/pro.3331
15. MJ. Vincent, E. Bergeron, S. Benjannet, et al., (2005) Chloroquine is a potent inhibitor of SARS coronavirus infection and spread.Virol. J, 2, 69. DOI: 10.1186/1743-422X-2-69.
16. He, Z., Chen, L., You, J., Qin, L., & Chen, X. (2009). Antiretroviral protease inhibitors potentiate chloroquine antimalarial activity in malaria parasites by regulating intracellular glutathione metabolism. Exp. Par., 123(2), 122-127. DOI: 10.1016/j.exppara.2009.06.008.
17. Sastry GM., Adzhigirey M., Sherman W., (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of computer-aidedmolecular design, 27 (3), 221–234. DOI: 10.1007/s10822-013-9644-8.
18. Zhang L., Lin D., Sun X., et al. (2020) Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors Science (New York, N.Y.) 368, 6489, 409–412. https://doi. org/10.1126/science.abb3405.
19. Arya R., Das A., Prashar V., Kumar M., (2020) Potential inhibitors against papain-like protease of novel coronavirus (SARS-CoV-2) from FDA approved drugs. J. Biological and Medicinal Chemistry. DOI: 10.26434/chemrxiv.11860011.v1.
20. Shang J., Ye G., Shi K., et al, (2020) Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221–224. DOI: 10.1038/s41586-020-2179-y.
21. Kim S., Thiessen PA., Bolton EE., et al, (2016) PubChem Substance and Compound databases Nucleicacids research, 44, D1202-13. DOI: 10.1093/nar/gkv951.
22. Genheden S., Ryde U., (2015) The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery 10(5), 449–461. DOI: 10.1517/17460441.2015.1032936.
23. Wang J., Morin P., Wang W., Kollman PA., (2001) Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA. J Am Chem Soc, 123(22), 5221–5230. DOI: 10.1021/ja003834q.
24. Hou T., Wang J., Li Y., Wang W., (2011) Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations, J. Chem Inf Model, 51(1), 69–82. DOI: 10.1021/ci100275a.
25. Sitkoff D., Sharp KA., Honig B., (1994) Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys Chem, 98(7), 1978–1988. DOI: 10.1021/j100058a043.
26. Wang J., Hou T., (2012) Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations, J. Chem Inf Model, 52(5), 1199–1212 (2012). DOI: 10.1021/ci300064d.
27. Turner P. J. C. f. C., (2005) Land-Margin Research, and Technology, B., OR. XMGRACE, Version 5.1. 19.
28. Lipinski CA., Lombardo F., Dominy BW., Feeney PJ., (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Advanced Drug Delivery Reviews, 23, 3–25. DOI: 10.1016/S0169-409X(96)00423-1.
29. Ibrahim IM., Abdelmalek DH., Elshahat ME., Elfiky AA., (2020) COVID-19 spike-host cell receptor GRP78 binding site prediction, Journal of infection, 80(5),554–562. DOI: 10.1016/j.jinf.2020.02.026.
30. Mcclain CB., Vabret N., (2020) SARS-CoV-2: the many pros of targeting PLpro, Signal Transduction and Targeted Therapy, 5(1), 223. DOI: 10.1038/s41392-020-00335-z.
31. Rut W., Lv Z., Zmudzinski M., et al., (2020) Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design, Science Advances, 6(42). DOI: 10.1126/sciadv.abd4596.
32. V. Gramany, FI. Khan, A. Govender, et al. (2016) Cloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus, J. Biomolecular Structure and Dynamics, 34(8), 1681–1692. DOI: 10.1080/07391102.2015.1089186.
33. Beg A., Khan FI., Lobb KA. , et al., (2019) High throughput screening, docking, and molecular dynamics studies to identify potential inhibitors of human calcium/calmodulin-dependent protein kinase IV, J. Biomolecular Structure and Dynamics, 37(8), 2179–2192. DOI: 10.1080/07391102.2018.1479310.
34. Shubham S., Pakhuri M., Omprakash S., et al., (2019) Computationally guided identification of Akt-3, a serine/threonine kinase inhibitors: Insights from homology modelling, structure-based screening, molecular dynamics and quantum mechanical calculations, J. biomolecular structure and dynamics, 38(14), 4179–4188. DOI: 10.1080/07391102.2019.1675536.
35. Islam R., Parves R., Paul AS., et al., (2020) A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2, J. biomolecular structure and dynamics, 39(9), 3213–3224. DOI: 10.1080/07391102.2020.1761883.
36. Cruz Jorddy N., Costa F. S., José Khayat S., Kuca A., Barros A. L. , Carlos Neto A. M. J. C, (2019) Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13, J. Biomol. Struct. Dyn., 37(6), 1616–1627. DOI: 10.1080/07391102.2018.1462734.