Computational study for identifying promising therapeutic agents of hydroxychloroquine analogues against SARS‐CoV‐2

References

• Adeoye, A. O., Oso, B. J., Olaoye, I. F., Tijjani, H., & Adebayo, A. I. (2020). Repurposing of chloroquine and some clinically approved antiviral drugs as effective therapeutics to prevent cellular entry and replication of coronavirus. Journal of Biomolecular Structure and Dynamics,
   PubMed Web of Science ®Google Scholar
• Agostini, M. L., Andres, E. L., Sims, A. C., Graham, R. L., Sheahan, T. P., Lu, X., Smith, E., Case, J., Feng, J., & Jordan, R. (2018). Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease. mBio, 9, e00221-18. https://doi.org/10.1128/mBio.00221-18
   PubMed Web of Science ®Google Scholar
• Amsden, G. (2005). Anti-inflammatory effects of macrolides-an underappreciated benefit in the treatment of community-acquired respiratory tract infections and chronic inflammatory pulmonary conditions? The Journal of Antimicrobial Chemotherapy, 55(1), 10–21. https://doi.org/10.1093/jac/dkh519
   PubMed Web of Science ®Google Scholar
• Barron, M. G., Jackson, C. R., & Awkerman, J. A. (2012). Evaluation of in silico development of aquatic toxicity species sensitivity distributions. Aquatic Toxicology (Amsterdam, Netherlands), 116–117, 1–7. https://doi.org/10.1016/j.aquatox.2012.02.006
   PubMed Web of Science ®Google Scholar
• Beigelman, A., Mikols, C. L., Gunsten, S. P., Cannon, C. L., Brody, S. L., & Walter, M. J. (2010). Azithromycin attenuates airway inflammation in a mouse model of viral bronchiolitis. Respiratory Research, 11(1), 90. https://doi.org/10.1186/1465-9921-11-90
   PubMedGoogle Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). admetSAR: A comprehensive source and free tool for assessment of chemical ADMET properties. ACS Publications.
   Google Scholar
• Chen, J., Liu, D., Liu, L., Liu, P., Xu, Q., Xia, L., Ling, Y., Huang, D., Song, S., Zhang, D., Qian, Z., Li, T., Shen, Y., & Lu, H. (2020). A pilot study of hydroxychloroquine in treatment of patients with moderate COVID-19. Zhejiang Da Xue Xue Bao. Yi Xue Ban. Journal of Zhejiang University. Medical Sciences, 49(2), 215–219. https://doi.org/10.3785/j.issn.1008-9292.2020.03.03
   PubMedGoogle Scholar
• Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., Xia, J., Yu, T., Zhang, X., & Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. Lancet (London, England), 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
   PubMed Web of Science ®Google Scholar
• Choudhary, R., & Sharma, A. K. (2020). Potential use of hydroxychloroquine, ivermectin and azithromycin drugs in fighting COVID-19: Trends, scope and relevance. New Microbes and New Infections, 35, 100684. https://doi.org/10.1016/j.nmni.2020.100684
   PubMed Web of Science ®Google Scholar
• Colson, P., Rolain, J.-M., Lagier, J.-C., Brouqui, P., & Raoult, D. (2020). Chloroquine and hydroxychloroquine as available weapons to fight COVID-19. International Journal of Antimicrobial Agents, 55(4), 105932. https://doi.org/10.1016/j.ijantimicag.2020.105932
   PubMed Web of Science ®Google Scholar
• Chu, C. M., Cheng, V. C., Hung, I. F., Wong, M. M., Chan, K. H., Chan, K. S., Kao, R. Y., Poon, L. L., Wong, C. L., Guan, Y., Peiris, J. S., Yuen, K. Y., & HKU/UCH SARS Study Group. (2004). Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings. Thorax, 59(3), 252–256. https://doi.org/10.1136/thorax.2003.012658
   Google Scholar
• Devaux, C. A., Rolain, J.-M., Colson, P., & Raoult, D. (2020). New insights on the antiviral effects of chloroquine against coronavirus: What to expect for COVID-19? International Journal of Antimicrobial Agents, 55(5), 105938. https://doi.org/10.1016/j.ijantimicag.2020.105938
   PubMed Web of Science ®Google Scholar
• Duan, K., Liu, B., Li, C., Zhang, H., Yu, T., Qu, J., Zhou, M., Chen, L., Meng, S., Hu, Y., Peng, C., Yuan, M., Huang, J., Wang, Z., Yu, J., Gao, X., Wang, D., Yu, X., Li, L., … Yang, X. (2020). Effectiveness of convalescent plasma therapy in severe COVID-19 patients. Proceedings of the National Academy of Sciences of the United States of America, 117(17), 9490–9496. https://doi.org/10.1073/pnas.2004168117
   PubMed Web of Science ®Google Scholar
• Elfiky, A. A. (2020). Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study. Life Sciences, 253, 117592. https://doi.org/10.1016/j.lfs.2020.117592
   PubMed Web of Science ®Google Scholar
• Fanin, A., Calegari, J., Beverina, A., Tiraboschi, S., & di Autoformazione Metodologica, G. (2020). Hydroxychloroquine and azithromycin as a treatment of COVID-19. Internal and Emergency Medicine, 15(5), 841–843. https://doi.org/10.1007/s11739-020-02388-y.
   Google Scholar
• Fantini, J., Di Scala, C., Chahinian, H., & Yahi, N. (2020). Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection. International Journal of Antimicrobial Agents, 55(5), 105960. https://doi.org/10.1016/j.ijantimicag.2020.105960
   PubMed Web of Science ®Google Scholar
• Gao, J., Tian, Z., & Yang, X. (2020). Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Bioscience Trends. https://doi.org/10.5582/bst.2020.01047
   Web of Science ®Google Scholar
• Gheblawi, M., Wang, K., Viveiros, A., Nguyen, Q., Zhong, J. C., Turner, A. J., Raizada, M. K., Grant, M. B., & Oudit, G. Y. (2020). Angiotensin-converting enzyme 2: SARS-CoV-2 receptor and regulator of the renin-angiotensin system: Celebrating the 20th anniversary of the discovery of ACE2. Circulation Research, 126(10), 1456–1474. https://doi.org/10.1161/CIRCRESAHA.120.317015
   PubMed Web of Science ®Google Scholar
• Giudicessi, J. R., Noseworthy, P. A., Friedman, P. A., & Ackerman, M. J. (2020). Urgent Guidance for Navigating and Circumventing the QTc-Prolonging and Torsadogenic Potential of Possible Pharmacotherapies for Coronavirus Disease 19 (COVID-19). Mayo Clinic proceedings, 95(6), 1213–1221. https://doi.org/10.1016/j.mayocp.2020.03.024
   Google Scholar
• Goel, R. K., Singh, D., Lagunin, A., & Poroikov, V. (2011). PASS-assisted exploration of new therapeutic potential of natural products. Medicinal Chemistry Research, 20(9), 1509–1514. https://doi.org/10.1007/s00044-010-9398-y
   Web of Science ®Google Scholar
• Guo, D. (2020). Old Weapon for New Enemy: Drug Repurposing for Treatment of Newly Emerging Viral Diseases. Virologica Sinica, 35(3), 253–255. https://doi.org/10.1007/s12250-020-00204-7
   Google Scholar
• Haider, Z., Subhani, M. M., Farooq, M. A., Ishaq, M., Khalid, M., Khan, R. S. A., & Niazi, A. K. (2020). In silico discovery of novel inhibitors against main protease (Mpro) of SARS-CoV-2 using pharmacophore and molecular docking based virtual screening from ZINC database. Preprints.
   Google Scholar
• Hasan, A., Paray, B. A., Hussain, A., Qadir, F. A., Attar, F., Aziz, F. M., Sharifi, M., Derakhshankhah, H., Rasti, B., Mehrabi, M., Shahpasand, K., Saboury, A. A., & Falahati, M. (2021). A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin. Journal of Biomolecular Structure & Dynamics, 39(8), 3025–3033. https://doi.org/10.1080/07391102.2020.1754293
   PubMed Web of Science ®Google Scholar
• Hashem, A. M., Alghamdi, B. S., Algaissi, A. A., Alshehri, F. S., Bukhari, A., Alfaleh, M. A., & Memish, Z. A. (2020). Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review. Travel Medicine and Infectious Disease, 35, 101735. https://doi.org/10.1016/j.tmaid.2020.101735
   PubMed Web of Science ®Google Scholar
• Igwe, K., Ikpeazu, O., Amaku, F., & Otuokere, I. (2020). Repurposing hydroxychloroquine as a model drug for the prediction of potential SARS-CoV-2 inhibitor. European Journal of Engineering Research and Science, 5(9), 1031–1036. https://doi.org/10.24018/ejers.2020.5.9.2056
   Google Scholar
• Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52(7), 1757–1768. https://doi.org/10.1021/ci3001277
   PubMed Web of Science ®Google Scholar
• Khan, M., Santhosh, S. R., Tiwari, M., Lakshmana Rao, P. V., & Parida, M. (2010). Assessment of in vitro prophylactic and therapeutic efficacy of chloroquine against Chikungunya virus in vero cells. Journal of Medical Virology, 82(5), 817–824. https://doi.org/10.1002/jmv.21663
   PubMed Web of Science ®Google Scholar
• Koes, D. R., & Camacho, C. J. (2012). ZINCPharmer: Pharmacophore search of the ZINC database. Nucleic Acids Research, 40(Web Server issue), W409–414. https://doi.org/10.1093/nar/gks378
   PubMed Web of Science ®Google Scholar
• Kwiek, J. J., Haystead, T. A., & Rudolph, J. (2004). Kinetic mechanism of quinone oxidoreductase 2 and its inhibition by the antimalarial quinolines. Biochemistry, 43(15), 4538–4547. https://doi.org/10.1021/bi035923w
   PubMed Web of Science ®Google Scholar
• Lagunin, A., Stepanchikova, A., Filimonov, D., & Poroikov, V. (2000). PASS: Prediction of activity spectra for biologically active substances. Bioinformatics (Oxford, England), 16(8), 747–748. https://doi.org/10.1093/bioinformatics/16.8.747
   PubMed Web of Science ®Google Scholar
• Lindner, H. A., Fotouhi-Ardakani, N., Lytvyn, V., Lachance, P., Sulea, T., & Menard, R. (2005). The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme. Journal of Virology, 79(24), 15199–15208. https://doi.org/10.1128/JVI.79.24.15199-15208.2005
   PubMed Web of Science ®Google Scholar
• Liu, J., Can, R., Xu, M., Wang, X., Zhang, H., & Hu, H. (2020). Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro. Cell Discovery, 6, 1–4. doi:10.1038/s41421-020-0156.
   PubMed Web of Science ®Google Scholar
• McChesney, E. W. (1983). Animal toxicity and pharmacokinetics of hydroxychloroquine sulfate. The American Journal of Medicine, 75(1), 11–18. https://doi.org/10.1016/0002-9343(83)91265-2
   PubMedGoogle Scholar
• Meanwell, N. A. (2016). Improving drug design: An update on recent applications of efficiency metrics, strategies for replacing problematic elements, and compounds in nontraditional drug space. Chemical Research in Toxicology, 29(4), 564–616. https://doi.org/10.1021/acs.chemrestox.6b00043
   PubMed Web of Science ®Google Scholar
• Mittal, M., Goel, R. K., Bhargava, G., & Mahajan, M. P. (2008). PASS-assisted exploration of antidepressant activity of 1,3,4-trisubstituted-beta-lactam derivatives. Bioorganic & Medicinal Chemistry Letters, 18(20), 5347–5349. https://doi.org/10.1016/j.bmcl.2008.09.064
   PubMed Web of Science ®Google Scholar
• Mittal, L., Zhang, L., Feng, R., & Werth, V. P. (2018). Antimalarial drug toxicities in patients with cutaneous lupus and dermatomyositis: A retrospective cohort study. Journal of the American Academy of Dermatology, 78(1), 100–106 e101. https://doi.org/10.1016/j.jaad.2017.09.061
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662. https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
   Web of Science ®Google Scholar
• Nisha, C. M., Kumar, A., Nair, P., Gupta, N., Silakari, C., Tripathi, T., & Kumar, A. (2016). Molecular docking and in silico ADMET study reveals acylguanidine 7a as a potential inhibitor of β-secretase. Advances in Bioinformatics, 2016, 9258578. https://doi.org/10.1155/2016/9258578
   PubMedGoogle Scholar
• Owusu, M., Annan, A., Corman, V. M., Larbi, R., Anti, P., Drexler, J. F., Agbenyega, O., Adu-Sarkodie, Y., & Drosten, C. (2014). Human coronaviruses associated with upper respiratory tract infections in three rural areas of Ghana. PLoS One, 9(7), e99782. https://doi.org/10.1371/journal.pone.0099782
   PubMed Web of Science ®Google Scholar
• Pastick, K. A., Okafor, E. C., Wang, F., Lofgren, S. M., Skipper, C. P., Nicol, M. R., Pullen, M. F., Rajasingham, R., McDonald, E. G., & Lee, T. C. (2020). Hydroxychloroquine and chloroquine for treatment of SARS-CoV-2 (COVID-19). Open Forum Infectious Diseases, 7(4), 1–9. https://doi.org/10.1093/ofid/ofaa130
   Web of Science ®Google Scholar
• Pelle, M. T., & Callen, J. P. (2002). Adverse cutaneous reactions to hydroxychloroquine are more common in patients with dermatomyositis than in patients with cutaneous lupus erythematosus. Archives of Dermatology, 138(9), 1231–1233. https://doi.org/10.1001/archderm.138.9.1231
   PubMedGoogle Scholar
• Perlman, S. (2020). Another decade, another coronavirus. Mass Medical Soc.
   Google Scholar
• Perlman, S., & Netland, J. (2009). Coronaviruses post-SARS: Update on replication and pathogenesis. Nature Reviews. Microbiology, 7(6), 439–450. https://doi.org/10.1038/nrmicro2147
   PubMed Web of Science ®Google Scholar
• Perricone, C., Triggianese, P., Bartoloni, E., Cafaro, G., Bonifacio, A. F., Bursi, R., Perricone, R., & Gerli, R. (2020). The anti-viral facet of anti-rheumatic drugs: Lessons from COVID-19. Journal of Autoimmunity, 111, 102468. https://doi.org/10.1016/j.jaut.2020.102468
   PubMed Web of Science ®Google Scholar
• Prasanth, D. S. N. B. K., Murahari, M., Chandramohan, V., Bhavya, G., Lakshmana Rao, A., Panda, S. P., Rao, G. S. N. K., Chakravarthi, G., Teja, N., Suguna Rani, P., Ashu, G., Purnadurganjali, C., Akhil, P., Vedita Bhavani, G., & Jaswitha, T. (2021). In-silico strategies of some selected phytoconstituents from Melissa officinalis as SARS CoV-2 main protease and spike protein (COVID-19) inhibitors. Molecular Simulation, 47(6), 457–414. https://doi.org/10.1080/08927022.2021.1880576
   Web of Science ®Google Scholar
• Prasanth, D., Murahari, M., Chandramohan, V., Panda, S. P., Atmakuri, L. R., & Guntupalli, C. (2020). In silico identification of potential inhibitors from Cinnamon against main protease and spike glycoprotein of SARS CoV-2. Journal of Biomolecular Structure and Dynamics, 39(13), 4618–4632. https://doi.org/10.1080/07391102.2020.1779129
   Google Scholar
• Principi, N., & Esposito, S. (2020). Chloroquine or hydroxychloroquine for prophylaxis of COVID-19. The Lancet. Infectious diseases, 20(10), 1118. https://doi.org/10.1016/S1473-3099(20)30296-6
   PubMed Web of Science ®Google Scholar
• Randolph, V. B., Winkler, G., & Stollar, V. (1990). Acidotropic amines inhibit proteolytic processing of flavivirus prM protein. Virology, 174(2), 450–458. https://doi.org/10.1016/0042-6822(90)90099-D
   PubMed Web of Science ®Google Scholar
• Ray, W. A., Murray, K. T., Hall, K., Arbogast, P. G., & Stein, C. M. (2012). Azithromycin and the risk of cardiovascular death. New England Journal of Medicine, 366(20), 1881–1890. https://doi.org/10.1056/NEJMoa1003833
   PubMed Web of Science ®Google Scholar
• Sander, T., Freyss, J., von Korff, M., Reich, J. R., & Rufener, C. (2009). OSIRIS, an entirely in-house developed drug discovery informatics system. Journal of Chemical Information and Modeling, 49(2), 232–246. https://doi.org/10.1021/ci800305f
   PubMed Web of Science ®Google Scholar
• Schrezenmeier, E., & Dorner, T. (2020). Mechanisms of action of hydroxychloroquine and chloroquine: Implications for rheumatology. Nature Reviews. Rheumatology, 16(3), 155–166. https://doi.org/10.1038/s41584-020-0372-x
   PubMed Web of Science ®Google Scholar
• Tailor, R., Elaraoud, I., Good, P., Hope-Ross, M., & Scott, R. A. (2012). A case of severe hydroxychloroquine-induced retinal toxicity in a patient with recent onset of renal impairment: A review of the literature on the use of hydroxychloroquine in renal impairment. Case Reports in Ophthalmological Medicine, 2012, 182747. https://doi.org/10.1155/2012/182747
   PubMedGoogle Scholar
• Tortorici, M. A., Walls, A. C., Lang, Y., Wang, C., Li, Z., Koerhuis, D., Boons, G. J., Bosch, B. J., Rey, F. A., de Groot, R. J., & Veesler, D. (2019). Structural basis for human coronavirus attachment to sialic acid receptors. Nature Structural & Molecular Biology, 26(6), 481–489. https://doi.org/10.1038/s41594-019-0233-y
   PubMed Web of Science ®Google Scholar
• Vincent, M. J., Bergeron, E., Benjannet, S., Erickson, B. R., Rollin, P. E., Ksiazek, T. G., Seidah, N. G., & Nichol, S. T. (2005). Chloroquine is a potent inhibitor of SARS coronavirus infection and spread. Virology Journal, 2(1), 69–10. https://doi.org/10.1186/1743-422X-2-69
   PubMed Web of Science ®Google Scholar
• Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W., & Xiao, G. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research, 30(3), 269–271. https://doi.org/10.1038/s41422-020-0282-0
   PubMed Web of Science ®Google Scholar
• World Health Organization. (2008). International health regulations (2005). World Health Organization.
   Google Scholar
• Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica, B, 10(5), 766–788. https://doi.org/10.1016/j.apsb.2020.02.008
   PubMed Web of Science ®Google Scholar
• Xu, X., Han, M., Li, T., Sun, W., Wang, D., Fu, B., Zhou, Y., Zheng, X., Yang, Y., Li, X., Zhang, X., Pan, A., & Wei, H. (2020). Effective treatment of severe COVID-19 patients with tocilizumab. Proceedings of the National Academy of Sciences of the United States of America, 117(20), 10970–10975. https://doi.org/10.1073/pnas.2005615117
   Google Scholar
• Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (New York, N.Y.), 367(6485), 1444–1448. https://doi.org/10.1126/science.abb2762
   Google Scholar
• Yang, H., Lou, C., Sun, L., Li, J., Cai, Y., Wang, Z., Li, W., Liu, G., & Tang, Y. (2019). admetSAR 2.0: Web-service for prediction and optimization of chemical ADMET properties. Bioinformatics (Oxford, England), 35(6), 1067–1069. https://doi.org/10.1093/bioinformatics/bty707
   PubMed Web of Science ®Google Scholar
• Yao, X., Ye, F., Zhang, M., Cui, C., Huang, B., Niu, P., Liu, X., Zhao, L., Dong, E., Song, C., Zhan, S., Lu, R., Li, H., Tan, W., & Liu, D. (2020). In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clinical Infectious Diseases, 71(15), 732–739. https://doi.org/10.1093/cid/ciaa237
   PubMed Web of Science ®Google Scholar
• Zhang, H., Penninger, J. M., Li, Y., Zhong, N., & Slutsky, A. S. (2020). Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: Molecular mechanisms and potential therapeutic target. Intensive Care Medicine, 46(4), 586–590. https://doi.org/10.1007/s00134-020-05985-9
   PubMed Web of Science ®Google Scholar
• Zhang, J.-J., Shen, X., Yan, Y.-M., Yan, W., & Cheng, Y.-X. (2020). Discovery of anti-SARS-CoV-2 agents from commercially available flavor via docking screening.
   Google Scholar
• Zhou, D., Dai, S. M., & Tong, Q. (2020). COVID-19: A recommendation to examine the effect of hydroxychloroquine in preventing infection and progression. The Journal of Antimicrobial Chemotherapy, 75(7), 1667–1670. https://doi.org/10.1093/jac/dkaa114
   PubMed Web of Science ®Google Scholar
• Zhou, F., Yu, T., Du, R., Fan, G., Liu, Y., Liu, Z., Xiang, J., Wang, Y., Song, B., Gu, X., Guan, L., Wei, Y., Li, H., Wu, X., Xu, J., Tu, S., Zhang, Y., Chen, H., & Cao, B. (2020). Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: A retrospective cohort study. The Lancet, 395(10229), 1054–1062. https://doi.org/10.1016/S0140-6736(20)30566-3
   PubMed Web of Science ®Google Scholar