Repurposing drugs and identification of inhibitors of integral proteins (spike protein and main protease) of SARS-CoV-2

References

• Abdullahi, M., Olotu, F. A., & Soliman, M. E. (2018). Allosteric inhibition abrogates dysregulated LFA-1 activation: Structural insight into mechanisms of diminished immunologic disease. Computational Biology and Chemistry, 73, 49–56. https://doi.org/10.1016/j.compbiolchem.2018.02.002
   PubMed Web of Science ®Google Scholar
• Babine, R. E., & Bender, S. L. (1997). Molecular recognition of proteinminus signLigand complexes: Applications to drug design. Chemical Reviews, 97(5), 1359–1472. https://doi.org/10.1021/cr960370z
   PubMed Web of Science ®Google Scholar
• Basconi, J. E., & Shirts, M. R. (2013). Effects of temperature control algorithms on transport properties and kinetics in molecular dynamics simulations. Journal of Chemical Theory and Computation, 9(7), 2887–2899.
   PubMed Web of Science ®Google Scholar
• Basu, A., Sarkar, A., & Maulik, U. (2020). Computational approach for the design of potential spike protein binding natural compounds in SARS- CoV2. Pharmacodynamics, 4, 1–22. https://doi.org/10.21203/rs.3.rs-33181/v1[Epub ahead of print].
   Google Scholar
• Begley, D. J., & Brightman, M. W. (2011). Structural and functional aspects of the blood-brain barrier. Peptide Transport and Delivery into the Central Nervous System’, 61(5), 39–78.
   Google Scholar
• Burley, S. K., Berman, H. M., Christie, C., Duarte, J. M., Feng, Z., Westbrook, J., Young, J., & Zardecki, C. (2018). RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. Protein Science : A Publication of the Protein Society, 27(1), 316–330. https://doi.org/10.1002/pro.3331
   PubMed Web of Science ®Google Scholar
• Cao, B., Wang, Y., Wen, D., Liu, W., Wang, J., Fan, G., Ruan, L., Song, B., Cai, Y., Wei, M., Li, X., Xia, J., Chen, N., Xiang, J., Yu, T., Bai, T., Xie, X., Zhang, L., Li, C., … Wang, C. (2020). A trial of lopinavir–ritonavir in adults hospitalized with severe COVID. New England Journal of Medicine, 382(19), 1787–1799. https://doi.org/10.1056/NEJMoa2001282
   PubMed Web of Science ®Google Scholar
• Centres for Disease Control and Prevention. (2020). Information for clinicians on therapeutic options for COVID-19 patients. Retrieved September 21, 2020, from https://www.cdc.gov/coronavirus/2019-ncov/hcp/therapeutic-options.html
   Google 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. The Lancet), 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
   PubMed Web of Science ®Google Scholar
• Chetty, S., Bhakat, S., Martin, A. J. M., & Soliman, M. E. S. (2016). Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: Molecular dynamics insights. Journal of Biomolecular Structure & Dynamics, 34(1), 135–151. https://doi.org/10.1080/07391102.2015.1018326
   PubMed Web of Science ®Google Scholar
• da Silva, C. H. T. P., Campo, V. L., Carvalho, I., & Taft, C. A. (2006). Molecular modeling, docking and ADMET studies applied to the design of a novel hybrid for treatment of Alzheimer's disease. Journal of Molecular Graphics & Modelling, 25(2), 169–175. https://doi.org/10.1016/j.jmgm.2005.12.002
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• de Wit, E., van Doremalen, N., Falzarano, D., & Munster, V. J. (2016). SARS and MERS: Recent insights into emerging coronaviruses. Nature Reviews Microbiology, 14(8), 523–534. https://doi.org/10.1038/nrmicro.2016.81
   PubMed Web of Science ®Google Scholar
• Gonnet, P. (2007). P-SHAKE: A quadratically convergent SHAKE. Journal of Computational Physics, 220(2), 740–747. https://doi.org/10.1016/j.jcp.2006.05.032
   Web of Science ®Google Scholar
• Grosdidier, A., Zoete, V., & Michielin, O. (2011). SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res, 39(suppl_2), W270–7. https://doi.org/10.1093/nar/gkr366
   PubMed Web of Science ®Google Scholar
• Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeerschd, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(8), 1–17.
   PubMedGoogle Scholar
• Heaney, R. P. (2001). Factors influencing the measurement of bioavailability, taking calcium as a model. The Journal of Nutrition, 131(4 Suppl), 1344S–1348S. https://doi.org/10.1093/jn/131.4.1344S
   PubMedGoogle Scholar
• Hess, B. (2002). Convergence of sampling in protein simulations. Physical Review, 65(3), 031910. https://coronavirus.jhu.edu/map.html
   Google Scholar
• Idowu, K., Ramharack, P., Nlooto, M., & Gordon, M. (2019). The pharmacokinetic properties of HIV-1 protease inhibitors: A computational perspective on herbal phytochemicals. Heliyon, 5(10), e02565.
   PubMed Web of Science ®Google Scholar
• Idowu, K., Ramharack, P., Nlooto, M., & Gordon, M. (2020). Molecular dynamic mechanism(s) of inhibition of bioactive antiviral phytochemical compounds targeting cytochrome P450 3A4 and P-glycoprotein. Journal of Biomolecular Structure and Dynamics, 3, 1221–1233.
   Google Scholar
• Izaguirre, J. A., Catarello, D. P., Wozniak, J. M., & Skeel, R. D. (2001). Langevin stabilization of molecular dynamics. The Journal of Chemical Physics, 114(5), 2090–2098. https://doi.org/10.1063/1.1332996
   Web of Science ®Google Scholar
• Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/10.1038/s41586-020-2223-y
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Jun, L., Jiwan, G., Jinfang, Y., Sisi, S., Huan, Z., Shilong, F., Qi, Z., Xuanling, S., Qisheng, W., Linqi, Z., & Xinquan, W. (2020). Crystal structure of the 2019-1 nCoV spike receptor-binding domain bound with the ACE2 receptor. https://doi.org/10.1101/2020.02.19.956235
   Google Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–1213. https://doi.org/10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• Kremers, P. (2002). In vitro tests for predicting drug-drug interactions: The need for validated procedures. Pharmacology & Toxicology, 91(5), 209–217. https://doi.org/10.1034/j.1600-0773.2002.910501.x
   PubMedGoogle Scholar
• Kumi, R. O., Soremekun, O. S., Issahaku, A. R., Fisayo, C. A., Olotu, A., & Soliman, M. E. S. (2020). Exploring the ring potential of 2,4-diaminopyrimidine derivatives towards the identification of novel caspase-1 inhibitors in Alzheimer’s disease therapy. Journal of molecular modeling, 26(68), 1–17.
   Google Scholar
• Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., Xing, X., Xiang, N., Wu, Y., Li, C., Chen, Q., Li, D., Liu, T., Zhao, J., Liu, M., … Feng, Z. (2020). Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. New England Journal of Medicine, 382(13), 1199–1207. https://doi.org/10.1056/NEJMoa2001316
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4–17. https://doi.org/10.1016/j.addr.2012.09.019
   Web of Science ®Google Scholar
• Liu, C., Zhou, Q., Li, Y., Garner, L. V., Watkins, S. P., Carter, L. J., Smoot, J., Gregg, A. C., Daniels, A. D., Jervey, S., & Albaiu, D. (2020). Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Central Science, 6(3), 315–331. https://doi.org/10.1021/acscentsci.0c00272
   PubMed Web of Science ®Google Scholar
• Maurya, V. K., Kumar, S., Bhatt, M. L. B., & Saxena, S. K. (2020). Therapeutic development and drugs for the treatment of COVID-19. Nature Public Health Emergency Collection, 109–126. https://doi.org/10.1007/978-981-15-4814-7_10
   Google Scholar
• Nair, P. C., & Miners, J. O. (2014). Molecular dynamics simulations: From structure function relationships to drug discovery. In Silico Pharmacology, 2(4), 1–4.
   PubMedGoogle Scholar
• Remko, M., Boháč, A., & Kováčiková, L. (2011). Molecular structure, pKa, lipophilicity, solubility, absorption, polar surface area, and blood brain barrier penetration of some antiangiogenic agents. Structural Chemistry, 22(3), 635–648. https://doi.org/10.1007/s11224-011-9741-z
   Web of Science ®Google Scholar
• Ren, Z., Yan, L., Zhang, N., Guo, Y., Yang, C., Lou, Z., & Rao, Z. (2013). The newly emerged SARS-Like coronavirus HCoV-EMC also has an "Achilles' heel": Current effective inhibitor targeting a 3C-like protease. Protein & Cell, 4(4), 248–250. 249. https://doi.org/10.1007/s13238-013-2841-3
   PubMed Web of Science ®Google Scholar
• Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19). (2020, February 16–24). World Health Organisation.
   Google Scholar
• Robert, I. F. (1993). Mechanism of action of hydroxychloroquine as antirheumatic drug. Seminar in Arthritis and Rheumatism, 23(2), 82–91.
   PubMed Web of Science ®Google Scholar
• Rodríguez-Morales, P., Alfonso, J., MacGregor, K., Kanagarajah, S., Patel, D. & Schlagenhauf, (2020). Going global – Travel and the 2019 novel coronavirus. Travel Medicine and Infectious Disease, 33, 2020.
   Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Seifert, E. (2014). OriginPro 9.1: Scientific data analysis and graphing software-software review. Journal of Chemical Information and Modeling, 54(5), 1552–1552. https://doi.org/10.1021/ci500161d
   PubMed Web of Science ®Google Scholar
• Senathilake, K., Samarakoon, S., & Tennekoon, K. (2020). Virtual screening of inhibitors against spike glycoprotein of 2019 novel corona virus: A drug repurposing approach. https://doi.org/10.20944/preprints202003.0042.v1)
   Google Scholar
• Shen, M., Zhou, Y., Ye, J., Al-Maskri, A. A. A., Kang, Y., Zeng, S., & Cai, S. (2020). Recent advances and perspectives of nucleic acid detection for coronavirus. Journal of Pharmaceutical Analysis, 10(2), 97–101. https://doi.org/10.1016/j.jpha.2020.02.010
   PubMed Web of Science ®Google Scholar
• Sindhu, T., & Srinivasan, P. (2015). Exploring the binding properties of agonists interacting with human TGR5 using structural modelling, molecular docking and dynamics simulations. RSC Advances, 5(19), 14202–14213. https://doi.org/10.1039/C4RA16617E
   Web of Science ®Google Scholar
• St. John, S. E., Tomar, S., Stauffer, S. R., & Mesecar, A. D. (2015). Targeting zoonotic viruses: Structure-based inhibition of the 3C-like protease from bat coronavirus HKU4-The likely reservoir host to the human coronavirus that causes Middle East Respiratory Syndrome (MERS)). Bioorganic & Medicinal Chemistry, 23(17), 6036–6048. https://doi.org/10.1016/j.bmc.2015.06.039
   PubMed Web of Science ®Google Scholar
• Wang, F., Chen, C., Tan, W., Yang, K., & Yang, H. (2016). Structure of main protease from human coronavirus NL63: Insights for wide spectrum anti-coronavirus drug design. Scientific Reports, 6, 22677–22677. https://doi.org/10.1038/srep22677
   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. (2020). Coronavirus disease 2019 (COVID-19): Situation report, 38. https://apps.who.int/iris/handle/10665/331226
   Google Scholar
• Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367(6483), 1260–1263. https://doi.org/10.1126/science.abb2507
   PubMed Web of Science ®Google Scholar
• Xu, J., Zhao, S., Teng, T., Abdalla, A. E., Zhu, W., Xie, L., Wang, Y., & Guo, X. (2020). Systematic comparison of two animal-to-human transmitted human coronaviruses: SARS-CoV-2 and SARS-CoV. Viruses, 12(2), 244. https://doi.org/10.3390/v12020244
   PubMed Web of Science ®Google Scholar
• Yamashita, F., & Hashida, M. (2004). In silico approaches for predicting ADME properties of drugs. Drug Metabolism and Pharmacokinetics, 19(5), 327–338. https://doi.org/10.2133/dmpk.19.327
   PubMedGoogle Scholar
• Yang, H. T., Xie, W., Xue, X., Yang, K., Ma, J., Liang, W., Zhao, Q., Zhou, Z., Pei, D., Ziebuhr, J., & Hilgenfeld, R. (2005). Design of wide-spectrum inhibitors targeting coronavirus main proteases. Plos Biology, 3, 2044–2044.
   Web of Science ®Google Scholar
• Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., Sun, L., Mo, L., Ye, S., Pang, H., Gao, G. F., Anand, K., Bartlam, M., Hilgenfeld, R., & 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 of the United States of America, 100(23), 13190–13195. https://doi.org/10.1073/pnas.1835675100
   PubMed Web of Science ®Google Scholar
• Yang, Z., Lasker, K., Schneidman-Duhovny, D., Webb, B., Huang, C. C., Pettersen, E. F., Goddard, T. D., Meng, E. C., Sali, A., & Ferrin, T. E. (2012). UCSF Chimera, MODELLER, and IMP: An integrated modeling system. Journal of Structural Biology, 179(3), 269–278. https://doi.org/10.1016/j.jsb.2011.09.006
   PubMed Web of Science ®Google Scholar
• Ylilauri, M., & Pentikäinen, O. T. (2013). MMGBSA as a tool to understand the binding affinities of filamin-peptide interactions. Journal of Chemical Information and Modeling, 53(10), 2626–2633. https://doi.org/10.1021/ci4002475
   PubMed Web of Science ®Google Scholar
• Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., Tan, W; China Novel Coronavirus Investigating and Research Team. (2020). A novel coronavirus from patients with pneumonia in China, 2019. New England Journal of Medicine, 382(8), 727–733.
   Google Scholar