In silico discovery of novel inhibitors from Northern African natural products database against main protease (Mpro) of SARS-CoV-2

References

• Arun, K. G., Sharanya, C. S., Abhithaj, J., Francis, D., & Sadasivan, C. (2021). Drug repurposing against SARS-CoV-2 using E-pharmacophore based virtual screening, molecular docking and molecular dynamics with main protease as the target. Journal of Biomolecular Structure & Dynamics, 39(13), 4647–4658. https://doi.org/10.1080/07391102.2020.1779819
   PubMed Web of Science ®Google Scholar
• Astuti Ysrafil, I. 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response. Diabetes & Metabolic Syndrome: Clinical Research & Reviews, 14(4), 407–412. https://doi.org/10.1016/j.dsx.2020.04.020
   PubMed Web of Science ®Google Scholar
• Beck, D. A. C., & Daggett, V. (2004). Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods (San Diego, Calif.), 34(1), 112–120. https://doi.org/10.1016/j.ymeth.2004.03.008
   PubMed Web of Science ®Google Scholar
• Bojkova, D., Klann, K., Koch, B., Widera, M., Krause, D., Ciesek, S., Cinatl, J., & Münch, C. (2020). Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature, 583(7816), 469–472. https://doi.org/10.1038/s41586-020-2332-7
   PubMed Web of Science ®Google Scholar
• Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of Medical Virology, 92(4), 418–423. https://doi.org/10.1002/jmv.25681
   PubMed Web of Science ®Google Scholar
• Chen, C. Z., Xu, M., Pradhan, M., Gorshkov, K., Petersen, J. D., Straus, M. R., Zhu, W., Shinn, P., Guo, H., Shen, M., Klumpp-Thomas, C., Michael, S. G., Zimmerberg, J., Zheng, W., & Whittaker, G. R. (2020). Identifying SARS-CoV-2 entry inhibitors through drug repurposing screens of SARS-S and MERS-S pseudotyped particles. ACS Pharmacology & Translational Science, 3(6), 1165–1175. https://doi.org/10.1021/acsptsci.0c00112
   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
• Cruz, J. N., Costa, J. F. S., Khayat, A. S., Kuca, K., Barros, C. A. L., & 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. Journal of Biomolecular Structure & Dynamics, 37(6), 1616–1627. https://doi.org/10.1080/07391102.2018.1462734
   PubMed Web of Science ®Google Scholar
• Galzitskaya, O. V., & Garbuzynskiy, S. O. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 144–154. https://doi.org/10.1002/prot.20851.
   Google Scholar
• 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. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Gentile, D., Patamia, V., Scala, A., Sciortino, M. T., Piperno, A., & Rescifina, A. (2020). Putative inhibitors of SARS-COV-2 main protease from a library of marine natural products: A virtual screening and molecular modeling study. Marine Drugs, 18(4), 225. https://doi.org/10.3390/md18040225
   PubMed Web of Science ®Google Scholar
• Ghose, A. K., Viswanadhan, V. N., & Wendoloski, J. J. (1999). A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. Journal of Combinatorial Chemistry, 1(1), 55–68. https://doi.org/10.1021/cc9800071
   PubMedGoogle Scholar
• Gorbalenya, A. E. (2020). The species severe acute respiratory syndrome-related coronavirus: Classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology, 5(4), 536–544. https://doi.org/10.1038/s41564-020-0695-z
   PubMed Web of Science ®Google Scholar
• Guo, Z. (2017). The modification of natural products for medical use. Acta Pharmaceutica Sinica B, 7(2), 119–136. https://doi.org/10.1016/j.apsb.2016.06.003
   PubMed Web of Science ®Google Scholar
• Ishak, S., Aris, S., Halim, K., Ali, M., Leow, T., Kamarudin, N., Masomian, M., & Rahman, R. (2017). Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure. Molecules, 22(10), 1574–13.1574. https://doi.org/10.3390/molecules2210
   PubMed Web of Science ®Google Scholar
• Islam, R. A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 0(0), 000. https://doi.org/10.1080/07391102.2020.1761883
   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 SARS-CoV-2 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
• Jukič, M., Škrlj, B., Tomšič, G., Pleško, S., Podlipnik, Č., & Bren, U. (2021). Prioritisation of compounds for 3clpro inhibitor development on SARS-CoV-2 variants. Molecules, 26(10), 3003. https://doi.org/10.3390/molecules2610
   PubMed Web of Science ®Google Scholar
• Khailany, R. A., Safdar, M., & Ozaslan, M. (2020). Genomic characterization of a novel SARS-CoV-2. Gene Reports, 19, 100682. https://doi.org/10.1016/j.genrep.2020.100682
   PubMed Web of Science ®Google Scholar
• Kneller, D. W. (2020). Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography. Nature Communications, 11(1), 7–12. https://doi.org/10.1038/s41467-020-16954-7
   PubMed Web of Science ®Google Scholar
• Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., & Vriend, G. (2004). Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins Structure, 57(4), 678–683. https://doi.org/10.1002/prot.20251
   PubMed Web of Science ®Google Scholar
• Lee, J. Y., Orlikova, B., & Diederich, M. (2015). Signal transducers and activators of transcription (STAT) regulatory networks in marine organisms: From physiological observations towards marine drug discovery. Marine Drugs, 13(8), 4967–4984. https://doi.org/10.3390/md13084967
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. https://doi.org/10.1016/S0169-409X(96)00423-1
   Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1–3), 3–26.
   PubMed Web of Science ®Google Scholar
• Lira, S. P. d., Seleghim, M. H. R., Williams, D. E., Marion, F., Hamill, P., Jean, F., Andersen, R. J., Hajdu, E., & Berlinck, R. G. S. (2007). A SARS-coronovirus 3CL protease inhibitor isolated from the marine sponge Axinella cf. corrugata: Structure elucidation and synthesis. Journal of the Brazilian Chemical Society, 18(2), 440–443. 2007, https://doi.org/10.1590/S0103-50532007000200030
   Web of Science ®Google Scholar
• Lobanov, M. Y., Bogatyreva, N. S., & Galzitskaya, O. V. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808. https://doi.org/10.1021/jm060522a
   PubMed Web of Science ®Google Scholar
• Ma, J., Peng, J., Wang, S., & Xu, J. (2012). A conditional neural fields model for protein threading. Bioinformatics, 28(12), i59–i66. https://doi.org/10.1093/bioinformatics/bts213
   PubMed Web of Science ®Google Scholar
• Malve, H. (2016 Apr-Jun). Exploring the ocean for new drug developments: Marine pharmacology. Journal of Pharmacy & Bioallied Sciences, 8(2), 83–91. 2016,https://doi.org/10.4103/0975-7406.171700
   PubMed Web of Science ®Google Scholar
• Martínez, L. (2015). Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS One, 10(3), e0119264–10. https://doi.org/10.1371/journal.pone.0119264
   PubMed Web of Science ®Google Scholar
• Mayer, A. M. S., Glaser, K. B., Cuevas, C., Jacobs, R. S., Kem, W., Little, R. D., McIntosh, J. M., Newman, D. J., Potts, B. C., & Shuster, D. E. (2010). The odyssey of marine pharmaceuticals: A current pipeline perspective. Trends in Pharmacological Sciences, 31(6), 255–265. 2010, https://doi.org/10.1016/j.tips.2010.02.005
   PubMed Web of Science ®Google Scholar
• Mohapatra, S., Nath, P., Chatterjee, M., Das, N., Kalita, D., Roy, P., & Satapathi, S. (2020). Repurposing therapeutics for COVID-19: Rapid prediction of commercially available drugs through machine learning and docking. PLoS One, 15(11), e0241543–13. https://doi.org/10.1371/journal.pone.0241543
   PubMed Web of Science ®Google Scholar
• Moussaoui, O., Byadi, S., Eddine Hachim, M., Sghyar, R., Bahsis, L., Moslova, K., Aboulmouhajir, A., Rodi, Y. K., Podlipnik, Č., Hadrami, E. M. E., & Chakroune, S. (2021). Selective synthesis of novel quinolones-amino esters as potential antibacterial and antifungal agents: Experimental, mechanistic study, docking and molecular dynamic simulations. Journal of Molecular Structure, 1241, 130652. https://doi.org/10.1016/j.molstruc.2021.130652
   Web of Science ®Google Scholar
• Muteeb, G., Alshoaibi, A., Aatif, M., Rehman, M. T., & Qayyum, M. Z. (2020). Screening marine algae metabolites as high-affinity inhibitors of SARS-CoV-2 main protease (3CLpro): An in silico analysis to identify novel drug candidates to combat COVID-19 pandemic. Applied Biological Chemistry, 63(1) https://doi.org/10.1186/s13765-020-00564-4.
   Google Scholar
• Nosé, S. (1980). Molecular dynamics simulations at constant temperature and pressure. Computational Simulation in Materials Science, 2384, 21–41. https://doi.org/10.1007/978-94-011-3546-7_2
   Google Scholar
• Ntie-Kang, F., Telukunta, K. K., Döring, K., Simoben, C. V., A Moumbock, A. F., Malange, Y. I., Njume, L. E., Yong, J. N., Sippl, W., & Günther, S. (2017). NANPDB: A resource for natural products from Northern African sources. Journal of Natural Products, 80(7), 2067–2076. https://doi.org/10.1021/acs.jnatprod.7b00283
   PubMed Web of Science ®Google Scholar
• Pal, M., Berhanu, G., Desalegn, C., & Kandi, V. (2020). Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): An update. Cureus, 2(3) https://doi.org/10.7759/cureus.7423
   Google Scholar
• Park, J.-Y., Kim, J. H., Kwon, J. M., Kwon, H.-J., Jeong, H. J., Kim, Y. M., Kim, D., Lee, W. S., & Ryu, Y. B. (2013). Dieckol, a SARS-CoV 3CL(pro) inhibitor, isolated from the edible brown algae Ecklonia cava. Bioorganic & Medicinal Chemistry, 21(13), 3730–3737. https://doi.org/10.1016/j.bmc.2013.04.026
   PubMed Web of Science ®Google Scholar
• Singh, T. U., Parida, S., Lingaraju, M. C., Kesavan, M., Kumar, D., & Singh, R. K. (2020). Drug repurposing approach to fight COVID-19. Pharmacological Reports: PR, 72(6), 1479–1508. https://doi.org/10.1007/s43440-020-00155-6
   PubMed Web of Science ®Google Scholar
• Snijder, E. J., Bredenbeek, P. J., Dobbe, J. C., Thiel, V., Ziebuhr, J., Poon, L. L. M., Guan, Y., Rozanov, M., Spaan, W. J. M., & Gorbalenya, A. E. (2003). Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. Journal of Molecular Biology, 331(5), 991–1004. https://doi.org/10.1016/S0022-2836(03)00865-9
   PubMed Web of Science ®Google Scholar
• Tu, Y.-F., Chien, C.-S., Yarmishyn, A. A., Lin, Y.-Y., Luo, Y.-H., Lin, Y.-T., Lai, W.-Y., Yang, D.-M., Chou, S.-J., Yang, Y.-P., Wang, M.-L., & Chiou, S.-H. (2020). A review of sars-cov-2 and the ongoing clinical trials. International Journal of Molecular Sciences, 21(7), 2657. https://doi.org/10.3390/ijms21072657
   PubMed Web of Science ®Google Scholar
• Veber, D. F., Johnson, S. R., Cheng, H. Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. https://doi.org/10.1021/jm020017n
   PubMed Web of Science ®Google Scholar
• Wang, L., Wang, Y., Ye, D., & Liu, Q. (2020). Review of the 2019 novel coronavirus (SARS-CoV-2) based on current evidence. International Journal of Antimicrobial Agents, 55(6), 105948. https://doi.org/10.1016/j.ijantimicag.2020.105948
   PubMed Web of Science ®Google Scholar
• Xiong, G., Wu, Z., Yi, J., Fu, L., Yang, Z., Hsieh, C., Yin, M., Zeng, X., Wu, C., Lu, A., Chen, X., Hou, T., & Cao, D. (2021). ADMETlab 2.0: An integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Research, 49(W1), W5–W14. https://doi.org/10.1093/nar/gkab255
   PubMed Web of Science ®Google Scholar
• Yasuhara-Bell, J., & Lu, Y. (2010). Marine compounds and their antiviral activities. Antiviral Research, 86(3), 231–240. https://doi.org/10.1016/j.antiviral.2010.03.009
   PubMed Web of Science ®Google Scholar
• Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (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
   PubMed Web of Science ®Google Scholar
• Zheng, J. (2020). SARS-coV-2: An emerging coronavirus that causes a global threat. International Journal of Biological Sciences, 16(10), 1678–1685. https://doi.org/10.7150/ijbs.45053
   PubMed Web of Science ®Google Scholar