Microbial based natural compounds as potential inhibitors for SARS-CoV-2 Papain-like protease (PLpro): a molecular docking and dynamic simulation study

References

• Balkrishna, A., Mittal, R., & Arya, V. (2021). Computational evidences of phytochemical mediated disruption of PLpro driven replication of SARS-CoV-2: A therapeutic approach against COVID-19. Current Pharmaceutical Biotechnology, 22(10), 1350–1359. https://doi.org/10.2174/1389201021999201110204116
   PubMed Web of Science ®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
• 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(1), 42717–42713. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Farmer, P. B., & Suhadolnik, R. J. (1972). Nucleoside antibiotics. Biosynthesis of arabinofuranosyladenine by Streptomyces antibioticus. Biochemistry, 11(5), 911–916. https://doi.org/10.1021/bi00755a034
   PubMed Web of Science ®Google Scholar
• Gao, X., Qin, B., Chen, P., Zhu, K., Hou, P., Wojdyla, J. A., Wang, M., & Cui, S. (2021). Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharmaceutica Sinica B, 11(1), 237–245. https://doi.org/10.1016/j.apsb.2020.08.014
   PubMed Web of Science ®Google Scholar
• Hoshino, T., Hayashi, T., & Uchiyama, T. (1994). Pseudodeoxyviolacein, a new red pigment produced by the tryptophan metabolism of Chromobacterium violaceum. Bioscience, Biotechnology, and Biochemistry, 58(2), 279–282. https://doi.org/10.1271/bbb.58.279
   PubMed Web of Science ®Google Scholar
• Kandeel, M., Abdelrahman, A. H., Oh-Hashi, K., Ibrahim, A., Venugopala, K. N., Morsy, M. A., & Ibrahim, M. A. (2021). Repurposing of FDA-approved antivirals, antibiotics, anthelmintics, antioxidants, and cell protectives against SARS-CoV-2 papain-like protease. Journal of Biomolecular Structure & Dynamics, 39(14), 5129–5128. https://doi.org/10.1080/07391102.2020.1784291
   PubMed Web of Science ®Google Scholar
• Kumar, Y., Singh, H., & Patel, C. N. (2020). In silico prediction of potential inhibitors for the main protease of SARS-CoV-2 using molecular docking and dynamics simulation based drug-repurposing. Journal of Infection and Public Health, 13(9), 1210–1223. https://doi.org/10.1016/j.jiph.2020.06.016
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Lynn, A., & Open Source Drug Discovery Consortium. (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Mitra, K., Ghanta, P., Acharya, S., Chakrapani, G., Ramaiah, B., & Doble, M. (2021). Dual inhibitors of SARS-CoV-2 proteases: Pharmacophore and molecular dynamics based drug repositioning and phytochemical leads. Journal of Biomolecular Structure & Dynamics, 39(16), 6324–6314. https://doi.org/10.1080/07391102.2020.1796802
   PubMed Web of Science ®Google Scholar
• Nakatani, S., Naoe, A., Yamamoto, Y., Yamauchi, T., Yamaguchi, N., & Ishibashi, M. (2003). Isolation of bisindole alkaloids that inhibit the cell cycle from Myxomycetes Arcyria ferruginea and Tubifera casparyi. Bioorganic & Medicinal Chemistry Letters, 13(17), 2879–2881. https://doi.org/10.1016/S0960-894X(03)00592-4
   PubMed Web of Science ®Google Scholar
• Novak, J., Rimac, H., Kandagalla, S., Grishina, M. A., & Potemkin, V. A. (2021). Can natural products stop the SARS-CoV-2 virus? A docking and molecular dynamics study of a natural product database. Future Medicinal Chemistry, 13(4), 363–378. https://doi.org/10.4155/fmc-2020-0248
   PubMed Web of Science ®Google Scholar
• Patridge, E., Gareiss, P., Kinch, M. S., & Hoyer, D. (2016). An analysis of FDA-approved drugs: Natural products and their derivatives. Drug Discovery Today, 21(2), 204–207. https://doi.org/10.1016/j.drudis.2015.01.009
   PubMed Web of Science ®Google Scholar
• Prajapat, M., Sarma, P., Shekhar, N., Avti, P., Sinha, S., Kaur, H., Kumar, S., Bhattacharyya, A., Kumar, H., Bansal, S., & Medhi, B. (2020). Drug targets for corona virus: A systematic review. Indian Journal of Pharmacology, 52(1), 56–65. https://doi.org/10.4103/ijp.IJP_115_20
   PubMed Web of Science ®Google Scholar
• Qin, L. L., Zhou, B., Ding, W., & Ma, Z. (2018). Bioactive metabolites from marine-derived Streptomyces sp. A68 and its Rifampicin resistant mutant strain R-M1. Phytochemistry Letters, 23, 46–51. https://doi.org/10.1016/j.phytol.2017.11.002
   Web of Science ®Google Scholar
• Sayed, A. M., Alhadrami, H. A., El-Gendy, A. O., Shamikh, Y. I., Belbahri, L., Hassan, H. M., Abdelmohsen, U. R., & Rateb, M. E. (2020). Microbial natural products as potential inhibitors of SARS-CoV-2 main protease (Mpro). Microorganisms, 8(7), 970. https://doi.org/10.3390/microorganisms8070970
   PubMed Web of Science ®Google Scholar
• Sharma, P., Joshi, T., Mathpal, S., Joshi, T., Pundir, H., Chandra, S., & Tamta, S. (2020). Identification of natural inhibitors against Mpro of SARS-CoV-2 by molecular docking, molecular dynamics simulation, and MM/PBSA methods. Journal of Biomolecular Structure and Dynamics, 39(18), 1–12. https://doi.org/10.1080/07391102.2020.1842806
   Google Scholar
• Shin, D., Mukherjee, R., Grewe, D., Bojkova, D., Baek, K., Bhattacharya, A., Schulz, L., Widera, M., Mehdipour, A. R., Tascher, G., Geurink, P. P., Wilhelm, A., van der Heden van Noort, G. J., Ovaa, H., Müller, S., Knobeloch, K.-P., Rajalingam, K., Schulman, B. A., Cinatl, J., … Dikic, I. (2020). Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature, 587(7835), 657–662. https://doi.org/10.1038/s41586-020-2601-5
   PubMed Web of Science ®Google Scholar
• Singh, P., Chauhan, S. S., Pandit, S., Sinha, M., Gupta, S., Gupta, A., & Parthasarathi, R. (2021). The dual role of phytochemicals on SARS-CoV-2 inhibition by targeting host and viral proteins. Journal of Traditional and Complementary Medicine, 11(5), 383-470. https://doi.org/10.1016/j.jtcme.2021.09.001
   Google Scholar
• Sunseri, J., & Koes, D. R. (2016). Pharmit: Interactive exploration of chemical space. Nucleic Acids Research, 44(W1), W442–W448.https://doi.org/10.1093/nar/gkw287.
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• van Santen, J. A., Jacob, G., Singh, A. L., Aniebok, V., Balunas, M. J., Bunsko, D., Neto, F. C., Castaño-Espriu, L., Chang, C., Clark, T. N., Cleary Little, J. L., Delgadillo, D. A., Dorrestein, P. C., Duncan, K. R., Egan, J. M., Galey, M. M., Haeckl, F. P. J., Hua, A., Hughes, A. H., … Linington, R. G. (2019). The natural products atlas: An open access knowledge base for microbial natural products discovery. ACS Central Science, 5(11), 1824–1833. https://doi.org/10.1021/acscentsci.9b00806
   PubMed Web of Science ®Google Scholar
• Wang, J. N., Zhang, H. J., Li, J. Q., Ding, W. J., & Ma, Z. J. (2018). Bioactive indolocarbazoles from the marine-derived Streptomyces sp. DT-A61. Journal of Natural Products, 81(4), 949–956. https://doi.org/10.1021/acs.jnatprod.7b01058
   PubMed Web of Science ®Google Scholar
• Wang, X., Abbas, M., Zhang, Y., Elshahawi, S. I., Ponomareva, L. V., Cui, Z., Van Lanen, S. G., Sajid, I., Voss, S. R., Shaaban, K. A., & Thorson, J. S. (2019). Baraphenazines A-G, divergent fused phenazine-based metabolites from a Himalayan Streptomyces. Journal of Natural Products, 82(6), 1686–1693. https://doi.org/10.1021/acs.jnatprod.9b00289
   PubMed Web of Science ®Google Scholar
• WHO. (2021). Severe Acute Respiratory Syndrome (SARS). Retrieved February 8, 2021, from https://www.who.int/health-topics/severe-acute-respiratory-syndrome
   Google Scholar
• WHO. (2021). WHO Coronavirus Disease (COVID-19) Dashboard. Retrieved February 8, 2021, from https://COVID19.who.int/
   Google Scholar
• Williams, D. E., Bernan, V. S., Ritacco, F. V., Maiese, W. M., Greenstein, M., & Andersen, R. J. (1999). Holyrines A and B, possible intermediates in staurosporine biosynthesis produced in culture by a marine actinomycete obtained from the North Atlantic Ocean. Tetrahedron Letters, 40(40), 7171–7174. https://doi.org/10.1016/S0040-4039(99)01495-1
   Web of Science ®Google Scholar
• Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E. C., & Zhang, Y.-Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/10.1038/s41586-020-2008-3
   PubMed Web of Science ®Google Scholar
• Zhou, Y., Hou, Y., Shen, J., Huang, Y., Martin, W., & Cheng, F. (2020). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discovery, 6(1), 14–18. https://doi.org/10.1038/s41421-020-0153-3
   PubMed Web of Science ®Google Scholar
• Zhou, B., Qin, L. L., Ding, W. J., & Ma, Z. J. (2018). Cytotoxic indolocarbazoles alkaloids from the streptomyces sp. A65. Tetrahedron, 74(7), 726–730. https://doi.org/10.1016/j.tet.2017.12.048
   Web of Science ®Google Scholar
• Zumla, A., Chan, J. F., Azhar, E. I., Hui, D. S., & Yuen, K. Y. (2016). Coronaviruses – Drug discovery and therapeutic options. Nature Reviews. Drug Discovery, 15(5), 327–347. https://doi.org/10.1038/nrd.2015.37
   PubMed Web of Science ®Google Scholar