Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID‐19 virus main protease and spike protein

References

• AlAjmi, M. F., Azhar, A., Owais, M., Rashid, S., Hasan, S., Hussain, A., & Rehman, M. T. (2021). Antiviral potential of some novel structural analogs of standard drugs repurposed for the treatment of COVID-19. Journal of Biomolecular Structure & Dynamics, 39(17), 6676–6688. https://doi.org/10.1080/07391102.2020.1799865
   PubMed Web of Science ®Google Scholar
• AlAjmi, M. F., Rehman, M. T., Hussain, A., & Rather, G. M. (2018). Pharmacoinformatics approach for the identification of Polo-like kinase-1 inhibitors from natural sources as anti-cancer agents. International Journal of Biological Macromolecules, 116, 173–181.
   PubMed Web of Science ®Google Scholar
• Al-Saleem, M. S., Al-Wahaibi, L. H., Rehman, M. T., AlAjmi, M. F., Alkahtani, R. A., & Abdel-Mageed, W. M. (2020). Phenolic compounds of Heliotropium europaeum and their biological activities. Pharmacognosy Magazine, 16, S108–S116.
   Web of Science ®Google Scholar
• Al-Shabib, N. A., Khan, J. M., Malik, A., Alsenaidy, M. A., Rehman, M. T., Alajmi, M. F., Al-Senaidy, A. M., Husain, F. M., & Khan, R. H. (2018). Molecular insight into binding behavior of polyphenol (rutin) with beta lactoglobulin: Spectroscopic, molecular docking and MD simulation studies. Journal of Molecular Liquids, 269, 511–520. https://doi.org/10.1016/j.molliq.2018.07.122
   Web of Science ®Google Scholar
• Al-Wahaibi, L. H., Rehman, M. T., Al-Saleem, M. S., Basudan, O. A., El-Gamal, A. A., AlAjmi, M. F., Backheet, E. Y., Khalifa, A. A., & Abdel-Mageed, W. M. (2021). Phenolics from the heartwood of Tecoma mollis as potential inhibitors of COVID-19 virus main protease and spike proteins: An in silico study. Pharmacognosy Magazine, 17, S278–S286.
   Web of Science ®Google Scholar
• Arshia, A. H., Shadravan, S., Solhjoo, A., Sakhteman, A., & Sami, A. (2021). De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations. Computers in Biology and Medicine, 139, 104967.
   PubMed Web of Science ®Google Scholar
• Bister, B., Bischoff, D., Ströbele, M., Riedlinger, J., Reicke, A., Wolter, F., Bull, A. T., Zähner, H., Fiedler, H. P., & Süssmuth, R. D. (2004). Abyssomicin C-A polycyclic antibiotic from a marine Verrucosispora strain as an inhibitor of the p-aminobenzoic acid/tetrahydrofolate biosynthesis pathway. Angewandte Chemie International Edition, 43(19), 2574–2576. https://doi.org/10.1002/anie.200353160
   PubMed Web of Science ®Google Scholar
• Branka, A. C. (2000). Nose-Hoover chain method for nonequilibrium molecular dynamics simulation. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 61(5A), 4769–4773. https://doi.org/10.1103/physreve.61.4769
   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
• Debbab, A., Aly, A. H., Lin, W. H., & Proksch, P. (2010). Bioactive compounds from marine bacteria and fungi. Microbial Biotechnology, 3(5), 544–563.
   PubMed Web of Science ®Google Scholar
• Freundlich, J. S., Lalgondar, M., Wei, J. R., Swanson, S., Sorensen, E. J., Rubin, E. J., & Sacchettini, J. C. (2010). The abyssomicin C family as in vitro inhibitors of Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland), 90(5), 298–300. https://doi.org/10.1016/j.tube.2010.08.002
   PubMed Web of Science ®Google Scholar
• Gerwick, W. H., & Fenner, A. M. (2013). Drug discovery from marine microbes. Microbial Ecology, 65(4), 800–806.
   PubMed Web of Science ®Google Scholar
• Grant, B. J., Skjaerven, L., & Yao, X. ‐Q. (2021). The Bio3D packages for structural bioinformatics. Protein Science, 30(1), 20–30. https://doi.org/10.1002/pro.3923
   PubMed Web of Science ®Google Scholar
• Gurushankar, K., Rimac, H., Potemkin, V., & Grishina, M. (2021). Investigation of the newly characterized baimantuoluoamide a and baimantuoluoamide b alkaloids as potential cyclin-dependent kinase 4 (CDK4) inhibitors using molecular docking and molecular dynamics simulations. Journal of Molecular Structure, 1230, 129925
   Google Scholar
• Havasi, A., Visan, S., Cainap, C., Cainap, S. S., Mihaila, A. A., & Pop, L. A. (2022). Influenza A, Influenza B, and SARS-CoV-2 similarities and differences - a focus on diagnosis. Frontiers in Microbiology, 13, 908525.
   PubMed Web of Science ®Google Scholar
• Huang, J., & MacKerell, A. D., Jr. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145. https://doi.org/10.1002/jcc.23354
   PubMed Web of Science ®Google Scholar
• Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., Cheng, Z., Yu, T., Xia, J., Wei, Y., Wu, W., Xie, X., Yin, W., Li, H., Liu, M., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet (London, England), 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
   PubMed Web of Science ®Google Scholar
• Iacob, S., & Iacob, D. G. (2020). SARS-CoV-2 treatment approaches: Numerous options, no certainty for a versatile virus. Frontiers in Pharmacology, 11, 1224.
   PubMed Web of Science ®Google Scholar
• Ichiye, T., & Karplus, M. (1991). Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins, 11(3), 205–217. https://doi.org/10.1002/prot.340110305
   PubMed Web of Science ®Google Scholar
• Igarashi, Y., Yu, L., Miyanaga, S., Fukuda, T., Saitoh, N., Sakurai, H., Saiki, I., Alonso-Vega, P., & Trujillo, M. E. (2010). Abyssomicin I, a modified polycyclic polyketide from Streptomyces sp. CHI39. Journal of Natural Products, 73(11), 1943–1946. https://doi.org/10.1021/np100292h
   PubMed Web of Science ®Google Scholar
• Iqbal, D., Rehman, M. T., Bin Dukhyil, A., Rizvi, S., Al Ajmi, M. F., Alshehri, B. M., Banawas, S., Khan, M. S., Alturaiki, W., & Alsaweed, M. (2021). High-throughput screening and molecular dynamics simulation of natural product-like compounds against Alzheimer’s disease through multitarget approach. Pharmaceuticals (Basel, Switzerland), 14(9), 937–955. https://doi.org/10.3390/ph14090937
   PubMedGoogle Scholar
• Jabir, N. R., Rehman, M. T., Tabrez, S., Alserihi, R. F., AlAjmi, M. F., Khan, M. S., Husain, F. M., & Ahmed, B. A. (2021). Identification of butyrylcholinesterase and monoamine oxidase B targeted ligands and their putative application in alzheimer’s treatment: A computational strategy. Current Pharmaceutical Design, 27(20), 2425–2434.
   PubMed Web of Science ®Google Scholar
• Jairajpuri, D. S., Hussain, A., Nasreen, K., Mohammad, T., Anjum, F., Tabish Rehman, M., Mustafa Hasan, G., Alajmi, M. F., & Imtaiyaz Hassan, M. (2021). Identification of natural compounds as potent inhibitors of SARS-CoV-2 main protease using combined docking and molecular dynamics simulations. Saudi Journal of Biological Sciences, 28(4), 2423–2431.
   PubMed 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 SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293.
   PubMed Web of Science ®Google Scholar
• Jolliffe, I. T. (2002). Principal component analysis. Springer series in statistics. Springer-Verlag.
   Google Scholar
• Jomhori, M., Mosaddeghi, H., & Farzin, H. (2021). Tracking the interaction between single-wall carbon nanotube and SARS-Cov-2 spike glycoprotein: A molecular dynamics simulations study. Computers in Biology and Medicine, 136, 104692.
   PubMed Web of Science ®Google Scholar
• Kandagalla, S., Rimac, H., Gurushankar, K., Novak, J., Grishina, M., & Potemkin, V. (2022). Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches. PeerJ. 10, e13374. https://doi.org/10.7717/peerj.13374
   PubMed Web of Science ®Google Scholar
• Keller, S., Nicholson, G., Drahl, C., Sorensen, E., Fiedler, H. P., & Süssmuth, R. D. (2007). Abyssomicins G and H and atrop-abyssomicin C from the marine Verrucosispora strain AB-18-032. The Journal of Antibiotics, 60(6), 391–394. https://doi.org/10.1038/ja.2007.54
   PubMed Web of Science ®Google Scholar
• Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., & Wang, X. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215–220. https://doi.org/10.1038/s41586-020-2180-5
   PubMed Web of Science ®Google Scholar
• León, B., Navarro, G., Dickey, B. J., Stepan, G., Tsai, A., Jones, G. S., Morales, M. E., Barnes, T., Ahmadyar, S., Tsiang, M., Geleziunas, R., Cihlar, T., Pagratis, N., Tian, Y., Yu, H., & Linington, R. G. (2015). Abyssomicin 2 reactivates latent HIV-1 by a PKC- and HDAC-independent mechanism. Organic Letters, 17(2), 262–265.
   PubMed Web of Science ®Google Scholar
• Lim, W. W., Wu, P., Bond, H. S., Wong, J. Y., Ni, K., Seto, W. H., Jit, M., & Cowling, B. J. (2019). Determinants of methicillin-resistant Staphylococcus aureus (MRSA) prevalence in the Asia-Pacific region: A systematic review and meta-analysis. Journal of Global Antimicrobial Resistance, 16, 17–27.
   PubMed Web of Science ®Google Scholar
• Lu, W. Y., Li, H. J., Li, Q. Y., & Wu, Y. C. (2021). Application of marine natural products in drug research. Bioorganic & Medicinal Chemistry, 35, 116058. https://doi.org/10.1016/j.bmc.2021.116058
   PubMed Web of Science ®Google Scholar
• Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101(5), 4177–4189. https://doi.org/10.1063/1.467468
   Web of Science ®Google Scholar
• Murugesan, S., Kottekad, S., Crasta, I., Sreevathsan, S., Usharani, D., Perumal, M. K., & Mudliar, S. N. (2021). Targeting COVID-19 (SARS-CoV-2) main protease through active phytocompounds of ayurvedic medicinal plants - Emblica officinalis (Amla), Phyllanthus niruri Linn. (Bhumi Amla) and Tinospora cordifolia (Giloy) - A molecular docking and simulation study. Computers in Biology and Medicine, 136, 104683. https://doi.org/10.1016/j.compbiomed.2021.104683
   PubMed 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), 79. https://doi.org/10.1186/s13765-020-00564-4
   PubMed Web of Science ®Google Scholar
• Naqvi, A., Fatima, K., Mohammad, T., Fatima, U., Singh, I. K., Singh, A., Atif, S. M., Hariprasad, G., Hasan, G. M., & Hassan, M. I. (2020). Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochimica et Biophysica Acta. Molecular Basis of Disease, 1866(10), 165878. https://doi.org/10.1016/j.bbadis.2020.165878
   PubMed Web of Science ®Google Scholar
• Niu, X. M., Li, S. H., Görls, H., Schollmeyer, D., Hilliger, M., Grabley, S., & Sattler, I. (2007). Abyssomicin E, a highly functionalized polycyclic metabolite from Streptomyces species. Organic Letters, 9(13), 2437–2440.
   PubMed Web of Science ®Google Scholar
• O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33–46.
   PubMed Web of Science ®Google Scholar
• Pfizer. (2021). Reduced risk of hospitalization or death by 89% in interim analysis of phase 2/3 EPIC-HR study. https://www.pfizer.com/news/press-release/press-release-detail/pfizers-novel-covid-19-oral-antiviral-treatment-candidate.
   Google Scholar
• Pushpakom, S., Iorio, F., Eyers, P. A., Escott, K. J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., Norris, A., Sanseau, P., Cavalla, D., & Pirmohamed, M. (2019). Drug repurposing: Progress, challenges and recommendations. Nature Reviews. Drug Discovery, 18(1), 41–58.
   PubMed Web of Science ®Google Scholar
• Rabaan, A. A., Al-Ahmed, S. H., Haque, S., Sah, R., Tiwari, R., Malik, Y. S., Dhama, K., Yatoo, M. I., Bonilla-Aldana, D. K., & Rodriguez-Morales, A. J. (2020). SARS-CoV-2, SARS-CoV, and MERS-COV: A comparative overview. Le Infezioni in Medicina, 28(2), 174–184.
   PubMedGoogle Scholar
• Rehman, M. T., AlAjmi, M. F., & Hussain, A. (2021). Natural compounds as inhibitors of SARS-CoV-2 main protease (3CLpro): A molecular docking and simulation approach to combat COVID-19. Current Pharmaceutical Design, 27(33), 3577–3589.
   PubMed Web of Science ®Google Scholar
• Sadaka, C., Ellsworth, E., Hansen, P. R., Ewin, R., Damborg, P., & Watts, J. L. (2018). Review on abyssomicins: Inhibitors of the chorismate pathway and folate biosynthesis. Molecules (Basel, Switzerland), 23(6), 1371–1396. https://doi.org/10.3390/molecules23061371
   PubMed Web of Science ®Google Scholar
• Schoeman, D., & Fielding, B. C. (2019). Coronavirus envelope protein: Current knowledge. Virology Journal, 16(1), 69.
   PubMed Web of Science ®Google Scholar
• Shamsi, A., Mohammad, T., Khan, M. S., Shahwan, M., Husain, F. M., Rehman, M. T., Hassan, M. I., Ahmad, F., & Islam, A. (2019). Unraveling binding mechanism of Alzheimer’s drug rivastigmine tartrate with human transferrin: molecular docking and multi-spectroscopic approach towards neurodegenerative diseases. Biomolecules, 9(9), 495. https://doi.org/10.3390/biom9090495
   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.
   PubMed Web of Science ®Google Scholar
• Song, Y., Li, Q., Qin, F., Sun, C., Liang, H., Wei, X., Wong, N.-K., Ye, L., Zhang, Y., Shao, M., & Ju, J. (2017). Neoabyssomicins A–C, polycyclic macrolactones from the deep-sea derived Streptomyces koyangensis SCSIO 5802. Tetrahedron, 73(36), 5366–5372. https://doi.org/10.1016/j.tet.2017.07.034
   Web of Science ®Google Scholar
• Wang, X., Elshahawi, S. I., Cai, W., Zhang, Y., Ponomareva, L. V., Chen, X., Copley, G. C., Hower, J. C., Zhan, C. G., Parkin, S., Rohr, J., Van Lanen, S. G., Shaaban, K. A., & Thorson, J. S. (2017). Bi- and tetracyclic spirotetronates from the coal mine fire isolate streptomyces sp. LC-6-2. Journal of Natural Products, 80(4), 1141–1149.
   PubMed Web of Science ®Google Scholar
• Wang, Q., Song, F., Xiao, X., Huang, P., Li, L., Monte, A., Abdel-Mageed, W. M., Wang, J., Guo, H., He, W., Xie, F., Dai, H., Liu, M., Chen, C., Xu, H., Liu, M., Piggott, A. M., Liu, X., Capon, R. J., & Zhang, L. (2013). Abyssomicins from the South China Sea deep-sea sediment Verrucosispora sp.: Natural thioether Michael addition adducts as antitubercular prodrugs. Angewandte Chemie (International ed. in English), 52(4), 1231–1234.
   PubMed Web of Science ®Google Scholar
• Woodhead, M., Ewig, S., & Torres, A. (2003). Severe acute respiratory syndrome (SARS). The European Respiratory Journal, 21(5), 739–740. https://doi.org/10.1183/09031936.03.00035403
   PubMed Web of Science ®Google Scholar
• Worldometers. (2022). COVID-19 coronavirus pandemic. https://www.worldometers.info/coronavirus/
   Google Scholar
• Wu, Q., Sabokroo, N., Wang, Y., Hashemian, M., Karamollahi, S., & Kouhsari, E. (2021). Systematic review and meta-analysis of the epidemiology of vancomycin-resistance Staphylococcus aureus isolates. Antimicrobial Resistance and Infection Control, 10(1), 101.
   PubMed Web of Science ®Google Scholar
• Zaki, A. M., van Boheemen, S., Bestebroer, T. M., Osterhaus, A. D., & Fouchier, R. A. (2012). Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. The New England Journal of Medicine, 367(19), 1814–1820. https://doi.org/10.1056/NEJMoa1211721
   PubMed Web of Science ®Google Scholar
• Zhang, J., Li, B., Qin, Y., Karthik, L., Zhu, G., Hou, C., Jiang, L., Liu, M., Ye, X., Liu, M., Hsiang, T., Dai, H., Zhang, L., & Liu, X. (2020). A new abyssomicin polyketide with anti-influenza A virus activity from a marine-derived Verrucosispora sp. Applied Microbiology and Biotechnology, 104(4), 1533–1543.
   PubMed 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.
   PubMed Web of Science ®Google Scholar