Computational screening of natural products to identify potential inhibitors for human neuropilin-1 (NRP1) receptor to abrogate the binding of SARS-CoV-2 and host cell

References

• Abdalla, M., Eltayb, W. A., El-Arabey, A. A., Singh, K., & Jiang, X. (2022). Molecular dynamic study of SARS-CoV-2 with various S protein mutations and their effect on thermodynamic properties. Computers in Biology and Medicine, 141, 105025. https://doi.org/10.1016/j.compbiomed.2021.105025
   PubMed Web of Science ®Google Scholar
• Acter, T., Uddin, N., Das, J., Akhter, A., Choudhury, T. R., & Kim, S. (2020). Evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as coronavirus disease 2019 (COVID-19) pandemic: A global health emergency. The Science of the Total Environment, 730, 138996–138996. https://doi.org/10.1016/j.scitotenv.2020.138996
   PubMed Web of Science ®Google Scholar
• Alameen, A. A., Abdalla, M., Alshibl, H. M., AlOthman, M. R., Alkhulaifi, M. M., Mirgany, T. O., & Elsayim, R. (2022). In-silico studies of glutathione peroxidase4 activators as candidate for multiple sclerosis management. Journal of Saudi Chemical Society, 26(6), 101554. https://doi.org/10.1016/j.jscs.2022.101554
   Web of Science ®Google Scholar
• Alamri, M. A., Tahir Ul Qamar, M., Mirza, M. U., Bhadane, R., Alqahtani, S. M., Muneer, I., Froeyen, M., & Salo-Ahen, O. M. H. (2021). Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro. Journal of Biomolecular Structure & Dynamics, 39(13), 4936–4948. https://doi.org/10.1080/07391102.2020.1782768
   PubMed Web of Science ®Google Scholar
• Alamri, M. A., Ul Qamar, M. T., Mirza, M. U., Alqahtani, S. M., Froeyen, M., & Chen, L.-L. (2020). Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches. Journal of Pharmaceutical Analysis, 10(6), 546–559. https://doi.org/10.1016/j.jpha.2020.08.012
   PubMed Web of Science ®Google Scholar
• Al-Jumaili, M. H. A., Siddique, F., Abul Qais, F., Hashem, H. E., Chtita, S., Rani, A., Uzair, M., & Almzaien, K. A. (2021). Analysis and prediction pathways of natural products and their cytotoxicity against HeLa cell line protein using docking, molecular dynamics and ADMET. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2021.2011785
   Google Scholar
• Ammar, S., Mahjoub, M. A., Charfi, N., Skandarani, I., Chekir-Ghedira, L., & Mighri, Z. (2007). Mutagenic, antimutagenic and antioxidant activities of a new class of β-Glucoside hydroxyhydroquinone from Anagallis monelli growing in Tunisia. Chemical & Pharmaceutical Bulletin, 55(3), 385–388. https://doi.org/10.1248/cpb.55.385
   PubMed Web of Science ®Google Scholar
• Cantuti-Castelvetri, L., Ojha, R., Pedro, L. D., Djannatian, M., Franz, J., Kuivanen, S., van der Meer, F., Kallio, K., Kaya, T., Anastasina, M., Smura, T., Levanov, L., Szirovicza, L., Tobi, A., Kallio-Kokko, H., Österlund, P., Joensuu, M., Meunier, F. A., Butcher, S. J., … Simons, M. (2020). Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science (New York, N.Y.), 370(6518), 856–860. https://doi.org/10.1126/science.abd2985
   PubMed Web of Science ®Google Scholar
• Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
   PubMed Web of Science ®Google Scholar
• Chapoval, S. P., & Keegan, A. D. (2021). Perspectives and potential approaches for targeting neuropilin 1 in SARS-CoV-2 infection. Molecular Medicine (Cambridge, Mass.), 27(1), 162. https://doi.org/10.1186/s10020-021-00423-y
   PubMed Web of Science ®Google Scholar
• Chen, F., Liu, H., Sun, H., Pan, P., Li, Y., Li, D., & Hou, T. (2016). Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking. Physical Chemistry Chemical Physics : PCCP, 18(32), 22129–22139. https://doi.org/10.1039/c6cp03670h
   PubMed Web of Science ®Google Scholar
• Choi, J. Y., & Smith, D. M. (2021). SARS-CoV-2 Variants of concern. Yonsei Medical Journal, 62(11), 961–968. https://doi.org/10.3349/ymj.2021.62.11.961
   PubMed Web of Science ®Google Scholar
• Chuckran, C. A., Liu, C., Bruno, T. C., Workman, C. J., & Vignali, D. A. (2020). Neuropilin-1: A checkpoint target with unique implications for cancer immunology and immunotherapy. Journal for ImmunoTherapy of Cancer, 8(2), e000967. https://doi.org/10.1136/jitc-2020-000967
   PubMed Web of Science ®Google Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx Chemical biology (pp. 243–250): Springer.
   Google Scholar
• Devaux, C. A., Lagier, J.-C., & Raoult, D. (2021). New insights into the physiopathology of COVID-19: SARS-CoV-2-associated gastrointestinal illness. Frontiers in Medicine, 8, 640073. https://doi.org/10.3389/fmed.2021.640073
   PubMed Web of Science ®Google Scholar
• Duong, D. (2021). Alpha, Beta, Delta, Gamma: What’s important to know about SARS-CoV-2 variants of concern? Canadian Medical Association.
   Web of Science ®Google Scholar
• Elfiky, A. A. (2020). SARS-CoV-2 spike-heat shock protein A5 (GRP78) recognition may be related to the immersed human coronaviruses. Frontiers in Pharmacology, 11, 1997. https://doi.org/10.3389/fphar.2020.577467
   Web of Science ®Google Scholar
• Gagnon, M. L., Bielenberg, D. R., Gechtman, Z. E., Miao, H.-Q., Takashima, S., Soker, S., & Klagsbrun, M. (2000). Identification of a natural soluble neuropilin-1 that binds vascular endothelial growth factor: In vivo expression and antitumor activity. Proceedings of the National Academy of Sciences of the United States of America, 97(6), 2573–2578. https://doi.org/10.1073/pnas.040337597
   PubMed Web of Science ®Google Scholar
• Gioelli, N., Neilson, L. J., Wei, N., Villari, G., Chen, W., Kuhle, B., Ehling, M., Maione, F., Willox, S., Brundu, S., Avanzato, D., Koulouras, G., Mazzone, M., Giraudo, E., Yang, X.-L., Valdembri, D., Zanivan, S., & Serini, G. (2022). Neuropilin 1 and its inhibitory ligand mini-tryptophanyl-tRNA synthetase inversely regulate VE-cadherin turnover and vascular permeability. Nature Communications, 13(1), 4188. https://doi.org/10.1038/s41467-022-31904-1
   PubMed Web of Science ®Google Scholar
• Goddard, T. D., Huang, C. C., & Ferrin, T. E. (2005). Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure (London, England : 1993), 13(3), 473–482. https://doi.org/10.1016/j.str.2005.01.006
   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. The Lancet, 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
   PubMed Web of Science ®Google Scholar
• Humayun, F., Khan, A., Ahmad, S., Yuchen, W., Wei, G., Nizam-Uddin, N., Hussain, Z., Khan, W., Zaman, N., Rizwan, M., Waseem, M., & Wei, D.-Q. (2022). Abrogation of SARS-CoV-2 interaction with host (NRP1) Neuropilin-1 receptor through high-affinity marine natural compounds to curtail the infectivity: A structural-dynamics data. Computers in Biology and Medicine, 141, 104714. https://doi.org/10.1016/j.compbiomed.2021.104714
   PubMed Web of Science ®Google Scholar
• Ibrahim, I. M., Abdelmalek, D. H., Elshahat, M. E., & Elfiky, A. A. (2020). COVID-19 spike-host cell receptor GRP78 binding site prediction. The Journal of Infection, 80(5), 554–562. https://doi.org/10.1016/j.jinf.2020.02.026
   PubMed Web of Science ®Google Scholar
• Khadake, S. N., Karamathulla, S., Jena, T. K., Monisha, M., Tuti, N. K., Khan, F. A., & Anindya, R. (2021). Synthesis and antibacterial activities of marine natural product ianthelliformisamines and subereamine synthetic analogues. Bioorganic & Medicinal Chemistry Letters, 39, 127883. https://doi.org/10.1016/j.bmcl.2021.127883
   PubMed Web of Science ®Google Scholar
• Khan, A., Kaushik, A. C., Ali, S. S., Ahmad, N., & Wei, D.-Q. (2019). Deep-learning-based target screening and similarity search for the predicted inhibitors of the pathways in Parkinson’s disease. RSC Advances, 9(18), 10326–10339. https://doi.org/10.1039/c9ra01007f
   PubMed Web of Science ®Google Scholar
• Khan, A., Khan, T., Ali, S., Aftab, S., Wang, Y., Qiankun, W., Khan, M., Suleman, M., Ali, S., Heng, W., Ali, S. S., Wei, D.-Q., & Mohammad, A. (2021). SARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines. Biomedicine & Pharmacotherapy, 143, 112176. https://doi.org/10.1016/j.biopha.2021.112176
   PubMed Web of Science ®Google Scholar
• Khan, A., Waris, H., Rafique, M., Suleman, M., Mohammad, A., Ali, S. S., Khan, T., Waheed, Y., Liao, C., & Wei, D.-Q. (2022). The Omicron (B. 1.1. 529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data. International Journal of Biological Macromolecules, 200, 438–448. 10.1016/j.ijbiomac.2022.01.059
   PubMed Web of Science ®Google Scholar
• Lagorce, D., Bouslama, L., Becot, J., Miteva, M. A., & Villoutreix, B. O. (2017). FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics (Oxford, England), 33(22), 3658–3660. https://doi.org/10.1093/bioinformatics/btx491
   PubMed Web of Science ®Google Scholar
• Lauring, A. S., & Malani, P. N. (2021). Variants of SARS-CoV-2. JAMA, 326(9), 880–880. https://doi.org/10.1001/jama.2021.14181
   Web of Science ®Google Scholar
• Mayi, B. S., Leibowitz, J. A., Woods, A. T., Ammon, K. A., Liu, A. E., & Raja, A. (2021). The role of Neuropilin-1 in COVID-19. PLoS Pathogens, 17(1), e1009153. https://doi.org/10.1371/journal.ppat.1009153
   PubMed Web of Science ®Google Scholar
• Mohammed Hadi Ali, A.-J. (2021). The Impact of COVID-19 on Iraqi Community: a descriptive study based on data reported from the Ministry of Health in Iraq. The Journal of Infection in Developing Countries, (9), 15. https://doi.org/10.3855/jidc.15010
   Google Scholar
• Moutal, A., Martin, L. F., Boinon, L., Gomez, K., Ran, D., Zhou, Y., Stratton, H. J., Cai, S., Luo, S., Gonzalez, K. B., Perez-Miller, S., Patwardhan, A., Ibrahim, M. M., & Khanna, R. (2021). SARS-CoV-2 Spike protein co-opts VEGF-A/neuropilin-1 receptor signaling to induce analgesia. Pain, 162(1), 243–252. https://doi.org/10.1097/j.pain.0000000000002097
   PubMed Web of Science ®Google Scholar
• Petrenko, V. A., Gillespie, J. W., De Plano, L. M., & Shokhen, M. A. (2022). Phage-displayed mimotopes of SARS-CoV-2 spike protein targeted to authentic and alternative cellular receptors. Viruses, 14(2), 384. https://doi.org/10.3390/v14020384
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Rabie, A. M. (2021). CoViTris2020 and ChloViD2020: a striking new hope in COVID-19 therapy. Molecular Diversity, 25(3), 1839–1854. https://doi.org/10.1007/s11030-020-10169-0
   PubMed Web of Science ®Google Scholar
• Rabie, A. M. (2021). Two antioxidant 2, 5-disubstituted-1, 3, 4-oxadiazoles (CoViTris2020 and ChloViD2020): successful repurposing against COVID-19 as the first potent multitarget anti-SARS-CoV-2 drugs. New Journal of Chemistry, 45(2), 761–771. https://doi.org/10.1039/D0NJ03708G
   Web of Science ®Google Scholar
• Roe, D. R., & Cheatham, T. E. III, (2013). PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Rose, P. W., Prlić, A., Altunkaya, A., Bi, C., Bradley, A. R., Christie, C. H., … Feng, Z. (2016). The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Research, gkw1000.
   Web of Science ®Google Scholar
• Sarkar, C., Abdalla, M., Mondal, M., Khalipha, A. B. R., & Ali, N. (2021). Ebselen suitably interacts with the potential SARS-CoV-2 targets: an in-silico approach. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2021.1971562
   Web of Science ®Google Scholar
• Simoben, C. V., Qaseem, A., Moumbock, A. F., Telukunta, K. K., Günther, S., Sippl, W., & Ntie‐Kang, F. (2020). Pharmacoinformatic investigation of medicinal plants from East Africa. Molecular Informatics, 39(11), 2000163. https://doi.org/10.1002/minf.202000163
   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
• Ul Qamar, M. T., Alqahtani, S. M., Alamri, M. A., & Chen, L.-L. (2020). Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. Journal of Pharmaceutical Analysis, 10(4), 313–319. https://doi.org/10.1016/j.jpha.2020.03.009
   PubMed Web of Science ®Google Scholar
• Wang, Y., Khan, A., Chandra Kaushik, A., Junaid, M., Zhang, X., & Wei, D.-Q. (2019). The systematic modeling studies and free energy calculations of the phenazine compounds as anti-tuberculosis agents. Journal of Biomolecular Structure & Dynamics, 37(15), 4051–4069. https://doi.org/10.1080/07391102.2018.1537896
   PubMed Web of Science ®Google Scholar
• Wu, C-r., Yin, W-c., Jiang, Y., & Xu, H. E. (2022). Structure genomics of SARS-CoV-2 and its Omicron variant: drug design templates for COVID-19. Acta Pharmacologica Sinica, https://doi.org/10.1038/s41401-021-00851-w
   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
   PubMed Web of Science ®Google Scholar