Vol 67 No 2 (2022): Journal of the Chilean Chemical Society
Original Research Papers
DETERMINATION OF PROTEINS ASSOCIATED WITH COVID-19 BASED LIGAND DESIGNING AND MOLECULAR MODELING
Published
June 24, 2022
Keywords
- Covid-19; RBD or Receptor binding domain; Gillan‘s leaves plants, ACE2 or Angiotensin Converting Enzyme-2; PD or protease domain
How to Cite
Mollaamin, F. (2022). DETERMINATION OF PROTEINS ASSOCIATED WITH COVID-19 BASED LIGAND DESIGNING AND MOLECULAR MODELING. Journal of the Chilean Chemical Society, 67(2), 5468-5476. Retrieved from https://jcchems.com/index.php/JCCHEMS/article/view/1907
Copyright (c) 2022 SCh
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Abstract
Towards to recognize a strong inhibitor we accomplished docking studies on the major virus protease with 4 natural product species as anti Covid-19(SARS-CoV-2), namely “Vidarabine”, “Cytarabine”, “Gemcitabine” and “Matrine” from which are extractive from Gillan’s leaves plants. These are known as Chuchaq, Trshvash, Cote-Couto and Khlvash in Iran. Among these four studied compounds, Cytarabine appear as suitable compound with high effectiveness inhibitors to this protease. With docking simulation and NMR investigation we demonstrated, these compounds exhibit a suitable binding energy around 9 Kcal/mol with various ligand proteins modes in the binding to COVID-19 viruses. However, these data need further in both, vivo & vitro evaluation for repurposing these drugs against COVID-19 viruses.
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Monajjemi M., (2015) Cell membrane causes the lipid bilayers to behave as variable capacitors: A resonance with self-induction of helical proteins , Biophysical Chemistry, 207, 114 –127
Mirza, M. U. et al. (2016) Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins. Scientific reports 6, 37313
Nain, Z., Karim, M. M., Sen, M. K. & Adhikari, U. K. (2019) Structural Basis and Designing of Peptide Vaccine using PE-PGRS Family Protein of Mycobacterium ulcerans–An Integrated Vaccinomics Approach. bioRxiv, 795146
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Paraskevis, D. et al. (2020) Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the
hypothesis of emergence as a result of a recent recombination event. Infection, Genetics and Evolution,
104212.
Pandey, R. K., Bhatt, T. K. & Prajapati, V. K. (2018) Novel immunoinformatics approaches to design multi-epitope subunit vaccine for malaria by investigating anopheles salivary protein. Scientific reports 8, 1-11
Rothe, C. et al. (2020) Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. New
England Journal of Medicine
Schwede, T., Kopp, J., Guex, N. & Peitsch, M. C. (2003) SWISS-MODEL: an automated protein
homology-modeling server. Nucleic acids research 31, 3381-3385 (2003).
Surya, W., Li, Y., Torres, J. (2018), Structural model of the SARS coronavirus E channel in LMPG micelles, Biochim Biophys Acta , 1860: 1309-1317
Santos, Y.M., Barraza, S.J., Wilson, M.W., Agius, M.P., Mielech, A.M., Davis, N.M., Baker, S.C.,Larsen, S.D., Mesecar, A.D. (2014) X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases. J.Med.Chem. 57, 2393-2412, https://doi.org/10.1021/jm401712t.
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Saikatendu, K.S., Joseph, J.S., Subramanian, V., Neuman, B.W., Buchmeier, M.J., Stevens, R.C., Kuhn, P. (2007) Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein. J Virol 81: 3913-3921
Shahid, F., Ashfaq, U. A., Javaid, A. & Khalid, H. (2020) Immunoinformatics guided rational design of a next generation multi epitope based peptide (MEBP) vaccine by exploring Zika virus proteome. Infection, Genetics and Evolution 80, 104199
Tahir ul Qamar, M. et al. (2018) Peptide vaccine against chikungunya virus: immuno- informatics combined with molecular docking approach. Journal of translational medicine 16, 298
Walker, J. M. The proteomics protocols handbook. (Springer, 2005).
Waterhouse, A. et al. (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research 46, W296-W303
Zhenming Jin, Xiaoyu Du, […] Haitao Yang , (2020), Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors , Nature volume 582, pages289–293
Zhang, C.; Zheng, W.; Huang, X.; Bell, E.W.; Zhou, X.; Zhang, Y. (2020) Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. Journal of Proteome Research, 19, 1351-1360, https://doi.org/10.1021/ acs.jproteome.0c00129.
Báez-Santos, Y.M., Barraza, S.J., Wilson, M.W.,Agius, M.P., Mielech, A.M., Davis, N.M., Baker, S.C., Larsen, S.D., Mesecar, A.D. (2014) X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases. Journal of Medicinal Chemistry, 57, 2393-2412, http://dx.doi.org/10.1021/jm401712t.
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Sayers, E. W. (2008) GenBank. 2 Nucleic acids research 37, D26-D31
Bailey, T. L., Johnson, J., Grant, C. E. & Noble, W. S. (2015) the MEME suite. Nucleic acids research 43, W39-W49 (2015).
Bailey, T. L. et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic acids research 37, W202-W208 .
Biasini, M. et al. (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic acids research 42, W252-W258 (2014).
Bailey, T. L., Williams, N., Misleh, C. & Li, W. W. (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic acids research 34, W369-W373 .
Cheng F. (2019) In Silico Oncology Drug Repositoning and Polypharmacology. Methods Mol Biol 2019;1878:243-61.
Doytchinova, I. A., Flower, D. R. VaxiJen: (2007)a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC bioinformatics 8, 4
Deléage, G. (2017) ALIGNSEC: viewing protein secondary structure predictions within large multiple sequence alignments. Bioinformatics
Desmond Molecular Dynamics System, D. E. Shaw Research. (2020). Maestro-Desmond interoperability tools. New York, NY: Schrodinger. ECT Register. (2020, April 10). https://www.clinicaltrialsregister.eu/ ctrsearch/search? query=covid-19
De Gregorio, E., Rappuoli, R., (2012) Vaccines for the future: learning from human immunology. Microbial biotechnology 5, 149-155.
Dai, L., Song, J., Lu, X., Deng, Y.Q., Musyoki, A.M., Cheng, H., Zhang, Y., Yuan, Y., Song, H., Haywood, ., Xiao, H., Yan, J., Shi, Y., Qin, C.F., Qi, J., Gao, G.F.(2016) Structures of the Zika Virus Envelope Protein and Its Complex with a Flavivirus Broadly Protective Antibody. Cell Host Microbe , 19: 696-704
Gordon, D.E., Jang, G.M., Bouhaddou, M., Xu, J., Obernier, K., O’Meara, M.J.,..., & Krogan, N.J. (2020). A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv doi: https://doi.org/10.1101/2020.03.22.002386
Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S.,..., & Pöhlmann, S. (2020).SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. doi: https://doi.org/10.1016/j.cell.2020.02.052.
Hilgenfeld, R., (2014), From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J., 281,4085-4096, https://doi.org/10.1111/febs.12936.
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). Bioorg. Med. Chem. 23, 6036-6048, https://doi.org/10.1016/ j.bmc.2015.06.039.
Kazazian Jr, H. H., Woodhead, A. P. (1973) Hemoglobin A synthesis in the developing fetus. New England Journal of Medicine 289, 58-62
Khan, A. et al. (2018) Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches. PloS one 13 (2018).
Källberg, M. et al. Template-based protein structure modeling using the RaptorX web server. (2012) Nature Protocols 7, 1511-1522, doi:10.1038/nprot.2012.085 (2012).
Lehmann, K.C., Gulyaeva, A., Zevenhoven-Dobbe, J.C., Janssen, G.M., Ruben, M., Overkleeft, H.S., van Veelen, P.A., Samborskiy, D.V., Kravchenko, A.A., Leontovich, A.M., Sidorov, I.A., Snijder, E.J., Posthuma, C.C., Gorbalenya, A.E. (2015) Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses. Nucleic Acids Res, 43, 8416-8434, https://doi.org/10.1093/nar/gkv838.
Li, S. et al. (2020) Regulation of the ER Stress Response by the Ion Channel Activity of the Infectious Bronchitis
Coronavirus Envelope Protein Modulates Virion Release, Apoptosis, Viral Fitness, and Pathogenesis.
Frontiers in Microbiology 10, 3022.
Meier, C., Aricescu, A.R., Assenberg, R., Aplin, R.T., Gilbert, R.J.C., Grimes, J.M., Stuart, D.I.(2006) The Crystal Structure of Orf-9B, a Lipid Binding Protein from the Sars Coronavirus., Structure 14: 1157
Monajjemi, M., Shahriari, S., Mollaamin, F.,(2020) Evaluation of Coronavirus Families & Covid-19 Proteins: Molecular Modeling Study, Biointerface Res. Appl. Chem., Volume 10, Issue 5,
Monajjemi, M., Mollaamin, F., Shojae, S., (2020) An overview on Coronaviruses family from past to Covid-19: introduce some inhibitors as antiviruses from Gillan’s plants, Biointerface Res. Appl. Chem., Volume 10, Issue 3,
Monajjemi M., (2015) Cell membrane causes the lipid bilayers to behave as variable capacitors: A resonance with self-induction of helical proteins , Biophysical Chemistry, 207, 114 –127
Mirza, M. U. et al. (2016) Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins. Scientific reports 6, 37313
Nain, Z., Karim, M. M., Sen, M. K. & Adhikari, U. K. (2019) Structural Basis and Designing of Peptide Vaccine using PE-PGRS Family Protein of Mycobacterium ulcerans–An Integrated Vaccinomics Approach. bioRxiv, 795146
Patronov, A., Doytchinova, (2013) I. T-cell epitope vaccine design by immunoinformatics. Open biology 3, 120139.
Paraskevis, D. et al. (2020) Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the
hypothesis of emergence as a result of a recent recombination event. Infection, Genetics and Evolution,
104212.
Pandey, R. K., Bhatt, T. K. & Prajapati, V. K. (2018) Novel immunoinformatics approaches to design multi-epitope subunit vaccine for malaria by investigating anopheles salivary protein. Scientific reports 8, 1-11
Rothe, C. et al. (2020) Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. New
England Journal of Medicine
Schwede, T., Kopp, J., Guex, N. & Peitsch, M. C. (2003) SWISS-MODEL: an automated protein
homology-modeling server. Nucleic acids research 31, 3381-3385 (2003).
Surya, W., Li, Y., Torres, J. (2018), Structural model of the SARS coronavirus E channel in LMPG micelles, Biochim Biophys Acta , 1860: 1309-1317
Santos, Y.M., Barraza, S.J., Wilson, M.W., Agius, M.P., Mielech, A.M., Davis, N.M., Baker, S.C.,Larsen, S.D., Mesecar, A.D. (2014) X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases. J.Med.Chem. 57, 2393-2412, https://doi.org/10.1021/jm401712t.
Sevajol, M.,Subissi, L., Decroly, E., Canard, B., Imbert, I. (2014) Insights into RNA synthesis, capping, and proofreading mechanisms of SARS-coronavirus. Virus Res. 194, 90–99, https://doi.org/10.1016 /j.virusres. 2014.10.008.
Schrodinger. (2020). € Schrodinger Release 2020-1: BioLuminate € . New York, NY. https://www.schrodinger.com/
Saadi, M., Karkhah, A.,Nouri, H. R.(2017) Development of a multi-epitope peptide vaccine inducing robust T cell responses against brucellosis using immunoinformatics based approaches. Infection, Genetics and Evolution 51, 227-234
Saikatendu, K.S., Joseph, J.S., Subramanian, V., Neuman, B.W., Buchmeier, M.J., Stevens, R.C., Kuhn, P. (2007) Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein. J Virol 81: 3913-3921
Shahid, F., Ashfaq, U. A., Javaid, A. & Khalid, H. (2020) Immunoinformatics guided rational design of a next generation multi epitope based peptide (MEBP) vaccine by exploring Zika virus proteome. Infection, Genetics and Evolution 80, 104199
Tahir ul Qamar, M. et al. (2018) Peptide vaccine against chikungunya virus: immuno- informatics combined with molecular docking approach. Journal of translational medicine 16, 298
Walker, J. M. The proteomics protocols handbook. (Springer, 2005).
Waterhouse, A. et al. (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research 46, W296-W303
Zhenming Jin, Xiaoyu Du, […] Haitao Yang , (2020), Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors , Nature volume 582, pages289–293
Zhang, C.; Zheng, W.; Huang, X.; Bell, E.W.; Zhou, X.; Zhang, Y. (2020) Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. Journal of Proteome Research, 19, 1351-1360, https://doi.org/10.1021/ acs.jproteome.0c00129.
