209
Views
3
CrossRef citations to date
0
Altmetric
Research Articles

In silico evaluation of NO donor heterocyclic vasodilators as SARS-CoV-2 Mpro protein inhibitor

ORCID Icon, ORCID Icon, ORCID Icon, , , ORCID Icon, & show all
Pages 280-297 | Received 28 Apr 2021, Accepted 08 Nov 2021, Published online: 23 Nov 2021

References

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Akaberi, D., Krambrich, J., Ling, J., Luni, C., Hedenstierna, G., Järhult, J. D., Lennerstrand, J., & Lundkvist, Å. (2020). Mitigation of the replication of SARS-CoV-2 by nitric oxide in vitro. Redox Biology, 37, 101734. https://doi.org/10.1016/j.redox.2020.101734
  • Åkerström, S., Gunalan, V., Keng, C. T., Tan, Y.-J., & Mirazimi, A. (2009). Dual effect of nitric oxide on SARS-CoV replication: Viral RNA production and palmitoylation of the S protein are affected. Virology, 395(1), 1–9. https://doi.org/10.1016/j.virol.2009.09.007
  • Akerström, S., Mousavi-Jazi, M., Klingström, J., Leijon, M., Lundkvist, A., & Mirazimi, A. (2005). Nitric oxide inhibits the replication cycle of severe acute respiratory syndrome coronavirus. Journal of Virology, 79(3), 1966–1969.https://doi.org/10.1128/JVI.79.3.1966-1969.2005
  • Al-Sehemi, A. G., Pannipara, M., Parulekar, R. S., Patil, O., Choudhari, P. B., Bhatia, M. S., Zubaidha, P. K., & Tamboli, Y. (2021). Potential of NO donor furoxan as SARS-CoV-2 main protease (Mpro) inhibitors: In silico analysis. Journal of Biomolecular Structure & Dynamics, 39(15), 5804–5818. https://doi.org/10.1080/07391102.2020.1790038
  • Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics, 17(4), 412–425. https://doi.org/10.1002/prot.340170408
  • Baildya, N., Ghosh, N. N., & Chattopadhyay, A. P. (2020). Inhibitory activity of hydroxychloroquine on COVID-19 main protease: An insight from MD-simulation studies. Journal of Molecular Structure, 1219, 128595. https://doi.org/10.1016/j.molstruc.2020.128595
  • Basha, G. M., Parulekar, R. S., Al-Sehemi, A. G., Pannipara, M., Siddaiah, V., Kumari, S., Choudhari, P. B., & Tamboli, Y. (2021). Design and in silico investigation of novel Maraviroc analogues as dual inhibition of CCR-5/SARS-CoV-2 Mpro. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2021.1955742
  • BIOVIA. (2020). DassaultSystèmes, [discovery studio]. DassaultSystèmes.
  • Chen, L., Liu, P., Gao, H., Sun, B., Chao, D., Wang, F., Zhu, Y., Hedenstierna, G., & Wang, C. G. (2004). Inhalation of nitric oxide in the treatment of severe acute respiratory syndrome: A rescue trial in Beijing. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 39(10), 1531–1535. https://doi.org/10.1086/425357
  • Elmaaty, A. A., Darwish, K. M., Khattab, M., Elhady, S. S., Salah, M., Hamed, M. I., Al‐Karmalawy, A. A., & Saleh, M. M. (2021). In a search for potential drug candidates for combating COVID-19: Computational study revealed salvianolic acid B as a potential therapeutic targeting 3CLpro and spike proteins. Journal of Biomolecular Structure and Dynamics, 1–28. https://doi.org/10.1080/07391102.2021.1918256
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
  • Fershtat, L. L., & Makhova, N. N. (2017). Molecular hybridization tools in the development of furoxan-based NO-donor prodrugs. ChemMedChem, 12(9), 622–638. https://doi.org/10.1002/cmdc.201700113
  • Frostell, C. G., & Hedenstierna, G. (2021). Nitric oxide and COVID-19: Dose, timing and how to administer it might be crucial. Acta Anaesthesiologica Scandinavica, 65(5), 576–577. https://doi.org/10.1111/aas.13788
  • Gasco, A., Fruttero, R., Sorba, G., Di Stilo, A., & Calvino, R. (2004). NO donors: Focus on furoxan derivatives. Pure and Applied Chemistry, 76(5), 973–981. https://doi.org/10.1351/pac200476050973
  • Ghosh, A. K., Brindisi, M., Shahabi, D., Chapman, M. E., & Mesecar, A. D. (2020). Drug development and medicinal chemistry efforts toward SARS-coronavirus and covid-19 therapeutics. ChemMedChem, 15(11), 907–932. https://doi.org/10.1002/cmdc.202000223
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12 < 1463::AID-JCC4 > 3.0.CO;2-H
  • Maffei, D., & Choi, S. (2020). Gilead Announces Results From Phase 3 Trial of Investigational Antiviral Remdesivir in Patients With Severe COVID-19. https://www.gilead.com/news-and-press/press-room/press-releases/2020/4/gilead-announces-results-from-phase-3-trial-of-investigational-antiviral-remdesivir-in-patients-with-severe-covid-19
  • https://www.visualcapitalist.com/every-vaccine-treatment-covid-19-so-far/. (2020).
  • https://www.wwpdb.org/pdb?id=pdb_00006w63
  • Huynh, T., Wang, H., & Luan, B. (2020). In silico exploration of the molecular mechanism of clinically oriented drugs for possibly inhibiting SARS-CoV-2's main protease. The Journal of Physical Chemistry Letters, 11(11), 4413–4420. https://doi.org/10.1021/acs.jpclett.0c00994
  • 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
  • Joshi, T., Sharma, P., Joshi, T., Pundir, H., Mathpal, S., & Chandra, S. (2021). Structure-based screening of novel lichen compounds against SARS Coronavirus main protease (Mpro) as potentials inhibitors of COVID-19. Molecular Diversity, 25(3), 1665–1677. https://doi.org/10.1007/s11030-020-10118-x
  • Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105(28), 6474–6487. https://doi.org/10.1021/jp003919d
  • Kanhed, A. M., Patel, D. V., Teli, D. M., Patel, N. R., Chhabria, M. T., & Yadav, M. R. (2021). Identification of potential Mpro inhibitors for the treatment of COVID-19 by using systematic virtual screening approach. Molecular Diversity, 25(1), 383–401. https://doi.org/10.1007/s11030-020-10130-1
  • Keyaerts, E., Vijgen, L., Chen, L., Maes, P., Hedenstierna, G., & Van Ranst, M. (2004). Inhibition of SARS-coronavirus infection in vitro by S-nitroso-N-acetylpenicillamine, a nitric oxide donor compound. International Journal of Infectious Diseases, 8(4), 223–226. https://doi.org/10.1016/j.ijid.2004.04.012
  • Kumari, R., Kumar, R., Open Source Drug Discovery Consortium, & Lynn, A. (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
  • Lin, F. Y., & MacKerell, A. D. Jr. (2017). Do halogen-hydrogen bond donor interactions dominate the favorable contribution of halogens to ligand-protein binding? The Journal of Physical Chemistry, B, 121(28), 6813–6821. https://doi.org/10.1021/acs.jpcb.7b04198
  • Mannick, J. B. (1995). The antiviral role of nitric oxide. Research in Immunology, 146(9), 693–697. https://doi.org/10.1016/0923-2494(96)84920-0
  • Mohanta, T. K., Mishra, A. K., Khan, A., Hashem, A., Abd-Allah, E. F., & Al-Harrasi, A. (2021). Virtual 2-D map of the fungal proteome. Scientific Reports, 11(1), 6676.https://doi.org/10.1038/s41598-021-86201-6
  • Parulekar, R. S., & Sonawane, K. D. (2018a). Insights into the antibiotic resistance and inhibition mechanism of aminoglycoside phosphotransferase from Bacillus cereus: In silico and in vitro perspective. Journal of Cellular Biochemistry, 119(11), 9444–9461. https://doi.org/10.1002/jcb.27261
  • Parulekar, R. S., & Sonawane, K. D. (2018b). Molecular modeling studies to explore the binding affinity of virtually screened inhibitor toward different aminoglycoside kinases from diverse MDR strains. Journal of Cellular Biochemistry, 119(3), 2679–2695. https://doi.org/10.1002/jcb.26435
  • 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
  • Pooladanda, V., Thatikonda, S., & Godugu, C. (2020). The current understanding and potential therapeutic options to combat COVID-19. Life Sciences, 254, 117765. https://doi.org/10.1016/j.lfs.2020.117765
  • Reiss, C. S., & Komatsu, T. (1998). Does nitric oxide play a critical role in viral infections? Journal of Virology, 72(6), 4547–4551.https://doi.org/10.1128/JVI.72.6.4547-4551.1998.
  • Saura, M., Zaragoza, C., McMillan, A., Quick, R. A., Hohenadl, C., Lowenstein, J. M., & Lowenstein, C. J. (1999). An antiviral mechanism of nitric oxide: Inhibition of a viral protease. Immunity, 10(1), 21–28. https://doi.org/10.1016/S1074-7613(00)80003-5
  • Shigeta, S., & Yamase, T. (2005). Current status of anti-SARS agents. Antiviral Chemistry & Chemotherapy, 16(1), 23–31. https://doi.org/10.1177/095632020501600103
  • Swami, P., Tamboli, Y., & Zubaidha, P. (2020). Synthesis and bioactivity studies of novel oxopiperazine NO donors. International Conference on “Drug Discovery and Development: Lab to Clinic” (DDD LC-2020). Nanded, Maharashtra: SRTM University.
  • Swami, P. M., Zubaidha, P. K., & Tiwari, G. B. (2019). Synthesis of novel nitric oxide releasing furoxan hybrids from biologically active bicyclic amine and their antioxidant activity. Asian Journal of Chemistry, 31(8), 1724–1728. https://doi.org/10.14233/ajchem.2019.21948
  • USA National Library of Medicine. (2020). Nitric Oxide Inhalation Therapy for COVID-19 Infections in the ED (NO COV-ED). https://clinicaltrials.gov/ct2/show/NCT04338828
  • Van Aalten, D. M., Bywater, R., Findlay, J. B., Hendlich, M., Hooft, R. W., & Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design, 10(3), 255–262. https://doi.org/10.1007/BF00355047
  • WHO novel coronavirus (2019-nCoV) situation report. (2020).
  • Worldometer. (2021). COVID-19 CORONAVIRUS PANDEMIC. https://www.worldometers.info/coronavirus
  • www.rcsb.org
  • www.vlifesciences.com
  • Zaki, A. A., Al-Karmalawy, A. A., El-Amier, Y. A., & Ashour, A. (2020). Molecular docking reveals the potential of Cleome amblyocarpa isolated compounds to inhibit COVID-19 virus main protease. New Journal of Chemistry, 44(39), 16752–16758. https://doi.org/10.1039/D0NJ03611K
  • Zaki, A. A., Ashour, A., Elhady, S. S., Darwish, K. M., & Al-Karmalawy, A. A. (2021). Calendulaglycoside A showing potential activity against SARS-CoV-2 main protease: Molecular docking, molecular dynamics, and SAR studies. Journal of Traditional and Complementary Medicine, 1–19. https://doi.org/10.1016/j.jtcme.2021.05.001
  • 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

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.