463
Views
3
CrossRef citations to date
0
Altmetric
Research Articles

Investigation of berberine and its derivatives in Sars Cov-2 main protease structure by molecular docking, PROTOX-II and ADMET methods: in machine learning and in silico study

ORCID Icon, ORCID Icon, , , ORCID Icon, , ORCID Icon & ORCID Icon show all
Pages 9366-9381 | Received 21 Jul 2022, Accepted 24 Oct 2022, Published online: 11 Nov 2022

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
  • Aldahham, B. J. M., Al-Khafaji, K., Saleh, M. Y., Abdelhakem, A. M., Alanazi, A. M., & Islam, M. A. (2022). Identification of naphthyridine and quinoline derivatives as potential Nsp16-Nsp10 inhibitors: a pharmacoinformatics study. Journal of Biomolecular Structure and Dynamics, 40(9), 3899–3906. https://doi.org/10.1080/07391102.2020.1851305
  • Banerjee, P., Eckert, O. A., Schrey, K. A., & Preissner, R. (2018). ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263. https://doi.org/10.1093/nar/gky318.
  • Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B., & Lindahl, E. (2010). Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459–466. https://doi.org/10.1021/ct900549r
  • Bodiwala, H. S., Sabde, S., Mitra, D., Bhutani, K. K., & Singh, P. (2011). Synthesis of 9-substituted derivatives of berberine as anti-HIV agents. European Journal of Medicinal Chemistry, 46(4), 1045–1049. https://doi.org/10.1016/j.ejmech.2011.01.016.
  • Cui, H.-M., Zhang, Q.-Y., Wang, J.-L., Chen, J.-L., Zhang, Y.-L., & Tong, X.-L. (2014). In vitro studies of berberine metabolism and its effect of enzyme induction of HepG2 cells. Journal of Ethnopharmacology, 158, 388–396. https://doi.org/10.1016/j.jep.2014.10.018
  • 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.
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
  • Davies, M., Nowotka, M., Papadatos, G., Dedman, N., Gaulton, A., Atkinson, F., Bellis, L., & Overington, J. P. (2015). ChEMBL web services: streamlining access to drug discovery data and utilities. Nucleic Acids Research, 43(W1), W612–W620. volumehttps://doi.org/10.1093/nar/gkv352
  • Domitrović, R., Jakovac, H., & Blagojević, G. (2011). Hepatoprotective activity of berberine is mediated by inhibition of TNF-α, COX2, and iNOS expression in CCl4-intoxicated mice. Toxicology, 280(1-2), 33–43. https://doi.org/10.1016/j.tox.2010.11.005
  • Fan, J., Li, B., Ge, T., Zhang, Z., Lv, J., Zhao, J., Wang, P., Liu, W., Wang, X., Mlyniec, K., & Cui, B. (2017). Berberine produces antidepressantlike effects in ovariectomized mice. Scientific Reports, 7(1), 1310. https://doi.org/10.1038/s41598-017-01035-5
  • Fan, J., Zhang, K., Jin, Y., Li, B., Gao, S., Zhu, J., & Cui, R. (2019). Pharmacological effects of berberine on mood disorders. Journal of Cellular and Molecular Medicine, 23(1), 21–28. https://doi.org/10.1111/jcmm.13930
  • Feng, Q., Li, L., & Wang, X. (2020). Identifying pathways and networks associated with the SARS-CoV-2 cell receptor ACE2 based on gene expression profiles in normal and SARS-CoV-2-ınfected human tissues. Frontiers in Molecular Biosciences, 7(305), 568954. https://doi.org/10.3389/fmolb.2020.568954
  • Galvez, E. M., Perez, M., Domingo, P., Nunez, D., Cebolla, V. L., Matt, M., & Pardo, J. (2013). Pharmacological/biological effects of berberine. Nat Prod, 1301-1329. https://doi.org/10.1007/978-3-642-22144-6_182
  • Guo, Y., Pope, C., Cheng, X., Zhou, H., & Klaassen, C. D. (2011). Dose-response of berberine on hepatic cytophromes P450 mRNA expression and activities in mice. Journal of Ethnopharmacology, 138(1), 111–118. https://doi.org/10.1016/j.jep.2011.08.058
  • Heberle, H., Meirelles, G. V., da Silva, F. R., Telles, G. P., & Minghim, R. (2015). InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics, 16, 169. https://doi.org/10.1186/s12859-015-0611-3
  • Joshi, P. V., Shirkhedkar, A. A., Prakash, K., & Maheshwari, V. L. (2011). Antidiarrheal activity, chemical and toxicity profile of Berberis aristata. Pharmaceutical Biology, 49(1), 94–100. https://doi.org/10.3109/13880209.2010.50029
  • Khan, T., Paul, B. K., Hasan, M. T., Islam, M. R., Arefin, M. A., Ahmed, K., Islam, M. K., & Moni, M. A. (2021). Significant pathway and biomarker identification of pancreatic cancer associated lung cancer. Informatics in Medicine Unlocked, 25, 100637. volume https://doi.org/10.1016/j.imu.2021.100637
  • Kim, H., Shin, H., Park, H., Kim, Y., Yun, G. Y., Park, S., Shin, H., & Kim, K. (2008). In vitro inhibition of coronavirus replications by the traditionally used medicinal herbal extracts, Cimicifuga rhizoma, Meliae cortex, Coptidis rhizoma, and Phellodendron cortex. Journal of Clinical Virology: The Official Publication of the Pan American Society for Clinical Virology, 41(2), 122–128. https://doi.org/10.1016/j.jcv.2007.10.011.
  • Kumar, N., Gupta, S., Chand Yadav, T., Pruthi, V., Kumar Varadwaj, P., & Goel, N. (2019). Extrapolation of phenolic compounds as multi-target agents against cancer and inflammation. Journal of Biomolecular Structure & Dynamics, 37(9), 2355–2369. https://doi.org/10.1080/07391102.2018.1481457
  • Laskowski, R. A. (1995). A program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of Molecular Graphics, 13(5), 323–330.
  • Liu, D., Meng, X., Wu, D., Qiu, Z., & Luo, H. (2019). A natural isoquinoline alkaloid with antitumor activity: studies of the biological activities of berberine. Frontiers in Pharmacology, 10(9), 1-12. https://doi.org/10.3389/fphar.2019.00009
  • Ma, Y.-G., Liang, L., Zhang, Y.-B., Wang, B.-F., Bai, Y.-G., Dai, Z.-J., Xie, M.-J., & Wang, Z.-W. (2017). Berberine reduced blood pressure and improved vasolidation in diabetic rat. Journal of Molecular Endocrinology, 59(3), 191–204. https://doi.org/10.1530/JME-17-0014
  • Motiwale, M., Yadav, N. S., Kumar, S., Kushwaha, T., Choudhir, G., Sharma, S., & Singour, P. K. (2022). Finding potent inhibitors for COVID-19 main protease (Mpro): an in silico approach using SARS-CoV-3CL protease inhibitors for combating CORONA. Journal of Biomolecular Structure & Dynamics, 40(4), 1534–1545. https://doi.org/10.1080/07391102.2020.1829501
  • Najaran, H., Bafrani, H. H., Hamid Rashtbari, H., Izadpanah, F., Rajabi, M. R., Kashani, H. H., & Mohammadi, A. (2019). Evaluation of the serum sex hormones levels and alkaline phosphatase activity in rats’ testis after administering of berberine in experimental varicocele. Oriental Pharmacy and Experimental Medicine, 19(2), 157–165. https://doi.org/10.1007/s13596-019-00369-x
  • Pang, Y.-N., Liang, Y.-W., Feng, T.-S., Zhao, S., Wu, H., Chai, Y.-S., Lei, F., Ding, Y., Xing, D.-M., & Du, L.-J. (2014). Transportation of berberine into HepG-2, Hela and SY5Y cells: a correlation to its ant-cancer effect. PLoS One, 9(11), e112937. https://doi.org/10.1371/journal.pone.0112937
  • Peng, L., Kang, S., Yin, Z., Jia, R., Song, X., Li, L., Li, Z., Zou, Y., Liang, X., Li, L., He, C., Ye, G., Yin, L., Shi, F., Lv, C., & Jing, B. (2015). Antibacterial activity and mechanism of berberine against Streptococcus agalactiae. International Journal of Clinical and Experimental Pathology, 8(5), 5217–5223. ()
  • Rafi, M. O., Al-Khafaji, K., Tok, T. T., & Rahman, M. S. (2022). Computer-based identification of potential compounds from Salviae miltiorrhizae against Neirisaral adhesion A regulatory protein. Journal of Biomolecular Structure and Dynamics, 40(10), 4301–4313. https://doi.org/10.1080/07391102.2020.1856189
  • Shamsi, A., Shahwan, M., Khan, M. S., Husain, F. M., Alhumaydhi, F. A., Aljohani, A. S. M., Rehman, M. T., Hassan, M. I., & Islam, A. (2021). Elucidating the ınteraction of human ferritin with quercetin and naringenin: Implication of natural products in neurodegenerative diseases: Molecular docking and dynamics simulation ınsight. ACS Omega, 6(11), 7922–7930. https://doi.org/10.1021/acsomega.1c00527
  • Shukla, R., Munjal, N. S., & Singh, T. R. (2019). Identification of novel small molecules against GSK3β for Alzheimer’s disease using chemoinformatics approach. Journal of Molecular Graphics and Modelling, 91, 91–104. https://doi.org/10.1016/j.jmgm.2019.06.008
  • Steiner, J. E., Menezes, R. B., Ricci, T. V., & de Oliveira, A. S. (2009). PCA tomography and ıts application to nearby galactic nuclei. Proceedings of the International Astronomical Union, 5(S267), 85–89. https://doi.org/10.1017/S1743921310005612
  • 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.
  • Wang, J. T., Peng, J. G., Zhang, J. Q., Wang, Z. X., Zhang, Y., Zhou, X. R., Miao, J., & Tang, L. (2019). Novel berberine-based derivatives with potent hypoglycemic activity. Bioorganic & Medicinal Chemistry Letters, 29(23), 126709. https://doi.org/10.1016/j.bmcl.2019.12670
  • Wang, Y., & Zidichouski, J. A. (2018). Update on the benefits and mechanisms of action of the bioactive vegetal alkaloid berberine on lipid metabolism and homeostasis. Cholesterol, 2018, 1–17. https://doi.org/10.1155/2018/7173920
  • Yan, Y., Fu, Y., Wu, S., Qin, H., Zhen, X., Song, M., Weng, Y., Wang, P., Chen, X., & Jiang, Z. (2018). Anti-influenza activity of berberine improves prognosis by reducing viral replication in mice. Phytotherapy Research: PTR, 32(12), 2560–2567. https://doi.org/10.1002/ptr.6196.
  • Yap, C. W. (2011). PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of Computational Chemistry, 32(7), 1466–1474.
  • Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: a fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/10.1002/jcc.21816

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.