In silico identification of 20S proteasome-β5 subunit inhibitors using structure-based virtual screening

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, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Agamah, F. E., Mazandu, G. K., Hassan, R., Bope, C. D., Thomford, N. E., Ghansah, A., & Chimusa, E. R. (2019). Computational/in silico methods in drug target and lead prediction. Briefings in Bioinformatics, 21(5), 1663–1675. https://doi.org/10.1093/bib/bbz103
   Web of Science ®Google Scholar
• AutoDock Vina—Molecular Docking and Virtual Screening Program (n.d.). Retrieved April 29, 2020, from http://vina.scripps.edu/
   Google Scholar
• Bai, Q., Tan, S., Xu, T., Liu, H., Huang, J., & Yao, X. (2021). MolAICal: A soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm. Briefings in Bioinformatics, 22(3), bbaa161. https://doi.org/10.1093/bib/bbaa161
   Web of Science ®Google Scholar
• Bank, R. P. D. (n.d.) RCSB PDB: Homepage. Retrieved April 29, 2020, from https://www.rcsb.org/
   Google Scholar
• Chen, D., Frezza, M., Schmitt, S., Kanwar, J., & Dou, Q. P. (2011). Bortezomib as the first proteasome inhibitor anticancer drug: Current status and future perspectives. Current Cancer Drug Targets, 11(3), 239–253. https://doi.org/10.2174/156800911794519752
   PubMed Web of Science ®Google Scholar
• Chen, X., Dou, Q. P., Liu, J., & Tang, D. (2021). Targeting ubiquitin–Proteasome system with copper complexes for cancer therapy. Frontiers in Molecular Biosciences, 8, 649151. https://doi.org/10.3389/fmolb.2021.649151
   PubMed Web of Science ®Google Scholar
• Crawford, L. J., Walker, B., & Irvine, A. E. (2011). Proteasome inhibitors in cancer therapy. Journal of Cell Communication and Signaling, 5(2), 101–110. https://doi.org/10.1007/s12079-011-0121-7
   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(1), 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2019). SwissTargetPrediction: Updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Research, 47(W1), W357–W364. https://doi.org/10.1093/nar/gkz382
   PubMed Web of Science ®Google Scholar
• Di Giovanni, C., Ettari, R., Sarno, S., Rotondo, A., Bitto, A., Squadrito, F., Altavilla, D., Schirmeister, T., Novellino, E., Grasso, S., Zappalà, M., & Lavecchia, A. (2016). Identification of noncovalent proteasome inhibitors with high selectivity for chymotrypsin-like activity by a multistep structure-based virtual screening. European Journal of Medicinal Chemistry, 121, 578–591. https://doi.org/10.1016/j.ejmech.2016.05.049
   PubMed Web of Science ®Google Scholar
• El Yaagoubi, O. M., Lahmadi, A., Bouyahya, A., Filali, H., Samaki, H., El Antri, S., & Aboudkhil, S. (2021). Antitumor effect of Inula viscosa extracts on DMBA-induced skin carcinoma are mediated by proteasome inhibition. BioMed Research International, 2021, e6687589. https://doi.org/10.1155/2021/6687589
   PubMed Web of Science ®Google Scholar
• El Yaagoubi, O. M., Oularbi, L., Bouyahya, A., Samaki, H., El Antri, S., & Aboudkhil, S. (2021). The role of the ubiquitin-proteasome pathway in skin cancer development: 26S proteasome-activated NF-κB signal transduction. Cancer Biology & Therapy, 22(10–12), 479–492. https://doi.org/10.1080/15384047.2021.1978785
   PubMed Web of Science ®Google Scholar
• Filali, H., El Yaagoubi, O. M., Lahmadi, A., Quessar, A., Antri, S. E., Samaki, H., & Aboudkhil, S. (2022). Functional and quantitative evaluation of the 20S proteasome in serum and intracellular in145 moroccan patients with hematologic malignancies. Clinical Proteomics, 19(1), 1. https://doi.org/10.1186/s12014-022-09375-9
   PubMed Web of Science ®Google Scholar
• Goodwin, R. J. A., Bunch, J., & McGinnity, D. F. (2017). Chapter six—Mass spectrometry imaging in oncology drug discovery. In R. R. Drake & L. A. McDonnell (Eds.), Advances in cancer research (Vol. 134, pp. 133–171). Academic Press. https://doi.org/10.1016/bs.acr.2016.11.005
   Google Scholar
• Han, J.-J., Yang, X., Wang, Q., Tang, L., Yu, F., Huang, X., Wang, Y., Liu, J.-X., & Xie, Q. (2019). The β5 subunit is essential for intact 26S proteasome assembly to specifically promote plant autotrophic growth under salt stress. New Phytologist, 221(3), 1359–1368. https://doi.org/10.1111/nph.15471
   PubMed Web of Science ®Google Scholar
• Hsu, K.-C., Chen, Y.-F., Lin, S.-R., & Yang, J.-M. (2011). iGEMDOCK: A graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. BMC Bioinformatics, 12(1), S33. https://doi.org/10.1186/1471-2105-12-S1-S33
   PubMedGoogle Scholar
• IGEMDOCK (n.d.). Retrieved May 11, 2020, from http://gemdock.life.nctu.edu.tw/dock/igemdock.php
   Google Scholar
• Ito, S. (2020). Proteasome inhibitors for the treatment of multiple myeloma. Cancers, 12(2), 265. https://doi.org/10.3390/cancers12020265
   PubMed Web of Science ®Google Scholar
• Khan, M. L., & Stewart, A. K. (2011). Carfilzomib: A novel second-generation proteasome inhibitor. Future Oncology, 7(5), 607–612. https://doi.org/10.2217/fon.11.42
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today. Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Machado, D., Girardini, M., Viveiros, M., & Pieroni, M. (2018). Challenging the drug-likeness dogma for new drug discovery in tuberculosis. Frontiers in Microbiology, 9, 1367. https://doi.org/10.3389/fmicb.2018.01367
   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. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Olsson, M. A., Söderhjelm, P., & Ryde, U. (2016). Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. Journal of Computational Chemistry, 37(17), 1589–1600. https://doi.org/10.1002/jcc.24375
   PubMed Web of Science ®Google Scholar
• Park, J., Cho, J., & Song, E. J. (2020). Ubiquitin–proteasome system (UPS) as a target for anticancer treatment. Archives of Pharmacal Research, 43(11), 1144–1161. https://doi.org/10.1007/s12272-020-01281-8
   PubMed Web of Science ®Google Scholar
• Park, J. E., Miller, Z., Jun, Y., Lee, W., & Kim, K. B. (2018). Next-generation proteasome inhibitors for cancer therapy. Translational Research: The Journal of Laboratory and Clinical Medicine, 198, 1–16. https://doi.org/10.1016/j.trsl.2018.03.002
   PubMed Web of Science ®Google Scholar
• Pawar, A., Basler, M., Goebel, H., Alvarez Salinas, G. O., Groettrup, M., & Böttcher, T. (2020). Competitive metabolite profiling of natural products reveals subunit specific inhibitors of the 20S proteasome. ACS Central Science, 6(2), 241–246. https://doi.org/10.1021/acscentsci.9b01170
   PubMed Web of Science ®Google Scholar
• PreADMET | Prediction of ADME/Tox (n.d.). PreADMET | Prediction of ADME/Tox. Retrieved May 24, 2021, from https://preadmet.bmdrc.kr/
   Google Scholar
• PyMOL | Pymol.Org (n.d.). Retrieved May 12, 2020, from https://pymol.org/2/
   Google Scholar
• Rausch, J. L., Ali, A. A., Lee, D. M., Gebreyohannes, Y. K., Mehalek, K. R., Agha, A., Patil, S. S., Tolstov, Y., Wellens, J., Dhillon, H. S., Makielski, K. R., Debiec-Rychter, M., Schöffski, P., Wozniak, A., & Duensing, A. (2020). Differential antitumor activity of compounds targeting the ubiquitin-proteasome machinery in gastrointestinal stromal tumor (GIST) cells. Scientific Reports, 10(1), 5178. https://doi.org/10.1038/s41598-020-62088-7
   PubMed Web of Science ®Google Scholar
• Saavedra-García, P., Martini, F., & Auner, H. W. (2020). Proteasome inhibition in multiple myeloma: Lessons for other cancers. American Journal of Physiology. Cell Physiology, 318(3), C451–C462. https://doi.org/10.1152/ajpcell.00286.2019
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Sherman, D. J., & Li, J. (2020). Proteasome inhibitors: Harnessing proteostasis to combat disease. Molecules, 25(3), 671. https://doi.org/10.3390/molecules25030671
   PubMed Web of Science ®Google Scholar
• Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334–395. https://doi.org/10.1124/pr.112.007336
   PubMed Web of Science ®Google Scholar
• Tan, C. R. C., Abdul-Majeed, S., Cael, B., & Barta, S. K. (2019). Clinical pharmacokinetics and pharmacodynamics of bortezomib. Clinical Pharmacokinetics, 58(2), 157–168. https://doi.org/10.1007/s40262-018-0679-9
   PubMed Web of Science ®Google Scholar
• Téléchargements—MGLTools (n.d.). Retrieved April 29, 2020, from http://mgltools.scripps.edu/downloads
   Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Viana Nunes, A. M., das Chagas Pereira de Andrade, F., Filgueiras, L. A., de Carvalho Maia, O. A., Cunha, R. L. O. R., Rodezno, S. V. A., Maia Filho, A. L. M., de Amorim Carvalho, F. A., Braz, D. C., & Mendes, A. N. (2020). preADMET analysis and clinical aspects of dogs treated with the Organotellurium compound RF07: A possible control for canine visceral leishmaniasis? Environmental Toxicology and Pharmacology, 80, 103470. https://doi.org/10.1016/j.etap.2020.103470
   PubMed Web of Science ®Google Scholar
• Wahiba, E., Marc, P. W., Anass, K., Haya, A., Jalal, N., Soumaya, B., & Sayeh, E. (2021). Immuno-informatics-based identification of novel potential B cell and T cell epitopes to fight Zika virus infections. Infectious Disorders-Drug Targets, 21(4), 572–581.
   PubMedGoogle Scholar
• Wei, X., Zeng, W., Xie, K., Diao, P., & Tang, P. (2018). Potential use of chymotrypsin-like proteasomal activity as a biomarker for prostate cancer. Oncology Letters, 15(4), 5149–5154. https://doi.org/10.3892/ol.2018.7936
   PubMed Web of Science ®Google Scholar
• Yun, Y., Lee, S.-Y., Choi, W. H., Park, J.-C., Lee, D. H., Kim, Y. K., Lee, J. H., Lee, J.-Y., Lee, M. J., & Kim, Y. H. (2020). Proteasome activity in the plasma as a novel biomarker in mild cognitive impairment with chronic tinnitus. Journal of Alzheimer’s Disease, 78(1), 195–205. https://doi.org/10.3233/JAD-200728
   PubMed Web of Science ®Google Scholar
• Zhang, J., Ye, Z., Chen, W., Culpepper, J., Jiang, H., Ball, L. E., Mehrotra, S., Blumental-Perry, A., Tew, K. D., & Townsend, D. M. (2020). Altered redox regulation and S-glutathionylation of BiP contribute to bortezomib resistance in multiple myeloma. Free Radical Biology & Medicine, 160, 755–767. https://doi.org/10.1016/j.freeradbiomed.2020.09.013
   PubMed Web of Science ®Google Scholar