Computational investigation of imidazo[2,1-b]oxazole derivatives as potential mutant BRAF kinase inhibitors: 3D-QSAR, molecular docking, molecular dynamics simulation, and ADMETox studies

References

• Abdel-Maksoud, M. S., Ammar, U. M., El-Gamal, M. I., Gamal El-Din, M. M., Mersal, K. I., Ali, E. M., Yoo, K. H., Lee, K.-T., & Oh, C.-H. (2019). Design, synthesis, and anticancer activity of imidazo[2,1-b]oxazole-based RAF kinase inhibitors. Bioorganic Chemistry, 93, 103349. https://doi.org/10.1016/j.bioorg.2019.103349
   PubMed Web of Science ®Google Scholar
• Agrawal, N., Akbani, R., Aksoy, B. A., Ally, A., Arachchi, H., Asa, S. L., Auman, J. T., Balasundaram, M., Balu, S., Baylin, S. B., Behera, M., Bernard, B., Beroukhim, R., Bishop, J. A., Black, A. D., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J., … Zou, L. (2014). Integrated genomic characterization of papillary thyroid carcinoma. Cell, 159(3), 676–690. https://doi.org/10.1016/j.cell.2014.09.050
   PubMed Web of Science ®Google Scholar
• Alvarez, M. R. S., Grijaldo, S. J. B., Nacario, R. C., Rabajante, J. F., Heralde, F. M., 3rdLebrilla, C. B., & Completo, G. C. (2023). In silico screening-based discovery of inhibitors against glycosylation proteins dysregulated in cancer. Journal of Biomolecular Structure and Dynamics, 41(5), 1540–1552. https://doi.org/10.1080/07391102.2021.2022534
   PubMed Web of Science ®Google Scholar
• Boutalaka, M., Mokhliss, Y., Koubi, Y., El Alaouy, M. H., Maghat, H., & Lakhlifi, T. (2021). 2D-QSAD study of the anticancer activity of naphthoquinone derivatives against cancer cell line T47D (breast ductal carcinoma). RHAZES: Green and Applied Chemistry, 13, 52–65. https://doi.org/10.48419/IMIST.PRSM/rhazes-v13.28853
   Google Scholar
• Brastianos, P. K., Taylor-Weiner, A., Manley, P. E., Jones, R. T., Dias-Santagata, D., Thorner, A. R., Lawrence, M. S., Rodriguez, F. J., Bernardo, L. A., Schubert, L., Sunkavalli, A., Shillingford, N., Calicchio, M. L., Lidov, H. G. W., Taha, H., Martinez-Lage, M., Santi, M., Storm, P. B., Lee, J. Y. K., … Santagata, S. (2014). Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas. Nature Genetics, 46(2), 161–165. https://doi.org/10.1038/ng.2868
   PubMed Web of Science ®Google Scholar
• Chapman, P. B., Hauschild, A., Robert, C., Haanen, J. B., Ascierto, P., Larkin, J., Dummer, R., Garbe, C., Testori, A., Maio, M., Hogg, D., Lorigan, P., Lebbe, C., Jouary, T., Schadendorf, D., Ribas, A., O'Day, S. J., Sosman, J. A., Kirkwood, J. M., … McArthur, G. A. (2011). Improved survival with vemurafenib in melanoma with BRAF V600E mutation. New England Journal of Medicine, 364(26), 2507–2516. https://doi.org/10.1056/NEJMoa1103782
   PubMed Web of Science ®Google Scholar
• Chetty, S., Ramesh, M., Singh-Pillay, A., & Soliman, M. E. (2017). Recent advancements in the development of anti-tuberculosis drugs. Bioorganic & Medicinal Chemistry Letters, 27(3), 370–386. https://doi.org/10.1016/j.bmcl.2016.11.084
   PubMed Web of Science ®Google Scholar
• Clark, D. E. (2003). In silico prediction of blood–brain barrier permeation. Drug Discovery Today. 8(20), 927–933. https://doi.org/10.1016/s1359-6446(03)02827-7
   PubMed Web of Science ®Google Scholar
• Clark, M., Cramer, R. D., & Opdenbosch, N. V. (1989). (1012). Validation of the general purpose tripos 5.2 force field. Journal of Computational Chemistry, 10(8), 982–1012. https://doi.org/10.1002/jcc.540100804
   Web of Science ®Google Scholar
• Cramer, R. D., Patterson, D. E., & Bunce, J. D. (1988). Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. Journal of the American Chemical Society, 110(18), 5959–5967. https://doi.org/10.1021/ja00226a005
   PubMed Web of Science ®Google Scholar
• Dai, M., Liu, D., Liu, M., Zhou, F., Li, G., Chen, Z., & Cai, H. (2020). Patients with cancer appear more vulnerable to SARS-COV-2: A multi-center study during the COVID-19 outbreak. Cancer Discovery, 10(6), 783-791. https://doi.org/10.1158/2159-8290.cd-20-0422
   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
• Dassault Systèmes BIOVIA. (2017). Discovery studio modeling environment. Dassault Systèmes.
   Google Scholar
• de Oliveira, O. V., Cristina Andreazza Costa, M., Marques da Costa, R., Giordano Viegas, R., Paluch, A. S., & Miguel Castro Ferreira, M. (2023). Traditional herbal compounds as Candidates to inhibit the SARS-CoV-2 main protease: An in silico study. Journal of Biomolecular Structure and Dynamics, 41(5), 1603–1616. https://doi.org/10.1080/07391102.2021.2023646
   PubMed Web of Science ®Google Scholar
• Dienstmann, R., & Tabernero, J. (2011). BRAF as a target for cancer therapy. Anti-Cancer Agents in Medicinal Chemistry, 11(3), 285–295. https://doi.org/10.2174/187152011795347469
   PubMed Web of Science ®Google Scholar
• Dummer, R., Ascierto, P. A., Gogas, H. J., Arance, A., Mandala, M., Liszkay, G., Garbe, C., Schadendorf, D., Krajsova, I., Gutzmer, R., Chiarion-Sileni, V., Dutriaux, C., de Groot, J. W. B., Yamazaki, N., Loquai, C., Moutouh-de Parseval, L. A., Pickard, M. D., Sandor, V., Robert, C., & Flaherty, K. T. (2018). Encorafenib plus binimetinib versus vemurafenib or encorafenib in patients with BRAF-mutant melanoma (COLUMBUS): A multicentre, open-label, randomised phase 3 trial. Lancet Oncology. 19(5), 603–615. https://doi.org/10.1016/S1470-2045(18)30142-6
   PubMed Web of Science ®Google Scholar
• Finn, L., Markovic, S. N., & Joseph, R. W. (2012). Therapy for metastatic melanoma: The past, present, and future. BMC Medicine, 10(23), 1-10. https://doi.org/10.1186/1741-7015-10-23
   PubMedGoogle Scholar
• Fiskus, W., & Mitsiades, N. (2016). B-Raf inhibition in the clinic: Present and future. Annual Review of Medicine, 67(1), 29–43. https://doi.org/10.1146/annurev-med-090514-030732
   PubMedGoogle Scholar
• Fransén, K., Klintenäs, M., Österström, A., Dimberg, J., Monstein, H. J., & Söderkvist, P. (2004). Mutation analysis of the BRAF, ARAF and RAF-1 genes in human colorectal adenocarcinomas. Carcinogenesis, 25(4), 527–533. https://doi.org/10.1093/carcin/bgh049
   PubMed Web of Science ®Google Scholar
• Ghaleb, A., Aouidate, A., Ayouchia, H. B. E., Aarjane, M., Anane, H., & Stiriba, S.-E. (2022). In silico molecular investigations of pyridine NOxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADMET screening. Journal of Biomolecular Structure and Dynamics, 40(1), 143–153. https://doi.org/10.1080/07391102.2020.1808530
   PubMed Web of Science ®Google Scholar
• Golbraikh, A., & Tropsha, A. (2002). Beware of q2! Journal of Molecular Graphics and Modelling, 20(4), 269–276. https://doi.org/10.1016/s1093-3263(01)00123-1
   PubMed Web of Science ®Google Scholar
• Holderfield, M., Deuker, M. M., McCormick, F., & McMahon, M. (2014). Targeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond. Nature Reviews Cancer, 14(7), 455–467. https://doi.org/10.1038/nrc3760
   PubMed Web of Science ®Google Scholar
• Jang, S., & Atkins, M. B. (2013). Treatment of BRAF-mutant melanoma: The role of vemurafenib and other therapies. Clinical Pharmacology & Therapeutics, 95(1), 24–31. https://doi.org/10.1038/clpt.2013.197
   PubMed Web of Science ®Google Scholar
• Klebe, G., Abraham, U., & Mietzner, T. (1994). Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. Journal of Medicinal Chemistry, 37(24), 4130–4146. https://doi.org/10.1021/jm00050a010
   PubMed Web of Science ®Google Scholar
• Kramer, B., Rarey, M., & Lengauer, T. (1999). Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins: Structure, Function, and Genetics, 37(2), 228–241. 0134(19991101)37:23.0.co;2-8. https://doi.org/10.1002/(sici)1097-
   PubMed Web of Science ®Google Scholar
• Li, Z., Jiang, J. D., & Kong, W. J. (2014). Berberine up-regulates hepatic low-density lipoprotein receptor through Ras-independent but AMP-activated protein kinase-dependent Raf-1 activation. Biological and Pharmaceutical Bulletin, 37(11), 1766–1775. https://doi.org/10.1248/bpb.b14-00412
   PubMed Web of Science ®Google Scholar
• Luo, C., Xie, P., & Marmorstein, R. (2008). Identification of BRAF inhibitors through in silico screening. Journal of Medicinal Chemistry, 51(19), 6121–6127. https://doi.org/10.1021/jm800539g
   PubMed Web of Science ®Google Scholar
• Mayer, J. C. P., Sauer, A. C., Iglesias, B. A., Acunha, T. V., Back, D. F., Rodrigues, O. E. D., & Dornelles, L. (2017). Ferrocenylethenyl-substituted 1,3,4-oxadiazolyl-1,2,4-oxadiazoles: Synthesis, characterization and DNA-binding assays. Journal of Organometallic Chemistry, 841, 1–11.https://doi.org/10.1016/j.jorganchem.2017.04
   Web of Science ®Google Scholar
• Menzies, A. M., Haydu, L. E., Visintin, L., Carlino, M. S., Howle, J. R., Thompson, J. F., Kefford, R. F., Scolyer, R. A., & Long, G. V. (2012). Distinguishing clinicopathologic features of patients with V600E and V600K BRAF-mutant metastatic melanoma. Clinical Cancer Research, 18(12), 3242–3249. https://doi.org/10.1158/1078-0432.CCR-12-0052
   PubMed Web of Science ®Google Scholar
• Murray, C. W., & Rees, D. C. (2016). Opportunity knocks: Organic chemistry for fragment-based drug discovery (FBDD). Angewandte Chemie International Edition, 55(2), 488–492. https://doi.org/10.1002/anie.201506783
   PubMed Web of Science ®Google Scholar
• Peng, X.-M., L. V., Damu, G., & He Zhou, C. (2013). Current developments of coumarin compounds in medicinal chemistry. Current Pharmaceutical Design, 19(21), 3884–3930. https://doi.org/10.2174/1381612811319210013
   PubMed Web of Science ®Google Scholar
• Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Prakash, A., Borkotoky, S., & Dubey, V. K. (2023). Targeting two potential sites of SARS-CoV-2 mainprotease through computational drug repurposing. Journal of Biomolecular Structure and Dynamics. 41(7), 014–3024. https://doi.org/10.1080/07391102.2022.2044907
   Web of Science ®Google Scholar
• Roy, K. (2007). On some aspects of validation of predictive quantitative structure-activity relationship models. Expert Opinion on Drug Discovery, 2(12), 1567–1577. https://doi.org/10.1517/17460441.2.12.1567
   PubMed Web of Science ®Google Scholar
• Smith, R. A., Dumas, J., Adnane, L., & Wilhelm, S. M. (2006). Recent advances in the research and development of RAF kinase inhibitors. Current Topics in Medicinal Chemistry, 6(11), 1071–1089. https://doi.org/10.2174/156802606777812077
   PubMed Web of Science ®Google Scholar
• Srivastav, A. K., Jaiswal, J., & Kumar, U. (2023). In silico bioprospecting of antiviral compounds from marine fungi and mushroom for rapid development of nutraceuticals against SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 41(5), 1574–1585. https://doi.org/10.1080/07391102.2021.2023048
   PubMed Web of Science ®Google Scholar
• Studio. d. (2017). Life science modeling and studio. Discovery Simulations.
   Google Scholar
• Sysak, A., & Obmińska-Mrukowicz, B. (2017). Isoxazole ring as a useful scaffold in a search for new therapeutic agents. European Journal of Medicinal Chemistry, 137, 292–309. https://doi.org/10.1016/j.ejmech.2017.06.002
   PubMed Web of Science ®Google Scholar
• Taha, M., Rahim, F., Zaman, K., Anouar, E. H., Uddin, N., Nawaz, F., Sajid, M., Khan, K. M., Shah, A. A., Wadood, A., Rehman, A. U., & Alhibshi, A. H. (2023). Synthesis, in vitro biological screening and docking study of benzo[d]oxazole bis Schiff base derivatives as a potent anti-Alzheimer agent. Journal of Biomolecular Structure and Dynamics, 41(5), 1649–1664. https://doi.org/10.1080/07391102.2021.2023640
   PubMed Web of Science ®Google Scholar
• Tripos. (2011). SYBYL-X suite (version 2.0). St. Tripos, Inc.
   Google Scholar
• Tsai, K.-C., Chen, Y.-C., Hsiao, N.-W., Wang, C.-L., Lin, C.-L., Lee, Y.-C., Li, M., & Wang, B. (2010). (1544). A comparison of different electrostatic potentials on prediction accuracy in CoMFA and CoMSIA studies. European Journal of Medicinal Chemistry, 45(4), 1544–1551. –1551. https://doi.org/10.1016/j.ejmech.2009.12.063
   PubMed Web of Science ®Google Scholar
• Uehling, D. E., & Harris, P. A. (2015). Recent progress on MAP kinase pathway inhibitors. Bioorganic & Medicinal Chemistry Letters, 25(19), 4047–4056. https://doi.org/10.1016/j.bmcl.2015.07.093
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (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
• Villanueva, J., Vultur, A., Lee, J. T., Somasundaram, R., Fukunaga-Kalabis, M., Cipolla, A. K., Wubbenhorst, B., Xu, X., Gimotty, P. A., Kee, D., Santiago-Walker, A. E., Letrero, R., D'Andrea, K., Pushparajan, A., Hayden, J. E., Brown, K. D., Laquerre, S., McArthur, G. A., Sosman, J. A., Nathanson, K. L., & Herlyn, M. (2010). Acquired resistance to BRAF inhibitors mediated by a RAF kinase switch in melanoma can be overcome by cotargeting MEK and IGF-1R/PI3K. Cancer Cell, 18(6), 683–695. https://doi.org/10.1016/j.ccr.2010.11.023
   PubMed Web of Science ®Google Scholar
• Wang, Q., Zhao, Y., Chen, X., & Hong, A. (2022). Virtual screening of approved clinic drugs with main protease (3CLpro) reveals potential inhibitory effects on SARS-CoV2. Journal of Biomolecular Structure & Dynamics, 40(2), 685–695. https://doi.org/10.1080/07391102.2020.1817786
   PubMed Web of Science ®Google Scholar
• Wenglowsky, S., Moreno, D., Laird, E. R., Gloor, S. L., Ren, L., Risom, T., Rudolph, J., Sturgis, H. L., & Voegtli, W. C. (2012). Pyrazolopyridine inhibitors of B-Raf(V600E). Part 4: Rational design and kinase selectivity profile of cell potent type II inhibitors. Bioorganic & Medicinal Chemistry, 22(19), 6237–6241. https://doi.org/10.1016/j.bmcl.2012.08.007
   Web of Science ®Google Scholar
• Wilhelm, S., Carter, C., Lynch, M., Lowinger, T., Dumas, J., Smith, R. A., Schwartz, B., Simantov, R., & Kelley, S. (2007). Erratum: Discovery and development of sorafenib: A multikinase inhibitor for treating cancer. Nature Reviews Drug Discovery, 6(2), 168–168. https://doi.org/10.1038/nrd2262
   Web of Science ®Google Scholar
• Williams, T. E., Subramanian, S., Verhagen, J., McBride, C. M., Costales, A., Sung, L., Antonios-McCrea, W., McKenna, M., Louie, A. K., Ramurthy, S., Levine, B., Shafer, C. M., Machajewski, T., Renhowe, P. A., Appleton, B. A., Amiri, P., Chou, J., Stuart, D., Aardalen, K., & Poon, D. (2015). Discovery of RAF265: A potent mut-B-RAF inhibitor for the treatment of metastatic melanoma. ACS Medicinal Chemistry Letters, 6(9), 961–965. https://doi.org/10.1021/ml500526p
   PubMed Web of Science ®Google Scholar
• Yokota, T., Ura, T., Shibata, N., Takahari, D., Shitara, K., Nomura, M., Kondo, C., Mizota, A., Utsunomiya, S., Muro, K., & Yatabe, Y. (2011). BRAF mutation is a powerful prognostic factor in advanced and recurrent colorectal cancer. British Journal of Cancer, 104(5), 856–862. https://doi.org/10.1038/bjc.2011.19
   PubMed Web of Science ®Google Scholar