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Research Article

Identification of potentially high drug-like VEGFR2/c-Met dual-target type II kinase inhibitors with symmetric skeletons based on structural screening

, , , &
Pages 1249-1267 | Received 23 Dec 2022, Accepted 29 Mar 2023, Published online: 12 Apr 2023

References

  • Alanazi, M. M., Elkady, H., Alsaif, N. A., Obaidullah, A. J., Alanazi, W. A., Al-Hossaini, A. M., Alharbi, M. A., Eissa, I. H., & Dahab, M. A. (2022). Discovery of new quinoxaline-based derivatives as anticancer agents and potent VEGFR-2 inhibitors: Design, synthesis, and in silico study. Journal of Molecular Structure, 1253, 132220. https://doi.org/10.1016/j.molstruc.2021.132220
  • Alanazi, M. M., Mahdy, H. A., Alsaif, N. A., Obaidullah, A. J., Alkahtani, H. M., Al-Mehizia, A. A., Alsubaie, S. M., Dahab, M. A., & Eissa, I. H. (2021). New bis ([1,2,4] triazolo) [4,3-a:3',4'-c] quinoxaline derivatives as VEGFR-2 inhibitors and apoptosis inducers: Design, synthesis, in silico studies, and anticancer evaluation. Bioorganic Chemistry, 112, 104949. https://doi.org/10.1016/j.bioorg.2021.104949
  • Awazu, Y., Nakamura, K., Mizutani, A., Kakoi, Y., Iwata, H., Yamasaki, S., Miyamoto, N., Imamura, S., Miki, H., & Hori, A. (2013). A novel inhibitor of c-Met and VEGF receptor tyrosine kinases with a broad spectrum of in vivo antitumor activities. Molecular Cancer Therapeutics, 12(6), 913–924. https://doi.org/10.1158/1535-7163.MCT-12-1011
  • Banerjee, P., Eckert, A. O., Schrey, A. K., & 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
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
  • Birchmeier, C., Birchmeier, W., Gherardi, E., & Vande Woude, G. F. (2003). Met, metastasis, motility and more. Nature Reviews. Molecular Cell Biology, 4(12), 915–925. https://doi.org/10.1038/nrm1261
  • Cai, Z. W., Wei, D., Schroeder, G. M., Cornelius, L. A., Kim, K., Chen, X. T., Schmidt, R. J., Williams, D. K., Tokarski, J. S., An, Y., Sack, J. S., Manne, V., Kamath, A., Zhang, Y., Marathe, P., Hunt, J. T., Lombardo, L. J., Fargnoli, J., & Borzilleri, R. M. (2008). Discovery of orally active pyrrolopyridine- and aminopyridine-based Met kinase inhibitors. Bioorganic & Medicinal Chemistry Letters, 18(11), 3224–3229. https://doi.org/10.1016/j.bmcl.2008.04.047
  • Cee, V. J., Cheng, A. C., Romero, K., Bellon, S., Mohr, C., Whittington, D. A., Bak, A., Bready, J., Caenepeel, S., Coxon, A., Deak, H. L., Fretland, J., Gu, Y., Hodous, B. L., Huang, X., Kim, J. L., Lin, J., Long, A. M., Nguyen, H., … Geuns-Meyer, S. (2009). Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase. Bioorganic & Medicinal Chemistry Letters, 19(2), 424–427. https://doi.org/10.1016/j.bmcl.2008.11.056
  • Chadha, N., & Silakari, O. (2016). Active site fingerprinting and pharmacophore screening strategies for the identification of dual inhibitors of protein kinase C (ΡΚCβ) and poly (ADP-ribose) polymerase-1 (PARP-1). Molecular Diversity, 20(3), 747–761. https://doi.org/10.1007/s11030-016-9676-9
  • Claridge, S., Raeppel, F., Granger, M.-C., Bernstein, N., Saavedra, O., Zhan, L., Llewellyn, D., Wahhab, A., Deziel, R., Rahil, J., Beaulieu, N., Nguyen, H., Dupont, I., Barsalou, A., Beaulieu, C., Chute, I., Gravel, S., Robert, M.-F., Lefebvre, S., … Vaisburg, A. (2008). Discovery of a novel and potent series of thieno[3,2-b] pyridine-based inhibitors of c-Met and VEGFR2 tyrosine kinases. Bioorganic & Medicinal Chemistry Letters, 18(9), 2793–2798. https://doi.org/10.1016/j.bmcl.2008.04.009
  • Comoglio, P. M., Giordano, S., & Trusolino, L. (2008). Drug development of MET inhibitors: Targeting oncogene addiction and expedience. Nature Reviews. Drug Discovery, 7(6), 504–516. https://doi.org/10.1038/nrd2530
  • Dain Md Opo, F. A., Alsaiari, A. A., Rahman Molla, M. H., Ahmed Sumon, M. A., Yaghmour, K. A., Ahammad, F., Mohammad, F., & Simal-Gandara, J. (2022). Identification of novel natural drug candidates against BRAF mutated carcinoma; An integrative in-silico structure-based pharmacophore modeling and virtual screening process. Frontiers in Chemistry, 10, 986376. https://doi.org/10.3389/fchem.2022.986376
  • D’Angelo, N. D., Bellon, S. F., Booker, S. K., Cheng, Y., Coxon, A., Dominguez, C., Fellows, I., Hoffman, D., Hungate, R., Kaplan-Lefko, P., Lee, M. R., Li, C., Liu, L., Rainbeau, E., Reider, P. J., Rex, K., Siegmund, A., Sun, Y., Tasker, A. S., … Kim, T.-S. (2008). Design, synthesis, and biological evaluation of potent c-Met inhibitors. Journal of Medicinal Chemistry, 51(18), 5766–5779. https://doi.org/10.1021/jm8006189
  • Fu, Y., Liu, Y.-X., Kang, T., Sun, Y.-N., Li, J.-Z., & Ye, F. (2019). Identification of novel inhibitors of p-hydroxyphenylpyruvate dioxygenase using receptor-based virtual screening. Journal of the Taiwan Institute of Chemical Engineers, 103, 33–43. https://doi.org/10.1016/j.jtice.2019.08.005
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Gharaghani, S., Khayamian, T., & Ebrahimi, M. (2013). Molecular dynamics simulation study and molecular docking descriptors in structure-based QSAR on acetylcholinesterase (AChE) inhibitors. SAR and QSAR in Environmental Research, 24(9), 773–794. https://doi.org/10.1080/1062936X.2013.792877
  • Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17. https://doi.org/10.1186/1758-2946-4-17
  • Hasan, J., Byers, R., & Jayson, G. C. (2002). Intra-tumoural microvessel density in human solid tumours. British Journal of Cancer, 86(10), 1566–1577. https://doi.org/10.1038/sj.bjc.6600315
  • Hassan, A., Badr, M., Abdelhamid, D., Hassan, H. A., Abourehab, M., & Abuo-Rahma, G. (2022). Design, synthesis, in vitro antiproliferative evaluation and in silico studies of new VEGFR-2 inhibitors based on 4-piperazinylquinolin-2(1H)-one scaffold. Bioorganic Chemistry, 120, 105631. https://doi.org/10.1016/j.bioorg.2022.105631
  • Heyman, H. R., Frey, R. R., Bousquet, P. F., Cunha, G. A., Moskey, M. D., Ahmed, A. A., Soni, N. B., Marcotte, P. A., Pease, L. J., Glaser, K. B., Yates, M., Bouska, J. J., Albert, D. H., Black-Schaefer, C. L., Dandliker, P. J., Stewart, K. D., Rafferty, P., Davidsen, S. K., Michaelides, M. R., & Curtin, M. L. (2007). Thienopyridine urea inhibitors of KDR kinase. Bioorganic & Medicinal Chemistry Letters, 17(5), 1246–1249. https://doi.org/10.1016/j.bmcl.2006.12.015
  • Holmes, K., Roberts, O. L., Thomas, A. M., & Cross, M. J. (2007). Vascular endothelial growth factor receptor-2: Structure, function, intracellular signalling and therapeutic inhibition. Cellular Signalling, 19(10), 2003–2012. https://doi.org/10.1016/j.cellsig.2007.05.013
  • Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D., Jr. (2017). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/10.1038/nmeth.4067
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–28. https://doi.org/10.1016/0263-7855(96)00018-5
  • Kim, K. S., Zhang, L., Schmidt, R., Cai, Z.-W., Wei, D., Williams, D. K., Lombardo, L. J., Trainor, G. L., Xie, D., Zhang, Y., An, Y., Sack, J. S., Tokarski, J. S., Darienzo, C., Kamath, A., Marathe, P., Zhang, Y., Lippy, J., Jeyaseelan, R., … Borzilleri, R. M. (2008). Discovery of pyrrolopyridine-pyridone based inhibitors of Met kinase: Synthesis, X-ray crystallographic analysis, and biological activities. Journal of Medicinal Chemistry, 51(17), 5330–5341. https://doi.org/10.1021/jm800476q
  • Kumar, A., Rajendran, V., Sethumadhavan, R., & Purohit, R. (2013). Molecular dynamic simulation reveals damaging impact of RAC1 F28L mutation in the switch I region. PLoS One, 8(10), e77453. https://doi.org/10.1371/journal.pone.0077453
  • Lai, S., Chen, J. N., Huang, H. W., Zhang, X. Y., Jiang, H. L., Li, W., Wang, P. L., Wang, J., & Liu, F. N. (2018). Structure activity relationships of chrysoeriol and analogs as dual c-Met and VEGFR2 tyrosine kinase inhibitors. Oncology Reports, 40(3), 1650–1656. https://doi.org/10.3892/or.2018.6542
  • Li, J., Gu, W., Bi, X., Li, H., Liao, C., Liu, C., Huang, W., & Qian, H. (2017). Design, synthesis, and biological evaluation of thieno[2,3-d] pyrimidine derivatives as novel dual c-Met and VEGFR-2 kinase inhibitors. Bioorganic & Medicinal Chemistry, 25(24), 6674–6679. https://doi.org/10.1016/j.bmc.2017.11.010
  • Liang, J.-W.,Li, S.-L.,Wang, S.,Li, W.-Q., &Meng, F.-H. (2020). Synthesis and biological evaluation of novel (E)-N'-benzylidene hydrazides as novel c-Met inhibitors through fragment based virtual screening. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), 468–477. https://doi.org/10.1080/14756366.2019.170265531902266
  • Lima, L. R., Bastos, R. S., Ferreira, E. F. B., Leão, R. P., Araújo, P. H. F., Pita, S. S. D. R., De Freitas, H. F., Espejo-Román, J. M., Dos Santos, E. L. V. S., Ramos, R. D. S., Macêdo, W. J. C., & Santos, C. B. R. (2022). Identification of potential new Aedes aegypti juvenile hormone inhibitors from N-Acyl piperidine derivatives: A bioinformatics approach. International Journal of Molecular Sciences, 23(17), 9927. https://doi.org/10.3390/ijms23179927
  • Liu, X., Yao, W., Newton, R. C., & Scherle, P. A. (2008). Targeting the c-MET signaling pathway for cancer therapy. Expert Opinion on Investigational Drugs, 17(7), 997–1011. https://doi.org/10.1517/13543784.17.7.997
  • McTigue, M., Murray, B. W., Chen, J. H., Deng, Y. L., Solowiej, J., & Kania, R. S. (2012). Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 109(45), 18281–18289. https://doi.org/10.1073/pnas.1207759109
  • Miyamoto, N., Sakai, N., Hirayama, T., Miwa, K., Oguro, Y., Oki, H., Okada, K., Takagi, T., Iwata, H., Awazu, Y., Yamasaki, S., Takeuchi, T., Miki, H., Hori, A., & Imamura, S. (2013). Discovery of N-[5-({2-[(cyclopropylcarbonyl)amino] imidazo[1,2-b] pyridazin-6-yl} oxy)-2-methylphenyl]-1,3-dimethyl-1H-pyrazole-5-carboxamide (TAK-593), a highly potent VEGFR2 kinase inhibitor. Bioorganic & Medicinal Chemistry, 21(8), 2333–2345. https://doi.org/10.1016/j.bmc.2013.01.074
  • Modi, S. J., & Kulkarni, V. M. (2019). Vascular endothelial growth factor receptor (VEGFR-2)/KDR inhibitors: Medicinal chemistry perspective. Medicine in Drug Discovery, 2, 100009. https://doi.org/10.1016/j.medidd.2019.100009
  • Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012). Directory of useful decoys, enhanced (DUD-E): Better ligands and decoys for better benchmarking. Journal of Medicinal Chemistry, 55(14), 6582–6594. https://doi.org/10.1021/jm300687e
  • Nada, H., Lee, K., Gotina, L., Pae, A. N., & Elkamhawy, A. (2022). Identification of novel discoidin domain receptor 1 (DDR1) inhibitors using E-pharmacophore modeling, structure-based virtual screening, molecular dynamics simulation and MM-GBSA approaches. Computers in Biology and Medicine, 142, 105217. https://doi.org/10.1016/j.compbiomed.2022.105217
  • Neben, C. L., Lo, M., Jura, N., & Klein, O. D. (2019). Feedback regulation of RTK signaling in development. Developmental Biology, 447(1), 71–89. https://doi.org/10.1016/j.ydbio.2017.10.017
  • Oguro, Y., Miyamoto, N., Okada, K., Takagi, T., Iwata, H., Awazu, Y., Miki, H., Hori, A., Kamiyama, K., & Imamura, S. (2010). Design, synthesis, and evaluation of 5-methyl-4-phenoxy-5H-pyrrolo[3,2-d] pyrimidine derivatives: Novel VEGFR2 kinase inhibitors binding to inactive kinase conformation. Bioorganic & Medicinal Chemistry, 18(20), 7260–7273. https://doi.org/10.1016/j.bmc.2010.08.017
  • Okamoto, K., Ikemori-Kawada, M., Jestel, A., von König, K., Funahashi, Y., Matsushima, T., Tsuruoka, A., Inoue, A., & Matsui, J. (2014). Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization. ACS Medicinal Chemistry Letters, 6(1), 89–94. https://doi.org/10.1021/ml500394m
  • Parikh, P. K., & Ghate, M. D. (2018). Recent advances in the discovery of small molecule c-Met Kinase inhibitors. European Journal of Medicinal Chemistry, 143, 1103–1138. https://doi.org/10.1016/j.ejmech.2017.08.044
  • Pires, D. E., 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
  • Pradeepkiran, J. A., Kumar, K. K., Kumar, Y. N., & Bhaskar, M. (2015). Modeling, molecular dynamics, and docking assessment of transcription factor rho: A potential drug target in Brucella melitensis 16M. Drug Design, Development and Therapy, 9, 1897–1912. https://doi.org/10.2147/DDDT.S77020
  • Qian, F., Engst, S., Yamaguchi, K., Yu, P., Won, K. A., Mock, L., Lou, T., Tan, J., Li, C., Tam, D., Lougheed, J., Yakes, F. M., Bentzien, F., Xu, W., Zaks, T., Wooster, R., Greshock, J., & Joly, A. H. (2009). Inhibition of tumor cell growth, invasion, and metastasis by EXEL-2880 (XL880, GSK1363089), a novel inhibitor of HGF and VEGF receptor tyrosine kinases. Cancer Research, 69(20), 8009–8016. https://doi.org/10.1158/0008-5472.CAN-08-4889
  • Salmaso, V., & Moro, S. (2018). Bridging molecular docking to molecular dynamics in exploring ligand-protein recognition process: An overview. Frontiers in Pharmacology, 9, 923. https://doi.org/10.3389/fphar.2018.00923
  • Selvam, C., Mock, C. D., Mathew, O. P., Ranganna, K., & Thilagavathi, R. (2020). Discovery of vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors by ligand-based virtual high throughput screening. Molecular Informatics, 39(7), e1900150. https://doi.org/10.1002/minf.201900150
  • Shi, L., Wu, T. T., Wang, Z., Xue, J. Y., & Xu, Y. G. (2014). Discovery of quinazolin-4-amines bearing benzimidazole fragments as dual inhibitors of c-Met and VEGFR-2. Bioorganic & Medicinal Chemistry, 22(17), 4735–4744. https://doi.org/10.1016/j.bmc.2014.07.008
  • Shi, W., Qiang, H., Huang, D., Bi, X., Huang, W., & Qian, H. (2018). Exploration of novel pyrrolo[2,1-f] [1,2,4] triazine derivatives with improved anticancer efficacy as dual inhibitors of c-Met/VEGFR-2. European Journal of Medicinal Chemistry, 158, 814–831. https://doi.org/10.1016/j.ejmech.2018.09.050
  • Susanti, N., Damayanti, S., Kartasasmita, R. E., & Tjahjono, D. H. (2021). A search for cyclin-dependent kinase 4/6 inhibitors by pharmacophore-based virtual screening, molecular docking, and molecular dynamic simulations. International Journal of Molecular Sciences, 22(24), 13423. https://doi.org/10.3390/ijms222413423
  • Temml, V., Garscha, U., Romp, E., Schubert, G., Gerstmeier, J., Kutil, Z., Matuszczak, B., Waltenberger, B., Stuppner, H., Werz, O., & Schuster, D. (2017). Discovery of the first dual inhibitor of the 5-lipoxygenase-activating protein and soluble epoxide hydrolase using pharmacophore-based virtual screening. Scientific Reports, 7, 42751. https://doi.org/10.1038/srep42751
  • Tímár, J., &Döme, B. (2008). Antiangiogenic drugs and tyrosine kinases. Anti-Cancer Agents in Medicinal Chemistry, 8(5), 462–469. https://doi.org/10.2174/18715200878453303518537529
  • Toi, M., Matsumoto, T., & Bando, H. (2001). Vascular endothelial growth factor: Its prognostic, predictive, and therapeutic implications. The Lancet. Oncology, 2(11), 667–673. https://doi.org/10.1016/S1470-2045(01)00556-3
  • Tran, Q.-H., Nguyen, Q.-T., Vo, N.-Q.-H., Mai, T. T., Tran, T.-T.-N., Tran, T.-D., Le, M.-T., Trinh, D.-T T., & Thai, K.-M. (2022). Structure-based 3D-Pharmacophore modeling to discover novel interleukin 6 inhibitors: An in silico screening, molecular dynamics simulations and binding free energy calculations. PLoS One, 17(4), e0266632. https://doi.org/10.1371/journal.pone.0266632
  • Tripathy, R., Ghose, A., Singh, J., Bacon, E. R., Angeles, T. S., Yang, S. X., Albom, M. S., Aimone, L. D., Herman, J. L., & Mallamo, J. P. (2007). 1,2,3-Thiadiazole substituted pyrazolones as potent KDR/VEGFR-2 kinase inhibitors. Bioorganic & Medicinal Chemistry Letters, 17(6), 1793–1798. https://doi.org/10.1016/j.bmcl.2006.12.054
  • Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
  • 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
  • Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & Mackerell, A. D., Jr. (2010). CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690. https://doi.org/10.1002/jcc.21367
  • Wang, S., Jiang, J. H., Li, R. Y., & Deng, P. (2020). Docking-based virtual screening of TβR1 inhibitors: Evaluation of pose prediction and scoring functions. BMC Chemistry, 14(1), 52. https://doi.org/10.1186/s13065-020-00704-3
  • Xie, J., Meng, D., Li, Y., Li, R., & Deng, P. (2022). Virtual screening for potential discoidin domain receptor 1 (DDR1) inhibitors based on structural assessment. Molecular Diversity. https://doi.org/10.1007/s11030-022-10557-8
  • Xu, H., Wang, M., Wu, F., Zhuo, L., Huang, W., & She, N. (2020). Discovery of N-substituted-3-phenyl-1,6-naphthyridinone derivatives bearing quinoline moiety as selective type II c-Met kinase inhibitors against VEGFR-2. Bioorganic & Medicinal Chemistry, 28(12), 115555. https://doi.org/10.1016/j.bmc.2020.115555
  • Zhang, J., Jiang, X., Jiang, Y., Guo, M., Zhang, S., Li, J., He, J., Liu, J., Wang, J., & Ouyang, L. (2016). Recent advances in the development of dual VEGFR and c-Met small molecule inhibitors as anticancer drugs. European Journal of Medicinal Chemistry, 108, 495–504. https://doi.org/10.1016/j.ejmech.2015.12.016
  • Zhang, Y., Zhang, T. J., Tu, S., Zhang, Z. H., & Meng, F. H. (2020). Identification of novel Src inhibitors: Pharmacophore-based virtual screening, molecular docking and molecular dynamics simulations. Molecules, 25(18), 4094. https://doi.org/10.3390/molecules25184094
  • Zillhardt, M., Park, S. M., Romero, I. L., Sawada, K., Montag, A., Krausz, T., Yamada, S. D., Peter, M. E., & Lengyel, E. (2011). Foretinib (GSK1363089), an orally available multikinase inhibitor of c-Met and VEGFR-2, blocks proliferation, induces anoikis, and impairs ovarian cancer metastasis. Clinical Cancer Research, 17(12), 4042–4051. https://doi.org/10.1158/1078-0432.CCR-10-3387

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