In silico studies on potential TNKS inhibitors: a combination of pharmacophore and 3D-QSAR modelling, virtual screening, molecular docking and molecular dynamics

References

• Andrews, P. R., Craik, D. J., & Martin, J. L. (1984). Functional group contributions to drug–receptor interactions. Journal of Medicinal Chemistry, 27(12), 1648–1657. doi: 10.1021/jm00378a021
   PubMed Web of Science ®Google Scholar
• Athar, M., Lone, M. Y., Khedkar, V. M., & Jha, P. C. (2016). Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting nrf2-mediated gene transcription intended for anti-Parkinson drug design. Journal of Biomolecular Structure & Dynamics, 34(6), 1282–1297. doi: 10.1080/07391102
   PubMed Web of Science ®Google Scholar
• Balupuri, A., Balasubramanian, P. K., Gadhe, C. G., & Cho, S. J. (2014). Docking-based 3D-QSAR study of pyridyl aminothiazole derivatives as checkpoint kinase 1 inhibitors. Sar & QSAR in Environmental Research, 25(8), 651–671. doi:10.1080/1062936X.2014.923040
   PubMed Web of Science ®Google Scholar
• Balupuri, A., Gadhe, C. G., Balasubramanian, P. K., Kothandan, G., & Cho, S. J. (2014). In silico study on indole derivatives as anti HIV-1 agents: A combined docking, molecular dynamics and 3D-QSAR study. Archives of Pharmacal Research, 37(8), 1001–1015. doi: 10.1007/s12272-013-0313-1
   PubMed Web of Science ®Google Scholar
• Bregman, H., Chakka, N., Guzman-Perez, A., Gunaydin, H., Gu, Y., Huang, X., … DiMauro, E. F. (2013). Discovery of novel, induced-pocket binding oxazolidinones as potent, selective, and orally bioavailable tankyrase inhibitors. Journal of Medicinal Chemistry, 56(11), 4320–4342. doi:10.1021/jm4000038
   PubMed Web of Science ®Google Scholar
• Chai, T., & Draxler, R. R. (2014). Root mean square error (RMSE) or mean absolute error (MAE)? – Arguments against avoiding RMSE in the literature. Geoscientific Model Development, 7(3), 1247–1250. doi: 10.5194/gmd-7-1247-2014
   Web of Science ®Google Scholar
• Chen, B., Dodge, M. E., Tang, W., Lu, J., Ma, Z., Fan, C.-W., … Lum, L. (2009). Small molecule-mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer. Nature Chemical Biology, 5(2), 100–107. doi: 10.1038/nchembio.137
   PubMed Web of Science ®Google Scholar
• Chirico, N., & Gramatica, P. (2011). Real external predictivity of QSAR models: How to evaluate it? Comparison of different validation criteria and proposal of using the concordance correlation coefficient. Journal of Chemical Information and Modeling, 51(9), 2320–2335. doi: 10.1021/ci200211n
   PubMed Web of Science ®Google Scholar
• Cichero, E., Brullo, C., Bruno, O., & Fossa, P. (2016). Exhaustive 3D-QSAR analyses as a computational tool to explore the potency and selectivity profiles of thieno[3,2-d]pyrimidin-4(3H)-one derivatives as PDE7 inhibitors. RSC Advances, 6(66), 61088–61108. doi: 10.1039/c6ra12624c
   Web of Science ®Google Scholar
• Clark, M., Cramer, R. D., Jones, D. M., Patterson, D. E., & Simeroth, P. E. (1990). Comparative molecular field analysis (CoMFA). 2. Toward its use with 3d-structural databases. Tetrahedron Computer Methodology, 3(1), 47–59. doi: 10.1016/0898-5529(90)90120-W
   Google Scholar
• Cramer, R. D. (2003). Topomer CoMFA: A design methodology for rapid lead optimization. Journal of Medicinal Chemistry, 46(3), 374–388. doi: 10.1021/jm020194o
   PubMed 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.
   PubMed Web of Science ®Google Scholar
• Driehuis, E., & Clevers, H. (2017). WNT signaling events near the cell membrane and their pharmacological targeting for the treatment of cancer. British Journal of Pharmacology, 174(24), 4547–4563. doi: 10.1111/bph.13758
   PubMed Web of Science ®Google Scholar
• Ferri, M., Liscio, P., Carotti, A., Asciutti, S., Sardella, R., Macchiarulo, A., & Camaioni, E. (2017). Targeting Wnt-driven cancers: Discovery of novel tankyrase inhibitors. European Journal of Medicinal Chemistry, 142, 506–522. doi:10.1016/j.ejmech.2017.09.030
   PubMed Web of Science ®Google Scholar
• Golbraikh, A., & Tropsha, A. (2002). Beware of q2! Journal of Molecular Graphics &Amp; Modelling, 20(4), 269–276.
   PubMed Web of Science ®Google Scholar
• Haikarainen, T., Krauss, S., & Lehtiö, L. (2014). Tankyrases: Structure, function and therapeutic implications in cancer. Current Pharmaceutical Design, 20(41), 6472–6488.
   PubMed Web of Science ®Google Scholar
• Homeyer, N., & Gohlke, H. (2012). Free energy calculations by the molecular mechanics Poisson–Boltzmann surface area method. Molecular Informatics, 31(2), 114–122. doi:10.1002/minf.201100135
   PubMed Web of Science ®Google Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods: I. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82. doi: 10.1021/ci100275a
   PubMed Web of Science ®Google Scholar
• Huang, S.-M. A., Mishina, Y. M., Liu, S., Cheung, A., Stegmeier, F., Michaud, G. A., … Cong, F. (2009). Tankyrase inhibition stabilizes Axin and antagonizes Wnt signalling. Nature, 461(7264), 614–620. doi: 10.1038/nature08356
   PubMed Web of Science ®Google Scholar
• Huo, S. H., Wang, J. M., Cieplak, P., Kollman, P. A., & Kuntz, I. D. (2002). Molecular dynamics and free energy analyses of cathepsin D − inhibitor interactions: Insight into structure-based ligand design. Journal of Medicinal Chemistry, 45(7), 1412–1419. doi: 10.1021/jm010338j
   PubMed Web of Science ®Google Scholar
• Jain, A. N. (2004). Ligand-based structural hypotheses for virtual screening. Journal of Medicinal Chemistry, 47(4), 947–961. doi: 10.1021/jm030520f
   PubMed Web of Science ®Google Scholar
• Ji, L., Jiang, B., Jiang, X., Charlat, O., Chen, A., Mickanin, C., … Cong, F. (2017). The SIAH E3 ubiquitin ligases promote Wnt/β-catenin signaling through mediating Wnt-induced Axin degradation. Genes & Development, 31(9), 904–915. doi: 10.1101/gad.300053.117
   PubMed Web of Science ®Google Scholar
• Klebe, G., & Abraham, U. (1999). Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries. Journal of Computer-Aided Molecular Design, 13, 1–10.
   PubMed Web of Science ®Google Scholar
• Laura, M., Catherine, M. T., Michael, R., Fabienne, B., Edward, M., & Sebastian, G. (2016). Tankyrase requires SAM domain-dependent polymerization to support Wnt–β-catenin signaling. Molecular Cell, 63, 498–513. doi:10.1016/j.molcel.2016.06.019
   PubMed Web of Science ®Google Scholar
• LehtiÖ, L., Chi, N. W., & Krauss, S. (2013). Tankyrases as drug targets. FEBS Journal, 280(15), 3576–3593. doi: 10.1111/febs.12320
   PubMed Web of Science ®Google Scholar
• Liu, G. Y., Ju, X. L., Jin, C., & Liu, Z. Q. (2010). 3D-QSAR studies of insecticidal anthranilic diamides as ryanodine receptor activators using CoMFA, CoMSIA and DISCOtech. Chemosphere, 78(3), 300–306. doi: 10.1016/j.chemosphere.2009.10.038
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. doi: 10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Mandal, S. P., Mithuna, M., Garg, A., Sahetya, S. S., Nagendra, S. R., Sripad, H. S., … Kumar, B. R. P. (2016). Novel rhodanines with anticancer activity: Design, synthesis and CoMSIA study. RSC Advances, 6(63), 58641–58653. doi: 10.1039/c6ra08785j
   Web of Science ®Google Scholar
• Mitra, I., Roy, P. P., Kar, S., Ojha, P. K., & Roy, K. (2010). On further application of rm2 as a metric for validation of QSAR models. Journal of Chemometrics, 24(1), 22–33. doi: 10.1002/cem.1268
   Google Scholar
• Narwal, M., Venkannagari, H., & Lehtiö, L. (2012). Structural basis of selective inhibition of human tankyrases. Journal of Medicinal Chemistry, 55, 1360–1367. doi:10.1021/jm201510p
   PubMed Web of Science ®Google Scholar
• Natarajan, U., Kaliappan, I., & Singh, N. K. (2010). A facile design and efficient synthesis of Schiff’s bases of tetrazolo[1,5-a]quinoxalines as potential anti-inflammatory and anti-microbial agents. Der Pharma Chemica, 2, 159–167.
   Google Scholar
• Pratim, R. P., Paul, S., Mitra, I., & Roy, K. (2009). On two novel parameters for validation of predictive QSAR models. Molecules, 14(5), 1660–1701. doi: 10.3390/molecules14051660
   PubMed Web of Science ®Google Scholar
• Ranjan, P., Athar, M., Jha, P. C., & Krishna, K. V. (2018). Probing the opportunities for designing anthelmintic leads by sub-structural topology-based QSAR modelling. Molecular Diversity, 22(3), 669–683. doi:10.1007/s11030-018-9825-4.
   PubMed Web of Science ®Google Scholar
• Riccio, A. A., Mccauley, M., Langelier, M. F., & Pascal, J. M. (2016). Tankyrase sterile α motif domain polymerization is required for its role in Wnt signaling. Structure, 24(9), 1573–1581. doi:10.1016/j.str.2016.06.022
   PubMed Web of Science ®Google Scholar
• Riffell, J. L., Lord, C. J., & Ashworth, A. (2012). Tankyrase-targeted therapeutics: expanding opportunities in the PARP family. Nature Reviews Drug Discovery, 11(12), 923–936. doi: 10.1038/nrd3868
   PubMed Web of Science ®Google Scholar
• Roy, K., Ambure, P., & Aher, R. B. (2017). How important is to detect systematic error in predictions and understand statistical applicability domain of QSAR models? Chemometrics & Intelligent Laboratory Systems, 162, 44–54. doi:10.1016/j.chemolab.2017.01.010
   Web of Science ®Google Scholar
• Roy, P. P., Leonard, J. T., & Roy, K. (2008). Exploring the impact of size of training sets for the development of predictive QSAR models. Chemometrics & Intelligent Laboratory Systems, 90(1), 31–42. doi: 10.1016/j.chemolab.2007.07.004
   Web of Science ®Google Scholar
• Thomson, D. W., Wagner, A. J., Bantscheff, M., Benson, R. E., Dittus, L., Duempelfeld, B., … Muelbaier, M. (2017). Discovery of a highly selective tankyrase inhibitor displaying growth inhibition effects against a diverse range of tumor derived cell lines. Journal of Medicinal Chemistry, 60(13), 5455–5471. doi: 10.1021/acs.jmedchem.7b00137
   PubMed Web of Science ®Google Scholar
• Tropsha, A., Gramatica, P., & Gombar, V. (2003). The importance of being earnest: Validation is the absolute essential for successful application and interpretation of QSPR models. QSAR & Combinatorial Science, 22(1), 69–77. doi: 10.1002/qsar.200390007.
   Google Scholar
• Wang, T. C., Cheng, L. P., Huang, X. Y., Zhao, L., & Pang, W. (2017). Identification of potential tubulin polymerization inhibitors by 3D-QSAR, molecular docking and molecular dynamics. RSC Advances, 7(61), 38479–38489. doi: 10.1039/c7ra04314g
   Web of Science ®Google Scholar
• Weiser, J., Shenkin, P. S., & Still, W. C. (1999). Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry, 20(2), 217–230. doi: 10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
   Web of Science ®Google Scholar
• Wold, S., Ruhe, A., Wold, H., & Iii, W. J. D. (1984). The collinearity problem in linear regression. The partial least squares (PLS) approach to generalized inverses. SIAM Journal on Scientific and Statistical Computing, 5(3), 735–743.
   Web of Science ®Google Scholar
• Xu, W., Lau, Y. H., Fischer, G., Tan, Y. S., Chattopadhyay, A., de la Roche, M., … Itzhaki, L. S. (2017). Macrocyclized extended peptides: Inhibiting the substrate-recognition domain of tankyrase. Journal of the American Chemical Society, 139(6), 2245–2256. doi: 10.1021/jacs.6b10234
   PubMed Web of Science ®Google Scholar
• Xu, D., Liu, J., Fu, T., Shan, B., Qian, L., Pan, L., & Yuan, J. Y. (2017). USP25 regulates Wnt signaling by controlling the stability of tankyrases. Genes & Development, 31(10), 1024–1035. doi: 10.1101/gad.300889.117
   PubMed Web of Science ®Google Scholar
• Yamada, T., & Masuda, M. (2017). Emergence of TNIK inhibitors in cancer therapeutics. Cancer Science, 108(5), 818–823. doi: 10.1111/cas.13203
   PubMed Web of Science ®Google Scholar
• Yusuf, D., Davis, A. M., Kleywegt, G. J., & Schmitt, S. (2008). An alternative method for the evaluation of docking performance: RSR vs RMSD. Journal of Chemical Information and Modeling, 48(7), 1411–1422. doi: 10.1021/ci800084x
   PubMed Web of Science ®Google Scholar
• Zhan, T., Rindtorff, N., & Boutros, M. (2017). Wnt signaling in cancer. Oncogene, 36(11), 1461–1473. doi: 10.1038/onc.2016.304
   PubMed Web of Science ®Google Scholar