References
- Almahariq, M., Tsalkova, T., Mei, F. C., Chen, H., Zhou, J., Sastry, S. K., Schwede, F., & Cheng, X. (2013). A novel EPAC-specific inhibitor suppresses pancreatic cancer cell migration and invasion. Molecular Pharmacology, 83(1), 122–128. https://doi.org/https://doi.org/10.1124/mol.112.080689
- 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/https://doi.org/10.1093/nar/28.1.235
- Bullock, A. N., & Fersht, A. R. (2001). Rescuing the function of mutant p53. Nature Reviews. Cancer, 1(1), 68–76. https://doi.org/https://doi.org/10.1038/35094077
- Butler, J. S., & Loh, S. N. (2003). Structure, function, and aggregation of the zinc-free form of the p53 DNA binding domain. Biochemistry, 42(8), 2396–2403. https://doi.org/https://doi.org/10.1021/bi026635n
- Chen, I.-J., & Foloppe, N. (2010). Drug-like bioactive structures and conformational coverage with the LigPrep/ConfGen suite: Comparison to programs MOE and catalyst. Journal of Chemical Information and Modeling, 50(5), 822–839. https://doi.org/https://doi.org/10.1021/ci100026x
- Chen, Y., Dey, R., & Chen, L. (2010). Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer. Structure (London, England : 1993), 18(2), 246–256. https://doi.org/https://doi.org/10.1016/j.str.2009.11.011
- Cho, Y., Gorina, S., Jeffrey, P., & Pavletich, N. (1994). Crystal structure of a p53 tumor suppressor-DNA complex: Understanding tumorigenic mutations. Science (New York, N.Y.), 265(5170), 346–355. https://doi.org/https://doi.org/10.1126/science.8023157
- Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N ⋅log (N) method for Ewald sums in large systems. Journal of Chemical Physics, 98(12), 10089–10092.
- Dixon, S. L., Smondyrev, A. M., & Rao, S. N. (2006). PHASE: A novel approach to pharmacophore modeling and 3D database searching. Chemical Biology & Drug Design, 67(5), 370–372. https://doi.org/https://doi.org/10.1111/j.1747-0285.2006.00384.x
- Duffy, M. J., Synnott, N. C., & Crown, J. (2017). Mutant p53 as a target for cancer treatment. European Journal of Cancer (Oxford, England : 1990)), 83, 258–265. https://doi.org/https://doi.org/10.1016/j.ejca.2017.06.023
- Fischer, M. (2017). Census and evaluation of p53 target genes. Oncogene, 36(28), 3943–3956. https://doi.org/https://doi.org/10.1038/onc.2016.502
- Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/https://doi.org/10.1021/jm0306430
- Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/https://doi.org/10.1021/jm051256o
- Gourley, C., Green, J., Gabra, H., Vergote, I., Basu, B., Brenton, J. D., Björklund, U., Smith, A. M., Euler, M. & Von, (2016). PISARRO: A EUTROC phase Ib study of APR-246 in combination with carboplatin (C) and pegylated liposomal doxorubicin (PLD) in platinum sensitive relapsed high grade serous ovarian cancer (HGSOC). Journal of Clinical Oncology, 34(15_suppl), 5571–5571.
- Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/https://doi.org/10.1021/jm030644s
- Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., Groot, B. L., de, Grubmüller, H., & MacKerell, A. D. (2017). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/https://doi.org/10.1038/nmeth.4067
- Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J. F., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins Struct Proteins, 55(2), 351–367. https://doi.org/https://doi.org/10.1002/prot.10613
- Joerger, A. C., Bauer, M. R., Wilcken, R., Baud, M. G. J., Harbrecht, H., Exner, T. E., Boeckler, F. M., Spencer, J., & Fersht, A. R. (2015). Exploiting transient protein states for the design of small-molecule stabilizers of mutant p53. Structure (London, England: 1993)), 23(12), 2246–2255. https://doi.org/https://doi.org/10.1016/j.str.2015.10.016
- Joerger, A. C., & Fersht, A. R. (2008). Structural biology of the tumor suppressor p53. Annual Review of Biochemistry, 77(1), 557–582. https://doi.org/https://doi.org/10.1146/annurev.biochem.77.060806.091238
- Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., Xie, M., Zhang, Q., McMichael, J. F., Wyczalkowski, M. A., Leiserson, M. D. M., Miller, C. A., Welch, J. S., Walter, M. J., Wendl, M. C., Ley, T. J., Wilson, R. K., Raphael, B. J., & Ding, L. (2013). Mutational landscape and significance across 12 major cancer types. Nature, 502(7471), 333–339. https://doi.org/https://doi.org/10.1038/nature12634
- Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). PubChem Substance and Compound databases. Nucleic Acids Research, 44(D1), D1202–13. https://doi.org/https://doi.org/10.1093/nar/gkv951
- Kruiswijk, F., Labuschagne, C. F., & Vousden, K. H. (2015). p53 in survival, death and metabolic health: A lifeguard with a licence to kill. Nature Reviews. Molecular Cell Biology, 16(7), 393–405. https://doi.org/https://doi.org/10.1038/nrm4007
- Lambert, J. M. R., Gorzov, P., Veprintsev, D. B., Söderqvist, M., Segerbäck, D., Bergman, J., Fersht, A. R., Hainaut, P., Wiman, K. G., & Bykov, V. J. N. (2009). PRIMA-1 Reactivates Mutant p53 by Covalent Binding to the Core Domain. Cancer Cell, 15(5), 376–388. https://doi.org/https://doi.org/10.1016/j.ccr.2009.03.003
- Lambert, J. M. R., Moshfegh, A., Hainaut, P., Wiman, K. G., & Bykov, V. J. N. (2010). Mutant p53 reactivation by PRIMA-1MET induces multiple signaling pathways converging on apoptosis. Oncogene, 29(9), 1329–1338. https://doi.org/https://doi.org/10.1038/onc.2009.425
- Lehmann, S., Bykov, V. J. N., Ali, D., Andrén, O., Cherif, H., Tidefelt, U., Uggla, B., Yachnin, J., Juliusson, G., Moshfegh, A., Paul, C., Wiman, K. G., & Andersson, P.-O. (2012). Targeting p53 in Vivo: A first-in-human study with p53-targeting compound APR-246 in refractory hematologic malignancies and prostate cancer. Journal of Clinical Oncology : official Journal of the American Society of Clinical Oncology, 30(29), 3633–3639. https://doi.org/https://doi.org/10.1200/JCO.2011.40.7783
- Liu, X., Wilcken, R., Joerger, A. C., Chuckowree, I. S., Amin, J., Spencer, J., & Fersht, A. R. (2013). Small molecule induced reactivation of mutant p53 in cancer cells. Nucleic Acids Research, 41(12), 6034–6044. https://doi.org/https://doi.org/10.1093/nar/gkt305
- Lu, Q., Tan, Y.-H., & Luo, R. (2007). Molecular dynamics simulations of p53 DNA-binding domain. The Journal of Physical Chemistry. B, 111(39), 11538–11545. https://doi.org/https://doi.org/10.1021/jp0742261
- Maleki, V. S., Salim, K. Y., Danter, W. R., & Koropatnick, J. (2018). Novel anti-cancer drug COTI-2 synergizes with therapeutic agents and does not induce resistance or exhibit cross-resistance in human cancer cell lines. PLoS One, 13(1), e0191766 https://doi.org/https://doi.org/10.1371/journal.pone.0191766
- Martins, C. P., Brown-Swigart, L., & Evan, G. I. (2006). Modeling the Therapeutic Efficacy of p53 Restoration in Tumors. Cell, 127(7), 1323–1334. https://doi.org/https://doi.org/10.1016/j.cell.2006.12.007
- Muller, P. A. J., & Vousden, K. H. (2013). p53 mutations in cancer. Nat Cell Biol, 15(1), 2–8. https://doi.org/https://doi.org/10.1038/ncb2641
- Pant, V., & Lozano, G. (2014). Limiting the power of p53 through the ubiquitin proteasome pathway. Genes & Development, 28(16), 1739–1751. https://doi.org/https://doi.org/10.1101/gad.247452.114
- Parrales, A., & Iwakuma, T. (2015). Targeting oncogenic mutant p53 for cancer therapy. Frontiers in Oncology, 5, 288 https://doi.org/https://doi.org/10.3389/fonc.2015.00288
- Salim, K. Y., Vareki, S. M., Danter, W. R., San-Marina, S., & Koropatnick, J. (2016). COTI-2, a novel small molecule that is active against multiple human cancer cell lines in vitro and in vivo. Oncotarget, 7(27), 41363–41379.
- Salsbury, F. R. (2010). Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Curr Opin Pharmacol, 10(6), 738–744. https://doi.org/https://doi.org/10.1016/j.coph.2010.09.016
- Tate, J. G., Bamford, S., Jubb, H. C., Sondka, Z., Beare, D. M., Bindal, N., Boutselakis, H., Cole, C. G., Creatore, C., Dawson, E., Fish, P., Harsha, B., Hathaway, C., Jupe, S. C., Kok, C. Y., Noble, K., Ponting, L., Ramshaw, C. C., Rye, C. E., Speedy, H. E., … Forbes, S. A. (2019). COSMIC: The catalogue of somatic mutations in cancer. Nucleic Acids Research, 47(D1), D941–D947. https://doi.org/https://doi.org/10.1093/nar/gky1015
- Teague, S. J. (2003). Implications of protein flexibility for drug discovery. Nature Reviews. Drug Discovery, 2(7), 527–541. https://doi.org/https://doi.org/10.1038/nrd1129
- Tokino, T., & Nakamura, Y. (2000). The role of p53-target genes in human cancer. Critical Reviews in Oncology/Hematology, 33(1), 1–6. https://doi.org/https://doi.org/10.1016/s1040-8428(99)00051-7
- Umbaugh, C. S., Diaz‐Quiñones, A., Neto, M. F., Shearer, J. J., & Figueiredo, M. L. (2018). A dock derived compound against laminin receptor (37 LR) exhibits anti-cancer properties in a prostate cancer cell line model. Oncotarget, 9(5), 5958–5978. https://doi.org/https://doi.org/10.18632/oncotarget.23236
- 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/https://doi.org/10.1002/jcc.21367
- Ventura, A., Kirsch, D. G., McLaughlin, M. E., Tuveson, D. A., Grimm, J., Lintault, L., Newman, J., Reczek, E. E., Weissleder, R., & Jacks, T. (2007). Restoration of p53 function leads to tumour regression in vivo. Nature, 445(7128), 661–665. https://doi.org/https://doi.org/10.1038/nature05541
- Wiman, K. G. (2010). Pharmacological reactivation of mutant p53: From protein structure to the cancer patient. Oncogene, 29(30), 4245–4252. https://doi.org/https://doi.org/10.1038/onc.2010.188
- Xue, W., Zender, L., Miething, C., Dickins, R. A., Hernando, E., Krizhanovsky, V., Cordon-Cardo, C., & Lowe, S. W. (2007). Senescence and tumour clearance is triggered by p53 restoration in murine liver carcinomas. Nature, 445(7128), 656–660. https://doi.org/https://doi.org/10.1038/nature05529
- Zhang, Q., Bykov, V. J. N., Wiman, K. G., & Zawacka-Pankau, J. (2018). APR-246 reactivates mutant p53 by targeting cysteines 124 and 277. Cell Death & Disease, 9(5), 439 https://doi.org/https://doi.org/10.1038/s41419-018-0463-7
- Zilfou, J. T., & Lowe, S. W. (2009). Tumor suppressive functions of p53. Cold Spring Harbor Perspectives in Biology, 1(5), a001883–a001883.