In-silico design of peptide inhibitors of K-Ras target in cancer disease

References

• Ahearn, I., Haigis, K., Bar-Sagi, D., & Philips, M. (2012). Regulating the regulator: Post-translational modification of RAS. Nature Reviews Molecular Cell Biology, 13(1), 39–51. doi:10.1038/nrm3255
   Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins, 17(4), 412–425. doi:10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Bahar, I., Atilgan, A. R., Demirel, M. C., & Erman, B. (1998). Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability. Physical Review Letters, 80 (12), 2733–2736. doi:10.1103/PhysRevLett.80.2733
   Web of Science ®Google Scholar
• Bos, J. L. (1989). Ras oncogenes in human cancer: A review. Cancer Research, 49 (17), 4682–4689.
   PubMed Web of Science ®Google Scholar
• Carugo, O., & Pongor, S. (2008). A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Science, 10(7), 1470–1473. doi:10.1110/ps.690101
   Google Scholar
• Castellano, E., & Downward, J. (2011). RAS interaction with PI3K: More than just another effector pathway. Genes & Cancer, 2(3), 261–274. doi:10.1177/1947601911408079
   PubMedGoogle Scholar
• Chen, Y., Wang, J., Zhang, J., & Wang, W. (2017). Binding modes of Bcl-2 homology 3 (BH3) peptides with anti-apoptotic protein A1 and redesign of peptide inhibitors: A computational study. Journal of Biomolecular Structure and Dynamics, 36(15), 3967–3977. doi:10.1080/07391102.2017.1404933
   PubMed Web of Science ®Google Scholar
• Cox, A. D., & Der, C. J. (2010). Ras history: The saga continues. Small Gtpases, 1 (1), 2–27. doi:10.4161/sgtp.1.1.12178
   PubMedGoogle Scholar
• Cox, A. D., Fesik, S. W., Kimmelman, A. C., Luo, J., & Der, C. J. (2014). Drugging the undruggable RAS: Mission Possible?. Nature Reviews. Drug Discovery, 13 (11), 828–851. doi:10.1038/nrd4389
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N log (N) method for Ewald sums in large systems. The Journal of chemical Physics, 98(12), 10089–10092. doi:10.1063/1.464397
   Web of Science ®Google Scholar
• Dogan, S., Shen, R., Ang, D. C., Johnson, M. L., D'Angelo, S. P., Paik, P. K., … Ladanyi, M. (2012). Molecular epidemiology of EGFR and KRAS mutations in 3,026 lung adenocarcinomas: Higher susceptibility of women to smoking-related KRAS-mutant cancers. Clinical Cancer Research, 18 (22), 6169–6177. doi:10.1158/1078-0432.CCR-11-3265
   PubMed Web of Science ®Google Scholar
• El Osta, B. E., Behera, M., Kim, S., Berry, L. D., Sica, G., Pillai, R. N., … Ramalingam, S. S. (2017). Characteristics and outcomes of patients (pts) with metastatic KRAS mutant lung adenocarcinomas: Lung Cancer Mutation Consortium (LCMC) database. Journal of Clinical Oncology, 35 (15_suppl), 9021–9021. doi:10.1200/JCO.2017.35.15_suppl.9021
   Google Scholar
• Eskici, G., & Gur, M. (2013). Computational Design of New Peptide Inhibitors for Amyloid Beta (Ab) Aggregation in Alzheimer’s disease: Application of a Novel Methodology. PLoS One, 8(6), e66178. doi:10.1371/journal.pone.0066178
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of chemical Physics, 103(19), 8577–8593. doi:10.1063/1.470117
   Web of Science ®Google Scholar
• Gotz, A. W., Williamson, M. J., Xu, D., Poole, D., Le Grand, S., & Walker, R. C. (2012). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born. Journal of Chemical Theory and Computation, 8(5), 1542–1555. doi:10.1021/ct200909j
   PubMed Web of Science ®Google Scholar
• Hancock, J. F., & Prior, I. A. (2005). Electron microscopic imaging of Ras signaling domains. Methods, 37(2), 165–172. doi:10.1016/j.ymeth.2005.05.018
   PubMed Web of Science ®Google Scholar
• Helmer, D., & Schmitz, K. (2016). Peptides and peptide analogs to inhibit protein-protein interactions. Advances in Experimental Medicine and Biology, 917, 147–183.
   PubMedGoogle Scholar
• Hirakawa, T., & Ruley, H. E. (1988). Rescue of cells from Ras oncogene-induced growth arrest by a second, complementing, oncogene. Proceedings of the National Academy of Sciences of Sciences, 85 (5), 1519–1523. doi:10.1073/pnas.85.5.1519
   PubMed Web of Science ®Google Scholar
• Isa, D. M., Chin, S. P., Chong, W. L., Zain, S. M., Rahman, N. A., & Lee, V. S. (2019). Dynamics and binding interactions of peptide inhibitors of dengue virus entry. Journal of Biological Physics, 45 (1), 63–76. doi:10.1007/s10867-018-9515-6
   PubMed Web of Science ®Google Scholar
• Jackson, J. H., Cochrane, C. G., Bourne, J. R., Solski, P. A., Buss, J. E., & Der, C. J. (1990). Farnesol modification of Kirstenras exon 4B protein is essential for transformation. Proceedings of the National Academy of Sciences of Sciences, 87(8), 3042–3046. doi:10.1073/pnas.87.8.3042
   PubMed Web of Science ®Google Scholar
• Jordan, E. J., Kim, H. R., Arcila, M. E., Barron, D., Chakravarty, D., Gao, J., … Riely, G. J. (2017). Prospective comprehensive molecular characterization of lung adenocarcinomas for efficient patient matching to approved and emerging therapies. Cancer Discovery, 7 (6), 596–609. doi:10.1158/2159-8290.CD-16-1337
   PubMed Web of Science ®Google Scholar
• Keeton, A. B., Salter, E. A., & Piazza, G. A. (2017). The RAS–effector interaction as a drug target. Cancer Research, 77(2), 221–226. doi:10.1158/0008-5472.CAN-16-0938
   PubMed Web of Science ®Google Scholar
• Land, H., Parada, L. F., & Weinberg, R. A. (1983). Tumorigenic conversion of primary embryo fibroblasts requires at least two cooperating oncogenes. Nature, 304 (5927), 596–602. doi:10.1038/304596a0
   PubMed Web of Science ®Google Scholar
• Lu, S., Jang, H., Gu, S., Zhang, J., & Nussinov, R. (2016). Drugging Ras GTPase: A comprehensive mechanistic and signaling structural view. Chemical Society Reviews, 45 (18), 4929–4952. doi:10.1039/C5CS00911A
   PubMed Web of Science ®Google Scholar
• Lu, S., Jang, H., Muratcioglu, S., Gursoy, A., Keskin, O., Nussinov, R., & Zhang, J. (2016). Ras conformational ensembles, allostery, and signaling. Chemical Reviews, 116 (11), 6607–6665. doi:10.1021/acs.chemrev.5b00542
   PubMed Web of Science ®Google Scholar
• Lu, S., Ni, D., Wang, C., He, X., Lin, H., Wang, Z., & Zhang, J. (2019). Deactivation pathway of Ras GTPase underlies conformational substates as targets for drug design. ACS Catalysis, 9(8), 7188–7196. doi:10.1021/acscatal.9b02556
   Web of Science ®Google Scholar
• Madan, M. B., Kumar, S. S., & Balaram, P. (2002). A C–H· · · O Hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins. Journal of Molecular Biology, 322, 871–880. doi:10.1016/S0022-2836(02)00715-5
   PubMed Web of Science ®Google Scholar
• Maurer, T., Garrenton, L. S., Oh, A., Pitts, K., Anderson, D. J., Skelton, N. J., … Fang, G. (2012). Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity. In Proceedings of the National Academy of Sciences of the United States of America (pp. 5299–5304).
   Google Scholar
• Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. doi:10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Moodie, S. A., Willumsen, B. M., Weber, M. J., & Wolfman, A. (1993). Complexes of Ras.GTP with Raf-1 and mitogen-activated protein kinase kinase. Science, 260 (5114), 1658–1661. doi:10.1126/science.8503013
   PubMed Web of Science ®Google Scholar
• Nevola, L., & Giralt, E. (2015). Modulating protein-protein interactions: The potential of peptides. Chemical Communications, 51(16), 3302–3315. doi:10.1039/C4CC08565E
   PubMed Web of Science ®Google Scholar
• Ni, D., Li, X., He, X., Hoa, Z., Zhang, J., & Lu, S. (2019). Drugging K-RasG12C through covalent inhibitors: Mission possible? Pharmacology & Therapeutics, 202, 1–17. doi:10.1016/j.pharmthera.2019.06.007
   PubMed Web of Science ®Google Scholar
• Niida, A., Sasaki, S., Yonemori, K., Sameshima, T., Yaguchi, M., Asami, T., … Kamaura, M. (2017). Investigation of the structural requirements of K-Ras(G12D) selective inhibitory peptide KRpep-2d using alanine scans and cysteine bridging. Bioorganic & Medicinal Chemistry Letters, 27(12), 3302–3315.
   Web of Science ®Google Scholar
• Okada, T., Masuda, T., Shinkai, M., Kariya, K., & Kataoka, T. (1996). Post-translational modification of H-Ras is required for activation of, but not for association with, B-Raf. Journal of Biological Chemistry, 271 (9), 4671–4678. doi:10.1074/jbc.271.9.4671
   PubMed Web of Science ®Google Scholar
• Ostrem, J. M., Peters, U., Sos, M. L., Wells, J. A., & Shokat, K. M. (2013). K-Ras (G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature, 503 (7477), 548–551. doi:10.1038/nature12796
   PubMed Web of Science ®Google Scholar
• Piao, L., Chen, Z., Li, Q., Liu, R., Song, W., Kong, R., & Chang, S. (2019). Molecular dynamics simulations of wild type andmutants of SAPAP in complexed with Shank3. International Journal of Molecular Sciences, 20 (1), 224. doi:10.3390/ijms20010224
   PubMed Web of Science ®Google Scholar
• Rodriguez-Viciana, P., Warne, P. H., Dhand, R., Vanhaesebroeck, B., Gout, I., Fry, M. J., … Downward, J. (1994). Phosphatidylinositol-3-OH kinase as a direct target of Ras. Nature, 370 (6490), 527–532. doi:10.1038/370527a0
   PubMed Web of Science ®Google Scholar
• Ruley, H. E. (1983). Adenovirus early region 1A enables viral and cellular transforming genes to transform primary cells in culture. Nature, 304 (5927), 602–606. doi:10.1038/304602a0
   PubMed Web of Science ®Google Scholar
• Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. doi:10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Salomon-Ferrer, R., Case, D. A., & Walker, R. C. (2013). An overview of the Amber biomolecular simulation package. Wiley Interdisciplinary Reviews: Computational Molecular Science, 3(2), 198–210. doi:10.1002/wcms.1121
   Web of Science ®Google Scholar
• Seifert, E. (2014). OriginPro 9.1: Scientific data analysis and graphing software-software review. Journal of Chemical Information and Modeling, 54(5), 1552–1552. doi:10.1021/ci500161d
   PubMed Web of Science ®Google Scholar
• Shepherd, F. A., Domerg, C., Hainaut, P., Jänne, P. A., Pignon, J. P., Graziano, S., … Tsao, M. S. (2013). Pooled analysis of the prognostic and predictive effects of KRAS mutation status and KRAS mutation subtype in early-stage resected non-small-cell lung cancer in four trials of adjuvant chemotherapy. Journal of Clinical Oncology, 31 (17), 2173–2181. doi:10.1200/JCO.2012.48.1390
   PubMed Web of Science ®Google Scholar
• Smits, C., Czabotar, P. E., Hinds, M. G., & Day, C. L. (2008). Structural plasticity underpins promiscuous binding of the prosurvival protein A1. Structure, 16(5), 818–829. doi:10.1016/j.str.2008.02.009
   PubMed Web of Science ®Google Scholar
• Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2009). Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme. Bioorganic & Medicinal Chemistry, 17, 3369–3378. doi:10.1016/j.bmc.2009.03.055
   PubMed Web of Science ®Google Scholar
• Stephen, A. G., Esposito, D., Bagni, R. K., & McCormick, F. (2014). Dragging Ras back in the ring. Cancer Cell, 25 (3), 272–281. doi:10.1016/j.ccr.2014.02.017
   PubMed Web of Science ®Google Scholar
• Stokoe, D., & McCormick, F. (1997). Activation of c-Raf-1 by Ras and Src through different mechanisms: Activation in vivo and in vitro. The EMBO Journal, 16(9), 2384–2396. doi:10.1093/emboj/16.9.2384
   PubMed Web of Science ®Google Scholar
• Thapar, R., Williams, J., & Campbell, S. (2004). NMR characterization of full-length farnesylated and non-farnesylated H-Ras and its implications for Raf activation. Journal of Molecular Biology, 343(5), 1391–1408. doi:10.1016/j.jmb.2004.08.106
   PubMed Web of Science ®Google Scholar
• Tong, Y., Tempel, W., Shen, L., Arrowsmith, C. H., Edwards, A. M., Sundstrom, M., … Park, H. (2009). Human K-Ras (Q61H) in complex with a GTP analogue. Protein Data Bank (PDB). http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=B605E09A
   Google Scholar
• Trahey, M., & McCormick, F. (1987). A cytoplasmic protein stimulates normal N-Ras p21 GTPase, but does not affect oncogenic mutants. Science, 238 (4826), 542–545. doi:10.1126/science.2821624
   PubMed Web of Science ®Google Scholar
• van Hattum, H., & Waldmann, H. (2014). Chemical biology tools for regulating RAS signaling complexity in space and time. Chemistry & Biology, 21(9), 1185–1195. doi:10.1016/j.chembiol.2014.08.001
   PubMedGoogle Scholar
• Wennerberg, K., Rossman, K. L., & Der, C. J. (2005). The Ras superfamily at a glance. Journal of Cell Science, 118 (5), 843–846. doi:10.1242/jcs.01660
   PubMed Web of Science ®Google Scholar
• Wittinghofer, A., & Vetter, I. R. (2011). Structure-function relationships of the G domain, a canonical switch motif. Annual Review of Biochemistry, 80 (1), 943–971. doi:10.1146/annurev-biochem-062708-134043
   PubMedGoogle Scholar
• Wittinghofer, A., & Waldmann, H. (2000). Ras—A molecular switch involved in tumor formation. Angewandte Chemie, 39(23), 4192–4214. doi:10.1002/1521-3773(20001201)39:23<4192::AID-ANIE4192>3.0.CO;2-Y
   Google Scholar
• Yoshizawa, A., Sumiyoshi, S., Sonobe, M., Kobayashi, M., Fujimoto, M., Kawakami, F., … Haga, H. (2013). Validation of the IASLC/ATS/ERS lung adenocarcinoma classification for prognosis and association with EGFR and KRAS gene mutations: Analysis of 440 Japanese patients. Journal of Thoracic Oncology, 8 (1), 52–61. doi:10.1097/JTO.0b013e3182769aa8
   PubMed Web of Science ®Google Scholar
• Zwanzig, R. (1973). Nonlinear generalized Langevin equations. Journal of Statistical Physics, 9(3), 215–220. doi:10.1007/BF01008729
   Google Scholar