|
|
基于KRAS蛋白结构的药学研究——生物化学课程教育教学改革研究与实践
|
Abstract:
目的：本项目通过将生物化学领域里的结构生物学知识应用于药学研究，拓展了基于结构的药物分子分析与设计的理论与技术。通过对药物靶点蛋白结构的统计与分析，研究了KRAS相关蛋白质结构与功能之间的关系，以及药物分子靶向目标蛋白质的分子机制，完成其结构与功能之间关系的分析，指导化合物的合成，为新药设计奠定基础。方法：主要通过PDB、PDBePISA、UniProt等数据库和网络服务器以及Chem3D、UCSF Chimera、PyMol、Origin等软件对于KRAS相关蛋白质的一系列重要参数进行检索、计算和绘图等，收集、整理、分析KRAS蛋白质分子的结构域功能信息，研究药物分子靶向目标蛋白质的分子机制。结果：KRAS蛋白与其配体化合物的结合面积与化合物的分子量呈正相关(除少部分外)。此外，KRAS蛋白与其配体化合物的结合为非共价结合时，化合物的摩尔折射率和分配系数都对其理论结合能影响不大，几乎维持在？5 kcal/mol到5 kcal/mol之间，而且配体化合物通常结合在Switch-II Pocket (S-IIP)附近。而当KRAS蛋白与其配体化合物的结合为共价结合时，突变体的结合能几乎都为负值，绝对值显著增大，而非突变体的结合能变化不大，依旧维持在？5 kcal/mol到5 kcal/mol之间，且配体化合物往往结合于第12位的甘氨酸突变产生的半胱氨酸附近。结论：靶向KRAS的药物分子若能够与蛋白质中由第12位的甘氨酸突变产生的半胱氨酸形成共价结合，且分子量较大，则其与蛋白质的结合面积相对较大、结合较为牢固、特异性更强，或者药物分子可以以非共价结合的方式结合于S-IIP附近，可以增强对KRAS的抑制效应。
Aim: To explore the application of structural biology technology in the medicinal research area, structures of KRAS-compound complexes are analyzed for the design of novel potent drugs. This project studies the relationship between the structure and function of KRAS gene-related proteins and the molecular mechanism of inhibitors targeting KRAS protein through structural and statistical analysis; so as to analyze the relationship between the structure and function, guide the synthesis of compounds, and lay the foundation for the design of new drugs. Methods: Searching, calculation and figure representation are carried out by using mainly PDB, UniProt, PDBePISA and some other websites or software, such as Chem3D, UCSF Chimera, PyMol, Origin, etc., for series of important parameters of the related proteins of the KRAS gene. To study the molecular mechanism of inhibitors targeting the KRAS protein molecule, information regarding the biophysical properties of compounds and domain function of protein of interest is collected, analyzed and summarized. Results: Except for a few, the interface areas between KRAS protein and its ligand compounds are positively correlated with the molecular weights of the compounds. In addition, when the binding of KRAS protein and its ligand compounds is non-covalent, the ClogP (molar refractivity or partition coefficient) value of the compounds has little effect on the theoretical binding energy, which almost remains between ？5 and 5 kcal/mol. The ligand compound is often bound to the vicinity of Switch-II Pocket (S-lP). However, when the binding of KRAS protein and its ligand compound is covalent binding, the binding energy of the mutants was almost all negative and the absolute value increased significantly, while the binding energy of the non-mutants did not change significantly, still maintaining between ？5 and 5
| [1] | Hawkins, T. and Kihara, D. (2007) Function Prediction of Uncharacterized Proteins. Journal of Bioinformatics and Computational Biology, 5, 1-30. https://doi.org/10.1142/S0219720007002503 |
| [2] | Cruz L.M., Trefflich, S., Weiss, V.A. and Castro, M.A.A. (2017) Protein Function Prediction. In: Kaufmann, M., Klinger, C. and Savelsbergh, A., Eds., Functional Genomics, Humana Press, New York, 55-75.
https://doi.org/10.1007/978-1-4939-7231-9_5 |
| [3] | Parada, L.F., Tabin, C.J., Shih, C. and Weinberg, R.A. (1982) Human EJ Bladder Carcinoma Oncogene Is Homologue of Harvey Sarcoma Virus Ras Gene. Nature, 297, 474-478. https://doi.org/10.1038/297474a0 |
| [4] | Hunter J.C., Gurbani, D., Ficarro, S.B., Carrasco, M.A., Lim, S.M., Choi, H.G., Xie, T., Marto, J.A., Chen, Z., Gray, N.S. and Westover, K.D. (2014) In Situ Selectivity Profiling and Crystal Structure of SML-8-73-1, an Active Site Inhibitor of Oncogenic K-Ras G12C. Proceedings of the National Academy of Sciences of the United States of America, 111, 8895-8900. https://doi.org/10.1073/pnas.1404639111 |
| [5] | Hunter J.C., Manandhar, A., Carrasco, M.A., Gurbani, D., Gondi, S. and Westover, K.D. (2015) Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations. Molecular Cancer Research, 13, 1325-1335.
https://doi.org/10.1158/1541-7786.MCR-15-0203 |
| [6] | McGee, J.H., Shim, S.Y., Lee, S.J., Swanson, P.K., Jiang, S.Y., Durney, M.A. and Verdine, G.L. (2018) Exceptionally High-Affinity Ras Binders That Remodel Its Effector Domain. The Journal of Biological Chemistry, 293, 3265-3280.
https://doi.org/10.1074/jbc.M117.816348 |
| [7] | Kauke, M.J., Traxlmayr, M.W., Parker, J.A., Kiefer, J.D., Knihtila, R., McGee, J., Verdine, G., Mattos, C. and Wittrup, K.D. (2017) An Engineered Protein Antagonist of K-Ras/B-Raf Interaction. Scientific Reports, 7, Article No. 5831.
https://doi.org/10.1038/s41598-017-05889-7 |
| [8] | Dhirendra, K.S., Dwight, V.N. and Frank, M. (2017) RAS Proteins and Their Regulators in Human Disease. Cell, 170, 17-33. https://doi.org/10.1016/j.cell.2017.06.009 |
| [9] | Lu, S.Y., Jang, H., Gu, S., Zhang, J. and Nussinov, R. (2016) Drugging Ras GTPase: A Comprehensive Mechanistic and Signaling Structural View. Chemical Society Reviews, 45, 4929-4952. https://doi.org/10.1039/C5CS00911A |
| [10] | Maurer, T., Garrenton, L.S., Oh, A., Pitts, K., Anderson, D.J., Skelton, N.J., Fauber, B.P., Pan, B., Malek, S., Stokoe, D., Ludlam, M.J.C., Bowman, K.K., Wu, J.S., Giannetti, A.M., Starovasnik, M.A., Mellman, I., Jackson, P.K., Rudolph, J., Wang, W.R. and Fang, G.W. (2012) Small-Molecule Ligands Bind to a Distinct Pocket in Ras and Inhibit SOS-Mediated Nucleotide Exchange Activity. Proceedings of the National Academy of Sciences of the United States of America, 109, 5299-5304. |
| [11] | Hillig, R.C., Sautier, B., Schroeder, J., Moosmayer, D., Hilpmann, A., Stegmann, C.M., Werbeck, N.D., Briem, H., Boemer, U., Weiske, J., Badock, V., Mastouri, J., Petersen, K., Siemeister, G., Kahmann, J.D., Wegener, D., B？hnke, N., Eis, K., Graham, K., Wortmann, L., von Nussbaum, F. and Bader, B. (2019) Discovery of Potent SOS1 Inhibitors That Block RAS Activation via Disruption of the RAS-SOS1 Interaction. Proceedings of the National Academy of Sciences of the United States of America, 116, 2551-2560. https://doi.org/10.1073/pnas.1812963116 |
| [12] | 李歆, 王义俊, 刘平羽. 特异靶向KRAS-G12C突变的抗肿瘤药物研究进展[J]. 药学学报, 2021, 56(2): 374-382.
https://doi.org/10.16438/j.0513-4870.2020-1485 |
| [13] | Mukhopadhyay, S., Vander, H.M.G. and McCormick, F. (2021) The Metabolic Landscape of RAS-Driven Cancers from Biology to Therapy. Nature Cancer, 2, 271-283. https://doi.org/10.1038/s43018-021-00184-x |
| [14] | Schubbert, S., Shannon, K. and Bollag, G. (2007) Hyperactive Ras in Developmental Disorders and Cancer. Nature Reviews Cancer, 7, 295-308. https://doi.org/10.1038/nrc2109 |
| [15] | Liu, P.Y., Wang, Y.J. and Li, X. (2019) Targeting the Untargetable KRAS in Cancer Therapy. Acta Pharmaceutica Sinica B, 9, 871-879. https://doi.org/10.1016/j.apsb.2019.03.002 |
| [16] | Douglas, H. and Robert, A.W. (2011) Hallmarks of Cancer: The Next Generation. Cell, 144, 646-674.
https://doi.org/10.1016/j.cell.2011.02.013 |
| [17] | Pylayeva-Gupta, Y., Grabocka, E. and Bar-Sagi, D. (2011) RAS Oncogenes: Weaving a Tumorigenic Web. Nature Reviews Cancer, 11, 761-774. https://doi.org/10.1038/nrc3106 |
| [18] | Ying, H.Q., Kimmelman, A.C., Lyssiotis, C.A., Hua, S.J., Chu, G.C., Fletcher-Sananikone, E., Locasale, J.W., Son, J., Zhang, H.L., Coloff, J.L., Yan, H.Y., Wang, W., Chen, S.J., Viale, A., Zheng, H.W., Paik, J., Lim, C., Guimaraes, A.R., Martin, E.S., Chang, J., Hezel, A.F., Perry, S.R., Hu, J., Gan, B.Y., Xiao, Y.H., Asara, J.M., Weissleder, R., Wang, Y.A., Chin, L., Cantley, L.C. and DePinho, R.A. (2012) Oncogenic Kras Maintains Pancreatic Tumors through Regulation of Anabolic Glucose Metabolism. Cell, 149, 656-670. https://doi.org/10.1016/j.cell.2012.01.058 |
| [19] | Weijzen, S., Velders, M.P. and Kast, W.M. (1999) Modulation of the Immune Response and Tumor Growth by Activated Ras. Leukemia, 13, 502-513. https://doi.org/10.1038/sj.leu.2401367 |
| [20] | Patricelli, M.P., Janes, M.R., Li, L.S., Hansen, R., Peters, U., Kessler, L.V., Chen, Y., Kucharski, J.M., Feng, J., Ely, T., Chen, J.H., Firdaus, S.J., Babbar, A., Ren, P.D. and Liu, Y. (2016) Selective Inhibition of Oncogenic KRAS Output with Small Molecules Targeting the Inactive State. Cancer Discovery, 6, 316-329.
https://doi.org/10.1158/2159-8290.CD-15-1105 |
| [21] | Bryant, K.L., Mancias, J.D., Kimmelman, A.C. and Der, C.J. (2014) KRAS: Feeding Pancreatic Cancer Proliferation. Trends in Biochemical Sciences, 39, 91-100. https://doi.org/10.1016/j.tibs.2013.12.004 |
| [22] | Hofmann, M.H., Gerlach, D., Misale, S., Petronczki, M. and Kraut, N. (2022) Expanding the Reach of Precision Oncology by Drugging All KRAS Mutants. Cancer Discovery, 12, 924-937.
https://doi.org/10.1158/2159-8290.c.6549598.v1 |
| [23] | Haigis, K.M. (2017) KRAS Alleles: The Devil Is in the Detail. Trends in Cancer, 3, 686-697.
https://doi.org/10.1016/j.trecan.2017.08.006 |
| [24] | Reck, M., Carbone, D.P., Garassino, M. and Barlesi, F. (2021) Targeting KRAS in Non-Small Cell Lung Cancer: Recent Progress and New Approaches. Annals of Oncology, 32, 1101-1110. https://doi.org/10.1016/j.annonc.2021.06.001 |
| [25] | Sun, Q., Burke, J.P., Phan, J., Burns, M.C., Olejniczak, E.T., Waterson, A.G., Lee, T., Rossanese, O.W. and Fesik, S.W. (2012) Discovery of Small Molecules That Bind to K-Ras and Inhibit Sos-Mediated Activation. Angewandte Chemie International Edition, 51, 6140-6143. https://doi.org/10.1002/anie.201201358 |
| [26] | Wu, H.Z., Xiao, J.Q., Xiao, S.S. and Cheng, Y. (2019) KRAS: A Promising Therapeutic Target for Cancer Treatment. Current Topics in Medicinal Chemistry, 19, 2081-2097. https://doi.org/10.2174/1568026619666190905164144 |
| [27] | Ni, D., Li, X.Y., He, X.H., Zhang, H., Zhang, J. and Lu, S.Y. (2019) Drugging K-Ras G12C through Covalent Inhibitors: Mission Possible? Pharmacology and Therapeutics, 202, 1-17. https://doi.org/10.1016/j.pharmthera.2019.06.007 |
| [28] | Gupta, A.K., Wang, X., Pagba, C.V., Prakash, P., Sarkar-Banerjee, S., Putkey, J. and Gorfe, A.A. (2019) Multi-Target, Ensemble-Based Virtual Screening Yields Novel Allosteric KRAS Inhibitors at High Success Rate. Chemical Biology & Drug Design, 94, 1441-1456. https://doi.org/10.1111/cbdd.13519 |
| [29] | Huang, L.M., Guo, Z.X., Wang, F. and Fu, L.W. (2021) KRAS Mutation: From Undruggable to Druggable in Cancer. Signal Transduction and Targeted Therapy, 6, Article No. 386. https://doi.org/10.1038/s41392-021-00780-4 |
| [30] | Yan, W.P., Markegard, E., Dharmaiah, S., Urisman, A., Drew, M., Esposito, D., Scheffzek, K., Nissley, D.V., McCormick, F. and Simanshu, D.K. (2020) Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR. Cell Reports, 32, Article ID: 107909.
https://doi.org/10.1016/j.celrep.2020.107909 |
| [31] | Nnadi, C.I., Jenkins, M.L., Gentile, D.R., Bateman, L.A., Zaidman, D., Balius, T.E., Nomura, D.K., Burke, J.E., Shokat, K.M. and Nir, L. (2018) Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. Journal of Chemical Information and Modeling, 58, 464-471. https://doi.org/10.1021/acs.jcim.7b00399 |
| [32] | Kettle, J.G., Bagal, S.K., Bickerton, S., Bodnarchuk, M.S., Breed, J., Carbajo, R.J., Cassar, D.J., Chakraborty, A., Cosulich, S., Cumming, I., Davies, M., Eatherton, A., Evans, L., Feron, L., Fillery, S., Gleave, E.S., Goldberg, F.W., Harlfinger, S., Hanson, L., Howard, M., Howells, R., Jackson, A., Kemmitt, P., Kingston, J.K., Lamont, S., Lewis, H.J., Li, S., Liu, L., Ogg, D., Phillips, C., Polanski, R., Robb, G., Robinson, D., Ross, S., Smith, J.M., Tonge, M., Whiteley, R., Yang, J., Zhang, L. and Zhao, X. (2020) Structure-Based Design and Pharmacokinetic Optimization of Covalent Allosteric Inhibitors of the Mutant GTPase KRASG12C. Journal of Medicinal Chemistry, 63, 4468-4483.
https://doi.org/10.1021/acs.jmedchem.9b01720 |
| [33] | Dirk, K., Andreas, B., Jark, B., Gerhard, F., Sandra, D., Melanie, H., Barbara, M., Alexander, W.P. and McConnell, D.B. (2020) Drugging All RAS Isoforms with One Pocket. Future Medicinal Chemistry, 12, 1911-1923.
https://doi.org/10.4155/fmc-2020-0221 |
| [34] | Hansen, R., Peters, U., Babbar, A., Chen, Y., Feng, J., Janes, M.R., Li, L.S., Ren, P., Liu, Y. and Zarrinkar, P.P. (2018) The Reactivity-Driven Biochemical Mechanism of Covalent KRASG12C Inhibitors. Nature Structural & Molecular Biology, 25, 454-462. https://doi.org/10.1038/s41594-018-0061-5 |
| [35] | Goebel, L., Mueller, M.P., Goody, R.S. and Rauh, D. (2020) KRasG12C Inhibitors in Clinical Trials: A Short Historical Perspective. RSC Medicinal Chemistry, 11, 760-770. https://doi.org/10.1039/D0MD00096E |
| [36] | Ostrem, J.M.L. and Shokat, K.M. (2016) Direct Small-Molecule Inhibitors of KRAS: From Structural Insights to Mechanism-Based Design. Nature Reviews Drug Discovery, 15, 771-785. https://doi.org/10.1038/nrd.2016.139 |
| [37] | Mishto, M., Mansurkhodzhaev, A., Ying, G., Bitra, A., Cordfunke, R.A., Henze, S., Paul, D., Sidney, J., Urlaub, H., Neefjes, J., Sette, A., Zajonc, D.M. and Liepe, J. (2019) An in Silico—in Vitro Pipeline Identifying an HLA-A*02: 01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients. Frontiers in Immunology, 10, Article 2572. https://doi.org/10.3389/fimmu.2019.02572 |
| [38] | Kwan, A.K., Piazza, G.A., Keeton, A.B. and Leite, C.A. (2022) The Path to the Clinic: A Comprehensive Review on Direct KRASG12C Inhibitors. Journal of Experimental & Clinical Cancer Research, 41, Article No. 27.
https://doi.org/10.1186/s13046-021-02225-w |
| [39] | Cox, A.D., Fesik, S.W., Kimmelman, A.C., Luo, J. and Der, C.J. (2014) Drugging the Undruggable RAS: Mission Possible? Nature Reviews Drug Discovery, 13, 828-851. https://doi.org/10.1038/nrd4389 |
| [40] | Désage, A.L., Léonce, C., Swalduz, A. and Ortiz, C.S. (2022) Targeting KRAS Mutant in Non-Small Cell Lung Cancer: Novel Insights into Therapeutic Strategies. Frontiers in Oncology, 12, Article 796832.
https://doi.org/10.3389/fonc.2022.796832 |
| [41] | 许俨钊, 文辉, 崔华清. KRAS抑制剂的研究进展[J]. 药学学报, 2021, 56(6): 1562-1570.
https://doi.org/10.16438/j.0513-4870.2020-1834 |
| [42] | Bera, A.K., Lu, J., Lu, C., Li, L., Gondi, S., Yan, W., Nelson, A., Zhang, G. and Westover, K.D. (2020) GTP Hydrolysis Is Modulated by Arg34 in the RASopathy-Associated KRASP34R. Birth Defects Research, 112, 708-717.
https://doi.org/10.1002/bdr2.1647 |
| [43] | Lu, J., Harrison, R.A., Li, L., Zeng, M., Gondi, S., Scott, D., Gray, N.S., Engen, J.R. and Westover, K.D. (2017) KRAS G12C Drug Development: Discrimination between Switch II Pocket Configurations Using Hydrogen/Deuterium-Exchange Mass Spectrometry. Structure, 25, 1442-1448.E3. https://doi.org/10.1016/j.str.2017.07.003 |
| [44] | Ostrem, J.M., Peters, U., Sos, M.L., Wells, J.A. and Shokat, K.M. (2013) K-Ras (G12C) Inhibitors Allosterically Control GTP Affinity and Effector Interactions. Nature, 503, 548-551. https://doi.org/10.1038/nature12796 |
| [45] | Janes, M.R., Zhang, J.C., Li, L.S., Hansen, R., Peters, U., Guo, X., Chen, Y.C., Babbar, A., Firdaus, S.J., Darjania, L., Feng, J., Chen, J.H., Li, S.W., Li, S.S., Long, Y.O., Thach, C., Liu, Y., Zarieh, A., Ely, T., Kucharski, J.M., Kessler, L.V., Wu, T., Yu, K., Wang, Y., Yao, Y., Deng, X.H., Zarrinkar, P.P., Brehmer, D., Dhanak, D., Lorenzi, M.V., Hu-Lowe, D., Patricelli, M.P., Ren, P. and Liu, Y. (2018) Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor. Cell, 172, 578-589.E17. https://doi.org/10.1016/j.cell.2018.01.006 |
| [46] | Canon, J., Rex, K., Saiki, A.Y., Mohr, C., Cooke, K., Bagal, D., Gaida, K., Holt, T., Knutson, C.G., Koppada, N., Lanman, B.A., Werner, J., Rapaport, A.S., San, M.T., Ortiz, R., Osgood, T., Sun, J.R., Zhu, X., McCarter, J.D., Volak, L.P., Houk, B.E., Fakih, M.G., O’Neil, B.H., Price, T.J., Falchook, G.S., Desai, J., Kuo, J., Govindan, R., Hong, D.S., Ouyang, W., Henary, H., Arvedson, T., Cee, V.J. and Lipford, J.R. (2019) The Clinical KRAS(G12C) Inhibitor AMG 510 Drives Anti-Tumour Immunity. Nature, 575, 217-223. https://doi.org/10.1038/s41586-019-1694-1 |
| [47] | Boike, L., Henning, N.J. and Nomura, D.K. (2022) Advances in Covalent Drug Discovery. Nature Reviews Drug Discovery, 21, 881-898. https://doi.org/10.1038/s41573-022-00542-z |
| [48] | Wang, H., Chi, L.L., Yu, F.Q., Dai, H.L., Gao, C., Si, X.J., Wang, Z.J., Liu, L.M., Zheng, J.X., Shan, L.H., Liu, H.M. and Zhang, Q.R. (2023) Annual Review of KRAS Inhibitors in 2022. European Journal of Medicinal Chemistry, 249, Article ID: 115124. https://doi.org/10.1016/j.ejmech.2023.115124 |
