Identification and validation of novel PERK inhibitors

Journal of Chemical Information and Modeling

Volumn 54, Issue 5, 2014, Pages 1467-1475

  Wang, Qiantao ^a,b   Park, Jihyun ^a   Devkota, Ashwini K ^a   Cho, Eun Jeong ^a   Dalby, Kevin N ^a   Ren, Pengyu ^b  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b The University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COST EFFECTIVENESS; MOLECULAR DYNAMICS;

ACTIVE COMPOUNDS; CONFORMATIONAL FLEXIBILITY; EXPERIMENTAL VALIDATIONS; PHARMACOPHORE MODELING; STRUCTURE-BASED; TYPE II DIABETES; UNFOLDED PROTEIN RESPONSE; VIRTUAL SCREENING;

DIAGNOSIS;

PERK KINASE; PROTEIN KINASE INHIBITOR; PROTEIN KINASE R;

ANIMAL; ANTAGONISTS AND INHIBITORS; CHEMISTRY; COMPUTER INTERFACE; DOSE RESPONSE; DRUG DATABASE; DRUG SCREENING; ENZYME ACTIVE SITE; HIGH THROUGHPUT SCREENING; IC50; METABOLISM; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOUSE; REPRODUCIBILITY; VALIDATION STUDY;

ANIMALS; CATALYTIC DOMAIN; DATABASES, PHARMACEUTICAL; DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG EVALUATION, PRECLINICAL; EIF-2 KINASE; HIGH-THROUGHPUT SCREENING ASSAYS; INHIBITORY CONCENTRATION 50; MICE; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN KINASE INHIBITORS; REPRODUCIBILITY OF RESULTS; USER-COMPUTER INTERFACE;

EID: 84901607879     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500114r     Document Type: Article

References (40)

1. Hu, X.; Compton, J. R.; AbdulHameed, M. D. M.; Marchand, C. L.; Robertson, K. L.; Leary, D. H.; Jadhav, A.; Hershfield, J. R.; Wallqvist, A.; Friedlander, A. M.; Legler, P. M. 3-Substituted Indole Inhibitors Against Francisella tularensis FabI Identified by Structure-Based Virtual Screening J. Med. Chem. 2013, 56, 5275-5287
2. Ravindranathan, K. P.; Mandiyan, V.; Ekkati, A. R.; Bae, J. H.; Schlessinger, J.; Jorgensen, W. L. Discovery of novel fibroblast growth factor receptor 1 kinase inhibitor by structure-based virtual screening J. Med. Chem. 2010, 53, 1662-1672
3. Teli, M. K.; Rajanikant, G. K. Computational Repositioning and Experimental Validation of Approved Drugs for HIF-Prolyl Hydroxylase Inhibition J. Chem. Inf. Model. 2013, 53, 1818-1824
4. Sahner, J. H.; Groh, M.; Negri, M.; Haupenthal, J.; Hartmann, R. W. Novel small molecule inhibitors targeting the "switch region" of bacterial RNAP: Structure-based optimization of a virtual screening hit Eur. J. Med. Chem. 2013, 65, 223-231
5. Rea, V. E. A.; Lavecchia, A.; Di Giovanni, C.; Rossi, F. W.; Gorrasi, A.; Pesapane, A.; de Paulis, A.; Ragno, P.; Montuori, N. Discovery of new small molecules targeting the vitronectin binding site of the urokinase receptor that block cancer cell invasion Mol. Cancer Ther. 2013, 12, 1402-1416
6. Kaoud, T. S.; Yan, C.; Mitra, S.; Tseng, C.-C.; Jose, J.; Taliaferro, J. M.; Tuohetahuntila, M.; Devkota, A.; Sammons, R.; Park, J.; Park, H.; Shi, Y.; Hong, J.; Ren, P.; Dalby, K. N. From in Silico Discovery to Intracellular Activity: Targeting JNK-Protein Interactions with Small Molecules ACS Med. Chem. Lett. 2012, 3, 721-725
7. Taylor, S. S.; Kornev, A. P. Protein kinases: evolution of dynamic regulatory proteins Trends Biochem. Sci. 2011, 36, 65-77
8. Schnieders, M. J.; Kaoud, T. S.; Yan, C.; Dalby, K. N.; Ren, P. Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases Curr. Pharm. Des. 2012, 18, 1173-1185
9. Yan, C.; Kaoud, T.; Lee, S.; Dalby, K. N.; Ren, P. Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1 J. Phys. Chem. B 2011, 115, 1491-1502
10. Wang, H.; Blais, J.; Ron, D.; Cardozo, T. Structural determinants of PERK inhibitor potency and selectivity Chem. Biol. Drug Des. 2010, 76, 480-495
11. Wang, J.; Chen, L.; Sinha, S. H.; Liang, Z.; Chai, H.; Muniyan, S.; Chou, Y.-W.; Yang, C.; Yan, L.; Feng, Y.; Li, K. K.; Lin, M.-F.; Jiang, H.; Zheng, Y. G.; Luo, C. Pharmacophore-based virtual screening and biological evaluation of small molecule inhibitors for protein arginine methylation J. Med. Chem. 2012, 55, 7978-7987
12. Singh, J.; Chuaqui, C. E.; Boriack-Sjodin, P. A.; Lee, W.-C.; Pontz, T.; Corbley, M. J.; Cheung, H.-K.; Arduini, R. M.; Mead, J. N.; Newman, M. N.; Papadatos, J. L.; Bowes, S.; Josiah, S.; Ling, L. E. Successful shape-based virtual screening: the discovery of a potent inhibitor of the type I TGFbeta receptor kinase (TbetaRI) Bioorg. Med. Chem. Lett. 2003, 13, 4355-4359
13. Chao, W.-R.; Yean, D.; Amin, K.; Green, C.; Jong, L. Computer-aided rational drug design: a novel agent (SR13668) designed to mimic the unique anticancer mechanisms of dietary indole-3-carbinol to block Akt signaling J. Med. Chem. 2007, 50, 3412-3415
14. De Luca, L.; Ferro, S.; Damiano, F. M.; Supuran, C. T.; Vullo, D.; Chimirri, A.; Gitto, R. Structure-based screening for the discovery of new carbonic anhydrase VII inhibitors Eur. J. Med. Chem. 2014, 71, 105-111
15. Yang, S.-Y. Pharmacophore modeling and applications in drug discovery: challenges and recent advances Drug Discovery Today 2010, 15, 444-450
16. Walter, P.; Ron, D. The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation Science 2011, 334, 1081-1086
17. Tsai, Y. C.; Weissman, A. M. The Unfolded Protein Response, Degradation from the Endoplasmic Reticulum, and Cancer Genes Cancer 2010, 1, 764-778
18. Tabas, I.; Ron, D. Integrating the mechanisms of apoptosis induced by endoplasmic reticulum stress Nat. Cell Biol. 2011, 13 (3) 184-190
19. Lin, J.; LaVail, M., Misfolded Proteins and Retinal Dystrophies. In Retinal Degenerative Diseases; Anderson, R. E.; Hollyfield, J. G.; LaVail, M. M., Eds.; Springer: New York, 2010; Vol. 664, pp 115-121.
20. Fonseca, S. G.; Gromada, J.; Urano, F. Endoplasmic reticulum stress and pancreatic β-cell death Trends Endocrinol. Metab. 2011, 22 (7) 266-274
21. Carrasco, D. R.; Sukhdeo, K.; Protopopova, M.; Sinha, R.; Enos, M.; Carrasco, Daniel E.; Zheng, M.; Mani, M.; Henderson, J.; Pinkus, G. S.; Munshi, N.; Horner, J.; Ivanova, E. V.; Protopopov, A.; Anderson, K. C.; Tonon, G.; DePinho, R. A. The Differentiation and Stress Response Factor XBP-1 Drives Multiple Myeloma Pathogenesis Cancer Cell 2007, 11 (4) 349-360
22. Papandreou, I.; Denko, N. C.; Olson, M.; Van Melckebeke, H.; Lust, S.; Tam, A.; Solow-Cordero, D. E.; Bouley, D. M.; Offner, F.; Niwa, M.; Koong, A. C. Identification of an Ire1alpha endonuclease specific inhibitor with cytotoxic activity against human multiple myeloma Blood 2011, 117 (4) 1311-1314
23. Li, B.; Gao, B.; Ye, L.; Han, X.; Wang, W.; Kong, L.; Fang, X.; Zeng, Y.; Zheng, H.; Li, S.; Wu, Z.; Ye, L. Hepatitis B virus X protein (HBx) activates ATF6 and IRE1-XBP1 pathways of unfolded protein response Virus Res. 2007, 124, 44-49
24. Axten, J. M.; Medina, J. R.; Feng, Y.; Shu, A.; Romeril, S. P.; Grant, S. W.; Li, W. H. H.; Heerding, D. A.; Minthorn, E.; Mencken, T.; Atkins, C.; Liu, Q.; Rabindran, S.; Kumar, R.; Hong, X.; Goetz, A.; Stanley, T.; Taylor, J. D.; Sigethy, S. D.; Tomberlin, G. H.; Hassell, A. M.; Kahler, K. M.; Shewchuk, L. M.; Gampe, R. T. Discovery of 7-Methyl-5-(1-{[3-(trifluoromethyl)phenyl]acetyl}- 2,3-dihydro-1H -indol-5-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (GSK2606414), a Potent and Selective First-in-Class Inhibitor of Protein Kinase R (PKR)-like Endoplasmic Reticulum Kinase (PERK) J. Med. Chem. 2012, 55, 7193-7207
25. Planesas, J. S. M.; Claramunt, R. M.; Teixidó, J.; Borrell, J. I.; Pérez-Nueno, V. I. Improving VEGFR-2 Docking-Based Screening by Pharmacophore Postfiltering and Similarity Search Postprocessing J. Chem. Inf. Model. 2011, 51 (4) 777-787
26. Zhang, Y.; Yang, S.; Jiao, Y.; Liu, H.; Yuan, H.; Lu, S.; Ran, T.; Yao, S.; Ke, Z.; Xu, J.; Xiong, X.; Chen, Y.; Lu, T. An Integrated Virtual Screening Approach for VEGFR-2 Inhibitors J. Chem. Inf. Model. 2013, 53, 3163-3177
27. Park, J.; Dalby, K. N. High through put screening of PERK inhibitors. Unpublished work. College of Pharmacy, University of Texas at Austin: Austin, TX, 2012.
28. Cui, W.; Li, J.; Ron, D.; Sha, B. The structure of the PERK kinase domain suggests the mechanism for its activation Acta Crystallogr., Sect.D 2011, 67, 423-428
29. Dar, A. C.; Dever, T. E.; Sicheri, F. Higher-order substrate recognition of eIF2alpha by the RNA-dependent protein kinase PKR Cell 2005, 122, 887-900
30. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
31. Case, D. A.; Darden, T. A.; Cheatham, I. T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Goetz, A. W.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER12; University of California: San Francisco, CA, 2012.
32. Siew, N.; Elofsson, A.; Rychlewski, L.; Fischer, D. MaxSub: an automated measure for the assessment of protein structure prediction quality Bioinformatics 2000, 16, 776-785
33. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267 (3) 727-748
34. Verdonk, M. L.; Berdini, V.; Hartshorn, M. J.; Mooij, W. T. M.; Murray, C. W.; Taylor, R. D.; Watson, P. Virtual screening using protein-ligand docking: avoiding artificial enrichment J. Chem. Inf. Comput. Sci. 2004, 44, 793-806
35. Dixit, A.; Verkhivker, G. M. Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations J. Chem. Inf. Model. 2012, 52 (10) 2501-2515
36. Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking Sets for Molecular Docking J. Med. Chem. 2006, 49 (23) 6789-6801
37. Traxler, P.; Furet, P. Strategies toward the design of novel and selective protein tyrosine kinase inhibitors Pharmacol. Ther. 1999, 82, 195-206
38. Cross, S.; Baroni, M.; Carosati, E.; Benedetti, P.; Clementi, S. FLAP: GRID Molecular Interaction Fields in Virtual Screening. Validation using the DUD Data Set J. Chem. Inf. Model. 2010, 50 (8) 1442-1450
39. Irwin, J. J.; Shoichet, B. K. ZINC-A free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 2005, 45 (1) 177-182
40. Irwin, J. J.; Sterling, T.; Mysinger, M. M.; Bolstad, E. S.; Coleman, R. G. ZINC: A free tool to discover chemistry for biology J. Chem. Inf. Model. 2012, 52 (7) 1757-1768