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Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity.

Kwarcinski FE, Brandvold KR, Phadke S, Beleh OM, Johnson TK, Meagher JL, Seeliger MA, Stuckey JA, Soellner MB
ACS Chem Biol 11 1296-304 (2016)
Related entries: 4ybk, 4yc8

Cited: 30 times
EuropePMC logo PMID: 26895387

Abstract

In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity.

Reviews - 4ybj mentioned but not cited (2)

  1. Three-Dimensional Interactions Analysis of the Anticancer Target c-Src Kinase with Its Inhibitors. Jha V, Macchia M, Tuccinardi T, Poli G. Cancers (Basel) 12 E2327 (2020)
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Articles - 4ybj mentioned but not cited (4)

  1. Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity. Kwarcinski FE, Brandvold KR, Phadke S, Beleh OM, Johnson TK, Meagher JL, Seeliger MA, Stuckey JA, Soellner MB. ACS Chem Biol 11 1296-1304 (2016)
  2. Survey of solution dynamics in Src kinase reveals allosteric cross talk between the ligand binding and regulatory sites. Tong M, Pelton JG, Gill ML, Zhang W, Picart F, Seeliger MA. Nat Commun 8 2160 (2017)
  3. Targeting Dynamic ATP-Binding Site Features Allows Discrimination between Highly Homologous Protein Kinases. Chakraborty S, Inukai T, Fang L, Golkowski M, Maly DJ. ACS Chem Biol 14 1249-1259 (2019)
  4. Selective Proteolysis to Study the Global Conformation and Regulatory Mechanisms of c-Src Kinase. Agius MP, Ko KS, Johnson TK, Kwarcinski FE, Phadke S, Lachacz EJ, Soellner MB. ACS Chem Biol 14 1556-1563 (2019)


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  2. Mechanisms of Cardiovascular Toxicity of BCR-ABL1 Tyrosine Kinase Inhibitors in Chronic Myelogenous Leukemia. Gustafson D, Fish JE, Lipton JH, Aghel N. Curr Hematol Malig Rep 15 20-30 (2020)
  3. Cyclin-Dependent Kinase 4 and 6 Inhibitors in Cell Cycle Dysregulation for Breast Cancer Treatment. Susanti NMP, Tjahjono DH. Molecules 26 4462 (2021)
  4. Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective. Ahmad K, Rizzi A, Capelli R, Mandelli D, Lyu W, Carloni P. Front Mol Biosci 9 899805 (2022)
  5. Novel Tyrosine Kinase Targets in Urothelial Carcinoma. Torres-Jiménez J, Albarrán-Fernández V, Pozas J, Román-Gil MS, Esteban-Villarrubia J, Carrato A, Rosero A, Grande E, Alonso-Gordoa T, Molina-Cerrillo J. Int J Mol Sci 22 E747 (2021)

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  1. Conformational states dynamically populated by a kinase determine its function. Xie T, Saleh T, Rossi P, Kalodimos CG. Science 370 eabc2754 (2020)
  2. How and when does an anticancer drug leave its binding site? Tiwary P, Mondal J, Berne BJ. Sci Adv 3 e1700014 (2017)
  3. Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome. Rao S, Gurbani D, Du G, Everley RA, Browne CM, Chaikuad A, Tan L, Schröder M, Gondi S, Ficarro SB, Sim T, Kim ND, Berberich MJ, Knapp S, Marto JA, Westover KD, Sorger PK, Gray NS. Cell Chem Biol 26 818-829.e9 (2019)
  4. The impact of Thr91 mutation on c-Src resistance to UM-164: molecular dynamics study revealed a new opportunity for drug design. Ndagi U, Mhlongo NN, Soliman ME. Mol Biosyst 13 1157-1171 (2017)
  5. Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape. Re S, Oshima H, Kasahara K, Kamiya M, Sugita Y. Proc Natl Acad Sci U S A 116 18404-18409 (2019)
  6. Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors. Suebsuwong C, Pinkas DM, Ray SS, Bufton JC, Dai B, Bullock AN, Degterev A, Cuny GD. Bioorg Med Chem Lett 28 577-583 (2018)
  7. How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture. Fang L, Vilas-Boas J, Chakraborty S, Potter ZE, Register AC, Seeliger MA, Maly DJ. ACS Chem Biol 15 2005-2016 (2020)
  8. Emergence of a Promising Lead Compound in the Treatment of Triple Negative Breast Cancer: An Insight into Conformational Features and Ligand Binding Landscape of c-Src Protein with UM-164. Ndagi U, Mhlongo NN, Soliman ME. Appl Biochem Biotechnol 185 655-675 (2018)
  9. Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles. Aleem S, Georghiou G, Kleiner RE, Guja K, Craddock BP, Lyczek A, Chan AI, Garcia-Diaz M, Miller WT, Liu DR, Seeliger MA. Cell Chem Biol 23 1103-1112 (2016)
  10. Targeting the Src Pathway Enhances the Efficacy of Selective FGFR Inhibitors in Urothelial Cancers with FGFR3 Alterations. Lima NC, Atkinson E, Bunney TD, Katan M, Huang PH. Int J Mol Sci 21 E3214 (2020)
  11. Parallel Chemoselective Profiling for Mapping Protein Structure. Potter ZE, Lau HT, Chakraborty S, Fang L, Guttman M, Ong SE, Fowler DM, Maly DJ. Cell Chem Biol 27 1084-1096.e4 (2020)
  12. Selective targeting of the inactive state of hematopoietic cell kinase (Hck) with a stable curcumin derivative. Chakraborty MP, Bhattacharyya S, Roy S, Bhattacharya I, Das R, Mukherjee A. J Biol Chem 296 100449 (2021)
  13. Structure-Based Virtual Screening of High-Affinity ATP-Competitive Inhibitors Against Human Lemur Tyrosine Kinase-3 (LMTK3) Domain: A Novel Therapeutic Target for Breast Cancer. Sarma H, Mattaparthi VSK. Interdiscip Sci 11 527-541 (2019)
  14. Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers. Li F, Fahie MA, Gilliam KM, Pham R, Chen M. Nat Commun 13 3541 (2022)
  15. Synergy and Antagonism between Allosteric and Active-Site Inhibitors of Abl Tyrosine Kinase. Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Angew Chem Int Ed Engl 60 20196-20199 (2021)
  16. Validation of an Allosteric Binding Site of Src Kinase Identified by Unbiased Ligand Binding Simulations. Mingione VR, Foda ZH, Paung Y, Philipose H, Rangwala AM, Shan Y, Seeliger MA. J Mol Biol 434 167628 (2022)
  17. Conquering the challenges of genotypic and phenotypic tumor heterogeneity to realize the promise of personalized cancer therapy: the role of academia. Merajver S, Phadke S, Soellner M. Trans Am Clin Climatol Assoc 128 169-179 (2017)
  18. Insights into the modular design of kinase inhibitors and application to Abl and Axl. Phadke S, Lopez-Barcons L, Vandecan N, Wu Z, Johnson TK, Lachacz EJ, Merajver SD, Soellner MB. RSC Med Chem 13 64-71 (2022)
  19. Allosteric enhancement of the BCR-Abl1 kinase inhibition activity of nilotinib by cobinding of asciminib. Oruganti B, Lindahl E, Yang J, Amiri W, Rahimullah R, Friedman R. J Biol Chem 298 102238 (2022)


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