5D10

Kinase domain of cSrc in complex with RL236

Summary for 5D10

• Entry DOI: 10.2210/pdb5d10/pdb
• Descriptor: Proto-oncogene tyrosine-protein kinase Src, N-[4-({4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}oxy)phenyl]prop-2-enamide (3 entities in total)
• Functional Keywords: kinase inhibitor, drug resistance, transferase
• Biological source: Gallus gallus (Chicken)
• Cellular location: Cell membrane : P00523
• Total number of polymer chains: 2
• Total formula weight: 66414.59

Authors

Becker, C.,Mayer-Wrangowski, S.C.,Julian, E.,Rauh, D. (deposition date: 2015-08-03, release date: 2015-09-02, Last modification date: 2024-01-10)

Primary citation

Engel, J.,Richters, A.,Getlik, M.,Tomassi, S.,Keul, M.,Termathe, M.,Lategahn, J.,Becker, C.,Mayer-Wrangowski, S.,Grutter, C.,Uhlenbrock, N.,Krull, J.,Schaumann, N.,Eppmann, S.,Kibies, P.,Hoffgaard, F.,Heil, J.,Menninger, S.,Ortiz-Cuaran, S.,Heuckmann, J.M.,Tinnefeld, V.,Zahedi, R.P.,Sos, M.L.,Schultz-Fademrecht, C.,Thomas, R.K.,Kast, S.M.,Rauh, D.
Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach.
J.Med.Chem., 58:6844-6863, 2015

PubMed Abstract: Receptor tyrosine kinases represent one of the prime targets in cancer therapy, as the dysregulation of these elementary transducers of extracellular signals, like the epidermal growth factor receptor (EGFR), contributes to the onset of cancer, such as non-small cell lung cancer (NSCLC). Strong efforts were directed to the development of irreversible inhibitors and led to compound CO-1686, which takes advantage of increased residence time at EGFR by alkylating Cys797 and thereby preventing toxic effects. Here, we present a structure-based approach, rationalized by subsequent computational analysis of conformational ligand ensembles in solution, to design novel and irreversible EGFR inhibitors based on a screening hit that was identified in a phenotype screen of 80 NSCLC cell lines against approximately 1500 compounds. Using protein X-ray crystallography, we deciphered the binding mode in engineered cSrc (T338M/S345C), a validated model system for EGFR-T790M, which constituted the basis for further rational design approaches. Chemical synthesis led to further compound collections that revealed increased biochemical potency and, in part, selectivity toward mutated (L858R and L858R/T790M) vs nonmutated EGFR. Further cell-based and kinetic studies were performed to substantiate our initial findings. Utilizing proteolytic digestion and nano-LC-MS/MS analysis, we confirmed the alkylation of Cys797.

PubMed: 26275028
DOI: 10.1021/acs.jmedchem.5b01082

Experimental method

X-RAY DIFFRACTION (2.7 Å)