Development of covalent inhibitors that can overcome resistance to first-generation FGFR kinase inhibitors
Edited by Katerina Politi, Yale University, New Haven, CT, and accepted by the Editorial Board October 7, 2014 (received for review February 25, 2014)
Significance
Inhibitors of the FGF receptors (FGFRs) are currently under clinical investigation for the treatment of various cancers. All currently approved kinase inhibitors eventually are rendered useless by the emergence of drug-resistant tumors. We used structure-based drug design to develop the first, to our knowledge, selective, next-generation covalent FGFR inhibitors that can overcome the most common form of kinase inhibitor resistance, the mutation of the so-called “gatekeeper” residue located in the ATP-binding pocket. We also describe a novel kinase inhibitor design strategy that uses a single electrophile to target covalently cysteines that are located in different positions within the ATP-binding pocket. These results have important implications for the design of covalent FGFR inhibitors that can overcome clinical resistance.
Abstract
The human FGF receptors (FGFRs) play critical roles in various human cancers, and several FGFR inhibitors are currently under clinical investigation. Resistance usually results from selection for mutant kinases that are impervious to the action of the drug or from up-regulation of compensatory signaling pathways. Preclinical studies have demonstrated that resistance to FGFR inhibitors can be acquired through mutations in the FGFR gatekeeper residue, as clinically observed for FGFR4 in embryonal rhabdomyosarcoma and neuroendocrine breast carcinomas. Here we report on the use of a structure-based drug design to develop two selective, next-generation covalent FGFR inhibitors, the FGFR irreversible inhibitors 2 (FIIN-2) and 3 (FIIN-3). To our knowledge, FIIN-2 and FIIN-3 are the first inhibitors that can potently inhibit the proliferation of cells dependent upon the gatekeeper mutants of FGFR1 or FGFR2, which confer resistance to first-generation clinical FGFR inhibitors such as NVP-BGJ398 and AZD4547. Because of the conformational flexibility of the reactive acrylamide substituent, FIIN-3 has the unprecedented ability to inhibit both the EGF receptor (EGFR) and FGFR covalently by targeting two distinct cysteine residues. We report the cocrystal structure of FGFR4 with FIIN-2, which unexpectedly exhibits a “DFG-out” covalent binding mode. The structural basis for dual FGFR and EGFR targeting by FIIN3 also is illustrated by crystal structures of FIIN-3 bound with FGFR4 V550L and EGFR L858R. These results have important implications for the design of covalent FGFR inhibitors that can overcome clinical resistance and provide the first example, to our knowledge, of a kinase inhibitor that covalently targets cysteines located in different positions within the ATP-binding pocket.
Data Availability
Data deposition: Crystallography, atomic coordinates, and structure factors reported in this paper have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 4QQC, 4R6V, and 4R5S).
Acknowledgments
We thank Liping Wang for technical assistance and Dr. Sara Buhrlage for proofreading. This work was supported by Lung Specialized Programs of Research Excellence Grant 5 P50 CA090578-10 (to P.A.J. and N.S.G.) and National Institute of Dental and Craniofacial Research Grant R01 DE13686 (to M.M.).
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Cover image: Pictured is a rotifer (Brachionus calyciflorus) eating algal prey (Chlorella vulgaris), imaged with Nomarski interference contrast microscopy. Minoru Kasada et al. examined predator–prey dynamics in systems containing algae with different growth rates and predator defense abilities. The systems reached equilibrium between predator and prey, but different patterns of dominance emerged between the algal strains depending on differences in the reproductive costs of predator defense. The authors suggest that genetic variation within populations may influence the outcome of ecological and evolutionary interactions. See the article by Kasada et al. on pages 16035–16040. Image courtesy of Minoru Kasada.
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Data Availability
Data deposition: Crystallography, atomic coordinates, and structure factors reported in this paper have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 4QQC, 4R6V, and 4R5S).
Submission history
Published online: October 27, 2014
Published in issue: November 11, 2014
Keywords
Acknowledgments
We thank Liping Wang for technical assistance and Dr. Sara Buhrlage for proofreading. This work was supported by Lung Specialized Programs of Research Excellence Grant 5 P50 CA090578-10 (to P.A.J. and N.S.G.) and National Institute of Dental and Craniofacial Research Grant R01 DE13686 (to M.M.).
Notes
This article is a PNAS Direct Submission. K.P. is a guest editor invited by the Editorial Board.
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The authors declare no conflict of interest.
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