Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases

Persky, Nicole S.; Hernandez, Desiree; Carmo, Mariana Do; Brenan, Lisa; Cohen, Ofir; Kitajima, Shunsuke; Nayar, Utthara; Walker, Alec J.; Pantel, Sasha; Lee, Y.; Cordova, Jonathon; Sathappa, Murugappan; Zhu, Cong; Hayes, Tikvah K.; Ram, Prahlad T.; Pancholi, Priya; Mikkelsen, Tarej; Barbie, David A.; Yang, Xiaoping; Haq, Rizwan; Piccioni, Federica; Root, David E.; Johannessen, Cory M.

doi:10.1038/s41594-019-0358-z

Cited by 39 publications

(35 citation statements)

References 91 publications

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“…As kinase inhibitors are promiscuous, we identified a TNIK drug-resistant mutant that we could use as a tool to validate the NCB-0846-induced toxicity is specifically due to inhibiting the catalytic activity of TNIK. We tested numerous mutants that would be predicted to be resistant to an ATP competitive inhibitor (10,11, Supplementary Table S1) and identified that mutation of the TNIK pocket protector residue (-1 GXGXXG site, V31 in TNIK) to tryptophan (V31W) retained catalytic activity in the presence of NCB-0846 (as evaluated by phosphorylation of the TNIK substrate Merlin, Supplementary Fig. S2B).…”

Section: Resultsmentioning

confidence: 99%

TNIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin

Torres‐Ayuso

Nyswaner

et al. 2021

Cancer Discovery

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Lung squamous cell carcinoma (LSCC) is the second most prevalent type of lung cancer. Despite extensive genomic characterization, no targeted therapies are approved for the treatment of LSCC. Distal amplification of the 3q chromosome is the most frequent genomic alteration in LSCC, and there is an urgent need to identify efficacious druggable targets within this amplicon. We identify the protein kinase TNIK as a therapeutic target in LSCC. TNIK is amplified in approximately 50% of LSCC cases. TNIK genetic depletion or pharmacologic inhibition reduces the growth of LSCC cells in vitro and in vivo. In addition, TNIK inhibition showed antitumor activity and increased apoptosis in established LSCC patient-derived xenografts. Mechanistically, we identified the tumor suppressor Merlin/NF2 as a novel TNIK substrate and showed that TNIK and Merlin are required for the activation of focal adhesion kinase. In conclusion, our data identify targeting TNIK as a potential therapeutic strategy in LSCC. Significance: Targeted therapies have not yet been approved for the treatment of LSCC, due to lack of identification of actionable cancer drivers. We define TNIK catalytic activity as essential for maintaining LSCC viability and validate the antitumor efficacy of TNIK inhibition in preclinical models of LSCC. This article is highlighted in the In This Issue feature, p. 1307

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Section: Resultsmentioning

confidence: 99%

TNIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin

Torres‐Ayuso

Nyswaner

et al. 2021

Cancer Discovery

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“…The enhanced performance of ASMv1.0. The early version of variant detection software, ORFCallv1.0, was successfully used in analyzing many saturation mutagenesis screens [14][15][16][17] .…”

Section: Resultsmentioning

confidence: 99%

Defining protein variant functions using high-complexity mutagenesis libraries and enhanced mutant detection software ASMv1.0

Yang

Sharpe

et al. 2021

Preprint

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Open reading frame (ORF) variant libraries have advanced our ability to query the functions of a large number of variants of a protein simultaneously in a single experiment. Variant libraries targeting full-length ORFs typically consists of all possible single-amino-acid substitutions and a stop codon at each amino-acid position. Because a variant differs from the template ORF by merely a single codon variation, variant quantification presents the most profound challenge to this technology. Efforts such as dividing a library into sub-libraries for direct sequencing, or tag-directed subassembly are practical only for small ORFs. Our approach, however, features generating and screening libraries for genes sized up to 3600 bases, shotgun sequencing and an enhanced variant-detecting tool. Having processed screens of ~20 ORF variant libraries, our tool calls variants reliably, and also presents variant annotations in datafiles enabling analyses that have reshaped our strategies governing library design, screen deconvolution, sequencing and its analysis.

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“…Thus, analog-sensitive kinase technology might be applicable for nearly all protein kinases for which “gatekeeper” residue is defined [ 69 ]. The biological significance of “gatekeeper” residues for protein kinase activities is also supported by studies showing that these residues are often mutated in protein kinases resistant to clinically relevant protein kinase inhibitors [ 46 , 70 , 71 , 72 , 73 ]. In such protein kinases, the point mutations of the “gatekeeper” residues lead to perturbations in the hydrophobic pocket located at the back of the ATP binding site.…”

Section: Analog-sensitive Kinase Technologymentioning

confidence: 99%

Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome

Jurcik

Siváková

Cipakova

et al. 2020

IJMS

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Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.

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Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases

Cited by 39 publications

References 91 publications

TNIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin

TNIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin

Defining protein variant functions using high-complexity mutagenesis libraries and enhanced mutant detection software ASMv1.0

Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome

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