1
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Chakraborty S, Ahler E, Simon JJ, Fang L, Potter ZE, Sitko KA, Stephany JJ, Guttman M, Fowler DM, Maly DJ. Profiling of drug resistance in Src kinase at scale uncovers a regulatory network coupling autoinhibition and catalytic domain dynamics. Cell Chem Biol 2024; 31:207-220.e11. [PMID: 37683649 PMCID: PMC10902203 DOI: 10.1016/j.chembiol.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/03/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023]
Abstract
Kinase inhibitors are effective cancer therapies, but resistance often limits clinical efficacy. Despite the cataloging of numerous resistance mutations, our understanding of kinase inhibitor resistance is still incomplete. Here, we comprehensively profiled the resistance of ∼3,500 Src tyrosine kinase mutants to four different ATP-competitive inhibitors. We found that ATP-competitive inhibitor resistance mutations are distributed throughout Src's catalytic domain. In addition to inhibitor contact residues, residues that participate in regulating Src's phosphotransferase activity were prone to the development of resistance. Unexpectedly, we found that a resistance-prone cluster of residues located on the top face of the N-terminal lobe of Src's catalytic domain contributes to autoinhibition by reducing catalytic domain dynamics, and mutations in this cluster led to resistance by lowering inhibitor affinity and promoting kinase hyperactivation. Together, our studies demonstrate how drug resistance profiling can be used to define potential resistance pathways and uncover new mechanisms of kinase regulation.
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Affiliation(s)
- Sujata Chakraborty
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ethan Ahler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Jessica J Simon
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Linglan Fang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Zachary E Potter
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Katherine A Sitko
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jason J Stephany
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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2
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Mao W, Vandecan NM, Bingham CR, Tsang PK, Ulintz P, Sexton R, Bochar DA, Merajver SD, Soellner MB. Selective and Potent PROTAC Degraders of c-Src Kinase. ACS Chem Biol 2024; 19:110-116. [PMID: 38113191 DOI: 10.1021/acschembio.3c00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Using dasatinib linked to E3 ligase ligands, we identified a potent and selective dual Csk/c-Src PROTAC degrader. We then replaced dasatinib, the c-Src-directed ligand, with a conformation-selective analogue that stabilizes the αC-helix-out conformation of c-Src. Using the αC-helix-out ligand, we identified a PROTAC that is potent and selective for c-Src. We demonstrated a high degree of catalysis with our c-Src PROTACs. Using our c-Src PROTACs, we identified pharmacological advantages of c-Src degradation compared to inhibition with respect to cancer cell proliferation.
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Affiliation(s)
- Wuxiang Mao
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Nathalie M Vandecan
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Christopher R Bingham
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Pui Ki Tsang
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Peter Ulintz
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
| | - Rachel Sexton
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Daniel A Bochar
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sofia D Merajver
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
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3
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Nguyen V, Ahler E, Sitko KA, Stephany JJ, Maly DJ, Fowler DM. Molecular determinants of Hsp90 dependence of Src kinase revealed by deep mutational scanning. Protein Sci 2023; 32:e4656. [PMID: 37167432 PMCID: PMC10273359 DOI: 10.1002/pro.4656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
Hsp90 is a molecular chaperone involved in the refolding and activation of numerous protein substrates referred to as clients. While the molecular determinants of Hsp90 client specificity are poorly understood and limited to a handful of client proteins, strong clients are thought to be destabilized and conformationally extended. Here, we measured the phosphotransferase activity of 3929 variants of the tyrosine kinase Src in both the presence and absence of an Hsp90 inhibitor. We identified 84 previously unknown functionally dependent client variants. Unexpectedly, many destabilized or extended variants were not functionally dependent on Hsp90. Instead, functionally dependent client variants were clustered in the αF pocket and β1-β2 strand regions of Src, which have yet to be described in driving Hsp90 dependence. Hsp90 dependence was also strongly correlated with kinase activity. We found that a combination of activation, global extension, and general conformational flexibility, primarily induced by variants at the αF pocket and β1-β2 strands, was necessary to render Src functionally dependent on Hsp90. Moreover, the degree of activation and flexibility required to transform Src into a functionally dependent client varied with variant location, suggesting that a combination of regulatory domain disengagement and catalytic domain flexibility are required for chaperone dependence. Thus, by studying the chaperone dependence of a massive number of variants, we highlight factors driving Hsp90 client specificity and propose a model of chaperone-kinase interactions.
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Affiliation(s)
- Vanessa Nguyen
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Ethan Ahler
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Katherine A. Sitko
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Jason J. Stephany
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Dustin J. Maly
- Department of ChemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Douglas M. Fowler
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
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4
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Dunker W, Zaver SA, Pineda JMB, Howard CJ, Bradley RK, Woodward JJ. The proto-oncogene SRC phosphorylates cGAS to inhibit an antitumor immune response. JCI Insight 2023; 8:e167270. [PMID: 37166992 PMCID: PMC10371251 DOI: 10.1172/jci.insight.167270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/09/2023] [Indexed: 05/12/2023] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) is a DNA sensor and responsible for inducing an antitumor immune response. Recent studies reveal that cGAS is frequently inhibited in cancer, and therapeutic targets to promote antitumor cGAS function remain elusive. SRC is a proto-oncogene tyrosine kinase and is expressed at elevated levels in numerous cancers. Here, we demonstrate that SRC expression in primary and metastatic bladder cancer negatively correlates with innate immune gene expression and immune cell infiltration. We determine that SRC restricts cGAS signaling in human cell lines through SRC small molecule inhibitors, depletion, and overexpression. cGAS and SRC interact in cells and in vitro, while SRC directly inhibits cGAS enzymatic activity and DNA binding in a kinase-dependent manner. SRC phosphorylates cGAS, and inhibition of cGAS Y248 phosphorylation partially reduces SRC inhibition. Collectively, our study demonstrates that cGAS antitumor signaling is hindered by the proto-oncogene SRC and describes how cancer-associated proteins can regulate the innate immune system.
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Affiliation(s)
| | - Shivam A. Zaver
- Department of Microbiology and
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
| | - Jose Mario Bello Pineda
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Robert K. Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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5
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Gul M, Navid A, Fakhar M, Rashid S. SHP-1 tyrosine phosphatase binding to c-Src kinase phosphor-dependent conformations: A comparative structural framework. PLoS One 2023; 18:e0278448. [PMID: 36638102 PMCID: PMC9838854 DOI: 10.1371/journal.pone.0278448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/16/2022] [Indexed: 01/14/2023] Open
Abstract
SHP-1 is a cytosolic tyrosine phosphatase that is primarily expressed in hematopoietic cells. It acts as a negative regulator of numerous signaling pathways and controls multiple cellular functions involved in cancer pathogenesis. This study describes the binding preferences of SHP-1 (pY536) to c-Srcopen (pY416) and c-Srcclose (pY527) through in silico approaches. Molecular dynamics simulation analysis revealed more conformational changes in c-Srcclose upon binding to SHP-1, as compared to its active/open conformation that is stabilized by the cooperative binding of the C-SH2 domain and C-terminal tail of SHP-1 to c-Src SH2 and KD. In contrast, c-Srcclose and SHP-1 interaction is mediated by PTP domain-specific WPD-loop (WPDXGXP) and Q-loop (QTXXQYXF) binding to c-Srcclose C-terminal tail residues. The dynamic correlation analysis demonstrated a positive correlation for SHP-1 PTP with KD, SH3, and the C-terminal tail of c-Srcclose. In the case of the c-Srcopen-SHP-1 complex, SH3 and SH2 domains of c-Srcopen were correlated to C-SH2 and the C-terminal tail of SHP-1. Our findings reveal that SHP1-dependent c-Src activation through dephosphorylation relies on the conformational shift in the inhibitory C-terminal tail that may ease the recruitment of the N-SH2 domain to phosphotyrosine residue, resulting in the relieving of the PTP domain. Collectively, this study delineates the intermolecular interaction paradigm and underlying conformational readjustments in SHP-1 due to binding with the c-Src active and inactive state. This study will largely help in devising novel therapeutic strategies for targeting cancer development.
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Affiliation(s)
- Mehreen Gul
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ahmad Navid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Fakhar
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
- * E-mail:
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6
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Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Reply to Correspondence on "Synergy and Antagonism between Allosteric and Active-Site Inhibitors of Abl Tyrosine Kinase". Angew Chem Int Ed Engl 2022; 61:e202209518. [PMID: 36283971 DOI: 10.1002/anie.202209518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Indexed: 10/22/2023]
Abstract
Manley and co-workers provide data demonstrating that, at super-pharmacological concentrations (300 μM), a ternary complex between Abl, asciminib, and ATP-competitive inhibitors is possible. The work in our manuscript concerns the interplay of asciminib (and GNF-2) with ATP-competitive inhibitors at pharmacologically relevant concentrations (Cmax =1.6-3.7 μM for asciminib). Manley and co-workers do not question any of the studies that we reported, nor do they provide explanations for how our work fits into their preferred model. Herein, we consider the data presented by Manley and co-workers. In addition, we provide new data supporting the findings in our Communication. Asciminib and ATP-competitive inhibitors do not simultaneously bind Abl at pharmacologically relevant concentrations unless the conformation selectivity for both ligands is matched.
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Affiliation(s)
- Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Daniel A Bochar
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Nathalie M Vandecan
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Jessica Furtado
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
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7
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Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Reply to Correspondence on “Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase”. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Taylor K. Johnson
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Daniel A. Bochar
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Nathalie M. Vandecan
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Jessica Furtado
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Michael P. Agius
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Sameer Phadke
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Matthew B. Soellner
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
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8
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Agius MP, Ko K, Johnson TK, Phadke S, Soellner MB. Conformation-tunable ATP-competitive kinase inhibitors. Chem Commun (Camb) 2022; 58:3541-3544. [PMID: 35195624 DOI: 10.1039/d1cc06893h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule kinase inhibitors have shown immense clinical utility for diverse indications. While >60 kinase inhibitors have been approved (and many more in clinical trials), it remains unclear whether the clinical efficacy of a kinase inhibitor is solely dependent on enzymatic inhibition, or whether non-catalytic functions play a role in the efficacy of some kinase inhibitors. Here, we designed and synthesized a series of pyrazolopyrimidine kinase inhibitors that modulate the global kinase conformation of c-Src kinase. Expanding upon our findings from the pyrazolopyrimidine inhibitor series, we designed, synthesized, and evaluated three pair of conformation-selective kinase inhibitors, each with a unique hinge-binding scaffold. We profiled each pair of kinase inhibitors across 468 kinases and identified 38 kinases that could be studied using these pair of conformation-selective inhibitors. We also explore the binding of conformation-selective kinase inhibitors to mutant kinases of EGFR, FLT3, and KIT. Together, these studies yield important insight into the design of conformation-tunable kinase inhibitors and provide a toolset of compounds to study the role of protein conformation on kinase signaling.
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Affiliation(s)
- Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Kristin Ko
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
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9
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Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Synergy and Antagonism between Allosteric and Active-Site Inhibitors of Abl Tyrosine Kinase. Angew Chem Int Ed Engl 2021; 60:20196-20199. [PMID: 34292655 PMCID: PMC8405588 DOI: 10.1002/anie.202105351] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/05/2021] [Indexed: 11/06/2022]
Abstract
Allosteric inhibitors of Abl kinase are being explored in the clinic, often in combination with ATP-site inhibitors of Abl kinase. However, there are conflicting data on whether both ATP-competitive inhibitors and myristoyl-site allosteric inhibitors can simultaneously bind Abl kinase. Here, we determine whether there is synergy or antagonism between ATP-competitive inhibitors and allosteric inhibitors of Abl. We observe that clinical ATP-competitive inhibitors are not synergistic with allosteric ABL inhibitors, however, conformation-selective ATP-site inhibitors that modulate the global conformation of Abl can afford synergy. We demonstrate that kinase conformation is the key driver to simultaneously bind two compounds to Abl kinase. Finally, we explore the interaction of allosteric and conformation selective ATP-competitive inhibitors in a series of biochemical and cellular assays.
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Affiliation(s)
- Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Daniel A Bochar
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Nathalie M Vandecan
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Jessica Furtado
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
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10
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Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Taylor K. Johnson
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Daniel A. Bochar
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Nathalie M. Vandecan
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Jessica Furtado
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Michael P. Agius
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Sameer Phadke
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Matthew B. Soellner
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
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11
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Zhao D, Yin Z, Soellner MB, Martin BR. Scribble sub-cellular localization modulates recruitment of YES1 to regulate YAP1 phosphorylation. Cell Chem Biol 2021; 28:1235-1241.e5. [PMID: 33730553 DOI: 10.1016/j.chembiol.2021.02.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/04/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022]
Abstract
The multi-domain scaffolding protein Scribble (Scrib) regulates cell polarity and growth signaling at cell-cell junctions. In epithelial cancers, Scrib mislocalization and overexpression paradoxically transform Scrib from a basolateral tumor suppressor to a cytosolic driver of tumorigenicity. To address the function of Scrib (mis)localization, a Scrib-HaloTag fusion was genome engineered in polarized epithelial cells. Expression of the epithelial to mesenchymal transcription factor Snail displaced Scrib-HaloTag from cell junctions, mirroring the mislocalization observed in cancers. Interestingly, Snail expression promotes Yes-associated protein-1 (YAP1) nuclear localization independent of hippo pathway-regulated YAP-S127 phosphorylation. Furthermore, Scrib HaloPROTAC degradation attenuates YAP1-Y357 phosphorylation. Halo-ligand affinity purification mass spectrometry analysis identified the Src family kinase YES1 as a mislocalized Scrib interaction partner, preferentially recruiting the kinase active and open global conformation (αC helix in). Altogether, mislocalized Scrib enhances YAP1 phosphorylation by scaffolding active YES1.
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Affiliation(s)
- Dongyu Zhao
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhangyuan Yin
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew B Soellner
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brent R Martin
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Scorpion Therapeutics, Inc., 888 Boylston Street, Suite 1111, Boston, MA 02199, USA.
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12
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Potter ZE, Lau HT, Chakraborty S, Fang L, Guttman M, Ong SE, Fowler DM, Maly DJ. Parallel Chemoselective Profiling for Mapping Protein Structure. Cell Chem Biol 2020; 27:1084-1096.e4. [PMID: 32649906 PMCID: PMC7484201 DOI: 10.1016/j.chembiol.2020.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/27/2020] [Accepted: 06/19/2020] [Indexed: 01/01/2023]
Abstract
Solution-based structural techniques complement high-resolution structural data by providing insight into the oft-missed links between protein structure and dynamics. Here, we present Parallel Chemoselective Profiling, a solution-based structural method for characterizing protein structure and dynamics. Our method utilizes deep mutational scanning saturation mutagenesis data to install amino acid residues with specific chemistries at defined positions on the solvent-exposed surface of a protein. Differences in the extent of labeling of installed mutant residues are quantified using targeted mass spectrometry, reporting on each residue's local environment and structural dynamics. Using our method, we studied how conformation-selective, ATP-competitive inhibitors affect the local and global structure and dynamics of full-length Src kinase. Our results highlight how parallel chemoselective profiling can be used to study a dynamic multi-domain protein, and suggest that our method will be a useful addition to the relatively small toolkit of existing protein footprinting techniques.
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Affiliation(s)
- Zachary E Potter
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Sujata Chakraborty
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Linglan Fang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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13
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Fang L, Vilas-Boas J, Chakraborty S, Potter ZE, Register AC, Seeliger MA, Maly DJ. How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture. ACS Chem Biol 2020; 15:2005-2016. [PMID: 32479050 DOI: 10.1021/acschembio.0c00429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecule kinase inhibitors that stabilize distinct ATP binding site conformations can differentially modulate the global conformation of Src-family kinases (SFKs). However, it is unclear which specific ATP binding site contacts are responsible for modulating the global conformation of SFKs and whether these inhibitor-mediated allosteric effects generalize to other tyrosine kinases. Here, we describe the development of chemical probes that allow us to deconvolute which features in the ATP binding site are responsible for the allosteric modulation of the global conformation of Src. We find that the ability of an inhibitor to modulate the global conformation of Src's regulatory domain-catalytic domain module relies mainly on the influence it has on the conformation of a structural element called helix αC. Furthermore, by developing a set of orthogonal probes that target a drug-sensitized Src variant, we show that stabilizing Src's helix αC in an active conformation is sufficient to promote a Src-mediated, phosphotransferase-independent alteration in cell morphology. Finally, we report that ATP-competitive, conformation-selective inhibitors can influence the global conformation of tyrosine kinases beyond the SFKs, suggesting that the allosteric networks we observe in Src are conserved in kinases that have a similar regulatory architecture. Our study highlights that an ATP-competitive inhibitor's interactions with helix αC can have a major influence on the global conformation of some tyrosine kinases.
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Affiliation(s)
| | - Jessica Vilas-Boas
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | | | | | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
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