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Kim SH, Bulos ML, Adams JA, Yun BK, Bishop AC. Single Ion Pair Is Essential for Stabilizing SHP2's Open Conformation. Biochemistry 2024; 63:273-281. [PMID: 38251939 DOI: 10.1021/acs.biochem.3c00609] [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: 01/23/2024]
Abstract
Src-homology-2-domain-containing PTP-2 (SHP2) is a widely expressed signaling enzyme whose misregulation is associated with multiple human pathologies. SHP2's enzymatic activity is controlled by a conformational equilibrium between its autoinhibited ("closed") state and its activated ("open") state. Although SHP2's closed state has been extensively characterized, the putative structure of its open form has only been revealed in the context of a highly activated mutant (E76K), and no systematic studies of the biochemical determinants of SHP2's open-state stabilization have been reported. To identify amino-acid interactions that are critical for stabilizing SHP2's active state, we carried out a mutagenic study of residues that lie at potentially important interdomain interfaces of the open conformation. The open/closed equilibria of the mutants were evaluated, and we identified several interactions that contribute to the stabilization of SHP2's open state. In particular, our findings establish that an ion pair between glutamate 249 on SHP2's PTP domain and arginine 111 on an interdomain loop is the key determinant of SHP2's open-state stabilization. Mutations that disrupt the R111/E249 ion pair substantially shift SHP2's open/closed equilibrium to the closed state, even compared to wild-type SHP2's basal-state equilibrium, which strongly favors the closed state. To the best of our knowledge, the ion-pair variants uncovered in this study are the first known SHP2 mutants in which autoinhibition is augmented with respect to the wild-type protein. Such "hyperinhibited" mutants may provide useful tools for signaling studies that investigate the connections between SHP2 inhibition and the suppression of human disease progression.
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Affiliation(s)
- Sean H Kim
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Maya L Bulos
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Jennifer A Adams
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - B Koun Yun
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
| | - Anthony C Bishop
- Department of Chemistry and Program in Biochemistry & Biophysics, Amherst College, Amherst, Massachusetts 01002, United States
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Xu L, Mu X, Liu M, Wang Z, Shen C, Mu Q, Feng B, Xu Y, Hou T, Gao L, Jiang H, Li J, Zhou Y, Wang W. Novel thieno[2,3-b]quinoline-procaine hybrid molecules: A new class of allosteric SHP-1 activators evolved from PTP1B inhibitors. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Clausse V, Fang Y, Tao D, Tagad HD, Sun H, Wang Y, Karavadhi S, Lane K, Shi ZD, Vasalatiy O, LeClair CA, Eells R, Shen M, Patnaik S, Appella E, Coussens NP, Hall MD, Appella DH. Discovery of Novel Small-Molecule Scaffolds for the Inhibition and Activation of WIP1 Phosphatase from a RapidFire Mass Spectrometry High-Throughput Screen. ACS Pharmacol Transl Sci 2022; 5:993-1006. [PMID: 36268125 PMCID: PMC9578142 DOI: 10.1021/acsptsci.2c00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/28/2022]
Abstract
Wild-type P53-induced phosphatase 1 (WIP1), also known as PPM1D or PP2Cδ, is a serine/threonine protein phosphatase induced by P53 after genotoxic stress. WIP1 inhibition has been proposed as a therapeutic strategy for P53 wild-type cancers in which it is overexpressed, but this approach would be ineffective in P53-negative cancers. Furthermore, there are several cancers with mutated P53 where WIP1 acts as a tumor suppressor. Therefore, activating WIP1 phosphatase might also be a therapeutic strategy, depending on the P53 status. To date, no specific, potent WIP1 inhibitors with appropriate pharmacokinetic properties have been reported, nor have WIP1-specific activators. Here, we report the discovery of new WIP1 modulators from a high-throughput screen (HTS) using previously described orthogonal biochemical assays suitable for identifying both inhibitors and activators. The primary HTS was performed against a library of 102 277 compounds at a single concentration using a RapidFire mass spectrometry assay. Hits were further evaluated over a range of 11 concentrations with both the RapidFire MS assay and an orthogonal fluorescence-based assay. Further biophysical, biochemical, and cell-based studies of confirmed hits revealed a WIP1 activator and two inhibitors, one competitive and one uncompetitive. These new scaffolds are prime candidates for optimization which might enable inhibitors with improved pharmacokinetics and a first-in-class WIP1 activator.
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Affiliation(s)
- Victor Clausse
- Synthetic
Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuhong Fang
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Dingyin Tao
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Harichandra D. Tagad
- Laboratory
of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hongmao Sun
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Yuhong Wang
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Surendra Karavadhi
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Kelly Lane
- Chemistry
and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Zhen-Dan Shi
- Chemistry
and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Olga Vasalatiy
- Chemistry
and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Christopher A. LeClair
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Rebecca Eells
- Reaction
Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355, United States
| | - Min Shen
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Samarjit Patnaik
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ettore Appella
- Laboratory
of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nathan P. Coussens
- Molecular
Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Matthew D. Hall
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Daniel H. Appella
- Synthetic
Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, United States
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Buck SJ, Plaman BA, Bishop AC. Inhibition of SHP2 and SHP1 Protein Tyrosine Phosphatase Activity by Chemically Induced Dimerization. ACS OMEGA 2022; 7:14180-14188. [PMID: 35559188 PMCID: PMC9089384 DOI: 10.1021/acsomega.2c00780] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
Protein tyrosine phosphatases (PTPs), the enzymes that catalyze the dephosphorylation of phosphotyrosine residues, are important regulators of mammalian cell signaling, whose activity is misregulated in numerous human diseases. PTPs are also notoriously difficult to selectively modulate with small molecules, and relatively few small-molecule tools for controlling their activities in the context of complex signaling pathways have been developed. Here, we show that a chemical inducer of dimerization (CID) can be used to selectively and potently inhibit constructs of Src-homology-2-containing PTP 2 (SHP2) that have been engineered to contain dimerization domains. Our strategy was inspired by the naturally occurring mechanism of SHP2 regulation, in which the PTP activity of SHP2's catalytic domain is autoinhibited through an intramolecular interaction with the protein's N-terminal SH2 (N-SH2) domain. We have re-engineered this inhibitory interaction to function intermolecularly by independently fusing the SHP2 catalytic and N-SH2 domains to protein domains that heterodimerize upon the introduction of the CID rapamycin. We show that rapamycin-induced protein dimerization leads to potent inhibition of SHP2's catalytic activity, which is driven by increased proximity of the SHP2 catalytic and N-SH2 domains. We also demonstrate that CID-based inhibition of PTP activity can be applied to an oncogenic gain-of-function SHP2 mutant (E76K SHP2) and to the catalytic domain of the SHP2's closest homologue, SHP1. In sum, CID-driven inhibition of PTP activity provides a broadly applicable tool for inhibiting dimerizable forms of the SHP PTPs and represents a novel paradigm for selective PTP inhibition through inducible protein-protein interactions.
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Pomorski A, Krężel A. Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook. Metallomics 2021; 12:1179-1207. [PMID: 32658234 DOI: 10.1039/d0mt00093k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.
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Affiliation(s)
- Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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Kim JY, Plaman BA, Bishop AC. Targeting a Pathogenic Cysteine Mutation: Discovery of a Specific Inhibitor of Y279C SHP2. Biochemistry 2020; 59:3498-3507. [PMID: 32871078 PMCID: PMC7891893 DOI: 10.1021/acs.biochem.0c00471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
An
intriguing challenge of drug discovery is targeting pathogenic
mutant proteins that differ from their wild-type counterparts by only
a single amino acid. In particular, pathogenic cysteine mutations
afford promising opportunities for mutant-specific drug discovery,
due to the unique reactivity of cysteine’s sulfhydryl-containing
side chain. Here we describe the first directed discovery effort targeting
a pathogenic cysteine mutant of a protein tyrosine phosphatase (PTP),
namely Y279C Src-homology-2-containing PTP 2 (SHP2), which has been
causatively linked to the developmental disorder Noonan syndrome with
multiple lentigines (NSML). Through a screen of commercially available
compounds that contain cysteine-reactive functional groups, we have
discovered a small-molecule inhibitor of Y279C SHP2 (compound 99; IC50 ≈ 6 μM) that has no appreciable
effect on the phosphatase activity of wild-type SHP2 or that of other
homologous PTPs (IC50 ≫ 100 μM). Compound 99 exerts its specific inhibitory effect through irreversible
engagement of Y279C SHP2’s pathogenic cysteine residue in a
manner that is time-dependent, is substrate-independent, and persists
in the context of a complex proteome. To the best of our knowledge, 99 is the first specific ligand of a disease-causing PTP mutant
to be identified. This study therefore provides both a starting point
for the development of NSML-directed therapeutic agents and a precedent
for the identification of mutant-specific inhibitors of other pathogenic
PTP mutants.
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Affiliation(s)
- Jenny Y Kim
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
| | - Bailey A Plaman
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
| | - Anthony C Bishop
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
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