1
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Kwak C, Park C, Ko M, Im CY, Moon H, Park YH, Kim SY, Lee S, Kang MG, Kwon HJ, Hong E, Seo JK, Rhee HW. Identification of proteomic landscape of drug-binding proteins in live cells by proximity-dependent target ID. Cell Chem Biol 2022; 29:1739-1753.e6. [PMID: 36272407 DOI: 10.1016/j.chembiol.2022.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/29/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
Direct identification of the proteins targeted by small molecules can provide clues for disease diagnosis, prevention, and drug development. Despite concentrated attempts, there are still technical limitations associated with the elucidation of direct interactors. Herein, we report a target-ID system called proximity-based compound-binding protein identification (PROCID), which combines our direct analysis workflow of proximity-labeled proteins (Spot-ID) with the HaloTag system to efficiently identify the dynamic proteomic landscape of drug-binding proteins. We successfully identified well-known dasatinib-binding proteins (ABL1, ABL2) and confirmed the unapproved dasatinib-binding kinases (e.g., BTK and CSK) in a live chronic myeloid leukemia cell line. PROCID also identified the DNA helicase protein SMARCA2 as a dasatinib-binding protein, and the ATPase domain was confirmed to be the binding site of dasatinib using a proximity ligation assay (PLA) and in cellulo biotinylation assay. PROCID thus provides a robust method to identify unknown drug-interacting proteins in live cells that expedites the mode of action of the drug.
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Affiliation(s)
- Chulhwan Kwak
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Cheolhun Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Minjeong Ko
- Chemical Genomics Leader Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Chun Young Im
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Heegyum Moon
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Young-Hoon Park
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - So Young Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Seungyeon Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ho Jeong Kwon
- Chemical Genomics Leader Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea.
| | - Jeong Kon Seo
- Graduate School of Semiconductor Materials and Devices Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea; UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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2
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Rezende Miranda R, Zhang C. Reactivity-based chemical-genetic study of protein kinases. RSC Med Chem 2022; 13:783-797. [PMID: 35923719 PMCID: PMC9298188 DOI: 10.1039/d1md00389e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The human protein kinase superfamily comprises over 500 members that operate in nearly every signal transduction pathway and regulate essential cellular processes. Deciphering the functional roles of protein kinases with small-molecule inhibitors is essential to enhance our understanding of cell signaling and to facilitate the development of new therapies. However, it is rather challenging to identify selective kinase inhibitors because of the conserved nature of the ATP binding site. A number of chemical-genetic approaches have been developed during the past two decades to enable selective chemical perturbation of the activity of individual kinases. Herein, we review the development and application of chemical-genetic strategies that feature the use of covalent inhibitors targeting cysteine residues to dissect the cellular functions of protein kinases.
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Affiliation(s)
- Renata Rezende Miranda
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester New York 14623 USA
| | - Chao Zhang
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- USC Norris Comprehensive Cancer Center, University of Southern California Los Angeles California 90089 USA
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3
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Rodd ZA, Engleman EA, Truitt WA, Burke AR, Molosh AI, Bell RL, Hauser SR. CNO administration increases dopamine and glutamate in the medial prefrontal cortex of wistar rats: Further concerns for the validity of the CNO-activated DREADD procedure. Neuroscience 2022; 491:176-184. [DOI: 10.1016/j.neuroscience.2022.03.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/03/2022] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
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4
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Lorenz R, Wu J, Herberg FW, Taylor SS, Engh RA. Drugging the Undruggable: How Isoquinolines and PKA Initiated the Era of Designed Protein Kinase Inhibitor Therapeutics. Biochemistry 2021; 60:3470-3484. [PMID: 34370450 DOI: 10.1021/acs.biochem.1c00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In 1984, Japanese researchers led by the biochemist Hiroyoshi Hidaka described the first synthetic protein kinase inhibitors based on an isoquinoline sulfonamide structure (Hidaka et al. Biochemistry, 1984 Oct 9; 23(21): 5036-41. doi: 10.1021/bi00316a032). These led to the first protein kinase inhibitor approved for medical use (fasudil), an inhibitor of the AGC subfamily Rho kinase. With potencies strong enough to compete against endogenous ATP, the isoquinoline compounds established the druggability of the ATP binding site. Crystal structures of their protein kinase complexes, including with cAMP-dependent protein kinase (PKA), showed interactions that, on the one hand, could mimic ATP but, on the other hand, could be optimized for high potency binding, kinase selectivity, and diversification away from adenosine. They also showed the flexibility of the glycine-rich loop, and PKA became a major prototype for crystallographic and nuclear magnetic resonance (NMR) studies of protein kinase mechanism and dynamic activity control. Since fasudil, more than 70 kinase inhibitors have been approved for clinical use, involving efforts that progressively have introduced new paradigms of data-driven drug discovery. Publicly available data alone comprise over 5000 protein kinase crystal structures and hundreds of thousands of binding data. Now, new methods, including artificial intelligence techniques and expansion of protein kinase targeting approaches, together with the expiration of patent protection for optimized inhibitor scaffolds, promise even greater advances in drug discovery. Looking back to the time of the first isoquinoline hinge binders brings the current state-of-the-art into stark contrast. Appropriately for this Perspective article, many of the milestone papers during this time were published in Biochemistry (now ACS Biochemistry).
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Affiliation(s)
- Robin Lorenz
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Richard A Engh
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø 9012, Norway
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5
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Morgan CW, Dale IL, Thomas AP, Hunt J, Chin JW. Selective CRAF Inhibition Elicits Transactivation. J Am Chem Soc 2021; 143:4600-4606. [PMID: 33750116 PMCID: PMC8041278 DOI: 10.1021/jacs.0c11958] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Discovering molecules that regulate
closely related protein isoforms
is challenging, and in many cases the consequences of isoform-specific
pharmacological regulation remains unknown. RAF isoforms are commonly
mutated oncogenes that serve as effector kinases in MAP kinase signaling.
BRAF/CRAF heterodimers are believed to be the primary RAF signaling
species, and many RAF inhibitors lead to a “paradoxical activation”
of RAF kinase activity through transactivation of the CRAF protomer;
this leads to resistance mechanisms and secondary tumors. It has been
hypothesized that CRAF-selective inhibition might bypass paradoxical
activation, but no CRAF-selective inhibitor has been reported and
the consequences of pharmacologically inhibiting CRAF have remained
unknown. Here, we use bio-orthogonal ligand tethering (BOLT) to selectively
target inhibitors to CRAF. Our results suggest that selective CRAF
inhibition promotes paradoxical activation and exemplify how BOLT
may be used to triage potential targets for drug discovery before
any target-selective small molecules are known.
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Affiliation(s)
- Charles W Morgan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ian L Dale
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Andrew P Thomas
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - James Hunt
- Antibody Discovery & Protein Engineering, R&D, AstraZeneca, Cambridge CB21 6GH, United Kingdom
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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6
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Chemogenetics a robust approach to pharmacology and gene therapy. Biochem Pharmacol 2020; 175:113889. [DOI: 10.1016/j.bcp.2020.113889] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/26/2020] [Indexed: 12/20/2022]
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7
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Huber TD, Clinger JA, Liu Y, Xu W, Miller MD, Phillips GN, Thorson JS. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chem Biol 2020; 15:695-705. [PMID: 32091873 DOI: 10.1021/acschembio.9b00943] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural conservation among methyltransferases (MTs) and MT functional redundancy is a major challenge to the cellular study of individual MTs. As a first step toward the development of an alternative biorthogonal platform for MTs and other AdoMet-utilizing enzymes, we describe the evaluation of 38 human methionine adenosyltransferase II-α (hMAT2A) mutants in combination with 14 non-native methionine analogues to identify suitable bioorthogonal mutant/analogue pairings. Enabled by the development and implementation of a hMAT2A high-throughput (HT) assay, this study revealed hMAT2A K289L to afford a 160-fold inversion of the hMAT2A selectivity index for a non-native methionine analogue over the native substrate l-Met. Structure elucidation of K289L revealed the mutant to be folded normally with minor observed repacking within the modified substrate pocket. This study highlights the first example of exchanging l-Met terminal carboxylate/amine recognition elements within the hMAT2A active-site to enable non-native bioorthgonal substrate utilization. Additionally, several hMAT2A mutants and l-Met substrate analogues produced AdoMet analogue products with increased stability. As many AdoMet-producing (e.g., hMAT2A) and AdoMet-utlizing (e.g., MTs) enzymes adopt similar active-site strategies for substrate recognition, the proof of concept first generation hMAT2A engineering highlighted herein is expected to translate to a range of AdoMet-utilizing target enzymes.
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Affiliation(s)
- Tyler D. Huber
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | - Yang Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | | | | | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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8
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation. Angew Chem Int Ed Engl 2019; 58:17930-17952. [DOI: 10.1002/anie.201812164] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
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9
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Messina KJ, Kierzek R, Tracey MA, Bevilacqua PC. Small Molecule Rescue and Glycosidic Conformational Analysis of the Twister Ribozyme. Biochemistry 2019; 58:4857-4868. [PMID: 31742390 PMCID: PMC6901379 DOI: 10.1021/acs.biochem.9b00742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The number of self-cleaving ribozymes has increased sharply in recent years, giving rise to elaborations of the four known ribozyme catalytic strategies, α, β, γ, and δ. One such extension is utilized by the twister ribozyme, which is hypothesized to conduct δ, or general acid catalysis, via N3 of the syn adenine +1 nucleobase indirectly via buffer catalysis at biological pH and directly at lower pH. Herein, we test the δ catalysis role of A1 via chemical rescue and the catalytic relevance of the syn orientation of the nucleobase by conformational analysis. Using inhibited twister ribozyme variants with A1(N3) deaza or A1 abasic modifications, we observe >100-fold chemical rescue effects in the presence of protonatable biological small molecules such as imidazole and histidine, similar to observed rescue values previously reported for C75U/C76Δ in the HDV ribozyme. Brønsted plots for the twister variants support a model in which small molecules rescue catalytic activity via a proton transfer mechanism, suggesting that A1 in the wild type is involved in proton transfer, most likely general acid catalysis. Additionally, through glycosidic conformational analysis in an appropriate background that accommodates the bromine atom, we observe that an 8BrA1-modified twister ribozyme is up to 10-fold faster than a nonmodified A1 ribozyme, supporting crystallographic data that show that A1 is syn when conducting proton transfer. Overall, this study provides functional evidence that the nucleotide immediately downstream of the cleavage site participates directly or indirectly in general acid-base catalysis in the twister ribozyme while occupying the syn conformation.
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Affiliation(s)
- Kyle J. Messina
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Matthew A. Tracey
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Current Address: Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
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10
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemische Epigenetik: der Einfluss chemischer und chemo‐biologischer Techniken auf die Zielstruktur‐Validierung von Bromodomänen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
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11
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Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics. Proc Natl Acad Sci U S A 2019; 116:17245-17250. [PMID: 31409709 DOI: 10.1073/pnas.1905240116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The peptide natural product nisin has been used as a food preservative for 6 decades with minimal development of resistance. Nisin contains the unusual amino acids dehydroalanine and dehydrobutyrine, which are posttranslationally installed by class I lanthipeptide dehydratases (LanBs) on a linear peptide substrate through an unusual glutamyl-tRNA-dependent dehydration of Ser and Thr. To date, little is known about how LanBs catalyze the transfer of glutamate from charged tRNAGlu to the peptide substrate, or how they carry out the subsequent elimination of the peptide-glutamyl adducts to afford dehydro amino acids. Here, we describe the synthesis of inert analogs that mimic substrate glutamyl-tRNAGlu and the glutamylated peptide intermediate, and determine the crystal structures of 2 LanBs in complex with each of these compounds. Mutational studies were used to characterize the function of the glutamylation and glutamate elimination active-site residues identified through the structural analysis. These combined studies provide insights into the mechanisms of substrate recognition, glutamylation, and glutamate elimination by LanBs to effect a net dehydration reaction of Ser and Thr.
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12
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Leopold AV, Chernov KG, Shemetov AA, Verkhusha VV. Neurotrophin receptor tyrosine kinases regulated with near-infrared light. Nat Commun 2019; 10:1129. [PMID: 30850602 PMCID: PMC6408446 DOI: 10.1038/s41467-019-08988-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 02/11/2019] [Indexed: 12/14/2022] Open
Abstract
Optical control over the activity of receptor tyrosine kinases (RTKs) provides an efficient way to reversibly and non-invasively map their functions. We combined catalytic domains of Trk (tropomyosin receptor kinase) family of RTKs, naturally activated by neurotrophins, with photosensory core module of DrBphP bacterial phytochrome to develop opto-kinases, termed Dr-TrkA and Dr-TrkB, reversibly switchable on and off with near-infrared and far-red light. We validated Dr-Trk ability to reversibly light-control several RTK pathways, calcium level, and demonstrated that their activation triggers canonical Trk signaling. Dr-TrkA induced apoptosis in neuroblastoma and glioblastoma, but not in other cell types. Absence of spectral crosstalk between Dr-Trks and blue-light-activatable LOV-domain-based translocation system enabled intracellular targeting of Dr-TrkA independently of its activation, additionally modulating Trk signaling. Dr-Trks have several superior characteristics that make them the opto-kinases of choice for regulation of RTK signaling: high activation range, fast and reversible photoswitching, and multiplexing with visible-light-controllable optogenetic tools.
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Affiliation(s)
- Anna V Leopold
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | | | - Anton A Shemetov
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Vladislav V Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland.
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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13
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Ocasio CA, Warkentin AA, McIntyre PJ, Barkovich KJ, Vesely C, Spencer J, Shokat KM, Bayliss R. Type II Kinase Inhibitors Targeting Cys-Gatekeeper Kinases Display Orthogonality with Wild Type and Ala/Gly-Gatekeeper Kinases. ACS Chem Biol 2018; 13:2956-2965. [PMID: 30239186 DOI: 10.1021/acschembio.8b00592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Analogue-sensitive (AS) kinases contain large to small mutations in the gatekeeper position rendering them susceptible to inhibition with bulky analogues of pyrazolopyrimidine-based Src kinase inhibitors (e.g., PP1). This "bump-hole" method has been utilized for at least 85 of ∼520 kinases, but many kinases are intolerant to this approach. To expand the scope of AS kinase technology, we designed type II kinase inhibitors, ASDO2/6 (analogue-sensitive "DFG-out" kinase inhibitors 2 and 6), that target the "DFG-out" conformation of Cys-gatekeeper kinases with submicromolar potency. We validated this system in vitro against Greatwall kinase (GWL), Aurora-A kinase, and cyclin-dependent kinase-1 and in cells using M110C-GWL-expressing mouse embryonic fibroblasts. These Cys-gatekeeper kinases were sensitive to ASDO2/6 inhibition but not AS kinase inhibitor 3MB-PP1 and vice versa. These compounds, with AS kinase inhibitors, have the potential to inhibit multiple AS kinases independently with applications in systems level and translational kinase research as well as the rational design of type II kinase inhibitors targeting endogenous kinases.
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Affiliation(s)
- Cory A Ocasio
- Genome Damage and Stability Centre, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9RQ , U.K
| | - Alexander A Warkentin
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Patrick J McIntyre
- Department of Molecular and Cell Biology , University of Leicester , Henry Wellcome Building , Leicester LE1 9HN , U.K
| | - Krister J Barkovich
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Clare Vesely
- Genome Damage and Stability Centre, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9RQ , U.K
| | - John Spencer
- Department of Chemistry, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9QJ , U.K
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Richard Bayliss
- School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
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14
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Dejonghe W, Okamoto M, Cutler SR. Small Molecule Probes of ABA Biosynthesis and Signaling. PLANT & CELL PHYSIOLOGY 2018; 59:1490-1499. [PMID: 29986078 DOI: 10.1093/pcp/pcy126] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/26/2018] [Indexed: 05/07/2023]
Abstract
The phytohormone ABA mediates many physiological and developmental responses, and its key role in plant water relations has fueled efforts to improve crop water productivity by manipulating ABA responses. ABA's core signaling components are encoded by large gene families, which has hampered functional studies using classical genetic approaches due to redundancy. Chemical approaches can complement genetic approaches and have the advantage of delivering both biological probes and potential agrochemical leads; these benefits have spawned the discovery and design of new chemical modulators of ABA signaling and biosynthesis, which have contributed to the identification of ABA receptors and helped to define PYR1 and related subfamily III receptors as key cellular targets for chemically manipulating water productivity. In this review, we provide an overview of small molecules that have helped dissect both ABA signaling and metabolic pathways. We further discuss how the insights gleaned using ABA probe molecules might be translated to improvements in crop water productivity and future opportunities for development of small molecules that affect ABA metabolism and signaling.
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Affiliation(s)
- Wim Dejonghe
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-cho, Utsunomiya, Tochigi, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Sean R Cutler
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
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15
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Affiliation(s)
- Byron B. Au-Yeung
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Lin Shen
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, California 94143, USA;,
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, California 94143, USA;,
- Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA
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16
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Korntner S, Pomorski A, Krężel A, Bishop AC. Optimized allosteric inhibition of engineered protein tyrosine phosphatases with an expanded palette of biarsenical small molecules. Bioorg Med Chem 2018; 26:2610-2620. [PMID: 29673715 DOI: 10.1016/j.bmc.2018.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 01/14/2023]
Abstract
Protein tyrosine phosphatases (PTPs), which catalyze the dephosphorylation of phosphotyrosine in protein substrates, are important cell-signaling regulators, as well as potential drug targets for a range of human diseases. Chemical tools for selectively targeting the activities of individual PTPs would help to elucidate PTP signaling roles and potentially expedite the validation of PTPs as therapeutic targets. We have recently reported a novel strategy for the design of non-natural allosteric-inhibition sites in PTPs, in which a tricysteine moiety is engineered within the PTP catalytic domain at a conserved location outside of the active site. Introduction of the tricysteine motif, which does not exist in any wild-type PTP, serves to sensitize target PTPs to inhibition by a biarsenical compound, providing a generalizable strategy for the generation of allosterically sensitized (as) PTPs. Here we show that the potency, selectivity, and kinetics of asPTP inhibition can be significantly improved by exploring the inhibitory action of a range of biarsenical compounds that differ in interarsenical distance, steric bulk, and electronic structure. By investigating the inhibitor sensitivities of five asPTPs from four different subfamilies, we have found that asPTP catalytic domains can be broadly divided into two groups: one that is most potently inhibited by biarsenical compounds with large interarsenical distances, such as AsCy3-EDT2, and one that is most potently inhibited by compounds with relatively small interarsenical distances, such as FlAsH-EDT2. Moreover, we show that a tetrachlorinated derivative of FlAsH-EDT2, Cl4FlAsH-EDT2, targets asPTPs significantly more potently than the parent compound, both in vitro and in asPTP-expressing cells. Our results show that biarsenicals with altered interarsenical distances and electronic properties are important tools for optimizing the control of asPTP activity and, more broadly, suggest that diversification of biarsenical libraries can serve to increase the efficacy of these compounds in targeted control of protein function.
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Affiliation(s)
- Samuel Korntner
- Amherst College, Department of Chemistry, Amherst, MA 01002, USA
| | - Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Anthony C Bishop
- Amherst College, Department of Chemistry, Amherst, MA 01002, USA.
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17
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Leopold AV, Chernov KG, Verkhusha VV. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem Soc Rev 2018; 47:2454-2484. [PMID: 29498733 DOI: 10.1039/c7cs00404d] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein kinases are involved in the regulation of many cellular processes including cell differentiation, survival, migration, axon guidance and neuronal plasticity. A growing set of optogenetic tools, termed opto-kinases, allows activation and inhibition of different protein kinases with light. The optogenetic regulation enables fast, reversible and non-invasive manipulation of protein kinase activities, complementing traditional methods, such as treatment with growth factors, protein kinase inhibitors or chemical dimerizers. In this review, we summarize the properties of the existing optogenetic tools for controlling tyrosine kinases and serine-threonine kinases. We discuss how the opto-kinases can be applied for studies of spatial and temporal aspects of protein kinase signaling in cells and organisms. We compare approaches for chemical and optogenetic regulation of protein kinase activity and present guidelines for selection of opto-kinases and equipment to control them with light. We also describe strategies to engineer novel opto-kinases on the basis of various photoreceptors.
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Affiliation(s)
- Anna V Leopold
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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18
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Identification of Protein Substrates of Specific PARP Enzymes Using Analog-Sensitive PARP Mutants and a "Clickable" NAD + Analog. Methods Mol Biol 2018; 1608:111-135. [PMID: 28695507 DOI: 10.1007/978-1-4939-6993-7_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The PARP family of ADP-ribosyl transferases contains 17 members in human cells, most of which catalyze the transfer of the ADP-ribose moiety of NAD+ onto their target proteins. This posttranslational modification plays important roles in cellular signaling, especially during cellular stresses, such as heat shock, inflammation, unfolded protein responses, and DNA damage. Knowing the specific proteins that are substrates for individual PARPs, as well as the specific amino acid residues in a given target protein that are ADP-ribosylated, is a key step in understanding the biology of individual PARPs. Recently, we developed a robust NAD+ analog-sensitive approach for PARPs, which allows PARP-specific ADP-ribosylation of substrates that is suitable for subsequent copper-catalyzed azide-alkyne cycloaddition ("click chemistry") reactions. When coupled with proteomics and mass spectrometry, the analog-sensitive PARP approach can be used to identify the specific amino acids that are ADP-ribosylated by individual PARP proteins. In this chapter, we describe the key facets of the experimental design and application of the analog-sensitive PARP methodology to identify site-specific modification of PARP target proteins.
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19
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Zhang Y, Larraufie MH, Musavi L, Akkiraju H, Brown LM, Stockwell BR. Design of Small Molecules That Compete with Nucleotide Binding to an Engineered Oncogenic KRAS Allele. Biochemistry 2018; 57:1380-1389. [PMID: 29313669 PMCID: PMC5960803 DOI: 10.1021/acs.biochem.7b01113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RAS mutations are found in 30% of all human cancers, with KRAS the most frequently mutated among the three RAS isoforms (KRAS, NRAS, and HRAS). However, directly targeting oncogenic KRAS with small molecules in the nucleotide-binding site has been difficult because of the high affinity of KRAS for GDP and GTP. We designed an engineered allele of KRAS and a covalent inhibitor that competes for GTP and GDP. This ligand-receptor combination demonstrates that the high affinity of GTP and GDP for RAS proteins can be overcome with a covalent inhibitor and a suitably engineered binding site. The covalent inhibitor irreversibly modifies the protein at the engineered nucleotide-binding site and is able to compete with GDP and GTP. This provides a new tool for studying KRAS function and suggests strategies for targeting the nucleotide-binding site of oncogenic RAS proteins.
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Affiliation(s)
| | | | | | - Hemanth Akkiraju
- Quantitative Proteomics and Metabolomics Center, Columbia University , New York, New York 10027, United States
| | - Lewis M Brown
- Quantitative Proteomics and Metabolomics Center, Columbia University , New York, New York 10027, United States
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20
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Samejima K, Booth DG, Ogawa H, Paulson JR, Xie L, Watson CA, Platani M, Kanemaki MT, Earnshaw WC. Functional analysis after rapid degradation of condensins and 3D-EM reveals chromatin volume is uncoupled from chromosome architecture in mitosis. J Cell Sci 2018; 131:jcs.210187. [PMID: 29361541 PMCID: PMC5868952 DOI: 10.1242/jcs.210187] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/15/2018] [Indexed: 01/01/2023] Open
Abstract
The requirement for condensin in chromosome formation in somatic cells remains unclear, as imperfectly condensed chromosomes do form in cells depleted of condensin by conventional methodologies. In order to dissect the roles of condensin at different stages of vertebrate mitosis, we have established a versatile cellular system that combines auxin-mediated rapid degradation with chemical genetics to obtain near-synchronous mitotic entry of chicken DT40 cells in the presence and absence of condensin. We analyzed the outcome by live- and fixed-cell microscopy methods, including serial block face scanning electron microscopy with digital reconstruction. Following rapid depletion of condensin, chromosomal defects were much more obvious than those seen after a slow depletion of condensin. The total mitotic chromatin volume was similar to that in control cells, but a single mass of mitotic chromosomes was clustered at one side of a bent mitotic spindle. Cultures arrest at prometaphase, eventually exiting mitosis without segregating chromosomes. Experiments where the auxin concentration was titrated showed that different condensin levels are required for anaphase chromosome segregation and formation of a normal chromosome architecture. This article has an associated First Person interview with the first author of the paper. Summary: Rapid condensin depletion reveals that different condensin levels are required for mitotic chromosome architecture and segregation. Condensin is not required for chromatin volume compaction during mitosis.
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Affiliation(s)
- Kumiko Samejima
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Daniel G Booth
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Hiromi Ogawa
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - James R Paulson
- Department of Chemistry, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI 54901, USA
| | - Linfeng Xie
- Department of Chemistry, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI 54901, USA
| | - Cara A Watson
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Melpomeni Platani
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, ROIS, and Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
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21
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Long MC, Urul DA, Chawla S, Lin HY, Zhao Y, Haegele JA, Wang Y, Aye Y. Precision Electrophile Tagging in Caenorhabditis elegans. Biochemistry 2018; 57:216-220. [PMID: 28857552 PMCID: PMC5770885 DOI: 10.1021/acs.biochem.7b00642] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/30/2017] [Indexed: 11/30/2022]
Abstract
Adduction of an electrophile to privileged sensor proteins and the resulting phenotypically dominant responses are increasingly appreciated as being essential for metazoan health. Functional similarities between the biological electrophiles and electrophilic pharmacophores commonly found in covalent drugs further fortify the translational relevance of these small-molecule signals. Genetically encodable or small-molecule-based fluorescent reporters and redox proteomics have revolutionized the observation and profiling of cellular redox states and electrophile-sensor proteins, respectively. However, precision mapping between specific redox-modified targets and specific responses has only recently begun to be addressed, and systems tractable to both genetic manipulation and on-target redox signaling in vivo remain largely limited. Here we engineer transgenic Caenorhabditis elegans expressing functional HaloTagged fusion proteins and use this system to develop a generalizable light-controlled approach to tagging a prototypical electrophile-sensor protein with native electrophiles in vivo. The method circumvents issues associated with low uptake/distribution and toxicity/promiscuity. Given the validated success of C. elegans in aging studies, this optimized platform offers a new lens with which to scrutinize how on-target electrophile signaling influences redox-dependent life span regulation.
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Affiliation(s)
- Marcus
J. C. Long
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Daniel A. Urul
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Shivansh Chawla
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Hong-Yu Lin
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Yi Zhao
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Joseph A. Haegele
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Yiran Wang
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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22
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Chen R, Huang J, Yao R, Wang X, Wu B. Construction of metal–organic frameworks from 3-(6-oxo-6,9-dihydro-1H-purin-1-yl)propionate. J COORD CHEM 2017. [DOI: 10.1080/00958972.2017.1355459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rui Chen
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, P. R. China
| | - Ju Huang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, P. R. China
| | - Rui Yao
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, P. R. China
| | - Xing Wang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, P. R. China
| | - Benlai Wu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, P. R. China
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23
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Resolving Behavioral Output via Chemogenetic Designer Receptors Exclusively Activated by Designer Drugs. J Neurosci 2017; 36:9268-82. [PMID: 27605603 DOI: 10.1523/jneurosci.1333-16.2016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/13/2016] [Indexed: 12/26/2022] Open
Abstract
Designer receptors exclusively activated by designer drugs (DREADDs) have proven to be highly effective neuromodulatory tools for the investigation of neural circuits underlying behavioral outputs. They exhibit a number of advantages: they rely on cell-specific manipulations through canonical intracellular signaling pathways, they are easy and cost-effective to implement in a laboratory setting, and they are easily scalable for single-region or full-brain manipulations. On the other hand, DREADDs rely on ligand-G-protein-coupled receptor interactions, leading to coarse temporal dynamics. In this review we will provide a brief overview of DREADDs, their implementation, and the advantages and disadvantages of their use in animal systems. We also will provide numerous examples of their use across a broad variety of biomedical research fields.
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24
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Forster M, Gehringer M, Laufer SA. Recent advances in JAK3 inhibition: Isoform selectivity by covalent cysteine targeting. Bioorg Med Chem Lett 2017; 27:4229-4237. [PMID: 28844493 DOI: 10.1016/j.bmcl.2017.07.079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 01/01/2023]
Abstract
Janus kinases (JAKs) are a family of four cytosolic protein kinases with a high degree of structural similarity. Due to its very restricted role in immune regulation, JAK3 was promoted as an excellent target for immunosuppression for more than a decade, but clinical validation of this concept is still elusive. During the last years, speculation arose that kinase activity of JAK1, which cooperates with JAK3 in cytokine receptor signaling, may have a dominant role over the one of JAK3. Until recently, however, this issue could not be appropriately addressed due to a lack of highly isoform-selective tool compounds. With the recent resurgence of covalent drugs, targeting of a specific cysteine that distinguishes JAK3 from other JAK family members became an attractive design option. By applying this strategy, a set of JAK3 inhibitors with excellent selectivity against other JAK isoforms and the kinome was developed during the last three years and used to decipher JAK3-dependent signaling. The data obtained with these tool compounds demonstrates that selective JAK3 inhibition is sufficient to block downstream signaling. Since one of these inhibitors is currently under evaluation in phase II clinical studies against several inflammatory disorders, it will soon become apparent whether selective JAK3 inhibition translates into clinical efficacy.
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Affiliation(s)
- Michael Forster
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany.
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany.
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25
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Computational design of ligand-binding proteins. Curr Opin Struct Biol 2016; 45:67-73. [PMID: 27951448 DOI: 10.1016/j.sbi.2016.11.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/24/2016] [Accepted: 11/25/2016] [Indexed: 02/07/2023]
Abstract
Custom-designed ligand-binding proteins with novel functions hold the potential for numerous applications. In recent years, the developments of computational methods together with high-throughput experimental screening techniques have led to the generation of novel, high-affinity ligand-binding proteins for given ligands. In addition, naturally occurring ligand-binding proteins have been computationally designed to recognize new ligands while keeping their original biological functions at the same time. Furthermore, metalloproteins have been successfully designed for novel functions and applications. Though much has been learned in these successful design cases, advances in our understanding of protein dynamics and functions related to ligand binding and development of novel computational strategies are necessary to further increase the success rate of computational protein-ligand binding design.
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26
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Huber TD, Johnson BR, Zhang J, Thorson JS. AdoMet analog synthesis and utilization: current state of the art. Curr Opin Biotechnol 2016; 42:189-197. [PMID: 27506965 DOI: 10.1016/j.copbio.2016.07.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 11/25/2022]
Abstract
S-Adenosyl-l-methionine (AdoMet) is an essential enzyme cosubstrate in fundamental biology with an expanding range of biocatalytic and therapeutic applications. In recent years, technologies enabling the synthesis and utilization of novel functional AdoMet surrogates have rapidly advanced. Developments highlighted within this brief review include improved syntheses of AdoMet analogs, unique S-adenosyl-l-methionine isosteres with enhanced stability, and corresponding applications in epigenetics, proteomics and natural product/small molecule diversification ('alkylrandomization').
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Affiliation(s)
- Tyler D Huber
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, United States
| | - Brooke R Johnson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, United States
| | - Jianjun Zhang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, United States
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, United States.
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27
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Runcie AC, Chan KH, Zengerle M, Ciulli A. Chemical genetics approaches for selective intervention in epigenetics. Curr Opin Chem Biol 2016; 33:186-94. [PMID: 27423045 PMCID: PMC5061558 DOI: 10.1016/j.cbpa.2016.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/01/2016] [Accepted: 06/23/2016] [Indexed: 11/21/2022]
Abstract
Chemical genetics offers tools and opportunities to investigate epigenetic processes. Chemical probes targeting epigenetic proteins are increasingly being developed. Epigenetic targets pose distinct challenges to chemical genetics approaches. The ‘bump-and-hole’ approach allows for highly selective single-target inhibition. PROTACS can degrade target proteins to enhance efficacy and selectivity.
Chemical genetics is the use of biologically active small molecules (chemical probes) to investigate the functions of gene products, through the modulation of protein activity. Recent years have seen significant progress in the application of chemical genetics to study epigenetics, following the development of new chemical probes, a growing appreciation of the role of epigenetics in disease and a recognition of the need and utility of high-quality, cell-active chemical probes. In this review, we single out the bromodomain reader domains as a prime example of both the success, and challenges facing chemical genetics. The difficulty in generating single-target selectivity has long been a thorn in the side of chemical genetics, however, recent developments in advanced forms of chemical genetics promise to bypass this, and other, limitations. The ‘bump-and-hole’ approach has now been used to probe — for the first time — the BET bromodomain subfamily with single-target selectivity and may be applicable to other epigenetic domains. Meanwhile, PROTAC compounds have been shown to be significantly more efficacious than standard domain inhibitors, and have the potential to enhance target selectivity.
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Affiliation(s)
- Andrew C Runcie
- School of Life Sciences, University of Dundee, Division of Biological Chemistry and Drug Discovery, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Kwok-Ho Chan
- School of Life Sciences, University of Dundee, Division of Biological Chemistry and Drug Discovery, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Michael Zengerle
- School of Life Sciences, University of Dundee, Division of Biological Chemistry and Drug Discovery, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Alessio Ciulli
- School of Life Sciences, University of Dundee, Division of Biological Chemistry and Drug Discovery, James Black Centre, Dow Street, Dundee DD1 5EH, UK.
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28
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Welsh MA, Blackwell HE. Chemical probes of quorum sensing: from compound development to biological discovery. FEMS Microbiol Rev 2016; 40:774-94. [PMID: 27268906 DOI: 10.1093/femsre/fuw009] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 01/20/2023] Open
Abstract
Bacteria can utilize chemical signals to coordinate the expression of group-beneficial behaviors in a method of cell-cell communication called quorum sensing (QS). The discovery that QS controls the production of virulence factors and biofilm formation in many common pathogens has driven an explosion of research aimed at both deepening our fundamental understanding of these regulatory networks and developing chemical agents that can attenuate QS signaling. The inherently chemical nature of QS makes studying these pathways with small molecule tools a complementary approach to traditional microbiology techniques. Indeed, chemical tools are beginning to yield new insights into QS regulation and provide novel strategies to inhibit QS. Here, we review the most recent advances in the development of chemical probes of QS systems in Gram-negative bacteria, with an emphasis on the opportunistic pathogen Pseudomonas aeruginosa We first describe reports of novel small molecule modulators of QS receptors and QS signal synthases. Next, in several case studies, we showcase how chemical tools have been deployed to reveal new knowledge of QS biology and outline lessons for how researchers might best target QS to combat bacterial virulence. To close, we detail the outstanding challenges in the field and suggest strategies to overcome these issues.
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Affiliation(s)
- Michael A Welsh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
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29
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Han Y, Yuan ZF, Molden RC, Garcia BA. Monitoring Cellular Phosphorylation Signaling Pathways into Chromatin and Down to the Gene Level. Mol Cell Proteomics 2016; 15:834-53. [PMID: 26543102 PMCID: PMC4813704 DOI: 10.1074/mcp.m115.053421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/26/2015] [Indexed: 01/14/2023] Open
Abstract
Protein phosphorylation, one of the most common and important modifications of acute and reversible regulation of protein function, plays a dominant role in almost all cellular processes. These signaling events regulate cellular responses, including proliferation, differentiation, metabolism, survival, and apoptosis. Several studies have been successfully used to identify phosphorylated proteins and dynamic changes in phosphorylation status after stimulation. Nevertheless, it is still rather difficult to elucidate precise complex phosphorylation signaling pathways. In particular, how signal transduction pathways directly communicate from the outer cell surface through cytoplasmic space and then directly into chromatin networks to change the transcriptional and epigenetic landscape remains poorly understood. Here, we describe the optimization and comparison of methods based on thiophosphorylation affinity enrichment, which can be utilized to monitor phosphorylation signaling into chromatin by isolation of phosphoprotein containing nucleosomes, a method we term phosphorylation-specific chromatin affinity purification (PS-ChAP). We utilized this PS-ChAP(1) approach in combination with quantitative proteomics to identify changes in the phosphorylation status of chromatin-bound proteins on nucleosomes following perturbation of transcriptional processes. We also demonstrate that this method can be employed to map phosphoprotein signaling into chromatin containing nucleosomes through identifying the genes those phosphorylated proteins are found on via thiophosphate PS-ChAP-qPCR. Thus, our results showed that PS-ChAP offers a new strategy for studying cellular signaling and chromatin biology, allowing us to directly and comprehensively investigate phosphorylation signaling into chromatin to investigate if these pathways are involved in altering gene expression. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD002436.
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Affiliation(s)
- Yumiao Han
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, PA 19104-5157, USA
| | - Zuo-Fei Yuan
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, PA 19104-5157, USA
| | | | - Benjamin A Garcia
- From the ‡Epigenetics Program, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, PA 19104-5157, USA;
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30
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Alonso-Rodríguez E, Fernández-Piñar P, Sacristán-Reviriego A, Molina M, Martín H. An Analog-sensitive Version of the Protein Kinase Slt2 Allows Identification of Novel Targets of the Yeast Cell Wall Integrity Pathway. J Biol Chem 2016; 291:5461-5472. [PMID: 26786099 DOI: 10.1074/jbc.m115.683680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 12/12/2022] Open
Abstract
The yeast cell wall integrity MAPK Slt2 mediates the transcriptional response to cell wall alterations through phosphorylation of transcription factors Rlm1 and SBF. However, the variety of cellular functions regulated by Slt2 suggests the existence of a significant number of still unknown substrates for this kinase. To identify novel Slt2 targets, we generated and characterized an analog-sensitive mutant of Slt2 (Slt2-as) that can be specifically inhibited by bulky kinase inhibitor analogs. We demonstrated that Slt2-as is able to use adenosine 5'-[γ-thio]triphosphate analogs to thiophosphorylate its substrates in yeast cell extracts as well as when produced as recombinant proteins in Escherichia coli. Taking advantage of this chemical-genetic approach, we found that Slt2 phosphorylates the MAPK phosphatase Msg5 both in the N-terminal regulatory and C-terminal catalytic domains. Moreover, we identified the calcineurin regulator Rcn2, the 4E-BP (translation initiation factor eIF4E-binding protein) translation repressor protein Caf20, and the Golgi-associated adaptor Gga1 as novel targets for Slt2. The Slt2 phosphorylation sites on Rcn2 and Caf20 were determined. We also demonstrated that, in the absence of SLT2, the GGA1 paralog GGA2 is essential for cells to survive under cell wall stress and for proper protein sorting through the carboxypeptidase Y pathway. Therefore, Slt2-as provides a powerful tool that can expand our knowledge of the outputs of the cell wall integrity MAPK pathway.
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Affiliation(s)
- Esmeralda Alonso-Rodríguez
- From the Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28040 Madrid, Spain
| | - Pablo Fernández-Piñar
- From the Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28040 Madrid, Spain
| | - Almudena Sacristán-Reviriego
- From the Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28040 Madrid, Spain
| | - María Molina
- From the Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28040 Madrid, Spain.
| | - Humberto Martín
- From the Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28040 Madrid, Spain
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Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA. Remote control of therapeutic T cells through a small molecule-gated chimeric receptor. Science 2015; 350:aab4077. [PMID: 26405231 PMCID: PMC4721629 DOI: 10.1126/science.aab4077] [Citation(s) in RCA: 494] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/09/2015] [Indexed: 12/17/2022]
Abstract
There is growing interest in using engineered cells as therapeutic agents. For example, synthetic chimeric antigen receptors (CARs) can redirect T cells to recognize and eliminate tumor cells expressing specific antigens. Despite promising clinical results, these engineered T cells can exhibit excessive activity that is difficult to control and can cause severe toxicity. We designed "ON-switch" CARs that enable small-molecule control over T cell therapeutic functions while still retaining antigen specificity. In these split receptors, antigen-binding and intracellular signaling components assemble only in the presence of a heterodimerizing small molecule. This titratable pharmacologic regulation could allow physicians to precisely control the timing, location, and dosage of T cell activity, thereby mitigating toxicity. This work illustrates the potential of combining cellular engineering with orthogonal chemical tools to yield safer therapeutic cells that tightly integrate cell-autonomous recognition and user control.
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Affiliation(s)
- Chia-Yung Wu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA
| | - Kole T Roybal
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA
| | - Elias M Puchner
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - James Onuffer
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA.
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA. Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA.
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Gerdt JP, McInnis CE, Schell TL, Blackwell HE. Unraveling the contributions of hydrogen-bonding interactions to the activity of native and non-native ligands in the quorum-sensing receptor LasR. Org Biomol Chem 2015; 13:1453-62. [PMID: 25474181 DOI: 10.1039/c4ob02252a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quorum sensing (QS) via the synthesis and detection of N-acyl L-homoserine lactone (AHL) signals regulates important pathogenic and mutualistic phenotypes in many bacteria. Over the past two decades, the development of non-native molecules that modulate this cell-cell signaling process has become an active area of research. The majority of these compounds were designed to block binding of the native AHL signal to its cognate LuxR-type receptor, and much effort has focused on LasR in the opportunistic pathogen Pseudomonas aeruginosa. Despite a small set of reported LasR structural data, it remains unclear which polar interactions are most important for either (i) activation of the LasR receptor by its native AHL signal, N-(3-oxo)-dodecanoyl L-homoserine lactone (OdDHL), or (ii) activation or inhibition of LasR by related AHL analogs. Herein, we report our investigations into the activity of OdDHL and five synthetic analogs in wild-type LasR and in nine LasR mutants with modifications to key polar residues in their ligand binding sites. Our results allowed us to rank, for the first time, the relative importance of each LasR:OdDHL hydrogen bond for LasR activation and provide strong evidence for the five synthetic ligands binding LasR in a very similar orientation as OdDHL. By delineating the specific molecular interactions that are important for LasR modulation by AHLs, these findings should aid in the design of new synthetic modulators of LasR (and homologous LuxR-type receptors) with improved potencies and selectivities.
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Affiliation(s)
- Joseph P Gerdt
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA.
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33
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Abstract
The article by Gerdt and colleagues in this issue of Chemistry & Biology provides molecular insights into how nonlactone quorum sensing modulators either activate or deactivate LasR. Interestingly, an antagonist could flip into an agaonist upon mutation of a single residue in the autoinducer binding site.
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Friedel P, Kahle KT, Zhang J, Hertz N, Pisella LI, Buhler E, Schaller F, Duan J, Khanna AR, Bishop PN, Shokat KM, Medina I. WNK1-regulated inhibitory phosphorylation of the KCC2 cotransporter maintains the depolarizing action of GABA in immature neurons. Sci Signal 2015; 8:ra65. [PMID: 26126716 DOI: 10.1126/scisignal.aaa0354] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Activation of Cl(-)-permeable γ-aminobutyric acid type A (GABAA) receptors elicits synaptic inhibition in mature neurons but excitation in immature neurons. This developmental "switch" in the GABA function depends on a postnatal decrease in intraneuronal Cl(-) concentration mediated by KCC2, a Cl(-)-extruding K(+)-Cl(-) cotransporter. We showed that the serine-threonine kinase WNK1 [with no lysine (K)] forms a physical complex with KCC2 in the developing mouse brain. Dominant-negative mutation, genetic depletion, or chemical inhibition of WNK1 in immature neurons triggered a hyperpolarizing shift in GABA activity by enhancing KCC2-mediated Cl(-) extrusion. This increase in KCC2 activity resulted from reduced inhibitory phosphorylation of KCC2 at two C-terminal threonines, Thr(906) and Thr(1007). Phosphorylation of both Thr(906) and Thr(1007) was increased in immature versus mature neurons. Together, these data provide insight into the mechanism regulating Cl(-) homeostasis in immature neurons, and suggest that WNK1-regulated changes in KCC2 phosphorylation contribute to the developmental excitatory-to-inhibitory GABA sequence.
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Affiliation(s)
- Perrine Friedel
- Institut de Neurobiologie de la Méditerranée (INMED), INSERM Unité 901, 13273 Marseille, France. Aix-Marseille Université, UMR 901, 13273 Marseille, France
| | - Kristopher T Kahle
- Department of Neurosurgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Jinwei Zhang
- UK Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Nicholas Hertz
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143-0450, USA
| | - Lucie I Pisella
- Institut de Neurobiologie de la Méditerranée (INMED), INSERM Unité 901, 13273 Marseille, France. Aix-Marseille Université, UMR 901, 13273 Marseille, France
| | - Emmanuelle Buhler
- Aix-Marseille Université, UMR 901, 13273 Marseille, France. Plateforme Post-Génomique, INMED, 13273 Marseille, France
| | - Fabienne Schaller
- Aix-Marseille Université, UMR 901, 13273 Marseille, France. Plateforme Post-Génomique, INMED, 13273 Marseille, France
| | - JingJing Duan
- Department of Neurosurgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Arjun R Khanna
- Department of Neurosurgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Paul N Bishop
- School of Biochemistry, University of Bristol, Bristol BS8 1TH, UK
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143-0450, USA
| | - Igor Medina
- Institut de Neurobiologie de la Méditerranée (INMED), INSERM Unité 901, 13273 Marseille, France. Aix-Marseille Université, UMR 901, 13273 Marseille, France.
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Chio CM, Yu X, Bishop AC. Rational design of allosteric-inhibition sites in classical protein tyrosine phosphatases. Bioorg Med Chem 2015; 23:2828-38. [PMID: 25828055 PMCID: PMC4451255 DOI: 10.1016/j.bmc.2015.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/05/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
Abstract
Protein tyrosine phosphatases (PTPs), which catalyze the dephosphorylation of phosphotyrosine in protein substrates, are critical regulators of metazoan cell signaling and have emerged as potential drug targets for a range of human diseases. Strategies for chemically targeting the function of individual PTPs selectively could serve to elucidate the signaling roles of these enzymes and would potentially expedite validation of the therapeutic promise of PTP inhibitors. Here we report a novel strategy for the design of non-natural allosteric-inhibition sites in PTPs; these sites, which can be introduced into target PTPs through protein engineering, serve to sensitize target PTPs to potent and selective inhibition by a biarsenical small molecule. Building on the recent discovery of a naturally occurring cryptic allosteric site in wild-type Src-homology-2 domain containing PTP (Shp2) that can be targeted by biarsenical compounds, we hypothesized that Shp2's unusual sensitivity to biarsenicals could be strengthened through rational design and that the Shp2-specific site could serve as a blueprint for the introduction of non-natural inhibitor sensitivity in other PTPs. Indeed, we show here that the strategic introduction of a cysteine residue at a position removed from the Shp2 active site can serve to increase the potency and selectivity of the interaction between Shp2's allosteric site and the biarsenical inhibitor. Moreover, we find that 'Shp2-like' allosteric sites can be installed de novo in PTP enzymes that do not possess naturally occurring sensitivity to biarsenical compounds. Using primary-sequence alignments to guide our enzyme engineering, we have successfully introduced allosteric-inhibition sites in four classical PTPs-PTP1B, PTPH-1, FAP-1, and HePTP-from four different PTP subfamilies, suggesting that our sensitization approach can likely be applied widely across the classical PTP family to generate biarsenical-responsive PTPs.
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Affiliation(s)
- Cynthia M Chio
- Amherst College, Department of Chemistry, Amherst, MA 01002, United States
| | - Xiaoling Yu
- Amherst College, Department of Chemistry, Amherst, MA 01002, United States
| | - Anthony C Bishop
- Amherst College, Department of Chemistry, Amherst, MA 01002, United States.
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Chemical biology strategies for posttranslational control of protein function. ACTA ACUST UNITED AC 2015; 21:1238-52. [PMID: 25237866 DOI: 10.1016/j.chembiol.2014.08.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/08/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023]
Abstract
A common strategy to understand a biological system is to selectively perturb it and observe its response. Although technologies now exist to manipulate cellular systems at the genetic and transcript level, the direct manipulation of functions at the protein level can offer significant advantages in precision, speed, and reversibility. Combining the specificity of genetic manipulation and the spatiotemporal resolution of light- and small molecule-based approaches now allows exquisite control over biological systems to subtly perturb a system of interest in vitro and in vivo. Conditional perturbation mechanisms may be broadly characterized by change in intracellular localization, intramolecular activation, or degradation of a protein-of-interest. Here we review recent advances in technologies for conditional regulation of protein function and suggest further areas of potential development.
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37
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Agrochemical control of plant water use using engineered abscisic acid receptors. Nature 2015; 520:545-8. [DOI: 10.1038/nature14123] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/28/2014] [Indexed: 12/13/2022]
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Brand M, Measures AM, Wilson BG, Cortopassi WA, Alexander R, Höss M, Hewings DS, Rooney TPC, Paton RS, Conway SJ. Small molecule inhibitors of bromodomain-acetyl-lysine interactions. ACS Chem Biol 2015; 10:22-39. [PMID: 25549280 DOI: 10.1021/cb500996u] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains are protein modules that bind to acetylated lysine residues. Their interaction with histone proteins suggests that they function as "readers" of histone lysine acetylation, a component of the proposed "histone code". Bromodomain-containing proteins are often found as components of larger protein complexes with roles in fundamental cellular process including transcription. The publication of two potent ligands for the BET bromodomains in 2010 demonstrated that small molecules can inhibit the bromodomain-acetyl-lysine protein-protein interaction. These molecules display strong phenotypic effects in a number of cell lines and affect a range of cancers in vivo. This work stimulated intense interest in developing further ligands for the BET bromodomains and the design of ligands for non-BET bromodomains. Here we review the recent progress in the field with particular attention paid to ligand design, the assays employed in early ligand discovery, and the use of computational approaches to inform ligand design.
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Affiliation(s)
- Michael Brand
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Angelina M. Measures
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Brian G. Wilson
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Wilian A. Cortopassi
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | | | | | - David S. Hewings
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy P. C. Rooney
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S. Paton
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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39
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Warner JB, Muthusamy AK, Petersson EJ. Specific modulation of protein activity by using a bioorthogonal reaction. Chembiochem 2014; 15:2508-14. [PMID: 25256385 DOI: 10.1002/cbic.201402423] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Indexed: 11/06/2022]
Abstract
Unnatural amino acids with bioorthogonal reactive groups have the potential to provide a rapid and specific mechanism for covalently inhibiting a protein of interest. Here, we use mutagenesis to insert an unnatural amino acid containing an azide group (Z) into the target protein at positions such that a "click" reaction with an alkyne modulator (X) will alter the function of the protein. This bioorthogonally reactive pair can engender specificity of X for the Z-containing protein, even if the target is otherwise identical to another protein, allowing for rapid target validation in living cells. We demonstrate our method using inhibition of the Escherichia coli enzyme aminoacyl transferase by both active-site occlusion and allosteric mechanisms. We have termed this a "clickable magic bullet" strategy, and it should be generally applicable to studying the effects of protein inhibition, within the limits of unnatural amino acid mutagenesis.
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Affiliation(s)
- John B Warner
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323 (USA)
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40
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Gerdt JP, McInnis CE, Schell TL, Rossi FM, Blackwell HE. Mutational analysis of the quorum-sensing receptor LasR reveals interactions that govern activation and inhibition by nonlactone ligands. ACTA ACUST UNITED AC 2014; 21:1361-1369. [PMID: 25242287 DOI: 10.1016/j.chembiol.2014.08.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/05/2014] [Accepted: 08/18/2014] [Indexed: 01/03/2023]
Abstract
Gram-negative bacteria use N-acyl L-homoserine lactone (AHL) quorum-sensing (QS) signals to regulate the expression of myriad phenotypes. Non-native AHL analogs can strongly attenuate QS receptor activity and thereby QS signaling; however, we currently lack a molecular understanding of the mechanisms by which most of these compounds elicit their agonistic or antagonistic profiles. In this study, we investigated the origins of striking activity profile switches (i.e., receptor activator to inhibitor, and vice versa) observed upon alteration of the lactone head group in certain AHL analogs. Reporter gene assays of mutant versions of the Pseudomonas aeruginosa QS receptor LasR revealed that interactions between the ligands and Trp60, Tyr56, and Ser129 govern whether these ligands behave as LasR activators or inhibitors. Using this knowledge, we propose a model for the modulation of LasR by AHL analogs-encompassing a subtly different interaction with the binding pocket to a global change in LasR conformation.
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Affiliation(s)
- Joseph P Gerdt
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Christine E McInnis
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Trevor L Schell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Francis M Rossi
- Department of Chemistry, SUNY Cortland, Cortland, NY 13045, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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41
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Moore KE, Gozani O. An unexpected journey: lysine methylation across the proteome. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1395-403. [PMID: 24561874 DOI: 10.1016/j.bbagrm.2014.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/11/2014] [Indexed: 12/17/2022]
Abstract
The dynamic modification of histone proteins by lysine methylation has emerged over the last decade as a key regulator of chromatin functions. In contrast, our understanding of the biological roles for lysine methylation of non-histone proteins has progressed more slowly. Though recently it has attracted less attention, ε-methyl-lysine in non-histone proteins was first observed over 50 years ago. In that time, it has become clear that, like the case for histones, non-histone methylation represents a key and common signaling process within the cell. Recent work suggests that non-histone methylation occurs on hundreds of proteins found in both the nucleus and the cytoplasm, and with important biomedical implications. Technological advances that allow us to identify lysine methylation on a proteomic scale are opening new avenues in the non-histone methylation field, which is poised for dramatic growth. Here, we review historical and recent findings in non-histone lysine methylation signaling, highlight new methods that are expanding opportunities in the field, and discuss outstanding questions and future challenges about the role of this fundamental post-translational modification (PTM).
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Affiliation(s)
- Kaitlyn E Moore
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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42
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Abstract
The eukaryotic cell division cycle has been studied at the molecular level for over 30 years, most fruitfully in model organisms. In the past 5 years, developments in mass spectrometry-based proteomics have been applied to the study of protein interactions and post-translational modifications involving key cell cycle regulators such as cyclin-dependent kinases and the anaphase-promoting complex, as well as effectors such as centrosomes, the kinetochore and DNA replication forks. In addition, innovations in chemical biology, functional proteomics and bioinformatics have been employed to study the cell cycle at the proteome level. This review surveys the contributions of proteomics to cell cycle research. The near future should see the application of more quantitative proteomic approaches to probe the dynamic aspects of the molecular system that underlie the cell cycle in model organisms and in human cells.
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Affiliation(s)
- Vincent Archambault
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, UK.
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43
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Child MA. Chemical biology approaches for the study of apicomplexan parasites. Mol Biochem Parasitol 2013; 192:1-9. [PMID: 24333788 DOI: 10.1016/j.molbiopara.2013.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 11/28/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
Chemical biology and the techniques the field encompasses provide scientists with the means to address biological questions in ever-evolving and technically sophisticated ways. They facilitate the dissection of molecular mechanisms of cell phenomena on timescales not achievable by other means. Libraries of small molecules, bioorthogonal chemistries and technical advances in mass-spectrometry techniques enable the modern chemical biologist to tackle even the most difficult of biological questions. It is because of their broad applicability that these approaches are well suited to systems less tractable to more classical genetic methods. As such, the parasite community has embraced them with great success. Some of these successes and the continuing evolution of chemical biology applied to apicomplexans will be discussed.
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Affiliation(s)
- Matthew A Child
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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44
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Hertz NT, Wang BT, Allen JJ, Zhang C, Dar AC, Burlingame AL, Shokat KM. Chemical genetic approach for kinase-substrate mapping by covalent capture of thiophosphopeptides and analysis by mass spectrometry. ACTA ACUST UNITED AC 2013; 2:15-36. [PMID: 23836541 DOI: 10.1002/9780470559277.ch090201] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Mapping kinase-substrate interactions demands robust methods to rapidly and unequivocally identify substrates from complex protein mixtures. Toward this goal, we present a method in which a kinase, engineered to utilize synthetic ATPγS analogs, specifically thiophosphorylates its substrates in a complex lysate. The thiophosphate label provides a bio-orthogonal tag that can be used to affinity purify and identify labeled proteins. Following the labeling reaction, proteins are digested with trypsin; thiol-containing peptides are then covalently captured and non-thiol-containing peptides are washed from the resin. Oxidation-promoted hydrolysis, at sites of thiophosphorylation, releases phosphopeptides for analysis by tandem mass spectrometry. By incorporating two specificity gates-kinase engineering and peptide affinity purification-this method yields high-confidence substrate identifications. This method gives both the identity of the substrates and phosphorylation-site localization. With this information, investigators can analyze the biological significance of the phosphorylation mark immediately following confirmation of the kinase-substrate relationship. Here, we provide an optimized version of this technique to further enable widespread utilization of this technology. Curr. Protoc. Chem Biol. 2:15-36. © 2010 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nicholas T Hertz
- Chemistry and Chemical Biology Graduate Program, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California
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45
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Orthogonal ubiquitin transfer through engineered E1-E2 cascades for protein ubiquitination. ACTA ACUST UNITED AC 2013; 19:1265-77. [PMID: 23102221 DOI: 10.1016/j.chembiol.2012.07.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/26/2012] [Accepted: 07/31/2012] [Indexed: 11/20/2022]
Abstract
Protein modification by ubiquitin (UB) controls diverse cellular processes. UB is conjugated to cellular proteins by sequential transfer through an E1-E2-E3 enzymatic cascade. The cross-activities of 2 E1s, 50 E2s and thousands of E3s encoded by the human genome make it difficult to identify the substrate proteins of a specific E3 enzyme in the cell. One way to solve this problem is to engineer an orthogonal UB transfer (OUT) cascade in which the engineered UB (xUB) is relayed by engineered E1, E2 and E3 enzymes (xE1, xE2, xE3) to modify the substrate proteins of a specific E3. Here, we use phage display and mutagenesis to construct xUB-xE1 and xE1-xE2 pairs that are orthogonal to the native E1 and E2 enzymes. Our work on engineering the UB transfer cascades will enable us to use OUT to map the signal transduction networks mediated by protein ubiquitination.
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46
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Gravells P, Tomita K, Booth A, Poznansky J, Porter AC. Chemical genetic analyses of quantitative changes in Cdk1 activity during the human cell cycle. Hum Mol Genet 2013; 22:2842-51. [DOI: 10.1093/hmg/ddt133] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Selective kinase inhibitors as tools for neuroscience research. Neuropharmacology 2012; 63:1227-37. [DOI: 10.1016/j.neuropharm.2012.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 07/06/2012] [Accepted: 07/11/2012] [Indexed: 01/02/2023]
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Liu XQ, Li ZY, Yuan XJ, Wu BL. Two new 2-D coordination polymers based on a purine-containing carboxylate. J COORD CHEM 2012. [DOI: 10.1080/00958972.2012.724172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Xin-Qi Liu
- a Department of Chemistry , Zhengzhou University , Zhengzhou 450001 , P.R. China
- b Henan Vocational College of Chemical Technology , Zhengzhou 450052 , P.R. China
| | - Zhong-Yuan Li
- c Shenzhen Academy of Metrology & Quality Inspection , Shenzhen 518055 , P.R. China
| | - Xiao-Ju Yuan
- a Department of Chemistry , Zhengzhou University , Zhengzhou 450001 , P.R. China
| | - Ben-Lai Wu
- a Department of Chemistry , Zhengzhou University , Zhengzhou 450001 , P.R. China
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Manlandro CMA, Palanivel VR, Schorr EB, Mihatov N, Antony AA, Rosenwald AG. Mon2 is a negative regulator of the monomeric G protein, Arl1. FEMS Yeast Res 2012; 12:637-50. [PMID: 22594927 DOI: 10.1111/j.1567-1364.2012.00814.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 04/27/2012] [Accepted: 05/11/2012] [Indexed: 11/30/2022] Open
Abstract
Using site-directed mutants of ARL1 predicted to alter nucleotide binding, we examined phenotypes associated with the loss of ARL1 , including effects on membrane traffic and K (+) homeostasis. The GTP-restricted allele, ARL[Q72L] , complemented the membrane traffic phenotype (CPY secretion), but not the K (+) homeostasis phenotypes (sensitivity to hygromycin B, steady-state levels of K (+) , and accumulation of (86) Rb (+) ), while the XTP-restricted mutant, ARL1[D130N] , complemented the ion phenotypes, but not the membrane traffic phenotype. A GDP-restricted allele, ARL1[T32N] , did not effectively complement either phenotype. These results are consistent with a model in which Arl1 has three different conformations in vivo. We also explored the relationship between ARL1 and MON2 using the synthetic lethal phenotype exhibited by these two genes and demonstrated that MON2 is a negative regulator of the GTP-restricted allele of ARL1 , ARL1[Q72L] . Finally, we constructed several new alleles predicted to alter binding of Arl1 to the sole GRIP domain containing protein in yeast, Imh1, and found that ARL1[F52G] and ARL1[Y82G] were unable to complement the loss of ARL1 with respect to either the membrane traffic or K (+) homeostasis phenotypes. Our study expands understanding of the roles of Arl1 in vivo.
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Hengeveld RCC, Hertz NT, Vromans MJM, Zhang C, Burlingame AL, Shokat KM, Lens SMA. Development of a chemical genetic approach for human aurora B kinase identifies novel substrates of the chromosomal passenger complex. Mol Cell Proteomics 2012; 11:47-59. [PMID: 22267324 DOI: 10.1074/mcp.m111.013912] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
To understand how the chromosomal passenger complex ensures chromosomal stability, it is crucial to identify its substrates and to find ways to specifically inhibit the enzymatic core of the complex, Aurora B. We therefore developed a chemical genetic approach to selectively inhibit human Aurora B. By mutating the gatekeeper residue Leu-154 in the kinase active site, the ATP-binding pocket was enlarged, but kinase function was severely disrupted. A unique second site suppressor mutation was identified that rescued kinase activity in the Leu-154 mutant and allowed the accommodation of bulky N(6)-substituted adenine analogs. Using this analog-sensitive Aurora B kinase, we found that retention of the chromosomal passenger complex at the centromere depends on Aurora B kinase activity. Furthermore, analog-sensitive Aurora B was able to use bulky ATPγS analogs and could thiophosphorylate multiple proteins in cell extracts. Utilizing an unbiased approach for kinase substrate mapping, we identified several novel substrates of Aurora B, including the nucleosomal-binding protein HMGN2. We confirmed that HMGN2 is a bona fide Aurora B substrate in vivo and show that its dynamic association to chromatin is controlled by Aurora B.
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Affiliation(s)
- Rutger C C Hengeveld
- Department of Medical Oncology, University Medical Center, 3584 CG Utrecht, The Netherlands
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