scholarly journals Streamlined Target Deconvolution Approach Utilizing a Single Photoreactive Chloroalkane Capture Tag

2021 ◽  
Vol 16 (2) ◽  
pp. 404-413
Author(s):  
Rachel Friedman Ohana ◽  
Sergiy Levin ◽  
Robin Hurst ◽  
Michael M. Rosenblatt ◽  
Kristopher Zimmerman ◽  
...  
Keyword(s):  
Target Deconvolution

Suzuki–Miyaura cross-coupling for chemoproteomic applications

2020 ◽  
Author(s):  
Jian Cao ◽  
Ernest Armenta ◽  
Lisa Boatner ◽  
Heta Desai ◽  
Neil Chan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cross Coupling ◽  
Protein Profiling ◽  
Protein Labeling ◽  
Caspase 8 ◽  
Complex Cell ◽  
Bioorthogonal Chemistry ◽  
Reaction Conditions ◽  
Target Deconvolution ◽  
Palladium Catalyzed

Bioorthogonal chemistry is a mainstay of chemoproteomic sample preparation workflows. While numerous transformations are now available, chemoproteomic studies still rely overwhelmingly on copper-catalyzed azide –alkyne cycloaddition (CuAAC) or 'click' chemistry. Here we demonstrate that gel-based activity-based protein profiling (ABPP) and mass-spectrometry-based chemoproteomic profiling can be conducted using Suzuki–Miyaura cross-coupling. We identify reaction conditions that proceed in complex cell lysates and find that Suzuki –Miyaura cross-coupling and CuAAC yield comparable chemoproteomic coverage. Importantly, Suzuki–Miyaura is also compatible with chemoproteomic target deconvolution, as demonstrated using structurally matched probes tailored to react with the cysteine protease caspase-8. Uniquely enabled by the observed orthogonality of palladium-catalyzed cross-coupling and CuAAC, we combine both reactions to achieve dual protein labeling.

scholarly journals Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth

2019 ◽  
Vol 5 (1) ◽  
pp. eaau9060 ◽  
Author(s):  
Tsuyoshi Oshima ◽  
Yoshimi Niwa ◽  
Keiko Kuwata ◽  
Ashutosh Srivastava ◽  
Tomoko Hyoda ◽  
...  
Keyword(s):  
Cell Growth ◽  
Circadian Clock ◽  
Cancer Cell ◽  
Direct Interaction ◽  
Cancer Cell Growth ◽  
X Ray ◽  
Clock Proteins ◽  
Target Deconvolution ◽  
Phenotypic Screen ◽  
Dependent Inhibition

Compounds targeting the circadian clock have been identified as potential treatments for clock-related diseases, including cancer. Our cell-based phenotypic screen revealed uncharacterized clock-modulating compounds. Through affinity-based target deconvolution, we identified GO289, which strongly lengthened circadian period, as a potent and selective inhibitor of CK2. Phosphoproteomics identified multiple phosphorylation sites inhibited by GO289 on clock proteins, including PER2 S693. Furthermore, GO289 exhibited cell type–dependent inhibition of cancer cell growth that correlated with cellular clock function. The x-ray crystal structure of the CK2α-GO289 complex revealed critical interactions between GO289 and CK2-specific residues and no direct interaction of GO289 with the hinge region that is highly conserved among kinases. The discovery of GO289 provides a direct link between the circadian clock and cancer regulation and reveals unique design principles underlying kinase selectivity.

scholarly journals Chemoproteomics-based kinome profiling and target deconvolution of clinical multi-kinase inhibitors in primary chronic lymphocytic leukemia cells

Leukemia ◽  
2010 ◽  
Vol 25 (1) ◽  
pp. 89-100 ◽  
Author(s):  
U Kruse ◽  
C P Pallasch ◽  
M Bantscheff ◽  
D Eberhard ◽  
L Frenzel ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Kinase Inhibitors ◽  
Lymphocytic Leukemia ◽  
Leukemia Cells ◽  
Target Deconvolution ◽  
Primary Chronic Lymphocytic Leukemia

A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates

2017 ◽  
pp. 1-18 ◽  
Author(s):  
Jason R. Thomas ◽  
Scott M. Brittain ◽  
Jennifer Lipps ◽  
Luis Llamas ◽  
Rishi K. Jain ◽  
...  
Keyword(s):  
Small Molecule ◽  
Photoaffinity Labeling ◽  
Drug Candidates ◽  
Small Molecule Drug ◽  
Target Deconvolution

Drug Target Identification in Tissues by Thermal Proteome Profiling

2021 ◽  
Vol 62 (1) ◽  
Author(s):  
André Mateus ◽  
Nils Kurzawa ◽  
Jessica Perrin ◽  
Giovanna Bergamini ◽  
Mikhail M. Savitski
Keyword(s):  
Drug Target ◽  
Target Identification ◽  
Annual Review ◽  
Publication Date ◽  
Proteome Profiling ◽  
Biological Phenomena ◽  
Target Deconvolution ◽  
Drug Target Identification ◽  
Recent Developments ◽  
Fundamental Biology

Drug target deconvolution can accelerate the drug discovery process by identifying a drug's targets (facilitating medicinal chemistry efforts) and off-targets (anticipating toxicity effects or adverse drug reactions). Multiple mass spectrometry–based approaches have been developed for this purpose, but thermal proteome profiling (TPP) remains to date the only one that does not require compound modification and can be used to identify intracellular targets in living cells. TPP is based on the principle that the thermal stability of a protein can be affected by its interactions. Recent developments of this approach have expanded its applications beyond drugs and cell cultures to studying protein-drug interactions and biological phenomena in tissues. These developments open up the possibility of studying drug treatment or mechanisms of disease in a holistic fashion, which can result in the design of better drugs and lead to a better understanding of fundamental biology. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Exploiting polypharmacology for drug target deconvolution

2014 ◽  
Vol 111 (13) ◽  
pp. 5048-5053 ◽  
Author(s):  
Taranjit Singh Gujral ◽  
Leonid Peshkin ◽  
Marc W. Kirschner
Keyword(s):  
Drug Target ◽  
Target Deconvolution

Epigenetic drug target deconvolution by mass spectrometry–based technologies

2019 ◽  
Vol 26 (10) ◽  
pp. 854-857 ◽  
Author(s):  
Roberta Noberini ◽  
Tiziana Bonaldi
Keyword(s):  
Mass Spectrometry ◽  
Drug Target ◽  
Target Deconvolution ◽  
Epigenetic Drug

scholarly journals From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5702
Author(s):  
Quentin T. L. Pasquer ◽  
Ioannis A. Tsakoumagkos ◽  
Sascha Hoogendoorn
Keyword(s):  
Small Molecules ◽  
Chemical Biology ◽  
Target Identification ◽  
Biologically Active ◽  
Phenotypic Screening ◽  
Biological Processes ◽  
Chemical Probes ◽  
Target Deconvolution ◽  
Cellular Target ◽  
Screening Approaches

Biologically active small molecules have a central role in drug development, and as chemical probes and tool compounds to perturb and elucidate biological processes. Small molecules can be rationally designed for a given target, or a library of molecules can be screened against a target or phenotype of interest. Especially in the case of phenotypic screening approaches, a major challenge is to translate the compound-induced phenotype into a well-defined cellular target and mode of action of the hit compound. There is no “one size fits all” approach, and recent years have seen an increase in available target deconvolution strategies, rooted in organic chemistry, proteomics, and genetics. This review provides an overview of advances in target identification and mechanism of action studies, describes the strengths and weaknesses of the different approaches, and illustrates the need for chemical biologists to integrate and expand the existing tools to increase the probability of evolving screen hits to robust chemical probes.

scholarly journals The Role of Historical Bioactivity Data in the Deconvolution of Phenotypic Screens

2014 ◽  
Vol 19 (5) ◽  
pp. 696-706 ◽  
Author(s):  
Aurelie Bornot ◽  
Carolyn Blackett ◽  
Ola Engkvist ◽  
Clare Murray ◽  
Claus Bendtsen
Keyword(s):  
Small Molecule ◽  
Large Scale ◽  
Enrichment Analysis ◽  
Large Set ◽  
Phenotypic Response ◽  
Target Deconvolution ◽  
Small Molecule Compound ◽  
Genetic Compensation ◽  
Complex Target ◽  
Factor Α

A substantial challenge in phenotypic drug discovery is the identification of the molecular targets that govern a phenotypic response of interest. Several experimental strategies are available for this, the so-called target deconvolution process. Most of these approaches exploit the affinity between a small-molecule compound and its putative targets or use large-scale genetic manipulations and profiling. Each of these methods has strengths but also limitations such as bias toward high-affinity interactions or risks from genetic compensation. The use of computational methods for target and mechanism of action identification is a complementary approach that can influence each step of a phenotypic screening campaign. Here, we describe how cheminformatics and bioinformatics are embedded in the process from initial selection of a focused compound library from a large set of historical small-molecule screens through the analysis of screening results. We present a deconvolution method based on enrichment analysis and using known bioactivity data of screened compounds to infer putative targets, pathways, and biological processes that are consistent with the observed phenotypic response. As an example, the approach is applied to a cellular screen aiming at identifying inhibitors of tumor necrosis factor–α production in lipopolysaccharide-stimulated THP-1 cells. In summary, we find that the approach can contribute to solving the often very complex target deconvolution task.

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