scholarly journals Label-Free Proteome Profiling as a Quantitative Target Identification Technique for Bioactive Small Molecules

Biochemistry ◽  
2019 ◽  
Vol 59 (3) ◽  
pp. 213-215
Author(s):  
Kyung Tae Hong ◽  
Jun-Seok Lee
Keyword(s):  
Small Molecules ◽  
Target Identification ◽  
Label Free ◽  
Proteome Profiling ◽  
Identification Technique

scholarly journals Developments of bioorthogonal handle-containing photo-crosslinkers for photoaffinity labeling

MedChemComm ◽  
2017 ◽  
Vol 8 (8) ◽  
pp. 1585-1591 ◽  
Author(s):  
Haijun Guo ◽  
Zhengqiu Li
Keyword(s):  
Small Molecules ◽  
Target Identification ◽  
Photoaffinity Labeling ◽  
Proteome Profiling

“Minimalist” photo-crosslinkers (L3–L6) applied in affinity-based proteome profiling and bioimaging for target identification of small molecules.

Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50–1000 Mammalian Cells

2021 ◽  
Author(s):  
Kendall Martin ◽  
Tong Zhang ◽  
Tai-Tu Lin ◽  
Amber N. Habowski ◽  
Rui Zhao ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Label Free ◽  
One Pot ◽  
Proteome Profiling

scholarly journals Volumetric registration of magnetic nanoparticles for optimization of quantitative immunochromatographic assays for detection of small molecules

2018 ◽  
Vol 185 ◽  
pp. 10006 ◽  
Author(s):  
Natalia V. Guteneva ◽  
Sergey L. Znoyko ◽  
Alexey V. Orlov ◽  
Maxim P. Nikitin ◽  
Petr I. Nikitin
Keyword(s):  
Magnetic Nanoparticles ◽  
Small Molecules ◽  
Optical Methods ◽  
Magnetic Method ◽  
Label Free ◽  
Spectral Correlation ◽  
Entire Volume ◽  
Specificity And Sensitivity ◽  
Particle Quantification

Precise quantitative and highly sensitive detection of small molecules (haptens) is highly demanded in medicine, food quality control, in vitro diagnostics, criminalistics, environmental monitoring, etc. In the present work, the magnetic method of particle quantification and the optical methods of spectral correlation and spectral phase interferometry complement each other for optimization of a quantitative assay for measuring concentrations of small molecules. The assay employs magnetic nanoparticles as labels in rapid immunochromatographic format. The approach was demonstrated with fluorescein as a model molecule. The interferometric label-free biosensors were employed for selection of optimal reagents that produced high specificity and sensitivity. The method of magnetic particle quantification counted the magnetic labels over the entire volume of the immunochromatographic membrane to provide their distribution along the test strip. Such distribution was used for optimization of such parameters as concentrations of the used reagents and of antibody immobilized on the labels, amount of the labels and conjugates of haptens with protein carriers to realize the advanced quantitative immunochromatographic assay.

scholarly journals A Simple Displacement Aptamer Assay on Resistive Pulse Sensor for Small Molecule Detection

2020 ◽  
Author(s):  
Rhushabh Maugi ◽  
bernadette gamble ◽  
david bunka ◽  
Mark Platt
Keyword(s):  
Small Molecules ◽  
Small Molecule ◽  
Label Free ◽  
Resistive Pulse ◽  
Pulse Sensor ◽  
Label Free Detection ◽  
Ssdna Aptamer ◽  
Aptamer Assay ◽  
Small Molecule Detection ◽  
Surface Changes

A universal aptamer-based sensing strategy is proposed using DNA modified nanocarriers and Resistive Pulse Sensing for the rapid and label free detection of small molecules. The surface of a magnetic nanocarrier was first modified with a ssDNA aka linker which is designed to be partially complimentary in sequence to a ssDNA aptamer. The aptamer and linker form a stable dsDNA complex on the nanocarriers surface. Upon the addition of the target molecule, a conformational change takes place where the aptamer preferentially binds to the target over the linker; causing the aptamer to be released into solution. The RPS measures the change in velocity of the nanocarrier as its surface changes from dsDNA to ssDNA, and its velocity is used as a proxy for the concentration of the target. We illustrate the versatility of the assay by demonstrating the detection of the antibiotic Moxifloxacin, and chemotherapeutics Imatinib and Irinotecan.

scholarly journals Identification of Celecoxib targeted proteins using label-free thermal proteome profiling on rat hippocampus

2020 ◽  
Author(s):  
Elham Gholizadeh ◽  
Reza karbalaei ◽  
Ali Khaleghian ◽  
Mona Salimi ◽  
Ziaurrehman Tanoli ◽  
...  
Keyword(s):  
Rat Hippocampus ◽  
Label Free ◽  
Proteome Profiling

scholarly journals A New Big-Data Paradigm for Target Identification and Drug Discovery

2017 ◽  
Author(s):  
Neel S. Madhukar ◽  
Prashant K. Khade ◽  
Linda Huang ◽  
Kaitlyn Gayvert ◽  
Giuseppe Galletti ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Small Molecules ◽  
Clinical Application ◽  
Small Molecule ◽  
Target Identification ◽  
Clinical Development ◽  
Data Types ◽  
Public Data ◽  
Drug Target Identification ◽  
Approved Drugs

AbstractDrug target identification is one of the most important aspects of pre-clinical development yet it is also among the most complex, labor-intensive, and costly. This represents a major issue, as lack of proper target identification can be detrimental in determining the clinical application of a bioactive small molecule. To improve target identification, we developed BANDIT, a novel paradigm that integrates multiple data types within a Bayesian machine-learning framework to predict the targets and mechanisms for small molecules with unprecedented accuracy and versatility. Using only public data BANDIT achieved an accuracy of approximately 90% over 2000 different small molecules – substantially better than any other published target identification platform. We applied BANDIT to a library of small molecules with no known targets and generated ∼4,000 novel molecule-target predictions. From this set we identified and experimentally validated a set of novel microtubule inhibitors, including three with activity on cancer cells resistant to clinically used anti-microtubule therapies. We next applied BANDIT to ONC201 – an active anti- cancer small molecule in clinical development – whose target has remained elusive since its discovery in 2009. BANDIT identified dopamine receptor 2 as the unexpected target of ONC201, a prediction that we experimentally validated. Not only does this open the door for clinical trials focused on target-based selection of patient populations, but it also represents a novel way to target GPCRs in cancer. Additionally, BANDIT identified previously undocumented connections between approved drugs with disparate indications, shedding light onto previously unexplained clinical observations and suggesting new uses of marketed drugs. Overall, BANDIT represents an efficient and highly accurate platform that can be used as a resource to accelerate drug discovery and direct the clinical application of small molecule therapeutics with improved precision.

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 Identification and Validation of VEGFR2 Kinase as a Target of Voacangine by a Systematic Combination of DARTS and MSI

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 508 ◽  
Author(s):  
Yonghyo Kim ◽  
Yutaka Sugihara ◽  
Tae Young Kim ◽  
Sung Min Cho ◽  
Jin Young Kim ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Compound ◽  
Target Identification ◽  
Growth Factor Receptor ◽  
Docking Simulation ◽  
Kinase Domain ◽  
Label Free ◽  
Downstream Signaling ◽  
Systematic Strategy ◽  
Specific Localization

Although natural products are an important source of drugs and drug leads, identification and validation of their target proteins have proven difficult. Here, we report the development of a systematic strategy for target identification and validation employing drug affinity responsive target stability (DARTS) and mass spectrometry imaging (MSI) without modifying or labeling natural compounds. Through a validation step using curcumin, which targets aminopeptidase N (APN), we successfully standardized the systematic strategy. Using label-free voacangine, an antiangiogenic alkaloid molecule as the model natural compound, DARTS analysis revealed vascular endothelial growth factor receptor 2 (VEGFR2) as a target protein. Voacangine inhibits VEGFR2 kinase activity and its downstream signaling by binding to the kinase domain of VEGFR2, as was revealed by docking simulation. Through cell culture assays, voacangine was found to inhibit the growth of glioblastoma cells expressing high levels of VEGFR2. Specific localization of voacangine to tumor compartments in a glioblastoma xenograft mouse was revealed by MSI analysis. The overlap of histological images with the MSI signals for voacangine was intense in the tumor regions and showed colocalization of voacangine and VEGFR2 in the tumor tissues by immunofluorescence analysis of VEGFR2. The strategy employing DARTS and MSI to identify and validate the targets of a natural compound as demonstrated for voacangine in this study is expected to streamline the general approach of drug discovery and validation using other biomolecules including natural products.

Sign in / Sign up

Export Citation Format

Share Document