A5065929661- Monoclonal and Polyclonal Antibodies Research
- Click Chemistry and Applications
- Chemical Synthesis and Analysis
- Epigenetics and DNA Methylation
- Advanced biosensing and bioanalysis techniques
- Cancer-related gene regulation
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Cancer Cells and Metastasis
- Biotin and Related Studies
- RNA and protein synthesis mechanisms
- Autophagy in Disease and Therapy
- Metabolism, Diabetes, and Cancer
- Analytical Chemistry and Chromatography
- RNA modifications and cancer
- Kruppel-like factors research
- Advanced Biosensing Techniques and Applications
- Receptor Mechanisms and Signaling
- Mast cells and histamine
- Computational Drug Discovery Methods
- RNA Interference and Gene Delivery
- Synthesis and Biological Evaluation
- Synthetic Organic Chemistry Methods
- Genomics and Chromatin Dynamics
- Amino Acid Enzymes and Metabolism
Purdue University West Lafayette
2016-2025
Center for Cancer Research
2016-2025
University of Minnesota System
2024
Stanford University
2010-2016
University of Wisconsin–Madison
2006-2013
University of Illinois Urbana-Champaign
2008
We report the selection of DNA-encoded small molecule libraries against protein targets within cytosol and on surface live cells. The approach relies generation a covalent linkage DNA to by affinity labeling. This cross-linking event enables subsequent copurification tag recombinant protein. To access cells, cyclic cell-penetrating peptide is appended for delivery across cell membrane. As this assesses binding DELs in it provides strategy challenging that cannot be expressed purified as active.
Abstract The ability of breast cancer cells to transiently transition between epithelial and mesenchymal states contributes their metastatic potential. Therefore, driving tumor into a stable state, as opposed complete cell eradication, presents an opportunity pharmacologically limit disease progression by promoting asymptomatic state dormancy. Here, we compare reversible model epithelial–mesenchymal (EMT) induced TGFβ phenotype chronic exposure the ErbB kinase inhibitor lapatinib. Only...
Polycomb repressive complex 1 (PRC1) is critical for mediating gene expression during development. Five chromobox (CBX) homolog proteins, CBX2, CBX4, CBX6, CBX7, and CBX8, are incorporated into PRC1 complexes, where they mediate targeting to trimethylated lysine 27 of histone H3 (H3K27me3) via the N-terminal chromodomain (ChD). Individual CBX paralogs have been implicated as drug targets in cancer; however, high similarities sequence structure among ChDs provide a major obstacle developing...
Enrichment of DNA-encoded ligands under stringent, protein-denaturing conditions is enabled by crosslinking with electrophilic or photoreactive groups.
G protein-coupled receptors (GPCRs) are the largest superfamily of human membrane target proteins for approved drugs. GPCR ligands can have a complex array pharmacological activities. Among these activities, biased agonists potential to serve as both chemical probes understand specific aspects receptor signaling and therapeutic leads with more specific, desired activity. Challenges exist, however, in development new activators due, part, low throughput traditional screening approaches....
Electrospray ionization (ESI) of denatured proteins produces a broad distribution multiply-charged ions leading to multiple peaks in the mass spectrum. We investigated changes positive-mode ESI charge state produced by several chemical modifications proteins. Capping carboxylic acid groups with neutral functional yields little change compared unmodified The results indicate that carboxyl do not play significant role positive charging ESI. modification additional basic sites or fixed charges...
The identification of protein ligands from a DNA-encoded library is commonly conducted by an affinity selection assay. These assays are often not validated for robustness, raising questions about selections that fail to identify and the utility enrichment values ranking ligand potencies. Here, we report method optimizing utilizing potent selective peptidic highly related chromodomains CBX proteins. To optimize parameters, statistical analyses (Z′ factors) were used define ability assay...
Abstract Polycomb group (PcG) proteins are epigenetic regulators that facilitate both embryonic development and cancer progression. PcG form repressive complexes 1 2 (PRC1 PRC2). PRC2 trimethylates histone H3 lysine 27 (H3K27me3), a mark recognized by the N‐terminal chromodomain (ChD) of CBX subunit canonical PRC1. There five paralogs in humans. CBX2 particular is upregulated variety cancers, particularly advanced prostate cancers. Using inhibitors to understand target highly desirable;...
Nanoluciferase or engineered biotin ligase fusions to a protein target allow proximity-induced biotinylation of DNA-linked ligands. The approach benefits ligand enrichment from DNA-encoded chemical libraries (DELs) and live cell selections.
The carboxyl groups of tryptic peptides were derivatized with a tertiary or quaternary amine labeling reagent to generate more highly charged peptide ions that fragment efficiently by electron transfer dissociation (ETD). All groups-aspartic and glutamic acid side-chains as well C-termini-were an average reaction efficiency 99 %. This nearly complete avoids making complex mixtures even because partially-labeled products, it allows the use static modifications during database searching. Alkyl...
Twin peaks: A facile and economic route has been developed for the incorporation of deuterated benzophenones (a widely used photoaffinity tag) into probes. Attachment these mixed-isotope labels to immunosuppressive drug CsA facilitated mass spectrometric identification a target (see picture) from mixture proteins.
Abstract A sensing approach is applied to encode quantitative enzymatic activity information into DNA sequence populations. The method utilizes DNA‐linked peptide substrates as probes. Signal detection involves chemical manipulation of a probe population downstream sample exposure and application purifying, selective pressure for enzyme products. Selection‐induced changes in abundance indicate activity. protein kinase, protease, farnesyltransferase activities demonstrated. assays were...
The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant billions of chance discovery and refinement compressed into few weeks, provided powerful tool now dominates all aspects protein engineering. A challenge has been to extend this scientific advance synthetic chemical space: enable the directed evolution abiotic molecules. problem tackled many ways. These include expanding natural genetic code unnatural amino...
A sequential reaction methodology is employed for the complete derivatization of protein thiols, amines, and acids in high purity under denaturing conditions. Following standard thiol alkylation, amines are modified via reductive methylation with formaldehyde pyridine-borane. Protein subsequently amidated buffered conditions DMSO using coupling reagent (7-azabenzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate. The generality approach demonstrated four proteins several yielding...
Small-molecule binding assays to target proteins are a core component of drug discovery and development. While number assay formats available, significant drawbacks still remain in cost, sensitivity, throughput. To improve by capitalizing on the power DNA sequence analysis, we have developed an method that combines encoding with split-and-pool sample handling. The approach involves affinity labeling DNA-linked ligands protein target. Critically, event assesses ligand enables subsequent...
Polycomb repressive complexes (PRCs) are a heterogenous collection of dozens, if not hundreds, protein composed various combinations subunits. PRCs transcriptional repressors important for cell-type specificity during development, and as such, commonly mis-regulated in cancer. broadly characterized PRC1 with histone ubiquitin ligase activity, or PRC2 methyltransferase activity; however, the mechanism by which individual PRCs, particularly highly diverse set PRC1s, alter gene expression has...
As aberrant activity of protein kinases is observed in many disease states, these enzymes are common targets for therapeutics and detection levels. The development non-natural kinase substrates offers an approach to substrate competitive inhibitors, a class inhibitors with promise improved specificity. Also, approaches would benefit from Here, we apply substrate-mediated selection peptidomimetic DNA-encoded chemical library enrichment molecules that can be phosphorylated by the tyrosine...
Here, we describe an immunoassay approach for the detection of enzyme activity by quantitative PCR (qPCR) or parallel DNA sequencing which relies on activity-based probes linked to barcoding DNAs. We demonstrate this technique in serine hydrolase activities using a fluorophosphonate-oligonucleotide conjugate.
An engineered, orthogonal ligand receptor pair has been exploited as a method to covalently label fusion proteins with small molecule probes in live cells.
Abstract A sensing approach is applied to encode quantitative enzymatic activity information into DNA sequence populations. The method utilizes DNA‐linked peptide substrates as probes. Signal detection involves chemical manipulation of a probe population downstream sample exposure and application purifying, selective pressure for enzyme products. Selection‐induced changes in abundance indicate activity. protein kinase, protease, farnesyltransferase activities demonstrated. assays were...
Doppelspitze: Eine einfache Methode zum Einbau deuterierter Benzophenone (intensiv genutzte Photoaffinitätsmarker) in Sonden wurde entwickelt. Das Anhängen dieser Gemischtisotopenmarker an das Immunsuppressivum CsA erleichtert die massenspektrometrische Identifizierung eines CsA-Zielmoleküls (siehe Bild) einer Proteinmischung. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z600743_s.pdf or from author. Please note: The...