Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.
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http://dx.doi.org/10.4155/fmc-2016-0059 | DOI Listing |
J Am Chem Soc
January 2025
State Key Laboratory of Molecular Reaction Dynamics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
Directly probing the heterogeneous conformations of intracellular proteins within their native cellular environment remains a significant challenge in mass spectrometry (MS). Here, we establish an in-cell MS and ultraviolet photodissociation (UVPD) strategy that directly ejects proteins from living cells into a mass spectrometer, followed by 193 nm UVPD for structural analysis. Applying this approach to calmodulin (CaM), we reveal that it adopts more extended conformations within living cells compared with purified samples , highlighting the unique influence of intracellular environments on protein folding.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, P. R. China.
Host-guest supramolecular fluorescence probes have garnered significant attention in the detection and sensing of bioactive molecules due to their functionalization potential, adjustable physical properties, and high specificity. However, such probes that reliably, rapidly, and specifically measure neurotransmitter dynamics at the cellular and in vivo level have yet to be reported. Herein, we present a supramolecular fluorescent chemosensor designed for norepinephrine (NE) detection, showing an exceptional response and specificity through host-guest complexation.
View Article and Find Full Text PDFBioanalysis
January 2025
College of Chemistry, Beijing University of Chemical Technology, Beijing, China.
Ultrasmall and highly fluorescent gold nanoclusters (Au NCs) have been widely used for the construction of sensing and imaging platforms. Specifically, through a combination of surface functionalization and spectral analysis and/or imaging techniques, effective intracellular detection and imaging are realized. In this review, we summarize the recently adopted intracellular analysis and imaging events with Au NCs-based probes.
View Article and Find Full Text PDFAnal Chem
January 2025
Key Laboratory of Organosilicon Chemistry and Materials Technology of the Ministry of Education, Zhejiang Key Laboratory of Organosilicon Material Technology, College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China.
As many treatments kill tumor cells by inducing apoptosis, fluorescent probes that can detect apoptosis are crucial for effective feedback regarding tumor therapy outcomes (in particular, activatable probes for better imaging). Cathepsins are enzymes that are released from lysosomes into the cytoplasm during lysosomal membrane permeabilization-induced apoptosis of many tumor cells, making them potential biomarkers of apoptotic cells. Despite their potential, to the best of our knowledge, no cathepsin-activatable fluorescent probes have been reported for this purpose.
View Article and Find Full Text PDFAnal Chem
January 2025
School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China.
PIWI-interacting RNAs (piRNAs) are a class of small noncoding RNAs associated with PIWI proteins within the male germline, and they play significant roles in maintaining genome stability via the modulation of gene expression. The piRNAs are implicated in the progression of various cancers, but the simultaneous monitoring of multiple piRNAs remains a challenge. Herein, we construct a single-molecule biosensor based on polymerization-transcription-mediated target regeneration for the simultaneous one-pot detection of multiple piRNAs.
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