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Cancer Cell Jul 2017Small-molecule chemical probes or tools have become progressively more important in recent years as valuable reagents to investigate fundamental biological mechanisms... (Review)
Review
Small-molecule chemical probes or tools have become progressively more important in recent years as valuable reagents to investigate fundamental biological mechanisms and processes causing disease, including cancer. Chemical probes have also achieved greater prominence alongside complementary biological reagents for target validation in drug discovery. However, there is evidence of widespread continuing misuse and promulgation of poor-quality and insufficiently selective chemical probes, perpetuating a worrisome and misleading pollution of the scientific literature. We discuss current challenges with the selection and use of chemical probes, and suggest how biologists can and should be more discriminating in the probes they employ.
Topics: Humans; Molecular Probes; Neoplasms; Research Design
PubMed: 28697345
DOI: 10.1016/j.ccell.2017.06.005 -
Chemistry (Weinheim An Der Bergstrasse,... Oct 2022Discovery of protein-binding fragments for precisely defined binding sites is an unmet challenge to date. Herein, formylglycine is investigated as a molecular probe for...
Discovery of protein-binding fragments for precisely defined binding sites is an unmet challenge to date. Herein, formylglycine is investigated as a molecular probe for the sensitive detection of fragments binding to a spatially defined protein site . Formylglycine peptide 3 was derived from a phosphotyrosine-containing peptide substrate of protein tyrosine phosphatase PTP1B by replacing the phosphorylated amino acid with the reactive electrophile. Fragment ligation with formylglycine occurred in situ in aqueous physiological buffer. Structures and kinetics were validated by NMR spectroscopy. Screening and hit validation revealed fluorinated and non-fluorinated hit fragments being able to replace the native phosphotyrosine residue. The formylglycine probe identified low-affinity fragments with high spatial resolution as substantiated by molecular modelling. The best fragment hit, 4-amino-phenyl-acetic acid, was converted into a cellularly active, nanomolar inhibitor of the protein tyrosine phosphatase SHP2.
Topics: Acetates; Amino Acids; Binding Sites; Glycine; Molecular Probes; Peptides; Phosphotyrosine
PubMed: 35781901
DOI: 10.1002/chem.202201282 -
Annual Review of Physical Chemistry Apr 2015Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to... (Review)
Review
Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.
Topics: Animals; Humans; Models, Molecular; Molecular Probes; Protein Conformation; Proteins; Spectrophotometry, Infrared
PubMed: 25580624
DOI: 10.1146/annurev-physchem-040214-121802 -
Annual Review of Analytical Chemistry... Jun 2017Since its discovery in 1974, surface-enhanced Raman scattering (SERS) has gained momentum as an important tool in analytical chemistry. SERS is used widely for analysis... (Review)
Review
Since its discovery in 1974, surface-enhanced Raman scattering (SERS) has gained momentum as an important tool in analytical chemistry. SERS is used widely for analysis of biological samples, ranging from in vitro cell culture models, to ex vivo tissue and blood samples, and direct in vivo application. New insights have been gained into biochemistry, with an emphasis on biomolecule detection, from small molecules such as glucose and amino acids to larger biomolecules such as DNA, proteins, and lipids. These measurements have increased our understanding of biological systems, and significantly, they have improved diagnostic capabilities. SERS probes display unique advantages in their detection sensitivity and multiplexing capability. We highlight key considerations that are required when performing bioanalytical SERS measurements, including sample preparation, probe selection, instrumental configuration, and data analysis. Some of the key bioanalytical measurements enabled by SERS probes with application to in vitro, ex vivo, and in vivo biological environments are discussed.
Topics: Biomarkers; DNA; Humans; Lipids; Molecular Probes; Nanoparticles; Proteins; Spectrum Analysis, Raman
PubMed: 28301754
DOI: 10.1146/annurev-anchem-071015-041557 -
Amino Acids Nov 2011Protein scaffold molecules are powerful reagents for targeting various cell signal receptors, enzymes, cytokines and other cancer-related molecules. They belong to the... (Review)
Review
Protein scaffold molecules are powerful reagents for targeting various cell signal receptors, enzymes, cytokines and other cancer-related molecules. They belong to the peptide and small protein platform with distinct properties. For the purpose of development of new generation molecular probes, various protein scaffold molecules have been labeled with imaging moieties and evaluated both in vitro and in vivo. Among the evaluated probes Affibody molecules and analogs, cystine knot peptides, and nanobodies have shown especially good characteristics as protein scaffold platforms for development of in vivo molecular probes. Quantitative data obtained from positron emission tomography, single photon emission computed tomography/CT, and optical imaging together with biodistribution studies have shown high tumor uptakes and high tumor-to-blood ratios for these probes. High tumor contrast imaging has been obtained within 1 h after injection. The success of those molecular probes demonstrates the adequacy of protein scaffold strategy as a general approach in molecular probe development.
Topics: Animals; Biomarkers, Tumor; Humans; Molecular Imaging; Molecular Probes; Neoplasms; Protein Structure, Secondary; Proteins; Radionuclide Imaging
PubMed: 20174842
DOI: 10.1007/s00726-010-0503-9 -
Chemical Society Reviews Apr 2014"Aggregation-caused signal change" is a well-established mechanism by now and has been widely used as the basis for optical probe and sensor development. Compared to... (Review)
Review
"Aggregation-caused signal change" is a well-established mechanism by now and has been widely used as the basis for optical probe and sensor development. Compared to aggregation, its reverse process, disaggregation, has received much less attention and is not properly discussed in the literature so far. With the less established paradigm or mechanism, although some of the reported sensors and probes seem to work through disaggregation phenomena, the proper interpretation of the results and applying the concept to novel probe development is seriously hampered. The process from aggregation to disaggregation generally causes a recovery or enhancement of fluorescence signals, and thus provides an interesting new path to design "turn-on" probes. This tutorial review will provide the balanced comparison between aggregation and disaggregation mechanism, and focuses on the less explored advantages of "disaggregation" as a novel sensing mechanism and its recent applications in probe development.
Topics: Aptamers, Nucleotide; DNA; Fluorescent Dyes; Metals; Molecular Probes; Nanoparticles
PubMed: 24514005
DOI: 10.1039/c3cs60368g -
Scientific Reports Oct 2020Redox status influences the course of the inflammatory, metabolic, and proliferative liver diseases. Oxidative stress is thought to play a crucial and sustained role in...
Redox status influences the course of the inflammatory, metabolic, and proliferative liver diseases. Oxidative stress is thought to play a crucial and sustained role in the pathological progression of early steatosis to severe hepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. Oxidative stress induced by reactive oxygen species which are generated in the mitochondria can lead to chronic organelle damage in hepatocytes. Currently, the diagnosis of liver disease requires liver biopsy, which is invasive and associated with complications. The present report describes the development of a novel molecular probe, EDA-PROXYL, with higher reactivity and mitochondrial selectivity than standard carboxyl-PROXYL and carbamoyl-PROXYL probes. The membrane permeability of our probe improved in aqueous environments which led to increased accumulation in the liver and interaction of EDA-PROXYL with the carnitine transporter via the amine (NH) group further increased accumulation. This increased mitochondrial sensitivity and enhanced accumulation highlight the potential of EDA-PROXYL as a molecular probe for determining metabolic reactions of the mitochondria. Thus, this novel probe could be a tool for the evaluation of redox status of the mitochondria to assess the degree of liver injury and, ultimately, the response to pharmacological therapy.
Topics: Animals; Carcinoma, Hepatocellular; Hepatocytes; Liver; Liver Cirrhosis; Liver Neoplasms; Male; Mice; Mice, Inbred C57BL; Mitochondria; Molecular Probes; Oxidation-Reduction; Oxidative Stress; Reactive Oxygen Species
PubMed: 33020535
DOI: 10.1038/s41598-020-73336-1 -
BMC Bioinformatics Jun 2019DNA is a promising candidate for the construction of biological devices due to its unique properties, including structural simplicity, convenient synthesis, high...
BACKGROUND
DNA is a promising candidate for the construction of biological devices due to its unique properties, including structural simplicity, convenient synthesis, high flexibility, and predictable behavior. And DNA has been widely used to construct the advanced logic devices.
RESULTS
Herein, a molecular probe apparatus was constructed based on DNA molecular computing to perform fluorescent quenching and fluorescent signal recovery, with an ' ON/OFF' switching function. In this study, firstly, we program the streptavidin-mediated fluorescent quenching apparatus based on short-distance strand migration. The variation of fluorescent signal is acted as output. Then DNAzyme as a switching controller was involved to regulate the fluorescent signal increase. Finally, on this base, a cascade DNA logic gate consists of two logic AND operations was developed to enrich probe machine.
CONCLUSION
The designed probe computing model can be implemented with readout of fluorescence intensity, and exhibits great potential applications in the field of bioimaging as well as disease diagnosis.
Topics: Computer Simulation; DNA; DNA, Catalytic; Fluorescence; Logic; Molecular Probes; Signal Processing, Computer-Assisted; Streptavidin
PubMed: 31182004
DOI: 10.1186/s12859-019-2767-8 -
Molecules (Basel, Switzerland) Jan 2019A G-quadruplex (G4) is a well-known nucleic acid secondary structure comprising guanine-rich sequences, and has profound implications for various pharmacological and... (Review)
Review
A G-quadruplex (G4) is a well-known nucleic acid secondary structure comprising guanine-rich sequences, and has profound implications for various pharmacological and biological events, including cancers. Therefore, ligands interacting with G4s have attracted great attention as potential anticancer therapies or in molecular probe applications. To date, a large variety of DNA/RNA G4 ligands have been developed by a number of laboratories. As protein-targeting drugs face similar situations, G-quadruplex-interacting drugs displayed low selectivity to the targeted G-quadruplex structure. This low selectivity could cause unexpected effects that are usually reasons to halt the drug development process. In this review, we address the recent research on synthetic G4 DNA-interacting ligands that allow targeting of selected G4s as an approach toward the discovery of highly effective anticancer drugs.
Topics: Animals; Antineoplastic Agents; Binding Sites; DNA; Drug Design; G-Quadruplexes; Guanine; Humans; Ligands; Molecular Probes; Molecular Targeted Therapy; Neoplasms; Oncogenes; Structure-Activity Relationship; Telomere
PubMed: 30682877
DOI: 10.3390/molecules24030429 -
Cell Chemical Biology Oct 2017Mitochondrial superoxide (O) underlies much oxidative damage and redox signaling. Fluorescent probes can detect O, but are of limited applicability in vivo, while in...
Mitochondrial superoxide (O) underlies much oxidative damage and redox signaling. Fluorescent probes can detect O, but are of limited applicability in vivo, while in cells their usefulness is constrained by side reactions and DNA intercalation. To overcome these limitations, we developed a dual-purpose mitochondrial O probe, MitoNeoD, which can assess O changes in vivo by mass spectrometry and in vitro by fluorescence. MitoNeoD comprises a O-sensitive reduced phenanthridinium moiety modified to prevent DNA intercalation, as well as a carbon-deuterium bond to enhance its selectivity for O over non-specific oxidation, and a triphenylphosphonium lipophilic cation moiety leading to the rapid accumulation within mitochondria. We demonstrated that MitoNeoD was a versatile and robust probe to assess changes in mitochondrial O from isolated mitochondria to animal models, thus offering a way to examine the many roles of mitochondrial O production in health and disease.
Topics: Animals; Biological Transport; Cell Line; DNA; Male; Mass Spectrometry; Mice; Mitochondria; Models, Molecular; Molecular Probes; Nucleic Acid Conformation; Oxidation-Reduction; Superoxides
PubMed: 28890317
DOI: 10.1016/j.chembiol.2017.08.003