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Biological & Pharmaceutical Bulletin 2017In vivo molecular imaging is the visualization, characterization, and measurement of biological processes at the molecular and cellular levels in humans and other living... (Review)
Review
In vivo molecular imaging is the visualization, characterization, and measurement of biological processes at the molecular and cellular levels in humans and other living systems. Among the methodologies used in in vivo molecular imaging, two methodologies are of great interest from the view of high sensitivity. One is nuclear medical imaging, and distribution and kinetics of a radiolabeled molecular probe are measured using positron emission tomography (PET) and single-photon emission computed tomography (SPECT). The other is optical molecular imaging, and distribution and kinetics of a fluorescent probe are measured using a fluorescent imaging instrument. In this review, the development of imaging probes for these two methodologies is briefly discussed. In nuclear medical molecular imaging, based on structure-activity-biodistribution relationship studies for small molecule and the concept of "functional unit-binding multifunctional molecular probe" containing 3 functional units (target recognition unit, signal-releasing unit, linker unit) for peptides and proteins, we developed radiolabeled probes with high and specific accumulation to the target for neuroreceptors, β-amyloid plaques, and tau aggregates in the brain, tumors, atherosclerotic plaques, pancreatic β-cell, myocardial sympathetic nerves, and so on. We also discuss the progression of molecular imaging toward therapy (radiotheranotics). In in vivo optical molecular imaging, taking into account the characteristics of optical imaging, we designed tumor-specific optical imaging probes with characteristic imaging mechanism, including near-infrared (NIR) fluorescent probes and activatable probes. Furthermore, we developed a photoacoustic imaging probe, which enables highly sensitive and high-resolution imaging in deep tissues.
Topics: Animals; Fluorescent Dyes; Humans; Molecular Imaging; Molecular Probes
PubMed: 28966233
DOI: 10.1248/bpb.b17-00505 -
Cell Chemical Biology Aug 2020Dynamic proteins perform critical roles in cellular machines, including those that control proteostasis, transcription, translation, and signaling. Thus, dynamic... (Review)
Review
Dynamic proteins perform critical roles in cellular machines, including those that control proteostasis, transcription, translation, and signaling. Thus, dynamic proteins are prime candidates for chemical probe and drug discovery but difficult targets because they do not conform to classical rules of design and screening. Selectivity is pivotal for candidate probe molecules due to the extensive interaction network of these dynamic hubs. Recognition that the traditional rules of probe discovery are not necessarily applicable to dynamic proteins and their complexes, as well as technological advances in screening, have produced remarkable results in the last 2-4 years. Particularly notable are the improvements in target selectivity for small-molecule modulators of dynamic proteins, especially with techniques that increase the discovery likelihood of allosteric regulatory mechanisms. We focus on approaches to small-molecule screening that appear to be more suitable for highly dynamic targets and have the potential to streamline identification of selective modulators.
Topics: Allosteric Regulation; CREB-Binding Protein; HSP70 Heat-Shock Proteins; Models, Molecular; Molecular Probes; Protein Binding; Proteins; Small Molecule Libraries
PubMed: 32783965
DOI: 10.1016/j.chembiol.2020.07.019 -
Cell Chemical Biology Apr 2020Ferroptosis is a recently described form of cell death driven by iron-dependent lipid peroxidation. This type of cell death was first observed in response to treatment... (Review)
Review
Ferroptosis is a recently described form of cell death driven by iron-dependent lipid peroxidation. This type of cell death was first observed in response to treatment of tumor cells with a small-molecule chemical probe named erastin. Most subsequent advances in understanding the mechanisms governing ferroptosis involved the use of genetic screens and small-molecule probes. We describe herein the utility and limitations of chemical probes that have been used to analyze and perturb ferroptosis, as well as mechanistic studies of ferroptosis that benefitted from the use of these probes and genetic screens. We also suggest probes for ferroptosis and highlight mechanistic questions surrounding this form of cell death that will be a high priority for exploration in the future.
Topics: Amino Acid Transport System y+; Energy Metabolism; Ferroptosis; Humans; Iron; Lipid Peroxidation; Molecular Probes; Neoplasms; Phospholipid Hydroperoxide Glutathione Peroxidase; Signal Transduction
PubMed: 32294465
DOI: 10.1016/j.chembiol.2020.03.013 -
Molecules (Basel, Switzerland) Jan 2021A molecular probe with l-phenylalanine -nitroanilide and l-lysin 4-methylcoumaryl-7-amide, in which these amino acid derivatives are connected through a succinic-acid...
A molecular probe with l-phenylalanine -nitroanilide and l-lysin 4-methylcoumaryl-7-amide, in which these amino acid derivatives are connected through a succinic-acid spacer, was prepared. Trypsin and papain were detected by blue-fluorescence emission of generated 7-amino-4-methylcoumarin (AMC). α-Chymotrypsin and nattokinase were detected from both the blue-fluorescence emission of AMC and the UV absorbance of -nitroaniline. In addition, different time courses of -nitroaniline and AMC were observed between the reaction of with α-chymotrypsin and that with nattokinase. In the case of nattokinase, both the fluorescence emission and UV absorbance slowly increased. In contrast, the increasing UV absorbance was saturated at the early stage of the reaction of the present probe with chymotrypsin, whereas the fluorescence emission continuously increased in the following stages.
Topics: Aniline Compounds; Chymotrypsin; Fluorescent Dyes; Humans; Molecular Probes; Papain; Trypsin
PubMed: 33477543
DOI: 10.3390/molecules26020482 -
Theranostics 2022Exploring and understanding the interaction of changes in the activities of various enzymes, such as proteases, phosphatases, and oxidoreductases with tumor invasion,... (Review)
Review
Exploring and understanding the interaction of changes in the activities of various enzymes, such as proteases, phosphatases, and oxidoreductases with tumor invasion, proliferation, and metastasis is of great significance for early cancer diagnosis. To detect the activity of tumor-related enzymes, various molecular probes have been developed with different imaging methods, including optical imaging, photoacoustic imaging (PAI), magnetic resonance imaging, positron emission tomography, and so on. In this review, we first describe the biological functions of various enzymes and the selectively recognized chemical linkers or groups. Subsequently, we systematically summarize the design mechanism of imaging probes and different imaging methods. Finally, we explore the challenges and development prospects in the field of enzyme activity detection. This comprehensive review will provide more insight into the design and development of enzyme activated molecular probes.
Topics: Humans; Molecular Imaging; Molecular Probes; Neoplasms; Optical Imaging; Photoacoustic Techniques; Tomography, X-Ray Computed
PubMed: 35154500
DOI: 10.7150/thno.66676 -
Proceedings of the National Academy of... Aug 2023Trehalose plays a crucial role in the survival and virulence of the deadly human pathogen (). The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the sole...
Trehalose plays a crucial role in the survival and virulence of the deadly human pathogen (). The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the sole pathway for trehalose to enter . The substrate-binding protein, LpqY, which forms a stable complex with the translocator SugABC, recognizes and captures trehalose and its analogues in the periplasmic space, but the precise molecular mechanism for this process is still not well understood. This study reports a 3.02-Å cryoelectron microscopy structure of trehalose-bound LpqY-SugABC in the pretranslocation state, a crystal structure of LpqY in a closed form with trehalose bound and five crystal structures of LpqY in complex with different trehalose analogues. These structures, accompanied by substrate-stimulated ATPase activity data, reveal how LpqY recognizes and binds trehalose and its analogues, and highlight the flexibility in the substrate binding pocket of LpqY. These data provide critical insights into the design of trehalose analogues that could serve as potential molecular probe tools or as anti-TB drugs.
Topics: Humans; Cryoelectron Microscopy; Mycobacterium tuberculosis; Trehalose; ATP-Binding Cassette Transporters; Molecular Probes
PubMed: 37603751
DOI: 10.1073/pnas.2307625120 -
The Analyst Nov 2021We have designed and synthesized a multifunctional dendritic molecular probe that selectively detects Cu ions potentiometric and fluorometric techniques with low...
We have designed and synthesized a multifunctional dendritic molecular probe that selectively detects Cu ions potentiometric and fluorometric techniques with low detection limits (3.5 μM in potentiometry, 15 nM in fluorometry). The selective and reversible binding of the molecule with the Cu ion was used to make a solid-state microsensor (diameter of 25 μm) by incorporating the molecular probe into the carbon-based membrane as an ionophore for Cu(II). The Cu(II) microelectrode has a broad linear range of 10 μM to 1 mM with a near Nernstian slope of 30 mV/log [] and detection limit of 3.5 μM. The Cu(II) microsensor has a fast response time (1.5 s), and it has a broad working pH range from 3.5 to 6.0. The incorporation of the hydrophobic dendritic moiety makes the ionophore less prone to leaching in an aqueous matrix for potentiometric measurement. The cinnamaldehyde component of the molecule helps detection of Cu ions fluorometrically, as indicated by a change in fluorescence upon selective and reversible binding of the molecular probe to the Cu ions. The strategic design of the molecular probe allows us to detect Cu ions in drinking water by using this novel dendritic fluoroionophore and solid-state Cu - ion-selective microelectrode.
Topics: Drinking Water; Fluorometry; Ions; Molecular Probes; Potentiometry
PubMed: 34591042
DOI: 10.1039/d1an01417j -
Chembiochem : a European Journal of... Apr 2021RNA molecules can fold into complex two- and three-dimensional shapes that are critical for their function. Chemical probes have long been utilized to interrogate RNA... (Review)
Review
RNA molecules can fold into complex two- and three-dimensional shapes that are critical for their function. Chemical probes have long been utilized to interrogate RNA structure and are now considered invaluable resources in the goal of relating structure to function. Recently, the power of deep sequencing and careful chemical probe design have merged, permitting researchers to obtain a holistic understanding of how RNA structure can be utilized to control RNA biology transcriptome-wide. Within this review, we outline the recent advancements in chemical probe design for interrogating RNA structures inside cells and discuss the recent advances in our understanding of RNA biology through the lens of chemical probing.
Topics: DNA Adducts; DNA, Complementary; Molecular Probes; Nucleic Acid Conformation; RNA; RNA, Messenger; Transcriptome
PubMed: 32737940
DOI: 10.1002/cbic.202000340 -
Theranostics 2023Lipid droplets (LDs) are critical organelles associated with many physiological processes in eukaryotic cells. To visualize and study LDs, fluorescence imaging...
Lipid droplets (LDs) are critical organelles associated with many physiological processes in eukaryotic cells. To visualize and study LDs, fluorescence imaging techniques including the confocal imaging as well as the emerging super-resolution imaging of stimulated emission depletion (STED), have been regarded as the most useful methods. However, directly limited by the availability of advanced LDs fluorescent probes, the performances of LDs fluorescence imaging are increasingly unsatisfied with respect to the fast research progress of LDs. We herein newly developed a superior LDs fluorescent probe named as a powerful tool for LDs fluorescence imaging and biological study. Colocalization imaging of and LDs fluorescent probe Ph-Red was conducted in four cell lines. The LDs staining selectivity and the photostability of were also evaluated by comparing with the commercial LDs probe Nile Red. The in-situ fluorescence lifetime of in LDs was determined by time-gated detection. The cytotoxicity of was assessed by MTT assay. The STED saturation intensity as well as the power- and gate time-dependent resolution were tested by Leica SP8 STED super-resolution nanoscopy. The time-lapse 3D confocal imaging and time-lapse STED super-resolution imaging were then designed to study the complex physiological functions of LDs. Featuring with the advantages of the super-photostability, high LDs selectivity, long fluorescence lifetime and low STED saturation intensity, the fluorescent probe was capable of the long-term time-lapse three-dimensional (3D) confocal imaging to in-situ monitor LDs in 3D space and the time-lapse STED super-resolution imaging (up to 500 STED frames) to track the dynamics of LDs with nanoscale resolution (37 nm). Based on the state-of-the-art fluorescence imaging results, some new biological insights into LDs have been successfully provided. For instance, the long-term time-lapse 3D confocal imaging has surely answered an important and controversial question that the number of LDs would significantly decrease rather than increase upon starvation stimulation; the time-lapse STED super-resolution imaging with the highest resolution has impressively uncovered the fission process of nanoscale LDs for the first time; the starvation-induced change of LDs in size and in speed has been further revealed at nanoscale by the STED super-resolution imaging. All of these results not only highlight the utility of the newly developed fluorescent probe but also significantly promote the biological study of LDs.
Topics: Molecular Probes; Microscopy, Fluorescence; Fluorescent Dyes; Lipid Droplets; Optical Imaging
PubMed: 36593956
DOI: 10.7150/thno.79052 -
Dalton Transactions (Cambridge, England... Oct 2017The development of new methods to image the onset and progression of thrombosis is an unmet need. Non-invasive molecular imaging techniques targeting specific key... (Review)
Review
The development of new methods to image the onset and progression of thrombosis is an unmet need. Non-invasive molecular imaging techniques targeting specific key structures involved in the formation of thrombosis have demonstrated the ability to detect thrombus in different disease state models and in patients. Due to its high concentration in the thrombus and its essential role in thrombus formation, the detection of fibrin is an attractive strategy for identification of thrombosis. Herein we provide an overview of recent and selected fibrin-targeted probes for molecular imaging of thrombosis by magnetic resonance imaging (MRI), positron emission tomography (PET), single photon emission computed tomography (SPECT), and optical techniques. Emphasis is placed on work that our lab has explored over the last 15 years that has resulted in the progression of the fibrin-binding PET probe [Cu]FBP8 from preclinical studies into human trials.
Topics: Animals; Fibrin; Humans; Molecular Imaging; Molecular Probes; Peptides; Thrombosis
PubMed: 29051933
DOI: 10.1039/c7dt02634j