Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine

Large-scale synthesis of non-ionic bismuth chelate for computed tomography imaging in vivo

High atomic number elements-based X-ray computed tomography (CT) contrast agents offer a promising solution to address the inherent deficiencies of FDA-approved iodine contrast agents. However, they face substantial challenges in balancing imaging performance, safety, and large-scale production for clinical translation. Herein, inspired by the history of clinical gadolinium- and iodine-based contrast agents, we report a large-scale approach for synthesizing non-ionic bismuth (Bi) chelate for high-performance CT imaging in vivo. Bi-HPDO3A can be easily obtained from low-cost precursor within 4 steps at 6 g-scale. The non-ionic macrocyclic structure endows it with low osmolality, low viscosity, high stability, good renal clearable capability and biocompatibility. Additionally, Bi-HPDO3A realizes superior imaging performance across various in vivo applications, including gastrointestinal imaging, renal imaging, and computed tomography angiography (CTA). Especially, Bi-HPDO3A exhibits superior spectral imaging capability owing to the high K-edge of element Bi, achieving metal artifact-free CTA in vivo. The proposed Bi-HPDO3A that balances overall performance can serve as a high-performance CT contrast agent with potential for clinical translation.

Zebrafish navigating the metabolic maze: insights into human disease - assets, challenges and future implications

Zebrafish (Danio rerio) have become indispensable models for advancing our understanding of multiple metabolic disorders such as obesity, diabetes mellitus, dyslipidemia, and metabolic syndrome. This review provides a comprehensive analysis of zebrafish as a powerful tool for dissecting the genetic and molecular mechanisms of these diseases, focusing on key genes, like pparγ, lepr, ins, and srebp. Zebrafish offer distinct advantages, including genetic tractability, optical transparency in early development, and the conservation of key metabolic pathways with humans. Studies have successfully used zebrafish to uncover conserved metabolic mechanisms, identify novel disease pathways, and facilitate high-throughput screening of potential therapeutic compounds. The review also highlights the novelty of using zebrafish to model multifactorial metabolic disorders, addressing challenges such as interspecies differences in metabolism and the complexity of human metabolic disease etiology. Moving forward, future research will benefit from integrating advanced omics technologies to map disease-specific molecular signatures, applying personalized medicine approaches to optimize treatments, and utilizing computational models to predict therapeutic outcomes. By embracing these innovative strategies, zebrafish research has the potential to revolutionize the diagnosis, treatment, and prevention of metabolic disorders, offering new avenues for translational applications. Continued interdisciplinary collaboration and investment in zebrafish-based studies will be crucial to fully harnessing their potential for advancing therapeutic development.

Capsaicin from chili peppers and its analogues and their valued applications: An updated literature review

Chili peppers are widely sought after by consumers for not only their color, flavor, and nutritional properties but also their main component (capsaicin) various biological activities in diverse fields. Capsaicin (trans-8-methyl-N-vanillyl-6-nonenamide), the compound primarily responsible for the spicy flavor of peppers, remains a hot topic in the scientific community and shows the vast potential in various applications. Although many reviews focus comprehensively on capsaicin, most articles are limited to the medical field of capsaicin. This review provides an overview briefly of the capsaicin and its analogues in the fields of food, medicine and with a particular emphasis on their applications in agriculture and livestock farming. Overall, we aims is to expand the broad spectrum of applications for capsaicin and its analogues and explore their potential biological mechanisms. Finally, the challenges of capsaicin and future development prospects were discussed and proposed.

A Small-Molecule Drug for the Self-Checking of Mitophagy

Mitophagy, particularly in the context of drugs that disrupt mitochondrial membrane potential (MMP), represents a critical focus in pharmacology. However, the discovery and evaluation of MMP-disrupting drugs are often hampered using commercially available marker molecules that target similar or identical zones. These markers can significantly interfere with, obscure, or amplify the functional effects of MMP-targeting drugs, frequently leading to clinical failures. In response to this challenge, we propose a "one-two punch" drug design strategy that integrates both target-zone drug functionality and non-target zone biological reporting within a single small-molecule drug. We have developed a novel proof-of-concept mitophagy self-check drug (MitoSC) that exhibits dual-color and dual-localization properties. The functional component of this system is a variable MitoSC that disrupts mitochondrial membrane potential (MMP) homeostasis, thereby inducing mitophagy. Upon activation, this component transforms into a blue-fluorescent monomer (MitoSC-fun) specifically within the mitochondrial target zone. Concurrently, the biological reporting component is represented by a red-fluorescent monomer (MitoSC-rep) that localizes to lysosomes, the non-target zone. As mitophagy progresses, the fluorescent signals from MitoSC-rep (lysosomes) and MitoSC-fun (mitochondria) converge, enabling real-time monitoring of the mitophagic process. This strategy combines potent drug functionality with robust biological reporting, thereby minimizing interference and eliminating the complexities associated with external detection. Our findings underscore the potential of a single-molecule drug to exert target-zone specific actions while simultaneously providing non-target zone self-checking, offering a new perspective for drug design.

Target Discovery Driven by Chemical Biology and Computational Biology

Target identification is crucial for drug screening and development because it can reveal the mechanism of drug action and ensure the reliability and accuracy of the results. Chemical biology, an interdisciplinary field combining chemistry and biology, can assist in this process by studying the interactions between active molecular compounds and proteins and their physiological effects. It can also help predict potential drug targets or candidates, develop new biomarker assays and diagnostic reagents, and evaluate the selectivity and range of active compounds to reduce the risk of off-target effects. Chemical biology can achieve these goals using techniques such as changing protein thermal stability, enzyme sensitivity, and molecular structure and applying probes, isotope labeling and mass spectrometry. Concurrently, computational biology employs a diverse array of computational models to predict drug targets. This approach also offers innovative avenues for repurposing existing drugs. In this paper, we review the reported chemical biology and computational biology techniques for identifying different types of targets that can provide valuable insights for drug target discovery.

Chemical probes for the identification of the molecular targets of honokiol

Honokiol is a natural product with an interesting array of biological effects, including significant anti-tumor properties. However, full exploration of its therapeutic potential is hampered by its modest pharmacokinetic profile and by the lack of synthetic methods that allow to obtain specifically designed derivatives with improved properties. In addition, the specific molecular targets of honokiol remain poorly understood, a fact that limits the search of alternative hits for subsequent optimization programs. In this work we describe an optimized series of synthetic routes that allow to access to a variety of honokiol derivatives, including a set of minimalist photoaffinity probes to map potential protein targets in live cells. Chemical proteomic studies of the most potent probe revealed a defined set of proteins as the cellular targets of honokiol. Significantly, up to the 62 % of the identified proteins have described roles in cancer, highlighting their potential relationship with the antitumor effects of honokiol. Furthermore, several of the top hits have been validated as direct binding partners of honokiol by cellular thermal shift assay (CETSA). In sum, the work described herein provides the first landscape of the cellular targets of honokiol in living cells and contributes to define the specific molecular pathways affected by this natural product.

Tailoring near-infrared amyloid-β probes with high-affinity and low background based on CN and amphipathic regulatory strategies and in vivo imaging of AD mice

Amyloid-β (Aβ) species (Aβ fibrils and Aβ plaques), as one of the typical pathological markers of Alzheimer's disease (AD), plays a crucial role in AD diagnosis. Currently, some near-infrared I (NIR I) Aβ probes have been reported in AD diagnosis. However, they still face challenges such as strong background interference and the lack of effective probe design. In this study, we propose molecular design strategy that incorporates CN group and amphiphilic modulation to synthesize a series of amphiphilic NIR I Aβ probes, surpassing the commercial probe ThT and ThS. Theoretical calculations indicate that these probes exhibit stronger interaction with amino acid residues in the cavities of Aβ. Notably, the probes containing CN group display the ability of binding two distinct sites of Aβ, which dramatically enhanced the affinity to Aβ species. Furthermore, these probes exhibit minimal fluorescence in aqueous solution and offer ultra-high signal-to-noise ratio (SNR) for in vitro labeling, even in wash-free samples. Finally, the optimal probe DM-V2CN-PYC3 was utilized for in vivo imaging of AD mice, demonstrating its rapid penetration through the blood-brain barrier and labelling to Aβ species. Moreover, it enabled long-term monitoring for a duration of 120 min. These results highlight the enhanced affinity and superior performance of the designed NIR I Aβ probe for AD diagnosis. The molecular design strategy of CN and amphiphilic modulation presents a promising avenue for the development Aβ probes with low background in vivo/in vitro imaging for Aβ species.

TMT-based proteomic analysis of radiation lung injury in rats

Radiation-induced lung injury (RILI) is a common adverse effect of radiation therapy that negatively affects treatment progression and the quality of life of patients. Identifying biomarkers for RILI can provide reference for the prevention and treatment of RILI in clinical practice. In this study, to explore key proteins related to RILI, we constructed a rat model of RILI and analyzed RILI tissues and normal lung tissues using tandem mass spectrometry labeling and quantitative proteomics technology. We used Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, Gene Ontology (GO) enrichment and protein-protein interaction (PPI) networks for bioinformatics analysis of Differentially expressed proteins (DEPs). The results identified 185 differentially expressed proteins in lung tissue from the RILI group compared with the controls, including 110 up-regulated proteins and 75 down-regulated proteins. GO analysis showed that the differentially expressed proteins were involved oxidation-reduction process, cellular biosynthetic processes and extracellular matrix. KEGG results demonstrated that the differentially expressed proteins were mainly involved in the PI3K-Akt, ECM receptor interactions, arachidonic acid metabolism, glutathione metabolism and other pathways. These results on the functions and signaling pathways of the differentially expressed proteins provide a theoretical basis for further study of the mechanism of RILI.

Application of rare earth elements in dual-modality molecular probes

The unique 4f subshell electronic structure of rare earth elements endows them with exceptional properties in electrical, magnetic, and optical domains. These properties include prolonged fluorescence lifetimes, large Stokes shifts, distinctive spectral bands, and strong resistance to photobleaching, making them ideal for the synthesis of molecular probes. Each imaging technique possesses unique advantages and specific applicabilities but also inherent limitations due to its operational principles. Dual-modality molecular probes effectively address these limitations, particularly in applications involving high-resolution Magnetic Resonance Imaging (MRI) such as MRI/OI, MRI/PET, MRI/CT, and MRI/US. This review summarizes the applications, advantages, challenges, and current research status of rare earth elements in these four dual imaging modalities, providing a theoretical basis for the future development and application of rare earth elements in the field of dual-modality molecular probes.

Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome

Studies of molecular and cellular functions of small-molecule inhibitors in cancer treatment, eliciting effects by targeting genome and epigenome associated proteins, requires measurement of drug-target engagement in single-cell resolution. Here we present EpiChem for in situ single-cell joint mapping of small molecules and multimodal epigenomic landscape. We demonstrate single-cell co-assays of three small molecules together with histone modifications, chromatin accessibility or target proteins in human colorectal cancer (CRC) organoids. Integrated multimodal analysis reveals diverse drug interactions in the context of chromatin states within heterogeneous CRC organoids. We further reveal drug genomic binding dynamics and adaptive epigenome across cell types after small-molecule drug treatment in CRC organoids. This method provides a unique tool to exploit the mechanisms of cell type-specific drug actions.

Rapid Glutathione Analysis with SERS Microneedles for Deep Glioblastoma Tissue Differentiation

Rapid tissue differentiation at the molecular level is a prerequisite for precise surgical resection, which is of special value for the treatment of malignant tumors, such as glioblastoma (GBM). Herein, a SERS-active microneedle is prepared by modifying glutathione (GSH)-responsive molecules, 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB), on the surface of Au@Ag substrates for the distinction of different GBM tissues. Since the Raman signals on the surface of the DTNB@Au@Ag microneedle can be collected by both portable and benchtop Raman spectrometers, the distribution of GSH in different tissues at centimeter scale can be displayed through Raman spectroscopy and Raman imaging, and the entire analysis process can be accomplished within 12 min. Accordingly, in vivo brain tissues of orthotopic GBM xenograft mice and ex vivo tissues of GBM patients are accurately differentiated with the microneedle, and the results are well consistent with tissue staining and postoperative pathological reports. In addition, the outline of tumor, peritumoral, and normal tissues can be indicated by the DTNB@Au@Ag microneedle for at least 56 days. Considering that the tumor tissues are quickly discriminated at the molecular level without the restriction of depth, the DTNB@Au@Ag microneedle is promising to be a powerful intraoperative diagnostic tool for surgery navigation.

A Sequentially Activated Probe for Imaging of Superoxide Anion and Peroxynitrite in PC12 Cells under Oxidative Stress

Superoxide anion (O2·-) and peroxynitrite (ONOO-), two important oxidants under oxidative stress, coexist in complex cell and organism systems, playing crucial roles in various physiological and pathological processes, particularly in neurodegenerative diseases. Despite the absence of robust molecular tools capable of simultaneously visualizing O2·- and ONOO- in biosystems, the relationship between these two species remains understudied. Herein, we present sequentially activated fluorescent probe, DHX-SP, which exhibits exceptional selectivity and sensitivity toward O2·- and ONOO-. This probe enables precise imaging of these species in living PC12 cells under oxidative stress conditions using distinct fluorescence signal combinations. Furthermore, the probe DHX-SP has the ability to visualize changes in O2·- and ONOO- levels during ferroptosis of PC12 cells and in the Parkinson's disease model. These findings establish a connection between the crosstalk of the phosphorus group of O2·- and ONOO- in PC12 cells under oxidative stress.

A Self-Accelerating Naphthalimide-Based Probe Coupled with Upconversion Nanoparticles for Ultra-Accurate Tri-Mode Visualization of Hydrogen Peroxide

The design and development of ultra-accurate probe is of great significance to chemical sensing in complex practical scenarios. Here, a self-accelerating naphthalimide-based probe with fast response and high sensitivity toward hydrogen peroxide (H2O2) is designed. By coupling with the specially selected upconversion nanoparticles (UCNPs), an ultra-accurate colorimetric-fluorescent-upconversion luminescence (UCL) tri-mode platform is constructed. Owing to the promoted reaction process, this platform demonstrates rapid response (< 1 s), an ultra-low detection limit (4.34 nM), and superb anti-interferent ability even in presence of > 21 types of oxidants, explosives, metallic salts, daily compounds, colorful or fluorescent substances. In addition, the effectiveness of this design is further verified by a sponge-based sensing chip loaded with the UCNPs/probe in recognizing trace H2O2 vapor from interferents with the three characteristic colors existing simultaneously. The proposed design of probe and tri-mode visualization detection platform is expected to open up a brand-new methodology for ultra-accurate sensing.

Noninvasive Diagnosis of Kidney Dysfunction Using a Small-Molecule Manganese-Based Magnetic Resonance Imaging Probe

Contrast-enhanced magnetic resonance imaging (CE-MRI) is a promising approach for the diagnosis of kidney diseases. However, safety concerns, including nephrogenic systemic fibrosis, limit the administration of gadolinium (Gd)-based contrast agents (GBCAs) in patients who suffer from renal impairment. Meanwhile, nanomaterials meet biosafety concerns because of their long-term retention in the body. Herein, we propose a small-molecule manganese-based imaging probe Mn-PhDTA as an alternative to GBCAs to assess renal insufficiency for the first time. Mn-PhDTA was synthesized via a simple three-step reaction with a total yield of up to 33.6%, and a gram-scale synthesis can be realized. Mn-PhDTA has an r1 relaxivity of 2.72 mM-1 s-1 at 3.0 T and superior kinetic inertness over Gd-DTPA and Mn-EDTA with a dissociation time of 60 min in the presence of excess Zn2+. In vivo and in vitro experiments demonstrate their good stability and biocompatibility. In the unilateral ureteral obstruction rats, Mn-PhDTA provided significant MR signal enhancement, enabled distinguishing structure changes between the normal and damaged kidneys, and evaluated the renal function at different injured stages. Mn-PhDTA could act as a potential MRI contrast agent candidate for the replacement of GBCAs in the early detection of kidney dysfunction and analysis of kidney disease progression.

Functional chromophores synthesized via multicomponent Reactions: A review on their use as cell-imaging probes

This review aims to provide a comprehensive overview of recent advancements and applications of fluorescence imaging probes synthesized via MCRs (multicomponent reactions). These probes, also known as functional chromophores, belong to a currently investigated class of fluorophores that are presently being successfully applied in bioimaging experiments, especially in various living cell lineages. We describe some of the MCRs that have been employed in the synthesis of these probes and explore their applications in biological imaging, with an emphasis on cellular imaging. The review also discusses the challenges and future perspectives in the field, particularly considering the potential impact of MCR-based fluorescence imaging probes on advancing this field of research in the coming years. Considering that this area of research is relatively new and nearly a decade has passed since the first publication, this review also provides a historical perspective on this class of fluorophores, highlighting the pioneering works published between 2011 and 2016.

Visualization detection of mycotoxin patulin in fruit juices by a small-molecule fluorescent probe

The mycotoxin patulin is a common contaminant in rotten fruits, posing severe food safety risks and threats to human health. Developing a convenient, sensitive and reliable method for patulin detection is of utmost importance but remains challenging. In this study, we have successfully designed and synthesized a small-molecule fluorescent probe, FITC-Lys, which demonstrates good sensitivity in detecting patulin. Upon contact with patulin, the terminal Lys group of the FITC-Lys probe reacts with patulin, resulting in the formation of the fluorescein dimer that subsequently quenches fluorescence. This variation of fluorescence enables the visualization and sensitive detection of patulin. The probe exhibits good sensitivity with a low LOD of 8 ng mL-1 for the fluorescence spectrum method and a LOD of 12 ng mL-1 for the fluorescence imaging method. Moreover, we have validated the probe's capability for patulin detection in apple and pear juices, achieving good recoveries ranging from 98.60% to 103.80%. Notably, the probe FITC-Lys is the first small-molecule fluorescent probe that has proven successful in visualizing patulin in juices derived from decayed apples and pears. Consequently, this probe holds great potential as a practical tool for monitoring patulin in foodstuffs, thereby contributing to enhanced food safety standards.

TMT-Based Proteomics Analysis of Senescent Nucleus Pulposus from Patients with Intervertebral Disc Degeneration

Lower back pain, a leading cause of disability worldwide, is associated with intervertebral disc degeneration (IDD) in approximately 40% of cases. Although nucleus pulposus (NP) cell senescence is a major contributor to IDD, the underlying mechanisms remain unclear. We collected NP samples from IDD patients who had undergone spinal surgery. Healthy and senescent NP tissues (n = 3) were screened using the Pfirrmann grading system combined with immunohistochemistry, as well as hematoxylin and eosin, Safranin O, Alcian blue, and Masson staining. Differentially expressed proteins (DEPs) were identified using quantitative TMT-based proteomics technology. Bioinformatics analyses included gene ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) analyses. In addition, immunofluorescence was used to verify protein expression. In total, 301 DEPs were identified in senescent NP tissues, including 92 upregulated and 209 downregulated proteins. In GO, DEPs were primarily associated with NF-kappaB transcription factor, extracellular regions, cellular protein metabolic processes, and post-translational protein modification. The enriched KEGG pathways included TGF-β, Wnt, RAP1, interleukin-17, extracellular matrix-receptor adhesion, and PI3K/Akt signaling pathways. PPI analysis demonstrated interactions between multiple proteins. Finally, immunofluorescence verified the expressions of MMP3, LUM, TIMP1, and CDC42 in senescent NP cells. Our study provides valuable insights into the mechanisms underlying senescent NP tissues in IDD patients. DEPs provide a basis for further investigation of the effects of senescent factors on IDD.