Integrated Thermal Proteome Profiling and Affinity Ultrafiltration Mass Spectrometry (iTPAUMS): A Novel Paradigm for Elucidating the Mechanism of Action of Natural Products.

Natural products (NPs) are foundational to drug discovery, offering a rich repertoire of molecular diversity with multifaceted modes of action against a broad array of targets. Despite their potential, deconvoluting the intricate mechanism of action (MoA) of NPs, characterized by their multicomponent, multitarget, and multilevel interactions, remains a formidable challenge. Here, we introduce an innovative pipeline called integrated thermal proteome profiling and affinity ultrafiltration mass spectrometry (iTPAUMS). This approach combines the high-throughput capacity of thermal proteome profiling (TPP) with the specificity of affinity ultrafiltration mass spectrometry (AUMS), creating a powerful toolkit for elucidating complex MoAs of NPs. Significantly, our investigation represents a pioneering application of TPP to delineate the target group of NPs mixtures and overcome the long-standing obstacle of mapping specific component-target interactions through AUMS. Our findings demonstrate the utility of iTPAUMS in constructing a comprehensive component-target atlas, providing a robust analytical foundation for unraveling the intricate pharmacological landscapes of NPs and advancing drug discovery.

Simultaneous measurement of bidirectional magnetic field and temperature with a dual-channel sensor based on the whispering gallery mode.

What we believe is a novel dual-channel whispering gallery mode (WGM) sensor for concurrently measuring bidirectional magnetic field and temperature is proposed and demonstrated. Two sensing microcavities [magnetic fluid (MF)-infiltrated capillary and polydimethylsiloxane (PDMS)-coated microbottle, respectively, referred as Channel 1 (CH1) and Channel 2 (CH2)] are integrated into a silica capillary to facilitate the dual-channel design. Resonant wavelengths corresponding to CH1 and CH2 mainly depend on the change in the magneto-induced refractive index and the change in the thermo-induced parameter (volume and refractive index) of the employed functional materials, respectively. The MF-infiltrated capillary enables bidirectional magnetic field sensing with maximum sensitivities of 46 pm/mT and -3 pm/mT, respectively. The PDMS-coated structure can realize the temperature measurement with a maximum sensitivity of 79.7 pm/°C. The current work possesses the advantage of bidirectionally magnetic tunability besides the temperature response, which is expected to be used in field such as vector magnetic fields and temperature dual-parameter sensing.

Benzo(a)anthracene Targeting SLC1A5 to Synergistically Enhance PAH Mixture Toxicity.

Human exposure to polycyclic aromatic hydrocarbons (PAHs) as mutagenic and carcinogenic pollutants in the environment often occurs in the form of mixtures. Although the mixture effects of PAHs have been previously recognized, the toxicological mechanisms to explain them still remain quite unclear. This study combined metabolomics and chemical proteomics methods to comprehensively understand the mixture effects of a PAH mixture including benzo(a)anthracene (BaA), benzo(b)fluoranthene (BbF), benzo(a)pyrene (BaP), and chrysene (CHR). Among them, BaA has shown a strong synergistic effect with other PAHs. Interestingly, BaA alone is not a potent oxidative stress inducer in liver cells but dose-dependently amplifies oxidative damage caused by the PAH mixture. Global metabolomics analysis results revealed damage to the antioxidant glutathione synthesis, which was caused by the glutamine depletion caused by BaA in the mixture. Subsequently, the label-free chemical proteomics and cellular thermal shift analysis (CETSA) demonstrated that the PAH mixture altered the thermal shift of glutamine transporter SLC1A5. Furthermore, Western blotting and the isothermal titration calorimetry (ITC) interaction measurements showed nanomolar KD values between BaA and SLC1A5. Overall, this study showed that BaA synergistically contributed to PAH mixture induced oxidative damage by targeting SLC1A5 to inhibit glutamate transport into cells, resulting in the inhibition of glutathione synthesis.

Electrochemical stability of biodegradable Zn-Cu alloys through machine-learning accelerated high-throughput discovery.

Zn-Cu alloys have attracted great attention as biodegradable alloys owing to their excellent mechanical properties and biocompatibility, with corrosion characteristics being crucial for their suitability for biomedical applications. However, the unresolved identification of intermetallic compounds in Zn-Cu alloys affecting corrosion and the complexity of the application environment hamper the understanding of their electrochemical behavior. Utilizing high-throughput first-principles calculations and machine-learning accelerated evolutionary algorithms for screening the most stable compounds in Zn-Cu systems, a dataset encompassing the formation energy of 2033 compounds is generated. It reveals that most of the experimentally reported Zn-Cu compounds can be replicated, especially the structure of R32 CuZn5 is first discovered which possesses the lowest formation energy of -0.050 eV per atom. Furthermore, the simulated X-ray diffraction pattern matches perfectly with the experimental ones. By formulating 342 potential electrochemical reactions based on the binary compounds, the Pourbaix diagrams for Zn-Cu alloys are constructed to clarify the fundamental competition between different phases and ions. The calculated equilibrium potential of CuZn5 is higher than that of Zn through the forward reaction Zn + CuZn5 ⇌ CuZn5 + Zn2+ + 2e-, resulting in microcell formation owing to the stronger charge density localization in Zn compared to CuZn5. The presence of chlorine accelerates the corrosion of Zn through the reaction Zn + CuZn5 + 6Cl- + 6H2O ⇌ Cu + 6ZnOHCl + 6H+ + 12e-, where the formation of ZnOHCl disrupts the ZnO passive film and expands the corrosion pH range from 9.2 to 8.8. Our findings reveal an accurate quantitative corrosion mechanism for Zn-Cu alloys, providing an effective pathway to investigate the corrosion resistance of biodegradable alloys.

Discovery of a potent and selective PARP1 degrader promoting cell cycle arrest via intercepting CDC25C-CDK1 axis for treating triple-negative breast cancer.

PARP1 is a multifaceted component of DNA repair and chromatin remodeling, making it an effective therapeutic target for cancer therapy. The recently reported proteolytic targeting chimera (PROTAC) could effectively degrade PARP1 through the ubiquitin-proteasome pathway, expanding the therapeutic application of PARP1 blocking. In this study, a series of nitrogen heterocyclic PROTACs were designed and synthesized through ternary complex simulation analysis based on our previous work. Our efforts have resulted in a potent PARP1 degrader D6 (DC50 = 25.23 nM) with high selectivity due to nitrogen heterocyclic linker generating multiple interactions with the PARP1-CRBN PPI surface, specifically. Moreover, D6 exhibited strong cytotoxicity to triple negative breast cancer cell line MDA-MB-231 (IC50 = 1.04 µM). And the proteomic results showed that the antitumor mechanism of D6 was found that intensifies DNA damage by intercepting the CDC25C-CDK1 axis to halt cell cycle transition in triple-negative breast cancer cells. Furthermore, in vivo study, D6 showed a promising PK property with moderate oral absorption activity. And D6 could effectively inhibit tumor growth (TGI rate = 71.4 % at 40 mg/kg) without other signs of toxicity in MDA-MB-321 tumor-bearing mice. In summary, we have identified an original scaffold and potent PARP1 PROTAC that provided a novel intervention strategy for the treatment of triple-negative breast cancer.

Substrate engineering for wafer-scale two-dimensional material growth: strategies, mechanisms, and perspectives.

The fabrication of wafer-scale two-dimensional (2D) materials is a prerequisite and important step for their industrial applications. Chemical vapor deposition (CVD) is the most promising approach to produce high-quality films in a scalable way. Recent breakthroughs in the epitaxy of wafer-scale single-crystalline graphene, hexagonal boron nitride, and transition-metal dichalcogenides highlight the pivotal roles of substrate engineering by lattice orientation, surface steps, and energy considerations. This review focuses on the existing strategies and underlying mechanisms, and discusses future directions in epitaxial substrate engineering to deliver wafer-scale 2D materials for integrated electronics and photonics.

The coat protein of the ilarvirus prunus necrotic ringspot virus mediates long-distance movement.

The coat protein (CP) of plant viruses generally has multiple functions involving infection, replication, movement and pathogenicity. Functions of the CP of prunus necrotic ringspot virus (PNRSV), the causal agent of several threatening diseases of Prunus fruit trees, are poorly studied. Previously, we identified a novel virus in apple, apple necrotic mosaic virus (ApNMV), which is phylogenetically related to PNRSV and probably associated with apple mosaic disease in China. Full-length cDNA clones of PNRSV and ApNMV were constructed, and both are infectious in cucumber (Cucumis sativus L.), an experimental host. PNRSV exhibited higher systemic infection efficiency with more severe symptoms than ApNMV. Reassortment analysis of genomic RNA segments 1-3 found that RNA3 of PNRSV could enhance the long-distance movement of an ApNMV chimaera in cucumber, indicating the association of RNA3 of PNRSV with viral long-distance movement. Deletion mutagenesis of the PNRSV CP showed that the basic motif from amino acids 38 to 47 was crucial for the CP to maintain the systemic movement of PNRSV. Moreover, we found that arginine residues 41, 43 and 47 codetermine viral long-distance movement. The findings demonstrate that the CP of PNRSV is required for long-distance movement in cucumber, which expands the functions of ilarvirus CPs in systemic infection. For the first time, we identified involvement of Ilarvirus CP protein during long-distance movement.

Phytochrome higher order mutants reveal a complex set of light responses in the moss Physcomitrium patens.

Phytochromes are photoreceptors enabling plants to respond to various light conditions. Independent gene duplications resulted in small phytochrome families in mosses, ferns and seed plants. This phytochrome diversity is hypothesised to be critical for sensing and adapting to different light conditions, but experimental evidence for this idea is lacking for mosses and ferns. The moss model species Physcomitrium patens contains seven phytochromes grouped into three clades, PHY1/3, PHY2/4 and PHY5. Here, we used CRISPR/Cas9-generated single and higher order mutants to investigate their role in light regulation of protonema and gametophore growth, protonema branching and induction of gametophores. We found both specific and partially overlapping roles for the three phytochrome clades in regulating these responses in different light conditions. PHY1/3 clade phytochromes act as primary far-red light receptors, while PHY5 clade phytochromes are the primary red light receptors. PHY2/4 clade phytochromes have functions in both red and far-red light. We also observed that PHY1/3 and PHY2/4 clade phytochromes promote gametophore growth in simulated canopy shade and also play a role in blue light. Similar to seed plants, gene duplications in the phytochrome lineage in mosses were followed by functional diversification into red and far-red light-sensing phytochromes.

Three-Dimensional Fe Single-Atom Catalyst for High-Performance Cathode of Zn-Air Batteries.

Designing cost-effective and highly active oxygen reduction reaction (ORR) catalysts is critical for the development of Zn-air batteries (ZABs). Iron-nitrogen-carbon (Fe-N-C) catalysts with single-atom Fe-Nx active sites are considered as one of the most promising alternatives to noble Pt but are hindered by unsatisfactory activity and durability. Herein, a NaCl template-assisted in situ pyrolysis technique is utilized to massively fabricate Fe-N-C single-atom catalysts (SACs) anchored on the three-dimensional open-pore carbon networks (denoted as 3D SAFe). The 3D SAFe catalyst exhibits ultrahigh activity with a half-wave potential of 0.90 V (vs RHE), benefiting from the enhanced mass diffusion and the increased amount of effective Fe-N4 sites. Consequently, the ZABs assembled with 3D SAFe deliver high peak power density up to 156 mW cm-2 and outstanding durability of 80 h, suggesting the application potential of the 3D SAFe catalyst. This work inspires the rational design and synthesis of highly efficient SACs for ZABs.

Glyoxalase I-4 functions downstream of NAC72 to modulate downy mildew resistance in grapevine.

Glyoxalase I (GLYI) is part of the glyoxalase system; its major function is the detoxification of α-ketoaldehydes, including the potent and cytotoxic methylglyoxal (MG). Methylglyoxal disrupts mitochondrial respiration and increases production of reactive oxygen species (ROS), which also increase during pathogen infection of plant tissues; however, there have been few studies relating the glyoxalase system to the plant pathogen response. We used the promoter of VvGLYI-4 to screen the upstream transcription factors and report a NAC (NAM/ATAF/CUC) domain-containing transcription factor VvNAC72 in grapevine, which is localized to the nucleus. Our results show that VvNAC72 expression is induced by downy mildew, Plasmopara viticola, while the transcript level of VvGLYI-4 decreases. Further analysis revealed that VvNAC72 can bind directly to the promoter region of VvGLYI-4 via the CACGTG element, leading to inhibition of VvGLYI-4 transcription. Stable overexpression of VvNAC72 in grapevine and tobacco showed a decreased expression level of VvGLYI-4 and increased content of MG and ROS, as well as stronger resistance to pathogen stress. Taken together, these results demonstrate that grapevine VvNAC72 negatively modulates detoxification of MG through repression of VvGLYI-4, and finally enhances resistance to downy mildew, at least in part, via the modulation of MG-associated ROS homeostasis through a salicylic acid-mediated defense pathway.

A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus).

Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.

Slowing Hot-Electron Relaxation in Mix-Phase Nanowires for Hot-Carrier Photovoltaics.

Hot carrier harvest could save 30% energy loss in solar cells. So far, however, it is still unreachable as the photoexcited hot carriers are short-lived, ∼1 ps, determined by a rapid relaxation process, thus invalidating any reprocessing efforts. Here, we propose and demonstrate a feasible route to reserve hot electrons for efficient collection. It is accomplished by an intentional mix of cubic zinc-blend and hexagonal wurtzite phases in III-V semiconductor nanowires. Additional energy levels are then generated above the conduction band minimum, capturing and storing hot electrons before they cool down to the band edges. We also show the superiority of core/shell nanowire (radial heterostructure) in extracting hot electrons. The strategy disclosed here may offer a unique opportunity to modulate hot carriers for efficient solar energy harvest.

Exploring the Absorption Mechanisms of Imidazolium-Based Ionic Liquids to Epigallocatechin Gallate.

Imidazolium-based ionic liquids are wildly used in natural product adsorption and purification. In this work, one typical polymeric ionic liquid (PIL) was synthesized by using L-proline as the anion, which exhibited excellent adsorption capacity toward tea polyphenol epigallocatechin gallate (EGCG). The adsorption conditions were optimized with the response surface method (RSM). Under the optimum conditions, the adsorption capacity of the PIL for EGCG can reach as high as 552 mg/g. Dynamics and isothermal research shows that the adsorption process of EGCG by the PIL particularly meets the quasi-second-order kinetic equation and monolayer adsorption mechanism. According to thermodynamic parameter analysis, the adsorption process is endothermic and spontaneous. The results of theoretical calculation by molecular docking also demonstrated the interaction mechanisms between EGCG and the ionic liquid. Considering the wide application of imidazolium-based ionic liquids in component adsorption and purification, the present study can not only be extended to other similar experimental mechanism validation, but also be representative for guiding the synthesis of PIL and optimization of adsorption conditions.

Synthesis of Tropine-Based Functionalized Acidic Ionic Liquids and Catalysis of Esterification.

Some traditional acidic ionic liquids (AILs) have shown great catalytic potential in esterification; meanwhile, the design and application of more new AILs are expected at present.Tropine-based functionalized acidic ionic liquids (FAILs) were synthesized to realize esterification catalysis for the first time; with aspirin synthesis as the template reaction, key influences on the substrate conversion and product yield of the synthesis, such as IL type, ratio of salicylic acid to acetic anhydride, temperature, reaction time and amount of IL, were investigated. The new tropine-based FAILs exhibited excellent performance in catalytic synthesis of aspirin with 88.7% yield and 90.8% selectivity. Multiple recovery and re-usage of N-(3-propanesulfonic acid) tropine is the cation, and p-toluenesulfonic acid is the anion. ([Trps][OTs]) shows satisfactory results. When [Trps][OTs] was used to catalyze different esterification reactions, it also showed good results. The above studies proved that ionic liquid [Trps][OTs] could serve as an ideal green solvent for esterification reaction, which serves as a suitable substitute for current catalysts.

Evolution of volatile profile and aroma potential of 'Gold Finger' table grapes during berry ripening.

BACKGROUND: 'Gold Finger' is a grape cultivar with a finger-like shape and a milk flavor. The process by which its aroma profile evolves during ripening is unclear. Thus, changes in the free and bound volatile compounds present in 'Gold Finger' grapes during ripening were investigated using headspace sampling-solid-phase microextraction-gas chromatography-mass spectroscopy (HS-SPME-GC-MS). RESULTS: A total of 83 volatile aroma components were identified in the grapes, with aldehydes, esters, acids, and alcohols being the main components. The total aroma compound content exhibited significant differences between the bound and free forms. The total content of bound volatile compounds did not change significantly during fruit development, although the free aroma compound content was significantly higher than the bound content. The total content of free aldehydes, free alcohols, bound norisoprenoids, and ketones gradually increased for up to 70 days after flowering (DAF), while the total free ester, terpene, and acid content decreased. The characteristic aroma compounds of 'Gold Finger' grapes were identified as hexanal, (E)-2-hexenal, and ethyl hexanoate. CONCLUSIONS: These results give a foundation for the further development of 'Gold Finger' grapes and provide a theoretical basis for the selection and breeding of novel aromatic grape varieties. © 2021 Society of Chemical Industry.

Metabolomics and In Silico Docking-Directed Discovery of Small-Molecule Enzyme Targets.

The identification of target proteins for small molecules is of great importance in drug discovery and for understanding the cellular mode of action (MOA) of toxicants. Herein, a "bottom-up" oriented target finding strategy is proposed based on the principle that the targeted enzymes can be inferred according to their phenotypic changes at the metabolome level. Meanwhile, computer-assisted in silico molecular docking analysis was performed to evaluate the binding affinities between the chemicals and the target enzymes to further rank the possible targets. In this study, triphenyl phosphate (TPhP) was used as an example to illustrate the workflow. After a comprehensive metabolome and lipidome analysis, 51 related metabolic enzymes were selected for ranking binding energies, wherein 25 proteins exhibited a higher affinity for TPhP than for their endogenous substrates. Two proteins, hydroxyacyl-coenzyme A dehydrogenase (HADH) and 3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10), were further confirmed by surface phasma resonance (SPR) and isothermal titration calorimetry (ITC) analysis, displayed Kd values at low micromolar levels for TPhP. Overall, the proposed strategy has provided a feasible means for discovering enzymatic targets for the large-scale small-molecule sets, with the advantages of closely associating with the phenotype change, reducing the cost of groping, and improving the accuracy of target prediction.

Single Cell Metabolite Detection Using Inertial Microfluidics-Assisted Ion Mobility Mass Spectrometry.

Single-cell metabolite measurement remains highly challenging due to difficulties related to single cell isolation, metabolite detection, and identification of low levels of metabolites. Here, as a first step of the technological development, we propose a novel strategy integrating spiral inertial microfluidics and ion mobility mass spectrometry (IM-MS) for single-cell metabolite detection and identification. Cells in methanol suspension are inertially focused into a single stream in the spiral microchannel. This stream of separated cells is delivered to the nanoelectrospray needle to be lysed and ionized and subsequently analyzed in real time by IM-MS. This analytical system enables six to eight single-cell metabolic fingerprints to be collected per minute, including gas-phase collisional cross section (CCS) measurements as an additional molecular descriptor, giving increased confidence in metabolite identification. As a proof of concept, the metabolic profiles of three types of cancer cells (U2OS, HepG2, and HepG2.215) were successfully screened, and 19 distinct lipids species were identified with CCS value filtering. Furthermore, principal component analysis (PCA) showed differentiation of the three cancer cell lines, mainly due to cellular surface phospholipids. Taken together, our technology platform offers a simple and efficient method for single-cell lipid profiling, with additional ion mobility separation of lipids significantly improving the confidence toward identification of metabolites.

Substitutionally Doped MoSe2 for High-Performance Electronics and Optoelectronics.

2D materials, of which the carrier type and concentration are easily tuned, show tremendous superiority in electronic and optoelectronic applications. However, the achievements are still quite far away from practical applications. Much more effort should be made to further improve their performance. Here, p-type MoSe2 is successfully achieved via substitutional doping of Ta atoms, which is confirmed experimentally and theoretically, and outstanding homojunction photodetectors and inverters are fabricated. MoSe2 p-n homojunction device with a low reverse current (300 pA) exhibits a high rectification ratio (104 ). The analysis of dark current reveals the domination of the Shockley-Read-Hall (SRH) and band-to-band tunneling (BTB) current. The homojunction photodetector exhibits a large open-circuit voltage (0.68 V) and short-circuit currents (1 µA), which is suitable for micro-solar cells. Furthermore, it possesses outstanding responsivity (0.28 A W-1 ), large external quantum efficiency (42%), and a high signal-to-noise ratio (≈107 ). Benefiting from the continuous energy band of homojunction, the response speed reaches up to 20 µs. Besides, the Ta-doped MoSe2 inverter exhibits a high voltage gain (34) and low power consumption (127 nW). This work lays a foundation for the practical application of 2D material devices.

Extrinsic Photoconduction Induced Short-Wavelength Infrared Photodetectors Based on Ge-Based Chalcogenides.

2D layered photodetectors have been widely researched for intriguing optoelectronic properties but their application fields are limited by the bandgap. Extending the detection waveband can significantly enrich functionalities and applications of photodetectors. For example, after breaking through bandgap limitation, extrinsic Si photodetectors are used for short-wavelength infrared or even long-wavelength infrared detection. Utilizing extrinsic photoconduction to extend the detection waveband of 2D layered photodetectors is attractive and desirable. However, extrinsic photoconduction has yet not been observed in 2D layered materials. Here, extrinsic photoconduction-induced short-wavelength infrared photodetectors based on Ge-based chalcogenides are reported for the first time and the effectiveness of intrinsic point defects are demonstrated. The detection waveband of room-temperature extrinsic GeSe photodetectors with the assistance of Ge vacancies is broadened to 1.6 µm. Extrinsic GeSe photodetectors have an excellent external quantum efficiency (0.5%) at the communication band of 1.31 µm and polarization-resolved capability to subwaveband radiation. Moreover, room-temperature extrinsic GeS photodetectors with a detection waveband to the communication band of 1.55 µm further verify the versatility of intrinsic point defects. This approach provides design strategies to enrich the functionalities of 2D layered photodetectors.

System Biology-Guided Chemical Proteomics to Discover Protein Targets of Monoethylhexyl Phthalate in Regulating Cell Cycle.

Chemical proteomics methods have been used as effective tools to identify novel protein targets for small molecules. These methods have great potential to be applied as environmental toxicants to figure out their mode of action. However, these assays usually generate dozens of possible targets, making it challenging to validate the most important one. In this study, we have integrated the cellular thermal shift assay (CETSA), quantitative proteomics, metabolomics, computer-assisted docking, and target validation methods to uncover the protein targets of monoethylhexyl phthalate (MEHP). Using the mass spectrometry implementation of CETSA (MS-CETSA), we have identified 74 possible protein targets of MEHP. The Gene Ontology (GO) enrichment integration was further conducted for the target proteins, the cellular dysregulated proteins, and the metabolites, showing that cell cycle dysregulation could be one primary change due to the MEHP-induced toxicity. Flow cytometry analysis confirmed that hepatocytes were arrested at the G1 stage due to the treatment with MEHP. Subsequently, the potential protein targets were ranked by their binding energy calculated from the computer-assisted docking with MEHP. In summary, we have demonstrated the development of interactomics workflow to simplify the redundant information from multiomics data and identified novel cell cycle regulatory protein targets (CPEB4, ANAPC5, and SPOUT1) for MEHP.