Novel Strategy for Screening Target Proteins by the Common Drugs─Sofosbuvir-Specific Profiling of HCV Patient Serum.

It is the scientific basis of precision medicine to study all of the targets of drugs based on the interaction between drugs and proteins. It is worth paying attention to unknown proteins that interact with drugs to find new targets for the design of new drugs. Herein, we developed a protein profiling strategy based on drug-protein interactions and drug-modified magnetic nanoparticles and took hepatitis C virus (HCV) and its corresponding drug sofosbuvir (SOF) as an example. A SOF-modified magnetic separation medium (Fe3O4@POSS@SOF) was prepared, and a gradient elution strategy was employed and optimized to profile specific proteins interacted with SOF. A series of proteomic analyses were performed to profile proteins based on SOF-protein interactions (SPIs) in the serum of HCV patients to evaluate the specificity of the profiling strategy. As a result, five proteins were profiled with strong SPIs and exhibited high relevance with liver tissue, which were potentially new drug targets. Among them, HSP60 was used to confirm the highly specific interactions between the SOF and its binding proteins by Western blotting analysis. Besides, 124 and 29 differential proteins were profiled by SOF material from three HCV patient serum and pooled 20 HCV patient serum, respectively, by comparing with healthy human serum. In comparison with those profiled by the polyhedral oligomeric silsesquioxane (POSS) material, differential proteins profiled by the SOF material were highly associated with liver diseases through GO analysis and pathway analysis. Furthermore, four common differential proteins profiled by SOF material but not by POSS material were found to be identical and expressed consistently in both pooled serum samples and independent serum samples, which might potentially be biomarkers of HCV infection. Taken together, our study proposes a highly specific protein profiling strategy to display distinctive proteomic profiles, providing a novel idea for drug design and development.

Magnetic resin composites for the enrichment of proteins, peptides and phosphopeptides.

There is growing interest in the development of materials for enriching proteins and phosphoproteins from complex sample matrices for mass spectrometric analysis. Herein, we designed and synthesized two types of magnetic resin composites, i.e., MTS9200@Fe3O4 and FPA90CL@Fe3O4, and assessed their applications as adsorbents for enriching proteins, peptides and phosphopeptides. With the combination of Fe3+-IMAC interaction (MTS9200) or electrostatic attraction (FPA90CL) of resins and the adsorption of Fe3O4, the prepared composites exhibited higher capacities for adsorbing a protein (bovine serum albumin, at 195.71 and 135.03 mg g-1 for MTS9200@Fe3O4 and FPA90CL@Fe3O4, respectively) than MTS9200, FPA90CL and Fe3O4. In addition, due to the contributions of the hydrophobic skeleton of resins and Fe3O4, the magnetic resin composites allowed for efficient enrichment of peptides. Moreover, through Fe3+-IMAC interaction or electrostatic attraction of resins and Fe-O MOAC interaction of Fe3O4 with phosphate groups, phosphopeptides could also be captured. Furthermore, we employed the prepared composites for enriching proteins and phosphopeptides from human serum, where 466 and 506 proteins, and 434 and 356 phosphorylation sites, were detected from human serum after being processed with FPA90CL@Fe3O4 and MTS9200@Fe3O4, respectively. Together, our work revealed the great potential of magnetic resin composites as enrichment materials for proteomics and phosphoproteomics analysis.

Selective profiling of liver-related specific proteins based on sofosbuvir-modified magnetic separation material.

It has great significance in profiling specific proteins throughout for better understanding of complex pathological processes and in-depth pharmacological studies. In this work, an efficient protein profiling strategy was developed based on the specific protein-drug interaction. Sofosbuvir (SOF), as a first-line drug for the treatment of hepatitis C, was modified onto the surface of nanoparticles through stable chemical bonds to fabricate a novel magnetic separation material denoted as Fe3O4@SiO2@PAA@SOF. With sequence coverage as the screening parameter, nine proteins were profiled from fetal bovine serum (FBS) of which eight were liver related. Similarly, the strategy was applied to hepatocellular carcinoma (HCC) patient serum. Eight proteins were profiled and all of them were liver related, demonstrating the superb specificity and selectivity of this strategy for profiling liver-related proteins by virtue of protein-SOF interaction. When serum proteins from HCC patients were compared to those from healthy people, one unique differential protein (D3DQX7) was profiled, which was liver related and was a potential target for ameliorating liver diseases. For further research, this material design concept and protein profiling strategy can be extended to employ other drugs for corresponding studies. Sofosbuvir, as a therapeutic drug for liver diseases, was modified onto the surface of magnetic nanoparticles to fabricate the specific selective separation material (Fe3O4@SiO2@PAA@SOF). Based on protein-SOF interaction, the material was applied to adsorb specific proteins from different serum samples. After MS analysis, specific proteins, most of which were liver related, were successfully profiled from FBS and HCC patient serum, fully demonstrating the superb specificity and selectivity of this protein profiling strategy.

Design and application of hydrophilic bimetallic metal-organic framework magnetic nanoparticles for rapid capture of exosomes.

Functional materials with good biocompatibility have been widely used in the study of genomics, proteomics and disease diagnosis, which has improved the progress of life science. In this paper, the material not only exhibited a strong affinity to the phosphate groups on the exosomal membrane due to the coexistence of Zr-O clusters and Ti4+, but also owned great hydrophilicity to reduce non-specific adsorption of contaminated proteins, achieving the separation and purification of exosomes from complex biosamples. The model exosomes extracted by ultracentrifugation (UC) were used to evaluate the feasibility of Fe3O4@UiO-66-NH2@PA-Ti4+ capturing exosomes. The process of Fe3O4@UiO-66-NH2@PA-Ti4+ capturing exosomes was simple to operate with a high recovery rate (97.3%) within a short time (5 min). Then Fe3O4@UiO-66-NH2@PA-Ti4+ was further applied to capture exosomes in media and urine followed by the downstream proteomics analysis. 348 and 284 exosomal proteins were identified for cell medium and urine, respectively. This work shows great potential of the material for subsequent function research of disease-related exosomes by separating exosomes rapidly and efficiently.

Dual-functionalized magnetic bimetallic metal-organic framework composite for highly specific enrichments of phosphopeptides and glycopeptides.

In this work, a dual-functionalized magnetic bimetallic metal-organic framework composite denoted as Fe3O4@SiO2@(Zr-Ti-MOF)10-NH2 was ingeniously designed and fabricated by a facial layer-by-layer assembly technique. The composite not only exhibited strong affinity for phosphopeptide due to the coexistence of Zr-O clusters and Ti-O clusters, but also owned great hydrophilicity for glycopeptides relying on abundant hydrophilic NH2 groups, meeting the demand for simultaneously enrichment and sequential elution of phosphopeptides and glycopeptides. As expected, the synthesized composite showed great selectivity (1:2000 M ratio of ß-casein:BSA; 1:50 M ratio of IgG:BSA), good sensitivity (1 fmol µL-1 for both α-casein and IgG), and good capacity (80 mg g-1 for α-casein and 200 mg g-1 for IgG). By using sequential elution strategy, 29 phosphopeptides and 24 glycopeptides from α-casein and IgG digests mixture could be simultaneously enriched and respectively detected through a single-step enrichment and sequential elution method. Furthermore, the composite was successfully applied to the analysis of intricate biological samples. 4 endogenous phosphopeptides and 20 phosphopeptides were trapped from human serum and non-fat milk tryptic digest respectively. From 0.5 mg of tryptic digest of rat brain, 141 N-linked glycopeptides corresponding to 127 glycoproteins and 918 phosphopeptides corresponding to 397 phosphoproteins were enriched simultaneously and identified respectively, proving the Fe3O4@SiO2@(Zr-Ti-MOF)10-NH2 to be a dependable candidate for the simultaneously enrichment of trace phosphopeptides and glycopeptides in intricate biological samples.

Layer-by-layer assembled magnetic bimetallic metal-organic framework composite for global phosphopeptide enrichment.

The highly selective enrichment of phosphopeptides is vital for the research of phosphorylated proteomics. Herein, a magnetic bimetallic metal-organic framework (MOF) with Zr-O and Ti-O clusters (denoted as Fe3O4@SiO2@(Zr-Ti-PTA)15) has been fabricated using a layer-by-layer assembly approach via the coordination of metal ions with carboxyl groups. The composite has large specific surface area (135.84 m2 g-1) and superparamagnetism (62.03 emu g-1). Compared with single-metal cluster MOF, the Fe3O4@SiO2@(Zr-Ti-PTA)15 showed higher binding capacity (100 mg g-1), enhanced affinity, better selectivity (nß-casein : nBSA = 1 : 2000) and sensitivity (0.3 fmol/µL) towards phosphopeptides due to the combination of the dual metal clusters. Furthermore, the Fe3O4@SiO2@ (Zr-Ti-PTA)15 was successfully applied to extracting phosphopeptides from non-fat milk tryptic digest, and 10 mono-phosphopeptides and 22 multi-phosphopeptides were captured. As a result, 1294 phosphopeptides (476 multi-phosphopeptides and 818 mono-phosphopeptides) were selectively extracted and detected from tryptic digest of rat brain extract, indicating its great application potential in phosphorylated proteomics research.

Programmable Bidirectional Folding of Metallic Thin Films for 3D Chiral Optical Antennas.

3D structures with characteristic lengths ranging from nanometer to micrometer scale often exhibit extraordinary optical properties, and have been becoming an extensively explored field for building new generation nanophotonic devices. Albeit a few methods have been developed for fabricating 3D optical structures, constructing 3D structures with nanometer accuracy, diversified materials, and perfect morphology is an extremely challenging task. This study presents a general 3D nanofabrication technique, the focused ion beam stress induced deformation process, which allows a programmable and accurate bidirectional folding (-70°-+90°) of various metal and dielectric thin films. Using this method, 3D helical optical antennas with different handedness, improved surface smoothness, and tunable geometries are fabricated, and the strong optical rotation effects of single helical antennas are demonstrated.

Multi-Direction-Tunable Three-Dimensional Meta-Atoms for Reversible Switching between Midwave and Long-Wave Infrared Regimes.

We introduce an electromechanically tunable metasurface composed of an array of three-dimensional nanosplit-rings for reversible and large-range changes of optical characteristics in infrared (IR) regime. When a current is induced or withdrawn, each nanosplit ring in the surface can deform in multi directions and consequently become a closed (OFF) or an open (ON) state. Theoretical and experimental results manifest that, as the metasurface is dynamically manipulated between the ON and OFF states, the corresponding resonance absorption will reversibly switch between the long wave (around 10.4 µm) and midwave (around 6.3 µm) IR regimes, two key IR spectral windows, and the reversible relative reflection changes can reach up to 95%.

Epothilone B induces apoptosis and enhances apoptotic effects of ABT-737 on human cancer cells via PI3K/AKT/mTOR pathway.

PURPOSE: Epothilone B and its derivatives are tested in multiple clinical trials. Epothilone B induces neurotoxic effect in clinical trials; however, low-dose epothilone B regimen can promote neuroprotection and neurogenesis. Thus, the study of new combination chemotherapy regimen incorporating low-dose epothilone B with other chemotherapeutic agents might help to develop epothilone B-based approaches to cancer treatment and avoid the neurotoxicity of epothilone B. METHODS: Cell proliferation was assessed by SRB cell viability assay. Apoptosis was analyzed by propidium iodide (PI) staining. Mitochondrial membrane depolarization was evaluated using JC-1 staining. The expression of proteins was detected by western blotting. RESULTS: In this study, we demonstrated that the combination of ABT-737 and low-dose epothilone B showed synergistic anti-proliferation effects on human cancer cells. In addition, epothilone B + ABT-737 synergy was through mitochondria-mediated apoptosis pathway. Furthermore, combination treatment markedly induced the activation of caspase-3 and the cleavage of PARP. The activation of PI3K/Akt/mTOR pathway is associated with resistance to epothilone B. Our data showed that epothilone B plus ABT-737 resulted in a blockade of the PI3K/AKT/mTOR signaling pathway. CONCLUSIONS: These data indicate that ABT-737 may be a pertinent sensitizer to epothilone B, and the strategy of combining epothilone B with ABT-737 appears to be an attractive option for overcoming the resistance and neurotoxicity of epothilone B.

Evodiamine induces apoptosis and enhances apoptotic effects of erlotinib in wild-type EGFR NSCLC cells via S6K1-mediated Mcl-1 inhibition.

Erlotinib is effective in NSCLC patients with known drug-sensitizing EGFR mutations, but its clinical efficacy in patients with wild-type EGFR or acquired resistance to erlotinib remains modest. Evodiamine is a chemical extracted from the Evodia rutaecarpa (Juss.) Benth, we showed that evodiamine could induce anti-proliferation and apoptosis in four wild-type EGFR NSCLC cell lines, and combining evodiamine with erlotinib might successfully inhibit cell proliferation and survival in wild-type EGFR NSCLC cells, characterized as erlotinib-resistant. In addition, evodiamine plus erlotinib significantly increased the apoptotic rate of NSCLC cells, as compared to single agent treatment alone. Further investigation of the mechanism underlying these effects revealed that evodiamine plus erlotinib might downregulate Mcl-1 expression through the mTOR/S6K1 control of its translation. Thus, our study has revealed evodiamine as a pertinent sensitizer to erlotinib and the strategy of combining erlotinib with evodiamine appears to be an attractive option for reversing resistance to erlotinib.