PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues.

A series of C-3 and C-28 MeON-neoglycosides of oleanolic acid were designed and synthesized by neoglycosylation as potential antiproliferative agents. Their cytotoxicity was evaluated in vitro against five human cancer cell lines: human non-small cell lung cancer cell line (A549), human melanoma cell line (A375), human colon cancer cell line (HCT116), human liver carcinoma cell line (HepG2), human breast adenocarcinoma cell line (MCF-7) by the Cell Counting Kit-8 (CCK-8) assay. Most of C-3 and C-28 MeON-neoglycosides of oleanolic acid exhibited notably inhibitory effects against the tested cancer cells and more sensitive to HepG2 cells than 5-Fluorouracil (5-FU). Structure-activities relationship (SAR) analysis revealed that sugar types and the d/l configuration of sugars would significantly affect their antiproliferative activities of neoglycosides. Among them, compound 8a (28-N-methoxyaminooleanane-β-d-glucoside) exhibited the most potent antiproliferative activities against HepG2 cells with IC50 values of 2.1 µM. Further pharmacological experiments revealed that compound 8a could cause morphological changes and cell cycle arrest at G0/G1 phase and induce apoptosis in HepG2 cells. These results suggested that neoglycosylation could provide a rapid strategy for the discovery of potential antiproliferative agents and their possible pharmacological mechanisms need more further research.

BRD9 and TAF1(2) have been regarded as significant targets of drug design for clinically treating acute myeloid leukemia, malignancies, and inflammatory diseases. In this study, multiple short molecular dynamics simulations combined with the molecular mechanics generalized Born surface area method were employed to investigate the binding selectivity of three ligands, 67B, 67C, and 69G, to BRD9/TAF1(2) with IC50 values of 230/59 nM, 1400/46 nM, and 160/410 nM, respectively. The computed binding free energies from the MM-GBSA method displayed good correlations with that provided by the experimental data. The results indicate that the enthalpic contributions played a critical factor in the selectivity recognition of inhibitors toward BRD9 and TAF1(2), indicating that 67B and 67C could more favorably bind to TAF1(2) than BRD9, while 69G had better selectivity toward BRD9 over TAF1(2). In addition, the residue-based free energy decomposition approach was adopted to calculate the inhibitor-residue interaction spectrum, and the results determined the gatekeeper (Y106 in BRD9 and Y1589 in TAF1(2)) and lipophilic shelf (G43, F44, and F45 in BRD9 and W1526, P1527, and F1528 in TAF1(2)), which could be identified as hotspots for designing efficient selective inhibitors toward BRD9 and TAF1(2). This work is also expected to provide significant theoretical guidance and insightful molecular mechanisms for the rational designs of efficient selective inhibitors targeting BRD9 and TAF1(2).

Secreted proteins are widely spread in living organisms and cells. Since secreted proteins are easy to be detected in body fluids, urine, and saliva in clinical diagnosis, they play important roles in biomarkers for disease diagnosis and vaccine production. In this study, we propose a novel predictor for accurate high-throughput identification of mammalian secreted proteins that is based on sequence-derived features. We combine the features of amino acid composition, sequence motifs, and physicochemical properties to encode collected proteins. Detailed feature analyses prove the effectiveness of the considered features. Based on the differences across various species of secreted proteins, we introduce the species-specific scheme, which is expected to further explore the intrinsic attributes of specific secreted proteins. Experiments on benchmark datasets prove the effectiveness of our proposed method. The test on independent testing dataset also promises a good generalization capability. When compared with the traditional universal model, we experimentally demonstrate that the species-specific scheme is capable of significantly improving the prediction performance. We use our method to make predictions on unreviewed human proteome, and find 272 potential secreted proteins with probabilities that are higher than 99%. A user-friendly web server, named iMSPs (identification of Mammalian Secreted Proteins), which implements our proposed method, is designed and is available for free for academic use at: http://www.inforstation.com/webservers/iMSP/.

Both HDACs and Mnks play important role in translating multiple oncogenic signaling pathways during oncogenesis. As HDAC and Mnk are highly expressed in a variety of tumors; thus simultaneous inhibit HDAC and Mnk can increase the inhibition of tumor cell proliferation and provide a new way of inhibiting tumor growth. Based on the previous work and the merge pharmacophore method; we designed and synthesized a series of 4,6-disubstituted pyrido[3,2-d]pyrimidine derivatives as HDAC and Mnk dual inhibitors. Among them; compound A12 displayed good HDAC and Mnk inhibitory activity. In vitro antiproliferative assay; compound A12 exhibited the best antiproliferative activity against human prostate cancer PC-3 cells. Docking study revealed that the pyrido[3,2-d]pyrimidine framework and hydroxamic acid motif of compound A12 were essential for maintaining the activity of HDAC and Mnk. These result indicated that A12 was a potent Mnk /HDAC inhibitor and will be further researched.

Euphorbia factors, lathyrane-type diterpenoids isolated from the medical herb Euphorbia lathyris L. (Euphorbiaceae), have been associated with intestinal irritation toxicity, but the mechanisms underlying this phenomenon are still unknown. The objective of this study was to evaluate the transcriptome and miRNA profiles of human colon adenocarcinoma Caco-2 cells in response to Euphorbia factors L1 (EFL1) and EFL2. Whole transcriptomes of mRNA and microRNA (miRNA) were obtained using second generation high-throughput sequencing technology in response to 200 μM EFL treatment for 72 h, and the differentially expressed genes and metabolism pathway were enriched. Gene structure changes were analyzed by comparing them with reference genome sequences. After 72 h of treatment, 16 miRNAs and 154 mRNAs were differently expressed between the EFL1 group and the control group, and 47 miRNAs and 1101 mRNAs were differentially expressed between the EFL2 group and the control. Using clusters of orthologous protein enrichment, the sequenced mRNAs were shown to be mainly involved in transcription, post-translational modification, protein turnover, chaperones, signal transduction mechanisms, intracellular trafficking, secretion, vesicular transport, and the cytoskeleton. The differentially expressed mRNA functions and pathways were enriched in transmembrane transport, T cell extravasation, the IL-17 signaling pathway, apoptosis, and the cell cycle. The differentially expressed miRNA EFLs caused changes in the structure of the gene, including alternative splicing, insertion and deletion, and single nucleotide polymorphisms. This study reveals the underlying mechanism responsible for the toxicity of EFLs in intestinal cells based on transcriptome and miRNA profiles of gene expression and structure.

The CD13 inhibitor ubenimex is used as an adjuvant drug with chemotherapy for the treatment of cancer due to its function as an immunoenhancer, but it has limitations in its cytotoxic efficacy. The proteasome inhibitor ixazomib is a landmark drug in the treatment of multiple myeloma with a high anti-cancer activity. Herein, we conjugated the pharmacophore of ubenimex and the boric acid of ixazomib to obtain a dual CD13 and proteasome inhibitor 7 (BC-05). BC-05 exhibited potent inhibitory activity on both human CD13 (IC50 = 0.13 μM) and the 20S proteasome (IC50 = 1.39 μM). Although BC-05 displayed lower anti-proliferative activity than that of ixazomib in vitro, an advantage was established in the in vivo anti-cancer efficacy and prolongation of survival time, which may be due to its anti-metastatic and immune-stimulating activity. A pharmacokinetic study revealed that BC-05 is a potentially orally active agent with an F% value of 24.9%. Moreover, BC-05 showed more favorable safety profiles than those of ixazomib in preliminary toxicity studies. Overall, the results indicate that BC-05 is a promising drug candidate for the treatment of multiple myeloma.

Accumulation of α-synuclein (α-Syn) is a remarkable pathology for Parkinson's disease (PD), therefore clearing it is possibly a promising strategy for treating PD. Aberrant copper (Cu(II)) homeostasis and oxidative stress play critical roles in the abnormal aggregation of α-Syn in the progress of PD. It is reported that the polyphenol (-)-epi-gallocatechin gallate (EGCG) can inhibit α-Syn fibrillation and aggregation, disaggregate α-Syn mature fibrils, as well as protect α-Syn overexpressed-PC12 cells against damage. Also, previous studies have reported that EGCG can chelate many divalent metal ions. What we investigate here is whether EGCG can interfere with the Cu(II) induced fibrillation of α-Syn and protect the cell viability. In this work, on a molecular and cellulaire basis, we demonstrated that EGCG can form a Cu(II)/EGCG complex, leading to the inhibition of Cu(II)-induced conformation transition of α-Syn from random coil to β-sheet, which is a dominant structure in α-Syn fibrils and aggregates. Moreover, we found that the mixture of Cu(II) and EGCG in a molar ratio from 0.5 to 2 can efficiently inhibit this process. Furthermore, we demonstrated that in the α-Syn transduced-PC12 cells, EGCG can inhibit the overexpression and fibrillation of α-Syn in the cells, and reduce Cu(II)-induced reactive oxygen species (ROS), protecting the cells against Cu(II)-mediated toxicity.

To address drug resistance to influenza virus neuraminidase inhibitors (NAIs), a series of novel boron-containing N-substituted oseltamivir derivatives were designed and synthesized to target the 150-cavity of neuraminidase (NA). In NA inhibitory assays, it was found that most of the new compounds exhibited moderate inhibitory potency against the wild-type NAs. Among them, compound 2c bearing 4-(3-boronic acid benzyloxy)benzyl group displayed weaker or slightly improved activities against group-1 NAs (H1N1, H5N1, H5N8 and H5N1-H274Y) compared to that of oseltamivir carboxylate (OSC). Encouragingly, 2c showed 4.6 times greater activity than OSC toward H5N1-H274Y NA. Moreover, 2c exerted equivalent or more potent antiviral activities than OSC against H1N1, H5N1 and H5N8. Additionally, 2c demonstrated low cytotoxicity in vitro and no acute toxicity at the dose of 1000 mg/kg in mice. Molecular docking of 2c was employed to provide a possible explanation for the improved anti-H274Y NA activity, which may be due to the formation of key additional hydrogen bonds with surrounding amino acid residues, such as Arg152, Gln136 and Val149. Taken together, 2c appeared to be a promising lead compound for further optimization.

Peptidyl-prolyl cis/trans isomerase Pin1 plays a key role in amplifying and translating multiple oncogenic signaling pathways during oncogenesis. The blockade of Pin1 provided a unique way of disrupting multiple oncogenic pathways and inducing apoptosis. Aiming to develop potent Pin1 inhibitors, a series of benzimidazole derivatives were designed and synthesized. Among the derivatives, compounds 6h and 13g showed the most potent Pin1 inhibitory activity with IC50 values of 0.64 and 0.37 μM, respectively. In vitro antiproliferative assay demonstrated that compounds 6d, 6g, 6h, 6n, 6o and 7c exhibited moderate antiproliferative activity against human prostate cancer PC-3 cells. Taken together, these unique benzimidazole derivatives exhibited great potential to be further explored as potent Pin1 inhibitors with improved potency.

To investigate the anti-atherosclerosis related mechanism of blueberries, the phenolic acids (PAs) content, antioxidant and anti-inflammatory activities, as well as the microRNA (miRNA) regulation of polyphenol fractions in blueberry samples from China were studied. Sixteen batches of blueberries including 14 commercialized cultivars (Reka, Patriot, Brigitta, Bluecrop, Berkeley, Duke, Darrow, Northland, Northblue, Northcountry, Bluesource, Southgood, O'Neal, and Misty) were used in this study. Seven PAs in the polyphenol fractions from 16 blueberry samples in China were quantified by high performance liquid chromatography/tandem mass spectrometry (HPLC/MS²). The antioxidant activities of blueberry polyphenols were tested by (1,1-diphenyl-2-picrylhydrazyl [DPPH]) assay. The anti-inflammatory (tumor necrosis factor-α [TNF-α] and interleukin-6 [IL-6]) activities of the polyphenol fractions of the blueberries were investigated by using lipopolysaccharide (LPS) induced RAW 264.7 macrophages. The correlation analysis showed that the antioxidant (1,1-diphenyl-2-picrylhydrazyl [DPPH]) and anti-inflammatory (tumor necrosis factor-α [TNF-α] and interleukin-6 [IL-6]) activities of the polyphenol fractions of the blueberries were in accordance with their PA contents. Although the polyphenol-enriched fractions of blueberries could inhibit the microRNAs (miRNAs) (miR-21, miR-146a, and miR-125b) to different extents, no significant contribution from the PAs was observed. The inhibition of these miRNAs could mostly be attributed to the other compounds present in the polyphenol-enriched fraction of the blueberries. This is the first study to evaluate the PAs content, antioxidant and anti-inflammatory activities, and miRNA regulation of Chinese blueberries.

Fibrillar accumulation of A53T mutant α-synuclein (A53T-AS) in Lewy bodies is a symptom of Parkinsonism. Inhibitions of the overexpression and fibrillar aggregation of α-synuclein (AS) in vivo could be a promising strategy for treating Parkinson's disease (PD). In this study, at concentrations lower than 1 mM, trehalose decreased the A53T-AS expression level in transduced PC12 cells. Although H₂O₂ and aluminum ions increased the expression level and neurotoxicity of A53T-AS in cells, proper trehalose concentrations inhibited the event. These studies adequately prove that trehalose at an appropriate dose would be potentially useful for PD treatment.

Metastasis is the major cause of death in colorectal cancer and it has been proven that inhibiting an interaction between adenomatous polyposis coli (APC) and Rho guanine nucleotide exchange factor 4 (Asef) efficaciously restrain metastasis. However, current inhibitors cannot achieve a satisfying effect in vivo and need to be optimized. In the present study, we applied molecular dynamics (MD) simulations and extensive analyses to apo and holo APC systems in order to reveal the inhibitor mechanism in detail and provide insights into optimization. MD simulations suggested that apo APC takes on a broad array of conformations and inhibitors stabilize conformation selectively. Representative structures in trajectories show specific APC-ligand interactions, explaining the different binding process. The stability and dynamic properties of systems elucidate the inherent factors of the conformation selection mechanism. Binding free energy analysis quantitatively confirms key interface residues and guide optimization. This study elucidates the conformation selection mechanism in APC-Asef inhibition and provides insights into peptide-based drug design.

Lysozyme is a key effector molecule of the innate immune system in both vertebrate and invertebrate. It is classified into six types, one of which is the goose-type (g-type). To date, no study on g-type lysozyme in crustacean has been documented. Here, we report the identification and characterization of a g-type lysozyme (named LysG1) from the shrimp inhabiting a deep-sea hydrothermal vent in Manus Basin. LysG1 possesses conserved structural features of g-type lysozymes. The recombinant LysG1 (rLysG1) exhibited no muramidase activity and killed selectively Gram-negative bacteria in a manner that depended on temperature, pH, and metal ions. rLysG1 bound target bacteria via interaction with bacterial cell wall components, notably lipopolysaccharide (LPS), and induced cellular membrane permeabilization, which eventually caused cell lysis. The endotoxin-binding capacity enabled rLysG1 to alleviate the inflammatory response induced by LPS. Mutation analysis showed that the bacterial binding and killing activities of rLysG1 required the integrity of the conserved α3 and 4 helixes of the protein. Together, these results provide the first insight into the activity and working mechanism of g-type lysozyme in crustacean and deep-sea organisms.

This study aimed to construct objective and accurate geographical discriminant models for tea leaves based on multielement concentrations in combination with chemometrics tools. Forty mineral elements in 87 tea samples from three growing regions in Guizhou Province (China), namely Meitan and Fenggang (MTFG), Anshun (AS) and Leishan (LS) were analyzed. Chemometrics evaluations were conducted using a one-way analysis of variance (ANOVA), principal component analysis (PCA), linear discriminant analysis (LDA), and orthogonal partial least squares discriminant analysis (OPLS-DA). The results showed that the concentrations of the 28 elements were significantly different among the three regions (p < 0.05). The correct classification rates for the 87 tea samples were 98.9% for LDA and 100% for OPLS-DA. The variable importance in the projection (VIP) values ranged between 1.01⁻1.73 for 11 elements (Sb, Pb, K, As, S, Bi, U, P, Ca, Na, and Cr), which can be used as important indicators for geographical origin identification of tea samples. In conclusion, multielement analysis coupled with chemometrics can be useful for geographical origin identification of tea leaves.

The effects of chlorogenic acid (CA) (6, 30, and 150 μM/g protein) on the physicochemical and functional properties of Coregonus peled myofibrillar protein (MP) through oxidation using a hydroxyl radical oxidation system (0.01 mM FeCl3, 0.01 mM Asc, and 1 mM H2O2) were investigated. The result showed that CA inhibited the increase in protein carbonyl content but did not prevent losses in sulfhydryl and free amine contents caused by oxidation. The presence of CA also increased conformational changes in the secondary and tertiary structures of oxidized MP. Oxidized MP containing 6 μM/g CA had superior functional properties (solubility, emulsifying, foaming, and gel properties), while oxidized MP containing 150 μM/g CA aggregated, resulting in insolubility and a poor gel network.