Investigating the anti-atherosclerotic effects and potential mechanism of Dalbergia odorifera in ApoE-deficient mice using network pharmacology combined with metabolomics.

Dalbergia odorifera (DO) is a precious rosewood species in Southern Asia, and its heartwood is used in China as an official plant for invigorating blood circulation and eliminating stasis. This study aims to evaluate the efficacy of DO on atherosclerosis (AS), and further explore its active components and potential mechanisms. The apolipoprotein-E (ApoE)-deficient mice fed a high-fat diet were used as model animals, and the pathological changes in mice with or without DO treatment were compared to evaluate the pharmacodynamics of DO on AS. The mechanisms were preliminarily expounded by combining with metabolomics and network pharmacology. Moreover, the bioactive components and targets were assessed by cell experiments and molecular docking, respectively. Our findings suggested that DO significantly modulated blood lipid levels and alleviated intimal hyperplasia in atherosclerotic-lesioned mice, and the mechanisms may involve the regulation of 18 metabolites that changed during the progression of AS, thus affecting 3 major metabolic pathways and 3 major signaling pathways. Moreover, the interactions between 16 compounds with anti-proliferative effect and hub targets in the 3 signaling pathways were verified using molecular docking. Collectively, our findings preliminarily support the therapeutic effect of DO in atherosclerosis, meanwhile explore the active constituents and potential pharmacological mechanisms, which is conducive to its reasonable exploitation and utilization.

Neural Correlates of Early-Life Urbanization and Their Spatial Relationships with Gene Expression, Neurotransmitter, and Behavioral Domain Atlases.

Previous neuroimaging research has established associations between urban exposure during early life and alterations in brain function and structure. However, the molecular mechanisms and behavioral relevance of these associations remain largely unknown. Here, we aimed to address this question using a combined analysis of multimodal data. Initially, we calculated amplitude of low-frequency fluctuations (ALFF) and gray matter volume (GMV) using resting-state functional and structural MRI to investigate their associations with early-life urbanization in a large sample of 511 healthy young adults. Then, we examined the spatial relationships of the identified neural correlates of early-life urbanization with gene expression, neurotransmitter, and behavioral domain atlases. Results showed that higher early-life urbanization scores were correlated with increased ALFF of the right fusiform gyrus and decreased GMV of the left dorsal medial prefrontal cortex and left precuneus. Remarkably, the identified neural correlates of early-life urbanization were spatially correlated with expression of gene categories primarily involving immune system process, signal transduction, and cellular metabolic process. Concurrently, there were significant associations between the neural correlates and specific neurotransmitter systems including dopamine, acetylcholine, and serotonin. Finally, we found that the ALFF correlates were associated with behavioral terms including "perception," "sensory," "cognitive control," and "reasoning." Apart from expanding existing knowledge of early-life urban environmental risk for mental disorders and health in general, our findings may contribute to an emerging framework for integrating social science, neuroscience, genetics, and public policy to respond to the major health challenge of world urbanization.

Brain Structural and Functional Damage Network Localization of Suicide.

BACKGROUND: Extensive neuroimaging research on brain structural and functional correlates of suicide has produced inconsistent results. Despite increasing recognition that damage in multiple different brain locations that causes the same symptom can map to a common brain network, there is still a paucity of research investigating network localization of suicide. METHODS: To clarify this issue, we initially identified brain structural and functional damage locations in relation to suicide from 63 published studies with 2135 suicidal and 2606 nonsuicidal individuals. By applying novel functional connectivity network mapping to large-scale discovery and validation resting-state functional magnetic resonance imaging datasets, we mapped these affected brain locations to 3 suicide brain damage networks corresponding to different imaging modalities. RESULTS: The suicide gray matter volume damage network comprised widely distributed brain areas primarily involving the dorsal default mode, basal ganglia, and anterior salience networks. The suicide task-induced activation damage network was similar to but less extensive than the gray matter volume damage network, predominantly implicating the same canonical networks. The suicide resting-state activity damage network manifested as a localized set of brain regions encompassing the orbitofrontal cortex and middle cingulate cortex. CONCLUSIONS: Our findings not only may help reconcile prior heterogeneous neuroimaging results, but also may provide insights into the neurobiological mechanisms of suicide from a network perspective, which may ultimately inform more targeted and effective strategies to prevent suicide.

Metabolomics and lipidomics combined with serum pharmacochemistry uncover the potential mechanism of Huang-Lian-Jie-Du decoction alleviates atherosclerosis in ApoE-/- mice.

ETHNOPHARMACOLOGICAL RELEVANCE: Atherosclerosis (AS) is one of the main cardiovascular diseases (CVDs) leading to an increase in global mortality, and its key pathological features are lipid accumulation and oxidative stress. Huang-Lian-Jie-Du decoction (HLJDD), a representative formula for clearing heat and detoxifying, has been shown to reduce aortic lipid plaque and improve AS. However, multiple components and multiple targets of HLJDD pose a challenge in comprehending its comprehensive mechanism in the treatment of AS. AIM OF THE STUDY: This study was designed to illustrate the anti-AS mechanisms of HLJDD in an apolipoprotein E-deficient (ApoE-/-) mouse model from a metabolic perspective. MATERIALS AND METHODS: ApoE-/- mice were kept on a high-fat diet (HFD) to induce AS. Serum total cholesterol (TC), total triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) levels were determined to evaluate the influence of HLJDD on dyslipidemia. Oil red O was used to stain mouse aortic lipid plaques, and hematoxylin and eosin (HE) staining was used to assess the pathological changes in the aortic roots. Metabolomics and lipidomics combined with serum pharmacochemistry were performed to research the HLJDD mechanism of alleviating AS. RESULTS: In this study, HLJDD treatment improved serum biochemical levels and histopathological conditions in AS mice. A total of 6 metabolic pathways (arginine biosynthesis, glycerophospholipid, sphingolipid, arachidonic acid, linoleic acid, and glycerolipid metabolism) related to 25 metabolic biomarkers and 41 lipid biomarkers were clarified, and 22 prototype components migrating to blood were identified after oral administration of HLJDD. CONCLUSION: HLJDD improved AS induced by HFD in ApoE-/- mice. The effects of HLJDD were mainly attributed to regulating lipid metabolism by regulating the metabolic pathways of glycerophospholipids, sphingolipids, arachidonic acid, linoleic acid, and glycerolipids and reducing the levels of oxidative stress by upregulating arginine biosynthesis.

Discovery of Pyxinol Amide Derivatives Bearing Amino Acid Residues as Nonsubstrate Allosteric Inhibitors of P-Glycoprotein-Mediated Multidrug Resistance.

Nonsubstrate allosteric inhibitors of P-glycoprotein (Pgp), which are considered promising modulators for overcoming multidrug resistance (MDR), are relatively unknown. Herein, we designed and synthesized amino acids bearing amide derivatives of pyxinol, the main ginsenoside metabolite produced by the human liver, and examined their MDR reversal abilities. A potential nonsubstrate inhibitor (7a) was identified to undergo high-affinity binding to the putative allosteric site of Pgp at the nucleotide-binding domains. Subsequent assays confirmed that 7a (25 µM) was able to suppress both basal and verapamil-stimulated Pgp-ATPase activities (inhibition rates of 87 and 60%, respectively) and could not be pumped out by Pgp, indicating that it was a rare nonsubstrate allosteric inhibitor. Moreover, 7a interfered with Pgp-mediated Rhodamine123 efflux while exhibiting high selectivity for Pgp. Notably, 7a also markedly enhanced the therapeutic efficacy of paclitaxel, with a tumor inhibition ratio of 58.1%, when used to treat nude mice bearing KBV xenograft tumors.

Dual cross-linked starch hydrogel for eugenol encapsulation and the formation of hydrogen bonds on textural hydrogel.

Physical and chemical cross-linked hydrogels combining N, N'-Methylenebisacrylamide (MBA)-grafted starch (MBAS) and sorbitol were successfully prepared and encapsulated with eugenol in this work. The dense porous structure with diameter of 10-15 µm and strong skeleton after restructuring inside the hydrogel was confirmed by SEM. The band shifts between 3258 cm-1 and 3264 cm-1 clarified the presence of a large number of hydrogen bonds in physical and chemical cross-linked hydrogels. The robust structure of the hydrogel was confirmed by mechanical and thermal property measurements. Molecular docking techniques were used to help understand the bridging pattern between three raw materials and to assess the advantageous conformation, which demonstrate sorbitol is beneficial to improve the characteristics of textural hydrogel by the formation of hydrogen bonds, creating a denser network, structural recombination and new intermolecular hydrogen bonds between starch and sorbitol afforded considerably junction zones. Compared to ordinary starch-based hydrogels, eugenol-loaded starch-sorbitol hydrogels (ESSG) exhibited a more attractive internal structure, swelling properties, viscoelasticity. Moreover, the ESSG showed excellent antimicrobial activity for typical undesired microorganisms in foods.

Green preparation of 3D micronetwork eugenol-encapsuled porous starch for improving the performance of starch-based antibacterial film.

In order to find a non-enzymatically treated alternative wall material with effective encapsulation properties, and to reduce the use of conventional non-biodegradable plastics, a novel 3D-micronetwork porous starch (3D-MPS) was created via a modified sacrificial template method to encapsulate eugenol (3D-EMPS) and used to incorporate with TiO2-starch film, for significantly improving the performance of starch-based antibacterial film. At the template SiO2 nanoparticles concentration of 0.1 %, the 3D-MPS exhibited anticipated alveolate structure with internal aperture of approximately 10 µm confirmed by SEM. With addition of 3D-EMPS, higher tensile strength (29.70 Mpa) and water barrier property (924 g/cm2·24 h) of the composite film was obtained. Moreover, molecular docking technique was used to model the intermolecular forces, which showed that the major forces maintaining the internal bonding of the composite film were hydrogen bonding and the interaction between eugenol and 3D-MPS skeleton in 3D-EMPS. Meanwhile, the composite film demonstrated the expected eugenol retardation and antimicrobial capacity against S. aureus, E. coli, and B. subtilis. Finally, the composite films were used for evaluating the feasibility in the actual food, which largely extended its shelf life compared to the negative control. This high-performance film revealed their potential for packaging materials application.

Developments in molecular docking technologies for application of polysaccharide-based materials: A review.

With the increasing pollution of the planet, the search for natural multifunctional alternatives to petroleum-based plastics has assumed to be a great important proposition. Polysaccharides, an inexhaustible natural resource with good biocompatibility as well as mechanical properties, are considered as an ideal alternative to petroleum-based materials. However, blind experimentation and development will inevitably lead to waste of raw materials and contamination of reagents. Therefore, researchers desire a technology which can assist in predicting and screening experimental materials at the higher level. Molecular docking simulations, an emerging computer technology that can effectively predict the structure of interactions between molecules and analyze the optimal conformation, are a common aid for materials and drug design. In this review, we describe the origins and development of molecular docking techniques, mainly performed an overview of various molecular docking software on their applications in the field of different polysaccharide materials.

Design, synthesis, and discovery of Eudistomin Y derivatives as lysosome-targeted antiproliferation agents.

Eudistomin Y is a novel class of ß-carbolines of marine origin with potential antiproliferation activity against MDA-MB-231 cells (triple-negative breast carcinoma). However, the subcellular target or the detailed mechanism against cancer cell proliferation has not yet been identified. In this study, based on its special structure, a novel series of Eudistomin Y fluorescent derivatives were designed and synthesized by enhancing the electron-donor effect of N-9 to endow it with fluorescent properties through N-alkylation. The structure-activity relationships against the proliferation of cancer cells were also analyzed. A quarter of Eudistomin Y derivatives showed much higher potency against cancer cell proliferation than the original Eudistomin Y1. Fluorescent derivative H1k with robust antiproliferative activity could arrest MDA-MB-231 cells in the G2-M phase. The subcellular localization studies of the probes, including H1k, and Eudistomin Y1 were performed in MDA-MB-231 cells, and the co-localization and competitive inhibition assays revealed their lysosome-specific localization. Moreover, H1k could dose-dependently increase the autophagy signal and downregulate the expression of cyclin-dependent kinase (CDK1) and cyclin B1 which principally regulated the G2-M transition. Furthermore, the specific autophagy inhibitor 3-methyladenine significantly inhibited the H1k-triggered antiproliferation of cancer cells and the downregulation of CDK1 and cyclin B1. Overall, the lysosome is identified as the subcellular target of Eudistomin Y for the first time, and derivative H1k showed robust antiproliferative activity against MDA-MB-231 cells by decreasing Cyclin B1-CDK1 complex via a lysosome-dependent pathway.

ANP32B promotes lung cancer progression by regulating VDAC1.

It has been reported before that acidic leucine-rich nuclear phosphoprotein 32 family member B (ANP32B) plays roles in many cancers, yet no report of its role in lung cancer exists. In this study, we documented an elevation of ANP32B within lung cancer tissues and cells. Knockdown of ANP32B hindered the proliferation as well as migration of lung cancer cells, whereas overexpression of ANP32B helps to promote the malignant progression of lung cancer. ANP32B also regulates lung cancer cells' apoptosis and cell cycling. In addition, voltage-dependent anion channel 1 (VDAC1) has been found to be a downstream targeted gene of ANP32B and is positively regulated by ANP32B in lung cancer cells. According to our research, the expression of VDAC1 was positively associated with ANP32B expression in lung adenocarcinoma (r = 0.61, P < 0.001) samples by Pearson's correlation coefficient analysis. Furthermore, rescue experiments demonstrated that VDAC1 could rescue the effect of ANP32B expression on lung cancer cell proliferation and migration. Our results suggest that ANP32B overexpression facilitates lung cancer progression by increasing the expression of VDAC1. As such, we have revealed a novel mechanism regulating the connection between ANP32B and VDAC1 and a potential role of ANP32B as an oncogene and a clinical therapeutic target in lung cancer.

Cerebral blood flow changes and their genetic mechanisms in major depressive disorder: a combined neuroimaging and transcriptome study.

BACKGROUND: Extensive research has shown abnormal cerebral blood flow (CBF) in patients with major depressive disorder (MDD) that is a heritable disease. The objective of this study was to investigate the genetic mechanisms of CBF abnormalities in MDD. METHODS: To achieve a more thorough characterization of CBF changes in MDD, we performed a comprehensive neuroimaging meta-analysis of previous literature as well as examined group CBF differences in an independent sample of 133 MDD patients and 133 controls. In combination with the Allen Human Brain Atlas, transcriptome-neuroimaging spatial association analyses were conducted to identify genes whose expression correlated with CBF changes in MDD, followed by a set of gene functional feature analyses. RESULTS: We found increased CBF in the reward circuitry and default-mode network and decreased CBF in the visual system in MDD patients. Moreover, these CBF changes were spatially associated with expression of 1532 genes, which were enriched for important molecular functions, biological processes, and cellular components of the cerebral cortex as well as several common mental disorders. Concurrently, these genes were specifically expressed in the brain tissue, in immune cells and neurons, and during nearly all developmental stages. Regarding behavioral relevance, these genes were associated with domains involving emotion and sensation. In addition, these genes could construct a protein-protein interaction network supported by 60 putative hub genes with functional significance. CONCLUSIONS: Our findings suggest a cerebral perfusion redistribution in MDD, which may be a consequence of complex interactions of a wide range of genes with diverse functional features.

The Critical Role of 12-Methyl Group of Anthracycline Dutomycin to Its Antiproliferative Activity.

Anthracycline dutomycin is a tetracyclic quinone glycoside produced by Streptomyces minoensis NRRL B-5482. SW91 is a C-12 demethylated dutomycin derivative, which was identified in our previous research. In vitro cytotoxicity and apoptosis assays of these two compounds were conducted to demonstrate their antiproliferation activities. The results showed that both dutomycin and SW91 block cells at the S phase, whereas dutomycin shows more significant inhibition of cell growth. Their interactions with calf thymus DNA (CT-DNA) were investigated, with dutomycin exhibiting higher binding affinity. The molecular docking demonstrated that the 12-methyl group makes dutomycin attach to the groove of DNA. These findings suggest that dutomycin has binding higher affinity to DNA and impairs DNA replication resulting in more significant antitumor activity.

Identification and engineering on the nonconserved residues of metallo-ß-lactamase-type thioesterase to improve the enzymatic activity.

The standalone metallo-ß-lactamase-type thioesterase (MßL-TE), belongs to the group V nonreducing polyketide synthase agene cluster, catalyzes the rate-limiting step of product releasing. Our work first investigated on the orthologous MßL-TEs from different origins to determine which nonconserved amino acid residues are important to the hydrolysis efficiency. A series of chimeric MßL-TEs were constructed by fragment swapping and site-directed mutagenesis, in vivo enzymatic assay showed that two nonconserved residues A19 and E75 (numbering in HyTE) were critical to the catalytic performance. Protein structure modeling suggested that these two residues are located in different areas of HyTE. A19 is on the entrance to the active sites, whereas E75 resides in the linker between the two ß strands which hold the metal-binding sites. Combining with computational simulations and comparative enzymatic assay, different screening criteria were set up for selecting the variants on the two noncatalytic and nonconserved key residues to improve the catalytic activity. The rational design on A19 and E75 gave five candidates in total, two (A19F and E75Q) of which were thus found significantly improved the enzymatic performance of HyTE. The double-point mutant was constructed to further improve the activity, which was increased by 28.4-fold on product accumulation comparing to the wild-type HyTE. This study provides a novel approach for engineering on nonconserved residues to optimize enzymatic performance.