1.Integrating network toxicology, molecular docking, and molecular dynamics simulation to explore the mechanisms underlying depression induced by low‑chlorinated polychlorinated dibenzo‑p‑dioxins
Xueting YIN ; Boyi CHU ; Pengzhan YANG ; Chengpeng ZHANG
Sichuan Mental Health 2026;39(4):345-355
BackgroundPolychlorinated dibenzo‑p‑dioxins (PCDDs) is a type of global environmental pollutants, have been shown in numerous studies to exert neurotoxic effects. Nevertheless, existing research has predominantly focused on 2,3,7,8‑tetrachlorodibenzo‑p‑dioxin (2,3,7,8‑TCDD). Whether low‑chlorinated PCDDs (LC‑PCDDs), a subclass with fewer chlorine substitutions, can induce depression as well as the corresponding molecular mechanisms remains unclear. ObjectiveTo elucidate molecular mechanisms underlying depression induced by LC‑PCDDs, so as to provide evidence for environmental neuro-psychotoxicological risk assessment. Methods①Network toxicology. Four compounds, namely 2-monochlorodibenzo-p-dioxin (2-MCDD), dichlorodibenzo-p-dioxin (DCDD), 1,2,4‑trichlorodibenzo‑p‑dioxin (1,2,4-TrCDD), and 2,3,7-TrCDD, were selected as research subjects. Their toxic profiles were predicted using public databases, and target genes associated with LC-PCDDs and depression were retrieved. The overlapping targets were imported into the STRING database to construct a protein-protein interaction (PPI) network. Topological analysis was subsequently performed via the CytoNCA plugin in Cytoscape to identify hub targets. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for these hub targets were completed in DAVID. ②Molecular docking. Docking simulations were conducted using AutoDock Tools 1.5.7, and the binding poses and interaction profiles of the resultant protein-ligand complexes were visualized using PyMOL (TM) 3.1.6.1. ③Molecular dynamics simulation. A 100-ns production simulation for the top-ranked docked complex was carried out using GROMACS 2025. The protein was parameterized with the AMBER99SB-ILDN force field, the ligand topologies were generated using GAFF2, and the two were then merged to construct the protein-ligand complex system. The complex was solvated in TIP3P water, and the system was adjusted to physiological ionic strength by adding 0.15 mol/L Na⁺/Cl⁻. Following energy minimization and sequential 2-ns equilibrations in canonical and isothermal-isobaric ensembles, a 100-ns production run was executed at 310 K and 1 bar. Results①Network toxicology analysis identified 10 hub targets (ESR1, HSP90AA1, PPARG, EGFR, MAPK1, MAPK14, AR, PGR, CDK2, and TGFBR1), which were enriched in multiple critical signaling pathways. ②Molecular docking revealed that all four compounds exhibited strong binding affinities for hub targets, with 2-MCDD showing the highest binding affinity for PPARG (ΔG=-8.836 kcal/mol). ③Molecular dynamics simulations demonstrated that the ligand-receptor complex formed by 2-MCDD and PPARG maintained a stable binding conformation throughout the 100-ns simulation. ConclusionLC-PCDDs may serve as significant environmental risk factors for depression, participating in its pathogenesis by mediating a multidimensional regulatory network involving metabolism, oxidative damage and apoptosis. [Funded by Hubei Province Traditional Chinese Medicine Clinical Excellent Talents Project].
2.Spatiotemporally delivery of Cas9 ribonucleoprotein/DNAzyme logic systems using near-infrared upconversion nanomachine for precise immunotherapy.
Chao CHEN ; Shiyu DU ; Qianglan LU ; Xueting SHEN ; Shuai DING ; Lihua QU ; Yamei GAO ; Zhiqiang YIN ; Zhe LI ; Yujun SONG ; Xin HAN
Acta Pharmaceutica Sinica B 2025;15(10):5431-5443
Gene therapy, harnessing the power of CRISPR-Cas9 and/or DNAzyme systems, stands as a pivotal approach in cancer therapy, enabling the meticulous manipulation of genes pivotal to tumorigenesis and immunity. However, the pursuit of precise gene therapy encounters formidable hurdles. Herein, a near-infrared upconversion theranostic nanomachine is devised and tailors for CRISPR-Cas9/DNAzyme systems mediate precise gene therapy. An ingenious logic DNAzyme system consists of Chain 1 (C1)/Chain 2 (C2) and endogenous lncRNA is designed. We employ manganese modified upconversion nanoparticles for carrying ultraviolet-responsive C1-PC linker-C2 (C2P) chain and Cas9 ribonucleoprotein (RNP), with outermost coats with hyaluronic acid. Upon reaching tumor microenvironment (TME), the released Mn2+ ions orchestrate a trifecta: facilitating endosomal escape, activating cGAS-STING signaling, and enabling T1-magnetic resonance imaging. Under near-infrared irradiation, Cas9 RNP/C2P complex dissociates, releasing Cas9 RNP into the nucleus to perform gene editing of Ptpn2, while C1/C2 chains self-assemble with endogenous lncRNA to form a functional DNAzyme system, targeting PD-L1 mRNA for gene silencing. This strategy remodels the TME by activating cGAS-STING signaling and dual immune checkpoints blockade, thus realizing tumor elimination. Our theranostic nanomachine armed with the CRISPR-Cas9/DNAzyme logic systems, represents a resourceful and promising strategy for advancing cancer systemic immunotherapy and precise gene therapy.
3.Self-assembly in the transparent droplets formed during the screening of protein self-assembly conditions.
Tuodi ZHANG ; Xudong DENG ; Fengzhu ZHAO ; Wenpu SHI ; Liangliang CHEN ; Yaqing ZHOU ; Xueting WANG ; Chenyan ZHANG ; Dachuan YIN
Chinese Journal of Biotechnology 2021;37(4):1396-1405
Protein self-assemblies at the micro- and nano-scale are of great interest because of their morphological diversity and good biocompatibility. High-throughput screening of protein self-assembly at different scales and morphologies using protein crystallization screening conditions is an emerging method. When using this method to screen protein self-assembly conditions, some apparently transparent droplets are often observed, in which it is not clear whether self-assembly occurs. We explored the interaction between β-lactoglobulin and the protein crystallization kit Index™ C10 and observed the presence of micro- and nano-scale protein self-assemblies in the transparent droplets. The diverse morphology of the micro- and nano-scale self-assemblies in the transparent droplets formed by mixing different initial concentrations of β-lactoglobulin and Index™ C10 was further investigated by scanning electron microscope. Self-assembly process of fluorescence-labelled β-lactoglobulin was monitored continuously by laser confocal microscope, allowing real-time observation of the liquid-liquid phase separation phenomenon and the morphology of the final self-assemblies. The internal structure of the self-assemblies was gradually ordered over time by in-situ X-ray diffraction. This indicates that the self-assembly phenomenon within transparent droplets, observed in protein self-assembly condition screening experiments, is worthy of further in-depth exploration.
Crystallization
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Lactoglobulins
4.Prognostic value of arterial lactate combined with central venous-to-arterial carbon dioxide difference to arterial-to-central venous oxygen content difference ratio in septic shock patients
Xueting WANG ; Xuehua GAO ; Wen CAO ; Yin GUAN ; Yannian LUO ; Foyan LIAN ; Nannan HE ; Peijie LI
Chinese Critical Care Medicine 2020;32(1):39-43
Objective:To evaluate the prognostic value of arterial lactate (Lac) combined with central venous-to-arterial carbon dioxide difference to arterial-to-central venous oxygen content difference ratio (Pcv-aCO 2/Ca-cvO 2) in patients with septic shock following early fluid resuscitation. Methods:A total of 97 patients with septic shock admitted to intensive care unit (ICU) of Lanzhou University Second Hospital from January 2017 to December 2019 were enrolled. The Pcv-aCO 2/Ca-cvO 2 ratio was calculated from blood gas analysis of radial artery and superior vena cava which was performed before resuscitation and at 6 hours of resuscitation at the same time. The patients were divided into death group and survival group according to the 28-day prognosis. The baseline data, acute physiology and chronic health evaluation Ⅱ (APACHEⅡ) score, sequential organ failure score (SOFA), clinical therapy, lactate clearance rate (LCR) at 6 hours, the length of ICU stay, hemodynamics and oxygen metabolism parameters before and after resuscitation were compared between the two groups. Risk factors were analyzed by multivariate Cox regression for 28-day mortality of patients with septic shock. The receiver operating characteristic (ROC) curve was plotted to assess the prognostic values of these factors for 28-day mortality. Results:① Compared with the survival group, the patients in the death group showed significantly higher levels of APACHEⅡ score (23.96±4.31 vs. 17.70±3.92) and SOFA score (12.74±2.80 vs. 9.23±2.43, both P < 0.01), significantly higher proportions of mechanical ventilation [85.2% (23/27) vs. 50.0% (35/70)] and continuous renal replacement therapy [CRRT; 51.9% (14/27) vs. 25.7% (18/70), both P < 0.05], a significantly more fluid replacement at 6 hours (L: 2.92±0.24 vs. 2.63±0.25, P < 0.01), a significantly lower level of LCR at 6 hours [(11.61±7.76)% vs. (27.67±13.71)%, P < 0.01], and a shorter length of ICU stay (days: 6.37±2.70 vs. 7.67±2.31, P < 0.05). ② Compared with the survival group, the patients before resuscitation in the death group showed a significantly lower level of mean arterial pressure [MAP (mmHg, 1 mmHg = 0.133 kPa): 52.63±4.35 vs. 55.74±3.01, P < 0.01], significantly higher levels of Lac and Pcv-aCO 2/Ca-cvO 2 ratio [Lac (mmol/L): 7.13±1.75 vs. 5.22±1.36, Pcv-aCO 2/Ca-cvO 2 ratio: 1.67±0.29 vs. 1.48±0.22, both P < 0.01]; and the patients at 6 hours of resuscitation in the death group showed a significantly lower level of MAP (mmHg: 62.59±4.80 vs. 66.71±3.91, P < 0.01), significantly higher levels of central venous pressure (CVP), Lac, Pcv-aCO 2 and Pcv-aCO 2/Ca-cvO 2 ratio [CVP (mmHg): 10.74±1.40 vs. 8.80±0.75, Lac (mmol/L): 6.36±1.86 vs. 3.90±1.95, Pcv-aCO 2 (mmHg): 7.59±2.02 vs. 4.34±1.37, Pcv-aCO 2/Ca-cvO 2 ratio: 1.87±0.51 vs. 1.03±0.27, all P < 0.01]. ③ Multivariate Cox regression analysis showed that the independent risk factors for 28-day mortality in patients with septic shock were Lac and Pcv-aCO 2/Ca-cvO 2 ratio whether before or at 6 hours of resuscitation [Lac before resuscitation: relative risk ( RR) = 1.434, 95% confidence interval (95% CI) was 1.070-1.922, P = 0.016; Lac at 6 hours of resuscitation: RR = 1.564, 95% CI was 1.202-2.035, P = 0.001; Pcv-aCO 2/Ca-cvO 2 ratio before resuscitation: RR = 2.828, 95% CI was 1.108-4.207, P = 0.038; Pcv-aCO 2/Ca-cvO 2 ratio at 6 hours of resuscitation: RR = 4.386, 95% CI was 2.842-5.730, P = 0.000]. ④ ROC curve analysis showed that Lac and Pcv-aCO 2/Ca-cvO 2 ratio at 6 hours of resuscitation had predictive value for the prognosis of patients with septic shock, the area under ROC curve (AUC) was 0.849 (95% CI was 0.762-0.914) and 0.905 (95% CI was 0.828-0.955), respectively. However, the predictive value of Lac combined with Pcv-aCO 2/Ca-cvO 2 ratio in patients with septic shock was significantly higher than Lac [AUC (95% CI): 0.976 (0.923-0.996) vs. 0.849 (0.762-0.914), Z = 3.354, P = 0.001], the sensitivity was 97.14%, and the specificity was 88.89%. Conclusions:Lac and Pcv-aCO 2/Ca-cvO 2 ratio are independent risk factors for predicting 28-day mortality in patients with septic shock. Lac combined with Pcv-aCO 2/Ca-cvO 2 ratio can assess the prognosis of patients with septic shock more accurately.

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