Unraveling the mystery of efficacy in Chinese medicine formula: New approaches and technologies for research on pharmacodynamic substances

Traditional Chinese medicine (TCM) is the key to unlock treasures of Chinese civilization. TCM and its compound play a beneficial role in medical activities to cure diseases, especially in major public health events such as novel coronavirus epidemics across the globe. The chemical composition in Chinese medicine formula is complex and diverse, but their effective substances resemble “mystery boxes”. Revealing their active ingredients and their mechanisms of action has become focal point and difficulty of research for herbalists. Although the existing research methods are numerous and constantly updated iteratively, there is remain a lack of prospective reviews. Hence, this paper provides a comprehensive account of existing new approaches and technologies based on previous studies with an in vitro to in vivo perspective. In addition, the bottlenecks of studies on Chinese medicine formula effective substances are also revealed. Especially, we look ahead to new perspectives, technologies and applications for its future development. This work reviews based on new perspectives to open horizons for the future research. Consequently, herbal compounding pharmaceutical substances study should carry on the essence of TCM while pursuing innovations in the field.     

Novel aromatic carboxamides from dehydroabietylamine as potential fungicides: Design,synthesis and antifungal evaluation

The present study was carried out to design and synthesize a number of novel aromatic carboxamide derivatives of dehydroabietylamine. The preliminary antifungal assay indicated that most of title compounds displayed moderate to good antifungal activity toward the six fungal strains in vitro. Compounds 3i, 3q, 4b and 4d showed significant antifungal activity against Sclerotinia sclerotiorum, with EC₅₀ values ranging from 0.067 ～ 0.393 mg/L. Compounds 3i, 4b and 4d also showed pronounced mycelial growth inhibition activities against B. cinerea and A. solani. Furthermore, in the in vivo assay, compound 4b exhibited brilliant protective activity against S. sclerotiorum-infected rape leaves. Meanwhile, the in vivo bioassay on tomato plants infected by B. cinerea showed that compound 3i and 4d displayed excellent protective activity at 200 mg/L, which were near to boscalid. Primary mechanistic study revealed that 4b could inhibit sclerotia formation as well as reduce the exopolysaccharide level. SEM and TEM analysis indicated that 4b possessed a strong ability to destroy the surface morphology of mycelia, cell structure and seriously interfere with the growth of the fungal pathogen. In addition, 4b exhibited good inhibitory activity (IC₅₀ = 23.3 ± 1.6 μM) toward succinate dehydrogenase (SDH). Molecular modeling study confirmed the binding modes between compound 4b and SDH. The above antifungal results and fungicidal mechanism study revealed that this class of dehydroabietylamine derivatives could be potential SDH inhibitors and lead compounds for novel fungicides development.     

QM/MM Study on Enzymatic Mechanism in Sinigrin Biosynthesis

As the major and abundant type of glucosinolates (GL) in plants, sinigrin has potential functions in promoting health and insect defense. The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds, which corresponds to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase (SOT). However, due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL, little is known about this sulfonation process. Fortunately, the crystal structure of SOT 18 from Arabidopsis thaliana (AtSOT18) containing the substance (sinigrin) similar to 3-methylthiopropyl GL has been determined. To understand the enzymatic mechanism, we employed molecular dynamics (MD) simulation and quantum mechanics combined with molecular mechanics (QM/MM) methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18. The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism. Moreover, Lys93, Thr96, Thr97, Tyr130, His155, and two enzyme peptide chains (Pro92-Lys93 and Gln95-Thr96-Thr97) play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry. Particularly, His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process. The presently proposed concerted dissociative mechanism explains the role of AtSOT18 in sinigrin biosynthesis, and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.     

基于硼酸酯的19F磁共振分子探针的设计合成及活体深组织活性氧物种的激活响应成像

活性氧簇(ROS), 如过氧化氢, 在生物体内的各种生理和病理过程中发挥着重要作用. 生物体内活性氧簇水平的异常与多种疾病(炎症、 肿瘤和器官损伤等)密切相关, 使ROS监测成为研究和诊断这些疾病的重要工具. 目前, 实现活体内深组织中的活性氧簇成像仍然面临挑战. 本文设计并合成了一种响应型的¹⁹F磁共振成像(MRI)探针(Gd-DPBF), 并将其用于实现对活体内通用活性氧簇的检测和成像. 该探针由钆螯合物通过活性氧簇响应的芳香硼酸酯键与含氟砌块相连接构成. 体外和体内成像实验结果证实, 该探针可以实现在活体荷瘤小鼠中针对肿瘤中高表达的活性氧进行检测和成像, 展示了其在生物体内对活性氧簇相关生理过程进行深组织、 零生物背景成像方面的潜力.     

碳酸酐酶靶向探针的研究进展

碳酸酐酶作为一类在肿瘤中高表达的酶, 参与肿瘤组织中乏氧、 微酸性等环境的调节, 已成为肿瘤诊断与治疗的一类重要靶点. 本文简要概述了碳酸酐酶的生物学功能, 并总结了目前针对碳酸酐酶所构建的不同类型的分子探针, 以及其在肿瘤成像与治疗应用中的研究进展. 最后, 对靶向碳酸酐酶探针研究所面临的挑战和未来可能的研究方向进行了展望.     

Rational hydrothermal synthesis of graphene quantum dots with optimized luminescent properties for sensing applications

Hydrothermal synthesis using graphene oxide (GO) as a precursor has been used to produce luminescent graphene quantum dots (GQDs). However, such a method usually requires many reagents and multistep pretreatments, while can give rise to GQDs with low quantum yield (QY). Here, we investigated the concentration, the temperature of synthesis, and the pH of the GO solution used in the hydrothermal method through factorial design experiments aiming to optimize the QY of GQDs to reach a better control of their luminescent properties. The best synthesis condition (2 mg/mL, 175 °C, and pH = 8.0) yielded GQDs with a relatively high QY (8.9%) without the need of using laborious steps or dopants. GQDs synthesized under different conditions were characterized to understand the role of each synthesis parameter in the materials' structure and luminescence properties. It was found that the control of the synthesis parameters enables the tailoring of the amount of specific oxygen functionalities onto the surface of the GQDs. By changing the synthesis' conditions, it was possible to prioritize the production of GQDs with more hydroxyl or carboxyl groups, which influence their luminescent properties. The as-developed GQDs with tailored composition were used as luminescent probes to detect Fe³⁺. The lowest limit of detection (0.136 μM) was achieved using GQDs with higher amounts of carboxylic groups, while wider linear range was obtained by GQDs with superior QY. Thus, our findings contribute to rationally produce GQDs with tailored properties for varied applications by simply adjusting the synthesis conditions and suggest a pathway to understand the mechanism of detection of GQDs-based optical sensors.     

二甲双胍化学反应性的密度泛函理论研究及实验研究

二甲双胍(MET)是一个非常优良的降血糖药,一直是治疗II型糖尿病(T2DM)的首选药物,但其脂溶性较差,也存在引起胃肠道不适等副作用,对其结构修饰和衍生化,特别是将其研制成前药(Prodrug)具有一定的临床意义。为了探明二甲双胍化学反应的性能特点,本文基于密度泛函理论（DFT）开展了二甲双胍的化学内禀性质研究,包括各种可能互变异构体的单点能和量子化学反应性指数。此外,还对各异构体互变过程的过渡态以及它们的反应路径进行了研究。在此基础上,本文还对二甲双胍与亲电试剂的化学反应机理进行了初探,并用化学合成反应来验证,从而让我们能够从理论上弄清楚二甲双胍化学反应的特殊性质。     

Synthesis and antimicrobial bioassays of 1,3,4-thiadiazole sulfone derivatives containing amide moiety: A study based on molecular dynamics (MD) simulations,MM/GBSA,and molecular docking

The backbone structure (1,3,4-thiadiazole sulfone derivatives containing amide moiety) of target compounds was determined by modification and optimization of the theoretical design based on commercial chemical carboxin, including molecular docking, scaffold hopping, ligand expansion, etc.In this paper, 23 target compounds were synthesized by the combination of theoretical design and chemical synthesis, and characterized by ¹H NMR, ¹³C NMR and HR MS. Addtionally, the antibacterical bioassay showed that most target compounds performed excellent inhibition on Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas oryzae pv. oryzae (Xoo) in vitro. Meanwhile, molecular docking, molecular dynamics (MD) simulations, and studies on ligand/protein (carboxin/2FBW and 4n/2FBW) complex systems were displayed, and the interaction patterns of ligand/protein complex system were predicted by molecular docking. Besides, the ligand/protein complex system was subject to MD simulation. The analysis of molecular dynamics such as RMSD values suggested that compound/2FBW complexes were stable. MM/GBSA (Molecular mechanics generalized born surface area) dynamic binding affinity results revealed that the active residues (TYR58, HIS26, ARG43, SER39, etc.) played an essential part in the binding of the compound(s) to form a stable low-energy ligand/protein complex, while the MD trajectories demonstrated that the interactions of drugs with 2FBW affected the tertiary structure and increased the stability of protein. Besides, compound 4n also showed control efficacies (curative and protective) on Xoo in vivo, where the curative efficacy was 35.91% and the protective efficacy was 18.97%. In a word, this study showed that 1,3,4-thiadiazole sulfone derivatives containing amide moiety designed based on the structure of carboxin were promising agricultural antibacterial agents, featuring certain stability of binding affinity to proteins and carboxin.