Quantitative ternary network-oriented discovery of Q-markers from traditional Chinese medicine prescriptions: Bu-Zhong-Yi-Qi-Tang as a case study.

BACKGROUND: The proposal of Q-markers for traditional Chinese medicine (TCM) represents a novel avenue of research pertaining to the quality control of TCM prescriptions. However, prior exploratory studies on Q-markers with multiple properties consistently neglected the consideration of weights, hampering our ability to accurately gauge the significance of each property and potentially leading to a flawed comprehension of Q-markers. PURPOSE: In this study, a quantitative ternary network strategy was firstly proposed to visually discover the Q-markers from TCM prescriptions, and it has been successfully applied into the quality control study of Bu-Zhong-Yi-Qi-Tang (BZYQT), a classical TCM prescription. METHODS: Firstly, the contents of 34 components in BZYQT, along with the kinetic features of 17 candidate Q-markers in biosamples (plasma and small intestinal contents), were characterized by UPLC-QqQ-MS/MS, and their immunomodulatory activities in macrophages and splenic lymphocytes were also assessed. Next, the obtained data were integrated into three properties: testability, bioavailability, effectiveness, and their weights were calculated using the entropy weight method to further establish a ternary network for quantitatively screening Q-markers. Subsequently, the identified Q-markers of BZYQT were utilized for the holistic quality evaluation of 36 batches of the commercial BZYQT preparation, Bu-Zhong-Yi-Qi-Pill (BZYQP) produced by three manufacturers, through similarity evaluation of the Q-marker-based fingerprint. RESULTS: Nine compounds (hesperidin, astragaloside IV, ononin, 18ß-glycyrrhizic acid, narirutin, calycosin, cimigenoside, astragaloside II, and liquiritin) showing three core properties, including testability, bioavailability, and effectiveness, were screened out as Q-markers of BZYQT based on their rankings in terms of regression area of the ternary network. Employing Q-markers as common peaks, the similarity values of 36 batches BZYQP ranged 0.914-0.998 under HPLC-UVD mode, and 0.631-1.000 under HPLC-ELSD mode, which were less than the similarity values evaluated by the conventional common peaks (HPLC-UVD mode: 0.946-0.990; HPLC-ELSD mode: 0.957-0.997). This observation suggests that the identified Q-markers are more representative as common peaks in chromatographic fingerprints for the holistic quality evaluation of TCM-related products from different manufacturers. CONCLUSION: The quantitative discovery of Q-markers from BZYQT laid an important foundation for holistic quality assessment of its related commercially available products, and our work offering a new strategy for ensuring the consistency and efficacy of TCM prescriptions.

A multi-module structure labelled molecular network orients the chemical profiles of traditional Chinese medicine prescriptions: Xiaoyao San, as an example.

Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) technology has emerged as a crucial tool for identifying components in traditional Chinese medicine (TCM). However, the characterization of the chemical profiles of TCM prescriptions (TCMPs) which often consist of multiple herbal medicines and contain diverse structural types, presents several challenges, such as component overlapping and time-consuming. In this study, a novel strategy known as the multi-module structure labelled molecular network (MSLMN), which integrates molecular networking, database annotation, and cluster analysis techniques, has been successfully proposed, which facilitates the identification of chemical constituents by leveraging a high-structural similarity ion list derived from the MSLMN. It has been effectively applied to analyze the chemical profile of Xiaoyao San (XYS), a classical TCMP. Through the MSLMN method, a total of 302 chemical constituents were identified, covering nine structural types in XYS. Furthermore, a validated and quantitative analytical method using UHPLC-QqQ-MS/MS technology was developed for 31 identified chemicals, encompassing all eight herbal medicines present in XYS, and the developed analytical approach was applied to investigate the content distribution across 40 different batches of commercially available XYS. In total, the proposed strategy has practical significance for improving the insight into the chemical profile of XYS and serves as a valuable approach for handling complex system data based on UHPLC-MS, particularly for TCMPs.

Four new prenylated flavonoids from the roots of Cudrania tricuspidata.

Four new prenylated flavonoids, cudraflavanones E-F (1-2) and cudraflavones F-G (6-7), together with eight known compounds were isolated from the roots of Cudrania tricuspidata. The structures of new compounds were elucidated on the basis of extensive spectroscopic analyses, including 1D and 2D NMR, HRESIMS and CD.

Virtual screening and biological evaluation of biofilm inhibitors on dual targets in quorum sensing system.

AIM: Resistance to conventional antibiotics has spurred interest in exploring new antimicrobial strategies. Suppressing quorum sensing within biofilm is a promising antimicrobial strategy. LasR in quorum sensing system of the Gram-negative bacteria, Pseudomonas aeruginosa, directly enhances virulence and antibiotic resistance, with QscR as its indirect suppressor, so targeting both of them can synergistically take the effect. METHODOLOGY/RESULTS: An in silico protocol combining pharmacophores with molecular docking was applied. Pharmacophores of QscR agonists and LasR antagonists were prepared for preliminary screening, followed by counter-screen using a pharmacophore model of LasR agonists and molecular docking of LasR. Four compounds with novel scaffolds were confirmed as potential biofilm inhibitors with preliminary experimental data. CONCLUSION: Novel biofilm inhibitors can be found with the method.

DAW22, a natural sesquiterpene coumarin isolated from Ferula ferulaeoides (Steud.) Korov. that induces C6 glioma cell apoptosis and endoplasmic reticulum (ER) stress.

2,3-Dihydro-7-hydroxy-2R*,3R*-dimethyl-2-[4,8-dimethyl-3(E),7-nonadienyl]-furo[3,2-c]coumarin (named DAW22), a sesquiterpene coumarin isolated from the roots of Ferula ferulaeoides (Steud.) Korov., has been reported to bear anti-proliferative activities toward different types of cancer cells. In this study, we demonstrated that DAW22 induced apoptosis in C6 glioma cells. Subsequently, we found that DAW22-induced apoptosis in C6 glioma cells occurred via the mitochondria-mediated and death-receptor pathways. Moreover, we found a massive cytoplasmic vacuolization, a dramatic change of endoplasmic reticulum (ER), up-regulation of CHOP and cleavage of caspase-12, suggesting that DAW22-induced apoptosis is involved in ER stress. In addition, we revealed that DAW22 treatment induced the activation of PERK, ATF6α and IRE1α. We further found that knockdown of CHOP affected DAW22-induced apoptosis, and DAW22-stimulated down-regulation of Bcl-2, caspase-8 activation and PARP cleavage were inhibited. Taken together, these results demonstrate that DAW22 induces apoptosis by ER stress and mitochondrial/death-receptor pathways, which may provide a new clue for exploiting this compound as a potential anti-neoplastic drug in future glioma cancer therapy.

Apoptotic and autophagic pathways with relevant small-molecule compounds, in cancer stem cells.

Accumulating evidence demonstrates existence of cancer stem cells (CSCs), which are suspected of contributing to cancer cell self-renewal capacity and resistance to radiation and/or chemotherapy. Including evasion of apoptosis and autophagic cell death, CSCs have revealed abilities to resist cell death, making them appealing targets for cancer therapy. Recently, molecular mechanisms of apoptosis and of autophagy in CSCs have been gradually explored, comparing them in stem cells and in cancer cells; distinct expression of these systems in CSCs may elucidate how these cells exert their capacity of unlimited self-renewal and hierarchical differentiation. Due to their proposed ability to drive tumour initiation and progression, CSCs may be considered to be potentially useful pharmacological targets. Further, multiple compounds have been verified as triggering apoptosis and/or autophagy, suppressing tumour growth, thus providing new strategies for cancer therapy. In this review, we summarized regulation of apoptosis and autophagy in CSCs to elucidate how key proteins participate in control of survival and death; in addition, currently well-studied compounds that target CSC apoptosis and autophagy are selectively presented. With increasing attention to CSCs in cancer therapy, researchers are now trying to find responses to unsolved questions as unambiguous as possible, which may provide novel insight into future anti-cancer regimes.

Systems biology network-based discovery of a small molecule activator BL-AD008 targeting AMPK/ZIPK and inducing apoptosis in cervical cancer.

The aim of this study was to discover a small molecule activator BL-AD008 targeting AMPK/ZIPK and inducing apoptosis in cervical cancer. In this study, we systematically constructed the global protein-protein interaction (PPI) network and predicted apoptosis-related protein connections by the Naïve Bayesian model. Then, we identified some classical apoptotic PPIs and other previously unrecognized PPIs between apoptotic kinases, such as AMPK and ZIPK. Subsequently, we screened a series of candidate compounds targeting AMPK/ZIPK, synthesized some compounds and eventually discovered a novel dual-target activator (BL-AD008). Moreover, we found BL-AD008 bear remarkable anti-proliferative activities toward cervical cancer cells and could induce apoptosis by death-receptor and mitochondrial pathways. Additionally, we found that BL-AD008-induced apoptosis was affected by the combination of AMPK and ZIPK. Then, we found that BL-AD008 bear its anti-tumor activities and induced apoptosis by targeting AMPK/ZIPK in vivo. In conclusion, these results demonstrate the ability of systems biology network to identify some key apoptotic kinase targets AMPK and ZIPK; thus providing a dual-target small molecule activator (BL-AD008) as a potential new apoptosis-modulating drug in future cervical cancer therapy.

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives.

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q (2) values of 0.753 and 0.770, and r (2) values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2'-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure-property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature.

Diphenyl ethers from Aspergillus sp. and their anti-Aß42 aggregation activities.

Two new compounds with the character of diphenyl ether structure, oxisterigmatocystin D (1) and 9-acetyldiorcinol B (6), were isolated from the endolichenic fungal strain Aspergillus sp. (No. 16-20-8-1), along with six known compounds, oxisterigmatocystin A (2), oxisterigmatocystin C (3), sterigmatocystin (4), diorcinol B (5), violaceol-I (7), and violaceol-II (8). The structures of the new compounds were determined by extensive NMR spectroscopic data, and the absolute configuration of 1 was established by single-crystal X-ray diffraction analysis. Moreover, the Aß42 aggregation inhibitory activities of 5-8 were evaluated by the standard thioflavin T (ThT) fluorescence assay using epigallocatechin gallate (EGCG) as the positive control. Compounds 7 and 8 displayed significant anti-Aß42 aggregation activity with IC50 values of 5.1 and 2.3µM, respectively. Preliminary structure-activity relationship of these diphenyl ethers as anti-Aß42 aggregation inhibitors was proposed.