Diverse polyacetylenes from Atractylodes chinensis and their anti-osteoclastogenesis activity.

The phytochemical investigation on Atractylodes chinensis afforded 15 polyacetylenes 1-15 and one meroterpenoid 16. Of the 16 isolates, compounds 4 and 9 are new ones, and compounds 8 and 16 are first reported from nature. In addition, the relative configuration of 1 and the available NMR data of compounds 1, 8, and 16 were first provided. Their structures were elucidated by extensive analysis of MS, UV, IR, and NMR spectroscopic data. Besides, all isolated compounds were evaluated for their effects on RANKL-induced osteoclastogenesis in BMMs. Among them, polyacetylenes 12-14 showed potent inhibitory activity with IC50 values of 0.67 ± 0.05 µM, 0.72 ± 0.31 µM, and 2.40 ± 0.41 µM, respectively. The current work demonstrates the polyacetylenes are the main active constituents of A. chinensis against osteoclastogenesis.

Oridonin Inhibits SARS-CoV-2 by Targeting Its 3C-Like Protease.

The current COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an enormous threat to public health. The SARS-CoV-2 3C-like protease (3CLpro), which is critical for viral replication and transcription, has been recognized as an ideal drug target. Herein, it is identified that three herbal compounds, Salvianolic acid A (SAA), (-)-Epigallocatechin gallate (EGCG), and Oridonin, directly inhibit the activity of SARS-CoV-2 3CLpro. Further, blocking SARS-CoV-2 infectivity by Oridonin is confirmed in cell-based experiments. By solving the crystal structure of 3CLpro in complex with Oridonin and comparing it to that of other ligands with 3CLpro, it is identified that Oridonin binds at the 3CLpro catalytic site by forming a C-S covalent bond, which is confirmed by mass spectrometry and kinetic study, blocking substrate binding through a nonpeptidomimetic covalent binding mode. Thus, Oridonin is a novel candidate to develop a new antiviral treatment for COVID-19.

Saucerneol attenuates nasopharyngeal carcinoma cells proliferation and metastasis through selectively targeting Grp94.

BACKGROUND: Nasopharyngeal carcinoma (NPC) is highly prevalent in southern China. The remote metastasis of advanced NPC requires chemotherapeutic treatments to reduce the mortality. Our previous work revealed that saucerneol (SN) showed cytotoxicity against several nasopharyngeal carcinoma (NPC) cells. This work aims to investigate the effect of SN in NPC growth and exploring the mechanism of action. STUDY DESIGN: Applying in vivo study, in vitro study and in silico study to indicate the mechanism of SN in inhibiting NPC growth. METHODS: Saucerneol (SN) toxicity was measured with MTT assay. NPC proliferation was measured with EdU and colony formation assays, cell cycle was detected with flow cytometry. NPC migration and invasion were measured with scratch assay and matrigel transwell method. Further, human NPC xenograft tumor models were established in nude mice to evaluate the therapeutic efficacy of SN in vivo. Toxicological analysis was performed on H&E staining and IHC. Quantitative real-time PCR and Western blot analyses were used to evaluate the expression levels of key molecules in PI3K/AKT/mTOR, MAPK, NF-κB, and HIF-1α signal pathways. Target predicting was conducted using computational method, and target identification was carried out by ATPase assay and TSA. RESULTS: SN, a potent NPC inhibitor that was previously isolated from Saururus chinensis in our lab, is proven to inhibit the proliferation and metastasis of HONE1 cell lines and inhibit the growth of human NPC xenografts in nude mice. Moreover, we further articulate the molecular mechanism of action for SN and, reveal that SN promotes the expression of cell cycle-dependent kinase inhibitory protein p21 Waf1/Cip1 through targeting Grp94 and then inhibiting PI3K/AKT signaling pathway as well as up-regulating p53 to disrupt the progression of HONE1 cells. CONCLUSION: SN significantly inhibits NPC cells proliferation and metastasis in vitro and in vivo via selectively inhibit Grp94 and then blocking PI3K/AKT/mTOR/HIF-1α signaling pathway. This study firstly provides a novel selective Grp94 inhibitor as a NPC candidate.

Discovery of phloroglucinols from Hypericum japonicum as ferroptosis inhibitors.

Ferroptosis is a new type of cell death, which involves central neuronal system. Inhibition of ferroptosis is a promising strategy to prevent and treat neurological diseases. Thirteen phloroglucinols (1-13) were obtained from the whole plants of Hypericum japonicum. Of them, compounds 1-3 are new ones. Their structures were elucidated by extensive analysis of spectroscopic data and X-ray diffraction. All the isolates were evaluated for their inhibitory effect on RSL3-induced ferroptosis. Two new compounds 2-3 showed significant inhibitory effect with EC50 of 0.48 ± 0.14 µM and 0.94 ± 0.14 µM, respectively. DPPH free radical scavenging abilities of all compounds were assessed to evaluate their antioxidant effect. This work first reports the anti-ferroptosis activity of phloroglucinols.

Diverse diterpenoids and sesquiterpenoids from Siegesbeckia pubescens and their activity against RANKL-induced osteoclastogenesis.

Phytochemical investigation of the aerial parts of Siegesbeckia pubescens led to seventeen diterpenoids (1-17) and twelve sesquiterpenoids (18-29). Their structures were varied including twelve ent-pimarane (1-12), three ent-kaurane (13-15), two acyclic diterpenoids (16-17), ten germacrene (18-27), one guaiane (28), and one caryolane (29) sesquiterpenoids. Eight of twenty-nine were new ones (1, 3, 4, 16-18, 23, and 28). Their structures were elucidated by extensive spectroscopic analysis. The absolute configurations of compounds 1 and 2 were identified using X-ray diffraction analysis, and of compounds 18, 23, and 28 were elucidated by the experimental and calculated electronic circular dichroism (ECD) spectra. All the isolated compounds (1-29) were assayed for their inhibition of RANKL-induced osteoclastogenesis in bone marrow macrophages (BMMs). Four sesquiterpenoids 18, 25, 26, and 27 exhibited potent inhibition of osteoclastogenesis with IC50 value of 0.51, 0.80, 0.50, and 0.83 µM, respectively. Here we demonstrated that S. pubescens may be a resource for discovery of anti-osteoporosis agents.

Discovery of ingenane and jatrophane diterpenoids from Euphorbia esula as inhibitors of RANKL-induced osteoclastogenesis.

Two new ingenane diterpenoids (1-2), four new jatrophane diterpenoids (3-6), and seven known analogues (7-13), were isolated from the 95% ethanol extract of Euphorbia esula. Their structures were determined by extensive spectroscopic methods and ECD data analysis. These compounds were assayed for their anti-osteoporotic activity in a bone marrow-derived macrophage (BMM) cell line, and compounds 2, 4, 7, 8, 9, and 11 significantly inhibited the formation of osteoclasts with IC50 values of 3.4, 4.3, 2.1, 0.5, 1.5, and 4.5 µM, respectively. These compounds also dose-dependently reduced the activity of nuclear factor activated T-cell cytoplasmic 1 (NFATc1). This study reveals the anti-osteoporotic effects of ingenane diterpenoids for the first time.

Chinese herbal medicine for premature ovarian insufficiency: A protocol for systematic review.

BACKGROUND: Premature ovarian insufficiency (POI) is the loss of function of the ovaries before age 40. Chinese herbal medicine (CHM) has been treating POI for long time. Therefore, we conduct this study to assess the efficacy and safety of CHM for POI. METHODS: Seven databases will be searched from inception to December 31, 2018: PubMed, Embase, Cochrane Library, Chinese National Knowledge Infrastructure (CNKI), China Biology Medicine disc (CBM), WanFang Database, and Chongqing Chinese Scientific Journal Database (CQVIP). Randomized controlled trials that used CHM will be included. Two reviewers will independently complete the study selection, data extraction, and study quality assessment according to Cochrane Collaboration. All the data will be analyzed using Review Manage 5.3 software. RESULTS: This study will generate a comprehensive summary on effectiveness and safety of CHM for POI. CONCLUSION: This study may be beneficial to health policymakers, clinicians, and patients with regard to the use of CHM in POI treatment. TRIAL REGISTRATION NUMBER: PROSPERO CRD 42019144629.

DeepChemStable: Chemical Stability Prediction with an Attention-Based Graph Convolution Network.

In the drug discovery process, unstable compounds in storage can lead to false positive or false negative bioassay conclusions. Prediction of the chemical stability of a compound by de novo methods is complex. Chemical instability prediction is commonly based on a model derived from empirical data. The COMDECOM (COMpound DECOMposition) project provides the empirical data for prediction of chemical stability. Models such as the extended-connectivity fingerprint and atom center fragments were built from the COMDECOM data and used for estimation of chemical stability, but deficits in the existing models remain. In this paper, we report DeepChemStable, a model employing an attention-based graph convolution network based on the COMDECOM data. The main advantage of this method is that DeepChemStable is an end-to-end model, which does not predefine structural fingerprint features, but instead, dynamically learns structural features and associates the features through the learning process of an attention-based graph convolution network. The previous ChemStable program relied on a rule-based method to reduce the false negatives. DeepChemStable, on the other hand, reduces the risk of false negatives without using a rule-based method. Because minimizing the rate of false negatives is a greater concern for instability prediction, this feature is a major improvement. This model achieves an AUC value of 84.7%, recall rate of 79.8%, and 10-fold stratified cross-validation accuracy of 79.1%.

Discovery of a New Pterocarpan-Type Antineuroinflammatory Compound from Sophora tonkinensis through Suppression of the TLR4/NFκB/MAPK Signaling Pathway with PU.1 as a Potential Target.

Neuroinflammation underlies many neuro-degenerative diseases. In this paper, we report the identification of a new pterocarpan-type anti-inflammatory compound named sophotokin isolated from Sophora tonkinensis. S. tonkinensis has been used traditionally for treatment of conditions related to inflammation. Our initial screening showed that sophotokin dose-dependently inhibits lipopolysaccharide (LPS)-stimulated production of NO, TNF-α, PGE2, and IL-1ß in microglial cells. This antineuroinflammatory effect was associated with sophotokin's blockade of LPS-induced production of the inflammatory mediators iNOS and COX-2. Western blot and qPCR analysis demonstrated that sophotokin inhibits both the p38-MAPK and NF-κB signal pathways. Further studies revealed that sophotokin also suppresses the expression of cluster differentiation 14 (CD14) in the toll-like receptor 4 (TLR4) signaling pathway. Following down-regulation of MyD88 and TRAF6, sophotokin inhibits the activation of the NF-κB and MAPK signal pathways in LPS-induced BV-2 cells. In silico studies suggested that sophotokin could interact with PU.1-DNA complex through hydrogen binding at sites 1 and 2 of the complex, blocking the DNA binding. This suggests that PU.1 may be a potential target of sophotokin. Taken together, these results suggest that sophotokin may have therapeutic potential for diseases related to neuroinflammation. The mechanism of antineuroinflammatory effects involves inhibition of the TLR4 signal pathway at the sites of NF-κB and MAPK with PU.1 as a likely upstream target.

Cembrane-type diterpenoids from Macaranga pustulata.

Three new cembrane-type diterpenoids, deheiculatins M-O (1-3), together with five known analogues (4-8), were isolated from the twigs of Macaranga pustulata King ex Hook. The structures of new compounds 1-3 were elucidated by extensive spectroscopic analyses, modified Mosher's method, and the experimental and calculated electronic circular dichroism (ECD) experiments. All the isolates were evaluated for their cytotoxicity on three human cancer cell lines (CNE1, CNE2, and HCT 116), and all of them showed weak cytotoxicity (IC50 > 20 µM).

TCMAnalyzer: A Chemo- and Bioinformatics Web Service for Analyzing Traditional Chinese Medicine.

Traditional Chinese medicine (TCM) has been widely used and proven effective in long term clinical practice. However, the molecular mechanism of action for many TCMs remains unclear due to the complexity of many ingredients and their interactions with biological receptors. This is one of the major roadblocks in TCM modernization. In order to solve this problem, we have developed TCMAnalyzer, which is a free web-based toolkit allowing a user to (1) identify the potential compounds that are responsible for the bioactivities for a TCM herb through scaffold-activity relation searches using structural search techniques, (2) investigate the molecular mechanism of action for a TCM herb at the systemic level, and (3) explore the potentially targeted bioactive herbs. The toolkit can result in TCM networks that demonstrate the relations among natural product molecules (small molecular ligands), putative protein targets, pathways, and diseases. These networks are graphically depicted to reveal the mechanism of actions for a TCM herb or to identify new molecular scaffolds for new chemotherapies. TCMAnalyzer is freely available at http://www.rcdd.org.cn/tcmanalyzer .

The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs.

The emergence of drug resistance is a major limitation of current antimalarials. The discovery of new druggable targets and pathways including those that are critical for multiple life cycle stages of the malaria parasite is a major goal for developing next-generation antimalarial drugs. Using an integrated chemogenomics approach that combined drug resistance selection, whole-genome sequencing, and an orthogonal yeast model, we demonstrate that the cytoplasmic prolyl-tRNA (transfer RNA) synthetase (PfcPRS) of the malaria parasite Plasmodium falciparum is a biochemical and functional target of febrifugine and its synthetic derivative halofuginone. Febrifugine is the active principle of a traditional Chinese herbal remedy for malaria. We show that treatment with febrifugine derivatives activated the amino acid starvation response in both P. falciparum and a transgenic yeast strain expressing PfcPRS. We further demonstrate in the Plasmodium berghei mouse model of malaria that halofuginol, a new halofuginone analog that we developed, is active against both liver and asexual blood stages of the malaria parasite. Halofuginol, unlike halofuginone and febrifugine, is well tolerated at efficacious doses and represents a promising lead for the development of dual-stage next-generation antimalarials.

ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase.

Febrifugine is the active component of the Chinese herb Chang Shan (Dichroa febrifuga Lour.), which has been used for treating malaria-induced fever for about 2,000 years. Halofuginone (HF), the halogenated derivative of febrifugine, has been tested in clinical trials for potential therapeutic applications in cancer and fibrotic disease. Recently, HF was reported to inhibit T(H)17 cell differentiation by activating the amino acid response pathway, through inhibiting human prolyl-transfer RNA synthetase (ProRS) to cause intracellular accumulation of uncharged tRNA. Curiously, inhibition requires the presence of unhydrolysed ATP. Here we report an unusual 2.0 Å structure showing that ATP directly locks onto and orients two parts of HF onto human ProRS, so that one part of HF mimics bound proline and the other mimics the 3' end of bound tRNA. Thus, HF is a new type of ATP-dependent inhibitor that simultaneously occupies two different substrate binding sites on ProRS. Moreover, our structure indicates a possible similar mechanism of action for febrifugine in malaria treatment. Finally, the elucidation here of a two-site modular targeting activity of HF raises the possibility that substrate-directed capture of similar inhibitors might be a general mechanism that could be applied to other synthetases.