Yun Tang

Yun Tang
East China University of Science and Technology | ECUST · School of Pharmacy

PhD

About

305
Publications
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6,205
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Publications

Publications (305)
Article
Mitochondria are important organelles in human cells, providing more than 95% of the energy. However, some drugs and environmental chemicals could induce mitochondrial dysfunction, which might cause complex diseases and even worsen the condition of patients with mitochondrial damage. Some drugs have been withdrawn from the market due to their sever...
Article
In recent years, the decline of honey bees and the collapse of bee colonies have caught the attention of ecologists, and the use of pesticides is one of the main reasons for the decline. Therefore, ecological risk assessment of pesticides is essential and necessary. In silico tools, such as QSAR models can play an important role in predicting physi...
Article
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The traditional Chinese medicines (TCMs) have been used to treat diseases over a long history, but it is still a great challenge to uncover the underlying mechanisms for their therapeutic effects due to the complexity of their ingredients. Based on a novel network pharmacology-based approach, we explored in this study the potential therapeutic targ...
Article
Although artemisinin combination therapies have succeeded in reducing the global burden of malaria, multidrug resistance of the deadliest malaria parasite, Plasmodium falciparum , is emerging worldwide. Innovative antimalarial drugs that kill all life-cycle stages of malaria parasites are urgently needed. Here, we report the discovery of the compou...
Article
MetaADEDB is an online database we developed to integrate comprehensive information on adverse drug events (ADEs). The first version of MetaADEDB was released in 2013 and has been widely used by researchers. However, it has not been updated for more than seven years. Here we reported its second version by collecting more and newer data from the U.S...
Article
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Background Arnebia euchroma (A. euchroma) is a traditional Chinese medicine (TCM) used for the treatment of blood diseases including leukemia. In recent years, many studies have been conducted on the anti-tumor effect of shikonin and its derivatives, the major active components of A. euchroma. However, the underlying mechanism of action (MoA) for a...
Article
Experimental screening of cocrystals is usually laborious and time-consuming, therefore it is urgent to develop effective in silico predictive models to guide cocrystal discovery. In this study, network-based recommendation models were proposed to predict new cocrystals for molecules in cocrystal network. The local random walk (LRW) recommender alg...
Article
The plasticity of cytochrome P450 enzymes (P450s) is known to contribute significantly to their catalytic capacity of metabolizing various substrates. Although numerous studies have been performed, factors governing the plasticity and dynamics of P450s are still not fully understood. In this study, taking CYP2B4 as an example, we dissect the protei...
Article
In this study, we developed a web server named NetInfer for prediction of targets, therapeutic and adverse effects via network-based inference methods. Compared with our previously developed standalone version of NetInfer, this web server provides a user-friendly interface. With the web server, users can easily predict potential target proteins, mi...
Article
Neurotoxicity is one of the main causes of drug withdrawal, and the biological experimental methods of detecting neurotoxic toxicity are time-consuming and laborious. In addition, the existing computational prediction models of neurotoxicity still have some shortcomings. In response to these shortcomings, we collected a large number of data set of...
Article
Free fatty acid receptor 1 (FFAR1), a member of class A in G-protein-coupled receptors (GPCRs), is a promising antidiabetic target. The crystal structure of FFAR1 revealed that one agonist (MK-8666) binds to the extracellular vestibule of this receptor, while another (AP8) occupies the surface pocket between transmembrane (TM) helices TM4 and TM5....
Preprint
Full-text available
Background: Arnebia euchroma (A. euchroma), a traditional Chinese medicine (TCM) for the treatment of blood diseases. In recent years, more and more researches have been conducted on the anti-tumor effect of shikonin and its derivatives, the major active components of A. euchroma. However, the underlying mechanism of action (MoA) for all the ingred...
Article
Full-text available
Drug discovery and development is a time-consuming and costly process. Therefore, drug repositioning has become an effective approach to address the issues by identifying new therapeutic or pharmacological actions for existing drugs. The drug's anatomical therapeutic chemical (ATC) code is a hierarchical classification system categorized as five le...
Article
As commonly-used cyclic oligomers, cyclodextrins are usually composed of 6 and 7 glucopyranose units (α-cyclodextrin and β-cyclodextrin). The binding constant is a significant parameter to estimate the association stability of inclusion complexes and evaluate the influence of cyclodextrins on guest compounds. In order to cover the shortage of exper...
Article
Epoxidation is one of the reactions in drug metabolism. Since epoxide metabolites would bind with proteins or DNA covalently, drugs should avoid epoxidation metabolism in the body. Due to the instability of epoxide, it is difficult to determine epoxidation experimentally. In silico models based on big data and machine learning methods are hence val...
Article
The farnesoid X receptor (FXR) is a bile acid-sensing transcription factor with indispensable roles in regulating kinds of metabolic processes. Nowadays, FXR has become a highly promising drug target for severe liver disorders, especially nonalcoholic steatohepatitis (NASH). A recent study showed that imatinib and its analogues were able to alloste...
Article
Structural alerts are a simple and easy way to identify toxic compounds being widely used in environmental toxicology research and drug discovery. With the emergence of big data techniques in recent years and their applications in chemistry and toxicology, computational approaches have become a promising method to identify structural alerts. In thi...
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Full-text available
The hydroxylation of non‐reactive C–H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochromes P450 (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio‐ and stereoselectivities of substrates hydroxylated by P450s remai...
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Background: Endocrine disrupting chemicals (EDCs) are xenobiotics that mimic the interaction of natural hormones and alter synthesis, transport, or metabolic pathways. The prospect of EDCs causing adverse health effects in humans and wildlife has led to the development of scientific and regulatory approaches for evaluating bioactivity. This need i...
Article
Renal clearance (CLr) plays an essential role in the elimination of drugs. In this study, 636 compounds were obtained from various sources to develop in silico models for the prediction of CLr. Step-wise multiple linear regression and random forest regression methods were employed to build global models and local models according to ionization stat...
Article
Our previous study had identified ciclopirox (CPX) as a promising lead compound for treatment of ischemic stroke. To find better neuroprotective agents, a series of N-hydroxypyridone derivatives based on CPX were designed, synthesized and evaluated in this study. Among these derivatives, compound 11 exhibits significant neuroprotection against oxyg...
Article
Full-text available
Plant-derived nature products, known as herb formulas, have been commonly used in Traditional Chinese Medicine (TCM) for disease prevention and treatment. The herbs have been traditionally classified into different categories according to the TCM Organ systems known as Meridians. Despite the increasing knowledge on the active components of the herb...
Article
In order to produce an effective and multi-targeted clinical drug that could prevent progressive neurodegeneration, a series of diosgenin carbamate derivatives were designed, synthesized and tested for their anti-inflammatory, antioxidant and anti-Aβ activities. The results demonstrated that compound M15 was the most promising derivative against in...
Article
Estrogen-related receptor alpha (ERRα), a member of nuclear receptors (NRs), participates in energy metabolism. Recent experiments identified that several agonists to increase the activity of ERRα, which have a therapeutic effect in improving insulin sensitivity and lowering blood glucose levels. However, the detailed molecular mechanism about how...
Article
Skin sensitization, frequently leading to allergic contact dermatitis (ACD), is authenticated to be a significant endpoint in the field of drug discovery and cosmetics. The initiation of ACD, also known as the skin sensitization mechanism, has been documented as an adverse outcome pathway (AOP), which can be studied experimentally and computational...
Preprint
Full-text available
Plant-derived nature products, known as herb formulas, have been commonly used in Traditional Chinese Medicine (TCM) for disease prevention and treatment. The herbs have been traditionally classified into different categories according to the TCM Organ systems known as Meridians. Despite the increasing knowledge on the active components of the herb...
Article
Full-text available
To reduce the endometrial toxicity and improve the efficacy of current selective estrogen receptor modulators used in breast cancer treatment by enhancing ERβ selectivity, inspired by active resveratrol oligomer, a series of analogs (5a–f, 6a–b, 7a–d, 8a–d) were designed, synthesized and biologically evaluated. Among them, the chiral indone analog...
Article
Breast cancer is one of the main diagnosis cancers annually worldwide. It is difficult to thorough cure due to drug resistance and the high possibility of metastasis. SM934 is a novel water-soluble artemisinin analog, and has been reported to have a promising therapeutic effect on multiple autoimmune diseases. In this study, SM934 was combined with...
Article
Overexpression of P-glycoprotein (P-gp) is one of the major causes for multidrug resistance (MDR), which has become a major obstacle in cancer therapy. One hopeful approach to reverse the MDR is to develop inhibitors of P-gp in expression and/or function. Here, we designed and synthesized a series of chalcone derivatives as P-gp inhibitors and eval...
Article
Skin sensitisation, one of the most frequent forms of human immune toxicity, is authenticated to be a significant endpoint in the field of drug discovery and cosmetics. Due to the drawbacks of traditional animal testing methods, in silico methods have advanced to study skin sensitisation. In this study, mechanism-based binary and ternary classifica...
Article
Full-text available
Background The antineoplastic activity of Chelidonium majus has been reported, but its mechanism of action (MoA) is unsuspected. The emerging theory of systems pharmacology may be a useful approach to analyze the complicated MoA of this multi-ingredient traditional Chinese medicine (TCM). Methods We collected the ingredients and related compound-t...
Article
Endocrine disruption (ED) has become a serious public health issue and also poses a significant threat to the ecosystem. Due to complex mechanisms of ED, traditional in silico models focusing on only one mechanism are insufficient for detection of endocrine disrupting chemicals (EDCs), let alone offering an overview of possible action mechanisms fo...
Article
Estrogen‐related receptor alpha (ERRα) has attracted increasing concerns. ERRα, orphan nuclear receptor, plays important roles in energy metabolism. Therefore, small molecule agonists of ERRα could be a potential therapeutic strategy in the treatment of metabolic diseases such as diabetes. Recently, Wei et al. identified cholesterol as the endogeno...
Article
Reproductive toxicity is an important regulatory endpoint in health hazard assessment. Because the in vivo tests are expensive, time consuming and require a large number of animals, which must be killed, in silico approaches as the alternative strategies have been developed to assess the potential reproductive toxicity (reproductive toxicity) of ch...
Article
Aquatic toxicity is a crucial endpoint for evaluating chemically adverse effects on ecosystems. Thus, we developed in silico methods for prediction of chemical aquatic toxicity in marine environment. At first, a diverse data set including different crustacean species was constructed. We then built local binary models using Mysidae data, and global...
Article
The cytochrome CYP3A4 and CYP3A5 share 84% sequence identity, but they exhibit different catalytic activities towards some substrates. Schisantherin E (SE) was recently identified as a selective substrate of CYP3A5, which exhibited catalytic efficiency that was more than 23 times higher than CYP3A4. At present, however, the structural determinants...
Article
The investigation of metabolically liable sites of xenobiotics mediated by UDP-glucuronosyltransferases (UGT) is important for lead optimization in early drug discovery. However, it is time-consuming and costly to identify potential susceptible sites experimentally. In silico approaches are hence developed to predict site of metabolism (SOM) of UGT...
Article
To tailor the solid state properties of rivaroxaban (RXB), microparticles were prepared using an anti-solvent precipitation technique. A mixture of hydroxypropyl methylcellulose (HPMC) and bovine serum albumin (BSA) was used for modification of the crystallization process. The solid state properties of RXB microparticles were characterized by techn...
Article
Full-text available
Chemical absorption, distribution, metabolism, excretion, and toxicity (ADMET), play key roles in drug discovery and development. A high-quality drug candidate should not only have sufficient efficacy against the therapeutic target, but also show appropriate ADMET properties at a therapeutic dose. A lot of in silico models are hence developed for p...
Article
The farnesoid X receptor (FXR) emerges as a promising drug target involved in regulating various metabolic pathways, yet some xenobiotic compounds binding to FXR would be an important determinant to induce the receptor dysfunctions that lead to undesirable side effects. Thus, it is critical to identify potential xenobiotics that disrupt normal FXR...
Article
Full-text available
Drug-target interaction (DTI) is the basis of drug discovery. However, it is time-consuming and costly to determine DTIs experimentally. Over the past decade, various computational methods were proposed to predict potential DTIs with high efficiency and low costs. These methods can be roughly divided into several categories, such as molecular docki...
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Full-text available
Vitamin K1 (VK1) plays an important role in the modulation of bleeding disorders. It has been reported that ω-hydroxylation on the VK1 aliphatic chain is catalyzed by cytochrome P450 4F2 (CYP4F2), an enzyme responsible for the metabolism of eicosanoids. However, the mechanism of VK1 ω-hydroxylation by CYP4F2 has not been disclosed. In this study, w...
Article
Full-text available
Drug-likeness comprising ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties plays significant roles in early drug discovery. However, as for current strategies of lead optimization, in vitro potency is still the focus, which may cause “molecular obesity” (poor ADMET properties). Therefore, optimization of ADMET propert...
Article
admetSAR was developed as a comprehensive source and free tool for the prediction of chemical ADMET properties. Since its first release in 2012 containing 27 predictive models, admetSAR has been widely used in chemical and pharmaceutical fields. This update, admetSAR 2.0, focuses on extension and optimization of existing models with significant qua...
Article
Blood‐Brain Barrier (BBB) as a part of absorption protects the central nervous system by separating the brain tissue from the bloodstream. In recent years, BBB permeability has become a critical issue in chemical ADMET (absorption, distribution, metabolism, excretion, and toxicity) prediction, but almost all models were built with imbalanced datase...
Article
With industrial development and eventual commercial use, environmental chemicals through accidental spills and effluents appear more frequently in aquatic ecosystem and may produce an enormous effect on water, soil, wildlife and human health. Therefore, aquatic toxicity becomes an increasing important endpoint in the evaluation of environmental imp...
Article
Avoidance of structural alerts (SA) might reduce the risk of failure in drug discovery. However, there are still some marketed drugs containing SA, which indicates that SA should be analyzed carefully to avoid their excessive uses. Several detection systems, including automatic mining methods and expert systems, have been developed to identify SA....
Article
Full-text available
Traditional Chinese medicine (TCM) is typically prescribed as formula to treat certain symptoms. A TCM formula contains hundreds of chemical components, which makes it complicated to elucidate the molecular mechanisms of TCM. Here, we proposed a computational systems pharmacology approach consisting of network link prediction, statistical analysis,...
Article
To explore the network pharmacological mechanisms of four anti-vitiligo Uyghur medicines based on the Phlegmatic temperament theory. First, The anti-vitiligo Uyghur medicine formulas based on Phlegmatic temperament theory were collected. The pharmacokinetic characteristic of main compounds in four anti-vitiligo Uyghur medicines were obtained by usi...
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Full-text available
During drug development, safety is always the most important issue, including a variety of toxicities and adverse drug effects, which should be evaluated in preclinical and clinical trial phases. This review article at first simply introduced the computational methods used in prediction of chemical toxicity for drug design, including machine learni...
Article
Full-text available
Genotoxicity tests can detect compounds that have an adverse effect on the process of heredity. In vivo micronucleus assay, a genotoxicity test method, has been widely used to evaluate the presence and extent of chromosomal damage to human beings. Due to the high cost and laboriousness of experimental tests, computational approaches for predicting...
Article
Full-text available
Background: Vitiligo is a long-term skin disease characterized by the loss of pigment in the skin. The current therapeutic approaches are limited. Although the anti-vitiligo mechanisms of Vernonia anthelmintica (L.) remain ambiguous, the herb has been broadly used in Uyghur hospitals to treat vitiligo. The overall objective of the present study ai...
Article
Full-text available
Resistance to malaria parasites has quickly developed to almost all used antimalarial drugs. Cysteine protease falcipain-2 (FP-2) and Plasmodium falciparum dihydrofolate reductase (PfDHFR) have crucial roles, which are absolutely necessary, in the parasite life cycle. In this study, based on the uniform pharmacophores of reported PfDHFR inhibitors...
Article
The μ opioid receptor (OR), a member of the class A subfamily of G-protein coupled receptors (GPCRs), is a major target for the treatment of pain. G-protein biased μ-OR agonists promise to be developed as analgesics. Thus, TRV130, the first representative μ-OR ligand with G-protein bias, has entered into phase III clinical trials. To identify the d...
Article
G protein-coupled receptors (GPCRs) are the largest super family with more than 800 membrane receptors. Currently, over 30% of the approved drugs target human GPCRs. However, only approximately 30 human GPCRs have been resolved three-dimensional crystal structures, which limits traditional structure-based drug discovery. Recent advances in network-...
Article
In drug design and discovery, binding affinity and selectivity are two basic properties of a drug candidate. Opioid receptors (ORs) are the main targets of strong analgesics. Like some other class A members of G-protein-coupled receptors (GPCRs), ORs exhibit complex selectivity on their ligands. The diversity of binding activity and selectivity amo...
Article
Natural products with diverse chemical scaffolds have been recognized as an invaluable source of compounds in drug discovery and development. However, systematic identification of drug targets for natural products at the human proteome level via various experimental assays is highly expensive and time-consuming. In this study, we proposed a systems...
Article
A series of novel propargylamine-modified pyrimidinylthiourea derivatives (1-3) were designed and synthesized as multifunctional agents for Alzheimer's disease (AD) therapy, and their potential was evaluated through various biological experiments. Among these derivatives, compound 1b displayed good selective inhibitory activity against AChE (vs BuC...