A5100688144- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Biochemical and Molecular Research
- RNA and protein synthesis mechanisms
- Synthesis and biological activity
- Cancer therapeutics and mechanisms
- Heat Transfer Mechanisms
- Turbomachinery Performance and Optimization
- Lung Cancer Treatments and Mutations
- Microbial Natural Products and Biosynthesis
- HIV/AIDS drug development and treatment
- Natural product bioactivities and synthesis
- Chemical Synthesis and Analysis
- Video Analysis and Summarization
- Cytokine Signaling Pathways and Interactions
- Bioinformatics and Genomic Networks
- Skin Protection and Aging
- Machine Learning in Bioinformatics
- Cell death mechanisms and regulation
- Molecular Sensors and Ion Detection
- Innovative Microfluidic and Catalytic Techniques Innovation
- RNA modifications and cancer
- HER2/EGFR in Cancer Research
- PI3K/AKT/mTOR signaling in cancer
- Cancer-related molecular mechanisms research
East China University of Science and Technology
2016-2025
East China Normal University
2022-2025
Mianyang Central Hospital
2024-2025
University of Electronic Science and Technology of China
2024-2025
Hebei Medical University
2014-2025
Second Hospital of Hebei Medical University
2018-2025
Sichuan University
2007-2025
University of Shanghai for Science and Technology
2024-2025
Nankai University
2025
Nanjing Medical University
2018-2025
The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house model database. original version of includes more than 7000 pharmacophores derived from complex crystal structures with corresponding protein annotations. In this article, we present new server, which backend database six times larger earlier one, total 23 236 proteins covering 16 159 druggable models and 51 431 ligandable models....
In silico drug target identification, which includes many distinct algorithms for finding disease genes and proteins, is the first step in discovery pipeline. When 3D structures of targets are available, problem identification usually converted to best interaction mode between potential candidates small molecule probes. Pharmacophore, spatial arrangement features essential a interact with specific receptor, an alternative method achieving this goal apart from molecular docking method....
A fluorescent chemodosimeter for cysteine detection and bio-imaging has been described which displays an excellent selectivity over homocysteine, glutathione other amino acids.
PharmMapper is a web server for drug target identification by reversed pharmacophore matching the query compound against an annotated model database, which provides computational polypharmacology prediction approach repurposing and side effect risk evaluation. But due to inherent nondiscriminative feature of simple fit scores used results ranking, signal/noise ratio high, posing challenge predictive reliability. In this paper, we improved accuracy generating ligand–target pairwise score...
Abstract Biological processes (like microbial growth & physiological response) are usually dynamic and require the monitoring of metabolic variation at different time-points. Moreover, there is clear shift from case-control (N=2) study to multi-class (N>2) problem in current metabolomics, which crucial for revealing mechanisms underlying certain process, disease metastasis, etc. These time-course metabolomics have attracted great attention, data normalization essential removing...
Abstract Emerging and re-emerging RNA viruses occasionally cause epidemics pandemics worldwide, such as the on-going outbreak of novel coronavirus SARS-CoV-2. Herein, we identified two potent inhibitors human DHODH, S312 S416, with favorable drug-likeness pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various viruses, including influenza A virus, Zika Ebola particularly Notably, S416 is reported to be most inhibitor so far an EC 50 17 nmol/L SI value...
Tumor-associated macrophages (TAMs) play a critical role in modulating the tumor microenvironment and promote metastases. Our studies have demonstrated that ginsenoside Rh2 (G-Rh2), monomeric compound extracted from ginseng, is promising anti-tumor agent lung cancer cells. However, it remains unclear whetherG-Rh2 can modulate differentiation of TAMs its interaction with microenvironment. In this study, we investigated how G-Rh2 regulates phenotype affects migration non-small cell (NSCLC)...
Drug discovery and development affects various aspects of human health dramatically impacts the pharmaceutical market. However, investments in a new drug often go unrewarded due to long complex process research (R&D). With advancement experimental technology computer hardware, artificial intelligence (AI) has recently emerged as leading tool analyzing abundant high-dimensional data. Explosive growth size biomedical data provides advantages applying AI all stages R&D. Driven by big...
Abstract Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have developed. However, existing suffer from a serious long-tail problem, with large number GO families containing few annotated proteins. Herein, an innovative strategy named AnnoPRO was therefore constructed by enabling sequence-based multi-scale protein representation, dual-path encoding using pre-training, long short-term memory-based decoding. A variety...
Abstract Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing mechanistic understanding of protein functions. To enhance the progress in this field, spectrum computational methodologies has been cultivated. AlphaFold2 exhibited exceptional precision predicting wild-type structures, with performance exceeding that other methods. However, structures missense mutant proteins using remains challenging due to intricate substantial structural...
Abstract Background Target identification is important for modern drug discovery. With the advances in development of molecular docking, potential binding proteins may be discovered by docking a small molecule to repository with three-dimensional (3D) structures. To complete this task, reverse program and target database 3D structures are necessary. end, we have developed web server tool, TarFisDock ( Tar get Fis hing Dock ing) http://www.dddc.ac.cn/tarfisdock , which has been used widely...
On the basis of mechanism Hg2+-promoted hydrolysis, a new fluorescent chemodosimeter (Rho-Hg1) is reported for single-selective and parts per billion level-sensitive detection Hg2+ in natural waters. Moreover, fluorescence response Rho-Hg1 to has little interference from sulfur compounds such as cysteine glutathione could be used imaging living cells.
Interleukin-1beta-converting enzyme (ICE)/Ced-3 proteases play a critical role in apoptosis. One well characterized substrate of these is the DNA repair poly(ADP-ribose) polymerase. We report here that alpha-fodrin, an abundant membrane-associated cytoskeletal protein, cleaved rapidly and specifically during Fas- tumor necrosis factor-induced apoptosis; this cleavage mediated by ICE/Ced-3 protease distinct from polymerase protease. Studies cells treated with apoptotic stimuli reveal both...
Abstract Summary: ChemMapper is an online platform to predict polypharmacology effect and mode of action for small molecules based on 3D similarity computation. collects >350 000 chemical structures with bioactivities associated target annotations (as well as >3 non-annotated compounds virtual screening). Taking the user-provided structure query, top most similar in terms are returned pharmacology annotations. designed provide versatile services a variety chemogenomics, drug...
Abstract [6]-Gingerol, a natural component of ginger, exhibits anti-inflammatory and antitumorigenic activities. Despite its potential efficacy in cancer, the mechanism by which [6]-gingerol exerts chemopreventive effects remains elusive. The leukotriene A4 hydrolase (LTA4H) protein is regarded as relevant target for cancer therapy. Our silico prediction using reverse-docking approach revealed that LTA4H might be [6]-gingerol. We supported our showing suppresses anchorage-independent cell...
Background: As new biomarkers of coronary artery diseases (CAD) emerge via metabolomics, the underlying functional mechanisms remain to be elucidated. Functional metabolomics aims translate metabolomics-derived disease mechanisms. Methods: A cohort 2324 patients who underwent angiography from 4 independent centers was studied. combination ultra–performance liquid chromatography and quadrupole time-of-flight mass spectrometry in negative ion mode used for untargeted analysis metabolites...
We developed a novel approach called SHAFTS (SHApe-FeaTure Similarity) for 3D molecular similarity calculation and ligand-based virtual screening. adopts hybrid metric combined with shape colored (labeled) chemistry groups annotated by pharmacophore features ranking, which is designed to integrate the strength of matching volumetric overlay approaches. A feature triplet hashing method used fast alignment poses enumeration, optimal superposition between target query molecules can be...
A novel molecule T1 with efficient intramolecular charge transfer was designed as a fluorescent chemodosimeter for cysteine (Cys) and homocysteine (Hcy). Upon addition of Cys/Hcy, exhibited greatly enhanced fluorescence intensity well large absorption peak shift (70 nm), can be used bioimaging Cys/Hcy in living cells detection human plasma by visual color change. The mechanism proved (1)H NMR, mass spectrometry analysis Gaussian calculations.