ABSTRACT
The human bacterial pathogen Helicobacter pylori causes a range of gastric diseases. The killing rate of Helicobacter pylori is declining year by year because of high antibiotics resistance. It is urgent to develop new target and novel anti- Helicobacter pylori drugs. As an "energy pump" for bacterial cells, SecA is essential for bacterial growth and drives bacterial protein transmembrane transport, moreover SecA is absent in mammals, all of which nominate SecA as an attractive antimicrobial target. Here, we provided a structure-based virtual screening method to screen the 3D-diversity natural-product-like screening library against SecA for novel anti- Helicobacter pylori inhibitors with novel scaffolds. In this study, homology modeling was used to construct the three-dimensional structure of Helicobacter pylori SecA. Two rounds of molecular docking were then used to find new small-molecule inhibitors of SecA, identifying six lead candidates that maintained key interactions with the binding pocket. After that, molecular dynamics simulations were used to explore more accurate ligand-receptor binding modes in states close to natural conditions. Encouragingly, all six compounds were relatively stable during the simulation. Apart from that the binding free energy calculation based on MM/PBSA demonstrated favorable results of < -13.642 kcal/mol. Finally, ADME-T analysis indicated that these compounds were also sufficiently druggable. All six compounds can be well combined with the crystal structure, which further facilitate the development of SecA inhibitors and lead compounds against Helicobacter pylori.
Subject(s)
Anti-Infective Agents , Helicobacter pylori , Humans , Molecular Docking Simulation , Protein Binding , Molecular Dynamics SimulationABSTRACT
Synthetic Biology is one of the most promising fields of modern Biology and a frontier interdisciplinary subject in the 21st century. With the rapid development of synthetic biology, the International Genetically Engineered Machine (iGEM) competition has emerged. The iGEM competition, based on the subject foundation of Synthetic Biology, intends to solve the biological problems in our daily life by applying modern biological technology. In recent years, with the continuous increase of participating teams, the iGEM competition has received extensive attention and achieved great progress. On the basis of the development of Synthetic Biology, we analyzed the 2018-2020 award-winning projects of the iGEM competition and illustrated the role and significance of the iGEM competition in cultivating college students' innovative thinking and ability with the participation experience of the iGEM team of Southwest Jiaotong University as an example.
Subject(s)
Genetic Engineering , Synthetic Biology , Humans , Students , UniversitiesABSTRACT
Erianin is a natural small molecule dibenzyl compound extracted from Dendrobium officinale or Dendrobium chrysotoxum. Studies show erianin has many pharmacological functions such as antioxidant, antibacterial, antiviral, improving diabetic nephropathy, relaxing bronchial smooth muscle and anti-tumor. However, the erianin-mediated molecular mechanism is elusive, and the target protein of erianin is not clear yet. Here, we screened and identified that the target protein of erianin in human hepatoma HepG2 cells is human pyruvate carboxylase, and explored the anti-tumor signal pathway regulated by erianin in several cell lines. Firstly, the interaction between human pyruvate carboxylase and erianin was studied by bioinformatics and biochemical methods. Secondly, in vitro, erianin can specifically inhibit the activity of human pyruvate carboxylase, and the purified human pyruvate carboxylase can specifically bind to the activity probe of erianin. Thirdly, human pyruvate carboxylase is highly expressed in a variety of malignant tumors, and the inhibitory effect of erianin on tumor cells is positively correlated with the expression of human pyruvate carboxylase, and erianin can selectively inhibit the activity of pyruvate carboxylase. Finally, erianin can regulate the pyruvate carboxylase-mediated Wnt/ ß- Catenin pathway. All of which provide important data for the further study of the anticancer mechanism of erianin, and lay a solid foundation for the further development and utilization of erianin.
Subject(s)
Bibenzyls/pharmacology , Cell Movement/drug effects , Cell Proliferation/drug effects , Dendrobium/chemistry , Phenol/pharmacology , Pyruvate Carboxylase/metabolism , Blotting, Western , Cell Line, Tumor , Computational Biology , Fluorescent Antibody Technique , Gas Chromatography-Mass Spectrometry , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Neoplastic , Gene Knockdown Techniques , HEK293 Cells , Hep G2 Cells , Humans , Inhibitory Concentration 50 , Magnetic Resonance Spectroscopy , Molecular Docking Simulation , Plant Extracts/pharmacology , Pyruvate Carboxylase/antagonists & inhibitors , Pyruvate Carboxylase/drug effects , Wnt Signaling Pathway/drug effectsABSTRACT
High-pressure processing is a nonthermal method of food processing that is widely used in sterilization and enzyme inactivation. Although some works on technological parameters and quality evaluation have been performed, the mechanism of high pressure on food is still unclear. Due to the complexity of food ingredients, a tremendously important tripeptide in food proteins, orthorhombic l-glutathione, was employed in this work. In addition, in situ methods such as high-pressure Raman, infrared, and X-ray diffraction were used to investigate the structural changes in the pressure range of 0-10 GPa. Experimental results showed that the sample underwent two phase transitions in pressure intervals of 1.8-2.2 and 4.1-5.3 GPa. In addition, the strength of the hydrogen bonds (NHâ¯O; OHâ¯O; SHâ¯O; CHâ¯O) also changed in the two pressure intervals. This work may have potential research value for revealing the mechanism of high-pressure processing on food proteins.
