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Background: In recent years, since the molecular docking technique can greatly improve the efficiency and reduce the research cost, it has become a key tool in computer-assisted drug design to predict the binding affinity and analyze the interactive mode.Results: This study introduces the key principles, procedures and the widely-used applications for molecular docking. Also, it compares the commonly used docking applications and recommends which research areas are suitable for them. Lastly, it briefly reviews the latest progress in molecular docking such as the integrated method and deep learning. Conclusion: Limited to the incomplete molecular structure and the shortcomings of the scoring function, current docking applications are not accurate enough to predict the binding affinity. However, we could improve the current molecular docking technique by integrating the big biological data into scoring function.Author summary: Currently, molecular docking has become a key tool in computer-assisted drug design. Therefore, this review introduces the basic theories of molecular docking and compares the commonly used docking software. And then, we list the inspiring applications and latest progress in molecular docking. Finally we discuss the drawbacks of existing molecular docking techniques and the future research direction.Quantitative Biology 2019, 7(2): 83-89 https://doi.

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Mitochondrial dysfunction is a major and common mechanism in developing non-alcoholic fatty liver disease (NAFLD). Replacement of dysfunctional mitochondria by functional exogenous mitochondria may attenuate intrahepatic excessive lipid and recover hepatocyte function. However, no data shows that mitochondria can be systemically administrated to animals to date. Here we suggest that mitochondria isolated from hepatoma cells are used as a mitotherapy agent to treat mouse fatty liver induced by high-fat diets. When the mitochondria were intravenously injected into the mice, serum aminotransferase activity and cholesterol level decreased in a dose-dependent manner. Also, the mitotherapy reduced lipid accumulation and oxidation injury of the fatty liver mice, improved energy production, and consequently restored hepatocyte function. The mitotherapy strategy offers a new potential therapeutic approach for treating NAFLD.

Glial derived neurotrophic factor (GDNF) is a trophic factor for the nigra-striatal tract in experimental Parkinson's disease (PD). The neurotrophin must be administered by intra-cerebral injection, because GDNF does not cross the blood-brain barrier (BBB). In the present study, GDNF was re-engineered to enable receptor-mediated transport across the BBB following fusion of GDNF to the heavy chain of a chimeric monoclonal antibody (MAb) against the mouse transferrin receptor (TfR), and this fusion protein is designated cTfRMAb-GDNF. This fusion protein had been previously shown to retain low nM binding constants for both the GDNF receptor and the mouse TfR, and to rapidly enter the mouse brain in vivo following intravenous administration. Experimental PD in mice was induced by the intra-striatal injection of 6-hydroxydopamine, and mice were treated with either saline or the cTfRMAb-GDNF fusion protein every other day for 3 weeks, starting 1 hour after toxin injection. Fusion protein treatment caused a 44% decrease in apomorphine-induced rotation, a 45% reduction in amphetamine-induced rotation, a 121% increase in the vibrissae-elicited forelimb placing test, and a 272% increase in striatal tyrosine hydroxylase (TH) enzyme activity at 3 weeks after toxin injection. Fusion protein treatment caused no change in TH enzyme activity in either the contralateral striatum or the frontal cortex. In conclusion, following fusion of GDNF to a BBB molecular Trojan horse, GDNF trophic effects in brain in experimental PD are observed following intravenous administration.

Investigating the surface structure, including crystal surface and surface‐coating ligands, of nanoparticulate T1 contrast agent may help to understand the T1 relaxation enhancement in vitro and in vivo. This study presents a novel strategy to develop high‐performance T1 magnetic resonance imaging (MRI) contrast agents through optimizing the nanocrystal surface and the nanobio interface. Based on the optimized crystal surface, the novel manganese oxide nanocubes (MOCs) show significantly higher surface‐to‐volume ratio and an approximately threefold higher r1 value compared to traditional manganese oxide nanospheres. Concurrently, transferring MOCs into aqueous media by dopamine derivatization can avoid the oxidation of Mn(II) ions and provide abundant magnetic core. This optimized surface endows MOCs with a high chemical exchange efficiency during T1 relaxation. Of particular significance, a rationally designed pH‐induced charge‐switchable surfaces can be negatively charged and corona‐free in blood and positively charged surface in tumor sites. This unique feature improves the circulation behavior of this intelligent T1 contrast agent in blood and increases cancer cell uptake to achieve accurate detection of solid tumor, holding great potential in aiding early and precise tumor diagnosis. This study provides a novel tool for sophisticated design of high‐performance T1 MRI contrast agents in bioimaging applications.

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