| Cancer is a great obstacle toward human's health for more than half a century. Statistics indicates that treatments for patients who suffer from cancer had prolonged their life by only half a year in spite of great manpower, physical and financial resources input since 1950s. Basic research on targets related to cancer is of important significance to this extent. This thesis focus on two different targets related to cancer, utilizing Computer-Aided Drug Design (CADD) methods, mainly are molecular docking and homology modeling, to study the structure and function relationships of them.In Chapter 1, kinds of CADD methods were introduced. Mainly two categary were discussed, Ligand Based Drug Design (LBDD) and Receptor Based Drug Design (SBDD). LBDD were further divided into Pharmacophore Model and Quantitative Structure Activity Relationship (QSAR); and the corresponding SBDD were divided into Molecular Docking and de novo Design. When introducing different methods in CADD, software and toolkits that used in these fields were included. Parameters and quality control methods were discussed as well. Methods employed in this thesis were mainly homology modeling and molecular docking in SBDD.In Chapter 2, we focus on Heparinae. Heparinase is a target related to cancer metastasis and angiogenesis, inhibition of this target will slow down the rate of this process. In part 1 of Chapter 2, previous researches found that there is a Zinc ion binding site in Heparinaseâ…¡, and our new findings suggests that Calcium ion is important to enzyme activity. I located a calcium ion binding site (307DVDY310) from a serial of manually checked possible sites, and then I docked the substrate into the substrate binding site. With different binding pose, we proposed a hypothesis that there is different elimination mechanism with different metal ion, and account for it specifically. Biological experiments and results confirmed our suggestion about the calcium ion binding site. In part 2 of Chapter 2, previous researches revealed that Heparinaseâ…¢can cut down heparan sulfate specifically, while new observations from experiments found that it can cut down heparin as well. To confirm this, I first build the homology model of Heparinaseâ…¢, then docked the substrate, viz. heparin and heparan sulfate, into the model. We made it clear about the mode of action while the substrate is different. Then we located the heparin binding site (Tyr450, Lys458 and Arg460), and discovered the residue which has a selectivity upon heparan sulfate and heparin (Lys458), and another residue which is important for both heparan sulfate and heparin (Glu133).In Chapter 3, we focus on histone deacetylase. Histone deacetylase is protein that can influence the cell cycle, differentiation and apoptosis through the modification of acetyl level of histones. SIRT 1 is one of them; it is a NAD+-dependent protein deacetylase. In part 1 of Chapter 3,1 build the homology model of SIRT1 (with or without p53 peptide) first, and then docked the NAD+ and "nicotinamide/ADPR" into the corresponding model. We found some phenomenon. Ser265 and Asn346 can interact with NAD+. Ser275 is at the entrance of the NAD+ binding pocket. Nicotinamide can interact with Ile347 and Asp348, and it is binding in the C-pocket of SIRT1. All these are confirmed by the following biological experiment and results. In the part 2 of Chapter 3, a serial of compounds newly synthesized was discovered to be highly active toward the inhibition of histone deacetylaseâ… , while we do not understand the reasons below. I docked these compounds into a homology model build previously followed by a MM-GBSA calculation. We discovered two new receptor-ligand interactions:hydrogen bond between Asp99 and the ligand,Ï€-Ï€stacking between Tyr204 and the ligand. These two interactions can not only explain the high activity and the activity diverse, but also suggests some new thinking toward the design of new and more active histone deacetylase inhibitors. |
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