Detailed Discussion Of Families Docking Results And Drugs.

819 words - 3 pages

Estrogen receptor regulates gene expression on binding the steroid hormone estradiol. Ligands in this family are typically large, rigid molecules 2-3 polar groups, and easy to dock to. Perfect sampling and high scoring success is observed in almost all the 47 complexes in this family. Complexes with the native substrate include estradiol 1QKT, 1QKU, 1A52. Trypsin is a serine protease found in the small intestine. It has a highly charged binding site with a triad of three catalytic residues His57, Asp102 and Ser195. There is a Calcium ion in the binding site. A large amount of crystallographic data is available for this protein, primarily because it is easily available and storable. Sampling (RGD=100%, FAD=89%, FLX=82.6%) and scoring (RGD=86.9%, FAD=73.9, FLX=54.3) drop gracefully. RGD sampling is perfect, but drops in FAD, FLX indicating trypsin ligands might benefit from a finer conformational sampling of the ligand torsions. Neuraminidase is the target for flu drugs, especially important with the threat of avian and swine flu. The natural substrate is neuraminic acid, a 9-carbon sugar molecule. This is a highly charged binding site, which responds well to docking efforts. Even though ligands have an average of 9 rotatable bonds, almost perfect sampling (95-98%) and scoring (93-86%) success is achieved. Since this is a tetramer with four non-interfacial binding sites, only the monomer was retained in this testset. Xtalmin scores clearly indicate the loss of binding in the mutants, WT = -72.6, while R292K = -68.9 and E119G=-68.1. The same ordering is captured in the scores of the top ranked poses for the flex docking results WT=-70.8, while R292K = -72.4 and E119G=-76.4, although the trend is not high enough to get a good correlation. Perfect sampling is achieved for all three docking experiments in this family, with over 90% scoring success for all 3 experiments. These ligands are somewhat flexible with an average of 7.4 rotatable bonds. Thrombin is a serine protease that converts soluble fibrinogen into insoluble fibrin strands in the blood clotting cascade. Direct thrombin inhibitors (DTI’s) act as anti-coagulants include 1MU8, 1MUE (hirugen). This family shows high sampling success (RGD=100%, FAD=97%, FLX=90%) while the scoring success drop-off unexpectedly rapid (RGD=100%, FAD=71%, FLX=68%) [Explain]. Several ligands exhibit a critical hydrogen binding network that provides selectivity with trypsin, another serine protease with a similar binding site. Curiously, this family shows significantly...

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