선택한 단어 수는 입니다.
최소 단어 이상 선택하여야 합니다.
최소 단어 이상 선택하여야 합니다.
선택한 단어 수는 30입니다.
최대 10 단어까지만 선택 가능합니다.
최대 10 단어까지만 선택 가능합니다.
제안 방법
- 14-17 AMBER force field parameters were assigned to compute the van der Waals interactions and the internal energy of a ligand. Docking simulations with AutoDock were then carried out in the active site of DUSP4 to score and rank the compounds in the docking library according to their calculated binding affinities.
- This common feature in the binding modes indicates the necessity for an effective surrogate of the substrate phosphotyrosine group and simultaneously for the hydrophobic groups for binding to the loop structures as the key structural components of potent DUSP4 inhibitors. In order to examine the possibility of the allosteric inhibition of DUSP4 by the identified inhibitors, docking simulations were carried out with the grid maps for the receptor model so as to include the entire phosphatase domain of DUSP4. However, the binding configuration in which an inhibitor resides outside the active site was not observed for any of the new inhibitors.
- The concentrations of DUSP4 (500 nM) and DiFMUP (10 μM) was determined by selecting a concentration showing the typical Michaelis-Menten kinetics.
- The reaction was continued for 20 min at room temperature. The enzymatic activity was measured using the Perkin Elmer 2030 instrument with a wavelength of 355 and 460 nm as excitation and emission wavelengths, respectively. Initial velocities of reactions were estimated for various concentrations (0-50 μM) of inhibitors.
대상 데이터
- A total of 143 compounds were tested for inhibitors of DUSP4. The phosphatase assays were performed by using 6,8-difluoro-4-methyl-umbelliferyl phosphate (DiFMUP) as a fluorogenic substrate.
- Of the 260,000 compounds screened with docking simulations, 150 top-scored compounds were selected as virtual hits. 143 of them were available from the compound supplier and were tested for inhibitory activity against DUSP4 by in vitro enzyme assays.
데이터처리
- 5, 5, 10, 20, and 50 μM. The IC50 value of each inhibitor was measured from the direct regression analysis by using a four parameter sigmoidal curve in the OriginPro program.
- To estimate the accuracy of the scoring function used in virtual screening, we calculated the Pearson coefficient (R) between the calculated binding free energies of 1-5 and their corresponding experimental IC50 values. The calculated R value amounted to 0.
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