| Autor: |
Liu X; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States., Duan S; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States., Jin Y; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States., Walker E; Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States., Tsao M; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States., Jang JH; Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States., Chen Z; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States., Singh AK; Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, United States., Cantrell KL; Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States., Ingolfsson HI; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States., Buratto SK; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States., Bowers MT; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States. |
| Abstrakt: |
Abnormal cytosolic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is observed in multiple diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and Alzheimer's disease. Previous studies have shown that TDP-43 307-319 located at the C-terminal of TDP-43 can form higher-order oligomers and fibrils. Of particular interest are the hexamers that adopt a cylindrin structure that has been strongly correlated to neurotoxicity. In this study, we use the joint pharmacophore space (JPS) model to identify and generate potential TDP-43 inhibitors. Five JPS-designed molecules are evaluated using both experimental and computational methods: ion mobility mass spectrometry, thioflavin T fluorescence assay, circular dichroism spectroscopy, atomic force microscopy, and molecular dynamics simulations. We found that all five molecules can prevent the amyloid fibril formation of TDP-43 307-319 , but their efficacy varies significantly. Furthermore, among the five molecules, [AC0101] is the most efficient in preventing the formation of higher-order oligomers and dissociating preformed higher-order oligomers. Molecular dynamics simulations show that [AC0101] both is the most flexible and forms the most hydrogen bonds with the TDP-43 307-319 monomer. The JPS-designed molecules can insert themselves between the β-strands in the hexameric cylindrin structure of TDP-43 307-319 and can open its structure. Possible mechanisms for JPS-designed molecules to inhibit and dissociate TDP-43 307-319 oligomers on an atomistic scale are proposed. |
