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Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening.
Jones, Katherine F M; Demir, Özlem; Wyllie, Mackenzie K; Grillo, Michael J; Morris, Clare; Hirakis, Sophia P; Kardile, Rahul Dadabhau; Walters, Michael A; Harris, Reuben S; Amaro, Rommie E; Harki, Daniel A.
Afiliação
  • Jones KFM; Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
  • Demir Ö; Department of Chemistry and Biochemistry, University of California - San Diego, La Jolla, CA, USA.
  • Wyllie MK; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
  • Grillo MJ; Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
  • Morris C; Department of Chemistry and Biochemistry, University of California - San Diego, La Jolla, CA, USA.
  • Hirakis SP; Department of Chemistry and Biochemistry, University of California - San Diego, La Jolla, CA, USA.
  • Kardile RD; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
  • Walters MA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
  • Harris RS; Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA.
  • Amaro RE; Department of Biochemistry & Structural Biology, University of Texas Health Science Center San Antonio, San Antonio, TX, USA.
  • Harki DA; Howard Hughes Medical Institute, University of Texas Health Science Center San Antonio, San Antonio, TX, USA.
bioRxiv ; 2024 Apr 25.
Article em En | MEDLINE | ID: mdl-38712210
ABSTRACT
APOBEC3B cytosine deaminase contributes to the mutational burdens of tumors, resulting in tumor progression and therapy resistance. Small molecule APOBEC3B inhibitors have potential to slow or mitigate these detrimental outcomes. Through molecular dynamics (MD) simulations and computational solvent mapping analysis, we identified a novel putative allosteric pocket on the C-terminal domain of APOBEC3B (A3Bctd), and virtually screened the ChemBridge Diversity Set (N~110,000) against both the active and potential allosteric sites. Selected high-scoring compounds were subsequently purchased, characterized for purity and composition, and tested in biochemical assays, which yielded 13 hit compounds. Orthogonal NMR assays verified binding to the target protein. Initial selectivity studies suggest these compounds preferentially target A3Bctd over related deaminase APOBEC3A (A3A), and MD simulations indicate this selectivity may be due to the steric repulsion from H56 that is unique to A3A. Taken together, our studies represent the first virtual screening effort against A3Bctd that has yielded candidate inhibitors suitable for further development.

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: BioRxiv Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: BioRxiv Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Estados Unidos