Identification of a small-molecule inhibitor that selectively blocks DNA-binding by Trypanosoma brucei replication protein A1

  • Nat Commun. 2023 Jul 20;14(1):4390. doi: 10.1038/s41467-023-39839-x.
Aditi Mukherjee  1 ,  Zakir Hossain  2 ,  Esteban Erben  3  4 ,  Shuai Ma  5 ,  Jun Yong Choi  6  7  8 ,  Hee-Sook Kim  9  10
Affiliations
  • 1. Public Health Research Institute, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.
  • 2. Department of Chemistry and Biochemistry, Queens College, New York, NY, 11367, USA.
  • 3. Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Provincia de Buenos Aires, Argentina.
  • 4. Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín, Provincia de Buenos Aires, Argentina.
  • 5. Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
  • 6. Department of Chemistry and Biochemistry, Queens College, New York, NY, 11367, USA. [email protected].
  • 7. Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA. [email protected].
  • 8. Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA. [email protected].
  • 9. Public Health Research Institute, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA. [email protected].
  • 10. Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA. [email protected].
PMID: 37474515 DOI: 10.1038/s41467-023-39839-x
Abstract

Replication Protein A (RPA) is a broadly conserved complex comprised of the RPA1, 2 and 3 subunits. RPA protects the exposed single-stranded DNA (ssDNA) during DNA replication and repair. Using structural modeling, we discover an inhibitor, JC-229, that targets RPA1 in Trypanosoma brucei, the causative Parasite of African trypanosomiasis. The inhibitor is highly toxic to T. brucei cells, while mildly toxic to human cells. JC-229 treatment mimics the effects of TbRPA1 depletion, including DNA replication inhibition and DNA damage accumulation. In-vitro ssDNA-binding assays demonstrate that JC-229 inhibits the activity of TbRPA1, but not the human ortholog. Indeed, despite the high sequence identity with T. cruzi and Leishmania RPA1, JC-229 only impacts the ssDNA-binding activity of TbRPA1. Site-directed mutagenesis confirms that the DNA-Binding Domain A (DBD-A) in TbRPA1 contains a JC-229 binding pocket. Residue Serine 105 determines specific binding and inhibition of TbRPA1 but not T. cruzi and Leishmania RPA1. Our data suggest a path toward developing and testing highly specific inhibitors for the treatment of African trypanosomiasis.

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