An Exploration of Small Molecules That Bind Human Single-Stranded DNA Binding Protein 1

SIMPLE SUMMARY: Innovative approaches are required to combat the complexity and adaptability of cancerous cells. Proteins that bind to DNA play an important role in the ability of cancerous cells to survive traditional treatments. This study explores small molecules that bind to one specific protein in these mechanisms—human single-stranded DNA binding protein 1. Using complementary computational and experimental approaches, we discovered three small molecules that appear to prevent the protein from binding to DNA. The computational tools suggest how the compounds bind to human single-stranded DNA binding protein 1, and cellular studies indicate that the molecules may interfere with the cell’s ability to repair DNA at certain concentrations. Further work is necessary to understand how these compounds interact with cells, and to develop them into selective hSSB1 inhibitors. ABSTRACT: Human single-stranded DNA binding protein 1 (hSSB1) is critical to preserving genome stability, interacting with single-stranded DNA (ssDNA) through an oligonucleotide/oligosaccharide binding-fold. The depletion of hSSB1 in cell-line models leads to aberrant DNA repair and increased sensitivity to irradiation. hSSB1 is over-expressed in several types of cancers, suggesting that hSSB1 could be a novel therapeutic target in malignant disease. hSSB1 binding studies have focused on DNA; however, despite the availability of 3D structures, small molecules targeting hSSB1 have not been explored. Quinoline derivatives targeting hSSB1 were designed through a virtual fragment-based screening process, synthesizing them using AlphaLISA and EMSA to determine their affinity for hSSB1. In parallel, we further screened a structurally diverse compound library against hSSB1 using the same biochemical assays. Three compounds with nanomolar affinity for hSSB1 were identified, exhibiting cytotoxicity in an osteosarcoma cell line. To our knowledge, this is the first study to identify small molecules that modulate hSSB1 activity. Molecular dynamics simulations indicated that three of the compounds that were tested bound to the ssDNA-binding site of hSSB1, providing a framework for the further elucidation of inhibition mechanisms. These data suggest that small molecules can disrupt the interaction between hSSB1 and ssDNA, and may also affect the ability of cells to repair DNA damage. This test study of small molecules holds the potential to provide insights into fundamental biochemical questions regarding the OB-fold.