Identifying potential binding sites for complex formation between Tyrosyl-DNA phosphodiesterase 1 and poly...

DNA topoisomerases manage the supercoiled structure of the genomic DNA through breaking and rejoining DNA strands, which is a key step in many cellular processes. DNA topoisomerase I (TOPI) forms TOPI-DNA cleavage complex (TOPIcc) via formation of a transient covalent bond between TOPI and the DNA single strand. Inhibition of TOPI enzymatic activity is a successful approach for treating multiple types of cancer. Tyrosyl-DNA phosphodiesterase 1 (TDP1) helps release of TOPIccs via catalysis of TOPI-DNA phosphodiester bond hydrolysis. TDP1 is therefore functionally connected with activity of TOPI. Poly [ADP-ribose] polymerase 1 (PARP1) physically interacts with TDP1 to make TDP1 PARylated and enhances TDP1 recruitment to DNA damage sites, thus playing a functional role in TOPIcc repair. If unrepaired, TOPIcc can lead to single strand breaks, which cause cell death. Slowing down TDP1 activity can increase the efficacy of existing TOPI inhibitors and improve their clinical utility. Repair of TOPIccs can be negatively impacted by blocking the physical interactions between TDP1 and PARP1. Therefore, blocking the TDP1-PARP1 complex formations has the potential to enhance the antitumor activity of existing FDA approved TOP1 inhibitors and reduce their side effects. Towards this aim, we identified binding sites that are crucial for the TDP1-PARP1 complex formation using 700 ns long molecular dynamics (MD) simulations. We identified specific interactions between D115(TDP1) and K940 or K943 (PARP1) as well as R137(TDP1) and E883(PARP1) that might be important for the TDP1-PARP1 complex formation. We validated the complex formation between purified recombinant TDP1 and PARP1 proteins using surface plasmon resonance (SPR). We also used SPR to confirm that peptides corresponding to contact points between TDP1 and PARP1 prevent complex formation. Our findings lead the path for creating novel inhibitors that can prevent TDP1 binding to PARP1 and consequently improve the clinical efficacy of the current TOP1 inhibitors for cancer treatment.