Poly (ADP-ribose) polymerases (PARPs) are a family of DNA repair enzymes that bind damaged DNA and catalyze the transfer of the ADP-ribose moiety of nicotinamide adenine dinucleotide (NAD+) to acceptor proteins, including PARP itself, causing poly ADP-ribosylation (PARylation). This polymerization signals other DNA repair enzymes, maintaining cellular function and integrity. PARP inhibition has proven to be a successful strategy for the treatment of various tumors with four approved PARP inhibitors on the market and several in clinical trials. We utilized our internal DNA-encoded library (DEL) platform, comprising ~5 billion molecules, to discover inhibitors for PARP1, which is responsible for up to 90% of cellular PARP activity.
DNA-binding proteins can be challenging targets for DEL due to non-specific DNA interactions causing low signal-to-noise in the selection data. One solution is to remove the DNA-binding domain from the protein construct and simply screen without it (e.g., screening the catalytic domain of PARP1). However, removing portions of the target protein can disrupt the functional conformation and useful ligands may be missed. For example, PARP1 contains an autoinhibitory helical domain which is subjected to a conformational change upon DNA binding. Therefore, some PARP1 inhibitors, such as benzamide adenine dinucleotide (BAD) analogs, are only able bind PARP1 when the helical domain is deleted or shifted by the binding of damaged DNA.2 Unable to productively screen full length PARP1 via DEL, we successfully designed and screened a helical domain deleted construct to discover potent inhibitors.