Poster: Helical domain deletion enables discovery of potent PARP1 inhibitors from a DEL selection

Intro­duc­tion

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.