A High-Throughput Screen for Antiproliferative Peptides in Mammalian Cells Identifies Key Transcription Factor Families

Transcription factors (TFs) are a
promising therapeutic
target
for a multitude of diseases. TFs perform their cellular roles by participating
in multiple specific protein–protein interactions. For example,
homo- or heterodimerization of some TFs controls DNA binding, while
interactions between TFs and components of basal transcriptional machinery
or chromatin modifiers can also be critical. While, in theory, small
molecules could be used to disrupt specific protein–protein
interfaces required for TF function, in practice, it is difficult
to identify small molecules with the necessary specificity and efficacy,
likely due to the extensive protein–protein interfaces that
often underlie TF function. However, in contrast to small molecules,
peptides have the potential to provide both the specificity and efficacy
required to disrupt such interfaces. Here, we identified ∼15
peptides that inhibit the proliferation of leukemia cells using a
high-throughput pooled screen of a library of 80-mer protein regions
(peptides) derived from human nuclear-localized proteins. The antiproliferative
peptides were enriched for regions known to be involved in specific
TF dimerization, including the basic leucine zipper (bZIP) domain
family. One of these bZIP domains, JDP2;bZIP_1, from the TF JDP2,
was the top antiproliferative peptide, reducing the proliferation
of K562 cells by 2-fold. JDP2;bZIP_1 inhibited AP-1 transcriptional
activity and phenocopied JDP2 overexpression, suggesting that the
peptide affected proliferation through a native JDP2 mechanism. Unexpectedly,
given the strong conservation of the bZIP domain, residues outside
of the annotated dimerization domain were critical for the peptide’s
antiproliferative potency. The peptide-mediated antiproliferative
effect initiated erythrocyte differentiation in K562 cells and increased
G0/G1 cells across multiple cell line models. We also found that many
of the antiproliferative peptides identified in this study, including
JDP2;bZIP_1, did not require a nuclear localization signal to function,
a potential benefit for delivering these peptides in therapeutic applications.