Rational optimization of a transcription factor activation domain inhibitor

Abstract

Transcription factors are among the most attractive therapeutic targets, but are considered largely undruggable. Here we provide evidence that small molecule-mediated partitioning of the androgen receptor, an oncogenic transcription factor, into phase-separated condensates has therapeutic effect in prostate cancer models. We show that the phase separation capacity of the androgen receptor is driven by aromatic residues and short unstable helices in its intrinsically disordered activation domain. Based on this knowledge, we developed tool compounds that covalently attach aromatic moieties to cysteines in the receptors' activation domain. The compounds enhanced partitioning of the receptor into condensates, facilitated degradation of the receptor, inhibited androgen receptor-dependent transcriptional programs, and had antitumorigenic effect in models of prostate cancer and castration-resistant prostate cancer in vitro and in vivo. These results establish a generalizable framework to target the phase-separation capacity of intrinsically disordered regions in oncogenic transcription factors and other disease-associated proteins with therapeutic intent.

SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins

“…While our analysis is necessarily retrospective and correlative, it is in line with prior experimental work. ,− To explore this observation further, we performed all-atom simulations using the ABSINTH implicit solvent model of the p53 − with three phosphomimetic mutations (S15E, T18E, and S20E) and compared the result to previous simulations of the wildtype sequence (Figure A) . While glutamic acid is an imperfect analogue for the phosphate group, the results revealed that relatively modest changes in linear charge density can cause local and long-range changes in the...…”

“…Comparison of changes in local and global dimensions for wildtype vs phosphomimetic versions of p53. (A) Scaling maps where inter-residue distances for the phosphomimetic version of the p53 N-terminal domain (p53 − ) are normalized by distances for the wildtype protein. Despite differing by only three residues in the N-terminal quarter of the protein, the phosphomimetic version of p53 shows substantial differences in long-range and local dimensions, as shown by the emergence of both attractive (blue) and repulsive (red) interactions.…”

Kinetic stabilization of translation-repression condensates by a neuron-specific microexon

“…2f). These results indicate that, as observed for other intrinsically disordered proteins rich in aromatic residues [21][22][23] , the number and patterning of His residues determine the phase separation propensity of nCPEB4-NTD. In addition, they suggest that a decrease in pH leads to an increase in phase separation propensity by allowing protonated His side chains to engage in cation-π or electrostatic interactions as the cationic moiety.…”

SOURSOP: A Python package for the analysis of simulations of intrinsically disordered proteins

“…While our analysis is necessarily retrospective and correlative, it is in line with prior experimental work 57,72–75 . To explore this observation further, we performed all-atom simulations using the ABSINTH implicit solvent model of the p53 1-91 with three phosphomimetic mutations (S15E, T18E, S20E) and compared the result to previous simulations of the wildtype sequence ( Fig.…”