Pharmacological manipulation of transcription factor protein-protein interactions: opportunities and obstacles

Abstract

Much research on transcription factor biology and their genetic pathways has been undertaken over the last 30 years, especially in the field of developmental biology and cancer. Yet, very little is known about the molecular modalities of highly dynamic interactions between transcription factors, genomic DNA, and protein partners. Methodological breakthroughs such as RNA-seq (RNA-sequencing), ChIP-seq (chromatin immunoprecipitation sequencing), RIME (rapid immunoprecipitation mass spectrometry of endogenous proteins), and single-molecule imaging will dramatically accelerate the discovery rate of their molecular mode of action in the next few years. From a pharmacological viewpoint, conventional methods used to target transcription factor activity with molecules mimicking endogenous ligands fail to achieve high specificity and are limited by a lack of identification of new molecular targets. Protein-protein interactions are likely to represent one of the next major classes of therapeutic targets. Transcription factors, known to act mostly via protein-protein interaction, may well be at the forefront of this type of drug development. One hurdle in this field remains the difficulty to collate structural data into meaningful information for rational drug design. Another hurdle is the lack of chemical libraries meeting the structural requirements of protein-protein interaction disruption. As more attempts at modulating transcription factor activity are undertaken, valuable knowledge will be accumulated on the modality of action required to modulate transcription and how these findings can be applied to developing transcription factor drugs. Key discoveries will spawn into new therapeutic approaches not only as anticancer targets but also for other indications, such as those with an inflammatory component including neurodegenerative disorders, diabetes, and chronic liver and kidney diseases.

Keywords: Cancer; Genomics; Interactome; Pharmacology; Proteomics; Screening; Specificity; Transcription.

Figure 1

Advantages of targeting transcription factor protein-protein interactions over conventional targets. Targeting upstream cell-signaling nodes (e.g., kinase) lacks specificity because of the interconnected nature of cell signaling and its numerous feedback loops. Targeting transcription factors, downstream effectors of cell signaling, able to control specific gene groups via specific protein associations, is likely to be a more specific approach [13].

Figure 2

Mode of action of transcriptional activation inhibitors. Small compounds directly inhibiting transcriptional activation can act by targeting DNA (blue), or transcription factors/co-activators, either preventing DNA binding (red and green) or altering protein conformation or protein-protein interaction (yellow). Inspired from [16].

Figure 3

Transcription factor protein-protein interaction disruptors: heavier, more hydrophobic, and more rigid than regular drugs. Anticancer indications: a/ BRD4/histone interaction disruptor: BRD4 binds to acetylated lysine residues in histone tails, which act as activation markers for gene expression. (+)-JQ1 was modeled to fit a hydrophobic cavity in the BRD4 domain that accommodates acetylated lysines. Potential indications are squamous cancer and acute myeloid leukemia [86]. b/ HDM2(MDM2)/p53 interaction disruptors: Human or mouse double minute 2 protein binds to tumor suppressor p53, increasing its degradation. Tetra-substituted imidazole, Nutlin-3, disrupts complexes with nanomolar affinity [87]. Subsequent attempts at computational optimization based on existing PPI descriptors and X-ray crystallography have generated compounds with low/sub-micromolar affinities PB11 and BDM_4605 [60,72]. Potential indications are all p53-related cancers. c/ Bcl-2(Bcl-xL)/Bax(Bak) interaction disruptors: Bcl-2 or Bcl-xL binds to the BH3 (Bcl2-homology 3) domain of pro-apoptotic Bax and Bak proteins, preventing apoptosis. BH3-mimetic ABT-737 disrupts complexes with sub-micromolar affinity, inducing apoptosis. Potential indications are small-cell lung carcinoma and lymphoma [73]. Other indications: d/ STAT3 is a latent cytoplasmic transcription factor transducing signals from the cell membrane to the nucleus. STAT3 can dimerize via reciprocal interaction of its Src homology 2 domain (SH2), upon phosphorylation of a conserved tyrosine within the SH2 domain. STA-21 inhibits cytokine-dependent nuclear translocation of Stat3 in normal human keratinocytes in vitro by impeding STAT3 DNA binding and dimerization with mid-micromolar potency [88].