Small molecule probes to target the human Mediator complex

Abstract

The human Mediator complex is a central integrator for transcription and represents a primary interface that allows DNA-binding transcription factors to communicate their regulatory signals to the RNA polymerase II enzyme. Because Mediator is dynamic both in terms of subunit composition and structure, it presents challenges as a target for small molecule probes. Moreover, little high-resolution structural information exists for Mediator. Its global requirement for transcription, as well as its distinct, transcription factor specific interaction surfaces, however, suggest that development of probes that bind specific Mediator subunits might enable gene- and pathway-specific modulation of transcription. Here we provide a brief overview of the Mediator complex, highlighting biological and structural features that make it an attractive target for molecular probes. We then outline several chemical strategies that might be effective for targeting the complex.

Keywords: CDK8 module; Mediator complex; gene expression; probe discovery.

Figure 1

Mediator is the central scaffold around which the human transcription machinery assembles. (a) Schematic of the human “Pre-Initiation Complex” (PIC). Complexes are shown at same relative scale. (b) Structural model of the human PIC, based upon a cryo-EM study of a Mediator-pol II-TFIIF assembly.[18]

Figure 2

Model for how TFs activate transcription via Mediator. (a) TFs induce sweeping structural shifts upon binding Mediator. At left is the structure of Mediator without a TF bound, whereas at right are two views of a TF-bound state (in this case, p53-Mediator). A common feature of TF-bound Mediator structures is a large pocket domain (arrow) that corresponds to the pol II binding site. (b) Schematic of an inactive or active PIC. In the absence of a key regulatory TF, the PIC can assemble at the promoter but remains in an inactive or unproductive structural state. Upon TF-Mediator binding, Mediator adopts an active structural state, which activates the PIC and pol II transcribes the gene. Adapted from ref. [35].

Figure 3

The VP16 binding region of MED25 involves a deep hydrophobic pocket at the intersection of two α-helices and a β-barrel.

Figure 4

MED17 interacts with MED11 and MED22 along a hydrophobic groove. Insert: Two alpha helices from MED11 (magenta) and MED 22 (silver) project hydrophobic residues into the MED17 hydrophobic groove.

Figure 5

Distinct TFs bind different Mediator subunits. The CDK8 module (red) and the Mediator complex (blue) are shown, along with the subunit composition of each. Because different TFs regulate distinct cellular processes, the varied TF-Mediator interaction surfaces can be considered key control points for these TF-directed events. Examples of basic physiological processes, and the TFs that help regulate them, are shown at the bottom. The Mediator subunit target of the TF is also listed. The general locations shown for select subunits are for illustrative purposes only; the location of each Mediator subunit is not well defined, especially for human Mediator.

Figure 6

Three areas of contemporary chemistry that are impacting the discovery of functional molecules against protein-protein interfaces: a. structural homologs e.g. stapled peptides and related compounds form a family that are increasingly being referred to as “synthetic biologics”; b. small molecules from diversity-oriented synthesis and other approaches; c. weak ligands identified by high-concentration screening (fragments) that are optimized to give potent small molecules.

Figure 7

Examples of molecules active against targets in transcription and protein-protein interfaces.