Toward Understanding the Mechanism of Client-Selective Small Molecule Inhibitors of the Sec61 Translocon

Abstract

The Sec61 translocon mediates the translocation of numerous, newly synthesized precursor proteins into the lumen of the endoplasmic reticulum or their integration into its membrane. Recently, structural biology revealed conformations of idle or substrate-engaged Sec61, and likewise its interactions with the accessory membrane proteins Sec62, Sec63, and TRAP, respectively. Several natural and synthetic small molecules have been shown to block Sec61-mediated protein translocation. Since this is a key step in protein biogenesis, broad inhibition is generally cytotoxic, which may be problematic for a putative drug target. Interestingly, several compounds exhibit client-selective modes of action, such that only translocation of certain precursor proteins was affected. Here, we discuss recent advances of structural biology, molecular modelling, and molecular screening that aim to use Sec61 as feasible drug target.

FIGURE 1

Schematic representation of the two translocation modes of a secretory protein via the Sec61 translocon in mammals. Co‐translational translocation (right) is SRP‐dependent and involves the binding of the particle signal recognition protein (SRP) to the ribosome carrying a nascent chain signal sequence (SP or TMH). Subsequently, this ribosome‐nascent chain‐SRP complex docks to a membrane receptor named SR, and SRP dissociates from the ribosome. Then, the signal peptide can insert into Sec61 as a result of altered conformational dynamics of Sec61. Post‐translational translocation (left) is an SRP independent pathway where the binding of a completely synthesized polypeptide chain with low hydrophobicity SP to the Sec61 complex along with Sec62/Sec63 membrane proteins is facilitated by the chaperones BiP/Grp78. Their binding to the polypeptide assists its translocation to happen in a net forward direction. Thereof the signal peptidase is cleaved off the signal peptide followed by folding and N‐glycosylation of the translocated protein. In fungi, the cytosolic face of Sec63 is bound to two additional proteins, termed Sec71 and Sec72.

FIGURE 2

Schematic diagram showing the co‐translational translocation of a “weak” signal peptide, which needs extra help from accessory proteins (residing in the local membrane environment) such as heterotetrameric translocon‐associated protein (TRAP) complex, translocating chain‐associated membrane protein (TRAM), Sec62/Sec63 complex with or without BiP. The presence of these proteins alters the conformational dynamics of Sec61 to facilitate protein translocation or membrane integration.

FIGURE 3

Schematic illustration of Sec61α conformations in the resting state and during translocation. View onto the lateral gate side, where TMH2, TMH3, TMH4, TMH7, TMH8, and plug, respectively, are shown as tubes. A relative motion of the N‐ and rather static C‐terminal halves of Sec61α and a movement of the plug moiety lead to channel opening. The picture is based on the structures described in References [59, 166].

FIGURE 4

Chemical structures of Sec61 inhibitors.

FIGURE 5

Interaction sites between chemical inhibitors and Sec61α. All structures show the same view into the lateral gate or inhibitor binding site. Shown in atomic detail are the inhibitors and the interacting amino acids of adjacent TMHs and plug domain of Sec61α. Polar (blue) and hydrophobic (pink) residues are highlighted. The inhibitors are shown in brown with atom specific coloring. The used PDB structures are from Gérard et al. [105] (a), Rehan et al. [106] (d), Itskanov et al. [107] (b, c, e–g), and Pauwels et al. [108] (h), respectively. The below hyperlinks for these structures (a–h) enable users to inspect these 3D structures with the NCBI molecular graphics viewer [168]. (a) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?HDgD1srwnK3UG4wg6; (b) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?89rVzevvmgrD9Xsv6; (c) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?XHDaSRChNCMRdJXe9; (d) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?CMkPWKhBaoWKhw9L8; (e) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?Z82M7M5ozaUiTJCt7; (f) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?SSH1AAsZbeCbUrPe6; (g) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?skRmobkGCgkrg2cR8; (h) https://structure.ncbi.nlm.nih.gov/icn3d/share.html?Ub1jjjozhZ2HeUgD7.