Drug discovery by targeting the protein-protein interactions involved in autophagy

Abstract

Autophagy is a cellular process in which proteins and organelles are engulfed in autophagosomal vesicles and transported to the lysosome/vacuole for degradation. Protein-protein interactions (PPIs) play a crucial role at many stages of autophagy, which present formidable but attainable targets for autophagy regulation. Moreover, selective regulation of PPIs tends to have a lower risk in causing undesired off-target effects in the context of a complicated biological network. Thus, small-molecule regulators, including peptides and peptidomimetics, targeting the critical PPIs involved in autophagy provide a new opportunity for innovative drug discovery. This article provides general background knowledge of the critical PPIs involved in autophagy and reviews a range of successful attempts on discovering regulators targeting those PPIs. Successful strategies and existing limitations in this field are also discussed.

Keywords: Autophagy regulation; Drug discovery; Protein–protein interactions; Small-molecule regulators.

Graphical abstract

Figure 1

Illustration of three major types of autophagy. Macroautophagy delivers cellular contents to lysosome via the formation of autophagosomes. Chaperone-mediated autophagy is characterized by the chaperone-dependent targeting of specific cytosolic proteins containing the KFRQ motif to LAMP-2A on the lysosomal membrane for proteolysis. Microautophagy refers to a non-selective process that recruits and degrades targeted components by lysosomes.

Figure 2

Structural features of ATG8 family proteins and two examples of LC3 inhibitors. (A) Structural alignment of yeast Atg8 and human LC3A, LC3B, LC3C, GABARAP, GABARAPL1, and GABARAPL2. All protein backbones are shown as ribbon models in rainbow color scheme. (B) The crystal structure of LC3B (PDB entry 1UGM). (C) Illustration of the LIR-docking site (LDS) on LC3B, which comprises two hydrophobic pockets HP1 (orange) and HP2 (pink). (D) The crystal structure of LC3A in complex with dihydronovobiocin (PDB entry 6TBE). (E) The crystal structure of LC3B in complex with compound a4 (PDB entry 7ELG).

Figure 3

Autophagic processes that are known to be amenable to pharmacological intervention by PPI regulation.

Figure 4

Top-view of the stapled peptides (A) SP4, (B) i7-01s-20, and (C) SAH-EJ2. A hydrocarbon staple was added in each case to form an (i, i + 7) or (i, i + 4) linkage to enforce the helical structure of the peptide.

Figure 5

Assessment of the 21 drug discovery studies by targeting the PPIs in autophagy, where the AMSS score of each study is given in the last column. AMSS_1: Autophagosome quantification via microscopy analysis; AMSS_2: Autophagosome formation-related biochemical changes; AMSS_3: Autophagy substrate degradation; AMSS_4: Autophagic flux; AMSS_5: Lysosome function-related assays; AMSS_6: Target identification for chemical autophagy modulators; AMSS_7: Autophagy-dependent pharmacological effects; AMSS_8: Autophagy modulation confirmed in vitro; AMSS_9: Autophagy modulation confirmed in vivo.

Figure 6

Several general strategies for obtaining PPI regulators. (A) Identification of active hits through screening, including high-throughput screening and virtual screening. (B) Covalent modification of certain residues on the binding interface of the target PPI. (C) Design of peptide/peptidomimetic binders based on the structural information of the target PPI.