Autophagy, the lysosomal digestion of cytoplasmic proteins and organelles, may play a protective role in certain neurodegenerative and infectious diseases. It may also have an inhibitory role in certain cancers. Currently, the only small molecule known to regulate autophagy in mammalian brains is rapamycin. However, owing to the involvement of mTOR (mammalian target of rapamycin) proteins in many cellular processes, the long-term use of rapamycin is associated with many complications. Writing in Nature Chemical Biology, Sarkar and colleagues describe a new approach to identify novel modulators of mammalian autophagy, which might provide leads for the development of drugs for Huntington's disease.

With the aim of finding safer methods of modulating autophagy, the authors performed high-throughput screening of 50,729 compounds in yeast to identify small molecules that either enhanced or suppressed the effects of rapamycin on cell growth. This resulted in the identification of a structurally non-redundant set of 21 small-molecule inhibitors of rapamycin (SMIRs) and 12 small-molecule enhancers of rapamycin (SMERs).

To test the capacity of these compounds to modulate mammalian autophagy, independent of rapamycin, they assessed their ability to induce clearance of the autophagy substrate A53T α-synuclein, which is associated with a form of familial Parkinson's disease. Thirteen SMIRs were shown to slow the clearance of this autophagy substrate, whereas four SMERs enhanced it.

The authors then focused on a subset of autophagy-inducing SMERs that lacked toxicity in various cell lines. These might have therapeutic potential in neurodegenerative disorders such as Huntington's disease, the underlying cause of which is an expansion of a polyglutamine (polyQ) tract in the huntingtin protein. In cell models expressing the mutant huntingtin protein — another substrate for autophagy — each of the SMERs enhanced clearance of this substrate, reducing mutant protein aggregation and cell death. In a Drosophila model of Huntington's disease, the SMERs protected against neurodegeneration as assessed by the reduction in the number of visible rhabdomeres in the ommatidia of the eye over time.

Interestingly, unlike rapamycin, these compounds exerted no reduction in the phosphorylation of substrates of mTOR kinase, which suggests that their induction of autophagy is mediated through an mTOR-independent mechanism, or through an unknown component of the mTOR autophagy pathway downstream of mTOR. In addition, treatment of cell models with SMERs together with rapamycin resulted in an additive effect on the clearance of A53T α-synuclein and the reduction of mutant huntingtin aggregation.

This study illustrates the use of a high-throughput screening strategy to identify small molecule modulators of mammalian autophagy. Structure–activity relationship analysis of the identified SMERs has highlighted functional groups that are required for their specific activity, and additional candidates for therapeutic development.