Selective Stalling of Human Translation by Small Molecules

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ABSTRACT Protein targets for many human diseases remain “undruggable” due to their underlying biochemical behavior. These limits to discovery of small molecule drugs hold back the promise of developing affordable therapeutics. Here we propose to develop an entirely new mechanism of action that could enable targeting previously “undruggable” proteins, by selectively blocking their translation by the human ribosome. Most drugs and drug candidates known to modulate human translation target translation initiation factor complexes or upstream signaling pathways such as mammalian target of Rapamycin (mTOR). These generally modulate translation of a large number of mRNAs. To date, only one type of compound that selectively targets the ribosome–to induce premature stop codon readthrough–is being evaluated in the clinic. We recently demonstrated that small molecules can selectively stall the translation of human proteins, with very little off-target activity. The compound we analyzed, PF-06446846 (PF846), directly and selectively inhibits the translation of PCSK9 during translation elongation, by stalling the ribosome on the nascent polypeptide residing in the ribosome exit tunnel. However, it remains unclear how this and related compounds selectively stall translation. The few examples of off-target proteins we identified as stalled by PF846 (less than 0.4 percent of the human proteome) exhibit substantial primary structure variability, making it difficult to predict target sequences for future development of selective ribosome-targeting drugs. We have preliminary evidence that PF846 interacts with these diverse nascent chain sequences to induce ribosome stalling by subtly different mechanisms. We propose to elucidate the full molecular mechanism of PF846 stalling of translation, so that this family of compounds can be further optimized to target proteins whose expression or overexpression causes diverse human diseases for which no treatments are now available. This family of compounds could also be optimized to target viruses, which use human translation to synthesize their proteome. These efforts have the potential to open up an entirely new mechanism of action for human therapeutic development.