A Small Molecule Enzyme Replacement for the Treatment of CLN1

PROJECT SUMMARY Significance: CLN1 is a devastating neurodegenerative disorder affecting 1 in 100,000 children born worldwide. This untreatable disease is characterized by dramatic developmental decline, neuromuscular symptoms, vision loss, and neuronal death. Unfortunately, patients with this disease rarely survive past childhood. CLN1 is the result of a loss-of-function mutation in the gene PPT1 that encodes for the enzyme palmitoyl-protein thioesterase 1 (PPT1). PPT1 is a lysosomal enzyme responsible for removing S-palmitoyl groups from proteins. When it is dysfunctional, as is the case with CLN1, lipids and proteins accumulate in cells and have toxic effects in the central nervous system, heart, and skeletal system. There are currently no approved therapies for CLN1, and children with this disease experience an average life expectancy of 8-12 years. Objective: To address the critical unmet need for CLN1 therapeutics, we are developing the first small molecule PPT1 replacement therapy for systemic treatment of this disease. We have recently engineered a novel class of depalmitoylating molecules (DPALMs), which chemoselectively cleave S-palmitoyl groups from proteins in live cells. Using this technology, we aim to develop compounds that can restore PPT1-like thioesterase activity to CLN1 cells. Preliminary Data: We have identified a set of DPALM lead compounds that effectively depalmitoylate PPT1 substrates and reverse abnormal protein accumulation in CLN1 patient-derived cells. Furthermore, we found that DPALMs are effective at non-toxic doses and are well tolerated in vivo. Specific Aims: We will optimize the potency and drug-like characteristics of our lead compounds to generate a DPALM suitable for preclinical testing and IND enabling studies. In SPECIFIC AIM 1, we will generate a set of optimized DPALMs using joint synthesis and screening efforts. A modular and robust synthetic strategy will be used to generate new compounds, which will then be screened for depalmitoylation activity toward PPT1 substrates. In SPECIFIC AIM 2, we will evaluate the efficacy of optimized DPALMs in CLN1 model cell lines. Compounds will be tested for their ability to reduce the level of accumulated proteins, reverse abnormal lysosome morphology, and inhibit apoptosis in in vitro disease models. The proposed studies will enable the development of a highly active DPALM and accelerate the commercialization of this therapy for the treatment of CLN1.PROJECT NARRATIVE This proposal addresses the unmet need for a systemic therapy for CLN1 disease. We will optimize the potency and drug-like characteristics of our lead compounds to maximize their efficacy in restoring thioesterase activity in CLN1. This work will identify compounds suitable for in vivo evaluation and IND enabling studies.