Keywords: proprotein convertase subtilisin/kexin type 9 (PCSK9), serine protease, substrate specificity, single-nucleotide polymorphism, atherosclerosis, low-density lipoprotein (LDL), high-throughput screening (HTS), protein secretion, active site
ABSTRACTProprotein convertase subtilisin/kexin type 9 (PCSK9) downregulates the low-density lipoprotein (LDL) receptor (LDL-R), elevating LDL cholesterol (LDL-C) and accelerating atherosclerotic heart disease, making it a promising cardiovascular drug target. To achieve its maximal effect on the LDL-R, PCSK9 requires autoproteolysis. After cleavage, PCSK9 retains its prodomain in the active site as a self-inhibitor. Unlike other proprotein convertases, however, this retention is permanent, inhibiting any further protease activity for the remainder of its life cycle. Such inhibition has proven a major challenge toward a complete biochemical characterization of PCSK9's proteolytic function, which could inform therapeutic approaches against its hypercholesterolemic effects. To address this challenge, we employed a cell-based, highthroughput method using a luciferase readout to evaluate the single-turnover PCSK9 proteolytic event. We combined this method with saturation mutagenesis libraries to interrogate the sequence specificities of PCSK9 cleavage and proteolysisindependent secretion.Our results highlight several key differences in sequence identity between these two steps, complement known structural data, and suggest that PCSK9 selfproteolysis is the rate-limiting step of secretion.Additionally, we found that for missense single nucleotide polymorphisms (SNPs) within PCSK9, alterations in both proteolysis and secretion are common. Lastly, we show that some SNPs allosterically modulate PCSK9's substrate sequence specificity. Our findings indicate that PCSK9 proteolysis acts as a commonly perturbed but critical switch in controlling lipid homeostasis and provide a new hope for the development of small molecule PCSK9 inhibitors.On the cell surface of the hepatocyte, proprotein convertase subtilisin/kexin type 9 (PCSK9) binds to the LDL receptor (LDL-R), and upon internalization, chaperones the entire complex to the lysosome for degradation.(1,2) By preventing recycling of the LDL-R back to the cell surface, PCSK9 reduces the availability of the LDL-R to remove LDL cholesterol (LDL-C) from the bloodstream,(3,4) which ultimately promotes atherosclerotic heart disease.(5,6) Therapeutics targeting PCSK9 function lead to impressive reductions in LDL-C in patients and, for those with established heart disease, provide additional clinical benefit beyond standard therapy. (7,8) The large therapeutic window of PCSK9 inhibition along with the prevalence of the underlying disease justify a need for additional anti-PCSK9 therapies, particularly ones amenable to lower manufacturing Successful processing of the PCSK9 polypeptide is required for its maximal effect on the LDL-R.(9) PCSK9 contains a signal sequence to direct its translation to the ER, where it then folds into a self-cle...