Abstract Background Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a secreted protein that down-regulates hepatic low-density lipoprotein receptor (LDLR) by binding and shuttling LDLR to lysosomes for degradation. The development of therapy that inhibits PCSK9 has attracted considerable attention for the management of cardiovascular disease risk. However, only monoclonal antibodies of PCSK9 have reached the clinic use. Oral administration of small-molecule transcriptional inhibitors has the potential to become a therapeutic option. Methods Here, we developed a cell-based small molecule screening platform to identify transcriptional inhibitors of PCSK9. Through high-throughput screening and a series of evaluation, we found several active compounds. After detailed investigation on the pharmacological effect and molecular mechanistic characterization, 7030B-C5 was identified as a potential small-molecule PCSK9 inhibitor. Findings Our data showed that 7030B-C5 down-regulated PCSK9 expression and increased the total cellular LDLR protein and its mediated LDL-C uptake by HepG2 cells. In both C57BL/6 J and ApoE KO mice, oral administration of 7030B-C5 reduced hepatic and plasma PCSK9 level and increased hepatic LDLR expression. Most importantly, 7030B-C5 inhibited lesions in en face aortas and aortic root in ApoE KO mice with a slight amelioration of lipid profiles. We further provide evidences suggesting that transcriptional regulation of PCSK9 by 7030B-C5 mostly depend on the transcriptional factor HNF1α and FoxO3. Furthermore, FoxO1 was found to play an important role in 7030B-C5 mediated integration of hepatic glucose and lipid metabolism. Interpretation 7030B-C5 with potential suppressive effect of PCSK9 expression may serve as a promising lead compound for drug development of cholesterol/glucose homeostasis and cardiovascular disease therapy. Fund This work was supported by grants from the National Natural Science Foundation of China (81473214, 81402929, and 81621064), the Drug Innovation Major Project of China (2018ZX09711001-003-006, 2018ZX09711001-007 and 2018ZX09735001-002), CAMS Innovation Fund for Medical Sciences (2016-I2M-2-002, 2016-I2M-1-011 and 2017-I2M-1-008), Beijing Natural Science Foundation (7162129). Keywords: PCSK9, Small-molecule inhibitor, FoxO1/3, HNF1α, Lipid and glucose metabolism, Atherosclerosis __________________________________________________________________ Research in context. Evidence before this study To date, PCSK9 inhibitors are novel therapeutics for the treatment of cardiovascular disease in addition to statins. Two monoclonal antibodies alirocumab and evolocumab targeting PCSK9 have been approved by FDA, but they are expensive and requiring subcutaneous administration, limiting their widespread use. As small-molecule inhibitors targeting protein-protein interaction of PCSK9 and LDLR are difficult to develop, more options are needed. Added value of this study Here, we have developed a novel cell-based screening platform to discover inhibitors targeting PCSK9 transcription. Using a robust and pragmatic approach, we identified an effective small-molecule PCSK9 inhibitor 7030B-C5. Our data showed that 7030B-C5 down-regulated the expression of PCSK9 at both mRNA and protein levels and increased the cellular LDLR protein level and its mediated cellular LDL-C uptake. In both C57BL/6 J mice and ApoE KO mice, oral administration of 7030B-C5 significantly reduced hepatic PCSK9 expression/secretion and increased LDLR expression. Moreover, the compound profoundly reduced atherosclerosis progression, and showed dual benefits in lipid and glucose metabolism in an HNF1α and FoxO1/3-responsive elements-dependent manner. Implications of all the available evidence A small-molecule compound, 7030B-C5, with PCSK9 inhibitory and anti-atherosclerosis activity may potentially serve as a drug lead compound for cholesterol/glucose modulation and cardiovascular disease. Alt-text: Unlabelled box 1. Introduction Increases in hepatic low-density lipoprotein receptor (LDLR) play a pivotal role in enhancing the clearance of plasma low-density lipoprotein cholesterol (LDL-C) and are associated with reducing the risk of cardiovascular disorder [41][1]. Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a critical player in LDL-C metabolism through regulating the degradation of hepatic LDLRs [[42]2,[43]3]. PCSK9 is a liver-derived plasma protease which is initially synthesized as a 75 kDa precursor protein and converted into a 62 kDa mature form undergoing the autocatalytic cleavage process in the Golgi apparatus [[44]4,[45]5]. Circulating PCSK9 binds to the extracellular epidermal growth factor-like repeat A (EGF-A) domain of LDLR, causing its internalization [[46]2,[47]6]. Followed, the PCSK9/LDLR complex translocates to the endosome-lysosomal compartment where LDLR is degraded [[48]7,[49]8]. Reduced cell-surface expression of LDLR leads to increased circulating levels of LDL-C. In human subjects, early studies have shown that gain-of-function mutations in the PCSK9 gene lead to familial hypercholesterolemia [50][9], while loss-of-function mutations are associated with hypocholesterolemia and protection against coronary artery disease [51][10], [52][11], [53][12]. Thus, decreasing circulating PCSK9 level or activity to up-regulate hepatic LDLR level and to lower circulating LDL-C level will be beneficial for reducing the risk of cardiovascular disease in humans. The pivotal role of PCSK9 in the metabolism of LDL-C as well as the verified safety of PCSK9 inhibition led to the development of PCSK9 inhibitors. Recently, two PCSK9 monoclonal antibodies (mAbs) alirocumab and evolocumab which were reported to disrupt the PCSK9-LDLR interaction have been approved by the U.S. Food and Drug Administration (FDA) [54][13]. Alirocumab and evolocumab can be potentially used as monotherapy or add-on therapies to statins in patients with familial hypercholesterolemia or atherosclerotic cardiovascular disease, effectively reducing LDL-C up to 70% and with well-tolerated profile [55][14], [56][15], [57][16], [58][17]. Besides, these monoclonal antibodies significantly suppress circulating PCSK9 levels and consistently reduce LDL-C levels in patients [59][18]. However, it is estimated that the cost of PCSK9 mAb inhibitors was ~$14,000 per person per year in the US which limits its widespread use [60][19]. The small-molecule inhibitors can offer potentially more convenient routes of administration and lower costs. However, small-molecule inhibitors specific to inhibit PCSK9 activity remains challenging because it is difficult for small molecules to blockade the fairly large size of the flat interface between the catalytic subunit of PCSK9 and the EGF-A domain of LDLR [61][20]. Other promising approaches have been explored to discover small molecules with potential to become a therapeutic option by inhibiting PCSK9 protein synthesis. PF-06446846 was identified by Petersen et al. through phenotypic screening of a small-molecule compound collection, which directly and selectively inhibits translation of PCSK9 by stalling the 80S ribosome in the proximity of codon region [[62]21,[63]22]. Orally-administered PF-06446846 reduces plasma PCSK9 and LDL-C levels without liver toxicity symptoms in vivo [64][23]. However, its development was discontinued for competitive reasons [65][24]. The gene expression of PCSK9 is controlled by various transcriptional regulators such as sterol regulatory element binding protein (SREBP), hepatocyte nuclear factor 1α (HNF1α), and forkhead box O3 (FoxO3). A sterol regulatory element (SRE), which forms the target site for SREBPs, is present 330 bp upstream of the translation start site and functions as an important cis-element regulating PCSK9 transcription [66][25]. Cholesterol-lowering drugs, statins, which activate the SREBP2 pathway by inhibiting HMG-CoA reductase and subsequently activating the expression of LDLR, have also been proven to stimulate PCSK9 gene expression, thus diminish the beneficial effects of statin treatment [67][26]. Insulin and docosahexaenoic acid (DHA) could activate PCSK9 transcription via SREBP-1c [68][27], [69][28], [70][29]. In addition to SREBP regulation, HNF1α, a liver-enriched transcription factor, was found to bind HNF1 element within the PCSK9 promoter and activate PCSK9 expression in hepatic cells [71][30] and livers [[72]31,[73]32]. HINFP was reported as a positive regulator of PCSK9 transcription through facilitation of histone H4 acetylation at PCSK9 promoter [74][33]. FoxO3, a forkhead transcription factor, has been identified as a negative regulator of PCSK9 gene expression through epigenetic modulation. FoxO3 interacts with the insulin-response element (IRE) within PCSK9 promoter, recruiting the sirtuin-6 (Sirt6) protein to deacetylate histones and reducing the promoter binding capacity of HNF1α, thereby suppressing the PCSK9 gene expression in hepatic cells [75][34]. In this work, we developed a strategy to discover small-molecule inhibitors of PCSK9 expression at transcription level, and described the identification and mechanistic characterization of 7030B-C5, an active small-molecule inhibitor of PCSK9 transcription. Oral administration of the compound significantly reduced atherosclerosis progression, and showed dual benefits in both lipid and glucose metabolism, providing a promising lead compound for further development of novel drug candidate for small-molecule PCSK9 modulators. 2. Materials and methods 2.1. Cell cultures and cell viability assay HepG2 cells were cultured in Eagle minimal essential medium (MEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% (vol/vol) fetal bovine serum (FBS; Gibco, Grand Island, NY, USA), 1% sodium pyruvate and 1% nonessential amino acids (Invitrogen). HEK-293T cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Invitrogen) supplemented with 10% (vol/vol) FBS (Gibco). HepG2 cells were transfected with luciferase reporter constructs contained the PCSK9 gene promoter sequence spanning the region from −2112 to −1 bp (nucleotide +1 corresponds to the A of ATG start codon, the same as below). The stable pGL4-PCSK9-P transfected HepG2 cells were established by selection with G418 (700 μg/mL, Invitrogen). The cells were cultured at 37 °C in a humidified 5% CO[2] incubator. Cell viability was determined using MTT assay. HepG2 cells were treated with vehicle or positive compounds (0.39–100 μM) for 4 h followed by incubation with MTT reagent (1 mg/mL) at 37 °C for 4 h. The medium was removed, and the purple formazan crystals were dissolved in DMSO. The absorbance was measured at 550 nm using a Victor X5 multilabel plate reader (PerkinElmer, Waltham, MA, USA). 2.2. Construction of luciferase reporter system and high-throughput screening Human PCSK9 gene promoter was amplified by PCR using HepG2 genomic DNA as the template and cloned into pGL4-Basic vector (Promega, Madison, WI, USA) at Xho I and Hind III sites to get pGL4-PCSK9-P. And pGL4-PCSK9-P plasmid was used as the template for the PCR amplification of PCSK9 gene promoter fragments (D1-D7). The HNF1α mutant (HNF1α-mu) and HINFP mutant (HINFP-mu) were generated from construct D5 using the Fast MultiSite Mutagenesis System (TransGen, Beijing, China). Primers used for plasmid construction are listed in Supplemental Table I. The cells were transfected with the human PCSK9 promoter plasmid using Lipofectamine 2000 (Thermo Scientific, Wilmington, DE, USA) according to the manufacturer's instructions. After transfection, the cells were treated with compounds or vehicle control (0.1% DMSO) for 24 h. The luciferase activities were measured using the Luciferase Assay System (Promega) and detected by a Victor X5 multilabel plate reader (PerkinElmer). A collection of 6328 compounds was screened in the pGL4-PCSK9-P stably transfected cells at a concentration of 25 μg/mL for the primary screening. The screening compound library and the positive compounds 7030B-C5, 7031B-H9, 7045B-E7 and 7045B-F7 are from the center for National New Drug Screening (Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China). 2.3. Transfection with small interference RNA (siRNA) Three pre-designed siRNAs targeted to human HNF1α mRNA, FoxO3 mRNA, HINFP mRNA and one silencer negative control siRNA were obtained from Ambion. Transfection of siRNAs was carried out using the Lipofectamine RNAiMax reagent (Thermo Scientific) according to the manufacturer's instructions. The cells were incubated with serum-free OPTI-MEM medium, and transfected with the negative control (siNC) or specific siRNA at a final concentration of 100 nM. After 48 h of transfection, the cells were treated with the vehicle or 7030B-C5 (12.5 μM) for 24 h and harvested for further analysis. 2.4. Quantitative real-time PCR Total RNAs were isolated from cultured cells or tissues with the SV total RNA isolation system (Promega) and quantified by Nanodrop spectrophotometry (Thermo Scientific). RNA was reverse transcribed using TransScript First-Strand cDNA Synthesis SuperMix (TransGen). Quantitative real-time PCR (qPCR) was performed in the Bio-Rad CFX96 real-time system (Bio-Rad, Hercules, CA, USA) using the SYBR green Master Kit (Roche, Mannheim, Germany) as previously described [76][35]. qPCR primers are listed in Supplemental Table II. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used to normalize the mRNA levels of target genes. 2.5. Western blotting Whole-cell lysates were prepared using RIPA lysis buffer (50 mM Tris HCl, 150 mM NaCl, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS, pH 7.4) containing complete EDTA-free protease inhibitor cocktail (Roche). Protein samples were separated by 10% SDS-polyacrylamide gel electrophoresis (PAGE) and transferred onto a 0.45-μm polyvinylidene fluoride (PVDF) membrane (Millipore, Bedford, MA, USA). The membranes were incubated with primary antibodies to LDLR (Abcam, Cambridge, UK), PCSK9 (R&D Systems, Minneapolis, MN, USA) HNF1α (Cell Signaling Technology, Danvers, MA, USA), FoxO1 (Cell Signaling Technology), FoxO3 (Cell Signaling Technology), HINFP (Novus, Littleton, CO, USA) or GAPDH (ZSJQ-Bio, Beijing, China), followed by horse radish peroxidase (HRP)-conjugated secondary antibodies (ZSJQ-Bio). An enhanced chemiluminescence detection system (Millipore) was used for blot detection. The quantification of detection protein amounts was determined by Image J software, normalized to GAPDH. 2.6. DiI-LDL uptake assays After incubated with positive compounds, HepG2 cells were incubated with 2 mg/mL 1,1′-dioctadecyl-3,3,3′,3′- tetramethylindocarbocyanine perchlorate (DiI)-labeled LDL (Biomedical Technologies, Stoughton, MA, USA) for 4 h at 37 °C. Then cells were harvested, washed and resuspended in phosphate buffered saline (PBS). DiI fluorescence measurements were performed using an Epics XL flow cytometer (Beckman Coulter, Miami, FL, USA) as described previously [77][36]. 2.7. Chromatin immunoprecipitation assay (ChIP assay) Cells cultured in MEM medium were treated with vehicle or 7030B-C5 (12.5 μM) for 24 h. The ChIP assay was carried out using the ChIP Assay Kit (Cell Signaling Technology) according to the manufacturer's instructions. After 7030B-C5 treating, the cells were fixed in 1% formaldehyde for 10 min at room temperature. The chromatin was sheared to an average length of 150–900 bp by sonication. The chromatin extracts were immunoprecipitated at 4 °C overnight with anti-HNF1α, anti-FoxO3, or control IgG (Cell Signaling Technology). Immunocomplexes were isolated by binding to protein A-agarose beads. Precipitated DNA was isolated after ethanol precipitation. Quantitative real-time PCR was performed to analyze the promoter binding levels determined using the specific PCSK9 primers 5′-TCCAGCCCAGTTAGGATTTG-3′ and 5′-CGGAAACCTTCTAGGGTGTG-3′. 2.8. Animal experiments and quantification of atherosclerosis All experimental procedures involving animals were approved by the Institutional Laboratory Animal Care and Use Committee of Institute of Medicinal Biotechnology. C57BL/6 J mice, ApoE KO mice were purchased from Vital River Laboratory Animal Technology (Beijing, China). To investigate the oral acute toxicity of active compounds, male C57BL/6 J mice (~8 weeks old) fed normal chow were divided into four groups (5 mice/group), and intragastric injected with active compounds dissolved in H[2]O (100 mg/kg bodyweight/day, 300 mg/kg bodyweight/day, 500 mg/kg bodyweight/day, 1000 mg/kg bodyweight/day, respectively). Survival and behavioral characteristics were immediately observed as well as 10 min, 15 min, 30 min, 1 h, and 2 h for the first day. Then, it was observed for once a day lasting for a total of 7 days. To determine the effect of active compounds on PCSK9 expression in vivo, male C57BL/6 J mice (~8 weeks old) fed normal chow were divided into three groups (5 mice/group), and intragastric injected with vehicle and 7030B-C5 (30 mg/kg bodyweight/day), 7031B-H9 (50 mg/kg bodyweight/day), 7045B-E7 (100 mg/kg bodyweight/day), 7045B-F7 dissolved in H[2]O (100 mg/kg bodyweight/day) for 4 weeks, respectively. Mice were then sacrificed with 1% sodium pentobarbital (40 mg/kg) followed by collection of liver samples individually to determine PCSK9 and LDLR expression by western blot and real-time PCR. To study the effects of active compounds on atherosclerosis, male ApoE KO mice (~8 weeks old) were fed a high-fat diet (HFD) containing 0.15% cholesterol and 20% lard or a regular rodent chow as a control. And the male ApoE KO mice (~8 weeks old) fed a HFD were divided into three groups (10 mice/group), and intragastric injected with vehicle and 7030B-C5 (10 mg/kg bodyweight/day, 30 mg/kg bodyweight/day), 7031B-H9 (50 mg/kg bodyweight/day, 100 mg/kg bodyweight/day). After 8 weeks of feeding, blood samples were collected for determination of lipid profiles by 7100 automatic biochemical analyzer (HITACHI, Tokyo, Japan). After 12 weeks of feeding, the animals were sacrificed followed by collection of mouse aorta, liver and blood samples. Liver samples were used to determine hepatic protein expression by Western blot. Liver tissues were fixed in 4% neutral buffered formalin and embedded in OCT freezing medium. The tissues were sliced and stained with hematoxylin-eosin (H&E) staining for morphological analysis, Oil Red O to detect lipid accumulation. Blood samples were collected and detected as described above. And serum PCSK9 levels were determined by an ELISA assay kit (Sino Biological, Beijing, China). Aortas were collected and stained with Oil Red O solution. To determine lesions in aortic root, frozen sections of aortic root were prepared and then stained with Oil Red O solution. The lesions in en face aortas and aortic root were quantitatively determined by computer-assisted image analysis method (Image J) and showed as percent lesion area [78][37]. 2.9. Fast protein liquid chromatography (FPLC) Mice serum was fractionated using FPLC (Akta FPLC; GE Healthcare, Pittsburgh, PA, USA) using Superose 6 Increase 10/300 GL columns. Phosphate buffered saline (PBS; pH 7.4) eluent buffer was first passed through a 0.22 μm filter, and then the column was equilibrated at a rate of 0.25 mL/min. Serum sample aliquots of 500 μL were then injected into the column. Elutions were then carried out at a flow rate of 0.25 mL/min. 63 fractions, 0.3 mL each, were collected in separate eluant eppendorf tubes for subsequent cholesterol content analysis by 7100 automatic biochemical analyzer (HITACHI). 2.10. Hepatic transcriptome analysis Total RNA from ApoE KO mice livers were extracted using TRIzol reagent (Invitrogen). Subsequently, mRNA was purified from total RNA using the Oligotex mRNA Midi Kit (Qiagen, Hilden, Germany). Poly(A)+ mRNA was obtained using magnetic poly(A)+ Dynabeads (Invitrogen). For RNA-seq, the cDNA libraries were prepared with fragmented mRNA according to a TruseqTM RNA sample prep kit (Illumina, California, USA). The cDNA was then end-repaired, adenylated, and ligated to the sequencing adapters provided by Illumina. Finally, the libraries were enriched by PCR amplification and sequenced using an Illumina HiSeq 2000 platform (Majorbio Bio-Pharm, Shanghai, China). Sequence data has been deposited with the NCBI BioProject database under accession PRJNA602107. 2.11. Statistical analyses All experiments were repeated at least three times and representative results are shown in figures. The values are expressed as the mean ± SEM. Student's t-test was applied for comparing two groups and one-way ANOVA for multiple groups, followed by Bonferroni's correction as applicable (GraphPad Prism Software; Graph-Pad). P value of < 0.05 was considered significant. Error bars denote SEM. 3. Results 3.1. Discovery of novel PCSK9 inhibitors using cell-based high-throughput screening (HTS) assays In order to establish a luciferase reporter-based HTS assay to find modulators targeting PCSK9 gene transcriptional expression, a 2112-bp fragment of PCSK9 gene promoter region was directionally inserted into the upstream of luciferase reporter gene of pGL4-Basic vector to construct the recombinant plasmid pGL4-PCSK9-P ([79]Fig. 1a). Subsequently, the HTS assay was built by stably transfecting plasmid pGL4-PCSK9-P into HepG2 cells and quantitatively assessed by Z’ factor [80][38] using berberine (BBR) as a positive control. BBR is a known inhibitor of PCSK9 transcription [81][30] ([82]Fig. 1b and Suppl Fig. 1), which regulated PCSK9 expression through the modulation of transcriptional factors SREBP2 and HNF1α in hepatic cells. In our assay, BBR significantly repressed PCSK9 transcriptional activity in a dose-dependent manner, with an IC[50] of 10.26 μM (Suppl Fig. 1c). Besides, anacetrapib, a CETP inhibitor, which was reported to inhibit transcriptional activation of the PCSK9 gene by reducing the expression of mature form of SREBP2 [83][39], was used to evaluate the established in vitro HTS assay as well. The results showed that anacetrapib could also significantly reduce the PCSK9 transcriptional activity in a dose-dependent manner, with the IC[50] of 33.16 μM (Suppl Fig. 1d). In addition, the HTS assay achieved a good signal-to-background ratio with a low percent coefficient of variation, indicating that the model is suitable for high-throughput screening (Suppl Table 3). Fig. 1. [84]Fig. 1 [85]Open in a new tab Identification of novel PCSK9 inhibitors using cell-based high-throughput screening (HTS) assays. (a) The construction of recombinant plasmid pGL4-PCSK9-P. Human PCSK9 promoter region spanning −2112 to −1 bp, relative to the ATG start codon, was amplified by PCR, verified by DNA sequencing and cloned into pGL4-Basic vector between the Xho I and Hind III sites to produce pGL4-PCSK9-P. (b) The samples in compound library were screened by the established cell-based HTS assay for their capability of inhibiting PCSK9 transcription. In total, 6328 compounds at 25 μg/mL were screened. The red dot represented PCSK9 inhibitors 7030B-C5, 7031B-H9, 7045B-E7 and 7045B-F7 we identified. The blue dot represented positive control berberine (BBR). (c) HTS hit triage workflow resulting in the identification of 7030B-C5, 7031B-H9, 7045B-E7 and 7045B-F7, with the number of compounds selected at each step. (d) The inhibitory activity and chemical structure of a novel PCSK9 inhibitor 7030B-C5, 7031B-H9, 7045B-E7 and 7045B-F7. The stable pGL4-PCSK9-P transfected HepG2 cells were treated with 7030B-C5, 7031B-H9, 7045B-E7 or 7045B-F7 for 24 h and the luciferase activities were measured. The data represent the mean ± SEM of at least three independent experiments. (For interpretation of the references to color