Identification of Vitamin D3-Based Hedgehog Pathway Inhibitors That Incorporate an Aromatic A‑Ring Isostere

Previous structure–activity relationship studies for vitamin D3 (VD3) inhibition of Hedgehog (Hh) signaling directed the design, synthesis, and evaluation of a series of VD3-based analogues that contain an aromatic A-ring mimic. Characterization of these compounds in a series of cellular assays demonstrated their ability to potently and selectively down-regulate Hh pathway signaling. The most active of these, <b>17</b>, inhibited pathway signaling in Hh-dependent mouse fibroblasts (IC₅₀ = 0.74 ± 0.1 μM) and cultured cancer cells (IC₅₀ values 3.8 ± 0.1 to 5.2 ± 0.2 μM). In addition, <b>17</b> demonstrated reduced activation of the vitamin D receptor (VDR) compared to VD3 in these cellular models. These results suggest that VD3-based analogues with an aromatic A-ring are a valid scaffold for the development of more selective and potent Hh pathway inhibitors and identify <b>17</b> as an intriguing lead from this class of compounds for further development. In addition, our analysis of Hh pathway inhibitors in cancer cells suggests that the murine basal cell carcinoma cell line ASZ001 and the human medulloblastoma cell line DAOY are appropriate in vitro cancer models for early stage evaluation of pathway inhibition

Proteins meeting significance criteria for fold change in CERES participants who died, using three normalization formats.

Proteins meeting significance criteria for fold change in CERES participants who died, using three normalization formats.</p

Orthogonal correlations for aptamer and traditional assays in CERES participants.

Spearman rho correlations were analyzed for aptamer and traditional assays. Aptamer measures were analyzed in three data formats: raw data, median normalized, and ANML. X-axes show the aptamer measure in relative fluorescence units (RFU), and the y-axes show the traditional assay. CRP: c-reactive protein. FGF23: fibroblast growth factor 23. NT-proBNP: N-terminal pro-B-type natriuretic peptide. PTH: parathyroid hormone.</p

Biological and technical variability of SomaScan.

Short-term biological and intra-assay CVs for 4802 proteins are shown in 4 study participants who had samples available for both types of CVs from the CERES cohort.</p

SomaScan technical information.

BackgroundPatients with kidney failure suffer high mortality, and we currently lack markers for risk stratification for these patients. We carried out a quality control study of a modified aptamer assay (SomaScan v.4.0) that measures ~ 5000 proteins, in preparation for a larger study using this platform in cohorts with kidney failure.MethodsForty participants from the Cardiac, Endothelial Function and Arterial Stiffness in End-Stage Renal Disease (CERES study) were selected to analyze technical and short-term biological variability, orthogonal correlations and differential protein expression in plasma from patients who died during 2.5 year follow-up. Long-term (one year) variability was studied in 421 participants in the Chronic Renal Insufficiency Cohort. We evaluated 4849 aptamers (4607 unique proteins) using data formats including raw data and data formatted using Adaptive Normalization by Maximum Likelihood (ANML), an algorithm developed for SomaScan data in individuals with normal kidney function.ResultsIn ANML format, median[IQR] intra-assay coefficient of variation (CV) was 2.38%[1.76, 3.40] and inter-assay CV was 7.38%[4.61, 13.12]. Short-term within-subject CV was 5.76% [3.35, 9.72]; long-term CV was 8.71%[5.91, 13.37]. Spearman correlations between aptamer and traditional assays for PTH, NT-proBNP, FGF-23 and CRP were all > 0.7. Fold-change (FC) in protein levels among non-survivors, significant after Bonferroni correction, included SVEP1 (FC[95% CI] 2.14 [1.62, 2.82]), keratocan (1.74 [1.40, 2.15]) and LanC-like protein 1 (0.56 [0.45, 0.70]). Compared to raw aptamer data, technical and short-term biological variability in paired samples was lower in ANML-formatted data. ANML formatting had minimal impact on orthogonal correlations with traditional assays or the associations of proteins with the phenotype of mortality.ConclusionsSomaScan had excellent technical variability and low within-subject short-term variability. ANML formatting could facilitate comparison of biomarker results with other studies that utilize this format. We expect SomaScan to provide novel and reproducible information in patients with kidney failure on dialysis.</div

S2 File -

S2 Table 1 Proteins Excluded From Variability Analyses. S2 Table 2 Baseline Characteristics of CRIC Participants with Kidney Failure on Hemodialysis. S2 Table 3 Proteins with Intra-assay CV>20% Using Raw or ANML Data Format. S2 Table 4 Proteins with Inter-assay CV>40% Using Raw or ANML Data Format. S2 Table 5 Short-term Biological Variability Measured Separately in 4 CERES Participants. S2 Table 6 Long-term Variablity of Proteins in 421 CRIC Participants: Raw Data Format. S2 Table 7 Long-term Variablity of Proteins in 421 CRIC Participants: ANML Data Format. S2 Table 8 Correlations of Fold Change and P-values of Proteins in Non-survivors. S2 Table 9 Fold Change (FC) in Protein Level in Non-Survivors Compared to Survivors Using Raw Data. S2 Table 10 Fold Change (FC) in Protein Level in Non-Survivors Compared to Survivors Using Median Normalized Data. (ZIP)</p

Technical and biological variability of somascan in plasma samples of patients with kidney failure.

Coefficient of variation (CV) and spearman rho correlations between pairs of samples are shown above. Data are from CERES study with the exception of long-term within-subject variability, calculated from CRIC data.</p

Fold Change (FC) in protein levels among non-survivors compared to survivors in 40 CERES participants.

Fold Change (FC) in protein levels among non-survivors compared to survivors in 40 CERES participants.</p

Baseline characteristics of 40 participants with kidney failure.

Baseline characteristics of 40 participants with kidney failure.</p

Structure–Activity Relationships for Vitamin D3-Based Aromatic A‑Ring Analogues as Hedgehog Pathway Inhibitors

A structure–activity relationship study for a series of vitamin D3-based (VD3) analogues that incorporate aromatic A-ring mimics with varying functionality has provided key insight into scaffold features that result in potent, selective Hedgehog (Hh) pathway inhibition. Three analogue subclasses containing (1) a single substitution at the <i>ortho</i> or <i>para</i> position of the aromatic A-ring, (2) a heteroaryl or biaryl moiety, or (3) multiple substituents on the aromatic A-ring were prepared and evaluated. Aromatic A-ring mimics incorporating either single or multiple hydrophilic moieties on a six-membered ring inhibited the Hh pathway in both Hh-dependent mouse embryonic fibroblasts and cultured cancer cells (IC₅₀ values 0.74–10 μM). Preliminary studies were conducted to probe the cellular mechanisms through which VD3 and <b>5</b>, the most active analogue, inhibit Hh signaling. These studies suggested that the anti-Hh activity of VD3 is primarily attributed to the vitamin D receptor, whereas <b>5</b> affects Hh inhibition through a separate mechanism