| Literature DB >> 31810863 |
Helene J Bustad1, Karen Toska2, Caroline Schmitt3, Marta Vorland2, Lars Skjærven1, Juha P Kallio1, Sylvie Simonin3, Philippe Letteron4, Jarl Underhaug5, Sverre Sandberg6, Aurora Martinez7.
Abstract
Mutations in hydroxymethylbilane synthase (HMBS) cause acute intermittent porphyria (AIP), an autosomal dominant disease where typically only one HMBS allele is mutated. In AIP, the accumulation of porphyrin precursors triggers life-threatening neurovisceral attacks and at long-term, entails an increased risk of hepatocellular carcinoma, kidney failure, and hypertension. Today, the only cure is liver transplantation, and a need for effective mechanism-based therapies, such as pharmacological chaperones, is prevailing. These are small molecules that specifically stabilize a target protein. They may be developed into an oral treatment, which could work curatively during acute attacks, but also prophylactically in asymptomatic HMBS mutant carriers. With the use of a 10,000 compound library, we identified four binders that further increased the initially very high thermal stability of wild-type HMBS and protected the enzyme from trypsin digestion. The best hit and a selected analog increased steady-state levels and total HMBS activity in human hepatoma cells overexpressing HMBS, and in an Hmbs-deficient mouse model with a low-expressed wild-type-like allele, compared to untreated controls. Moreover, the concentration of porphyrin precursors decreased in liver of mice treated with the best hit. Our findings demonstrate the great potential of these hits for the development of a pharmacological chaperone-based corrective treatment of AIP by enhancing wild-type HMBS function independently of the patients' specific mutation.Entities:
Keywords: acute intermittent porphyria; autosomal dominant disease; heme synthesis; hydroxymethylbilane synthase; inborn error of metabolism; mouse model of AIP; pharmacological chaperones; protein stabilization
Mesh:
Substances:
Year: 2019 PMID: 31810863 PMCID: PMC7001003 DOI: 10.1016/j.ymthe.2019.11.010
Source DB: PubMed Journal: Mol Ther ISSN: 1525-0016 Impact factor: 11.454
Figure 1Screening and Validation of Stabilizing Hit Compounds for HMBS
(A) Representative differential scanning fluorimetry (DSF) profiles for HMBS in the absence and presence of hit compounds. The thermal upshift values (ΔTm) for the compounds are determined from the midpoint denaturation temperatures (Tm at y = 0.5) compared to the control sample with 2% DMSO (Tm = 76.6 ± 0.5°C). The profiles represent recombinant WT-HMBS incubated with the 0.04-mg/mL compound (average concentration 122 μM) in 2% DMSO (red, C5; blue, C6; see the formulas in Table 2) and the control sample without compound, with 2% DMSO (dotted gray). (B) Protection of hit compounds against limited tryptic proteolysis of WT-HMBS. Top: SDS-PAGE showing the effect of the indicated compounds (84 μM and 2% DMSO) on HMBS trypsination. std, low molecular weight standards; control n.t., no trypsin added; control DMSO, HMBS with 2% DMSO and trypsin. Bottom: quantification of the lowest 31.5-kDa band relative to the full-length HMBS at 42.5 kDa. *p < 0.05 and **p < 0.01 for differences compared to the DMSO control, calculated by unpaired two-tailed t test. Data are presented as mean ± SD.
Primary Hit Compounds
| Compound ID | ΔTm | Relative Activity, Standard | Relative Activity, Pre-Incubated at 70°C | Protection against Tryptic Proteolysis |
|---|---|---|---|---|
| Control | – | 1.00 | 1.00 | – |
| C4 | 1.6 | 1.04 ± 0.05 | 0.92 ± 0.07** | ND |
| C5 | 2.1 | 1.05 ± 0.02 | 1.04 ± 0.05 | |
| C6 | 1.6 | 0.98 ± 0.06 | 1.01 ± 0.06 | |
| C8 | 4.5 | 1.01 ± 0.03 | 0.92 ± 0.05** | ND |
| C9 | 3.8 | 0.98 ± 0.03 | 1.04 ± 0.07 | +/− |
| C11 | 1.6 | 1.00 ± 0.03 | 1.01 ± 0.04 | |
| C12 | 2.2 | 1.07 ± 0.05 | 0.94 ± 0.09 | +/− |
| C15 | 1.5 | 1.00 ± 0.02 | 0.91 ± 0.07* | ND |
| C16 | 2.0 | 1.04 ± 0.04 | 0.91 ± 0.03*** | ND |
| C17 | 2.3 | 1.09 ± 0.05 | 1.07 ± 0.04 | |
| C19 | 2.0 | 1.04 ± 0.02 | 0.95 ± 0.06 | +/− |
| C23 | 1.6 | 0.92 ± 0.05** | 0.96 ± 0.06* | ND |
| C24 | 2.3 | 1.08 ± 0.03 | 0.81 ± 0.06**** | ND |
The effect of the 13 primary hit compounds on the Tm of HMBS measured by DSF, enzymatic activity, and limited tryptic proteolysis of the enzyme. *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001 for significance compared with the DMSO control sample, calculated by unpaired two-tailed t test. Data are presented as mean ± SD.
The thermal upshift values (ΔTm) monitored by DSF. The average compound concentration in DSF screening was 122 μM (2% DMSO).
Activity assay performed at standard conditions, with 100 μM PBG at 37°C, 84 μM compound, and 2% DMSO, which was added in all controls.
Assay, including preincubation of HMBS with compound at 70°C, and subsequent standard activity assay, with 100 μM PBG at 37°C, 84 μM compound, and 2% DMSO.
+/−, ±2%; +, >4%; ++, 10% remaining full-length HMBS relative to DMSO; ND, not determined; see main text and Figure 1B for details.
Hit compounds selected for cell studies.
Hit Compounds Selected for Validation
| ID | Structure | KM (PBG) | Vmax |
|---|---|---|---|
| Control | – | 86 ± 5 | 61 ± 2 |
| C5 | 81 ± 5 | 55 ± 1** | |
| C6 | 69 ± 4* | 56 ± 1* | |
| C11 | 77 ± 5 | 59 ± 1 | |
| C17 | 81 ± 2 | 58 ± 2 |
Chemical structure of the four hit compounds selected for cellular studies and steady-state enzyme kinetic parameters of HMBS in the presence of the compounds. *p < 0.05 and **p < 0.01 for significant difference compared with the values for the control sample (with 2% DMSO), calculated by unpaired two-tailed t test. Data are presented as mean ± SD.
Effect of the compounds on the enzyme kinetic parameters for HMBS activity, measured at fixed compound concentration (84 μM in 2% DMSO) and variable PBG (0–1 mM) at 37°C, and fitted to Michaelis-Menten kinetics.
Figure 2Effect of the Hit Compounds C6 and Its Analog C6-3 on HMBS in HepG2 Cells and Concentration-Dependent Surface Plasmon Resonance
(A and B) Western blotting and immunoquantification of the relative amount of HMBS in cell lysates from WT-HMBS stably transfected HepG2 cells treated with either C6 (A) or its analog C6-3 (B; see molecular structure in Table 3 and main text thereafter) at the indicated concentrations. DMSO (2%) was included in all samples. Representative blots are shown, and the histograms below represent the quantification of the relative HMBS levels (n = 3) using GAPDH as the protein loading control. Concentration-dependent binding of C6 (C) and C6-3 (D) to HMBS measured by SPR. The half-maximal binding (S0.5) values were 83 ± 7 μM for C6, obtained by subsequent Octet measurements (C, inset), and 63 ± 3 μM for C6-3, obtained from the SPR binding isotherm (D). Data are presented as mean ± SD.
Compound Analogs of C6
| ID | IUPAC Name and Structure | MW | ΔTm | Protection against Tryptic Proteolysis | KM (PBG) | Vmax |
|---|---|---|---|---|---|---|
| Control | – | – | – | – | 86 ± 5 | 61 ± 2 |
| C6-1 | 5-benzyl-2-hydroxy-3-nitrobenzaldehyde | 257.24 | 6.6 | +/− | – | – |
| C6-2 | 4-[(2-chlorophenyl)methyl]-2-(hydroxymethyl)-6-nitrophenol | 293.7 | 4.7 | +/− | – | – |
| C6-3 | (4-chloro-3-nitrophenyl)(phenyl)methanone | 261.66 | 4.9 | +* | 84 ± 8 | 54 ± 2** |
The analogs of C6 were selected from the compound similarity search calculated using the Tanimoto coefficient. The Tanimoto coefficient is used to calculate the 2D similarity between sets of chemical structures. The effect of the analogs on both the ΔTm measured by DSF and on the limited tryptic proteolysis of HMBS was determined. Steady-state enzymatic kinetic parameters of HMBS in the presence of analogs were only determined for the analog that protected toward tryptic proteolysis (C6-3). *p < 0.05 and **p < 0.01 for significant difference compared with the values for the control sample (with 2% DMSO), calculated by unpaired two-tailed t test. Data are presented as mean ± SD. IUPAC, International Union of Pure and Applied Chemistry.
The thermal upshift values (ΔTm) monitored by DSF. The average compound concentration in DSF screening was 122 μM (2% DMSO).
+/−, ±2%; +, >4%.
Effect of the compounds on the enzyme kinetic parameters for HMBS activity, measured at fixed compound concentration (84 μM with 2% DMSO) and variable PBG (0–1 mM) at 37°C, and fitted to Michaelis-Menten kinetics.
Figure 3The Interaction of C6 and C6-3 with HMBS
(A) Potential binding pockets large enough to accommodate small-molecule compounds in HMBS. The structure of HMBS in the holoenzyme state (PDB: 3ECR) is shown in cartoon representation with the pockets (1 and 2) in pink spheres and cyan surface representation. The DPM cofactor is shown in purple and red spheres. (B) Top-score docked mode for C6, obtained for site 2 (blue sticks); see text for details. This pocket also scored highest for docking of C6-3. (C and D) Detailed view of the top-score docking mode of C6 (blue; C) and C6-3 (green; D) interacting with Arg195 in HMBS (PDB: 3ECR). In both panels, the DPM cofactor is located in the background, and Arg195, Val38, and Leu238 are denoted.
Figure 4The Effect on ALA/PBG Excretion of the Hit Compound and Analog in Hmbs-Deficient Mice
Three groups of Hmbs-deficient T1/T2−/− mice (n = 6 in each group) were treated for 12 days with 20 mg/kg/day of C5, C6, or the analog C6-3, given orally. I.p. injection of phenobarbital was given on days 10–12 to induce the heme biosynthesis and thus, precipitation of biochemical acute attack. The control group was given 10% DMSO and likewise induced with phenobarbital. Urine was collected on days 1 and 10–12, and livers were harvested after sacrifice. (A and B) Bars represent porphyrin precursors ALA (A) and PBG (B) from C5 (red), C6 (blue), and C6-3 (green) treatment, measured in the urine (u) pooled for all mice from each group. The control group is shown in white. (C) HMBS protein levels measured in liver lysates by western blot quantification. Scatterplots with mean representing HMBS protein levels in mice livers treated with C5 (red), C6 (blue), and C6-3 (green). *p < 0.05 for differences with the corresponding control (10% DMSO without compound; white circles), calculated by unpaired two-tailed t test. Data are presented as mean ± SD. (D) HMBS activity in liver lysates. Scatterplot with mean showing the hepatic HMBS activity after treatment with C6 (blue) and C6-3 (green). **p < 0.01 and ****p < 0.0001 for differences with the corresponding control (10% DMSO without compound; white circles), calculated by unpaired two-tailed t test. Data are presented as mean ± SD. (E and F) The relative concentrations of ALA (E) and PBG (F) were measured in liver tissue extracts after treatment with C6 (blue) and C6-3 (green). *p < 0.05 for differences with the corresponding control (10% DMSO without compound; white), calculated by unpaired two-tailed t test. Data are presented as mean ± SD.