SLC13A5 Inhibitor | BI01383298
Highlights
BI01383298 is a potent inhibitor of the human solute carrier SLC13A5, also known as sodium-coupled citrate transporter (hNaCT). Its potency and selectivity is improved over prior tools, even over related family members such as hSLC13A2 and hSLC13A3 or murine SLC13A5. BI01372674, bearing only a single substituent exchange, serves as a negative control.
Background information
Target Information
SLC13A5, also known as the sodium-coupled citrate transporter (NaCT), is part of the SLC13 family of sodium/sulphate carboxylate co-transporters that comprises of five members. SLC13A5, along with SLC13A2 and SLC13A3, transports di- and tricarboxylates using sodium as a co-ion. SLC13A1 and SLC13A4 are not thought to transport di- and tricarboxylates. SLC13A5 is predominantly expressed in the plasma membrane of hepatocytes where it transports citrate from the circulatory system into hepatocytes. Lower levels are also observed in brain and testes.4 SLC13A5 was first identified in Drosophila melanogaster where the name I’m Not Dead Yet or INDY was coined. Inactivation mutants of SLC13A5 in D. melanogaster and Caenorhabditus elegans led to increased lifespan.5 Data from mouse models have implicated that the protein may have a role in various disease settings such as obesity and diabetes. This was supported by data that demonstrated that knockout mice were protected from adiposity.6 Inhibition of the transporter also led to reduced lipid concentrations in a siRNA study,7 and a substrate analogue was used to lower blood glucose levels.1 More recently mutations in SLC13A5 have been linked to early-infantile epileptic encephalopathy,8 while silencing of the SLC13A5 gene inhibits proliferation of human hepatocarcinoma cells.9 Together, this data indicates that the development of pharmacological regulators of SLC13A5 may open new opportunities in the development of treatments for obesity, metabolic disorders and cancer.10,11
Structure of a SLC related to SLC13A5, as revealed by X-ray crystallography (PDB code 5UL7)
In vitro activity
BI01383298 displays an IC50 (hSLC13A5) = 56 nM and an IC50 (HepG2) = 24 nM, while being highly selective (IC50 > 100 µM for all other SLC13 family members, and for murine SLC13A5).
| Probe name / negative control | BI01383298 | BI01372674 |
| MW [Da] | 445.0 | 503.1 |
| HEK293-hSLC13A5 (IC50) [µM]a | 0.056 | >100 |
| HepG2 (IC50) [µM]b | 0.024 | >100 |
| HEK293-hSLC13A2 (IC50) [µM]a | >100 | n.d. |
| HEK293-hSLC13A3 (IC50) [µM]a | >100 | n.d. |
| HEK293-mSLC13A5 (IC50) [µM]a | >100 | >70 |
| HEK293-GLYT2 (IC50) [µM]c | >100 | n.d. |
Citrate uptake inhibition was measured for all citrate transporters and glycine uptake measured to GLYT2. Potency was assessed for the probe candidate and the negative control on uptake of 14C-citrate into cells over-expressing SLC13A5, SLC13A2, SLC13A3, mouse SLC13A5 and in HEPG2 cells.
a The IC50 were measured in a recombinant human SLC13A5 citrate uptake assay, using human embryonic kidney 293Flp-In-cells overexpressing the human SLC13A5 transporter
b The IC50s were obtained in a HepG2 citrate uptake assay.
c The IC50s were obtained in a human GlyT2 glycine uptake assay.
For all assays outlined for this molecule, detailed experimental conditions can be obtained via the “Contact us” form on opnMe.com.
In vitro DMPK and CMC parameters
BI01383298 is a permeable but poorly soluble tool compound with moderate microsomal stability. Efforts to improve the solubility led to the discovery of BI01372674, the negative control.
| Probe name / negative control | BI01383298 | BI01372674 |
| logP | 4.64 | 1.8 |
| Solubility @ pH 6.8 [µg/ml] | <1 | 70 |
| CACO permeability @ pH 7.4 [*10-6 cm/s] | 37 | 0.3 |
| CACO efflux ratio | 0.4 | 64 |
| Microsomal stability (human/mouse/rat) [% QH] | 48/50/45 | <23/<23/n.d. |
| Hepatocyte stability (human/mouse/rat) [% QH] | 28/95/84 | 10/47/52 |
| Plasma protein binding (human/mouse/rat) [%] | 99.2/-/- | 86.1/97.7/89.0 |
| hERG [inh. % @ 10 µM] | 17 | n.d. |
| CYP 3A4 (IC50) [µM] | >50 | >50 |
| CYP 2D6 (IC50) [µM] | >50 | >50 |
| CYP 1A2 (IC50) [µM] | >50 | >50 |
| CYP 3A4 (IC50) [µM] | >50 | >50 |
In vitro pharmacology
BI01383298, along with an active probe from the same structural class with better solubility and reference compound PF-06649298,1,3 and negative control BI01372674 in a thermostability assay, at various concentrations (Figure 4). It was shown that BI01383298 directly stabilizes hSLC13A5, and that both the probe and the negative control demonstrate target engagement in vitro. The thermostabilisation data was obtained with the Prometheus label-free system from Nanotemper.
Thermostabilisation of human SLC13A5 by BI0138298 at concentrations ranging from 0.1 mM to 10 mM (three biological samples, each measured in 4 or 8 replicates).
Negative control
BI01372674 is provided as the negative control. It bears only a single substituent exchange by comparison with the active probe, and is completely inactive on both hSLC13A5 and HepG2, IC50 >100 µM for both.
BI01372674, which serves as a negative control
Selectivity
BI01383298 was subjected to a selectivity panel profiling where it showed >100-fold selectivity for 42 out of 44 targets and still >10-fold selectivity for the other two ones.
| SELECTIVITY DATA AVILABLE | BI01383298 | BI01372674 |
SafetyScreen44™ with kind support of  | Yes | Yes |
| Invitrogen® | No | No |
| DiscoverX® | No | No |
| Dundee | No | No |
Download selectivity data:
BI01383298_selectivityData_0.xlsx
BI-2674_selectivityData.xlsx
Reference molecule(s)
PF-06649298 (see Reference 1)
Summary
BI01383298 is a potent and selective inhibitor of human SLC13A5 for in vitro use with no structural homology to the substrate.
Supplementary data
2 D structure formats available
SLC13A5 Inhibitor | BI01383298.png
SLC13A5 Inhibitor | BI01383298.smiles
SLC13A5 Inhibitor | BI01383298.sdf
Negative Control | BI01383298.png
References
Discovery and characterization of novel inhibitors of the sodium-coupled citrate transporter (NaCT or SLC13A5)
Huard K., Brown J., Jones J. C., Cabral S., Futatsugi K., Gorgoglione M., Lanba A., Vera N. B., Zhu Y., Yan Q., Zhou Y., Vernochet C., Riccardi K., Wolford A., Pirman D., Niosi M., Aspnes G., Herr M., Genung N. E., Magee T. V., Uccello D. P., Loria P., Di L., Gosset J. R., Hepworth D., Rolph T., Pfefferkorn J. A., Erion D. M.
Sci. Rep. 2015, 5, 17391.
Optimization of a Dicarboxylic Series for in Vivo Inhibition of Citrate Transport by the Solute Carrier 13 (SLC13) Family
Huard K., Gosset J. R., Montgomery J. I., Gilbert A., Hayward M. M., Magee T. V., Shawn Cabral, Uccello D.P., Bahnck K., Brown J., Purkal J., Gorgoglione M., Lanba A., Futatsugi K., Herr M., Genung N. E., Aspnes G., Polivkova J., Garcia-Irizarry C. N., Li Q., Canterbury D., Niosi M., Vera N. B., Li Z., Khunte B., Siderewicz J., Rolph T., Erion D. M.
J. Med. Chem. 2016, 59 (3), 1165-1175.
Deletion of the Mammalian INDY Homolog Mimics Aspects of Dietary Restriction and Protects against Adiposity and Insulin Resistance in Mice
Birkenfeld A. L., Lee H., Guebre-Egziabher F., Alves T. C., Jurczak M. J., Jornayvaz F. R., Zhang D., Hsiao J. J., Martin-Montalvo A., Fischer-Rosinsky A., Spranger J., Pfeiffer A. F., Jordan J., Fromm M. F., König J., Lieske S., Carmean C. M., Frederick D. W., Weismann D., Knauf F., Irusta P. M., De Cabo R., Helfand S. L., Samuel V. T., Shulman G. I.
Cell Metab. 2011, 14, 184-195.
Inhibition of citrate cotransporter Slc13a5/mINDY by RNAi improves hepatic insulin sensitivity and prevents diet-induced non-alcoholic fatty liver disease in mice
Brachs S., Winkel A. F., Tang H., Birkenfeld A. L., Brunner B., Jahn-Hofmann K., Margerie D., Ruetten H., Schmoll D., Spranger J.
Mol Metab. 2016, 5, 1072-1082.
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