Orally bioavailable PHGDH inhibitor
BI-9593
To our knowledge, BI-9593 is the first orally bioavailable PHGDH inhibitor, characterized by high potency (IC50 of 7 nM) and selectivity. With its unique profile, it complements the previously shared BI-4924 and its esterified prodrug BI-4916. Its stereoisomer BI-9594 has significantly reduced potency in both in vivo and cellular assays, and is suitable as a negative control.
More information
PHGDH (3-phosphoglycerate dehydrogenase) catalyzes the first step of de novo serine biosynthesis downstream of glycolysis and is the rate limiting enzyme for the pathway1. PHGDH converts 3-phosphoglycerate (3-PG) to 3-phosphohydroxypyruvate (3-PHP) in a NAD-dependent manner and is expressed in high levels in the brain, heart, kidneys, liver, and skeletal muscle. Patients with loss-of-function mutations in PHGDH suffer from neurodevelopmental symptoms such as microcephaly, a finding which is replicated in murine models with brain-specific PHGDH deletions2.
PHGDH is also amplified or overexpressed in a subset of tumors, most frequently melanoma and triple-negative breast cancers. Cells with amplified or overexpressed PHGDH show an elevated serine synthesis and are relatively resistant to serine starvation while showing some dependency on PHGDH activity3-6.
Although a plethora of published data support the contributions of the serine biosynthesis pathway to tumorigenesis, as well as to the development of the central nervous system, the precise molecular mechanisms of PHGDH’s role in disease remain unclear. BI-9395 can help elucidating the role of PHGDH in vivo, while BI-4924 and its prodrug BI-4916 with better permeability characteristics are suitable for cellular studies.
X-ray structure of BI-4924, a close analog of BI-9593, binding in PHGDH (PDB code:6RJ6)
BI-9593 displays an IC50 of 7 nM in a PHGDH FL His 500/500 NAD/3-PG diaphorase/resazurin assay and shows modulation of cellular 13C serine biosynthesis over 72 h with an IC50 of 1.4 µM.
| Probe name / negative control | BI-9593 | BI-9594 |
| MW [Da, free base]a | 489.4 | 489.4 |
| PHGDH FL His 500/500 NAD/3-PG Diaphorase/Resazurin Assay (IC50) [nM]b | 7 | 160 |
| PHGDH (3-Phosphoglycerate dehydrogenase length version with His-tag) 13C Serine MS Assay 50 µl (IC50) [nM] | 1,360 | > 100,000 |
a For the salt form you will get, please refer to the label on the vial and for the molecular weight of the salt, please refer to the FAQs
bPHGDH (3-phosphoglycerate dehydrogenase) FL His HighConc 500/500 NAD/3-PG diaphorase/resazurin Assay; the enzymatic activity of 3-Phosphoglycerate dehydrogenase (PHGDH) was measured in the direction of 3-phosphoglycerate (3-PG) oxidation to phosphohydroxypyruvate (PHP) by coupling the reaction with a resazurin reduction reaction, which uses NADH as cofactor, to allow fluorescence detection7
cAll assay conditions are in reference 1
Both BI-9593 and the negative control BI-9594 are highly permeable compounds without efflux liabilities. The excellent microsomal stability qualifies both compounds for in vivo profiling.
| Probe name / negative control | BI-9593 | BI-9594 |
| logD @ pH 11 | 2.2 | 1.2 |
| Solubility @ pH 7 [µg/mL] | 38 | 29 |
| Microsomal stability (human/mouse/rat) [% QH] | < 24/< 24/28 | < 24/< 24/< 23 |
| Hepatocyte stability (mouse) [% QH] | 15 | n.a. |
| Plasma Protein Binding (human/mouse) [%] | > 99.8 / > 99.9 | n.a. / 99.8 |
| BI-9593 | Mouse |
| Clearance [% QH]a | 6.0 |
| Mean residence time after i.v. dose [h]a | 6.2 |
| tmax [h]b | 1.7 |
| Cmax [nM]b | 29,200 |
| F [%]b | 100 |
| Vss [L/kg]a | 1.9 |
a i.v. dose: 1 mg/kg
b p.o. dose: 25 mg/kg
PK properties in mice are suitable for twice daily oral dosing in acute or sub-chronic in vivo experiments, resulting in >90% inhibition of de novo serine synthesis for up to 20 h in the spleen of mice treated with a single dose of 250mg/kg. The compound is well tolerated, as assessed by measuring body weight change.
MOLECULAR WEIGHT OF NEGATIVE CONTROL [DA]
489
BI-9594, is a stereoisomer with >20-fold and >70-fold lower potency in biochemical and cellular assays respectively and can be used as negative control.
BI-9594 which serves as a negative control
BI-9593 hits 4 out of 44 targets with > 50% inhibition. Two GPCRs namely A2A/H and CCKA/H are hit with 62% and 95% inhibition respectively. In addition, BZD/CENTR/R and PDE3A are hit with 68% and 85% inhibition respectively. The negative control BI-9594 hits 3 out of 44 targets with > 50% inhibition, showing a different selectivity pattern. It hits 5HT2B with 65%, CCKA/H with 59% and GCORTICOID/H with 67% inhibition.
| SELECTIVITY DATA AVILABLE | BI-9593 | BI-9594 |
SafetyScreen44™ with kind support of  | Yes | Yes |
| Invitrogen® | No | No |
| DiscoverX® | No | No |
| Dundee | No | No |
Download selectivity data:
BI-9593_selectivityData.xlsx
BI-9594_selectivityData.xlsx
The 1st generation PHGDH inhibitor BI-4924 can be used as a reference molecule.
BI-9593 is the first orally bioavailable PHGDH inhibitor suitable for cellular and in vivo profiling. BI-9594 is available as a negative control.
Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) Inhibitor BI-4924 Disrupts Serine Biosynthesis
Weinstabl H., Treu M., Rinnenthal J., Zahn S. K., Ettmayer P., Bader G., Dahmann G., Kessler D., Rumpel K., Mischerikow N., Savarese F., Gerstberger T., Mayer M., Zoephel A., Schnitzer R., Sommergruber W., Martinelli P., Arnhof H., Peric-Simov B., Hofbauer K. S., Garavel G., Scherbantin Y., Mitzner S., Fett T. N., Scholz G., Bruchhaus J., Burkard M., Kousek R., Ciftci T., Sharps B., Schrenk A., Harrer C., Hearing D., Wolkerstorfer B., Zhang X., Lv X., Du A., Li D., Li Y., Quant J., Pearson M., McConnell D. B.
Journal of Medicinal Chemistry 2019, 62 (17), 7976-7997.
l-Serine deficiency caused by genetic Phgdh deletion leads to robust induction of 4E-BP1 and subsequent repression of translation initiation in the developing central nervous system
Sayano T., Kawakami Y., Kusada W., Suzuki T., Kawano Y., Watanabe A., Takashima K., Arimoto Y., Esaki K., Wada A., Yoshizawa F., Watanabe M., Okamoto M., Hirabayashi Y., Furuya S.
FEBS J 2013, 280: 1502-1517.
Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis
Locasale J. W., Grassian A. R., Melman T., Lyssiotis C. A., Mattaini K. R., Bass A. J., Heffron G., Metallo C. M., Muranen T., Sharfi H., Sasaki A. T., Anastasiou D., Mullarky E., Vokes N. I., Sasaki M., Beroukhim R., Stephanopoulos G., Ligon A. H., Meyerson M., Richardson A. L., Chin L., Wagner G., Asara J. M., Brugge J. S., Cantley L. C., Vander Heiden M. G.
Nat Genet 2011, 43(9):869-74.
Functional genomics reveal that the serine synthesis pathway is essential in breast cancer
Possemato R., Marks K. M., Shaul Y. D., Pacold M. E., Kim D., Birsoy K., Sethumadhavan S., Woo H-K., Jang H. G., Jha A. K., Chen W. W., Barrett F. G., Stransky N., Tsun Z-Y., Cowley G. S., Barretina J., Kalaany N. Y., Hsu P. P., Ottina K., Chan A. M., Yuan B., Garraway L. A., Root D. E., Mino-Kenudson M., Brachtel E. F., Driggers E. M., Sabatini D. M.
Nature 2011, 476(7360):346-50.
Increased Serine Synthesis Provides an Advantage for Tumors Arising in Tissues Where Serine Levels Are Limiting
Sullivan M. R., Mattaini K. R., Dennstedt E. A., Nguyen A. A., Sivanand S., Reilly M. F., Meeth K., Muir A., Darnell A. M., Bosenberg M. W., Lewis C. A., Vander Heiden M. G.
Cell Metab 2019, 29(6):1410-1421.e4.
When you plan a publication, please use the following acknowledgement:
BI-9593 was kindly provided by Boehringer Ingelheim via its open innovation platform opnMe, available at https://www.opnme.com.