SOS1::KRAS inhibitor | BI-3406
Highlights
BI-3406 is a highly potent and selective SOS1::KRAS protein interaction inhibitor1. This small molecule reduces the formation of GTP-loaded KRAS and inhibits MAPK pathway signaling in vitro and in vivo. It has good solubility in water and is highly permeable in the Caco2 assay. Its PK properties make it suitable for in vivo testing in rodent species.
Background information
Target Information
Aberrant activation of Kirsten rat sarcoma viral oncogene homolog (KRAS) by deregulated upstream signaling, loss of GTPase-activating protein function, or oncogenic mutations results in increased GTP-bound KRAS and persistent signaling through downstream effector pathways in cancer.2,3 KRAS is the most frequently mutated oncogene in three of the deadliest cancers, as it occurs in approximately 90% of pancreatic cancer, 40% of colorectal cancer and 25% of non-small cell lung cancer cases (Data from cBioPortal v3.7.4 accessed Sept 14, 2021)11,12.
RAS family small GTP/GDP binding proteins, such as KRAS, have a weak intrinsic GTPase activity and slow nucleotide exchange rates. Two classes of enzymes have evolved to facilitate cycling between the active GTP-bound state and the inactive GDP-bound form. GTPase Activating Proteins (GAPs) increase the intrinsic GTPase activity of RAS family proteins, leading to the formation of GDP bound RAS (e.g. NF1), whereas guanine nucleotide exchange factors (GEFs), such as Son of Sevenless 1 (SOS1), directly interact with KRAS and release GDP, enabling GTP binding and re-activation. Cancer-associated mutations in KRAS further suppress the intrinsic and GAP-induced GTPase activity leading to an increased population of signaling competent GTP loaded KRAS molecules.3-6
Selective inhibition of SOS1, a GEF for the RAS family of small GTPases, significantly reduces formation of GTP-loaded KRAS (activated KRAS) and thereby inhibits downstream MAPK signaling. SOS1 needs to be recruited to the membrane where it binds to Shp2 and Grb2 to act as GEF. Depleting SOS1 decreased the survival of tumor cells carrying a KRAS mutation or amplification whereas, no effect was observed in KRAS non addicted wild-type cells.8
Reduction of RASGDP and an anti-proliferative cytostatic effect was demonstrated with this SOS1::KRAS inhibitor in KRAS addicted cell lines in vitro using 3D proliferation assays as well in vivo in KRAS mutant mouse models.
Preclinical data showed enhanced pathway modulation and synergistic anti-tumor effects following vertical pathway inhibition of BI-3406 with either Mitogen-activated protein kinase inhibitors (MEKi; e.g. trametinib, binimetinib, cobimetinib, selumetinib or BI 3011441) or KRASG12C inhibitors (MRTX849, AMG510 or BI 1823911). Furthermore, SOS1::KRAS treatment sensitizes tumor cells to enhanced DNA damage in combination with irinotecan.9
BI-3406 in complex with SOS1 (PDB code:6scm)
In vitro activity
BI-3406 inhibits the interaction of SOS1 with GDP-loaded KRAS with an IC50 of 5 nM. In KRAS mutant NCI-H358 cells, the small molecule SOS1::KRAS inhibitor inhibits pERK formation with an IC50 of 4 nM and cellular proliferation with an IC50 of 24 nM.1 The small molecule SOS1::KRAS inhibitor has no species selectivity versus mouse KRAS mutant cell lines.10
| Probe name / negative control | BI-3406 | BI-0178 |
| MW [Da] | 462.5 | 335.4 |
| SOS1 (IC50) [nM]a | 4 | >100,000 |
| pERK (DLD-1, KRASG13D) (IC50) [nM]a | 24 | n.a. |
| Proliferation (DLD-1, KRASG13D) (IC50) [nM]a | 36 | n.a. |
| Proliferation (H520, KRASwt) (IC50) [nM]a | >10,000 | n.a. |
a assay conditions see ref. 1,10
In vitro DMPK and CMC parameters
BI-3406 has good solubility in water at acidic or neutral pH. It showed high permeability in Caco2 assay but significant efflux in the MDCK permeability assay.
| Probe name / negative control | BI-3406 | BI-0178 |
| logP | 4.2 | n.d. |
| Solubility @ pH 6.8 [µg/ml] | 84 | 12 |
| CACO permeability @ pH 7.4 [*10-6 cm/s] | 15.3 | n.d. |
| CACO efflux ratio | 1.75 | n.d. |
| MDCK permeability Pappa-b/b-a @ 1µM [10-6 cm/s] | 1.7 | 40 |
| MDCK efflux ratio | 25 | 1.7 |
| Microsomal stability (human/mouse/rat) [% QH] | 44/81/48 | <23/78/78 |
| Hepatocyte stability (human/mouse/rat) [% QH] | 12/56/28 | n.d. |
| Plasma protein binding (human/mouse/rat) [%] | 98.8/98.4/99.0 | n.d. |
| hERG [inh. % @ 1 µM] | 11.2 | n.d. |
| CYP 3A4 (IC50) [µM] | >50 | >50 |
| CYP 2C8 (IC50) [µM] | 18 | 24.9 |
| CYP 2C9 (IC50) [µM] | 15 | >50 |
| CYP 2C19 (IC50) [µM] | 13 | >50 |
| CYP 2D6 (IC50) [µM] | 11 | 35.9 |
In vivo DMPK parameters
PK properties in rodent animal species are suitable for once or twice daily oral dosing in acute or sub-chronic in vivo experiments, but is expected to have low brain penetration1. BI-8668 has a good DMPK profile and showed 33% inhibition of fluid absorption at 3 µg/kg in an airway fluid absorption assay in Wistar rats.
| BI-3406 | Mouse | RAT |
| Clearance [% QH]b | 61 | 16 |
| Mean residence time after iv dose [h] | 0.5 | 2.6 |
| tmax [h] | 0.8 | 3.3 |
| Cmax, dose normalized [nM] | 85 | 237 |
| F [%] | 100 | 100 |
| Vss [l/kg] | 1.7 | 1.7 |
In vivo pharmacology
BI-3406 was studied in several KRAS mutant CRC, PDX and NSCLC PDX and CDX models.1,10
Negative control
BI-0178 which serves as a negative control
Selectivity
BI-3406 was shown to be selective versus SOS2 (IC50 > 10µ M), selective in a panel of 368 kinases (no off-target hits at 5 µM) and moderately selective in a panel of 44 other off-targets (10 hits at 10 µM, IC50 (alpha A1 antagonism)= 6 µM).
| SELECTIVITY DATA AVAILABLE | BI-3406 | BI-0178 |
SafetyScreen44™ with kind support of  | Yes | Yes |
| Invitrogen® | Yes | No |
| DiscoverX® | No | No |
| Dundee | No | No |
Download selectivity data:
BI-3406_selectivityData.xlsx
BI-0178_selectivityData.xlsx
Co-crystal structure of the BI probe compound and the target protein
The Xray crystal structure of target in complex with BI-3406 is available (PDB code: 1NVU).1
Reference molecule(s)
BAY-293
Summary
BI-3406 is a potent and selective Son of Sevenless 1 (SOS1) :: Kirsten rat sarcoma viral oncogene (KRAS) protein interaction inhibitor for research. The small molecule inhibitor BI-3406 binds to the catalytic site of SOS1, inhibiting the interaction with RAS‐GDP. This significantly reduces formation of GTP-loaded KRAS (activated KRAS), thereby inhibiting downstream MAPK signaling. The SOS1::KRAS inhibitor shows pharmacokinetic (PK) properties that are suitable for in vivo testing in rodent species but is expected to have low brain penetration1.
Supplementary data
2 D structure formats available
SOS1::KRAS inhibitor | BI-3406.png
SOS1::KRAS inhibitor | BI-3406.smiles
SOS1::KRAS inhibitor | BI-3406.sdf
Negative Control | BI-0178.png
References
BI-3406, a Potent and Selective SOS1-KRAS Interaction Inhibitor, Is Effective in KRAS-Driven Cancers through Combined MEK Inhibition
Hofmann M. H., Gmachl M., Ramharter J., Savarese F., Gerlach D., Marszalek J. R., Sanderson M. P., Kessler D., Trapani F., Arnhof H., Rumpel K., Botesteanu D.-A., Ettmayer P., Gerstberger T., Kofink C., Wunberg T., Zoephel A., Fu S.-C., Teh J. L., Böttcher J., Pototschnig N., Schachinger F., Schipany K., Lieb S., Vellano C. P., O'Connell J. C., Mendes R. L., Moll J., Petronczki M., Heffernan T. P., Pearson M., McConnell D. B., Kraut N.
Cancer Discov. 2021, Jan;11(1):142-157.
Abstract CT210: Trial in Process: Phase 1 studies of BI 1701963, a SOS1::KRAS Inhibitor, in combination with MEK inhibitors, irreversible KRASG12C inhibitors or irinotecan.
Hofmann M. H., Lu H., Duenzinger U., Gerlach D., Trapani F., Machado A. A., Daniele J. R., Huang J. K., Bristow C. A., Waizenegger I. C., Gmachl M., Rudolph D., Vellano C. P., Marotti M., Vucenovic V., Heffernan T. P., Marszalek J. R., Petronczki M. P., Kraut N.
Poster presentation at AACR 2021 Abstract
One Atom Makes All the Difference: Getting a Foot in the Door between SOS1 and KRAS
Ramharter J., Kessler D., Ettmayer P., Hofmann M. H., Gerstberger T., Gmachl M., Wunberg T., Kofink C., Sanderson M., Arnhof H., Bader G., Rumpel K., Zöphel A., Schnitzer R., Böttcher J., Jonathan C. O’Connell, Rachel L. Mendes, David Richard, Nikolai Pototschnig, Irene Weiner, Hela W., Hauer K., Haering D., Lamarre L., Wolkerstorfer B., Salamon C., Werni P., Munico-Martinez S., Meyer R., Kennedy M. D., Kraut N., McConnell D. B.
J. Med. Chem. 2021, 64, 6569–6580.
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data
Cerami E., Gao J., Dogrusoz U., Gross B. E., Sumer S. O., Aksoy B. A., Jacobsen A., Byrne C. J., Heuer M. L., Larsson E., Antipin Y., Reva B., Goldberg A. P., Sander C., Schultz N.
Cancer Discovery 2012, 2, 401-4.
How to cite opnMe?
When you plan a publication, please use the following acknowledgement:
BI-3406 was kindly provided by Boehringer Ingelheim via its open innovation platform opnMe, available at https://opnme.com.
