A German team has identified a compound that disrupts a protein-protein interaction that localizes K-Ras to the cell membrane, thus inhibiting tumor growth.1 The interface provides a new small molecule binding site for the handful of companies and academics working on ways to tackle the previously undruggable Ras family.

Ras proteins are molecular switches that control cell growth and proliferation. Mutations and other mechanisms that aberrantly activate Ras signaling can promote tumorigenesis.

Collectively, mutations in genes encoding the three Ras isoforms-K-Ras, v-Ha-ras Harvey rat sarcoma viral oncogene homolog (HRAS) or neuroblastoma Ras viral (v-Ras) oncogene (NRAS)-occur in nearly 20% of all cancers.

K-Ras is by far the most commonly mutated isoform, with activating mutations occurring in about 80% of pancreatic cancers.

"If one is diagnosed with pancreatic cancer based on a mutation in K-Ras, the life expectancy is months. And there is hardly anything the doctors can do," said Herbert Waldmann, professor of chemistry and managing director at the Max Planck Institute of Molecular Physiology.

"K-Ras is a particularly important driver in pancreatic cancer. This is essentially an untreatable cancer-there is a huge unmet clinical need," added John Hancock, integrative biology and pharmacology chair and professor at The University of Texas Health Science Center at Houston.

Until 2012, nobody had been able to target any form of Ras with a small molecule because the proteins lacked well-defined surface pockets suitable for binding drug molecules (see Box 1, "A complex question").

Last year, independent teams at Roche's Genentech Inc. unit and the Vanderbilt University School of Medicine identified small molecules that disrupted Ras, but the compounds were not potent and were not tested against oncogenic Ras.2-4

In April, a Kobe University team developed small molecule inhibitors of wild-type and oncogenic forms of Ras, but the compounds were far from drug-like in terms of potency.5,6

Now, a German team has overcome these shortcomings by targeting a distinct protein-protein interface that modulates oncogenic K-Ras activity.

K-Ras activation depends on its localization at the plasma membrane. Farnesyl protein transferases add a lipid modification called a prenyl group to the C-terminal end of K-Ras, which anchors K-Ras to the membrane. The phosphodiesterase d subunit (PDEd), a prenyl-binding protein, binds lipid-modified Ras and delivers it to the plasma membrane.7

With that mechanism in mind, Waldmann, Philippe Bastiaens and Alfred Wittinghofer led a structure-based initiative to identify small molecules that bind to PDEd and disrupt its interaction with K-Ras. The goal was to delocalize K-Ras from the plasma membrane and inhibit its activity.

Bastiaens is professor of systemic cell biology at the Max Planck Institute of Molecular Physiology, and Wittinghofer is professor emeritus at the institute.

A high throughput screen identified small molecules that bound to the prenyl-binding pocket of PDEd. The screen yielded several hits with a shared chemical scaffold. After validating these hits in secondary, in vitro PDEd-binding assays, the scientists solved the crystal structure of PDEd in complex with several compounds.

Using the cocrystal structures as guides, the team modified the initial hits to optimize interaction with and affinity for PDEd. For cellular studies the group selected one compound-deltarasin-that bound PDEd with a Kd of 38 nM in vitro but did not interact with off-target prenyl-binding proteins.

In cultured cells, deltarasin disrupted PDEd-K-Ras interactions. Deltarasin delocalized K-Ras from the plasma membrane in pancreatic ductal adenocarcinoma cell lines. The molecule also produced dose-dependent decreases in oncogenic K-Ras-driven proliferation and signaling compared with vehicle in pancreatic cancer cell lines. In xenograft mouse models, deltarasin abrogated oncogenic K-Ras-driven pancreatic tumor growth.

Results were published in Nature. The team also included scientists from Ruhr University Bochum.

Building momentum against Ras

Waldmann said a drug discovery project based on deltarasin is ongoing at the Lead Discovery Center GmbH, which is the drug discovery arm of the Max Planck Society.8

"Within the next two years we are going to profile and optimize several compound series, including deltarasin and analogs, to generate a lead package," said Thomas Hegendörfer, head of business development at Lead Discovery Center.

Hegendörfer said projects usually start to attract interest from industry after showing efficacy in therapeutically relevant animal models. In the case of deltarasin, however, he said there are already pharma suitors.

One reason for the early interest, said Waldmann, is that deltarasin is more potent than other reported Ras inhibitors. "It also differentiates between wild-type- and K-Ras-dependent cell lines," he said. "The target is entirely novel."

The deltarasin compound class is patented by the Max Planck Society and will be available for licensing from Max Planck Innovation GmbH.

Donner, A. SciBX 6(24); doi:10.1038/scibx.2013.588
Published online Jun 20, 2013


1.   Zimmermann, G. et al. Nature; published online May 22, 2013; doi:10.1038/nature12205
Contact: Herbert Waldmann, Max Planck Institute of Molecular Physiology, Dortmund, Germany
e-mail: herbert.waldmann@mpi-dortmund.mpg.de
Contact: Philippe I.H. Bastiaens, same affiliation as above
e-mail: philippe.bastiaens@mpi-dortmund.mpg.de
Contact: Alfred Wittinghofer, same affiliation as above
e-mail: alfred.wittinghofer@mpi-dortmund.mpg.de

2.   Sun, Q. et al. Angew. Chem. Int. Ed. 51, 6140-6143 (2012)

3.   Maurer, T. et al. Proc. Natl. Acad. Sci. USA 109, 5299-5304 (2012)

4.   Kotz, J. SciBX 5(21); doi:10.1038/scibx.2012.536

5.   Shima, F. et al. Proc. Natl. Acad. Sci. USA 110, 8182-8187 (2013)

6.   Haas, M.J. SciBX 6(19); doi:10.1038/scibx.2013.454

7.   Chandra, A. et al. Nat. Cell Biol. 14, 148-158 (2012)

8.   Edelson, S. SciBX 2(20); doi:10.1038/scibx.2009.815

9.   Hocker, H.J. et al. Proc. Natl. Acad. Sci. USA; published online June 4, 2013; doi:10.1073/pnas.1300016110
Contact: Alemayehu Gorfe, The University of Texas Health Science Center at Houston, Houston, Texas
e-mail: alemayehu.g.abebe@uth.tmc.edu
Contact: John F. Hancock, same affiliation as above
e-mail: john.f.hancock@uth.tmc.edu
Contact: Johnson Stanslas, University of Putra Malaysia, Selangor, Malaysia
e-mail: jstanslas@yahoo.co.uk


Genentech Inc., South San Francisco, Calif.

Kobe University, Kobe, Japan

Lead Discovery Center GmbH, Dortmund, Germany

Max Planck Innovation GmbH, Munich, Germany

Max Planck Institute of Molecular Physiology, Dortmund, Germany

Max Planck Society, Munich, Germany

Roche (SIX:ROG; OTCQX:RHHBY), Basel, Switzerland

Ruhr University Bochum, Bochum, Germany

University of Putra Malaysia, Selangor, Malaysia

The University of Texas Health Science Center at Houston, Houston, Texas

Vanderbilt University School of Medicine, Nashville, Tenn.