Inhibitors of Ras–SOS Interactions

Activating Ras mutations are found in about 30 % of human cancers. Ras activation is regulated by guanine nucleotide exchange factors, such as the son of sevenless (SOS), which form protein–protein interactions (PPIs) with Ras and catalyze the exchange of GDP by GTP. This is the rate‐limiting step in Ras activation. However, Ras surfaces lack any evident suitable pockets where a molecule might bind tightly, rendering Ras proteins still ‘undruggable’ for over 30 years. Among the alternative approaches is the design of inhibitors that target the Ras–SOS PPI interface, a strategy that is gaining increasing recognition for treating Ras mutant cancers. Herein we focus on data that has accumulated over the past few years pertaining to the design of small‐molecule modulators or peptide mimetics aimed at the interface of the Ras–SOS PPI. We emphasize, however, that even if such Ras–SOS therapeutics are potent, drug resistance may emerge. To counteract this development, we propose “pathway drug cocktails”, that is, drug combinations aimed at parallel (or compensatory) pathways. A repertoire of classified cancer, cell/tissue, and pathway/protein combinations would be beneficial toward this goal.

[1]  J. Sage,et al.  Control of Proliferation and Cancer Growth by the Hippo Signaling Pathway , 2015, Molecular Cancer Research.

[2]  Y. Yoshikawa,et al.  Current status of the development of Ras inhibitors. , 2015, Journal of biochemistry.

[3]  Ozlem Keskin,et al.  GTP-Dependent K-Ras Dimerization. , 2015, Structure.

[4]  Jay T. Groves,et al.  Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics , 2014, Science.

[5]  Philipp M. Cromm,et al.  Small-molecule modulation of Ras signaling. , 2014, Nature chemical biology.

[6]  Punit Upadhyaya,et al.  Direct Inhibitors of Ras-Effector Protein Interactions. , 2016, Mini reviews in medicinal chemistry.

[7]  S. Fesik,et al.  Drugging the undruggable RAS: Mission Possible? , 2014, Nature Reviews Drug Discovery.

[8]  Landon R. Whitby,et al.  Comprehensive peptidomimetic libraries targeting protein-protein interactions. , 2012, Accounts of chemical research.

[9]  Ruth Nussinov,et al.  'Pathway drug cocktail': targeting Ras signaling based on structural pathways. , 2013, Trends in molecular medicine.

[10]  Ozlem Keskin,et al.  The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas , 2015, Molecular Cancer Research.

[11]  Ozlem Keskin,et al.  A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway. , 2015, Biophysical journal.

[12]  S R Sprang,et al.  G proteins, effectors and GAPs: structure and mechanism. , 1997, Current opinion in structural biology.

[13]  I. Choi,et al.  Direct monitoring of the inhibition of protein-protein interactions in cells by translocation of PKCδ fusion proteins. , 2011, Angewandte Chemie.

[14]  Kevan M. Shokat,et al.  K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions , 2013, Nature.

[15]  R. Nussinov,et al.  "Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains. , 2006, Structure.

[16]  T. Elston,et al.  Divergent Roles of CAAX Motif-signaled Posttranslational Modifications in the Regulation and Subcellular Localization of Ral GTPases* , 2015, The Journal of Biological Chemistry.

[17]  Ruth Nussinov,et al.  GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site* , 2015, The Journal of Biological Chemistry.

[18]  Jacqueline Cherfils,et al.  Regulation of small GTPases by GEFs, GAPs, and GDIs. , 2013, Physiological reviews.

[19]  H. Lehrach,et al.  A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome , 2005, Cell.

[20]  D. Esposito,et al.  Dragging ras back in the ring. , 2014, Cancer cell.

[21]  M. Wigler,et al.  Human Sos1: a guanine nucleotide exchange factor for Ras that binds to GRB2. , 1993, Science.

[22]  P. Bastiaens,et al.  Small molecule inhibition of the KRAS–PDEδ interaction impairs oncogenic KRAS signalling , 2013, Nature.

[23]  A. Adjei,et al.  Blocking oncogenic Ras signaling for cancer therapy. , 2001, Journal of the National Cancer Institute.

[24]  Andre Hoelz,et al.  Structural Evidence for Feedback Activation by Ras·GTP of the Ras-Specific Nucleotide Exchange Factor SOS , 2003, Cell.

[25]  S. Liberles,et al.  Detection and structural characterization of ras oncoprotein-inhibitors complexes by electrospray mass spectrometry. , 1997, Bioorganic & medicinal chemistry.

[26]  H. Waldmann,et al.  Direkte Modulation von Aktivität und Funktion kleiner GTPasen , 2015 .

[27]  Frank McCormick,et al.  Targeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond , 2014, Nature Reviews Cancer.

[28]  Ruth Nussinov,et al.  High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site , 2015, Biophysical journal.

[29]  Matthias Stein,et al.  Design, Synthesis and Biological Evaluation of Sugar‐Derived Ras Inhibitors , 2005, Chembiochem : a European journal of chemical biology.

[30]  J. Meller,et al.  Combined Rational Design and a High Throughput Screening Platform for Identifying Chemical Inhibitors of a Ras-activating Enzyme* , 2015, The Journal of Biological Chemistry.

[31]  R. Nussinov,et al.  Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD. , 2015, Structure.

[32]  S H Kim,et al.  Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. , 1992, Science.

[33]  M. Barbacid,et al.  RAS oncogenes: the first 30 years , 2003, Nature Reviews Cancer.

[34]  Malcolm Anderson,et al.  Small molecule binding sites on the Ras:SOS complex can be exploited for inhibition of Ras activation. , 2015, Journal of medicinal chemistry.

[35]  R. Nussinov,et al.  Protein–protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach , 2005, Physical biology.

[36]  Shaoyong Lu,et al.  Harnessing Allostery: A Novel Approach to Drug Discovery , 2014, Medicinal research reviews.

[37]  Holger Sondermann,et al.  Regulation of Ras Signaling Dynamics by Sos-Mediated Positive Feedback , 2006, Current Biology.

[38]  I. Mellman,et al.  Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity , 2012, Proceedings of the National Academy of Sciences.

[39]  C. Ottmann,et al.  Modulators of protein-protein interactions. , 2014, Chemical reviews.

[40]  C. Der,et al.  Involvement of the Switch 2 Domain of Ras in Its Interaction with Guanine Nucleotide Exchange Factors (*) , 1996, The Journal of Biological Chemistry.

[41]  Carla Mattos,et al.  A comprehensive survey of Ras mutations in cancer. , 2012, Cancer research.

[42]  Norbert Perrimon,et al.  Direct inhibition of oncogenic KRAS by hydrocarbon-stapled SOS1 helices , 2015, Proceedings of the National Academy of Sciences.

[43]  Paramjit S. Arora,et al.  An Orthosteric Inhibitor of the Ras-Sos Interaction , 2011, Nature chemical biology.

[44]  I. Vetter,et al.  Structure-function relationships of the G domain, a canonical switch motif. , 2011, Annual review of biochemistry.

[45]  W. Kabsch,et al.  Refined crystal structure of the triphosphate conformation of H‐ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. , 1990, The EMBO journal.

[46]  Hong‐yu Li,et al.  Targeting mutant KRAS for anticancer therapeutics: a review of novel small molecule modulators. , 2013, Journal of medicinal chemistry.

[47]  Khozirah Shaari,et al.  Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function , 2013, Proceedings of the National Academy of Sciences.

[48]  T. Rabbitts,et al.  Intracellular antibody capture: A molecular biology approach to inhibitors of protein-protein interactions. , 2014, Biochimica et biophysica acta.

[49]  Suzanne Schubbert,et al.  Hyperactive Ras in developmental disorders and cancer , 2007, Nature Reviews Cancer.

[50]  Richard Bonneau,et al.  Rational Design of Topographical Helix Mimics as Potent Inhibitors of Protein–Protein Interactions , 2014, Journal of the American Chemical Society.

[51]  C. Sander,et al.  How does the switch II region of G‐domains work? , 1993, FEBS letters.

[52]  Ozlem Keskin,et al.  Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation , 2015, Expert review of proteomics.

[53]  J. Matthews,et al.  Protein-protein interactions in human disease. , 2005, Current opinion in structural biology.

[54]  R. Nussinov,et al.  The underappreciated role of allostery in the cellular network. , 2013, Annual review of biophysics.

[55]  T. Pawson,et al.  Protein-protein interactions define specificity in signal transduction. , 2000, Genes & development.

[56]  Shaoyong Lu,et al.  Recent computational advances in the identification of allosteric sites in proteins. , 2014, Drug discovery today.

[57]  K. Ji,et al.  How to Target Activated Ras Proteins: Direct Inhibition vs. Induced Mislocalization. , 2016, Mini reviews in medicinal chemistry.

[58]  Heidi Ledford Cancer: The Ras renaissance , 2015, Nature.

[59]  Qi Sun,et al.  Discovery of small molecules that bind to K-Ras and inhibit Sos-mediated activation. , 2012, Angewandte Chemie.

[60]  I. Vetter,et al.  The Guanine Nucleotide-Binding Switch in Three Dimensions , 2001, Science.

[61]  C. Ottmann,et al.  The renaissance of Ras. , 2014, ACS chemical biology.

[62]  Shaoyong Lu,et al.  ASBench: benchmarking sets for allosteric discovery , 2015, Bioinform..

[63]  L. Perkins,et al.  Ras oncoprotein inhibitors: the discovery of potent, ras nucleotide exchange inhibitors and the structural determination of a drug-protein complex. , 1997, Bioorganic & medicinal chemistry.

[64]  Yi Zheng,et al.  Rational design of small molecule inhibitors targeting the Ras GEF, SOS1. , 2014, Chemistry & biology.

[65]  K. Kaibuchi,et al.  Small GTP-binding proteins. , 1992, International review of cytology.

[66]  J. Wells,et al.  Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. , 2014, Chemistry & biology.

[67]  A. Wittinghofer,et al.  The interaction of Ras with GTPase‐activating proteins , 1997, FEBS letters.

[68]  R. Heumann,et al.  Bisphenol A binds to Ras proteins and competes with guanine nucleotide exchange: implications for GTPase-selective antagonists. , 2013, Journal of medicinal chemistry.

[69]  Jayajit Das,et al.  Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells , 2009, Cell.

[70]  Min Huang,et al.  Targeting ERK, an Achilles' Heel of the MAPK pathway, in cancer therapy , 2018, Acta pharmaceutica Sinica. B.

[71]  D. Lane,et al.  Drugging the p53 pathway: understanding the route to clinical efficacy , 2014, Nature Reviews Drug Discovery.

[72]  J. Cherfils,et al.  Ras superfamily GEFs and GAPs: validated and tractable targets for cancer therapy? , 2010, Nature Reviews Cancer.

[73]  Philipp M. Cromm,et al.  Direct Modulation of Small GTPase Activity and Function. , 2015, Angewandte Chemie.

[74]  L. Vassilev,et al.  Stapled α−helical peptide drug development: A potent dual inhibitor of MDM2 and MDMX for p53-dependent cancer therapy , 2013, Proceedings of the National Academy of Sciences.

[75]  R. Nussinov,et al.  Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region* , 2015, The Journal of Biological Chemistry.

[76]  Sarah R. Clippinger,et al.  Inhibition of Ras signaling by blocking Ras-effector interactions with cyclic peptides. , 2015, Angewandte Chemie.

[77]  S. K. R. Guduru,et al.  Small molecule modulators of protein-protein interactions: selected case studies. , 2014, Chemical reviews.

[78]  R. Nussinov,et al.  Principles of protein-protein interactions: what are the preferred ways for proteins to interact? , 2008, Chemical reviews.