Druggable orthosteric and allosteric hot spots to target protein-protein interactions.

Drug designing targeting protein-protein interactions is challenging. Because structural elucidation and computational analysis have revealed the importance of hot spot residues in stabilizing these interactions, there have been on-going efforts to develop drugs which bind the hot spots and out-compete the native protein partners. The question arises as to what are the key 'druggable' properties of hot spots in protein-protein interactions and whether these mimic the general hot spot definition. Identification of orthosteric (at the protein- protein interaction site) and allosteric (elsewhere) druggable hot spots is expected to help in discovering compounds that can more effectively modulate protein-protein interactions. For example, are there any other significant features beyond their location in pockets in the interface? The interactions of protein-protein hot spots are coupled with conformational dynamics of protein complexes. Currently increasing efforts focus on the allosteric drug discovery. Allosteric drugs bind away from the native binding site and can modulate the native interactions. We propose that identification of allosteric hot spots could similarly help in more effective allosteric drug discovery. While detection of allosteric hot spots is challenging, targeting drugs to these residues has the potential of greatly increasing the hot spot and protein druggability.

[1]  Saraswathi Vishveshwara,et al.  Oligomeric protein structure networks: insights into protein-protein interactions , 2005, BMC Bioinformatics.

[2]  A. Levine,et al.  One billion years of p53/p63/p73 evolution , 2009, Proceedings of the National Academy of Sciences.

[3]  R. Nussinov,et al.  Allostery: absence of a change in shape does not imply that allostery is not at play. , 2008, Journal of molecular biology.

[4]  E. Pasquale,et al.  Eph receptors inactivate R-Ras through different mechanisms to achieve cell repulsion , 2006, Journal of Cell Science.

[5]  T. Selwood,et al.  Allosteric Inhibition of Human Porphobilinogen Synthase* , 2009, The Journal of Biological Chemistry.

[6]  Jesús Avila,et al.  Early changes in hippocampal Eph receptors precede the onset of memory decline in mouse models of Alzheimer's disease. , 2009, Journal of Alzheimer's disease : JAD.

[7]  T. Schwartz,et al.  The minor binding pocket: a major player in 7TM receptor activation. , 2010, Trends in pharmacological sciences.

[8]  Olivier Sperandio,et al.  Rationalizing the chemical space of protein-protein interaction inhibitors. , 2010, Drug discovery today.

[9]  O. Dym,et al.  The modular architecture of protein-protein binding interfaces. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[10]  L. Lopiano,et al.  Binding of anti‐Parkinson's disease drugs to human serum albumin is allosterically modulated , 2010, IUBMB life.

[11]  R. Nussinov,et al.  Conformational ensembles, signal transduction and residue hot spots: application to drug discovery. , 2010, Current opinion in drug discovery & development.

[12]  Giorgio Palù,et al.  Disruption of protein–protein interactions: Towards new targets for chemotherapy , 2005, Journal of cellular physiology.

[13]  C. Prives,et al.  Blinded by the Light: The Growing Complexity of p53 , 2009, Cell.

[14]  Pedro A Fernandes,et al.  Hot spots—A review of the protein–protein interface determinant amino‐acid residues , 2007, Proteins.

[15]  A. Bogan,et al.  Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.

[16]  C. Mattos,et al.  Allosteric modulation of Ras positions Q61 for a direct role in catalysis , 2010, Proceedings of the National Academy of Sciences.

[17]  J. Sodroski,et al.  Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody , 1998, Nature.

[18]  Jonathan C. Fuller,et al.  Predicting druggable binding sites at the protein-protein interface. , 2009, Drug discovery today.

[19]  Ravi Salgia,et al.  The role of ephrins and Eph receptors in cancer. , 2004, Cytokine & growth factor reviews.

[20]  R. Abagyan,et al.  Three-dimensional Structure of the EphB2 Receptor in Complex with an Antagonistic Peptide Reveals a Novel Mode of Inhibition* , 2007, Journal of Biological Chemistry.

[21]  Dima Kozakov,et al.  Analysis of binding site hot spots on the surface of Ras GTPase. , 2011, Journal of molecular biology.

[22]  Y. Pommier,et al.  Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery. , 2005, Trends in pharmacological sciences.

[23]  E. Pasquale,et al.  Structure-activity relationship analysis of peptides targeting the EphA2 receptor. , 2010, Biochemistry.

[24]  C. Chennubhotla,et al.  Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES , 2006, Molecular systems biology.

[25]  E. Ruoslahti,et al.  An Eph receptor regulates integrin activity through R-Ras. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Bernard R Brooks,et al.  Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. , 2009, Current protein & peptide science.

[27]  J. Rhim,et al.  Activation of EphA receptor tyrosine kinase inhibits the Ras/MAPK pathway , 2001, Nature Cell Biology.

[28]  Jie Liang,et al.  Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. , 2004, Journal of molecular biology.

[29]  A. Lavie,et al.  A New Dimension to Ras Function: A Novel Role for Nucleotide-Free Ras in Class II Phosphatidylinositol 3-Kinase Beta (PI3KC2β) Regulation , 2012, PloS one.

[30]  K. Aoki,et al.  The Scaffold Protein Shoc2/SUR-8 Accelerates the Interaction of Ras and Raf* , 2010, The Journal of Biological Chemistry.

[31]  J. Hepler,et al.  RGS14 is a multifunctional scaffold that integrates G protein and Ras/Raf MAPkinase signalling pathways. , 2010, Cellular signalling.

[32]  Joël Janin,et al.  Protein modules and protein-protein interaction. Introduction. , 2002, Advances in protein chemistry.

[33]  R. Nussinov,et al.  Is allostery an intrinsic property of all dynamic proteins? , 2004, Proteins.

[34]  Michelle R Arkin,et al.  The road less traveled: modulating signal transduction enzymes by inhibiting their protein-protein interactions. , 2009, Current opinion in chemical biology.

[35]  D Reichmann,et al.  Binding hot spots in the TEM1-BLIP interface in light of its modular architecture. , 2007, Journal of molecular biology.

[36]  R. Nussinov,et al.  Allostery and population shift in drug discovery. , 2010, Current opinion in pharmacology.

[37]  A. Meola,et al.  Anti-EphA2 Antibodies with Distinct In Vitro Properties Have Equal In Vivo Efficacy in Pancreatic Cancer , 2010, Journal of oncology.

[38]  H. Hirai,et al.  A novel putative tyrosine kinase receptor encoded by the eph gene. , 1987, Science.

[39]  Takashi Kumasaka,et al.  Structural Basis for Conformational Dynamics of GTP-bound Ras Protein* , 2010, The Journal of Biological Chemistry.

[40]  P. Kuhn,et al.  Structure and thermodynamic characterization of the EphB4/Ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity. , 2006, Structure.

[41]  R. Nussinov,et al.  The different ways through which specificity works in orthosteric and allosteric drugs. , 2012, Current pharmaceutical design.

[42]  S. Vajda,et al.  Anchor residues in protein-protein interactions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  R. Nussinov,et al.  Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Oz Sharabi,et al.  What makes Ras an efficient molecular switch: a computational, biophysical, and structural study of Ras-GDP interactions with mutants of Raf. , 2010, Journal of molecular biology.

[45]  Elena B. Pasquale,et al.  Eph receptors and ephrins in cancer: bidirectional signalling and beyond , 2010, Nature Reviews Cancer.

[46]  C. Der,et al.  Ras history , 2010, Small GTPases.

[47]  Olivier Sperandio,et al.  Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments , 2008, The open biochemistry journal.

[48]  T. Kenakin.  Ligand Detection in the Allosteric World , 2010, Journal of biomolecular screening.

[49]  T. Schwartz,et al.  Allosteric enhancers, allosteric agonists and ago-allosteric modulators: where do they bind and how do they act? , 2007, Trends in pharmacological sciences.

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

[51]  Ozlem Keskin,et al.  Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example† †This article is part of a Molecular BioSystems themed issue on Computational and Systems Biology. , 2009, Molecular bioSystems.

[52]  Elena B Pasquale,et al.  An Ephrin Mimetic Peptide That Selectively Targets the EphA2 Receptor* , 2002, The Journal of Biological Chemistry.

[53]  Christopher D. Thanos,et al.  Hot-spot mimicry of a cytokine receptor by a small molecule , 2006, Proceedings of the National Academy of Sciences.

[54]  C. Post,et al.  Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding. , 2010, Journal of the American Chemical Society.

[55]  Doheon Lee,et al.  A feature-based approach to modeling protein–protein interaction hot spots , 2009, Nucleic acids research.

[56]  F. J. Luque,et al.  Binding site detection and druggability index from first principles. , 2009, Journal of medicinal chemistry.

[57]  Nobuyoshi Sugaya,et al.  Assessing the druggability of protein-protein interactions by a supervised machine-learning method , 2009, BMC Bioinformatics.

[58]  H. Xi,et al.  Eph receptors and ephrins as targets for cancer therapy , 2012, Journal of cellular and molecular medicine.

[59]  Cornel Catana,et al.  Inhibition of protein–protein interactions: The discovery of druglike β‐catenin inhibitors by combining virtual and biophysical screening , 2006, Proteins.

[60]  R. Nussinov,et al.  Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. , 2005, Journal of molecular biology.

[61]  Y. Yoshikawa,et al.  Solution Structure of the State 1 Conformer of GTP-bound H-Ras Protein and Distinct Dynamic Properties between the State 1 and State 2 Conformers* , 2011, The Journal of Biological Chemistry.

[62]  Mitsutoshi Nakada,et al.  EphB2/R-Ras signaling regulates glioma cell adhesion, growth, and invasion. , 2005, The American journal of pathology.

[63]  Robert Tampé,et al.  ABC proteins in antigen translocation and viral inhibition. , 2010, Nature chemical biology.

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

[65]  Ruth Nussinov,et al.  Energetic determinants of protein binding specificity: Insights into protein interaction networks , 2009, Proteomics.

[66]  Alan R. Fersht,et al.  Awakening guardian angels: drugging the p53 pathway , 2009, Nature Reviews Cancer.

[67]  N. Lin,et al.  Design, synthesis and characterization of novel small molecular inhibitors of ephrin-B2 binding to EphB4. , 2013, Biochemical pharmacology.

[68]  M. Karplus,et al.  Allostery and cooperativity revisited , 2008, Protein science : a publication of the Protein Society.

[69]  M. Stratton,et al.  The cancer genome , 2009, Nature.

[70]  R. Noberini,et al.  Targeting Eph receptors with peptides and small molecules: progress and challenges. , 2012, Seminars in cell & developmental biology.

[71]  Jin Chen,et al.  Eph receptors and Ephrins in cancer: common themes and controversies. , 2008, Cancer research.

[72]  L. Vassilev,et al.  Targeting protein–protein interactions for cancer therapy , 2005, Journal of Molecular Medicine.

[73]  J. Frisén,et al.  Ephrins and Eph receptors in stem cells and cancer. , 2010, Current opinion in cell biology.

[74]  Ozlem Keskin,et al.  HotPoint: hot spot prediction server for protein interfaces , 2010, Nucleic Acids Res..

[75]  C. Der,et al.  Inhibition of Ras for cancer treatment: the search continues. , 2011, Future medicinal chemistry.

[76]  R. Noberini,et al.  Distinctive binding of three antagonistic peptides to the ephrin-binding pocket of the EphA4 receptor. , 2012, The Biochemical journal.

[77]  R. Nussinov,et al.  Multiple‐Targeting and Conformational Selection in the Estrogen Receptor: Computation and Experiment , 2011, Chemical Biology and Drug Design.

[78]  G. Salvesen,et al.  Emerging principles in protease-based drug discovery , 2010, Nature Reviews Drug Discovery.

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

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

[81]  K. Garber.  Of Ephs and ephrins: companies target guidance molecules in cancer. , 2010, Journal of the National Cancer Institute.

[82]  K. Murai,et al.  Targeting the EphA4 receptor in the nervous system with biologically active peptides , 2003, Molecular and Cellular Neuroscience.

[83]  Joe W. Gray,et al.  Restriction of Receptor Movement Alters Cellular Response: Physical Force Sensing by EphA2 , 2010, Science.

[84]  C. Crews,et al.  Identification and Characterization of a Peptidic Ligand for Ras , 2010, Chembiochem : a European journal of chemical biology.

[85]  K. O'Byrne,et al.  Receptor tyrosine kinases and their activation in melanoma , 2011, Pigment cell & melanoma research.

[86]  Julie C. Mitchell,et al.  KFC Server: interactive forecasting of protein interaction hot spots , 2008, Nucleic Acids Res..

[87]  S. Saito,et al.  Relation between the conformational heterogeneity and reaction cycle of Ras: molecular simulation of Ras. , 2010, Biophysical journal.

[88]  Wolfgang Wenzel,et al.  Probing hot spots on protein-protein interfaces with all-atom free-energy simulation. , 2009, The Journal of chemical physics.

[89]  T. Blundell,et al.  Structural biology and drug discovery of difficult targets: the limits of ligandability. , 2012, Chemistry & biology.

[90]  D. Megías,et al.  Blocking ephrinB2 with highly specific antibodies inhibits angiogenesis, lymphangiogenesis, and tumor growth. , 2012, Blood.

[91]  R. Nussinov,et al.  The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins , 2005, Physical biology.

[92]  Ozlem Keskin,et al.  Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy , 2009, Bioinform..

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

[94]  Zhan Xiao,et al.  EphB4 promotes or suppresses Ras/MEK/ERK pathway in a context-dependent manner , 2012, Cancer biology & therapy.

[95]  Carlos J. Camacho,et al.  ANCHOR: a web server and database for analysis of protein–protein interaction binding pockets for drug discovery , 2010, Nucleic Acids Res..

[96]  Herren Wu,et al.  Structural and functional characterization of an agonistic anti-human EphA2 monoclonal antibody. , 2011, Journal of molecular biology.

[97]  X. Daura,et al.  Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery , 2010, BMC Structural Biology.

[98]  F. Guerlesquin,et al.  Protein–protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef protein , 2007, Proceedings of the National Academy of Sciences.

[99]  Andrea Mozzarelli,et al.  Exploring and exploiting allostery: Models, evolution, and drug targeting. , 2011, Biochimica et biophysica acta.

[100]  A. del Sol,et al.  Small‐world network approach to identify key residues in protein–protein interaction , 2004, Proteins.

[101]  Michelle R. Arkin,et al.  Small-molecule inhibitors of protein–protein interactions: progressing towards the dream , 2004, Nature Reviews Drug Discovery.

[102]  Gerhard Klebe,et al.  Strategies to search and design stabilizers of protein–protein interactions: A feasibility study , 2007, Proteins.

[103]  Salam A. Assi,et al.  Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces , 2010, PloS one.

[104]  E. Pasquale,et al.  Eph receptor-ephrin bidirectional signals that target Ras and Rho proteins. , 2004, Cellular signalling.

[105]  Jean Chmielewski,et al.  Inhibiting protein-protein interactions using designed molecules. , 2005, Current opinion in structural biology.

[106]  Laurie E. Grove,et al.  Structural conservation of druggable hot spots in protein–protein interfaces , 2011, Proceedings of the National Academy of Sciences.

[107]  Gideon Schreiber,et al.  Protein binding specificity versus promiscuity. , 2010, Current opinion in structural biology.

[108]  Laurence J. Miller,et al.  Seven Transmembrane Receptors as Shapeshifting Proteins: The Impact of Allosteric Modulation and Functional Selectivity on New Drug Discovery , 2010, Pharmacological Reviews.

[109]  C. Mattos,et al.  Shift in the equilibrium between on and off states of the allosteric switch in Ras-GppNHp affected by small molecules and bulk solvent composition. , 2012, Biochemistry.

[110]  J. Andrew McCammon,et al.  Mapping the Druggable Allosteric Space of G-Protein Coupled Receptors: a Fragment-Based Molecular Dynamics Approach , 2010, Chemical biology & drug design.

[111]  Di Wu,et al.  Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming. , 2011, Journal of theoretical biology.

[112]  Massimiliano Pontil,et al.  Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods , 2009, BMC Bioinformatics.

[113]  Colin Norman,et al.  What Don't We Know? , 2005, Science.

[114]  H. Wolfson,et al.  Protein functional epitopes: hot spots, dynamics and combinatorial libraries. , 2001, Current opinion in structural biology.

[115]  Richard S Larson,et al.  Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction. , 2005, Current protein & peptide science.

[116]  S. Koide,et al.  Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces. , 2008, Current opinion in structural biology.