Allo-network drugs: harnessing allostery in cellular networks.

[1]  J. Gutkind,et al.  Multiple Mitogen-Activated Protein Kinase Signaling Pathways Connect the Cot Oncoprotein to the c-junPromoter and to Cellular Transformation , 2000, Molecular and Cellular Biology.

[2]  H. Kitano.  Systems Biology: A Brief Overview , 2002, Science.

[3]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

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

[5]  C. Lindsley,et al.  The Akt/PKB family of protein kinases: a review of small molecule inhibitors and progress towards target validation. , 2005, Current topics in medicinal chemistry.

[6]  Péter Csermely,et al.  The efficiency of multi-target drugs: the network approach might help drug design. , 2004, Trends in pharmacological sciences.

[7]  Susan S. Taylor,et al.  Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A. , 2006, Analytical chemistry.

[8]  Lila M Gierasch,et al.  The changing landscape of protein allostery. , 2006, Current opinion in structural biology.

[9]  Patrick Cramer,et al.  Structure and TBP binding of the Mediator head subcomplex Med8–Med18–Med20 , 2006, Nature Structural &Molecular Biology.

[10]  J. Tegnér,et al.  Perturbations to uncover gene networks. , 2007, Trends in genetics : TIG.

[11]  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.

[12]  J. Engelman,et al.  Acquired resistance to tyrosine kinase inhibitors during cancer therapy. , 2008, Current opinion in genetics & development.

[13]  Daniel Panne,et al.  The enhanceosome. , 2008, Current opinion in structural biology.

[14]  R. Nussinov,et al.  Allosteric effects in the marginally stable von Hippel–Lindau tumor suppressor protein and allostery-based rescue mutant design , 2008, Proceedings of the National Academy of Sciences.

[15]  A. Hopkins.  Network pharmacology: the next paradigm in drug discovery. , 2008, Nature chemical biology.

[16]  Krin A. Kay,et al.  The implications of human metabolic network topology for disease comorbidity , 2008, Proceedings of the National Academy of Sciences.

[17]  Ruth Nussinov,et al.  MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions , 2008, Nucleic Acids Res..

[18]  Ozlem Keskin,et al.  PRISM: protein-protein interaction prediction by structural matching. , 2008, Methods in molecular biology.

[19]  H. Bourbon,et al.  Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex , 2008, Nucleic acids research.

[20]  István Simon,et al.  Malleable Machines in Transcription Regulation: The Mediator Complex , 2008, PLoS Comput. Biol..

[21]  J. Sodroski,et al.  Structural determinants for affinity enhancement of a dual antagonist peptide entry inhibitor of human immunodeficiency virus type-1. , 2008, Journal of medicinal chemistry.

[22]  K. Yamamoto,et al.  DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity , 2009, Science.

[23]  Chao Zhang,et al.  Inhibitor Hijacking of Akt Activation , 2009, Nature chemical biology.

[24]  T. Kenakin.  '7TM receptor allostery: putting numbers to shapeshifting proteins. , 2009, Trends in pharmacological sciences.

[25]  C. Craik,et al.  Trapping Moving Targets with Small Molecules , 2009, Science.

[26]  P. Parker,et al.  PKC maturation is promoted by nucleotide pocket occupation independently of intrinsic kinase activity , 2009, Nature Structural &Molecular Biology.

[27]  Csaba Böde,et al.  Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design. , 2008, Current protein & peptide science.

[28]  Joshua A. Grochow,et al.  Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture , 2009, Molecular systems biology.

[29]  Ruth Nussinov,et al.  Amplification of signaling via cellular allosteric relay and protein disorder , 2009, Proceedings of the National Academy of Sciences.

[30]  R. Nussinov,et al.  The origin of allosteric functional modulation: multiple pre-existing pathways. , 2009, Structure.

[31]  Arthur Christopoulos,et al.  Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders , 2009, Nature Reviews Drug Discovery.

[32]  M. Vidal,et al.  Edgetic perturbation models of human inherited disorders , 2009, Molecular systems biology.

[33]  Wladimir Labeikovsky,et al.  Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein , 2009, Cell.

[34]  R. Nussinov,et al.  Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms , 2009, Molecular bioSystems.

[35]  N. Hooper,et al.  Prion protein and Alzheimer disease , 2009, Prion.

[36]  R. Hamatake,et al.  RDEA119/BAY 869766: a potent, selective, allosteric inhibitor of MEK1/2 for the treatment of cancer. , 2009, Cancer research.

[37]  Olivier Lichtarge,et al.  Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors , 2010, Proceedings of the National Academy of Sciences.

[38]  D. Sabatini,et al.  Structure of the human mTOR complex I and its implications for rapamycin inhibition. , 2010, Molecular cell.

[39]  Nadine H. Elowe,et al.  An allosteric inhibitor of substrate recognition by the SCFCdc4 ubiquitin ligase , 2010, Nature Biotechnology.

[40]  C. Lindsley,et al.  Orthosteric- and allosteric-induced ligand-directed trafficking at GPCRs. , 2010, Current opinion in drug discovery & development.

[41]  Illés J. Farkas,et al.  Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery , 2010, Bioinform..

[42]  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.

[43]  B. Schulman,et al.  Crystal Structure of UBA2ufd-Ubc9: Insights into E1-E2 Interactions in Sumo Pathways , 2010, PloS one.

[44]  Nahum Sonenberg,et al.  Dissecting the role of mTOR: lessons from mTOR inhibitors. , 2010, Biochimica et biophysica acta.

[45]  K. Gregory,et al.  Discovery of a Novel Chemical Class of mGlu5 Allosteric Ligands with Distinct Modes of Pharmacology , 2010, ACS chemical neuroscience.

[46]  R. Nussinov,et al.  Induced Fit, Conformational Selection and Independent Dynamic Segments: an Extended View of Binding Events Opinion , 2022 .

[47]  D. Taatjes,et al.  p53 activates transcription by directing structural shifts within Mediator , 2010, Nature Structural &Molecular Biology.

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

[49]  C. Lindsley.  The Akt/PKB family of protein kinases: a review of small molecule inhibitors and progress towards target validation: a 2009 update. , 2010, Current topics in medicinal chemistry.

[50]  Timothy Hagen,et al.  Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety , 2010, Nature Biotechnology.

[51]  D. Taatjes,et al.  The human Mediator complex: a versatile, genome-wide regulator of transcription. , 2010, Trends in biochemical sciences.

[52]  Bruce J. Melancon,et al.  Small-molecule inhibition of Wnt signaling through activation of casein kinase 1α. , 2010, Nature chemical biology.

[53]  A. Iafrate,et al.  BRAF Gene Amplification Can Promote Acquired Resistance to MEK Inhibitors in Cancer Cells Harboring the BRAF V600E Mutation , 2010, Science Signaling.

[54]  David M Sabatini,et al.  mTOR and cancer: many loops in one pathway. , 2009, Current opinion in cell biology.

[55]  N. Zheng,et al.  Structural assembly of cullin-RING ubiquitin ligase complexes. , 2010, Current opinion in structural biology.

[56]  M. Ascano,et al.  Multimeric assembly and biochemical characterization of the Trax/Translin endonuclease complex , 2011, Nature Structural &Molecular Biology.

[57]  István A. Kovács,et al.  Network-Based Tools for the Identification of Novel Drug Targets , 2011, Science Signaling.

[58]  T. Kenakin,et al.  Analytical pharmacology: the impact of numbers on pharmacology. , 2011, Trends in pharmacological sciences.

[59]  H. Ng,et al.  The transcriptional and signalling networks of pluripotency , 2011, Nature Cell Biology.

[60]  P. Wintrode,et al.  Allosteric suppression of HIV-1 reverse transcriptase structural dynamics upon inhibitor binding. , 2011, Biophysical Journal.

[61]  C. Craik,et al.  Enzyme inhibition by allosteric capture of an inactive conformation. , 2011, Journal of molecular biology.

[62]  Daniel V. Veres,et al.  Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review , 2011 .

[63]  Albert-László Barabási,et al.  Controllability of complex networks , 2011, Nature.

[64]  W. El-Deiry,et al.  Off-Target Lapatinib Activity Sensitizes Colon Cancer Cells Through TRAIL Death Receptor Up-Regulation , 2011, Science Translational Medicine.

[65]  Herbert Schulz,et al.  Specific Gene Signatures and Pathways in Mesodermal Cells and Their Derivatives Derived from Embryonic Stem Cells , 2012, Stem Cell Reviews and Reports.

[66]  G. Shi,et al.  A Rit GTPase-p38 Mitogen-Activated Protein Kinase Survival Pathway Confers Resistance to Cellular Stress , 2011, Molecular and Cellular Biology.

[67]  Adam B Castoreno,et al.  Small molecule probes of cellular pathways and networks. , 2011, ACS chemical biology.

[68]  P Jeffrey Conn,et al.  "Molecular switches" on mGluR allosteric ligands that modulate modes of pharmacology. , 2011, Biochemistry.

[69]  S. Digumarthy,et al.  Genotypic and Histological Evolution of Lung Cancers Acquiring Resistance to EGFR Inhibitors , 2011, Science Translational Medicine.

[70]  Jonathan Chernoff,et al.  Faculty Opinions recommendation of COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. , 2011 .

[71]  Ruth Nussinov,et al.  Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review. , 2011, Current protein & peptide science.