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Volumn 40, Issue 9, 2015, Pages 491-496

Targeting disordered proteins with small molecules using entropy

Author keywords

Binding; Disordered proteins; Entropic expansion; Entropy; Small molecule

Indexed keywords

AMYLOID BETA PROTEIN; MYC PROTEIN; PROTEIN; PROTEIN BINDING;

EID: 84940467045     PISSN: 09680004     EISSN: 13624326     Source Type: Journal    
DOI: 10.1016/j.tibs.2015.07.004     Document Type: Review
Times cited : (81)

References (56)
  • 1
    • 84888862866 scopus 로고    scopus 로고
    • DGIdb: mining the druggable genome
    • Griffith M., et al. DGIdb: mining the druggable genome. Nat. Methods 2013, 10:1209-1210.
    • (2013) Nat. Methods , vol.10 , pp. 1209-1210
    • Griffith, M.1
  • 2
    • 29144531173 scopus 로고    scopus 로고
    • The druggable genome: an update
    • Russ A.P., Lampel S. The druggable genome: an update. Drug Discov. Today 2005, 10:1607-1610.
    • (2005) Drug Discov. Today , vol.10 , pp. 1607-1610
    • Russ, A.P.1    Lampel, S.2
  • 4
    • 79958072421 scopus 로고    scopus 로고
    • Intrinsically disordered proteins: regulation and disease
    • Babu M.M., et al. Intrinsically disordered proteins: regulation and disease. Curr. Opin. Struct. Biol. 2011, 21:432-440.
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 432-440
    • Babu, M.M.1
  • 5
    • 84870057622 scopus 로고    scopus 로고
    • Intrinsically disordered proteins: A 10-year recap
    • Tompa P. Intrinsically disordered proteins: A 10-year recap. Trends Biochem. Sci. 2012, 37:509-516.
    • (2012) Trends Biochem. Sci. , vol.37 , pp. 509-516
    • Tompa, P.1
  • 6
    • 77955327536 scopus 로고    scopus 로고
    • Intrinsically disordered proteins are potential drug targets
    • Metallo S.J. Intrinsically disordered proteins are potential drug targets. Curr. Opin. Chem. Biol. 2010, 14:481-488.
    • (2010) Curr. Opin. Chem. Biol. , vol.14 , pp. 481-488
    • Metallo, S.J.1
  • 7
    • 48249097986 scopus 로고    scopus 로고
    • Intrinsically disordered proteins in human diseases: introducing the D2 concept
    • Uversky V.N., et al. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu. Rev. Biophys. 2008, 37:215-246.
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 215-246
    • Uversky, V.N.1
  • 9
    • 0037188377 scopus 로고    scopus 로고
    • Intrinsic disorder and protein function
    • Dunker A.K., et al. Intrinsic disorder and protein function. Biochemistry 2002, 41:6573-6582.
    • (2002) Biochemistry , vol.41 , pp. 6573-6582
    • Dunker, A.K.1
  • 10
    • 84922341947 scopus 로고    scopus 로고
    • The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins
    • Sormanni P., et al. The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins. J. Mol. Biol. 2015, 427:982-996.
    • (2015) J. Mol. Biol. , vol.427 , pp. 982-996
    • Sormanni, P.1
  • 11
    • 84902500178 scopus 로고    scopus 로고
    • Controlling entropy to tune the functions of intrinsically disordered regions
    • Flock T., et al. Controlling entropy to tune the functions of intrinsically disordered regions. Curr. Opin. Struct. Biol. 2014, 26:62-72.
    • (2014) Curr. Opin. Struct. Biol. , vol.26 , pp. 62-72
    • Flock, T.1
  • 12
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson H.J., Wright P.E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 2005, 6:197-208.
    • (2005) Nat. Rev. Mol. Cell Biol. , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 13
    • 84870196501 scopus 로고    scopus 로고
    • Intrinsically disordered proteins
    • Tompa P., Han K. Intrinsically disordered proteins. Phys. Today 2012, 65:64.
    • (2012) Phys. Today , vol.65 , pp. 64
    • Tompa, P.1    Han, K.2
  • 14
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
    • Wright P.E., Dyson H.J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 1999, 293:321-331.
    • (1999) J. Mol. Biol. , vol.293 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 15
    • 79958741408 scopus 로고    scopus 로고
    • Intrinsically disordered proteins from A to Z
    • Uversky V.N. Intrinsically disordered proteins from A to Z. Int. J. Biochem. Cell Biol. 2011, 43:1090-1103.
    • (2011) Int. J. Biochem. Cell Biol. , vol.43 , pp. 1090-1103
    • Uversky, V.N.1
  • 16
    • 84903957091 scopus 로고    scopus 로고
    • Introducing protein intrinsic disorder
    • Habchi J., et al. Introducing protein intrinsic disorder. Chem. Rev. 2014, 114:6561-6588.
    • (2014) Chem. Rev. , vol.114 , pp. 6561-6588
    • Habchi, J.1
  • 17
    • 0037135111 scopus 로고    scopus 로고
    • The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics
    • Hardy J., Selkoe D.J. The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science 2002, 297:353-356.
    • (2002) Science , vol.297 , pp. 353-356
    • Hardy, J.1    Selkoe, D.J.2
  • 18
    • 61849185913 scopus 로고    scopus 로고
    • Recent developments in Alzheimer's disease therapeutics
    • Rafii M.S., Aisen P.S. Recent developments in Alzheimer's disease therapeutics. BMC Med. 2009, 7:7.
    • (2009) BMC Med. , vol.7 , pp. 7
    • Rafii, M.S.1    Aisen, P.S.2
  • 19
    • 84878994873 scopus 로고    scopus 로고
    • Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism
    • Cohen S.I., et al. Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:9758-9763.
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 9758-9763
    • Cohen, S.I.1
  • 20
    • 84895866256 scopus 로고    scopus 로고
    • Targeting the intrinsically disordered structural ensemble of α-synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease
    • Tóth G., et al. Targeting the intrinsically disordered structural ensemble of α-synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease. PLoS ONE 2014, 9:e87133.
    • (2014) PLoS ONE , vol.9 , pp. e87133
    • Tóth, G.1
  • 21
    • 67650523478 scopus 로고    scopus 로고
    • Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc
    • Hammoudeh D.I., et al. Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc. J. Am. Chem. Soc. 2009, 131:7390-7401.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 7390-7401
    • Hammoudeh, D.I.1
  • 22
    • 58849114460 scopus 로고    scopus 로고
    • Small-molecule perturbation of competing interactions between c-Myc and Max
    • Follis A.V., et al. Small-molecule perturbation of competing interactions between c-Myc and Max. Bioorg. Med. Chem. Lett. 2009, 19:807-810.
    • (2009) Bioorg. Med. Chem. Lett. , vol.19 , pp. 807-810
    • Follis, A.V.1
  • 23
    • 84862901143 scopus 로고    scopus 로고
    • Small-molecule modulators of c-Myc/Max and Max/Max interactions
    • Berg T. Small-molecule modulators of c-Myc/Max and Max/Max interactions. Curr. Top. Microbiol. Immunol. 2010, 348:139-149.
    • (2010) Curr. Top. Microbiol. Immunol. , vol.348 , pp. 139-149
    • Berg, T.1
  • 24
    • 84866671396 scopus 로고    scopus 로고
    • Mechanisms of small-molecule binding to intrinsically disordered proteins
    • Cuchillo R., Michel J. Mechanisms of small-molecule binding to intrinsically disordered proteins. Biochem. Soc Trans. 2012, 40:1004-1008.
    • (2012) Biochem. Soc Trans. , vol.40 , pp. 1004-1008
    • Cuchillo, R.1    Michel, J.2
  • 25
    • 77951281285 scopus 로고    scopus 로고
    • The role of conformational entropy in molecular recognition by calmodulin
    • Marlow M.S., et al. The role of conformational entropy in molecular recognition by calmodulin. Nat. Chem. Biol. 2010, 6:352-358.
    • (2010) Nat. Chem. Biol. , vol.6 , pp. 352-358
    • Marlow, M.S.1
  • 26
    • 84884277426 scopus 로고    scopus 로고
    • Thermodynamics of ligand-protein interactions: implications for molecular design
    • InTech, J.C. Moreno-Pirajan (Ed.)
    • Bronowska A. Thermodynamics of ligand-protein interactions: implications for molecular design. Thermodynamics - Interaction Studies - Solids, Liquids and Gases 2011, 1-49. InTech. J.C. Moreno-Pirajan (Ed.).
    • (2011) Thermodynamics - Interaction Studies - Solids, Liquids and Gases , pp. 1-49
    • Bronowska, A.1
  • 27
    • 84926158682 scopus 로고    scopus 로고
    • Applying thermodynamic profiling in lead finding and optimization
    • Klebe G. Applying thermodynamic profiling in lead finding and optimization. Nat. Rev. Drug Discov. 2015, 14:95-110.
    • (2015) Nat. Rev. Drug Discov. , vol.14 , pp. 95-110
    • Klebe, G.1
  • 28
    • 84877768087 scopus 로고    scopus 로고
    • Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design
    • Chodera J.D., Mobley D.L. Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annu. Rev. Biophys. 2013, 42:121-142.
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 121-142
    • Chodera, J.D.1    Mobley, D.L.2
  • 29
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities
    • Liu T., et al. BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007, 35(Suppl. 1):D198-D201.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D198-D201
    • Liu, T.1
  • 30
    • 14244271762 scopus 로고    scopus 로고
    • The Binding Database: overview and user's guide
    • Chen X., et al. The Binding Database: overview and user's guide. Biopolymers 2001, 61:127-141.
    • (2001) Biopolymers , vol.61 , pp. 127-141
    • Chen, X.1
  • 31
    • 0036169718 scopus 로고    scopus 로고
    • The Binding Database: data management and interface design
    • Chen X., et al. The Binding Database: data management and interface design. Bioinformatics 2002, 18:130-139.
    • (2002) Bioinformatics , vol.18 , pp. 130-139
    • Chen, X.1
  • 32
    • 0035658264 scopus 로고    scopus 로고
    • BindingDB: a web-accessible molecular recognition database
    • Chen X., et al. BindingDB: a web-accessible molecular recognition database. Comb. Chem. High Throughput Screen. 2001, 4:719-725.
    • (2001) Comb. Chem. High Throughput Screen. , vol.4 , pp. 719-725
    • Chen, X.1
  • 33
    • 0034733042 scopus 로고    scopus 로고
    • 2+ binding properties of novel C2 domains of plant phospholipase Dα and β
    • 2+ binding properties of novel C2 domains of plant phospholipase Dα and β. J. Biol. Chem. 2000, 275:19700-19706.
    • (2000) J. Biol. Chem. , vol.275 , pp. 19700-19706
    • Zheng, L.1
  • 34
    • 0032584589 scopus 로고    scopus 로고
    • Thermodynamics of binding of calcium, magnesium, and zinc to the N- methyl-D-aspartate receptor ion channel peptidic inhibitors, conantokin-G and conantokin-T
    • Prorok M., Castellino F.J. Thermodynamics of binding of calcium, magnesium, and zinc to the N- methyl-D-aspartate receptor ion channel peptidic inhibitors, conantokin-G and conantokin-T. J. Biol. Chem. 1998, 273:19573-19578.
    • (1998) J. Biol. Chem. , vol.273 , pp. 19573-19578
    • Prorok, M.1    Castellino, F.J.2
  • 35
    • 46449120133 scopus 로고    scopus 로고
    • Induced disorder in protein-ligand complexes as a drug-design strategy
    • Crespo A., Fernández A. Induced disorder in protein-ligand complexes as a drug-design strategy. Mol. Pharm. 2008, 5:430-437.
    • (2008) Mol. Pharm. , vol.5 , pp. 430-437
    • Crespo, A.1    Fernández, A.2
  • 36
    • 77958035712 scopus 로고    scopus 로고
    • Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3
    • Diehl C., et al. Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3. J. Am. Chem. Soc. 2010, 132:14577-14589.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 14577-14589
    • Diehl, C.1
  • 37
    • 34447503697 scopus 로고    scopus 로고
    • Conformational entropy in molecular recognition by proteins
    • Frederick K.K., et al. Conformational entropy in molecular recognition by proteins. Nature 2007, 448:325-329.
    • (2007) Nature , vol.448 , pp. 325-329
    • Frederick, K.K.1
  • 38
    • 44949167588 scopus 로고    scopus 로고
    • Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association
    • Chang C-E.A., et al. Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:7456-7461.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 7456-7461
    • Chang, C.-E.A.1
  • 39
    • 43649103922 scopus 로고    scopus 로고
    • (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
    • Baron R., McCammon J.A. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. ChemPhysChem 2008, 9:983-988.
    • (2008) ChemPhysChem , vol.9 , pp. 983-988
    • Baron, R.1    McCammon, J.A.2
  • 40
    • 70450191983 scopus 로고    scopus 로고
    • Dynamic activation of an allosteric regulatory protein
    • Tzeng S-R., Kalodimos C.G. Dynamic activation of an allosteric regulatory protein. Nature 2009, 462:368-372.
    • (2009) Nature , vol.462 , pp. 368-372
    • Tzeng, S.-R.1    Kalodimos, C.G.2
  • 41
    • 56049097680 scopus 로고    scopus 로고
    • Structural rationale for the coupled binding and unfolding of the c-Myc oncoprotein by small molecules
    • Follis A.V., et al. Structural rationale for the coupled binding and unfolding of the c-Myc oncoprotein by small molecules. Chem. Biol. 2008, 15:1149-1155.
    • (2008) Chem. Biol. , vol.15 , pp. 1149-1155
    • Follis, A.V.1
  • 42
    • 84856383832 scopus 로고    scopus 로고
    • Privileged scaffolds or promiscuous binders: a comparative study on rhodanines and related heterocycles in medicinal chemistry
    • Mendgen T., et al. Privileged scaffolds or promiscuous binders: a comparative study on rhodanines and related heterocycles in medicinal chemistry. J. Med. Chem. 2012, 55:743-753.
    • (2012) J. Med. Chem. , vol.55 , pp. 743-753
    • Mendgen, T.1
  • 44
    • 84864018938 scopus 로고    scopus 로고
    • The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-Myc
    • Michel J., Cuchillo R. The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-Myc. PLoS ONE 2012, 7:e41070.
    • (2012) PLoS ONE , vol.7 , pp. e41070
    • Michel, J.1    Cuchillo, R.2
  • 45
    • 84887305278 scopus 로고    scopus 로고
    • Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins
    • Jin F., et al. Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins. PLoS Comput. Biol. 2013, 9:e1003249.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003249
    • Jin, F.1
  • 46
    • 84867488138 scopus 로고    scopus 로고
    • Ordering of the N-terminus of human MDM2 by small molecule inhibitors
    • Michelsen K., et al. Ordering of the N-terminus of human MDM2 by small molecule inhibitors. J. Am. Chem. Soc. 2012, 134:17059-17067.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 17059-17067
    • Michelsen, K.1
  • 47
    • 84940467577 scopus 로고    scopus 로고
    • Elucidation of ligand-dependent modulation of disorder-order transitions in the oncoprotein MDM2
    • Bueren-Calabuig J.A., Michel J. Elucidation of ligand-dependent modulation of disorder-order transitions in the oncoprotein MDM2. PLoS Comput. Biol. 2015, 11:e1004282.
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004282
    • Bueren-Calabuig, J.A.1    Michel, J.2
  • 48
    • 84889565658 scopus 로고    scopus 로고
    • Phosphorylation drives a dynamic switch in serine/arginine-rich proteins
    • Xiang S., et al. Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 2013, 21:2162-2174.
    • (2013) Structure , vol.21 , pp. 2162-2174
    • Xiang, S.1
  • 49
    • 84884507134 scopus 로고    scopus 로고
    • A relationship between the aggregation rates of α-synuclein variants and the β-sheet populations in their monomeric forms
    • Camilloni C., Vendruscolo M. A relationship between the aggregation rates of α-synuclein variants and the β-sheet populations in their monomeric forms. J. Phys. Chem. B 2013, 117:10737-10741.
    • (2013) J. Phys. Chem. B , vol.117 , pp. 10737-10741
    • Camilloni, C.1    Vendruscolo, M.2
  • 50
    • 22844435320 scopus 로고    scopus 로고
    • Periplasmic protein HdeA exhibits chaperone-like activity exclusively within stomach pH range by transforming into disordered conformation
    • Hong W., et al. Periplasmic protein HdeA exhibits chaperone-like activity exclusively within stomach pH range by transforming into disordered conformation. J. Biol. Chem. 2005, 280:27029-27034.
    • (2005) J. Biol. Chem. , vol.280 , pp. 27029-27034
    • Hong, W.1
  • 51
    • 84961289040 scopus 로고    scopus 로고
    • The H50Q mutation induces a 10-fold decrease in the solubility of α-synuclein
    • Porcari R., et al. The H50Q mutation induces a 10-fold decrease in the solubility of α-synuclein. J. Biol. Chem. 2015, 290:2395-2404.
    • (2015) J. Biol. Chem. , vol.290 , pp. 2395-2404
    • Porcari, R.1
  • 52
    • 77954618278 scopus 로고    scopus 로고
    • Small-molecule inhibitors of c-Myc transcriptional factor suppress proliferation and induce apoptosis of promyelocytic leukemia cell via cell cycle arrest
    • Jeong K-C., et al. Small-molecule inhibitors of c-Myc transcriptional factor suppress proliferation and induce apoptosis of promyelocytic leukemia cell via cell cycle arrest. Mol. Biosyst. 2010, 6:1503-1509.
    • (2010) Mol. Biosyst. , vol.6 , pp. 1503-1509
    • Jeong, K.-C.1
  • 53
    • 33847662852 scopus 로고    scopus 로고
    • Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid beta-peptide
    • Haass C., Selkoe D.J. Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid beta-peptide. Nat. Rev. Mol. Cell. Biol. 2007, 8:101-112.
    • (2007) Nat. Rev. Mol. Cell. Biol. , vol.8 , pp. 101-112
    • Haass, C.1    Selkoe, D.J.2
  • 54
    • 72149118250 scopus 로고    scopus 로고
    • An analytical solution to the kinetics of breakable filament assembly
    • Knowles T.P.J. An analytical solution to the kinetics of breakable filament assembly. Science 2009, 1533:1533-1537.
    • (2009) Science , vol.1533 , pp. 1533-1537
    • Knowles, T.P.J.1
  • 55
    • 67650369989 scopus 로고    scopus 로고
    • Unfoldomics of human diseases: linking protein intrinsic disorder with diseases
    • Uversky V.N., et al. Unfoldomics of human diseases: linking protein intrinsic disorder with diseases. BMC Genomics 2009, 10(Suppl. 1):S7.
    • (2009) BMC Genomics , vol.10 , pp. S7
    • Uversky, V.N.1
  • 56
    • 84940467085 scopus 로고    scopus 로고
    • On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment
    • Giandanti A.D. On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment. Biophys. Bioeng. Lett. 2014, 7:27-32.
    • (2014) Biophys. Bioeng. Lett. , vol.7 , pp. 27-32
    • Giandanti, A.D.1


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