메뉴 건너뛰기




Volumn 10, Issue 9, 2014, Pages 716-722

Comprehensive analysis of loops at protein-protein interfaces for macrocycle design

Author keywords

[No Author keywords available]

Indexed keywords

MACROCYCLIC COMPOUND;

EID: 84906327241     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.1580     Document Type: Article
Times cited : (144)

References (44)
  • 1
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    • Wells, J.A. & McClendon, C.L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450, 1001-1009 (2007).
    • (2007) Nature , vol.450 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 2
    • 79953777824 scopus 로고    scopus 로고
    • Macrocycles are great cycles: Applications, opportunities, and challenges of synthetic macrocycles in drug discovery
    • Marsault, E. & Peterson, M.L. Macrocycles are great cycles: applications, opportunities, and challenges of synthetic macrocycles in drug discovery. J. Med. Chem. 54, 1961-2004 (2011).
    • (2011) J. Med. Chem. , vol.54 , pp. 1961-2004
    • Marsault, E.1    Peterson, M.L.2
  • 3
    • 84875138812 scopus 로고    scopus 로고
    • Getting in shape: Controlling peptide bioactivity and bioavailability using conformational constraints
    • Bock, J.E., Gavenonis, J. & Kritzer, J.A. Getting in shape: controlling peptide bioactivity and bioavailability using conformational constraints. ACS Chem. Biol. 8, 488-499 (2013).
    • (2013) ACS Chem. Biol. , vol.8 , pp. 488-499
    • Bock, J.E.1    Gavenonis, J.2    Kritzer, J.A.3
  • 4
    • 44949231073 scopus 로고    scopus 로고
    • Peptidomimetics a synthetic tool of drug discovery
    • Vagner, J., Qu, H. & Hruby, V.J. Peptidomimetics, a synthetic tool of drug discovery. Curr. Opin. Chem. Biol. 12, 292-296 (2008).
    • (2008) Curr. Opin. Chem. Biol. , vol.12 , pp. 292-296
    • Vagner, J.1    Qu, H.2    Hruby, V.J.3
  • 5
    • 57449084703 scopus 로고    scopus 로고
    • Exploring β-sheet structure and interactions with chemical model systems
    • Nowick, J.S. Exploring β-sheet structure and interactions with chemical model systems. Acc. Chem. Res. 41, 1319-1330 (2008).
    • (2008) Acc. Chem. Res. , vol.41 , pp. 1319-1330
    • Nowick, J.S.1
  • 6
    • 84875436143 scopus 로고    scopus 로고
    • Inhibition of α-helix-mediated protein-protein interactions using designed molecules
    • Azzarito, V., Long, K., Murphy, N.S. & Wilson, A.J. Inhibition of α-helix-mediated protein-protein interactions using designed molecules. Nat. Chem. 5, 161-173 (2013).
    • (2013) Nat. Chem. , vol.5 , pp. 161-173
    • Azzarito, V.1    Long, K.2    Murphy, N.S.3    Wilson, A.J.4
  • 7
    • 34548141882 scopus 로고    scopus 로고
    • Secondary structure based analysis and classification of biological interfaces: Identification of binding motifs in protein-protein interactions
    • Guharoy, M. & Chakrabarti, P. Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein-protein interactions. Bioinformatics 23, 1909-1918 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1909-1918
    • Guharoy, M.1    Chakrabarti, P.2
  • 8
    • 38549092067 scopus 로고    scopus 로고
    • HotSprint: Database of computational hot spots in protein interfaces
    • Guney, E., Tuncbag, N., Keskin, O. & Gursoy, A. HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res. 36, D662-D666 (2008).
    • (2008) Nucleic Acids Res. , vol.36
    • Guney, E.1    Tuncbag, N.2    Keskin, O.3    Gursoy, A.4
  • 9
    • 84863270608 scopus 로고    scopus 로고
    • Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists
    • Koes, D. et al. Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists. PLoS ONE 7, e32839 (2012).
    • (2012) PLoS ONE , vol.7
    • Koes, D.1
  • 10
    • 77958105231 scopus 로고    scopus 로고
    • Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors
    • Jochim, A.L. & Arora, P.S. Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors. ACS Chem. Biol. 5, 919-923 (2010).
    • (2010) ACS Chem. Biol. , vol.5 , pp. 919-923
    • Jochim, A.L.1    Arora, P.S.2
  • 11
    • 84885995896 scopus 로고    scopus 로고
    • HippDB: A database of readily targeted helical protein-protein interactions
    • Bergey, C.M., Watkins, A.M. & Arora, P.S. HippDB: a database of readily targeted helical protein-protein interactions. Bioinformatics 29, 2806-2807 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2806-2807
    • Bergey, C.M.1    Watkins, A.M.2    Arora, P.S.3
  • 12
    • 77957947345 scopus 로고    scopus 로고
    • Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?
    • London, N., Raveh, B., Movshovitz-Attias, D. & Schueler-Furman, O. Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins 78, 3140-3149 (2010).
    • (2010) Proteins , vol.78 , pp. 3140-3149
    • London, N.1    Raveh, B.2    Movshovitz-Attias, D.3    Schueler-Furman, O.4
  • 13
    • 32044470909 scopus 로고    scopus 로고
    • Structure and thermodynamic characterization of the EphB4/ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity
    • Chrencik, J.E. et al. Structure and thermodynamic characterization of the EphB4/ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity. Structure 14, 321-330 (2006).
    • (2006) Structure , vol.14 , pp. 321-330
    • Chrencik, J.E.1
  • 14
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme, T. & Baker, D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA 99, 14116-14121 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 15
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme, T., Kim, D. & Baker, D. Computational alanine scanning of protein-protein interfaces. Sci. STKE 2004, pl2 (2004).
    • (2004) Sci. STKE , vol.2004
    • Kortemme, T.1    Kim, D.2    Baker, D.3
  • 16
    • 77949617607 scopus 로고    scopus 로고
    • PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta
    • Chaudhury, S., Lyskov, S. & Gray, J.J. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics 26, 689-691 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 689-691
    • Chaudhury, S.1    Lyskov, S.2    Gray, J.J.3
  • 17
    • 38649087636 scopus 로고    scopus 로고
    • Spatial chemical conservation of hot spot interactions in protein-protein complexes
    • Shulman-Peleg, A., Shatsky, M., Nussinov, R. & Wolfson, H.J. Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol. 5, 43 (2007).
    • (2007) BMC Biol. , vol.5 , pp. 43
    • Shulman-Peleg, A.1    Shatsky, M.2    Nussinov, R.3    Wolfson, H.J.4
  • 18
    • 48549093368 scopus 로고    scopus 로고
    • MSDmotif: Exploring protein sites and motifs
    • Golovin, A. & Henrick, K. MSDmotif: exploring protein sites and motifs. BMC Bioinformatics 9, 312 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 312
    • Golovin, A.1    Henrick, K.2
  • 19
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan, A.A. & Thorn, K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280, 1-9 (1998).
    • (1998) J. Mol. Biol. , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 20
    • 0024246956 scopus 로고
    • Surface subunit interfaces and interior of oligomeric proteins
    • Janin, J., Miller, S. & Chothia, C. Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol. 204, 155-164 (1988).
    • (1988) J. Mol. Biol. , vol.204 , pp. 155-164
    • Janin, J.1    Miller, S.2    Chothia, C.3
  • 21
    • 1842405464 scopus 로고    scopus 로고
    • Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
    • Tsai, C.-J., Lin, S.L., Wolfson, H.J. & Nussinov, R. Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci. 6, 53-64 (1997).
    • (1997) Protein Sci. , vol.6 , pp. 53-64
    • Tsai, C.-J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 22
    • 0026335990 scopus 로고
    • Rational design of receptor-specific variants of human growth hormone
    • Cunningham, B.C. & Wells, J.A. Rational design of receptor-specific variants of human growth hormone. Proc. Natl. Acad. Sci. USA 88, 3407-3411 (1991).
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 3407-3411
    • Cunningham, B.C.1    Wells, J.A.2
  • 23
    • 0027132013 scopus 로고
    • Comparison of a structural and a functional epitope
    • Cunningham, B.C. & Wells, J.A. Comparison of a structural and a functional epitope. J. Mol. Biol. 234, 554-563 (1993).
    • (1993) J. Mol. Biol. , vol.234 , pp. 554-563
    • Cunningham, B.C.1    Wells, J.A.2
  • 24
    • 0029770041 scopus 로고    scopus 로고
    • Crystal structure of an antagonist mutant of human growth hormone, G120R, in complex with its receptor at 2.9 A resolution
    • Sundström, M. et al. Crystal structure of an antagonist mutant of human growth hormone, G120R, in complex with its receptor at 2.9 A resolution. J. Biol. Chem. 271, 32197-32203 (1996).
    • (1996) J. Biol. Chem. , vol.271 , pp. 32197-32203
    • Sundström, M.1
  • 25
    • 84862557429 scopus 로고    scopus 로고
    • A phase i first-in-human trial of bardoxolone methyl in patients with advanced solid tumors and lymphomas
    • Hong, D.S. et al. A phase I first-in-human trial of bardoxolone methyl in patients with advanced solid tumors and lymphomas. Clin. Cancer Res. 18, 3396-3406 (2012).
    • (2012) Clin. Cancer Res. , vol.18 , pp. 3396-3406
    • Hong, D.S.1
  • 26
    • 33747606306 scopus 로고    scopus 로고
    • Structure of the Keap1: Nrf2 interface provides mechanistic insight into Nrf2 signaling
    • Lo, S.-C., Li, X., Henzl, M.T., Beamer, L.J. & Hannink, M. Structure of the Keap1: Nrf2 interface provides mechanistic insight into Nrf2 signaling. EMBO J. 25, 3605-3617 (2006).
    • (2006) EMBO J. , vol.25 , pp. 3605-3617
    • Lo, S.-C.1    Li, X.2    Henzl, M.T.3    Beamer, L.J.4    Hannink, M.5
  • 27
    • 81355124042 scopus 로고    scopus 로고
    • Kinetic analyses of Keap1-Nrf2 interaction and determination of the minimal Nrf2 peptide sequence required for Keap1 binding using surface plasmon resonance
    • Chen, Y., Inoyama, D., Kong, A.-N.T., Beamer, L.J. & Hu, L. Kinetic analyses of Keap1-Nrf2 interaction and determination of the minimal Nrf2 peptide sequence required for Keap1 binding using surface plasmon resonance. Chem. Biol. Drug Des. 78, 1014-1021 (2011).
    • (2011) Chem. Biol. Drug Des. , vol.78 , pp. 1014-1021
    • Chen, Y.1    Inoyama, D.2    Kong, A.-N.T.3    Beamer, L.J.4    Hu, L.5
  • 28
    • 84877659801 scopus 로고    scopus 로고
    • Peptide inhibitors of the Keap1-Nrf2 protein-protein interaction with improved binding and cellular activity
    • Hancock, R., Schaap, M., Pfister, H. & Wells, G. Peptide inhibitors of the Keap1-Nrf2 protein-protein interaction with improved binding and cellular activity. Org. Biomol. Chem. 11, 3553-3557 (2013).
    • (2013) Org. Biomol. Chem. , vol.11 , pp. 3553-3557
    • Hancock, R.1    Schaap, M.2    Pfister, H.3    Wells, G.4
  • 29
    • 84878531946 scopus 로고    scopus 로고
    • Crystal-contact engineering to obtain a crystal form of the Kelch domain of human Keap1 suitable for ligand-soaking experiments
    • Hörer, S., Reinert, D., Ostmann, K., Hoevels, Y. & Nar, H. Crystal-contact engineering to obtain a crystal form of the Kelch domain of human Keap1 suitable for ligand-soaking experiments. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 69, 592-596 (2013).
    • (2013) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. , vol.69 , pp. 592-596
    • Hörer, S.1    Reinert, D.2    Ostmann, K.3    Hoevels, Y.4    Nar, H.5
  • 30
    • 47149092405 scopus 로고    scopus 로고
    • Targeting the p27 E3 ligase SCFSkp2 results in p27-and Skp2-mediated cell-cycle arrest and activation of autophagy
    • Chen, Q. et al. Targeting the p27 E3 ligase SCFSkp2 results in p27-and Skp2-mediated cell-cycle arrest and activation of autophagy. Blood 111, 4690-4699 (2008).
    • (2008) Blood , vol.111 , pp. 4690-4699
    • Chen, Q.1
  • 31
    • 25844441096 scopus 로고    scopus 로고
    • Structural basis of the Cks1-dependent recognition of p27Kip1 by the SCFSkp2 ubipuitin ligase
    • Hao, B. et al. Structural basis of the Cks1-dependent recognition of p27Kip1 by the SCFSkp2 ubipuitin ligase. Mol. Cell 20, 9-19 (2005).
    • (2005) Mol. Cell , vol.20 , pp. 9-19
    • Hao, B.1
  • 32
    • 0036829681 scopus 로고    scopus 로고
    • Three different binding sites of Cks1 are required for p27-ubiquitin ligation
    • Sitry, D. et al. Three different binding sites of Cks1 are required for p27-ubiquitin ligation. J. Biol. Chem. 277, 42233-42240 (2002).
    • (2002) J. Biol. Chem. , vol.277 , pp. 42233-42240
    • Sitry, D.1
  • 33
    • 28844455956 scopus 로고    scopus 로고
    • High-throughput screening for inhibitors of the Cks1-Skp2 interaction
    • Huang, K.S. & Vassilev, L.T. High-throughput screening for inhibitors of the Cks1-Skp2 interaction. Methods Enzymol. 399, 717-728 (2005).
    • (2005) Methods Enzymol. , vol.399 , pp. 717-728
    • Huang, K.S.1    Vassilev, L.T.2
  • 34
    • 84882353683 scopus 로고    scopus 로고
    • High-throughput screening AlphaScreen assay for identification of small-molecule inhibitors of ubiquitin E3 ligase SCFSkp2-Cks1
    • Ungermannova, D. et al. High-throughput screening AlphaScreen assay for identification of small-molecule inhibitors of ubiquitin E3 ligase SCFSkp2-Cks1. J. Biomol. Screen. 18, 910-920 (2013).
    • (2013) J. Biomol. Screen. , vol.18 , pp. 910-920
    • Ungermannova, D.1
  • 35
    • 84871569969 scopus 로고    scopus 로고
    • Specific small molecule inhibitors of Skp2-mediated p27 degradation
    • Wu, L. et al. Specific small molecule inhibitors of Skp2-mediated p27 degradation. Chem. Biol. 19, 1515-1524 (2012).
    • (2012) Chem. Biol. , vol.19 , pp. 1515-1524
    • Wu, L.1
  • 36
    • 84861847390 scopus 로고    scopus 로고
    • Structural insight into the regulation of MOF in the male-specific lethal complex and the non-specific lethal complex
    • Huang, J. et al. Structural insight into the regulation of MOF in the male-specific lethal complex and the non-specific lethal complex. Cell Res. 22, 1078-1081 (2012).
    • (2012) Cell Res. , vol.22 , pp. 1078-1081
    • Huang, J.1
  • 37
    • 79551625231 scopus 로고    scopus 로고
    • Structural basis for MOF and MSL3 recruitment into the dosage compensation complex by MSL1
    • Kadlec, J. et al. Structural basis for MOF and MSL3 recruitment into the dosage compensation complex by MSL1. Nat. Struct. Mol. Biol. 18, 142-149 (2011).
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 142-149
    • Kadlec, J.1
  • 38
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson, T. & Wells, J. A hot spot of binding energy in a hormone-receptor interface. Science 267, 383-386 (1995).
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.2
  • 39
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot spots in binding interfaces: Progress and challenges
    • DeLano, W.L. Unraveling hot spots in binding interfaces: progress and challenges. Curr. Opin. Struct. Biol. 12, 14-20 (2002).
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 14-20
    • Delano, W.L.1
  • 40
    • 0043245780 scopus 로고    scopus 로고
    • Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    • Gohlke, H., Kiel, C. & Case, D.A. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 330, 891-913 (2003).
    • (2003) J. Mol. Biol. , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, C.2    Case, D.A.3
  • 41
    • 34548779127 scopus 로고    scopus 로고
    • Hot spots - A review of the protein-protein interface determinant amino-acid residues
    • Moreira, I.S., Fernandes, P.A. & Ramos, M.J. Hot spots-a review of the protein-protein interface determinant amino-acid residues. Proteins 68, 803-812 (2007).
    • (2007) Proteins , vol.68 , pp. 803-812
    • Moreira, I.S.1    Fernandes, P.A.2    Ramos, M.J.3
  • 43
    • 48749094943 scopus 로고    scopus 로고
    • Structural determinants of the ADAM inhibition by TIMP-3: Crystal structure of the TACE-N-TIMP-3 complex
    • Wisniewska, M. et al. Structural determinants of the ADAM inhibition by TIMP-3: crystal structure of the TACE-N-TIMP-3 complex. J. Mol. Biol. 381, 1307-1319 (2008).
    • (2008) J. Mol. Biol. , vol.381 , pp. 1307-1319
    • Wisniewska, M.1
  • 44
    • 0021828928 scopus 로고
    • Hydrogen bonding and biological specificity analysed by protein engineering
    • Fersht, A.R. et al. Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314, 235-238 (1985).
    • (1985) Nature , vol.314 , pp. 235-238
    • Fersht, A.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.