메뉴 건너뛰기




Volumn 54, Issue 5, 2014, Pages 1425-1432

Computational screening and selection of cyclic peptide hairpin mimetics by molecular simulation and kinetic network models

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHEMICAL MODIFICATION; CONFORMATIONS; CROSSLINKING; DEGREES OF FREEDOM (MECHANICS); MOLECULAR DYNAMICS; POPULATION STATISTICS;

EID: 84901608851     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500102y     Document Type: Article
Times cited : (45)

References (58)
  • 1
    • 84890137047 scopus 로고    scopus 로고
    • Druggable protein-protein interactions - From hot spots to hot segments
    • London, N.; Raveh, B.; Schueler-Furman, O. Druggable protein-protein interactions-from hot spots to hot segments Curr. Opin. Chem. Biol. 2013, 17, 952-959
    • (2013) Curr. Opin. Chem. Biol. , vol.17 , pp. 952-959
    • London, N.1    Raveh, B.2    Schueler-Furman, O.3
  • 2
    • 84884546351 scopus 로고    scopus 로고
    • Synthesis of a Tetrasubstituted Tetrahydronaphthalene Scaffold for α-Helix Mimicry via a MgBr 2-Catalyzed Friedel-Crafts Epoxide Cycloalkylation
    • Naduthambi, D.; Bhor, S.; Elbaum, M. B.; Zondlo, N. J. Synthesis of a Tetrasubstituted Tetrahydronaphthalene Scaffold for α-Helix Mimicry via a MgBr 2-Catalyzed Friedel-Crafts Epoxide Cycloalkylation Org. Lett. 2013, 15, 4892-4895
    • (2013) Org. Lett. , vol.15 , pp. 4892-4895
    • Naduthambi, D.1    Bhor, S.2    Elbaum, M.B.3    Zondlo, N.J.4
  • 5
    • 57349151828 scopus 로고    scopus 로고
    • β-Hairpin Peptidomimetics: Design, Structures and Biological Activities
    • Robinson, J. A. β-Hairpin Peptidomimetics: Design, Structures and Biological Activities Acc. Chem. Res. 2008, 41, 1278-1288
    • (2008) Acc. Chem. Res. , vol.41 , pp. 1278-1288
    • Robinson, J.A.1
  • 6
    • 79952741178 scopus 로고    scopus 로고
    • Cilengitide: The first anti-angiogenic small molecule drug candidate. Design, synthesis and clinical evaluation
    • Mas-Moruno, C.; Rechenmacher, F.; Kessler, H. Cilengitide: the first anti-angiogenic small molecule drug candidate. Design, synthesis and clinical evaluation Anti-Cancer Agents Med. Chem. 2010, 10, 753-768
    • (2010) Anti-Cancer Agents Med. Chem. , vol.10 , pp. 753-768
    • Mas-Moruno, C.1    Rechenmacher, F.2    Kessler, H.3
  • 7
    • 0035850529 scopus 로고    scopus 로고
    • Interstrand Side Chain-Side Chain Interactions in a Designed β-Hairpin: Significance of Both Lateral and Diagonal Pairings
    • Syud, F. A.; Stanger, H. E.; Gellman, S. H. Interstrand Side Chain-Side Chain Interactions in a Designed β-Hairpin: Significance of Both Lateral and Diagonal Pairings J. Am. Chem. Soc. 2001, 123, 8667-8677
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 8667-8677
    • Syud, F.A.1    Stanger, H.E.2    Gellman, S.H.3
  • 9
    • 84890705499 scopus 로고    scopus 로고
    • Rational Optimization of Conformational Effects Induced by Hydrocarbon Staples in Peptides and their Binding Interfaces
    • Lama, D.; Quah, S. T.; Verma, C. S.; Lakshminarayanan, R.; Beuerman, R. W.; Lane, D. P.; Brown, C. J. Rational Optimization of Conformational Effects Induced By Hydrocarbon Staples in Peptides and their Binding Interfaces Sci. Rep. 2013, 3, 3451
    • (2013) Sci. Rep. , vol.3 , pp. 3451
    • Lama, D.1    Quah, S.T.2    Verma, C.S.3    Lakshminarayanan, R.4    Beuerman, R.W.5    Lane, D.P.6    Brown, C.J.7
  • 11
    • 84865181920 scopus 로고    scopus 로고
    • Configurational Preferences of Arylamide α-Helix Mimetics via Alchemical Free Energy Calculations of Relative Binding Affinities
    • Fuller, J. C.; Jackson, R. M.; Shirts, M. R. Configurational Preferences of Arylamide α-Helix Mimetics via Alchemical Free Energy Calculations of Relative Binding Affinities J. Phys. Chem. B 2012, 116, 10856-10869
    • (2012) J. Phys. Chem. B , vol.116 , pp. 10856-10869
    • Fuller, J.C.1    Jackson, R.M.2    Shirts, M.R.3
  • 12
    • 79952266181 scopus 로고    scopus 로고
    • A c-di-GMP Effector System Controls Cell Adhesion by Inside-Out Signaling and Surface Protein Cleavage
    • Newell, P. D.; Boyd, C. D.; Sondermann, H.; O'Toole, G. A. A c-di-GMP Effector System Controls Cell Adhesion by Inside-Out Signaling and Surface Protein Cleavage PLoS Biology 2011, 9, e1000587
    • (2011) PLoS Biology , vol.9 , pp. 1000587
    • Newell, P.D.1    Boyd, C.D.2    Sondermann, H.3    O'Toole, G.A.4
  • 14
    • 57349192372 scopus 로고    scopus 로고
    • A Hydrogen Bond Surrogate Approach for Stabilization of Short Peptide Sequences in Alpha-Helical Conformation
    • Henchey, L.; Jochim, A.; Arora, P. A Hydrogen Bond Surrogate Approach for Stabilization of Short Peptide Sequences in Alpha-Helical Conformation Acc. Chem. Res. 2008, 41, 1289-1300
    • (2008) Acc. Chem. Res. , vol.41 , pp. 1289-1300
    • Henchey, L.1    Jochim, A.2    Arora, P.3
  • 15
    • 0033598258 scopus 로고    scopus 로고
    • Synthesis and Activity of a New Generation of Ruthenium-Based Olefin Metathesis Catalysts Coordinated with 1,3-Dimesityl-4,5-dihydroimidazol-2- ylidene Ligands
    • Scholl, M.; Ding, S.; Lee, C. W.; Grubbs, R. H. Synthesis and Activity of a New Generation of Ruthenium-Based Olefin Metathesis Catalysts Coordinated with 1,3-Dimesityl-4,5-dihydroimidazol-2-ylidene Ligands Org. Lett. 1999, 1, 953-956
    • (1999) Org. Lett. , vol.1 , pp. 953-956
    • Scholl, M.1    Ding, S.2    Lee, C.W.3    Grubbs, R.H.4
  • 16
    • 84866327641 scopus 로고    scopus 로고
    • Structural Characterization of a Conserved, Calcium-Dependent Periplasmic Protease from Legionella pneumophila
    • Chatterjee, D.; Boyd, C. D.; O'Toole, G. A.; Sondermann, H. Structural Characterization of a Conserved, Calcium-Dependent Periplasmic Protease from Legionella pneumophila J. Bacteriol. 2012, 194, 4415-4425
    • (2012) J. Bacteriol. , vol.194 , pp. 4415-4425
    • Chatterjee, D.1    Boyd, C.D.2    O'Toole, G.A.3    Sondermann, H.4
  • 17
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
    • Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 19
    • 2542564912 scopus 로고    scopus 로고
    • Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules
    • Kollman, P. A. Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules Acc. Chem. Res. 1996, 29, 461-469
    • (1996) Acc. Chem. Res. , vol.29 , pp. 461-469
    • Kollman, P.A.1
  • 20
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational changes with a modified generalized born model
    • Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model Proteins: Struct., Funct., Bioinf. 2004, 55, 383-394
    • (2004) Proteins: Struct., Funct., Bioinf. , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 21
    • 76149136021 scopus 로고    scopus 로고
    • Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)
    • Voelz, V. A.; Bowman, G. R.; Beauchamp, K.; Pande, V. S. Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39) J. Am. Chem. Soc. 2010, 132, 1526-1528
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 1526-1528
    • Voelz, V.A.1    Bowman, G.R.2    Beauchamp, K.3    Pande, V.S.4
  • 22
    • 84864495493 scopus 로고    scopus 로고
    • Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment
    • Voelz, V. A.; Jäger, M.; Yao, S.; Chen, Y.; Zhu, L.; Waldauer, S. A.; Bowman, G. R. Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment J. Am. Chem. Soc. 2012, 134, 12565-12577
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 12565-12577
    • Voelz, V.A.1    Jäger, M.2    Yao, S.3    Chen, Y.4    Zhu, L.5    Waldauer, S.A.6    Bowman, G.R.7
  • 23
    • 77950789652 scopus 로고    scopus 로고
    • Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment
    • Voelz, V. A.; Singh, V. R.; Wedemeyer, W. J.; Lapidus, L. J.; Pande, V. S. Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment J. Am. Chem. Soc. 2010, 132, 4702-4709
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 4702-4709
    • Voelz, V.A.1    Singh, V.R.2    Wedemeyer, W.J.3    Lapidus, L.J.4    Pande, V.S.5
  • 25
    • 79960007037 scopus 로고    scopus 로고
    • Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
    • Buch, I.; Giorgino, T.; De Fabritiis, G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 10184-10189
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 10184-10189
    • Buch, I.1    Giorgino, T.2    De Fabritiis, G.3
  • 27
    • 0036890178 scopus 로고    scopus 로고
    • Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
    • Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation J. Comput. Chem. 2002, 23, 1623-1641
    • (2002) J. Comput. Chem. , vol.23 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 29
    • 52949088587 scopus 로고    scopus 로고
    • Statistically optimal analysis of samples from multiple equilibrium states
    • Shirts, M. R.; Chodera, J. D. Statistically optimal analysis of samples from multiple equilibrium states J. Chem. Phys. 2008, 129, 124105
    • (2008) J. Chem. Phys. , vol.129 , pp. 124105
    • Shirts, M.R.1    Chodera, J.D.2
  • 31
    • 0034623787 scopus 로고    scopus 로고
    • Screen savers of the world, unite!
    • Shirts, M.; Pande, V. S. Screen savers of the world, unite! Science 2000, 290, 1903-1904
    • (2000) Science , vol.290 , pp. 1903-1904
    • Shirts, M.1    Pande, V.S.2
  • 32
    • 84876005630 scopus 로고    scopus 로고
    • Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
    • Schwantes, C. R.; Pande, V. S. Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9 J. Chem. Theory Comput. 2013, 9, 2000-2009
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 2000-2009
    • Schwantes, C.R.1    Pande, V.S.2
  • 34
    • 84870182404 scopus 로고    scopus 로고
    • Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty
    • Bowman, G. R. Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty J. Chem. Phys. 2012, 137, 134111
    • (2012) J. Chem. Phys. , vol.137 , pp. 134111
    • Bowman, G.R.1
  • 36
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of b-hairpin formation
    • Munoz, V.; Thompson, P.; Hofrichter, J. Folding dynamics and mechanism of b-hairpin formation Nature 1997, 390, 196-199
    • (1997) Nature , vol.390 , pp. 196-199
    • Munoz, V.1    Thompson, P.2    Hofrichter, J.3
  • 38
    • 77952837884 scopus 로고    scopus 로고
    • Development of a Rotamer Library for Use in β-Peptide Foldamer Computational Design
    • Shandler, S. J.; Shapovalov, M. V.; Dunbrack, R. L., Jr.; DeGrado, W. F. Development of a Rotamer Library for Use in β-Peptide Foldamer Computational Design J. Am. Chem. Soc. 2010, 132, 7312-7320
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 7312-7320
    • Shandler, S.J.1    Shapovalov, M.V.2    Dunbrack Jr., R.L.3    Degrado, W.F.4
  • 44
    • 84858266350 scopus 로고    scopus 로고
    • Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design
    • Renfrew, P. D.; Choi, E. J.; Bonneau, R.; Kuhlman, B. Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design PLoS One 2012, 7, e32637
    • (2012) PLoS One , vol.7 , pp. 32637
    • Renfrew, P.D.1    Choi, E.J.2    Bonneau, R.3    Kuhlman, B.4
  • 46
    • 0034697649 scopus 로고    scopus 로고
    • An All-Hydrocarbon Cross-Linking System for Enhancing the Helicity and Metabolic Stability of Peptides
    • Schafmeister, C. E.; Po, J.; Verdine, G. L. An All-Hydrocarbon Cross-Linking System for Enhancing the Helicity and Metabolic Stability of Peptides J. Am. Chem. Soc. 2000, 122, 5891-5892
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 5891-5892
    • Schafmeister, C.E.1    Po, J.2    Verdine, G.L.3
  • 47
    • 65549127630 scopus 로고    scopus 로고
    • Design of Protein-Protein Interaction Inhibitors Based on Protein Epitope Mimetics
    • Robinson, J. A. Design of Protein-Protein Interaction Inhibitors Based on Protein Epitope Mimetics ChemBioChem. 2009, 10, 971-973
    • (2009) ChemBioChem. , vol.10 , pp. 971-973
    • Robinson, J.A.1
  • 48
    • 28344441228 scopus 로고    scopus 로고
    • Error analysis and efficient sampling in Markovian state models for molecular dynamics
    • Singhal, N.; Pande, V. S. Error analysis and efficient sampling in Markovian state models for molecular dynamics J. Chem. Phys. 2005, 123, 204909
    • (2005) J. Chem. Phys. , vol.123 , pp. 204909
    • Singhal, N.1    Pande, V.S.2
  • 49
    • 77950159292 scopus 로고    scopus 로고
    • Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models
    • Bowman, G. R.; Ensign, D. L.; Pande, V. S. Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models J. Chem. Theory Comput. 2010, 6, 787-794
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 787-794
    • Bowman, G.R.1    Ensign, D.L.2    Pande, V.S.3
  • 50
    • 82455174407 scopus 로고    scopus 로고
    • Atomistic Kinetic Model for Population Shift and Allostery in Biomolecules
    • Long, D.; Brüschweiler, R. Atomistic Kinetic Model for Population Shift and Allostery in Biomolecules J. Am. Chem. Soc. 2011, 133, 18999-19005
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 18999-19005
    • Long, D.1    Brüschweiler, R.2
  • 51
    • 0033572951 scopus 로고    scopus 로고
    • NMR-Based Quantification of β-Sheet Populations in Aqueous Solution through Use of Reference Peptides for the Folded and Unfolded States
    • Syud, F. A.; Espinosa, J. F.; Gellman, S. H. NMR-Based Quantification of β-Sheet Populations in Aqueous Solution through Use of Reference Peptides for the Folded and Unfolded States J. Am. Chem. Soc. 1999, 121, 11577-11578
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 11577-11578
    • Syud, F.A.1    Espinosa, J.F.2    Gellman, S.H.3
  • 53
    • 84887566303 scopus 로고    scopus 로고
    • Profound methyl effects in drug discovery and a call for new C-H methylation reactions
    • Schönherr, H.; Cernak, T. Profound methyl effects in drug discovery and a call for new C-H methylation reactions Angew. Chem., Int. Ed. 2013, 52, 12256-12267
    • (2013) Angew. Chem., Int. Ed. , vol.52 , pp. 12256-12267
    • Schönherr, H.1    Cernak, T.2
  • 57
    • 84871962988 scopus 로고    scopus 로고
    • N-Methylation of Peptides and Proteins: An Important Element for Modulating Biological Functions
    • Chatterjee, J.; Rechenmacher, F.; Kessler, H. N-Methylation of Peptides and Proteins: An Important Element for Modulating Biological Functions Angew. Chem., Int. Ed. 2012, 52, 254-269
    • (2012) Angew. Chem., Int. Ed. , vol.52 , pp. 254-269
    • Chatterjee, J.1    Rechenmacher, F.2    Kessler, H.3
  • 58
    • 0037438384 scopus 로고    scopus 로고
    • Stability of Cyclic β-Hairpins:- Asymmetric Contributions from Side Chains of a Hydrogen-Bonded Cross-Strand Residue Pair
    • Russell, S. J.; Blandl, T.; Skelton, N. J.; Cochran, A. G. Stability of Cyclic β-Hairpins:- Asymmetric Contributions from Side Chains of a Hydrogen-Bonded Cross-Strand Residue Pair J. Am. Chem. Soc. 2003, 125, 388-395
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 388-395
    • Russell, S.J.1    Blandl, T.2    Skelton, N.J.3    Cochran, A.G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.