메뉴 건너뛰기




Volumn 53, Issue 20, 2014, Pages 3336-3346

Quantum mechanics/molecular mechanics studies of the mechanism of falcipain-2 inhibition by the epoxysuccinate E64

Author keywords

[No Author keywords available]

Indexed keywords

DEVELOPING COUNTRIES; MALARIA CONTROL; MOLECULAR DYNAMICS; MOLECULAR MODELING; MOSQUITO CONTROL;

EID: 84901417389     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi500060h     Document Type: Article
Times cited : (21)

References (60)
  • 1
    • 84901423816 scopus 로고    scopus 로고
    • http://www.who.int/malaria/publications/world-malaria-report-2013/report/ en/index.html (2013).
    • (2013)
  • 2
    • 34249981805 scopus 로고    scopus 로고
    • Novel molecular targets for antimalarial chemotherapy
    • Jana, S. and Paliwal, J. (2007) Novel molecular targets for antimalarial chemotherapy Int. J. Antimicrob. Agents 30, 4-10
    • (2007) Int. J. Antimicrob. Agents , vol.30 , pp. 4-10
    • Jana, S.1    Paliwal, J.2
  • 3
    • 33947594387 scopus 로고    scopus 로고
    • Recent advances in antimalarial compounds and their patents
    • Mital, A. (2007) Recent advances in antimalarial compounds and their patents Curr. Med. Chem. 14, 759-773
    • (2007) Curr. Med. Chem. , vol.14 , pp. 759-773
    • Mital, A.1
  • 5
    • 4143139772 scopus 로고    scopus 로고
    • Selection of cysteine protease inhibitor-resistant malaria parasites is accompanied by amplification of falcipain genes and alteration in inhibitor transport
    • Singh, A. and Rosenthal, P. J. (2004) Selection of cysteine protease inhibitor-resistant malaria parasites is accompanied by amplification of falcipain genes and alteration in inhibitor transport J. Biol. Chem. 279, 35236-35241
    • (2004) J. Biol. Chem. , vol.279 , pp. 35236-35241
    • Singh, A.1    Rosenthal, P.J.2
  • 6
    • 0034666133 scopus 로고    scopus 로고
    • Characterization of native and recombinant falcipain-2, a principal trophozoite cysteine protease and essential hemoglobinase of Plasmodium falciparum
    • Shenai, B. R., Sijwali, P. S., Singh, A., and Rosenthal, P. J. (2000) Characterization of native and recombinant falcipain-2, a principal trophozoite cysteine protease and essential hemoglobinase of Plasmodium falciparum J. Biol. Chem. 275, 29000-29010
    • (2000) J. Biol. Chem. , vol.275 , pp. 29000-29010
    • Shenai, B.R.1    Sijwali, P.S.2    Singh, A.3    Rosenthal, P.J.4
  • 7
    • 0035644195 scopus 로고    scopus 로고
    • Expression and characterization of the Plasmodium falciparum haemoglobinase falcipain-3
    • Sijwali, P. S., Shenai, B. R., Gut, J., Singh, A., and Rosenthal, P. J. (2001) Expression and characterization of the Plasmodium falciparum haemoglobinase falcipain-3 Biochem. J. 360, 481-489
    • (2001) Biochem. J. , vol.360 , pp. 481-489
    • Sijwali, P.S.1    Shenai, B.R.2    Gut, J.3    Singh, A.4    Rosenthal, P.J.5
  • 8
    • 84857769803 scopus 로고    scopus 로고
    • Falcipain Inhibition as a Promising Antimalarial Target
    • Marco, M. and Miguel Coteron, J. (2012) Falcipain Inhibition as a Promising Antimalarial Target Curr. Top. Med. Chem. 12, 408-444
    • (2012) Curr. Top. Med. Chem. , vol.12 , pp. 408-444
    • Marco, M.1    Miguel Coteron, J.2
  • 10
    • 79961149911 scopus 로고    scopus 로고
    • Peptidomimetic nitriles as selective inhibitors for the malarial cysteine protease falcipain-2
    • Ehmke, V., Kilchmann, F., Heindl, C., Cui, K., Huang, J., Schirmeister, T., and Diederich, F. (2011) Peptidomimetic nitriles as selective inhibitors for the malarial cysteine protease falcipain-2 MedChemComm 2, 800-804
    • (2011) MedChemComm , vol.2 , pp. 800-804
    • Ehmke, V.1    Kilchmann, F.2    Heindl, C.3    Cui, K.4    Huang, J.5    Schirmeister, T.6    Diederich, F.7
  • 12
    • 84865585931 scopus 로고    scopus 로고
    • Synthesis and Molecular Modeling Studies of Derivatives of a Highly Potent Peptidomimetic Vinyl Ester as Falcipain-2 Inhibitors
    • Ettari, R., Micale, N., Grazioso, G., Bova, F., Schirmeister, T., Grasso, S., and Zappala, M. (2012) Synthesis and Molecular Modeling Studies of Derivatives of a Highly Potent Peptidomimetic Vinyl Ester as Falcipain-2 Inhibitors ChemMedChem 7, 1594-1600
    • (2012) ChemMedChem , vol.7 , pp. 1594-1600
    • Ettari, R.1    Micale, N.2    Grazioso, G.3    Bova, F.4    Schirmeister, T.5    Grasso, S.6    Zappala, M.7
  • 15
    • 35848959471 scopus 로고    scopus 로고
    • Dipeptidyl-α,β-epoxyesters as potent irreversible inhibitors of the cysteine proteases cruzain and rhodesain
    • Gonzalez, F. V., Izquierdo, J., Rodriguez, S., McKerrow, J. H., and Hansell, E. (2007) Dipeptidyl-α,β-epoxyesters as potent irreversible inhibitors of the cysteine proteases cruzain and rhodesain Bioorg. Med. Chem. Lett. 17, 6697-6700
    • (2007) Bioorg. Med. Chem. Lett. , vol.17 , pp. 6697-6700
    • Gonzalez, F.V.1    Izquierdo, J.2    Rodriguez, S.3    McKerrow, J.H.4    Hansell, E.5
  • 16
    • 79960196428 scopus 로고    scopus 로고
    • Structural Basis for the Regulation of Cysteine-Protease Activity by a New Class of Protease Inhibitors in Plasmodium
    • Hansen, G., Heitmann, A., Witt, T., Li, H., Jiang, H., Shen, X., Heussler, V. T., Rennenberg, A., and Hilgenfeld, R. (2011) Structural Basis for the Regulation of Cysteine-Protease Activity by a New Class of Protease Inhibitors in Plasmodium Structure 19, 919-929
    • (2011) Structure , vol.19 , pp. 919-929
    • Hansen, G.1    Heitmann, A.2    Witt, T.3    Li, H.4    Jiang, H.5    Shen, X.6    Heussler, V.T.7    Rennenberg, A.8    Hilgenfeld, R.9
  • 17
    • 61449267734 scopus 로고    scopus 로고
    • Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: Implications for substrate specificity
    • Kerr, I. D., Lee, J. H., Pandey, K. C., Harrison, A., Sajid, M., Rosenthal, P. J., and Brinen, L. S. (2009) Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: Implications for substrate specificity J. Med. Chem. 52, 852-857
    • (2009) J. Med. Chem. , vol.52 , pp. 852-857
    • Kerr, I.D.1    Lee, J.H.2    Pandey, K.C.3    Harrison, A.4    Sajid, M.5    Rosenthal, P.J.6    Brinen, L.S.7
  • 19
    • 0019731722 scopus 로고
    • 2+ on the inhibition of calcium-activated neutral protease by leupeptin, anti-pain and epoxysuccinate derivates
    • 2+ on the inhibition of calcium-activated neutral protease by leupeptin, anti-pain and epoxysuccinate derivates FEBS Lett. 136, 119-122
    • (1981) FEBS Lett. , vol.136 , pp. 119-122
    • Suzuki, K.1    Tsuji, S.2    Ishiura, S.3
  • 22
    • 1542328053 scopus 로고    scopus 로고
    • Design, synthesis, and evaluation of aza-peptide epoxides as selective and potent inhibitors of caspases-1, -3, -6, and-8
    • James, K. E., Asgian, J. L., Li, Z. Z., Ekici, O. D., Rubin, J. R., Mikolajczyk, J., Salvesen, G. S., and Powers, J. C. (2004) Design, synthesis, and evaluation of aza-peptide epoxides as selective and potent inhibitors of caspases-1, -3, -6, and-8 J. Med. Chem. 47, 1553-1574
    • (2004) J. Med. Chem. , vol.47 , pp. 1553-1574
    • James, K.E.1    Asgian, J.L.2    Li, Z.Z.3    Ekici, O.D.4    Rubin, J.R.5    Mikolajczyk, J.6    Salvesen, G.S.7    Powers, J.C.8
  • 23
    • 0032491264 scopus 로고    scopus 로고
    • Design and synthesis of dipeptidyl α',β '-epoxy ketones, potent irreversible inhibitors of the cysteine protease cruzain
    • Roush, W. R., Gonzalez, F. V., McKerrow, J. H., and Hansell, E. (1998) Design and synthesis of dipeptidyl α ',β '-epoxy ketones, potent irreversible inhibitors of the cysteine protease cruzain Bioorg. Med. Chem. Lett. 8, 2809-2812
    • (1998) Bioorg. Med. Chem. Lett. , vol.8 , pp. 2809-2812
    • Roush, W.R.1    Gonzalez, F.V.2    McKerrow, J.H.3    Hansell, E.4
  • 24
    • 0024577165 scopus 로고
    • Mode of bindinf of E64-C, a potent thiol protease inhibitor, to papain as determined by X-ray crystals analysis of the complex
    • Matsumoto, K., Yamamoto, D., Ohishi, H., Tomoo, K., Ishida, T., Inoue, M., Sadatome, T., Kitamura, K., and Mizuno, H. (1989) Mode of bindinf of E64-C, a potent thiol protease inhibitor, to papain as determined by X-ray crystals analysis of the complex FEBS Lett. 245, 177-180
    • (1989) FEBS Lett. , vol.245 , pp. 177-180
    • Matsumoto, K.1    Yamamoto, D.2    Ohishi, H.3    Tomoo, K.4    Ishida, T.5    Inoue, M.6    Sadatome, T.7    Kitamura, K.8    Mizuno, H.9
  • 25
    • 0023950936 scopus 로고
    • Irreversible inhibition of papain by epoxysuccinyl peptides. Carbon-13 NMR characterization of the site of alkylation
    • Yabe, Y., Guillaume, D., and Rich, D. H. (1988) Irreversible inhibition of papain by epoxysuccinyl peptides. Carbon-13 NMR characterization of the site of alkylation J. Am. Chem. Soc. 110, 4043-4044
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 4043-4044
    • Yabe, Y.1    Guillaume, D.2    Rich, D.H.3
  • 26
    • 0036882396 scopus 로고    scopus 로고
    • Irreversible inhibitors of serine, cysteine, and threonine proteases
    • Powers, J. C., Asgian, J. L., Ekici, O. D., and James, K. E. (2002) Irreversible inhibitors of serine, cysteine, and threonine proteases Chem. Rev. 102, 4639-4750
    • (2002) Chem. Rev. , vol.102 , pp. 4639-4750
    • Powers, J.C.1    Asgian, J.L.2    Ekici, O.D.3    James, K.E.4
  • 27
    • 38349070259 scopus 로고    scopus 로고
    • Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria
    • Ghosh, R., Chakraborty, S., Chakrabarti, C., Dattagupta, J. K., and Biswas, S. (2008) Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria FEBS J. 275, 421-434
    • (2008) FEBS J. , vol.275 , pp. 421-434
    • Ghosh, R.1    Chakraborty, S.2    Chakrabarti, C.3    Dattagupta, J.K.4    Biswas, S.5
  • 28
    • 0026463878 scopus 로고
    • Crystal-structure of papain-E64-C complex-binding diversity of E64-C to papain S(2) and S(3) subsites
    • Kim, M. J., Yamamoto, D., Matsumoto, K., Inoue, M., Ishida, T., Mizuno, H., Sumiya, S., and Kitamura, K. (1992) Crystal-structure of papain-E64-C complex-binding diversity of E64-C to papain S(2) and S(3) subsites Biochem. J. 287, 797-803
    • (1992) Biochem. J. , vol.287 , pp. 797-803
    • Kim, M.J.1    Yamamoto, D.2    Matsumoto, K.3    Inoue, M.4    Ishida, T.5    Mizuno, H.6    Sumiya, S.7    Kitamura, K.8
  • 29
    • 0037014129 scopus 로고    scopus 로고
    • Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: Crystal structure of cathepsin B-E64c complex
    • Yamamoto, A., Tomoo, K., Matsugi, K., Hara, T., In, Y., Murata, M., Kitamura, K., and Ishida, T. (2002) Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: Crystal structure of cathepsin B-E64c complex Biochim. Biophys. Acta 1597, 244-251
    • (2002) Biochim. Biophys. Acta , vol.1597 , pp. 244-251
    • Yamamoto, A.1    Tomoo, K.2    Matsugi, K.3    Hara, T.4    In, Y.5    Murata, M.6    Kitamura, K.7    Ishida, T.8
  • 32
    • 46949103330 scopus 로고    scopus 로고
    • Atomistic insights into the inhibition of cysteine proteases: First QM/MM calculations clarifying the regiospecificity and the inhibition potency of epoxide- and aziridine-based inhibitors
    • Mladenovic, M., Junold, K., Fink, R. F., Thiel, W., Schirmeister, T., and Engels, B. (2008) Atomistic insights into the inhibition of cysteine proteases: First QM/MM calculations clarifying the regiospecificity and the inhibition potency of epoxide- and aziridine-based inhibitors J. Phys. Chem. B 112, 5458-5469
    • (2008) J. Phys. Chem. B , vol.112 , pp. 5458-5469
    • Mladenovic, M.1    Junold, K.2    Fink, R.F.3    Thiel, W.4    Schirmeister, T.5    Engels, B.6
  • 33
    • 0000180596 scopus 로고
    • Reactions of α,β-epoxy carbonyl-compounds with methanethiolate-regioselectivity and rate
    • Bihovsky, R. (1992) Reactions of α,β-epoxy carbonyl-compounds with methanethiolate-regioselectivity and rate J. Org. Chem. 57, 1029-1031
    • (1992) J. Org. Chem. , vol.57 , pp. 1029-1031
    • Bihovsky, R.1
  • 36
    • 0029744988 scopus 로고    scopus 로고
    • Mechanistic studies on the inactivation of papain by epoxysuccinyl inhibitors
    • Meara, J. P. and Rich, D. H. (1996) Mechanistic studies on the inactivation of papain by epoxysuccinyl inhibitors J. Med. Chem. 39, 3357-3366
    • (1996) J. Med. Chem. , vol.39 , pp. 3357-3366
    • Meara, J.P.1    Rich, D.H.2
  • 37
    • 0017100947 scopus 로고
    • Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of carbonium-ion reaction lysozyme
    • Warshel, A. and Levitt, M. (1976) Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of carbonium-ion reaction lysozyme J. Mol. Biol. 103, 227-249
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 39
    • 60349127442 scopus 로고    scopus 로고
    • QM/MM Methods for Biomolecular Systems
    • Senn, H. M. and Thiel, W. (2009) QM/MM Methods for Biomolecular Systems Angew. Chem., Int. Ed. 48, 1198-1229
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 1198-1229
    • Senn, H.M.1    Thiel, W.2
  • 40
    • 84876719258 scopus 로고    scopus 로고
    • Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology
    • van der Kamp, M. W. and Mulholland, A. J. (2013) Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology Biochemistry 52, 2708-2728
    • (2013) Biochemistry , vol.52 , pp. 2708-2728
    • Van Der Kamp, M.W.1    Mulholland, A.J.2
  • 42
    • 0000831054 scopus 로고    scopus 로고
    • The Dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
    • Field, M. J., Albe, M., Bret, C., Proust-De Martin, F., and Thomas, A. (2000) The Dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials J. Comput. Chem. 21, 1088-1100
    • (2000) J. Comput. Chem. , vol.21 , pp. 1088-1100
    • Field, M.J.1    Albe, M.2    Bret, C.3    Proust-De Martin, F.4    Thomas, A.5
  • 46
    • 34547625687 scopus 로고    scopus 로고
    • Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms
    • Nam, K., Cui, Q., Gao, J., and York, D. M. (2007) Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms J. Chem. Theory Comput. 3, 486-504
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 486-504
    • Nam, K.1    Cui, Q.2    Gao, J.3    York, D.M.4
  • 47
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W. L., Maxwell, D. S., and TiradoRives, J. (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118, 11225-11236
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tiradorives, J.3
  • 49
    • 84986513644 scopus 로고
    • A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
    • Field, M. J., Bash, P. A., and Karplus, M. (1990) A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations J. Comput. Chem. 11, 700-733
    • (1990) J. Comput. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 50
    • 84988053595 scopus 로고
    • A combined abinitio quantum-mechanical and molecular mechanical method for carryng out simulations on complex molecular-systems: Applications to the CH3CL + CL- Exchange-reaction and gas-phase protonation of polyethers
    • Singh, U. C. and Kollman, P. A. (1986) A combined abinitio quantum-mechanical and molecular mechanical method for carryng out simulations on complex molecular-systems: Applications to the CH3CL + CL- Exchange-reaction and gas-phase protonation of polyethers J. Comput. Chem. 7, 718-730
    • (1986) J. Comput. Chem. , vol.7 , pp. 718-730
    • Singh, U.C.1    Kollman, P.A.2
  • 51
    • 33845926809 scopus 로고    scopus 로고
    • Improving the QM/MM description of chemical processes: A dual level strategy to explore the potential energy surface in very large systems
    • Martí, S., Moliner, V., and Tuñón, I. (2005) Improving the QM/MM description of chemical processes: A dual level strategy to explore the potential energy surface in very large systems J. Chem. Theory Comput. 1, 1008-1016
    • (2005) J. Chem. Theory Comput. , vol.1 , pp. 1008-1016
    • Martí, S.1    Moliner, V.2    Tuñón, I.3
  • 52
    • 84869489010 scopus 로고    scopus 로고
    • Mechanism of falcipain-2 inhibition by α,β-unsaturated benzo 1,4-diazepin-2-one methyl ester
    • Grazioso, G., Legnani, L., Toma, L., Ettari, R., Micale, N., and De Micheli, C. (2012) Mechanism of falcipain-2 inhibition by α,β- unsaturated benzo 1,4-diazepin-2-one methyl ester J. Comput.-Aided Mol. Des. 26, 1035-1043
    • (2012) J. Comput.-Aided Mol. Des. , vol.26 , pp. 1035-1043
    • Grazioso, G.1    Legnani, L.2    Toma, L.3    Ettari, R.4    Micale, N.5    De Micheli, C.6
  • 53
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. 1 the method
    • Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method J. Comput. Chem. 13, 1011-1021
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 54
    • 0342929614 scopus 로고
    • Non-physical sampling distributions in monte-carlo free-energy estimation: Umbrella sampling
    • Torrie, G. M. and Valleau, J. P. (1977) Non-physical sampling distributions in monte-carlo free-energy estimation: Umbrella sampling J. Comput. Phys. 23, 187-199
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 55
  • 56
    • 0000501629 scopus 로고    scopus 로고
    • Mapped interpolation scheme for single-point energy corrections in reaction rate calculations and a critical evaluation of dual-level reaction path dynamics methods
    • Chuang, Y. Y., Corchado, J. C., and Truhlar, D. G. (1999) Mapped interpolation scheme for single-point energy corrections in reaction rate calculations and a critical evaluation of dual-level reaction path dynamics methods J. Phys. Chem. A 103, 1140-1149
    • (1999) J. Phys. Chem. A , vol.103 , pp. 1140-1149
    • Chuang, Y.Y.1    Corchado, J.C.2    Truhlar, D.G.3
  • 57
    • 43049141516 scopus 로고    scopus 로고
    • The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals
    • Zhao, Y. and Truhlar, D. G. (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals Theor. Chem. Acc. 120, 215-241
    • (2008) Theor. Chem. Acc. , vol.120 , pp. 215-241
    • Zhao, Y.1    Truhlar, D.G.2
  • 59
    • 0037422363 scopus 로고    scopus 로고
    • Effectiveness of Diffuse Basis Functions for Calculating Relative Energies by Density Functional Theory
    • Lynch, B. J., Zhao, Y., and Truhlar, D. G. (2003) Effectiveness of Diffuse Basis Functions for Calculating Relative Energies by Density Functional Theory J. Phys. Chem. A 107, 1384-1388
    • (2003) J. Phys. Chem. A , vol.107 , pp. 1384-1388
    • Lynch, B.J.1    Zhao, Y.2    Truhlar, D.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.