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Volumn 64, Issue 17, 2007, Pages 2285-2305

Computational inhibitor design against malaria plasmepsins

Author keywords

Inhibitor design; Linear interaction energy method; Malaria; Molecular dynamics; Plasmepsin; Reaction mechanism

Indexed keywords

PLASMEPSIN I; PLASMEPSIN II;

EID: 34548348687     PISSN: 1420682X     EISSN: 15691632     Source Type: Journal    
DOI: 10.1007/s00018-007-7102-2     Document Type: Review
Times cited : (48)

References (98)
  • 1
    • 15044338866 scopus 로고    scopus 로고
    • The global distribution of clinical episodes of Plasmodium falciparum malaria
    • Snow, R. W., Guerra, C. A., Noor, A. M., Myint, H. Y., and Hay, S. I. (2005) The global distribution of clinical episodes of Plasmodium falciparum malaria. Nature 434, 214-217.
    • (2005) Nature , vol.434 , pp. 214-217
    • Snow, R.W.1    Guerra, C.A.2    Noor, A.M.3    Myint, H.Y.4    Hay, S.I.5
  • 2
    • 16844376016 scopus 로고    scopus 로고
    • Drug therapy: Effectiveness of antimalarial drugs
    • Baird, J. K. (2005) Drug therapy: effectiveness of antimalarial drugs. N. Engl. J. Med. 352, 1565-1577.
    • (2005) N. Engl. J. Med , vol.352 , pp. 1565-1577
    • Baird, J.K.1
  • 3
    • 26844565462 scopus 로고    scopus 로고
    • Malaria vaccines 1985-2005: A full circle?
    • Targett, G. A. (2005) Malaria vaccines 1985-2005: a full circle? Trends Parasitol. 21, 499-503.
    • (2005) Trends Parasitol , vol.21 , pp. 499-503
    • Targett, G.A.1
  • 4
    • 0037033989 scopus 로고    scopus 로고
    • Malaria in 2002
    • Greenwood, B., and Mutabingwa, T. (2002) Malaria in 2002. Nature 415, 670-672.
    • (2002) Nature , vol.415 , pp. 670-672
    • Greenwood, B.1    Mutabingwa, T.2
  • 5
    • 23944525290 scopus 로고    scopus 로고
    • Malaria vaccines evaluation and implementation
    • Greenwood, B. (2005) Malaria vaccines evaluation and implementation. Acta Trop. 95, 298-304.
    • (2005) Acta Trop , vol.95 , pp. 298-304
    • Greenwood, B.1
  • 8
    • 5644228594 scopus 로고    scopus 로고
    • Alonso, P. L., Sacarlal, J., Aponte, J. J., Leach, A., Macete, E., Milman, J., Mandomando, I., Spiessens, B., Guinovart, C., Espasa, M., Bassat, Q., Aide, P., Ofori-Anyinam, O., Navia, M. M., Corachan, S., Ceuppens, M., Dubois, M. C., Demoitie, M. A., Dubovsky, F., Menendez, C., Tornieporth, N., Ballou, W. R., Thompson, R., and Cohen, J. (2004) Efficacy of the RTS,S/ AS02A vaccine against Plasmodium falciparum infection and disease in young African children: randomised controlled trial. Lancet 364, 1411-1420.
    • Alonso, P. L., Sacarlal, J., Aponte, J. J., Leach, A., Macete, E., Milman, J., Mandomando, I., Spiessens, B., Guinovart, C., Espasa, M., Bassat, Q., Aide, P., Ofori-Anyinam, O., Navia, M. M., Corachan, S., Ceuppens, M., Dubois, M. C., Demoitie, M. A., Dubovsky, F., Menendez, C., Tornieporth, N., Ballou, W. R., Thompson, R., and Cohen, J. (2004) Efficacy of the RTS,S/ AS02A vaccine against Plasmodium falciparum infection and disease in young African children: randomised controlled trial. Lancet 364, 1411-1420.
  • 9
    • 28844483001 scopus 로고    scopus 로고
    • Alonso, P. L., Sacarlal, J., Aponte, J. J., Leach, A., Macete, E., Aide, P., Sigauque, B., Milman, J., Mandomando, I., Bassat, Q., Guinovart, C., Espasa, M., Corachan, S., Lievens, M., Navia, M. M., Dubois, M. C., Menendez, C., Dubovsky, F., Cohen, J., Thompson, R., and Ballou, W. R. (2005) Duration of protection with RTS,S/AS02A malaria vaccine in prevention of Plasmodium falciparum disease in Mozambican children: single-blind extended follow-up of a randomised controlled trial. Lancet 366, 2012-2018.
    • Alonso, P. L., Sacarlal, J., Aponte, J. J., Leach, A., Macete, E., Aide, P., Sigauque, B., Milman, J., Mandomando, I., Bassat, Q., Guinovart, C., Espasa, M., Corachan, S., Lievens, M., Navia, M. M., Dubois, M. C., Menendez, C., Dubovsky, F., Cohen, J., Thompson, R., and Ballou, W. R. (2005) Duration of protection with RTS,S/AS02A malaria vaccine in prevention of Plasmodium falciparum disease in Mozambican children: single-blind extended follow-up of a randomised controlled trial. Lancet 366, 2012-2018.
  • 10
    • 33646446147 scopus 로고    scopus 로고
    • Functional characterization and target validation of alternative complex I of Plasmodium falciparum mitochondria
    • Biagini, G. A., Viriyavejakul, P., O'Neill, P. M., Bray, P. G., and Ward, S. A. (2006) Functional characterization and target validation of alternative complex I of Plasmodium falciparum mitochondria. Antimicrob. Agents Chemother. 50, 1841-1851.
    • (2006) Antimicrob. Agents Chemother , vol.50 , pp. 1841-1851
    • Biagini, G.A.1    Viriyavejakul, P.2    O'Neill, P.M.3    Bray, P.G.4    Ward, S.A.5
  • 11
    • 29744444853 scopus 로고    scopus 로고
    • Parasite mitochondria as a target of chemotherapy-inhibitory effect of licochalcone A on the Plasmodium falciparum respiratory chain
    • Kotwal, G. J. and Lahiri, D. K, Eds, pp, New York Academy of Sciences, New York
    • Mi-Ichi, F., Miyadera, H., Kobayashi, T., Takamiya, S., Waki, S., Iwata, S., Shibata, S., and Kita, K. (2005) Parasite mitochondria as a target of chemotherapy-inhibitory effect of licochalcone A on the Plasmodium falciparum respiratory chain. In: Natural Products and Molecular Therapy (Kotwal, G. J. and Lahiri, D. K., Eds.), pp 46-54, New York Academy of Sciences, New York.
    • (2005) Natural Products and Molecular Therapy , pp. 46-54
    • Mi-Ichi, F.1    Miyadera, H.2    Kobayashi, T.3    Takamiya, S.4    Waki, S.5    Iwata, S.6    Shibata, S.7    Kita, K.8
  • 12
    • 21044454794 scopus 로고    scopus 로고
    • Aquaporins from pathogenic protozoan parasites: Structure, function and potential for chemotherapy
    • Beitz, E. (2005) Aquaporins from pathogenic protozoan parasites: structure, function and potential for chemotherapy. Biol. Cell 97, 373-383.
    • (2005) Biol. Cell , vol.97 , pp. 373-383
    • Beitz, E.1
  • 13
    • 19344363970 scopus 로고    scopus 로고
    • Polyamine transport in parasites: A potential target for new antiparasitic drug development. Comp. Biochem. Physiol. C Comp
    • Reguera, R. M., Tekwani, B. L., and Balana-Fouce, R. (2005) Polyamine transport in parasites: a potential target for new antiparasitic drug development. Comp. Biochem. Physiol. C Comp. Pharmacol. Toxicol. 140, 151-164.
    • (2005) Pharmacol. Toxicol , vol.140 , pp. 151-164
    • Reguera, R.M.1    Tekwani, B.L.2    Balana-Fouce, R.3
  • 15
    • 33646447331 scopus 로고    scopus 로고
    • Antimalarial activity of allicin, a biologically active compound from garlic cloves
    • Coppi, A., Cabinian, M., Mirelman, D., and Sinnis, P. (2006) Antimalarial activity of allicin, a biologically active compound from garlic cloves. Antimicrob. Agents Chemother. 50, 1731-1737.
    • (2006) Antimicrob. Agents Chemother , vol.50 , pp. 1731-1737
    • Coppi, A.1    Cabinian, M.2    Mirelman, D.3    Sinnis, P.4
  • 16
    • 32944470879 scopus 로고    scopus 로고
    • Ersmark, K., Nervall, M., Gutierrez-de-Teran, H., Hamelink, E., Janka, L. K., Clemente, J. C., Dunn, B. M., Gogoll, A., Samuelsson, B., Åqvist, J., and Hallberg, A. (2006) Macrocyclic inhibitors of the malarial aspartic proteases plasmepsin I, II, and IV. Bioorg. Med. Chem. 14, 2197-2208.
    • Ersmark, K., Nervall, M., Gutierrez-de-Teran, H., Hamelink, E., Janka, L. K., Clemente, J. C., Dunn, B. M., Gogoll, A., Samuelsson, B., Åqvist, J., and Hallberg, A. (2006) Macrocyclic inhibitors of the malarial aspartic proteases plasmepsin I, II, and IV. Bioorg. Med. Chem. 14, 2197-2208.
  • 18
    • 33646932438 scopus 로고    scopus 로고
    • The A/T-specific DNA alkylating agent adozelesin inhibits Plasmodium falciparum growth in vitro and protects mice against Plasmodium chabaudi adami infection
    • Yanow, S. K., Purcell, L. A., and Spithill, T. W. (2006) The A/T-specific DNA alkylating agent adozelesin inhibits Plasmodium falciparum growth in vitro and protects mice against Plasmodium chabaudi adami infection. Mol. Biochem. Parasitol. 148, 52-59.
    • (2006) Mol. Biochem. Parasitol , vol.148 , pp. 52-59
    • Yanow, S.K.1    Purcell, L.A.2    Spithill, T.W.3
  • 19
    • 0025754304 scopus 로고
    • Hemoglobin degradation in the human malaria pathogen Plasmodium falciparum: A catabolic pathway initiated by a specific aspartic protease
    • Goldberg, D. E., Slater, A. F., Beavis, R., Chait, B., Cerami, A., and Henderson, G. B. (1991) Hemoglobin degradation in the human malaria pathogen Plasmodium falciparum: a catabolic pathway initiated by a specific aspartic protease. J. Exp. Med. 173, 961-9.
    • (1991) J. Exp. Med , vol.173 , pp. 961-969
    • Goldberg, D.E.1    Slater, A.F.2    Beavis, R.3    Chait, B.4    Cerami, A.5    Henderson, G.B.6
  • 20
    • 12544251879 scopus 로고    scopus 로고
    • The role of Plasmodium falciparum food vacuole plasmepsins
    • Liu, J., Gluzman, I. Y., Drew, M. E., and Goldberg, D. E. (2005) The role of Plasmodium falciparum food vacuole plasmepsins. J. Biol. Chem. 280, 1432-1437.
    • (2005) J. Biol. Chem , vol.280 , pp. 1432-1437
    • Liu, J.1    Gluzman, I.Y.2    Drew, M.E.3    Goldberg, D.E.4
  • 21
    • 11144237489 scopus 로고    scopus 로고
    • Genetic disruption of the Plasmodium falciparum digestive vacuole plasmepsins demonstrates their functional redundancy
    • Omara-Opyene, A. L., Moura, P. A., Sulsona, C. R., Bonilla, J. A., Yowell, C. A., Fujioka, H., Fidock, D. A., and Dame, J. B. (2004) Genetic disruption of the Plasmodium falciparum digestive vacuole plasmepsins demonstrates their functional redundancy. J. Biol. Chem. 279, 54088-54096.
    • (2004) J. Biol. Chem , vol.279 , pp. 54088-54096
    • Omara-Opyene, A.L.1    Moura, P.A.2    Sulsona, C.R.3    Bonilla, J.A.4    Yowell, C.A.5    Fujioka, H.6    Fidock, D.A.7    Dame, J.B.8
  • 22
    • 33745041171 scopus 로고    scopus 로고
    • Plasmodium falciparum ensures its amino acid supply with multiple acquisition pathways and redundant proteolytic enzyme systems
    • Liu, J., Istvan, E. S., Gluzman, I. Y., Gross, J., and Goldberg, D. E. (2006) Plasmodium falciparum ensures its amino acid supply with multiple acquisition pathways and redundant proteolytic enzyme systems. Proc. Natl. Acad. Sci. USA. 103, 8840-8845.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 8840-8845
    • Liu, J.1    Istvan, E.S.2    Gluzman, I.Y.3    Gross, J.4    Goldberg, D.E.5
  • 23
    • 0041620630 scopus 로고    scopus 로고
    • C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: Synthesis and theoretical predictions
    • Ersmark, K., Feierberg, I., Bjelic, S., Hulten, J., Samuelsson, B., Åqvist, J., and Hallberg, A. (2003) C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions. Bioorg. Med. Chem. 11, 3723-3733.
    • (2003) Bioorg. Med. Chem , vol.11 , pp. 3723-3733
    • Ersmark, K.1    Feierberg, I.2    Bjelic, S.3    Hulten, J.4    Samuelsson, B.5    Åqvist, J.6    Hallberg, A.7
  • 24
    • 0037133223 scopus 로고    scopus 로고
    • Identification and characterization of allophenylnorstatine-based inhibitors of plasmepsin II, an antimalarial target
    • Nezami, A., Luque, I., Kimura, T., Kiso, Y., and Freire, E. (2002) Identification and characterization of allophenylnorstatine-based inhibitors of plasmepsin II, an antimalarial target. Biochemistry 41, 2273-2280.
    • (2002) Biochemistry , vol.41 , pp. 2273-2280
    • Nezami, A.1    Luque, I.2    Kimura, T.3    Kiso, Y.4    Freire, E.5
  • 25
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
    • Gohlke, H., and Klebe, G. (2002) Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem. Int. Ed. 41, 2645-2676.
    • (2002) Angew. Chem. Int. Ed , vol.41 , pp. 2645-2676
    • Gohlke, H.1    Klebe, G.2
  • 26
    • 1642357706 scopus 로고    scopus 로고
    • Themany roles of computation in drug discovery
    • Jorgensen, W. L. (2004) Themany roles of computation in drug discovery. Science 303, 1813-1818.
    • (2004) Science , vol.303 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 27
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., and Olson, A. J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19, 1639-1662.
    • (1998) J. Comput. Chem , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 28
    • 6244283606 scopus 로고    scopus 로고
    • Critical evaluation of search algorithms for automated molecular docking and database screening
    • Ewing, T. J. A., and Kuntz, I. D. (1997) Critical evaluation of search algorithms for automated molecular docking and database screening. J. Comput. Chem. 18, 1175-1189.
    • (1997) J. Comput. Chem , vol.18 , pp. 1175-1189
    • Ewing, T.J.A.1    Kuntz, I.D.2
  • 29
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M., Kramer, B., Lengauer, T., and Klebe, G. (1996) A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261, 470-489.
    • (1996) J. Mol. Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 31
    • 1642310340 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    • Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., and Banks, J. L. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 47, 1750-1759.
    • (2004) J. Med. Chem , vol.47 , pp. 1750-1759
    • Halgren, T.A.1    Murphy, R.B.2    Friesner, R.A.3    Beard, H.S.4    Frye, L.L.5    Pollard, W.T.6    Banks, J.L.7
  • 32
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G., Willett, P., Glen, R. C., Leach, A. R., and Taylor, R. (1997) Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267, 727-748.
    • (1997) J. Mol. Biol , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 34
    • 10044294023 scopus 로고    scopus 로고
    • An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
    • Wang, R. X., Lu, Y. P., Fang, X. L., and Wang, S. M. (2004) An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci. 44, 2114-2125.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 2114-2125
    • Wang, R.X.1    Lu, Y.P.2    Fang, X.L.3    Wang, S.M.4
  • 35
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge, M. D., Murray, C. W., Auton, T. R., Paolini, G. V., and Mee, R. P. (1997) Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput. Aided Mol. Des. 11, 425-445.
    • (1997) J. Comput. Aided Mol. Des , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 36
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang, R. X., Lai, L. H., and Wang, S. M. (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput. Aided Mol. Des. 16, 11-26.
    • (2002) J. Comput. Aided Mol. Des , vol.16 , pp. 11-26
    • Wang, R.X.1    Lai, L.H.2    Wang, S.M.3
  • 37
    • 26444588137 scopus 로고    scopus 로고
    • DrugScore(CSD)- knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
    • Velec, H. F. G., Gohlke, H., and Klebe, G. (2005) DrugScore(CSD)- knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J. Med. Chem. 48, 6296-6303.
    • (2005) J. Med. Chem , vol.48 , pp. 6296-6303
    • Velec, H.F.G.1    Gohlke, H.2    Klebe, G.3
  • 39
    • 0035957732 scopus 로고    scopus 로고
    • Mechanisms of tetraethylammonium ion block in the KcsA potassium channel
    • Luzhkov, V. B., and Åqvist, J. (2001) Mechanisms of tetraethylammonium ion block in the KcsA potassium channel. FEBS Lett. 495, 191-6.
    • (2001) FEBS Lett , vol.495 , pp. 191-196
    • Luzhkov, V.B.1    Åqvist, J.2
  • 40
    • 0028155689 scopus 로고
    • New method for predicting binding affinity in computer-aided drug design
    • Åqvist, J., Medina, C., and Samuelsson, J. E. (1994) New method for predicting binding affinity in computer-aided drug design. Protein Eng. 7, 385-391.
    • (1994) Protein Eng , vol.7 , pp. 385-391
    • Åqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 41
    • 0035665229 scopus 로고    scopus 로고
    • The linear interaction energy method for predicting ligand binding free energies
    • Åqvist, J., and Marelius, J. (2001) The linear interaction energy method for predicting ligand binding free energies. Comb. Chem. High Throughput Screen. 4, 613-626.
    • (2001) Comb. Chem. High Throughput Screen , vol.4 , pp. 613-626
    • Åqvist, J.1    Marelius, J.2
  • 42
    • 0036280661 scopus 로고    scopus 로고
    • Ligand binding affinities from MD simulations
    • Åqvist, J., Luzhkov, V. B., and Brandsdal, B. O. (2002) Ligand binding affinities from MD simulations. Acc. Chem. Res. 35, 358-365.
    • (2002) Acc. Chem. Res , vol.35 , pp. 358-365
    • Åqvist, J.1    Luzhkov, V.B.2    Brandsdal, B.O.3
  • 43
    • 7444257387 scopus 로고    scopus 로고
    • Efficient evaluation of binding free energy using continuum electrostatics solvation
    • Huang, D., and Caflisch, A. (2004) Efficient evaluation of binding free energy using continuum electrostatics solvation. J. Med. Chem. 47, 5791-5797.
    • (2004) J. Med. Chem , vol.47 , pp. 5791-5797
    • Huang, D.1    Caflisch, A.2
  • 44
    • 2342636434 scopus 로고    scopus 로고
    • General model for estimation of the inhibition of protein kinases using Monte Carlo simulations
    • Tominaga, Y., and Jorgensen, W. L. (2004) General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. J. Med. Chem. 47, 2534-2549.
    • (2004) J. Med. Chem , vol.47 , pp. 2534-2549
    • Tominaga, Y.1    Jorgensen, W.L.2
  • 45
    • 0035950792 scopus 로고    scopus 로고
    • New linear interaction method for binding affinity calculations using a continuumsolvent model
    • Zhou, R. H., Friesner, R. A., Ghosh, A., Rizzo, R. C., Jorgensen, W. L., and Levy, R. M. (2001) New linear interaction method for binding affinity calculations using a continuumsolvent model. J. Phys. Chem. B 105, 10388-10397.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 10388-10397
    • Zhou, R.H.1    Friesner, R.A.2    Ghosh, A.3    Rizzo, R.C.4    Jorgensen, W.L.5    Levy, R.M.6
  • 46
    • 1942539324 scopus 로고    scopus 로고
    • Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics: Application to HIV-1 protease inhibitors
    • Zoete, V., Michielin, O., and Karplus, M. (2003) Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics: application to HIV-1 protease inhibitors. J. Comput. Aided Mol. Des. 17, 861-880.
    • (2003) J. Comput. Aided Mol. Des , vol.17 , pp. 861-880
    • Zoete, V.1    Michielin, O.2    Karplus, M.3
  • 47
    • 0026596911 scopus 로고
    • Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603
    • Lee, F. S., Chu, Z. T., Bolger, M. B., and Warshel, A. (1992) Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Eng. 5, 215-228.
    • (1992) Protein Eng , vol.5 , pp. 215-228
    • Lee, F.S.1    Chu, Z.T.2    Bolger, M.B.3    Warshel, A.4
  • 48
    • 0342321950 scopus 로고    scopus 로고
    • Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA and PDLD/S-LRA calculations of ligands binding to an HIV protease
    • Sham, Y., Chu, Z. T., Tao, H., and Warshel, A. (2000) Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins 39, 393-407.
    • (2000) Proteins , vol.39 , pp. 393-407
    • Sham, Y.1    Chu, Z.T.2    Tao, H.3    Warshel, A.4
  • 50
    • 33751344549 scopus 로고    scopus 로고
    • Calculations of solute and solvent entropies from molecular dynamics simulations
    • Carlsson, J., and Åqvist, J. (2006) Calculations of solute and solvent entropies from molecular dynamics simulations. Phys. Chem. Chem. Phys. 8, 5385-5395.
    • (2006) Phys. Chem. Chem. Phys , vol.8 , pp. 5385-5395
    • Carlsson, J.1    Åqvist, J.2
  • 53
    • 33747177314 scopus 로고    scopus 로고
    • Plasmepsins as potential targets for new antimalarial therapy
    • Ersmark, K., Samuelsson, B., and Hallberg, A. (2006) Plasmepsins as potential targets for new antimalarial therapy. Med. Res. Rev. 26, 626-666.
    • (2006) Med. Res. Rev , vol.26 , pp. 626-666
    • Ersmark, K.1    Samuelsson, B.2    Hallberg, A.3
  • 55
    • 33750087338 scopus 로고    scopus 로고
    • Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor
    • Gutiérrez-de-Terán, H., Nervall, M., Dunn, B. M., Clemente, J. C., and Áqvist, J. (2006) Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor. FEBS Lett. 580, 5910-5916.
    • (2006) FEBS Lett , vol.580 , pp. 5910-5916
    • Gutiérrez-de-Terán, H.1    Nervall, M.2    Dunn, B.M.3    Clemente, J.C.4    Áqvist, J.5
  • 57
    • 2142647173 scopus 로고    scopus 로고
    • Design, synthesis, and computational affinity prediction of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii
    • Graffner-Nordberg, M., Kolmodin, K., Åqvist, J., Queener, S. F., and Hallberg, A. (2004) Design, synthesis, and computational affinity prediction of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii. Eur. J. Pharm. Sci. 22, 43-54.
    • (2004) Eur. J. Pharm. Sci , vol.22 , pp. 43-54
    • Graffner-Nordberg, M.1    Kolmodin, K.2    Åqvist, J.3    Queener, S.F.4    Hallberg, A.5
  • 58
    • 0035913056 scopus 로고    scopus 로고
    • Design, synthesis, computational prediction, and biological evaluation of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii
    • Graffner-Nordberg, M., Kolmodin, K., Åqvist, J., Queener, S. F., and Hallberg, A. (2001) Design, synthesis, computational prediction, and biological evaluation of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii. J. Med. Chem. 44, 2391-402.
    • (2001) J. Med. Chem , vol.44 , pp. 2391-2402
    • Graffner-Nordberg, M.1    Kolmodin, K.2    Åqvist, J.3    Queener, S.F.4    Hallberg, A.5
  • 60
    • 0032014129 scopus 로고    scopus 로고
    • Marelius, J., Graffner-Nordberg, M., Hansson, T., Hallberg, A., and Åqvist, J. (1998) Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases. J. Comput. Aided Drug Des. 12, 119-31.
    • Marelius, J., Graffner-Nordberg, M., Hansson, T., Hallberg, A., and Åqvist, J. (1998) Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases. J. Comput. Aided Drug Des. 12, 119-31.
  • 61
    • 0035905853 scopus 로고    scopus 로고
    • Estimation of binding affinities for HEPT and nevirapine analogues with HTV-1 reverse transcriptase via Monte Carlo simulations
    • Rizzo, R. C., Tirado-Rives, J., and Jorgensen, W. L. (2001) Estimation of binding affinities for HEPT and nevirapine analogues with HTV-1 reverse transcriptase via Monte Carlo simulations. J. Med. Chem. 44, 145-154.
    • (2001) J. Med. Chem , vol.44 , pp. 145-154
    • Rizzo, R.C.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 63
    • 0034722975 scopus 로고    scopus 로고
    • Validation of a model for the complex of HIV-1 reverse transcriptase with sustiva through computation of resistance profiles
    • Rizzo, R. C., Wang, D. P., Tirado-Rives, J., and Jorgensen, W. L. (2000) Validation of a model for the complex of HIV-1 reverse transcriptase with sustiva through computation of resistance profiles. J. Am. Chem. Soc. 122, 12898-12900.
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 12898-12900
    • Rizzo, R.C.1    Wang, D.P.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 64
    • 20644437755 scopus 로고    scopus 로고
    • Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method
    • Smith, R. H., Jorgensen, W. L., Tirado-Rives, J., Lamb, M. L., Janssen, P. A. J., Michejda, C. J., and Smith, M. B. K. (1998) Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method. J. Med. Chem. 41, 5272-5286.
    • (1998) J. Med. Chem , vol.41 , pp. 5272-5286
    • Smith, R.H.1    Jorgensen, W.L.2    Tirado-Rives, J.3    Lamb, M.L.4    Janssen, P.A.J.5    Michejda, C.J.6    Smith, M.B.K.7
  • 66
    • 0037187412 scopus 로고    scopus 로고
    • Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: Insight into structure-based ligand design
    • Huo, S., Wang, J., Cieplak, P., Kollman, P. A., and Kuntz, I. D. (2002) Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J. Med. Chem. 45, 1412-1419.
    • (2002) J. Med. Chem , vol.45 , pp. 1412-1419
    • Huo, S.1    Wang, J.2    Cieplak, P.3    Kollman, P.A.4    Kuntz, I.D.5
  • 67
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
    • Srinivasan, J., Cheatham, T. E., Cieplak, P., Kollman, P. A., and Case, D. A. (1998) Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120, 9401-9409.
    • (1998) J. Am. Chem. Soc , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 68
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
    • Kuhn, B., and Kollman, P. A. (2000) Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J. Med. Chem. 43, 3786-3791.
    • (2000) J. Med. Chem , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 70
    • 8744303696 scopus 로고    scopus 로고
    • Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site
    • Bjelic, S., and Åqvist, J. (2004) Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site. Biochemistry 43, 14521-14528.
    • (2004) Biochemistry , vol.43 , pp. 14521-14528
    • Bjelic, S.1    Åqvist, J.2
  • 71
    • 33746869326 scopus 로고    scopus 로고
    • Catalysis and linear free energy relationships in aspartic proteases
    • Bjelic, S., and Åqvist, J. (2006) Catalysis and linear free energy relationships in aspartic proteases. Biochemistry 45, 7709-7723.
    • (2006) Biochemistry , vol.45 , pp. 7709-7723
    • Bjelic, S.1    Åqvist, J.2
  • 72
    • 0035521154 scopus 로고    scopus 로고
    • Aspartic proteases of Plasmodium falciparum and other parasitic protozoa as drug targets
    • Coombs, G. H., Goldberg, D. E., Klemba, M., Berry, C., Kay, J., and Mottram, J. C. (2001) Aspartic proteases of Plasmodium falciparum and other parasitic protozoa as drug targets. Trends Parasitol. 17, 532-537.
    • (2001) Trends Parasitol , vol.17 , pp. 532-537
    • Coombs, G.H.1    Goldberg, D.E.2    Klemba, M.3    Berry, C.4    Kay, J.5    Mottram, J.C.6
  • 73
    • 0037154180 scopus 로고    scopus 로고
    • Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidine
    • Banerjee, R., Liu, J., Beatty, W., Pelosof, L., Klemba, M., and Goldberg, D. E. (2002) Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidine. Proc. Natl. Acad. Sci. USA. 99, 990-995.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 990-995
    • Banerjee, R.1    Liu, J.2    Beatty, W.3    Pelosof, L.4    Klemba, M.5    Goldberg, D.E.6
  • 74
    • 0036882390 scopus 로고    scopus 로고
    • Structure and mechanism of the pepsin-like family of aspartic peptidases
    • Dunn, B. M. (2002) Structure and mechanism of the pepsin-like family of aspartic peptidases. Chem. Rev. 102, 4431-4458.
    • (2002) Chem. Rev , vol.102 , pp. 4431-4458
    • Dunn, B.M.1
  • 75
    • 0038184354 scopus 로고    scopus 로고
    • HIV-1 protease: Mechanism and drug discovery
    • Brik, A., and Wong, C. H. (2003) HIV-1 protease: mechanism and drug discovery. Org. Biomol. Chem. 1, 5-14.
    • (2003) Org. Biomol. Chem , vol.1 , pp. 5-14
    • Brik, A.1    Wong, C.H.2
  • 77
    • 0035940264 scopus 로고    scopus 로고
    • Energetics and dynamics of enzymatic reactions
    • Villa, J., and Warshel, A. (2001) Energetics and dynamics of enzymatic reactions. J. Phys. Chem. B 105, 7887-7907.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 7887-7907
    • Villa, J.1    Warshel, A.2
  • 78
    • 4243810035 scopus 로고
    • Simulation of enzymereactions using valence-bond force-fields and other hybrid quantum-classical approaches
    • Åqvist, J., and Warshel, A. (1993) Simulation of enzymereactions using valence-bond force-fields and other hybrid quantum-classical approaches. Chem. Rev. 93, 2523-2544.
    • (1993) Chem. Rev , vol.93 , pp. 2523-2544
    • Åqvist, J.1    Warshel, A.2
  • 79
    • 21244497608 scopus 로고    scopus 로고
    • Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
    • Friesner, R. A., and Guallar, V. (2005) Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annu. Rev. Phys. Chem. 56, 389-427.
    • (2005) Annu. Rev. Phys. Chem , vol.56 , pp. 389-427
    • Friesner, R.A.1    Guallar, V.2
  • 80
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C. (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31, 3381-3385.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 81
    • 0038324472 scopus 로고    scopus 로고
    • Inhibitors of the Plasmodium falciparum parasite aspartic protease plasmepsin II as potential antimalarial agents
    • Boss, C., Richard-Bildstein, S., Weller, T., Fischli, W., Meyer, S., and Binkert, C. (2003) Inhibitors of the Plasmodium falciparum parasite aspartic protease plasmepsin II as potential antimalarial agents. Curr. Med. Chem. 10, 883-907.
    • (2003) Curr. Med. Chem , vol.10 , pp. 883-907
    • Boss, C.1    Richard-Bildstein, S.2    Weller, T.3    Fischli, W.4    Meyer, S.5    Binkert, C.6
  • 82
    • 21244486379 scopus 로고    scopus 로고
    • X-ray structure of plasmepsin II complexed with a potent achiral inhibitor
    • Prade, L., Jones, A. F., Boss, C., Bildstein, S. R., Meyer, S., Binkert, C., and Bur, D. (2005) X-ray structure of plasmepsin II complexed with a potent achiral inhibitor. J. Biol. Chem. 280, 23837-23843.
    • (2005) J. Biol. Chem , vol.280 , pp. 23837-23843
    • Prade, L.1    Jones, A.F.2    Boss, C.3    Bildstein, S.R.4    Meyer, S.5    Binkert, C.6    Bur, D.7
  • 83
    • 33746276423 scopus 로고    scopus 로고
    • Hof, F., Schutz, A., Fah, C., Meyer, S., Bur, D., Liu, J., Goldberg, D. E., and Diederich, F. (2006) Starving the malaria parasite: inhibitors active against the aspartic proteases plasmepsins I, II, and IV. Angew. Chem. Int. Ed. 45, 2138-2141.
    • Hof, F., Schutz, A., Fah, C., Meyer, S., Bur, D., Liu, J., Goldberg, D. E., and Diederich, F. (2006) Starving the malaria parasite: inhibitors active against the aspartic proteases plasmepsins I, II, and IV. Angew. Chem. Int. Ed. 45, 2138-2141.
  • 86
    • 0037436389 scopus 로고    scopus 로고
    • Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum
    • Asojo, O. A., Gulnik, S. V., Afonina, E., Yu, B., Ellman, J. A., Haque, T. S., and Silva, A. M. (2003) Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum. J. Mol. Biol. 327, 173-181.
    • (2003) J. Mol. Biol , vol.327 , pp. 173-181
    • Asojo, O.A.1    Gulnik, S.V.2    Afonina, E.3    Yu, B.4    Ellman, J.A.5    Haque, T.S.6    Silva, A.M.7
  • 87
    • 0032924352 scopus 로고    scopus 로고
    • Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from Plasmodium falciparum
    • Bernstein, N. K., Cherney, M. M., Loetscher, H., Ridley, R. G., and James, M. N. G. (1999) Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from Plasmodium falciparum. Nat. Struct. Biol. 6, 32-37.
    • (1999) Nat. Struct. Biol , vol.6 , pp. 32-37
    • Bernstein, N.K.1    Cherney, M.M.2    Loetscher, H.3    Ridley, R.G.4    James, M.N.G.5
  • 91
    • 0037780064 scopus 로고    scopus 로고
    • High-affinity inhibition of a family of Plasmodium falciparum proteases by a designed adaptive inhibitor
    • Nezami, A., Kimura, T., Hidaka, K., Kiso, A., Liu, J., Kiso, Y., Goldberg, D. E., and Freire, E. (2003) High-affinity inhibition of a family of Plasmodium falciparum proteases by a designed adaptive inhibitor. Biochemistry 42, 8459-8464.
    • (2003) Biochemistry , vol.42 , pp. 8459-8464
    • Nezami, A.1    Kimura, T.2    Hidaka, K.3    Kiso, A.4    Liu, J.5    Kiso, Y.6    Goldberg, D.E.7    Freire, E.8
  • 92
    • 0031282557 scopus 로고    scopus 로고
    • Plasmodium falciparum, P. vivax, and P. malariae: A comparison of the active site properties of plasmepsins cloned and expressed from three different species of the malaria parasite
    • Westling, J., Yowell, C. A., Majer, P., Erickson, J. W., Dame, J. B., and Dunn, B. M. (1997) Plasmodium falciparum, P. vivax, and P. malariae: a comparison of the active site properties of plasmepsins cloned and expressed from three different species of the malaria parasite. Exp. Parasitol. 87, 185-193.
    • (1997) Exp. Parasitol , vol.87 , pp. 185-193
    • Westling, J.1    Yowell, C.A.2    Majer, P.3    Erickson, J.W.4    Dame, J.B.5    Dunn, B.M.6
  • 95
    • 0002496235 scopus 로고    scopus 로고
    • Calculation of ligand binding free energies from molecular dynamics simulations
    • Marelius, J., Hansson, T., and Åqvist, J. (1998) Calculation of ligand binding free energies from molecular dynamics simulations. Int. J. Quantum Chem. 69, 77-88.
    • (1998) Int. J. Quantum Chem , vol.69 , pp. 77-88
    • Marelius, J.1    Hansson, T.2    Åqvist, J.3
  • 96
    • 0030134110 scopus 로고    scopus 로고
    • On the validity of electrostatic linear response in polar solvents
    • Åqvist, J., and Hansson, T. (1996) On the validity of electrostatic linear response in polar solvents. J. Phys. Chem. 100, 9512-9521.
    • (1996) J. Phys. Chem , vol.100 , pp. 9512-9521
    • Åqvist, J.1    Hansson, T.2
  • 98
    • 8644243887 scopus 로고    scopus 로고
    • Search for substrate-based inhibitors fitting the S-2′ space of malarial aspartic protease plasmepsin II
    • Kiso, A., Hidaka, K., Kimura, T., Hayashi, Y., Nezami, A., Freire, E., and Kiso, Y. (2004) Search for substrate-based inhibitors fitting the S-2′ space of malarial aspartic protease plasmepsin II. J. Pept. Sci. 10, 641-647.
    • (2004) J. Pept. Sci , vol.10 , pp. 641-647
    • Kiso, A.1    Hidaka, K.2    Kimura, T.3    Hayashi, Y.4    Nezami, A.5    Freire, E.6    Kiso, Y.7


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