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Volumn 35, Issue 4, 2009, Pages 311-324

Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs)

Author keywords

ArgusLab 4.0; AScore; Influenza virus neuraminidase; Inhibitors

Indexed keywords

ARGUSLAB 4.0; ASCORE; BINDING AFFINITIES; BINDING MODES; INFLUENZA VIRUS; INFLUENZA VIRUS NEURAMINIDASE; INHIBITORS; PROTEIN STRUCTURES; STRUCTURE-BASED;

EID: 68149157302     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020802430752     Document Type: Article
Times cited : (29)

References (44)
  • 1
    • 0001387044 scopus 로고    scopus 로고
    • D.B.N. Fields, M. Knipe, and P. Howley, eds, Lippincott-Raven, Philadelphia
    • B.R. Murphy and R.G. Webster, in Fields Virology, D.B.N. Fields, M. Knipe, and P. Howley, eds., Lippincott-Raven, Philadelphia, 1996, pp. 1397-1445.
    • (1996) Fields Virology , pp. 1397-1445
    • Murphy, B.R.1    Webster, R.G.2
  • 2
    • 0019119577 scopus 로고
    • A Revision of the system of nomenclature for influenza viruses: A WHO memorandum
    • World Health Organization
    • World Health Organization, A Revision of the system of nomenclature for influenza viruses: a WHO memorandum, Bull. World Health Organ. 58 (1980), pp. 585-591.
    • (1980) Bull. World Health Organ , vol.58 , pp. 585-591
  • 3
    • 0028013177 scopus 로고
    • Improved sensitivity of profile searches through the use of sequence weights and gap excision
    • J.D. Thompson, D.G. Higgins, and T.J. Gibson, Improved sensitivity of profile searches through the use of sequence weights and gap excision, Comput. Appl. Biosci. 10 (1994), pp. 19-29.
    • (1994) Comput. Appl. Biosci , vol.10 , pp. 19-29
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 5
    • 25644439259 scopus 로고    scopus 로고
    • Global influenza program surveillance network. Evolution of H5N1 avian influenza viruses in Asia
    • World Health Organization
    • World Health Organization, Global influenza program surveillance network. Evolution of H5N1 avian influenza viruses in Asia, Emerg. Infect. Dis. 11 (2005), pp. 1515-1521.
    • (2005) Emerg. Infect. Dis , vol.11 , pp. 1515-1521
  • 6
    • 0031048319 scopus 로고    scopus 로고
    • Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: Design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity
    • C. Kim, W. Lew, M. Williams, H. Liu, L. Zhang, S. Swaminathan, N. Bischofberger, M. Chen, D. Mendel, and C. Tai, et al., Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity, J. Am. Chem. Soc. 119 (1997), pp. 681-690.
    • (1997) J. Am. Chem. Soc , vol.119 , pp. 681-690
    • Kim, C.1    Lew, W.2    Williams, M.3    Liu, H.4    Zhang, L.5    Swaminathan, S.6    Bischofberger, N.7    Chen, M.8    Mendel, D.9    Tai, C.10
  • 8
    • 33847038372 scopus 로고    scopus 로고
    • Susceptibility of highly pathogenic A (H5N1) avian influenza viruses to the neuraminidase inhibitors and adamantanes
    • A.C. Hurt, P. Selleck, N. Komadina, R. Shaw, L. Brown, and I.G. Barr, Susceptibility of highly pathogenic A (H5N1) avian influenza viruses to the neuraminidase inhibitors and adamantanes, Antiviral Res. 73 (2007), pp. 228-231.
    • (2007) Antiviral Res , vol.73 , pp. 228-231
    • Hurt, A.C.1    Selleck, P.2    Komadina, N.3    Shaw, R.4    Brown, L.5    Barr, I.G.6
  • 9
    • 33947274552 scopus 로고    scopus 로고
    • Characterization of drug-resistant recombinant influenza A/H1N1 viruses selected in vitro with peramivir and zanamivir
    • M. Baz, Y. Abed, and G. Boivin, Characterization of drug-resistant recombinant influenza A/H1N1 viruses selected in vitro with peramivir and zanamivir, Antiviral Res. 74 (2007), pp. 159-162.
    • (2007) Antiviral Res , vol.74 , pp. 159-162
    • Baz, M.1    Abed, Y.2    Boivin, G.3
  • 10
    • 33847648935 scopus 로고    scopus 로고
    • Can immunity induced by the human influenza virus N1 neuraminidase provide some protection from avian influenza H5N1 viruses? PLOS
    • L. Gillim-Ross and K. Subbarao, Can immunity induced by the human influenza virus N1 neuraminidase provide some protection from avian influenza H5N1 viruses? PLOS Medicine 4 (2007), pp. 226-228.
    • (2007) Medicine , vol.4 , pp. 226-228
    • Gillim-Ross, L.1    Subbarao, K.2
  • 13
    • 0025895628 scopus 로고
    • Three-dimensional structure of the neuraminidase of influenza virus A/Tokyo/3/67 at 22 Å resolution
    • J.N. Varghese and P.M. Colman, Three-dimensional structure of the neuraminidase of influenza virus A/Tokyo/3/67 at 22 Å resolution, J. Mol. Biol. 221 (1991), pp. 473-486.
    • (1991) J. Mol. Biol , vol.221 , pp. 473-486
    • Varghese, J.N.1    Colman, P.M.2
  • 14
    • 0020629047 scopus 로고
    • Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution
    • J.N. Varghese, W.G. Laver, and P.M. Colman, Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution, Nature 303 (1983), pp. 35-40.
    • (1983) Nature , vol.303 , pp. 35-40
    • Varghese, J.N.1    Laver, W.G.2    Colman, P.M.3
  • 15
    • 0029099621 scopus 로고
    • Structure-based inhibitors of influenza virus sialidase. A benzoic acid lead with novel interaction
    • S. Singh, M.J. Jedrzejas, G.M. Air, M. Luo, W.G. Laver, and W.J. Brouillette, Structure-based inhibitors of influenza virus sialidase. A benzoic acid lead with novel interaction, J. Med. Chem. 38 (1995), pp. 3217-3225.
    • (1995) J. Med. Chem , vol.38 , pp. 3217-3225
    • Singh, S.1    Jedrzejas, M.J.2    Air, G.M.3    Luo, M.4    Laver, W.G.5    Brouillette, W.J.6
  • 16
    • 0028925854 scopus 로고
    • A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies
    • C.L. White, M.N. Janakiraman, W.G. Laver, C. Philippon, A. Vasella, G.M. Air, and M. Luo, A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies, J. Mol. Biol. 245 (1995), pp. 623-634.
    • (1995) J. Mol. Biol , vol.245 , pp. 623-634
    • White, C.L.1    Janakiraman, M.N.2    Laver, W.G.3    Philippon, C.4    Vasella, A.5    Air, G.M.6    Luo, M.7
  • 19
    • 34250335685 scopus 로고    scopus 로고
    • Structural information and computational methods used in design of neuraminidase inhibitors, Curr. Comput
    • C. Sangma and S. Hannongbua, Structural information and computational methods used in design of neuraminidase inhibitors, Curr. Comput. Aided Drug Design 3 (2007), pp. 113-132.
    • (2007) Aided Drug Design , vol.3 , pp. 113-132
    • Sangma, C.1    Hannongbua, S.2
  • 20
    • 34548134462 scopus 로고    scopus 로고
    • A computational H5N1 neuraminidase model and its binding to commercial drugs
    • P. Nimmanpipug, J. Jitonnom, C. Ngaojampa, S. Hannongbua, and V.S. Lee, A computational H5N1 neuraminidase model and its binding to commercial drugs, Mol. Simul. 33 (2007), pp. 487-493.
    • (2007) Mol. Simul , vol.33 , pp. 487-493
    • Nimmanpipug, P.1    Jitonnom, J.2    Ngaojampa, C.3    Hannongbua, S.4    Lee, V.S.5
  • 21
    • 33646160618 scopus 로고    scopus 로고
    • Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands
    • D-Q. Wei, Q-S. Du, H. Sun, and K-C. Chou, Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands, Biochem. Biophys. Res. Commun. 344 (2006), pp. 1048-1055.
    • (2006) Biochem. Biophys. Res. Commun , vol.344 , pp. 1048-1055
    • Wei, D.-Q.1    Du, Q.-S.2    Sun, H.3    Chou, K.-C.4
  • 23
    • 0033376021 scopus 로고    scopus 로고
    • I. Muegge, The effects of small changes in protein structure on predicted binding modes of known inhibitors of influenza virus neuraminidase: PMF-Scoring in DOCK4, Med. Chem. Res. 9 (1999, pp. 490-500; (b) A.M. Abu Hammada, F.U. Afifia, and M.O. Taha, Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions, J. Mol. Graph. Model. 26 (2007, pp. 443-456; (c) L. Birch, C.W. Murray, M.J. Hartshorn, I.J. Tickle, and M.L. Verdonk, Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase, J. Comput. Aided Mol. Design 16 (2002, pp. 855-869; (d) C.W. Murray, C.A. Baxter, and A.D. Frenkel, The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase, J. Comput. Aided Mol. Design 13 (1999, pp. 547-562; (e) M.R. Landon, R.E. Amaro, R. Baron, C.H. Ngan, D.Ozonoff, J.A. McCammon, and S. Vajda, Novel druggable hot
    • (a) I. Muegge, The effects of small changes in protein structure on predicted binding modes of known inhibitors of influenza virus neuraminidase: PMF-Scoring in DOCK4, Med. Chem. Res. 9 (1999), pp. 490-500; (b) A.M. Abu Hammada, F.U. Afifia, and M.O. Taha, Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions, J. Mol. Graph. Model. 26 (2007), pp. 443-456; (c) L. Birch, C.W. Murray, M.J. Hartshorn, I.J. Tickle, and M.L. Verdonk, Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase, J. Comput. Aided Mol. Design 16 (2002), pp. 855-869; (d) C.W. Murray, C.A. Baxter, and A.D. Frenkel, The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase, J. Comput. Aided Mol. Design 13 (1999), pp. 547-562; (e) M.R. Landon, R.E. Amaro, R. Baron, C.H. Ngan, D.Ozonoff, J.A. McCammon, and S. Vajda, Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble, Chem. Biol. Drug. Des. 71 (2008) pp. 106-116.
  • 24
    • 0038209544 scopus 로고    scopus 로고
    • Pyrrolidinobenzoic acid inhibitors of influenza virus neuraminidase: Modifications of essential pyrrolidinone ring substituents
    • W.J. Brouillette, S. Bajpai, S. Ali, S. Velu, V. Atigadda, B. Lommer, J. Finley, M. Luo, and G. Air, Pyrrolidinobenzoic acid inhibitors of influenza virus neuraminidase: modifications of essential pyrrolidinone ring substituents, Bioorg. Med. Chem. 11 (2003), pp. 2739-2749.
    • (2003) Bioorg. Med. Chem , vol.11 , pp. 2739-2749
    • Brouillette, W.J.1    Bajpai, S.2    Ali, S.3    Velu, S.4    Atigadda, V.5    Lommer, B.6    Finley, J.7    Luo, M.8    Air, G.9
  • 25
    • 0023475950 scopus 로고
    • Threedimensional structure of neuraminidase of subtype N9 from an avian influenza virus
    • A.T. Baker, J.N. Varghese, W.G. Laver, G.M. Air, and P.M. Colman, Threedimensional structure of neuraminidase of subtype N9 from an avian influenza virus, Proteins 2 (1987), pp. 111-117.
    • (1987) Proteins , vol.2 , pp. 111-117
    • Baker, A.T.1    Varghese, J.N.2    Laver, W.G.3    Air, G.M.4    Colman, P.M.5
  • 26
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
    • A.R. Leach, B.K. Shoichet, and C.E. Peishoff, Prediction of protein-ligand interactions. Docking and scoring: successes and gaps, J. Med. Chem. 49 (2006), pp. 5851-5852.
    • (2006) J. Med. Chem , vol.49 , pp. 5851-5852
    • Leach, A.R.1    Shoichet, B.K.2    Peishoff, C.E.3
  • 27
    • 29044433371 scopus 로고    scopus 로고
    • Recent advances in docking and scoring, Curr. Comput
    • E.M. Krovat, T. Steindl, and T. Langer, Recent advances in docking and scoring, Curr. Comput. Aided Drug Design 1 (2005), pp. 93-102.
    • (2005) Aided Drug Design , vol.1 , pp. 93-102
    • Krovat, E.M.1    Steindl, T.2    Langer, T.3
  • 28
    • 14044262243 scopus 로고    scopus 로고
    • V. Mohan, A.C. Gibbs, M.D. Cummings, E.P. Jaeger, and R.L. DesJarlais, Docking: successes and challenges, Curr. Pharm. Design 11 (2005), pp. 323-333.
    • V. Mohan, A.C. Gibbs, M.D. Cummings, E.P. Jaeger, and R.L. DesJarlais, Docking: successes and challenges, Curr. Pharm. Design 11 (2005), pp. 323-333.
  • 29
    • 10644254613 scopus 로고    scopus 로고
    • Planaria Software LLC, Seattle, WA
    • M.A. Thompson, ArgusLab 4.0.1, Planaria Software LLC, Seattle, WA, http://www.arguslab.com
    • ArgusLab 4.0.1
    • Thompson, M.A.1
  • 31
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • H.J. Böhm, The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure, J. Comput. Aided Mol. Design 8 (1994), pp. 243-256.
    • (1994) J. Comput. Aided Mol. Design , vol.8 , pp. 243-256
    • Böhm, H.J.1
  • 32
    • 0030255303 scopus 로고    scopus 로고
    • Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
    • A.N. Jain, Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities, J. Comput. Aided Mol. Design 10 (1996), pp. 427-440.
    • (1996) J. Comput. Aided Mol. Design , vol.10 , pp. 427-440
    • Jain, A.N.1
  • 33
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • M.D. Eldridge, C.W. Murray, T.R. Auton, G.V. Paolini, and R.P. Mee, Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes, J. Comput. Aided Mol. Design 11 (1997), pp. 425-445.
    • (1997) J. Comput. Aided Mol. Design , 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
  • 34
    • 0029995624 scopus 로고    scopus 로고
    • VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands
    • R.D. Head, M.L. Smythe, T.I. Oprea, C.L. Waller, S.M. Green, and G.R. Marshall, VALIDATE: a new method for the receptor-based prediction of binding affinities of novel ligands, J. Am. Chem. Soc. 118 (1996), pp. 3959-3969.
    • (1996) J. Am. Chem. Soc , vol.118 , pp. 3959-3969
    • Head, R.D.1    Smythe, M.L.2    Oprea, T.I.3    Waller, C.L.4    Green, S.M.5    Marshall, G.R.6
  • 35
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
    • H.J. Böhm, Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs, J. Comput. Aided Mol. Design 12 (1998), p. 309.
    • (1998) J. Comput. Aided Mol. Design , vol.12 , pp. 309
    • Böhm, H.J.1
  • 36
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • I. Muegge and Y.C. Martin, A general and fast scoring function for protein-ligand interactions: a simplified potential approach, J. Med. Chem. 42 (1999), pp. 791-804.
    • (1999) J. Med. Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 37
    • 0033566211 scopus 로고    scopus 로고
    • I. Muegge, Y.C. Martin, P.J. Hajduk, and S.W. Fesik, Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein, J. Med. Chem. 42 (1999), pp. 2498-2503.
    • I. Muegge, Y.C. Martin, P.J. Hajduk, and S.W. Fesik, Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein, J. Med. Chem. 42 (1999), pp. 2498-2503.
  • 38
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
    • R. Wang, Y. Gao, and L. Lai, SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex, J. Mol. Model. 4 (1998), pp. 379-394.
    • (1998) J. Mol. Model , vol.4 , pp. 379-394
    • Wang, R.1    Gao, Y.2    Lai, L.3
  • 39
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • R. Wang, L. Lai, and S. Wang, Further development and validation of empirical scoring functions for structure-based binding affinity prediction, J. Comput. Aided Mol. Design 16 (2002), pp. 11-26.
    • (2002) J. Comput. Aided Mol. Design , vol.16 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 40
    • 40349087133 scopus 로고    scopus 로고
    • Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
    • N. Moitessier, P. Englebienne, D. Lee, J. Lawandi, and C.R. Corbeil, Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go, British J. Pharmacol. 153 (2008), pp. S7-S26.
    • (2008) British J. Pharmacol , vol.153
    • Moitessier, N.1    Englebienne, P.2    Lee, D.3    Lawandi, J.4    Corbeil, C.R.5
  • 41
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson, Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function, J. Comp. Chem. 19 (1999), pp. 1639-1662.
    • (1999) J. Comp. 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
  • 42
    • 0028805201 scopus 로고
    • A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase
    • M.J. Jedrzejas, S. Singh, W.J. Brouillette, G.M. Air, and M. Luo, A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase, Proteins 23 (1995), pp. 264-277.
    • (1995) Proteins , vol.23 , pp. 264-277
    • Jedrzejas, M.J.1    Singh, S.2    Brouillette, W.J.3    Air, G.M.4    Luo, M.5
  • 43
    • 34548261773 scopus 로고    scopus 로고
    • Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus
    • Q-S. Du, S-Q. Wang, and K-C. Chou, Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus, Biochem. Biophys. Res. Commun. 362 (2007), pp. 525-531.
    • (2007) Biochem. Biophys. Res. Commun , vol.362 , pp. 525-531
    • Du, Q.-S.1    Wang, S.-Q.2    Chou, K.-C.3
  • 44
    • 46149126359 scopus 로고    scopus 로고
    • Another look at the molecular mechanism of the resistance of H5N1 influenza A virus neuraminidase (NA) to oseltamivir (OTV)
    • M.L. Mihajlovic and P.M. Mitrasinovic, Another look at the molecular mechanism of the resistance of H5N1 influenza A virus neuraminidase (NA) to oseltamivir (OTV), Biophys. Chem. 136 (2008), pp. 152-158.
    • (2008) Biophys. Chem , vol.136 , pp. 152-158
    • Mihajlovic, M.L.1    Mitrasinovic, P.M.2


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