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Volumn 7, Issue 4, 2004, Pages 404-410

Structure-guided fragment screening for lead discovery

Author keywords

Fragment based; Lead optimization; X ray crystallography

Indexed keywords

ENZYME INHIBITOR; LIGAND; TRIOSEPHOSPHATE ISOMERASE; CARRIER PROTEIN; LEAD BINDING PROTEINS; LEAD-BINDING PROTEINS;

EID: 4644349994     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review
Times cited : (55)

References (50)
  • 1
    • 0034255751 scopus 로고    scopus 로고
    • Isn't combinatorial chemistry just chemistry?
    • Hird N: Isn't combinatorial chemistry just chemistry? Drug Disc Today (2000) 5(8):307-308.
    • (2000) Drug Disc Today , vol.5 , Issue.8 , pp. 307-308
    • Hird, N.1
  • 2
    • 0035324944 scopus 로고    scopus 로고
    • Molecular complexity and its impact on the probability of finding leads for drug discovery
    • Hann MM, Leach AR, Harper G: Molecular complexity and its impact on the probability of finding leads for drug discovery. J Chem Inf Comput Sci(2001) 41(3):856-864. Using a very simple model, this paper elegantly demonstrates how large compounds have a much lower probability of forming complementary interactions with a binding site than small compounds.
    • (2001) J Chem Inf Comput Sci , vol.41 , Issue.3 , pp. 856-864
    • Hann, M.M.1    Leach, A.R.2    Harper, G.3
  • 3
    • 0033576601 scopus 로고    scopus 로고
    • The design of leadlike combinatorial libraries
    • Teague SJ, Davis AM, Leeson PD, Oprea T: The design of leadlike combinatorial libraries. Angew Chem Int Ed (1999) 38(24)3743-3748. Describes the differences between drug-like and lead-like compounds (in terms of their molecular weight and ClogP values) and argues that screening libraries should contain lead-like compounds (lower molecular weight and lower ClogP) rather than drug-like compounds.
    • (1999) Angew Chem Int Ed , vol.38 , Issue.24 , pp. 3743-3748
    • Teague, S.J.1    Davis, A.M.2    Leeson, P.D.3    Oprea, T.4
  • 4
    • 1942453243 scopus 로고    scopus 로고
    • Ligand efficiency: A useful metric for lead selection
    • Hopkins AL, Groom CR, Alex A: Ligand efficiency: A useful metric for lead selection. Drug Disc Today (2004) 9(10):430-431.
    • (2004) Drug Disc Today , vol.9 , Issue.10 , pp. 430-431
    • Hopkins, A.L.1    Groom, C.R.2    Alex, A.3
  • 5
    • 0036051992 scopus 로고    scopus 로고
    • High-throughput crystallography for lead discovery in drug design
    • Blundell TL, Jhoti H, Abell C: High-throughput crystallography for lead discovery in drug design. Nat Rev Drug Disc (2002) 1(1):45-54.
    • (2002) Nat Rev Drug Disc , vol.1 , Issue.1 , pp. 45-54
    • Blundell, T.L.1    Jhoti, H.2    Abell, C.3
  • 6
    • 1642288258 scopus 로고    scopus 로고
    • Novel inhibitors of DNA gyrase: 3D structure-based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening
    • Boehm HJ, Boehringer M, Bur D, Gmuender H, Huber W, Klaus W, Kostrewa D, Kuehne H, Luebbers T, Meunier-Keller N, Mueller F: Novel inhibitors of DNA gyrase: 3D structure-based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. J Med Chem (2000) 43(14)5664-2674. Early fragment-based lead discovery application following an integrated approach using virtual screening with LUDI, NMR and other biophysical methods, and crystallography to find potent leads against a difficult target.
    • (2000) J Med Chem , vol.43 , Issue.14 , pp. 5664-12674
    • Boehm, H.J.1    Boehringer, M.2    Bur, D.3    Gmuender, H.4    Huber, W.5    Klaus, W.6    Kostrewa, D.7    Kuehne, H.8    Luebbers, T.9    Meunier-Keller, N.10    Mueller, F.11
  • 7
    • 0036558207 scopus 로고    scopus 로고
    • Structure-based screening of low-affinity compounds
    • Carr R, Jhoti H: Structure-based screening of low-affinity compounds. Drug Disc Today (2002) 7(9):522-527.
    • (2002) Drug Disc Today , vol.7 , Issue.9 , pp. 522-527
    • Carr, R.1    Jhoti, H.2
  • 8
    • 0033213957 scopus 로고    scopus 로고
    • The SHAPES strategy: An NMR-based approach for lead generation in drug discovery
    • Fejzo J, Lepre CA, Peng JW, Bemis GW, Ajay, Murcko MA, Moore JM: The SHAPES strategy: An NMR-based approach for lead generation in drug discovery. Chem Biol (1999) 6(10):755-769. An early example of the use of ligand-based NMR screening to focus enzymatic assays.
    • (1999) Chem Biol , vol.6 , Issue.10 , pp. 755-769
    • Fejzo, J.1    Lepre, C.A.2    Peng, J.W.3    Bemis, G.W.4    Ajay5    Murcko, M.A.6    Moore, J.M.7
  • 10
    • 0029836953 scopus 로고    scopus 로고
    • Discovering high-affinity ligands for proteins: SAR by NMR
    • Shuker SB, Hajduk PJ, Meadows RP, Fesik SW: Discovering high-affinity ligands for proteins: SAR by NMR. Science (1996) 274(5292):1531-1534. A key paper on target-based NMR, describing how the technique was used to identify leads against FK506 binding protein. Two fragment hits were found to interact in two distinct pockets and were then joined to form potent leads.
    • (1996) Science , vol.274 , Issue.5292 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 11
    • 2342589483 scopus 로고    scopus 로고
    • New lead generation strategies for protein kinase inhibitors - Fragment based screening approaches
    • Gill A: New lead generation strategies for protein kinase inhibitors - fragment based screening approaches. Mini Rev Med Chem (2004) 4(3):301-311.
    • (2004) Mini Rev Med Chem , vol.4 , Issue.3 , pp. 301-311
    • Gill, A.1
  • 12
    • 0024745871 scopus 로고
    • The price of lost freedom: Entropy of bimolecular complex formation
    • Finkelstein AV, Janin J: The price of lost freedom: Entropy of bimolecular complex formation. Protein Eng (1989) 3(1):1 -3. A paper on the loss of rigid-body entropy upon the binding of a ligand to a target. Using simple models, the authors demonstrate that this loss should be independent of the molecular weight of the ligand.
    • (1989) Protein Eng , vol.3 , Issue.1 , pp. 1-3
    • Finkelstein, A.V.1    Janin, J.2
  • 13
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • Gilson MK, Given JA, Bush BL, Mccammon JA: The statistical-thermodynamic basis for computation of binding affinities: A critical review. Biophys J (1997) 72(3):1047-1069.
    • (1997) Biophys J , vol.72 , Issue.3 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    Mccammon, J.A.4
  • 14
    • 0036821028 scopus 로고    scopus 로고
    • The consequences of translational and rotational entropy lost by small molecules on binding to proteins
    • Murray CW, Verdonk ML: The consequences of translational and rotational entropy lost by small molecules on binding to proteins. J Comput Aided Mol Des (2002) 16(10):741-753.
    • (2002) J Comput Aided Mol Des , vol.16 , Issue.10 , pp. 741-753
    • Murray, C.W.1    Verdonk, M.L.2
  • 15
    • 0026848170 scopus 로고
    • In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach
    • Verlinde CL, Rudenko G, Hol WG: In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach. J Comput Aided Mol Des (1992) 6(2):131-147.
    • (1992) J Comput Aided Mol Des , vol.6 , Issue.2 , pp. 131-147
    • Verlinde, C.L.1    Rudenko, G.2    Hol, W.G.3
  • 16
    • 0001928830 scopus 로고    scopus 로고
    • Antitrypanosomiasis drug development based on structures of glycolitic enzymes
    • Veerapandian P (Ed), Marcel Dekker Inc, New York, NY, USA
    • Vertinde CLMJ, Kim H, Bernstein BE, Mande SC, Hol WGJ: Antitrypanosomiasis drug development based on structures of glycolitic enzymes. In: Structure-Based Drug Design. Veerapandian P (Ed), Marcel Dekker Inc, New York, NY, USA (1997):365-394. An early paper discussing the use of X-ray crystallography for lead discovery.
    • (1997) Structure-Based Drug Design , pp. 365-394
    • Vertinde, C.L.M.J.1    Kim, H.2    Bernstein, B.E.3    Mande, S.C.4    Hol, W.G.J.5
  • 18
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G, Wiltett P, Glen RC, Leach AR, Taylor R: Development and validation of a genetic algorithm for flexible docking. J Mol Biol (1997) 267(3):727-748.
    • (1997) J Mol Biol , vol.267 , Issue.3 , pp. 727-748
    • Jones, G.1    Wiltett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 21
    • 0037463033 scopus 로고    scopus 로고
    • NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors
    • Meyer B, Peters T: NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew Chem Int Ed (2003) 42(8):864-890.
    • (2003) Angew Chem Int Ed , vol.42 , Issue.8 , pp. 864-890
    • Meyer, B.1    Peters, T.2
  • 22
    • 0035253553 scopus 로고    scopus 로고
    • MS/NMR: A structure-based approach for discovering protein ligands and for drug design by coupling size exclusion chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy
    • Moy FJ, Haraki K, Mobilio D, Walker G, Powers R, Tabei K, Tong H, Siegel MM: MS/NMR: A structure-based approach for discovering protein ligands and for drug design by coupling size exclusion chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. Anal Chem (2001) 73(3):571 -581.
    • (2001) Anal Chem , vol.73 , Issue.3 , pp. 571-581
    • Moy, F.J.1    Haraki, K.2    Mobilio, D.3    Walker, G.4    Powers, R.5    Tabei, K.6    Tong, H.7    Siegel, M.M.8
  • 24
    • 0035753065 scopus 로고    scopus 로고
    • High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: Utility in pharmaceutical design
    • Woods VL Jr, Hamuro Y: High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: Utility in pharmaceutical design. J Cell Biochem (2001) 84(S37):89-98.
    • (2001) J Cell Biochem , vol.84 , Issue.S37 , pp. 89-98
    • Woods Jr., V.L.1    Hamuro, Y.2
  • 25
    • 1442333529 scopus 로고    scopus 로고
    • Modeling data from titration, amide H/D exchange, and mass spectrometry to obtain protein-ligand binding constants
    • Zhu MM, Rempel DL, Gross ML: Modeling data from titration, amide H/D exchange, and mass spectrometry to obtain protein-ligand binding constants. J Am Soc Mass Soectrom (2004) 15(3):388-397.
    • (2004) J Am Soc Mass Soectrom , vol.15 , Issue.3 , pp. 388-397
    • Zhu, M.M.1    Rempel, D.L.2    Gross, M.L.3
  • 27
    • 0021871375 scopus 로고
    • A computational-procedure for determining energetically favorable binding-sites on biologically Important macromolecules
    • Goodford PJ: A computational-procedure for determining energetically favorable binding-sites on biologically Important macromolecules. J Med Chem (1985) 28(7):849-857.
    • (1985) J Med Chem , vol.28 , Issue.7 , pp. 849-857
    • Goodford, P.J.1
  • 28
    • 0029895576 scopus 로고    scopus 로고
    • X-SITE: Use of empirically derived atomic packing preferences to Identify favourable Interaction regions in the binding sites of proteins
    • Laskowski RA, Thornton JM, Humblet C, Singh J: X-SITE: Use of empirically derived atomic packing preferences to Identify favourable Interaction regions in the binding sites of proteins. J Mol Biol (1996) 259(1):175-201.
    • (1996) J Mol Biol , vol.259 , Issue.1 , pp. 175-201
    • Laskowski, R.A.1    Thornton, J.M.2    Humblet, C.3    Singh, J.4
  • 29
    • 0035823226 scopus 로고    scopus 로고
    • SuperStar: Comparison of CSD and PDB-based Interaction fields as a basis for the prediction of protein-ligand interactions
    • Boer DR, Kroon J, Cole JC, Smith B, Verdonk ML: SuperStar: Comparison of CSD and PDB-based Interaction fields as a basis for the prediction of protein-ligand interactions. J Mol Biol (2001) 312(1)275-287.
    • (2001) J Mol Biol , vol.312 , Issue.1 , pp. 275-287
    • Boer, D.R.1    Kroon, J.2    Cole, J.C.3    Smith, B.4    Verdonk, M.L.5
  • 30
    • 0033047007 scopus 로고    scopus 로고
    • SuperStar: A knowledge-based approach for identifying interaction sites in proteins
    • Verdonk ML, Cole JC, Taylor R: SuperStar: A knowledge-based approach for identifying interaction sites In proteins. J Mol Biol (1999) 289(4):1093-1108.
    • (1999) J Mol Biol , vol.289 , Issue.4 , pp. 1093-1108
    • Verdonk, M.L.1    Cole, J.C.2    Taylor, R.3
  • 32
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • Allen FH: The Cambridge Structural Database: A quarter of a million crystal structures and rising. Acta Crystallogr B (2002) 58:380-388.
    • (2002) Acta Crystallogr B , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 33
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • Miranker A, Karplus M: Functionality maps of binding sites: A multiple copy simultaneous search method. Proteins (1991) 11(1):29-34.
    • (1991) Proteins , vol.11 , Issue.1 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 34
    • 0026813925 scopus 로고
    • The computer-program LUDI: A new method for the de novo design of enzyme-inhibitors
    • Bohm HJ: The computer-program LUDI: A new method for the de novo design of enzyme-inhibitors. J Comput Aided Mol Des (1992) 6(1):61-78.
    • (1992) J Comput Aided Mol Des , vol.6 , Issue.1 , pp. 61-78
    • Bohm, H.J.1
  • 35
    • 0041418274 scopus 로고    scopus 로고
    • Recent advances in de novo design strategy for practical lead identification
    • Honma T: Recent advances in de novo design strategy for practical lead identification. Med Res Rev (2003) 23(5):606-632.
    • (2003) Med Res Rev , vol.23 , Issue.5 , pp. 606-632
    • Honma, T.1
  • 39
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M, Kramer B, Lengauer T, Klebe G: A fast flexible docking method using an incremental construction algorithm. J Mol Biol (1996) 261(3):470-489.
    • (1996) J Mol Biol , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 41
    • 0040196029 scopus 로고    scopus 로고
    • Further development of a genetic algorithm for ligand docking and its application to screening combinatorial libraries
    • Parrill AL, Reddy MR (Eds), American Chemical Society, Washington, DC, USA
    • Jones G, Wiltett P, Glen RC, Leach AR, Taylor R: Further development of a genetic algorithm for ligand docking and its application to screening combinatorial libraries. In: Rational Drug Design, Novel Methodology and Practical Applications. ACS Symposium Series Vol 719. Parrill AL, Reddy MR (Eds), American Chemical Society, Washington, DC, USA (1999):271-291.
    • (1999) Rational Drug Design, Novel Methodology and Practical Applications. ACS Symposium Series , vol.719 , pp. 271-291
    • Jones, G.1    Wiltett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 42
    • 0033672647 scopus 로고    scopus 로고
    • A recursive algorithm for efficient combinatorial library docking
    • Rarey M, Lengauer T: A recursive algorithm for efficient combinatorial library docking. Perspect Drug Disc Design (2000) 20(1):63-81.
    • (2000) Perspect Drug Disc Design , vol.20 , Issue.1 , pp. 63-81
    • Rarey, M.1    Lengauer, T.2
  • 43
    • 0032196541 scopus 로고    scopus 로고
    • CombiDOCK: Structure-based combinatorial docking and library design
    • Sun Y, Ewing TJ, Skillman AG, Kuntz ID: CombiDOCK: Structure-based combinatorial docking and library design. J Comput Aided Mol Des (1998) 12(6):597-604.
    • (1998) J Comput Aided Mol Des , vol.12 , Issue.6 , pp. 597-604
    • Sun, Y.1    Ewing, T.J.2    Skillman, A.G.3    Kuntz, I.D.4
  • 44
    • 2442647742 scopus 로고    scopus 로고
    • BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38 and HIV protease
    • Pierce AC, Rao G, Bernis GW: BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38 and HIV protease. J Med Chem (2004) 47(11):2768-2775.
    • (2004) J Med Chem , vol.47 , Issue.11 , pp. 2768-2775
    • Pierce, A.C.1    Rao, G.2    Bernis, G.W.3
  • 48
  • 50
    • 0038751777 scopus 로고    scopus 로고
    • The structural revolution
    • Verdonk ML: The structural revolution. Curr Drug Disc (2003) 5(3):44-46.
    • (2003) Curr Drug Disc , vol.5 , Issue.3 , pp. 44-46
    • Verdonk, M.L.1


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