메뉴 건너뛰기




Volumn 78, Issue 16, 2010, Pages 3281-3291

Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments

Author keywords

19F NMR; Active site mapping; Fluorine; Fragment based screening; GRID; Pharmacophoric fingerprint

Indexed keywords

FLUORINE; SERINE PROTEINASE; TRYPSIN;

EID: 78349294513     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22836     Document Type: Article
Times cited : (30)

References (47)
  • 1
    • 34848848499 scopus 로고    scopus 로고
    • Fluorine in pharmaceuticals: looking beyond intuition
    • Müller K, Faeh C, Diederich F. Fluorine in pharmaceuticals: looking beyond intuition. Science 2007; 317: 1881-1886.
    • (2007) Science , vol.317 , pp. 1881-1886
    • Müller, K.1    Faeh, C.2    Diederich, F.3
  • 2
    • 70349124638 scopus 로고    scopus 로고
    • Design and NMR-based screening of LEF, a library of chemical fragments with different local environment of fluorine
    • Vulpetti A, Hommel U, Landrum G, Lewis R, Dalvit C. Design and NMR-based screening of LEF, a library of chemical fragments with different local environment of fluorine. J Am Chem Soc 2009; 131: 12949-12959.
    • (2009) J Am Chem Soc , vol.131 , pp. 12949-12959
    • Vulpetti, A.1    Hommel, U.2    Landrum, G.3    Lewis, R.4    Dalvit, C.5
  • 4
    • 0002899752 scopus 로고
    • Modified spin-echo method for measuring nuclear relaxation times
    • Meiboom S, Gill D. Modified spin-echo method for measuring nuclear relaxation times. Rev Sci Instrum 1958; 29: 688-691.
    • (1958) Rev Sci Instrum , vol.29 , pp. 688-691
    • Meiboom, S.1    Gill, D.2
  • 5
    • 48749144559 scopus 로고
    • Evaluation of a new broadband decoupling sequence: WALTZ-16
    • Shaka AJ, Keeler J, Freeman R. Evaluation of a new broadband decoupling sequence: WALTZ-16. J Magn Reson 1983; 53: 313-340.
    • (1983) J Magn Reson , vol.53 , pp. 313-340
    • Shaka, A.J.1    Keeler, J.2    Freeman, R.3
  • 6
    • 0029824559 scopus 로고    scopus 로고
    • Reaction of active methylene compounds with α-fluoroalkyl ketones or esters: a convenient synthesis of 4-trifluoromethylpyridines and meta-trifluoromethylphenols
    • Guan H-P, Hu C-M. Reaction of active methylene compounds with α-fluoroalkyl ketones or esters: a convenient synthesis of 4-trifluoromethylpyridines and meta-trifluoromethylphenols. Synthesis 1996; 86: 1363-1370.
    • (1996) Synthesis , vol.86 , pp. 1363-1370
    • Guan, H.1    Hu, C.2
  • 7
    • 16644368493 scopus 로고    scopus 로고
    • APRV-a program for automated data processing, refinement and visualization
    • Kroemer M, Dreyer MK, Wendt KU. APRV-a program for automated data processing, refinement and visualization. Acta Crystallogr Sect D 2004; 60: 1679-1682.
    • (2004) Acta Crystallogr Sect D , vol.60 , pp. 1679-1682
    • Kroemer, M.1    Dreyer, M.K.2    Wendt, K.U.3
  • 8
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D 2004; 60: 2126-2132.
    • (2004) Acta Crystallogr Sect D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 9
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr Sect D 1997; 53: 240-255.
    • (1997) Acta Crystallogr Sect D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 11
    • 20544433165 scopus 로고
    • van der Waals volumes and radii
    • Bondi A. van der Waals volumes and radii. J Phys Chem 1964; 68: 441-451.
    • (1964) J Phys Chem , vol.68 , pp. 441-451
    • Bondi, A.1
  • 12
    • 17044421336 scopus 로고    scopus 로고
    • Orthogonal multipolar interactions in structural chemistry and biology
    • Paulini R, Müller K, Diederich F. Orthogonal multipolar interactions in structural chemistry and biology. Angew Chem Int Ed Engl 2005; 44: 1788-1805.
    • (2005) Angew Chem Int Ed Engl , vol.44 , pp. 1788-1805
    • Paulini, R.1    Müller, K.2    Diederich, F.3
  • 13
    • 50549086578 scopus 로고    scopus 로고
    • A fluorine scan of non-peptidic inhibitors of neprilysin: fluorophobicand fluorophilic regions in an enzyme active site
    • Morgenthaler M, Aebi JD, Gruninger F, Mon D, Wagner B, Kansy M, Dietrich F. A fluorine scan of non-peptidic inhibitors of neprilysin: fluorophobicand fluorophilic regions in an enzyme active site. JFluor Chem 2008; 129: 852-865.
    • (2008) JFluor Chem , vol.129 , pp. 852-865
    • Morgenthaler, M.1    Aebi, J.D.2    Gruninger, F.3    Mon, D.4    Wagner, B.5    Kansy, M.6    Dietrich, F.7
  • 14
    • 70350515927 scopus 로고    scopus 로고
    • Fluorine bonding-how does it work in protein-ligand interactions?
    • Zhou P, Zou J, Tian F, Shang Z. Fluorine bonding-how does it work in protein-ligand interactions? J Chem Inf Model 2009; 49: 2344-2355.
    • (2009) J Chem Inf Model , vol.49 , pp. 2344-2355
    • Zhou, P.1    Zou, J.2    Tian, F.3    Shang, Z.4
  • 15
    • 78349265177 scopus 로고    scopus 로고
    • Molecular Operating Environment (MOE). Available at:. Accessed on August 1
    • Molecular Operating Environment (MOE). Available at:. Accessed on August 1, 2009.
    • (2009)
  • 16
    • 70350422335 scopus 로고    scopus 로고
    • NMR methods in fragment screening: theory and a comparison with other biophysical techniques
    • Dalvit C. NMR methods in fragment screening: theory and a comparison with other biophysical techniques. Drug Discov Today 2009; 14: 1051-1057.
    • (2009) Drug Discov Today , vol.14 , pp. 1051-1057
    • Dalvit, C.1
  • 17
    • 0038207989 scopus 로고    scopus 로고
    • Fluorine-NMR experiments for high-throughput screening: theoretical aspects, practical considerations, and range of applicability
    • Dalvit C, Fagerness PE, Hadden DTA, Sarver RW, Stockman BJ. Fluorine-NMR experiments for high-throughput screening: theoretical aspects, practical considerations, and range of applicability. JAm Chem Soc 2003; 125: 7696-7703.
    • (2003) JAm Chem Soc , vol.125 , pp. 7696-7703
    • Dalvit, C.1    Fagerness, P.E.2    Hadden, D.T.A.3    Sarver, R.W.4    Stockman, B.J.5
  • 18
    • 36049036606 scopus 로고    scopus 로고
    • Ligand- and substrate-based 19F NMR screening: principles and applications to drug discovery
    • Dalvit C. Ligand- and substrate-based 19F NMR screening: principles and applications to drug discovery. Prog NMR Spectrosc 2007; 51: 243-271.
    • (2007) Prog NMR Spectrosc , vol.51 , pp. 243-271
    • Dalvit, C.1
  • 19
    • 84890711200 scopus 로고    scopus 로고
    • Guide to fluorine NMR for organic chemists
    • Wiley; Hoboken, New Jersey, USA
    • Dolbier WR, Jr. Guide to fluorine NMR for organic chemists. Wiley; Hoboken, New Jersey, USA, 2009.
    • (2009)
    • Dolbier Jr, W.R.1
  • 20
    • 0037663879 scopus 로고    scopus 로고
    • A fluorine scan of thrombin inhibitors to map the fluorophilicity/fluorophobicity of an enzyme active site: evidence for C-F. C=O interactions
    • Olsen JA, Banner DW, Seiler P, Obst Sander U, D'Arcy A, Stihle M, Müller K, Dietrich F. A fluorine scan of thrombin inhibitors to map the fluorophilicity/fluorophobicity of an enzyme active site: evidence for C-F. C=O interactions. Angew Chem Int Ed Engl 2003; 42: 2507-2511.
    • (2003) Angew Chem Int Ed Engl , vol.42 , pp. 2507-2511
    • Olsen, J.A.1    Banner, D.W.2    Seiler, P.3    Obst Sander, U.4    D'Arcy, A.5    Stihle, M.6    Müller, K.7    Dietrich, F.8
  • 21
    • 0001401527 scopus 로고
    • Quantitative predictions of tautomeric equilibria for 2-, 3-, and 4-substituted pyridines in both the gas phase and aqueous solution: combination of AM1 with reaction field theory
    • Karelson MM, Katritzky AZ, Szafran M, Zerner MC. Quantitative predictions of tautomeric equilibria for 2-, 3-, and 4-substituted pyridines in both the gas phase and aqueous solution: combination of AM1 with reaction field theory. J Org Chem 1989; 54: 6030-6034.
    • (1989) J Org Chem , vol.54 , pp. 6030-6034
    • Karelson, M.M.1    Katritzky, A.Z.2    Szafran, M.3    Zerner, M.C.4
  • 22
    • 0000304948 scopus 로고
    • Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory
    • Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Ringnalda M, Goddard WA, III, Honig B. Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory. J Am Chem Soc 1994; 116: 11875-11882.
    • (1994) J Am Chem Soc , vol.116 , pp. 11875-11882
    • Tannor, D.J.1    Marten, B.2    Murphy, R.3    Friesner, R.A.4    Sitkoff, D.5    Nicholls, A.6    Ringnalda, M.7    Goddard III, W.A.8    Honig, B.9
  • 23
    • 0030180875 scopus 로고    scopus 로고
    • New model for calculation of solvation free energies: correction of self-consistent reaction field continuum dielectric theory for short-range hydrogen-bonding effects
    • Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringnalda MN, Sitkoff D, Honig B. New model for calculation of solvation free energies: correction of self-consistent reaction field continuum dielectric theory for short-range hydrogen-bonding effects. J Phys Chem 1996; 100: 11775-11788.
    • (1996) J Phys Chem , vol.100 , pp. 11775-11788
    • Marten, B.1    Kim, K.2    Cortis, C.3    Friesner, R.A.4    Murphy, R.B.5    Ringnalda, M.N.6    Sitkoff, D.7    Honig, B.8
  • 24
    • 77954065505 scopus 로고    scopus 로고
    • Tautomer preference in PDB complexes and its impact on structure-based drug discovery
    • Milletti F, Vulpetti A. Tautomer preference in PDB complexes and its impact on structure-based drug discovery. J Chem Inf Model 2010; 50: 1062-1074.
    • (2010) J Chem Inf Model , vol.50 , pp. 1062-1074
    • Milletti, F.1    Vulpetti, A.2
  • 26
    • 0028932309 scopus 로고
    • Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors
    • Mattos C, Giammona DA, Petsko GA, Ringe D. Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors. Biochemistry 1995; 34: 3193-3203.
    • (1995) Biochemistry , vol.34 , pp. 3193-3203
    • Mattos, C.1    Giammona, D.A.2    Petsko, G.A.3    Ringe, D.4
  • 28
    • 0020484541 scopus 로고
    • Crystallographic study of the binding of a trifluoroacetyl dipeptide anilide inhibitor with elastase
    • Hughes DL, Sieker LC, Bieth J, Dimicoli JL. Crystallographic study of the binding of a trifluoroacetyl dipeptide anilide inhibitor with elastase. J Mol Biol 1982; 162: 645-658.
    • (1982) J Mol Biol , vol.162 , pp. 645-658
    • Hughes, D.L.1    Sieker, L.C.2    Bieth, J.3    Dimicoli, J.L.4
  • 30
    • 0025378039 scopus 로고
    • Interaction of the peptide CF3-Leu-Ala-NH-C6H4-CF3 (TFLA) with porcine pancreatic elastase. X-ray studies at 18 Å
    • de la Sierra IL, Papamichael E, Sakarellos C, Dimicoli JL, Prange T. Interaction of the peptide CF3-Leu-Ala-NH-C6H4-CF3 (TFLA) with porcine pancreatic elastase. X-ray studies at 18 Å. J Mol Recognit 1990; 3: 36-44.
    • (1990) J Mol Recognit , vol.3 , pp. 36-44
    • de la Sierra, I.L.1    Papamichael, E.2    Sakarellos, C.3    Dimicoli, J.L.4    Prange, T.5
  • 32
    • 70450240765 scopus 로고    scopus 로고
    • The crystal structure of oxylipin-conjugated barley LTP1 highlights the unique plasticity of the hydrophobic cavity of these plant lipid-binding proteins
    • Bakan B, Hamberg M, Larue V, Prangé T, Marion D, Lascombe MB. The crystal structure of oxylipin-conjugated barley LTP1 highlights the unique plasticity of the hydrophobic cavity of these plant lipid-binding proteins. Biochem Biophys Res Commun 2009; 18: 780-785.
    • (2009) Biochem Biophys Res Commun , vol.18 , pp. 780-785
    • Bakan, B.1    Hamberg, M.2    Larue, V.3    Prangé, T.4    Marion, D.5    Lascombe, M.B.6
  • 34
  • 35
    • 0033136831 scopus 로고    scopus 로고
    • Use of organic solvents and small molecules for locating binding sites on proteins in solution
    • Dalvit C, Floersheim P, Zurini M, Widmer A. Use of organic solvents and small molecules for locating binding sites on proteins in solution. J Biomol NMR 1999; 14: 23-32.
    • (1999) J Biomol NMR , vol.14 , pp. 23-32
    • Dalvit, C.1    Floersheim, P.2    Zurini, M.3    Widmer, A.4
  • 36
    • 0030965629 scopus 로고    scopus 로고
    • Organic solvents identify specific ligand binding sites on protein surfaces
    • Liepinsh E, Otting G. Organic solvents identify specific ligand binding sites on protein surfaces. Nat Biotechnol 1997; 15: 264-268.
    • (1997) Nat Biotechnol , vol.15 , pp. 264-268
    • Liepinsh, E.1    Otting, G.2
  • 37
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: a multiple copy simultaneous search method (MCSS)
    • Miranker A, Karplus M. Functionality maps of binding sites: a multiple copy simultaneous search method (MCSS). Proteins 1991; 11: 29-34.
    • (1991) Proteins , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 38
    • 0027219536 scopus 로고
    • Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase
    • Caflisch A, Miranker A, Karplus M. Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. J Med Chem 1993; 36: 2142-2167.
    • (1993) J Med Chem , vol.36 , pp. 2142-2167
    • Caflisch, A.1    Miranker, A.2    Karplus, M.3
  • 39
    • 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 Chem Med 1985; 28: 849-857.
    • (1985) J Chem Med , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 40
    • 33947658802 scopus 로고    scopus 로고
    • Identification of hot spots within druggable binding regions by computational solvent mapping of proteins
    • Landon MR, Lancia DR, Jr, Yu J, Thiel SC, Vajda S. Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J Med Chem 2007; 50: 1231-1240.
    • (2007) J Med Chem , vol.50 , pp. 1231-1240
    • Landon, M.R.1    Lancia Jr, D.R.2    Yu, J.3    Thiel, S.C.4    Vajda, S.5
  • 41
    • 61449104961 scopus 로고    scopus 로고
    • Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques
    • Brenke R, Kozakov D, Chuang G-Y, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 2009; 25: 621-627.
    • (2009) Bioinformatics , vol.25 , pp. 621-627
    • Brenke, R.1    Kozakov, D.2    Chuang, G.3    Beglov, D.4    Hall, D.5    Landon, M.R.6    Mattos, C.7    Vajda, S.8
  • 42
    • 65449159794 scopus 로고    scopus 로고
    • Binding site detection and druggability index from first principles
    • Seco J, Luque FJ, Barril X. Binding site detection and druggability index from first principles. J Med Chem 2009; 52: 2363-2371.
    • (2009) J Med Chem , vol.52 , pp. 2363-2371
    • Seco, J.1    Luque, F.J.2    Barril, X.3
  • 43
    • 4744373354 scopus 로고    scopus 로고
    • Hydrogen bonding interactions of covalently bonded fluorine atoms: from crystallographic data to a new angular function in the GRID force field
    • Carosati E, Sciabola S, Cruciani G. Hydrogen bonding interactions of covalently bonded fluorine atoms: from crystallographic data to a new angular function in the GRID force field. J Med Chem 2004; 47: 5114-5125.
    • (2004) J Med Chem , vol.47 , pp. 5114-5125
    • Carosati, E.1    Sciabola, S.2    Cruciani, G.3
  • 44
    • 22244460783 scopus 로고    scopus 로고
    • Probing the subpockets of factor Xa reveals two binding modes for inhibitors based on a 2-carboxyindole scaffold: a study combining structure-activity relationship and X-ray crystallography
    • Nazaré M, Will DW, Matter H, Schreuder H, Ritter K, Urmann M, Essrich M, Bauer A, Wagner M, Czech J, Lorenz M, Laux V, Wehner V. Probing the subpockets of factor Xa reveals two binding modes for inhibitors based on a 2-carboxyindole scaffold: a study combining structure-activity relationship and X-ray crystallography. J Med Chem 2005; 48: 4511-4525.
    • (2005) J Med Chem , vol.48 , pp. 4511-4525
    • Nazaré, M.1    Will, D.W.2    Matter, H.3    Schreuder, H.4    Ritter, K.5    Urmann, M.6    Essrich, M.7    Bauer, A.8    Wagner, M.9    Czech, J.10    Lorenz, M.11    Laux, V.12    Wehner, V.13
  • 45
    • 18344364519 scopus 로고    scopus 로고
    • Structural requirements for factor Xa inhibition by 3-oxybenzamides with neutral P1 substituents: combining X-ray crystallography, 3D-QSAR, and tailored scoring functions
    • Matter H, Will DW, Nazaré M, Schreuder H, Laux V, Wehner V. Structural requirements for factor Xa inhibition by 3-oxybenzamides with neutral P1 substituents: combining X-ray crystallography, 3D-QSAR, and tailored scoring functions. J Med Chem 2005; 48: 3290-3312.
    • (2005) J Med Chem , vol.48 , pp. 3290-3312
    • Matter, H.1    Will, D.W.2    Nazaré, M.3    Schreuder, H.4    Laux, V.5    Wehner, V.6
  • 47
    • 67349109896 scopus 로고    scopus 로고
    • More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin
    • Baum B, Mohamed M, Zayed M, Gerlach C, Heine A, Hangauer D, Klebe G. More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin. J Mol Biol 2009; 390: 56-69.
    • (2009) J Mol Biol , vol.390 , pp. 56-69
    • Baum, B.1    Mohamed, M.2    Zayed, M.3    Gerlach, C.4    Heine, A.5    Hangauer, D.6    Klebe, G.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.