Molecular modeling of cardiac glycoside binding by the human sequence monoclonal antibody 1B3

Proteins: Structure, Function and Genetics

Volumn 60, Issue 3, 2005, Pages 382-391

  Paula, Stefan ^a,c   Monson, Nancy ^b   Ball Jr , William James ^a  

^a UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c NORTHERN KENTUCKY UNIVERSITY   (United States)

Author keywords

Antibody homology modeling; Computational docking; Congestive heart failure; Digitalis; Digitalis binding; Digitalis immunotherapy; Digoxin

Indexed keywords

16 ACETYLGITOXIN; ACETYLDIGITOXIN; AMINO ACID; BUFALIN; CARDIAC GLYCOSIDE; CERBEROSIDE; DIGITALIS; DIGITOXIGENIN; DIGITOXIN; DIGOXIGENIN; DIGOXIN; DIHYDRODIGOXIN; GITOXIN; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN LIGHT CHAIN; LANATOSIDE C; LIGAND; MONOCLONAL ANTIBODY; MONOCLONAL ANTIBODY 1B3; OUABAIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; COMPLEMENTARITY DETERMINING REGION; CONGESTIVE HEART FAILURE; DRUG BINDING; HUMAN; LIGAND BINDING; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

AMINO ACID SEQUENCE; ANTIBODIES, MONOCLONAL; ANTIBODY SPECIFICITY; BINDING SITES; BINDING SITES, ANTIBODY; CARDIAC GLYCOSIDES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DIGOXIN; HUMANS; IMAGING, THREE-DIMENSIONAL; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; MYOCARDIUM; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; STRUCTURE-ACTIVITY RELATIONSHIP;

DIGITALIS; MURINAE;

EID: 23044467529     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20484     Document Type: Article

References (37)

1. Farr CD, Tabet MR, Ball WR Jr, Fishwild DM, Wang X, Nair AC, Welsh WJ. Three-dimensional quantitative structure-activity relationship analysis of ligand binding to human sequence anti-digoxin monoclonal antibodies using comparative molecular field analysis. J Med Chem 2002;45:3257-3270.
2. Li-Saw-Hee FL, Lip GYH. Digoxin revisited. Q J Med 1998;91:259-264.
3. Lip GY, Metcalfe MJ, Dunn FG. Diagnosis and treatment of digoxin toxicity. Postgrad Med J 1993;69:337-339.
4. Martiny SS, Phelps SJ, Massey DL. Treatment of severe digitalis intoxication with digoxin-specific antibody fragments: a clinical review. Crit Care Med 1998;16:629-635.
5. Azrin, MA. The use of antiboides in clinical cardiology. Am Heart J 1992;124:753-768.
6. Hickey AR, Wenger TL, Carpenter VP, Tilson HH, Hlatky MA, Furberg CD, Kirkpatrick CH, Strauss HC, Smith TW. Digoxin immune Fab therapy in the management of digitalis intoxication: safety and efficacy results of an observational surveillance study. J Am Coll Cardiol 1991;17:590-598.
7. Riechmann L, Clark M, Waldmann H, Winter G. Reshaping human antibodies for therapy. Nature 1988;332:323-327.
8. Jones PT, Dear PH, Foote J, Neuberger MS, Winter G. Replacing the complementarily-determining regions in a human antibody with those from a mouse. Nature 1986;321:522-525.
9. Ball WR Jr, Kasturi R, Dey P, Tabet M, O'Donnell S, Hudson D, Fishwild D. Isolation and characterization of human monoclonal antibodies to digoxin. J Immunol 1999;163:2291-2298.
10. Xu D, Xu Y, Uberbacher EC. Computational tools for protein modeling. Curr Protein Pept Sci 2000;1:1-21.
11. Van Dongen M, Weigelt J, Uppenberg J, Schultz J, Wikstrom M. Structure-based screening and design in drug discovery. Drug Discov Today 2002;7:471-478.
12. Klabunde T, Hessler G. Drug design strategies for targeting G-protein-coupled receptors. Chembiochem 2002;3:928-944.
13. Martin AC, Cheetaham JC, Rees AR. Molecular modeling of antibody combining sites. Methods Enzymol 1991;203:121-153.
14. Jeffrey PD, Schildbach JF, Chang CY, Kussie PH, Margolies MN, Sheriff S. Structure and specificity of the anti-digoxin antibody 40-50. J Mol Biol 1995;248:344-360.
15. Jeffrey PD, Strong RK, Sieker LC, Chang CY, Campbell RL, Petsko GA, Haber E, Margolies MN, Sheriff S. 26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity. Proc Natl Acad Sci USA 1993;90:10310-10314.
16. Lonberg N, Taylor LD, Harding FA, Troustine M, Higgins KM, Schramm SR, Kuo CC, Mashayekh R, Wymore K, McCabe JG, Donna Munoz-O'Regan, O'Donnell SL, Lapachet ESG, Bengoechea T, Fishwild DM, Carmack CE, Kay RM, Haszar D. Antigen-specific human antibodies from mice comprising four distinct genetic modifications. Nature 1994;368:856-859.
17. Fishwild DM, O'Donnell SL, Bengoechea T, Hudson DV, Harding F, Bernhard SL, Jones D, Kay RM, Higgins KM, Schramm SR, Lonberg N. High-avidity human IgG kappa monoclonal antibodies from a novel strain of minilocus transgenic mice. Nat Biotechnol 1996;14:845-851.
18. + B cells. J Clin Invest 1997;99:1614-1627.
19. + B cells. J Clin Invest 1997;9:2488-2501.
20. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1997;74:5463-5467.
21. Whitelegg NR, Rees AR. WAM: an improved algorithm for modelling antibodies on the WEB. Protein Eng 2000;13:819-824.
22. Martin AC, Cheetham JC, Rees AR. Modeling antibody hypervariable loops: a combined algorithm. Proc Natl Acad Sci USA 1989;86:9268-9272.
23. Bruccoleri RE, Karplus M. Preddiction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 1987;26:137-168.
24. Levell SC, Davis IW, Arendall WB III, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richadson DC. Structure validation by Cα geometry: Φ, Ψ, and Cβ deviation. Proteins 2003;50:437-450.
25. Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968;23:283-438.
26. Levell SC, Word JM, Richardson JS, Richardson DC. The penultimate roatmer library. Proteins 2000;40:389-408.
27. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-1723.
28. Kabat EA, Wu TT, Perry HM, Gottesman KS, Foeller C. Sequences of proteins of immunological interest. 5th Ed. Public Health Service NIH USA; 1991.
29. Martin AC. Accessing the kabat antibody sequence database by computer. Proteins 1996;25:130-133.
30. Shirai H, Kidera A, Nakamura H. H3-rules: identification of CDR-H3 structures in antibodies. FEBS Lett 1999;455:188-197.
31. Baca M, Presta LG, O'Connor SJ, Wells JA. Antibody humanization using monovalent phage display. J Biol Chem 1997;272: 10678-10864.
32. Novotny J, Bruccoleri R, Newell J, Murphy D, Haber E, Karplus M. Molecular anatomy of the antibody binding site. J Biol Chem 1983;258:14433- 14437.
33. Chothia C, Gelfand I, Kister A. Structural determinants in the sequences of immunoglobulin variable domain. J Mol Biol 1998; 278:457-479.
34. Wilson IA, Stanfield RL. Antibody-antigen interactions: new structures and new conformational changes. Curr Opin Struct Biol 1994;4:857-867.
35. Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748.
36. Morea V, Tramontano A, Rustici M, Chothia C, Lesk AM. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J Mol Biol 1998;275:269-294.
37. Tanford C. The hydrophobic effect: formation of micelles and biological membranes. New York: John Wiley & Sons; 1980.