Replacing affinity with binding kinetics in QSAR studies resolves otherwise confounded effects

Journal of Chemometrics

Volumn 20, Issue 8-10, 2006, Pages 370-375

  Andersson, Karl ^a   Hämäläinen, Markku D ^a  

^a BIACORE AB   (Sweden)

Author keywords

Biacore; Biosensor; Off rate; On rate; Quantitative structure activity relationship; Surface plasmon resonance

Indexed keywords

BINDING ENERGY; BIOASSAY; COMPUTATIONAL CHEMISTRY; DISSOCIATION; MOLECULAR GRAPHICS; RATE CONSTANTS; SURFACE PLASMON RESONANCE;

ASSOCIATION RATES; BIACORE; BINDING AFFINITIES; BINDING KINETICS; DISSOCIATION RATES; OFF-RATE; ON-RATE; QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP STUDIES; SURFACE-PLASMON RESONANCE;

BIOSENSORS;

EID: 34249342240     PISSN: 08869383     EISSN: 1099128X     Source Type: Journal    
DOI: 10.1002/cem.1010     Document Type: Article

References (26)

1. Kubinyi H. Comparative molecular field analysis (CoMFA). In The Encyclopedia of Computational Chemistry, Vol. 1, Schleyer PvR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaefer HF, III, Schreiner PR (eds). John Wiley & Sons: Chichester, 1998; 448-460.
2. Demyttenaere-Kovatcheva A, Cronin MT, Benfenati E, Roncaglioni A, Lopiparo E. Identification of the structural requirements of the receptor-binding affinity of diphenolic azoles to estrogen receptors alpha and beta by three-dimensional quantitative structure-activity relationship and structure-activity relationship analysis. J. Med. Chem. 2005; 48(24): 7628-7636.
3. Bohl CE, Chang C, Mohler ML, Chen J, Miller DD, Swaan PW, Dalton JT. A ligand-based approach to identify quantitative structure-activity relationships for the androgen receptor. J. Med. Chem. 2004; 47(15): 3765-3776.
4. Box G. Signal-to-noise ratios, performance criteria, and transformations. Technometrics 1988; 30: 1-17.
5. Lundqvist T. The devil is still in details - driving early drug discovery forward with biophysical experimental methods. Curr. Opin. Drug Discov. Dev. 2005; 8: 513-519.
6. Shuman CF, Hamalainen MD, Danielson UH. Kinetic and thermodynamic characterization of HIV-1 protease inhibitors. J. Mol. Recognit. 2004; 17(2): 106-119.
7. Hall S, Strichartz G, Moczydlowski E, Ravindran A, Reicharrdt PB. The saxitoxins: sources, chemistry, and pharmacology. In Marine Toxins Origin, Structure and Molecular Pharmacology, Hall S, Strichartz G (eds), ACS Symposium Series. American Chemical Society: Washington, DC, 1990; 29-65.
8. Elg M, Gustafsson D, Deinum J. The importance of enzyme inhibition kinetics for the effect of thrombin inhibitors in a rat model of arterial thrombosis. Thromb. Haemost. 1997; 78(4): 1286-1292.
9. Park BW, Zhang HT, Wu C, Berezov A, Zhang X, Dua R, Wang Q, Kao G, O'Rourke DM, Greene MI, Murali R. Rationally designed anti-HER2/neu peptide mimetic disables P185HER2/neu tyrosine kinases in vitro and in vivo. Nat. Biotechnol. 2000; 18(2): 194-198.
10. Rich RL, Hoth LR, Geoghegan KF, Brown TA, LeMotte PK, Simons SP, Hensley P, Myszka DG. Kinetic analysis of estrogen receptor/ligand interactions. Proc. Natl. Acad. Sci. U.S.A. 2002; 99: 8562-8567.
11. Krogsgaard M, Prado N, Adams EJ, He XL, Chow DC, Wilson DB, Garcia KC, Davis MM. Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation. Mol. Cell. 2003; 12: 1367-1378.
12. Wu H, Pfarr DS, Tang Y, An LL, Patel NK, Watkins JD, Huse WD, Kiener PA, Young JF. Ultra-potent antibodies against respiratory syncytial virus: effects of binding kinetics and binding valence on viral neutralization. J. Mol. Biol. 2005; 350: 126-144.
13. Huber W. A new strategy for improved secondary screening and lead optimization using high-resolution SPR characterization of compound-target interactions. J. Mol. Recognit. 2005; 18(4): 273-281.
14. Lofas S. Optimizing the hit-to-lead process using SPR analysis. Assay Drug Dev. Technol. 2004; 2: 1-9.
15. Markgren P-O, Schaal W, Hamalainen MD, Karlén A, Hallberg A, Samuelsson B, Danielsson UH. Relationships between structure and interaction kinetics for HIV-1 protease inhibitors. J. Med. Chem. 2002; 45(25): 5430-5439.
16. Schaal W. Computational Studies of HIV-1 Protease Inhibitors. Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy, 2002, ISBN: 91-554-5213-2.
17. Andersson K, Choulier L, Hamalainen MD, van Regenmortel MHV, Altschuh D, Malmqvist M. Predicting the kinetics of peptide-antibody interactions using a multivariate experimental design of sequence and chemical space. J. Mol. Recognit. 2001; 14: 62-71.
18. De Genst E, Areskoug D, Decanniere K, Muyldermans S, Andersson K. Kinetic and affinity predictions of a protein-protein interaction using multivariate experimental design. J. Biol. Chem. 2002; 277(33): 29897-29907.
19. Andersson K. Characterization of Biomolecular Interactions Using a Multivariate Approach. Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, 2004, ISBN: 91-554-5999-4.
20. Hellberg S, Sjöström M, Skagerberg B, Wold S. Peptide quantitative structure-activity relationships, a multivariate approach. J. Med. Chem. 1987; 30: 1126-1135.
21. Deleage G, Roux B. An algorithm for protein secondary structure based on class prediction. Protein Eng. 1987; 1: 289-294.
22. Chatellier J, Rauffer-Bruyère N, Van Regenmortel MHV, Altschuh D, Weiss E. Comparative interaction kinetics of two recombinant Fabs and of the corresponding antibodies directed to the coat protein of tobacco mosaic virus. J. Mol. Recognit. 1996; 9: 39-51.
23. Choulier L, Rauffer-Bruyere N, Ben Khalifa M, Martin F, Vernet T, Altschuh D. Kinetic analysis of the effect on Fab binding of identical substitutions in a peptide and its parent protein. Biochemistry 1999; 38(12): 3530-3537.
24. Choulier L, Andersson K, Hamalainen MD, van Regenmortel MHV, Malmqvist M, Altschuh D. QSAR studies applied to the prediction of antigen-antibody interaction kinetics as measured by BIACORE. Protein Eng. 2002; 15(5): 373-382.
25. Freyhult EK, Andersson K, Gustafsson MG. Structural modeling extends QSAR analysis of antibody-lysozyme interactions to 3D-QSAR. Biophys. J. 2003; 84: 2264-2272.
26. Desmyter A, Transue TR, Ghahroudi MA, Thi M-HD, Poortmans F, Hamers R, Muyldermans S, Wyns L. Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme. Nat. Struct. Biol. 1996; 3(9): 803-811.