Method and system for determination of molecular interaction parameters

• US 7,373,255 B2
• Filed: 06/04/2004
• Issued: 05/13/2008
• Est. Priority Date: 06/06/2003
• Status: Active Grant

• Current Assignee: Cytiva Sweden AB (Danaher Corporation)
• Original Assignee: Biacore AB
• Inventors: Andersson, Karl, Karlsson, Robert, Wass, Christina
• Primary Examiner(s): Zeman; Mary K.
• Application Number:
  US10/861,098
• Publication Number:
  US 20050014179A1
• Time in Patent Office: 1,439 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: G01N 2333/912 transferring phosphorus containing groups, e.g. kinases (2.7)
• CPC Class Codes: G01N 2333/936 acting on beta-1, 4 bonds between N-acetylmuramic acid and 2-acetyl-amino 2-deoxy-D-glucose, e.g. lysozyme
• CPC Class Codes: G01N 2333/974 Thrombin
• CPC Class Codes: G01N 2333/988 Lyases (4.), e.g. aldolases, heparinase, enolases, fumarase
• CPC Class Codes: G01N 2500/04 Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
• CPC Class Codes: G01N 2500/20 cell-free systems
• CPC Class Codes: G01N 33/53 Immunoassay; Biospecific binding assay; Materials therefor
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 33/6854 Immunoglobulins
• CPC Class Codes: G01N 35/08 using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface

Abstract

A method of determining kinetic parameters for a reversible molecular interaction between a ligand immobilized to a solid support surface and a binding partner to the ligand in solution, comprises sequentially, without intermediate regeneration or renewal of the immobilized ligand, flowing a plurality of fluid volumes containing different known concentrations of the binding partner over the solid support surface, monitoring the momentary amount of binding partner bound to the solid support surface related to time and solution concentration of binding partner and collecting the binding data, and determining the kinetic parameters by globally fitting a predetermined kinetic model for the interaction between the binding partner and the immobilized ligand to the collected binding data, which model allows for mass transport limitation at the solid support surface. An analytical system for carrying out the method, a computer program, a computer program product and a computer system for performing the method are also disclosed.

Claims

1. A method of determining kinetic parameters for a reversible molecular interaction between a ligand immobilized to a solid support surface and a binding partner to the ligand in solution, comprising the steps of:

a) sequentially, without intermediate regeneration or renewal of the immobilized ligand, flowing a plurality of fluid volumes containing different known concentrations of the binding partner over the solid support surface to permit association of binding partner to the immobilized ligand,

b) flowing over the solid support surface a fluid volume free from binding partner to permit dissociation of binding partner from the ligand,

c) monitoring during steps a) and b) the momentary amount of binding partner bound to the solid support surface related to time and solution concentration of binding partner and collecting the binding data, wherein steps a) to c) are repeated at least once with the same or another sequence of binding partner concentrations, and

d) determining the kinetic parameters by simultaneously fitting a predetermined kinetic model for the interaction between the binding partner and the immobilized ligand to all the collected binding data, which model allows for mass transport limitation at the solid support surface.

2. The method according to claim 1, wherein step d) comprises determining the kinetic parameters by globally fitting the kinetic model to the collected binding data.

3. The method according to claim 1, wherein sequential binding data obtained from steps a) to c) are combined with at least one set of binding data for a single concentration of binding partner, and the combined binding data are fitted in step d) to the kinetic model.

4. The method according to claim 1, wherein step b) is performed after flowing the last fluid volume containing binding partner over the surface.

5. The method according to claim 1, wherein step b) is performed between two fluid volumes containing binding partner.

6. The method according to claim 1, wherein each volume containing binding partner is followed by a fluid volume free from binding partner.

7. The method according to claim 6, wherein one of the fluid volumes free from binding partner is flowed over the solid support surface for a longer time than the other fluid volumes free from binding partner.

8. The method according to claim 7, wherein the last fluid volume free from binding partner is flowed over the solid support surface for a longer time than the other fluid volumes free from binding partner.

9. The method according to claim 1, wherein the plurality of fluid volumes containing binding partner include fluid volumes with the same concentration of binding partner.

10. The method according to claim 1, wherein the fluid volumes containing binding partner contain successively increasing concentrations of binding partner.

11. The method according to claim 1, wherein step a) is stopped when an increased concentration of binding partner results in a predetermined marginal increase in the amount of bound binding partner at the sensor surface.

12. The method according to claim 1, wherein the kinetic model is a two-compartment model.

13. The method according to claim 1, wherein the kinetic model is adapted to an interaction mechanism selected from 1:

1 binding, parallel reactions, competing reactions, conformation change and bivalent analyte.

14. The method according to claim 1, wherein step a) is performed at least one other density of ligand at the solid support surface.

15. The method according to claim 1, wherein the flow over the solid support surface is maintained essentially constant.

16. The method according to claim 1, wherein the fluid volumes containing different known concentrations of the binding partner comprise volume segments taken from a concentration gradient of the binding partner.

17. The method according to claim 1, wherein the solid support surface is a sensor surface.

18. The method according to claim 1, wherein the detection at the solid support surface is based on evanescent wave sensing.

19. The method according to claim 18, wherein the detection at the solid support surface is based on surface plasmon resonance (SPR).

20. The method according to claim 1, wherein the detection at the solid support surface is based on detection of a label.

21. The method according to claim 1, wherein step d) is computer-implemented.

22. A method of determining kinetic parameters for reversible molecular interactions between a ligand immobilized to a solid support surface and a plurality of different binding partners to the ligand in solution, comprising the steps of:

a) sequentially, without intermediate regeneration or renewal of the immobilized ligand, flowing a plurality of fluid volumes containing different binding partners over the solid support surface to permit association of binding partners to the immobilized ligand,

b) after the addition of each fluid volume containing binding partner, flowing over the solid support surface a fluid volume free from binding partner to permit dissociation of binding partner from the ligand,

c) monitoring during steps a) and b) the momentary amount of binding partner bound to the solid support surface related to time and solution concentration of binding partner and collecting the binding data, wherein steps a) to c) are repeated at least once with the same or another sequence of binding partner concentrations, and

d) determining the kinetic parameters by simultaneously fitting a predetermined kinetic model for the interaction between each binding partner and the immobilized ligand to all the collected binding data, which model allows for mass transport limitation at the solid support surface.

23. The method according to claim 22, wherein step d) comprises determining the kinetic parameters by globally fitting the kinetic model to the collected binding data.

24. The method according to claim 22, wherein the solid support surface is a sensor surface.

25. The method according to claim 22, wherein the detection at the solid support surface is based on evanescent wave sensing.

26. The method according to claim 25, wherein the detection at the solid support surface is based on surface plasmon resonance (SPR).

27. The method according to claim 22, wherein the detection at the solid support surface is based on detection of a label.

28. The method according to claim 22, wherein step d) is computer-implemented.

29. A method of determining kinetic parameters for a reversible molecular interaction between a ligand immobilized to a sensor surface and a binding partner to the ligand in solution, comprising the steps of:

a) sequentially, without intermediate regeneration or renewal of the immobilized ligand, flowing a plurality of fluid volumes containing different concentrations of the binding partner over the solid support surface to permit association of binding partner to the immobilized ligand, wherein the fluid volumes containing binding partner are discrete segments of a concentration gradient of the binding partner separated by segments of fluid free from binding partner,

b) monitoring during step a) the momentary amount of binding partner bound to the solid support surface related to time and solution concentration of binding partner and collecting the binding data, wherein steps a) to b) are repeated at least once with the same or another sequence of binding partner concentration, and

c) determining the kinetic parameters by simultaneously fitting a predetermined kinetic model for the interaction between the binding partner and the immobilized ligand to all the collected binding data.

30. The method according to claim 29, wherein the kinetic model allows for mass transport limitation at the solid support surface.

31. The method according to claim 29, wherein the binding partner concentrations of all gradient segments are known, and a global fitting is performed in step c).

32. The method according to claim 29, wherein the binding partner concentrations of all gradient segments are not known, and the fitting performed in step c) includes local fitting of the binding partner concentration.

33. The method according to claim 29, wherein the solid support surface is a sensor surface.

34. The method according to claim 29, wherein the detection at the solid support surface is based on evanescent wave sensing.

35. The method according to claim 34, wherein the detection at the solid support surface is based on surface plasmon resonance (SPR).

36. The method according to claim 29, wherein the detection at the solid support surface is based on detection of a label.

37. The method according to claim 29, wherein step c) is computer-implemented.