Affinity Measurement with Biomolecular Interaction Analysis Biacore

What SPR Biosensors Measures Kinetics Affinity Thermodynamics Specificity Concentration How fast, strong & why… Is the binding of a lead compound How specific & selective... Is this drug binding to its receptor? How much... Biologically active compound is in a production batch?

Biacore History Founded 1984 as Pharmacia Biosensor AB Biacore System launched October 1990 Biacore Symposium 1991 Inline referencing started 1994 Became Biacore AB in 1996 Support of regulated environments from 2002 Entering the drug discovery market with S51 in 2002 Going into protein arrays with Biacore A100 and Flexchip in 2005

Probing Biological Affinities

The Corner-stones of the Technology Sensor Chips SPR Detection IFC Microfluidic

The SPR Detector

Total Internal Reflection & SPR Gold layer Evanescent field Total Internal Reflected light (TIR) TIR angle Incident Light High refractive index medium: Prism Low refractive index medium: Buffer

SPR detection Principle Result SPR detects refractive index changes close to the surface E.g. accumulation of 1 pg/mm2 gives a change of 1 µRIU or 1 RU All biomolecules have refractive properties, so no labeling required Result No need to separate bound from free This facilitates real-time measurements as a basis for taking kinetic data Work with un-altered analytes possible

Sensor Chips Sensor Chip specific matrix Glass Gold 50 nm

Sensor Chip CM5 Dextran matrix covered with carboxyl groupes (red circles) Captures ligands such as proteins, lipids, carbohydrates and nucleic acids (irreversible) Study of analytes ranging in size from small organic molecules, e.g. drug candidates, to large molecular assemblies or whole viruses.

Sensor Chip CM4 Similar to CM5 but with a lower degree of carboxymethylation resulting in low immobilization capacity and lower surface charge density. Allows to reduce non specific binding in case of complex mixture such as cell extract or culture medium. Advantageous for kinetic experiments where low immobilization levels are recommended.

Sensor Chip CM3 Similar to CM5 but with shorter dextran chains, giving a lower immobilization capacity of the surface. Allows the interaction to take place closer to the cell surface which can improve sensitivity when working with large molecules, molecular complexes, viruses or whole cells.

Sensor Chip SA CM dextran matrix pre-immobilized with streptavidin Captures biotinylated ligands such as carbohydrates, peptides, proteins and DNA (irreversible) Ideal for capture of large biotinylated DNA fragments and study of nucleic acid interactions

Sensor Chip NTA CM dextran matrix pre-immobilized with nitrilotriacetic acid (NTA) Capture of His-tagged ligands via metal chelation Controled steric orientation of ligand for optimal site exposure Regeneration by injection of EDTA to remove metal ions

Sensor Chip L1 CM dextran matrix modified with lipophilic anchor molecules For rapid and reproducible capture of lipid membrane vesicles such as liposomes, with retention of lipid bilayer structure Allows studies of transmembrane receptors in a membrane-like environment , for example.

The Steps in the Biacore Assay Surface preparation Analysis Cycle

Surface Preparation: Immobilization y t e i g d c p u r m o a n l y t e i g d Direct Capture Covalent coupling of Regeneration down to ligand capture molecule

Direct Immobilization

Various Coupling Chemistries

Amine Coupling - Sensorgram Activation = EDC/NHS injection  surface esters Ligand contact = reaction with amine groups on ligand Blocking = deactivation of free esters with ethanolamine Blocking Activation Ligand contact

High Affinity Capture

Capture Surfaces and Molecules Type Product/Molecule Comment Anti-Antibody RaM Fc anti-human Fc Available from Biacore Use affinity-pure products Anti-tag anti-GST anti-His Strep-MAB anti-Biotin E.g. Penta-His See IBA Anti-Fc Protein A / G / L - Biotin-binding Avidin family StrepTactin Streptavidin / Neutravidin Oligos Sequence specific Home made Sensor Chip SA, NTA, L1

Analysis Cycle Generates the desired data Sample injection Regeneration Evaluation

Analysis Cycle Done by Sample injection Results Regeneration Buffer flow, pH shift, salt & chaotrophic ions, detergents Similar concept as in affinity chromatography Results Re-use of biospecific surface Low amount of ligand needed Sample injection Regeneration Evaluation

The Result: the Sensorgram

Experiments without Kinetics Specificity Multi layer structure Concentration assays Affinity constants

Specificity Do two molecules interact with each other? Yes/No Answers. Different analytes are tested with the same ligand e.g. different lectins with immobilized thyroglobulin. Quantitative measurements, test a range of analyte concentration to determine the concentration dependency of the response.

Specificity Analysis Overplay plot of sensorgrams showing interaction between different lectins and immobilized thyroglobulin.

Multiple Binding Enhancement Sandwich assays Epitope mapping Enhancing lower detection limit of assays Sandwich assays Enhancing selectivity of test Epitope mapping Charting the surface of antigens with antibodies Multimolecular complexes Identify the logical sequence of binding events

Multiple Binding Analyte Ligand 2nd Binder 26000 27000 28000 29000 30000 31000 Response [RU] 50 100 150 200 250 300 350 400 Time [s]

Epitope Specificity of two mAbs against HIV1-p24 Immobilization of rabbit rabbit anti-mouse IgG1 A: baseline A-B: 1st mAb against HIV1-p24 B-C: blocking antibody C-D: HIV1-p24 D-E: 2nd mAb against HIV1-p24

Concentration Assays Concentration based on biological activity All concentration assays require a calibration curve Concentrations of unknowns samples are calculated from this 4 - 7 concentrations in duplicate Calibrants and unknowns in same matrix Moderate to high densities on sensor chip Direct binding formats Inhibition formats

= Calibration Curves Sample matrix for calibration curve Response x Sample x x x x Concentration = Sample matrix for calibration curve Sample matrix for unknown samples

Affinity Analysis How STRONG is the binding at equilibrium? » Quantify KD » Rank Antibodies » Find best Ab pairs

Affinity and Equilibrium Furosemide binding to carbonic anhydrase Referenced data Report Point towards end of injection Do secondary plot 5 10 15 20 60 120 Signal [RU] Time [s]

Determining Affinity Constants Plot Req against C Steady state model Concentration at 50% saturation is KD

Kinetic Analysis How FAST is the binding ? » ka kon (recognition) » kd koff (stability) » KD = kd/ka » Ab selection; wash steps

Same Affinity but different Kinetics All four compounds have the same affinity KD = 10 nM = 10-8M The same affinity can be the result from different kinetics ka [M-1s-1] kd [s-1] All target sites occupied 30 min 60 min 100 nM 1 µM 30 min 60 min 106 10-2 105 10-3 104 10-4 103 10-5 KD 10 nM

Rate Constants Association rate constant ka Dissociation rate constant kd Definition ka A + B AB kd AB A + B Unit [M-1s-1] [s-1] Describes Rate of complex formation, i.e. the number of AB formed per second in a 1 molar solution of A and B Stability of the complex i.e. the fraction of complexes that decays per second. Typical range 1x10-3 – 1x107 1x10-1 – 5x10-6

Equilibrium Constants Equilibrium dissociation constant KD Equilibrium association constant KA Definition Unit [M] [M-1] Describes Dissociation tendency High KD = low affinity Association tendency High KA = high affinity Typical range 1x10-5 – 1x10-12 1x105 – 1x1012 kd (A).(B) (AB) = ka (AB) ka = kd (A).(B)

Equilibrium and Kinetic Constants are related

Equilibrium and Kinetics in Biacore

Information in a Sensorgram

Extracting Rate Constants from Sensograms Measure binding curves Decide on a model to describe the interaction Fit the curve to a mathematical rate equation describing the model e.g. Obtain values for the constants ka, kd, Rmax Assess the fit overlay pots, residual plots acceptable statistics e.g. chi2 – curve fidelity Biological and experimental relevance of the calculated parameters dR dt = ka. C . (Rmax-R) – kd . R

Biacore and other Methods Conventional Assays Time Method Time Isotyping Day 1 ELISA One Day RIA Weeks + labelling Affinity Day 1&2 Kinetics Day 1&2 Na Na ELISA Weeks + labelling Epitope Map Overnight Biacore is much quicker than conventional methods

Summary Surface plasmon resonance detects binding events as changes in mass at the chip surface Real-time kinetic measurements Qualitative rankings Measurement of concentrations Information about structure-activity relationships No labeling and low volumes samples needed