Small-Molecule Kinetics

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1 Application Note No. 1 / September 1, 2014 Small-Molecule Kinetics Creoptix WAVE

2 Small-Molecule Kinetics: Binding of Sulfonamides to Carbonic Anhydrase II Summary Label-free interaction analysis of biomolecules using optical biosensors is a key technique in the drug discovery process. Optical biosensors are capable of measuring the reversible binding of biological molecules in a label-free manner and in real time, thus providing detailed thermodynamic and kinetic information. The screening of smallmolecule binding to targets demands highest sensitivity. By measuring the binding kinetics of small molecule inhibitors of Carbonic Anhydrase II, we here show that the Creoptix WAVE system provides best-in-class sensitivity thanks to waveguide-based interferometry and achieves outstanding resolution at even very low signal levels. This demonstrates that the Creoptix WAVE system enables characterization of small and weak binding molecules at high accuracy. through-put of a screen and avoiding any interference by the label. The accurate determination of binding constants for very small molecules (~ Da) is challenging for most label-free technologies currently available on the market. The small size of the molecule and the often weak binding requires very high sensitivity to obtain sufficient resolution at even low signal levels. Creoptix has introduced the WAVE system, an optical biosensor with outstanding sensitivity thanks to its proprietary waveguidebased interferometry approach 1,2. Introduction Detailed information on small-molecule-to-target interactions are crucial to a successful drugdiscovery process. Optical biosensors are an established method in both the pharma-ceutical industry as well as academia for the determination of thermodynamic and kinetic properties of such interactions. The reversible association of small molecules to immobilized target molecules can be monitored in real time, thus providing information on binding kinetics. Optical biosensors further allow the screening of compounds in a label-free manner, no chemical modification is required, thus increasing the In this application note, we investigate the binding of five small-molecule inhibitors interacting with the enzyme carbonic anhydrase II (CAII). CAII is an enzyme that catalyzes the reversible hydration of carbon dioxide to form bicarbonate with the release of a proton 3,4.

3 Material & Methods Carbonic anhydrase isotype II from bovine erythrocytes, sulfonamide inhibitors and the reagents for amine coupling (1-ethyl-3-(3- dimethylaminopropyl) carbodiimide (EDC) and N- hydroxysuccinimid (NHS)) were purchased from Sigma-Aldrich. Carbonic anhydrase II was immobilized on a WAVEchip (CMH type) through standard amine coupling to a dextran matrix. Phosphate buffered saline (PBS) containing 0.05% Tween 20 and 3% DMSO was used as running buffer. The flow rate was set to 10 ml/min for all steps during immobilization. The carboxymethyl groups of the dextran surface were activated by a 7 minute injection of an EDC/NHS mixture in water at a concentration of 200/50 mm. Protein was diluted into 10 mm acetate buffer ph 5 to a final concentration of 30 mg/ml and injected for 210 seconds over channel 1 only. Channel 2 was used as reference channel. Active sites were quenched for 7 minutes by deactivation with 1 M ethanolamine solution. 1 2 ❶ ❷ ❸ ❹ ❺ Figure 1: Carbonic Anhydrase II inhibitors tested: (1) Furosemide, (2) Acetazolamide, (3) Sulfanilamide, (4) Benzenesulfonamide and (5) Methylsulfonamide. Binding of the following carbonic anhydrase II inhibitors was measured; furosemide, acetazolamide, benzenesulfonamide, sulfanil-amide and methylsulfonamide (Fig. 1 and Tab. 1). The compounds were directly dissolved in running buffer to give a 1 mm stock solution with the exception of methylsulfonamide for which a 300 mm stock solution was prepared. A three-fold dilution series in running buffer was prepared with a total of 8 concentrations. A total of 5 buffer injections in-between compounds were used for double referencing of the sensor data. No regeneration of the ligand surface was required due to the fast dissociation rates. Association and dissociation were monitored for 70 and 210 seconds, respectively, at a flow rate of 60 ul/min. All experiments were performed at 25 C. Results Experimental setup and evaluation were accomplished using the Creoptix WAVEcontrol and Scrubber (BioLogic, Australia) software. The covalent immobi-lization of the carbonic anhydrase II through amine coupling resulted in a ligand density of approx pg/mm 2. Representative binding curves (raw un-smoothed data, double referenced) for the compounds are shown in Figure 2. The association and dissociation rate constants were obtained for compounds 1 to 4 by fitting of the experimental data to a 1:1 interaction model. The obtained kinetic constants and the calculated global KD s are shown in Table 1 and correlate well with the published values for these compounds 3,4 (data not shown). In addition, the equilibrium analysis of the binding data is shown as an inset in Figure 2. The response signal at equilibrium was plotted against the analyte concentration and fitted with a 1:1 binding isotherm. The obtained dissociation constants at equilibrium are summarized in Table 1. Note that for methylsulfonamide, the fast rate constants precluded the determination of the onand off-rates.

4 ❶ ❷ ❸ ❹ ❺ Figure 2. Representative binding data for carbonic anhydrase II inhibitors: (1) Furosemide, (2) Acetazolamide, (3) Sulfanilamide, (4) Benzenesulfonamide and (5) Methylsulfonamide. Data analysis with Scrubber Software. Compounds 1, 3 and 4 were tested in eight concentrations of a 3-fold dilution series from 45.7 nm to 100 M. Compound 2 was tested in eight concentrations of a 3-fold dilution series from nm to 1 M. Compound 5 was tested in five concentrations of a 3-fold dilution series from 37 M to 3 mm. Kinetic determination Equilibrium determination ID Compound Mw (Da) k on (M -1 s -1 ) k off (s -1 ) k m R max K D (µm) R max K D (µm) ❶ Furosemide x ❷ Acetazolamide x x ❸ Sulfanilamide x ❹ Benzenesulfonamide x ❺ Methylsulfonamide n.d. n.d. - n.d. n.d Table 1. Kinetic and thermodynamic data obtained for the binding of inhibitors to carbonic anhydrase II

5 Discussion The label-free analysis of molecular interactions plays an increasing role in today s drug discovery and life science research. However, the binding characterization of small molecules imposes a high hurdle to today s available instrumentation in label-free bio-sensing due to limited sensitivity. This is especially true in the case of weak binders as signal levels become too low for a sufficient resolution. Here we demonstrate that the Creoptix WAVE system is capable of accurately determining the binding characteristics of small molecule drugs using different sulfonamide-based inhibitors of Carbonic Anhydrase II as example. We also demonstrate the outstanding high sensitivity of the WAVE system by the high resolution of the low signals generated by methylsulfonamide a very small (Mw Da) and weakly binding inhibitor. These studies show that the Creoptix WAVE system becomes an invaluable tool for every drug discovery project as its outstanding sensitivity and resolution generate data of so far unreached accuracy and quality. References 1. Kunz, R. E. & Cottier, K. Optimizing integrated optical chips for label-free (bio-chemical sensing. Anal. Bioanal. Chem. 384, (2006). 2. P. Kozma, A. Hamori, K. Cottier, S. Kurunczi, R. Horvath, Grating coupled interferometry for optical sensing, Applied Physics B Lasers and Optics, Volume 97, Number 1, pp 5-8 (2009) 3. Papalia, G. A. et al. Comparative analysis of 10 small molecules binding to carbonic anhydrase II by different investigators using Biacore technology. Anal. Biochem. 359, (2006). 4. Myszka, D. G. Analysis of small-molecule interactions using Biacore S51 technology. Anal. Biochem. 329, (2004). Contacts for Ordering and Information Creoptix AG Einsiedlerstrasse Wadenswil Switzerland Phone Mobile info@creoptix.com

Small-Molecule Kinetics

Application Note No. 1 / February 4, 2015 Small-Molecule Kinetics Creoptix WAVE Small-Molecule Kinetics: Binding of Sulfonamides to Carbonic Anhydrase II Summary Label-free interaction analysis of biomolecules