Bis sulfone Reagents. Figure 1.

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Karen Newman
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Bis sulfone Reagents An intact IgG molecule has four accessible inter chain disulfide bonds that can be reduced to form eight free cysteine thiols, which can serve as sites for conjugation.

1 Bis sulfone Reagents An intact IgG molecule has four accessible inter chain disulfide bonds that can be reduced to form eight free cysteine thiols, which can serve as sites for conjugation. The reaction between reduced IgG and maleimide reagents yields conjugates composed of a mixture of species with between 0 and 8 payload moieties per antibody. Maleimide based conjugates have been shown to undergo retro addition reactions in the presence of competing thiols. In serum, this can result in de conjugation by exchange reactions with free thiol groups within circulating albumin. Maleimide, as well as other monoalkylation reagents also leave the cysteines from the original disulfides unbridged, introducing a potential for instability to the antibody. A promising solution to these problems is the utilization of bis reactive bridging reagents that are able to restore a covalent linkage between the two cysteines. This approach uses bis sulfone reagents that are selective for the cysteine sulfur atoms from a native disulfide that has been reduced (Figure 2). Mechanistically, the first step is elimination of sulfinic acid to form a conjugated double bond to initiate a sequence of addition elimination reactions (Figure 1). Figure 1. After initial Michael addition of the first thiol, a second elimination of sulfinic acid generates another conjugated double bond for the addition of second thiol. This leads to the formation of a three carbon bridge between two cysteine residues of a reduced native disulfide bond such as the interchain disulfide bonds of a mab. The reaction results in covalent re bridging of the disulfide bond via a three carbon bridge leaving the protein structurally intact. Figure 2.

2 ThioLinker TM Reagents The bis sulfone reagents have been known for almost 25 years, however their application was mostly limited to conjugation of hydrophilic PEGs to proteins. The limited application of these reagents is associated with their rather poor re bridging and conjugation efficiency, which can be attributed to the high hydrophobicity of bis sulfone reagents. Often, functionalization of hydrophobic toxins with a bis sulfone moiety makes the resulting conjugates practically insoluble in aqueous media. To overcome the solubility issue, large amount of organic cosolvents should be used to achieve desired degree of labeling and re bridging. We have developed unique, water soluble bis alkylating reagents that overcome the drawbacks associated with traditional bis sulfone reagents (Figure 3). Incorporation of sulfopropyl groups greatly improves not only solubility but also labeling and re bridging efficiency. In addition, upon functionalization of a payload with water soluble bis alkylating reagents, the aqueous solubility of resulting conjugate is greatly improved compared to unmodified molecule. Figure 3. Several amine, and carboxyl reactive building blocks and clickable reagents are available from Click Chemistry Tools as off shelf products. Upon request our team of chemists can prepare custom ThioLinker TM reagents according to your specification. Two step Approach This approach uses novel bis sulfone reagents to introduce a small bioorthogonal group. The payload, which is equipped with a complementary functional group reactive toward the linker, is then reacted with the protein linker conjugate to yield the desired ADC. In this approach, the first step takes advantage of the selectivity of the bridging reagents, which is used to introduce a new bioorthogonal reactive group that then provides superior reaction kinetics for a second, more complex conjugation reaction. A two step strategy that employs bioorthogonal ligation chemistry is outlined in Figure 4.

3 Figure 4. A distinct advantage of a two step approach is that it is compatible with payloads of any complexity and size as attachment of the payload is done independently from antibody modification. Another advantage of this approach is that it allows for the utilization of different payloads without altering the antibody modification step. In addition, using our meticulously designed, off shelf ThioLinker clickable reagents, very little or no optimization is required to prepare homogeneous ADCs.

4 Protein Modification with Bis- alkylating Reagents Protein Requirements The protein to be reacted with a bis- alkylating reagent must be highly purified and its molecular weight known (e.g kda). The protein must have available disulfide bonds. Proteins must be free of reducing agents (e.g. β- ME, DTT or TCEP) prior to labeling with a bis- alkylating reagent, if present these compounds must be removed (See Material Preparation). Material Preparation A. Preparation of PBS + 10 mm EDTA Buffer (ph 7.5) 1. Prepare PBS (100 mm Sodium Phosphate, 150 mm Sodium Chloride) + 10mM EDTA, ph 7.5. For long- term storage sterile- filter the solution. Do not add sodium azide or Proclin preservatives as these reagents interfere with protein A280 measurements. 2. Degassing and/or purging the buffer with nitrogen or argon is recommended for consistent labeling. B. Protein Preparation 1. If the lyophilized protein ( µg) to be labeled is pure and free of exogenous thiols (e.g. DTT or β- ME), resuspend in 500 µl PBS + 10 mm EDTA (ph 7.5) to obtain a mg/ml solution, proceed to Protein Reduction. 2. If the lyophilized protein is known to contain exogenous thiols (e.g. DTT, β- ME) resuspend in PBS + 10mM EDTA (ph 7.5) then proceed with buffer exchange, followed by Protein Reduction. 3. If the purified protein to be modified ( µg) is already in a suitable thiol- free buffer (e.g. MOPS, Tris- HCL, or PBS) at a concentration range from mg/ml, proceed to Protein Reduction. C. Equilibration of Desalting Column into PBS +10 mm EDTA (ph 7.5) 1. Choose a suitable desalting column. We recommend Pierce Zeba Spin Desalting Columns (7 k MWCO, 2mL). 2. Equilibrate the desalting column into PBS +10 mm EDTA (ph7.5) according to the manufacturer s instructions.

5 D. Buffer Exchange of Protein 1. Buffer exchange protein into PBS +10 mm EDTA (ph 7.5) equilibrated column according to the manufacturer s instructions. 2. Retain the eluate in the collection tube. Discard the used desalting column. 3. Protein is now buffer exchanged. Protein Reduction A. TCEP 1. Prior to labeling with a bis- alkylating reagent, proteins containing disulfide bonds must be reduced with TCEP to insure proper labeling. 2. Prepare mm TCEP stock solution in ultrapure water, vortex to dissolve crystals completely. 3. Add an appropriate volume of TCEP to the protein solution to reach a final TCEP concentration of times molar excess for each disulfide bond to be reduced. For IgG1, this corresponds to a molar excess of TCEP versus antibody. 4. Allow the reduction reaction to incubate for 60 minutes at room temperature. 5. Prepare 2 desalting columns. 6. Buffer exchange TCEP reduced protein TWICE, using 2 consecutive columns B. Immobilized TCEP Disulfide Reducing Gel 1. Using a pipette with the tip cut off, aliquot a volume of resin equal to 4 times the volume of protein solution to be reduced. 2. Centrifuge and wash the resin with PBS+10 mm EDTA (ph 7.5) according to the manufacturer s instructions. 3. Add the protein solution to the washed, packed resin. The volume ratio should be 2:1 compact resin: protein. 4. Pipette up and down to ensure proper mixing of the slurry. Do not vortex. 5. Incubate the slurry for 2-4 hours at 37 C 6. After reduction, centrifuge the resin according to the manufacturer s instructions. Remove the supernatant and proceed to the next step. (Note: for more efficient protein recovery, use a micro- spin column with a solid support to separate the reduced protein from the resin). Labeling Reaction The optimal amount of a bis- alkylating reagent reagent to use for each reaction depends on a number of factors. Usually 10- fold molar excess (2.5- fold molar excess per solvent accessible disulfide bond) of a reagent over IgG results in a DOL around 4, however labeling at

6 high protein concentrations (>5 mg/ml) might require only fold excess of a bis- alkylating reagent per solvent accessible disulfide bond. For Fab fragments labeling, the optimal molar excess of a bis- alkylating reagent is Determine molar excess of a bis- alkylating reagent to be used during the labeling reaction. 2. Determine the concentration of protein solution. 3. Add required amount of water- miscible solvent (e.g. DMSO) or ultrapure water to 5 mm stock solution, vortex vigorously for 2 minutes until the reagent is fully dissolved. Note: Bis- sulfone reagents are not water- soluble, water- miscible solvent should be used to make a stock solution. ThioLinker reagents are water- soluble, water or water- miscible solvent can be used to make a stock solution 4. Add the required volume of a bis- alkylating reagent to the protein solution to achieve the desired molar excess versus protein concentration. Pipette the mixture up and down several times to mix. Allow labeling reaction to proceed overnight at room temperature. Note: For the labeling of Fab fragments, the labeling reaction is usually complete after 4 hours. 5. Remove excess of a bis- alkylating reagent by desalting into PBS (or buffer of choice). Note: At this point in the procedure, EDTA is no longer required. Troubleshooting Problem Possible Cause Solution Incorrect protein Buffer exchange protein into reaction buffer concentration and/or (PBS ph mM EDTA) using spin columns possible contaminants in provided and confirm concentration of protein protein sample. prior to labeling. Poor or lower than expected thiol bridging Insufficient reduction Oxygen in reaction buffer Ensure that proteins are fully reduced. Check TCEP expiration and ensure that stocks are being made immediately before use De- gas buffer prior to use and/or purge with inert gas Protein oligomerization or aggregation Reducing agent is present during reaction Molar excess of a bis- alkylating reagent is too high for the protein of interest Make certain that desalting is effectively removing TCEP after reduction Desalt reduced protein solution twice Reduce the molar excess of a bis- alkylating reagent to 1.5x per disulfide contained in your protein. Zeba is a trademark of Pierce Biotechnology, USA

Data sheet. UV-Tracer TM Biotin-Maleimide. For Labeling of Thiol-groups with UV-detectable Biotin CLK-B Description

Data sheet. UV-Tracer TM Biotin-Maleimide. For Labeling of Thiol-groups with UV-detectable Biotin CLK-B Description Cat. No. CLK-B105-10 CLK-B105-100 Amount 10 mg 100 mg For in vitro use only! Quality guaranteed for 12 months Store at -20 C 1. Description UV-Tracer TM Biotin Maleimide for biotinylation reactions of