Supporting Information

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1 Supporting Information Systematic Evaluation and ptimization of Modification Reactions of ligonucleotides with Amines and Carboxylic Acids for the Synthesis of DA-Encoded Chemical Libraries Raphael M. Franzini, a Florent Samain, b Maaly Abd Elrahman, a Gediminas Mikutis, b Angela auer, a Mauro Zimmermann, a Jörg Scheuermann, a Jonathan all, a and Dario eri a* a Institute of Pharmaceutical Sciences, ET Zürich, Vladimir-Prelog Weg 1-5, 8093 Zürich, Switzerland. b Philochem AG, Liebernstrasse 3, 8112 telfingen, Switzerland. dario.neri@pharma.ethz.ch; Tel.: Table of Contents Figure S1 Solvent dependence of S 2 reaction S2 Figure S2 Dependence of pseudo-solid phase S 2-reaction on experimental parameters S3 Figure S3 Dependence of solid-phase S 2 reaction on experimental parameters S4 Figure S4 Effect of heating and microwave irradiation S5 Figure S5 Dependence of reductive amination on amine concentration S6 Figure S6 Dependence of reductive amination of ab 3 C concentration S7 Figure S7 Effect of organic solvents on reductive amination S8 Figure S8 DA-conjugates S9 Figure S9 Formation of EDC adducts S9 Figure S10 Possible mechanism for EDC adduct formation S10 Figure S11 Formation of ethyl carbamate side product S10 Table S1 Mass-spectrometric analysis of benzylamine test reactions S11 Table S2 Mass-spectrometry analysis of Table 1 S12 Table S3 Mass-spectrometry analysis of Table 2 S12 1

2 Figure S1. Dependence on solvents of product formation for the solid phase reaction between ClAc-DA and Bn 2 (Method B; c(bn 2 ) = 0.5 M, t = 2 h, T = room temperature). Peaks designated with * are termination sequences of DA solid-phase synthesis and are excluded from analysis of conversion rate. Similar solvent dependence was found for nucleophilic substitution on pseudo-solid phase (not shown). ipr was also tested as solvent and provided lower yields (not shown). PLC conditions: C18-XTerra column (5 μm, 10 on 10 x 150 mm, Waters, Milford, CT) and using a linear gradient from 5% to 32% MeC in 100 mm TEAA, p 7 over a period of 20 min. 2

3 Figure S2. Dependence of product formation on experimental conditions for the pseudo-solid phase reaction between ClAc-DA and Bn 2 (Method A). a) Dependence on the concentration of Bn 2. (Solvent = DMS, t = 2 h, T = room temperature). b) Dependence on the reaction time (Solvent = DMS, c(bn 2 ) = 0.25 M, T = room temperature). Bottom PLC trace is ClAc-DA after coupling of the acid but prior to S 2-reaction. Two peaks in the PLC were not included for the determination of the conversion yield (designated by *). These peaks corresponded to an impurity in the DA (peak 1) and unmodified DA- 2 (peak 2). The size of these peaks varied significantly between different batches of DA and reactions. The values in parenthesis indicated the conversion yields including these peaks for analysis. PLC conditions: C18-XTerra column (5 μm, 10 on 10 x 150 mm, Waters, Milford, CT) and using a linear gradient from 5% to 32% MeC in 100 mm TEAA, p 7 over a period of 20 min. 3

4 Figure S3. Dependence of product formation on experimental conditions for the reaction between ClAc-DA and Bn 2 on the solid phase (Method B). a) Dependence on the concentration of Bn 2 (Solvent = DMF, t = 2 h, T = room temperature). b) Dependence on the reaction time (Solvent = DMF, c(bn 2 ) = 0.5 M, T = room temperature). The DA on the solid-support is unpurified and contains incompletely synthesized DA sequences (failure sequences), which have no amine available for modification. Peaks below 9 min (designated by *) are therefore a result of incomplete DA-solid phase synthesis and are irrelevant for the conversion rate and were therefore excluded from the analysis of the conversion rate. PLC conditions: C18-XTerra column (5 μm, 10 on 10 x 150 mm, Waters, Milford, CT) and using a linear gradient from 5% to 32% MeC in 100 mm TEAA, p 7 over a period of 20 min. 4

5 Figure S4. Influence of heating and microwave irradiation on the product formation by nucleophilic substitution of ClAc-DA with benzylamine on solid support analyzed by mass spectrometry of PLC purified conjugate (Method D). a) eating to 50 C for 16 h. b) Microwave irradiation (10 pulses of 15 s at 900 W followed by cooling at room temperature for 5 min). LS-MS analysis was performed on a tandem-quadrupole mass-spectrometer (Quattro micro API, Waters, Milforf, CT) with electrospray ionization source (negative charge mode) and 400 mm hexafluoroisopropanol and 15 mm triethylamine in Me for elution. 5

6 Figure S5. Dependence on the concentration of Bn 2 of the rate of conversion of reductive amination of DA-C (Method C) [MPS buffer, p 7.4, 1 eq. Ac (relative to Bn 2 ), c(da) = 20 μm, c(ab 3 C) = 15 mm, t = 16 h, T = 37 C, 5% DMF]. PLC conditions: C18-XTerra column (5 μm, 10 on 10 x 150 mm, Waters, Milford, CT) and using a linear gradient from 5% to 20% MeC in 100 mm TEAA, p 7 over a period of 20 min. 6

7 Figure S6. Dependence on concentration of ab 3 C of the rate of conversion of reductive amination of DA-C with Bn 2 (Method C) (MPS buffer, p 7.4, c(bn 2 ) = 50 mm, c(ac) = 50 mm, c(da) = 20 μm, t = 16 h, T = 37 C, 5% DMF). PLC conditions: C18-XTerra column (5 μm, 10 on 10 x 150 mm, Waters, Milford, CT) and using a linear gradient from 5% to 20% MeC in 100 mm TEAA, p 7 over a period of 20 min. 7

8 Figure S7. Influence of the presence of organic solvents (DMF) on the rate of conversion of reductive amination of DA-C with Bn 2 in solution (Method C) (MPS buffer, p 7.4, c(bn 2 ) = 50 mm, c(ac) = 50 mm, c(ab 3 C) = 50 mm, c(da) = 20 μm, t = 16 h, T = 37 C). Left peak is DA-C (starting material) and right peak is product. PLC conditions: C18-XTerra column (5 μm, 10 on 10 x 150 mm, Waters, Milford, CT) and using a linear gradient from 5% to 20% MeC in 100 mm TEAA, p 7 over a period of 20 min. 8

9 DA-sequences for test reactions: Method A: Cl 12 P - -GGA GCT TGT GAA TTC TGG ATC TTA GGA CGT GTG TGA ATT GTC-3' Method B: 2 12 P - -GGA GCT TCT GAA TTC TGT GTG CTG XXX XXX CGA GTC CCA TGG CGC-3' Different sequences were used for the test reactions, X being variable monomers. Method C: P - -GGA GCT TGT GAA TTC TGG ATC TTA GGA CGT GTG TGA ATT GTC -3' Method D: 12 P - -GGA GCT TCT GAA TTC TGT GTG CTG CAC CTT CGA GTC CCA TGG CGC-3' Figure S8. DA-sequences and conjugates used for the test experiments used to evaluate the different bioconjugation methods. a) b) Figure S9. EDC-adduct formation during attachment of carboxylic acid to amine-modified DA on pseudo-solid phase analyzed by mass-spectrometry (deconvoluted mass). Left figure example of carboxylic acid for which EDC adduct formation was negligible; right figure: example of carboxylic acid for which mono- and bis-edc adducts were observed alongside the expected DA-conjugate. LS-MS analysis was performed on a tandem-quadrupole mass-spectrometer (Quattro micro API, Waters, Milforf, CT) with electrospray ionization source (negative charge mode) and 400 mm hexafluoroisopropanol and 15 mm triethylamine in Me for elution. 9

10 Figure S10. Possible formation of covalent adducts between DA and carbodiimides (e.g., ethyl-3,3-dimethylaminopropylcarbodiimide). b) + C EEDQ + + Starting Material Product Carbamate Figure S11. Formation of ethylcarbamate side product during amide bond formation with EEDQ as the coupling reagent. a) Example of PLC trace of product mixture of reaction of BnAc-DA with adamantylacetic acid. b) Starting products and product for amide bond forming reaction with EEDQ. 10

11 Table S1. Mass-spectrometric analysis of the test reactions for evaluating the substrate scope of the different bioconjugation methods (corresponds to conjugates of Figure 4b). Method A Method B Method C Method D AM AM AM AM AM AM AM AM AM a a AM AM a a b AM a Coupling yield was insufficient for mass determination. b The found mass is indicative for mono-methylation of the amidine-functionality during deprotection with aq. 2/Me 2. Deprotection with aq. 3 (14 h at 60 C) provided a conjugate with a found mass of Considering the symmetry of the amidine group, a mono-methyladduct may be a result of initial formation of dimetylamidine followed by hydrolysis of the amidine to the methylcarboxamide. The resolution of the LC-MS is insufficient to distinguish between the amidine and the carboxamide derivatives. 11

12 DA DA DA DA Table 2. Mass-spectrometric analysis of the test reactions for evaluating the substrate scope of the different bioconjugation methods (corresponds to conjugates of Table 1). S 2 CA S CA-2 CA-3 CA-4 CA-5 CA-6 CA-7 CA-8 CA-9 CA-10 CA F Cl a Masses were determined only for coupling yields >30% because of limited sensitivity of the instrument S S S Br Table 3. Mass-spectrometric analysis of the test reactions for evaluating the substrate scope of the different bioconjugation methods (corresponds to conjugates of Table 2). EDC (1 eq.)/ At (0.1eq.) DA EEDQ (4 eq.) PyBroP (2 eq.) DA EDC (1 eq.)/ At (0.1eq.) EEDQ (4 eq.) PyBroP (2 eq.) CA-1 CA S CA Cl F CA-4 CA CA a Masses were determined only for coupling yields >30% because of limited sensitivity of the instrument. 12