Study of On-Resin Convergent Synthesis of N-Linked. Glycopeptides Containing a Large High Mannose N- Linked Oligosaccharide

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1 Supporting Information Study of On-Resin Convergent Synthesis of N-Linked Glycopeptides Containing a Large High Mannose N- Linked Oligosaccharide Rui Chen and Thomas J. Tolbert* Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana tolbert@indiana.edu

2 Table of Contents: 1. Testing Allyl and 2-phenylisopropyl as orthogonal protecting groups for Asp side chain (p. 2) 2. Glycosylamine conversions (p. 7) 3. Recovery of unreacted Man 8 GlcNAc 2 (p. 8) 4. Glycopeptide 3:Fmoc-AKSAN(GlcNAc)E-NH 2 (p. 11) 5. Glycopeptide 4: Fmoc-AKSAN(Man 8 GlcNAc 2 )E-NH 2 (p. 12) 6. Glycopeptide 5: Fmoc-N(Man 8 GlcNAc 2 )STWFN-NH 2 (p. 13) 7. Glycopeptide 6:Fmoc-CN(Man 8 GlcNAc 2 )ISR-NH 2 (p. 14) 8. C34 peptide 7 (p. 15) 9. GlcNAc-C34 glycopeptide 8 (p. 16) 10. Man 8 GlcNAc 2 -C34 glycopeptide 9 (p. 17) 11. High mannose glycan Man 8 GlcNAc 2 (p. 18) 12. Reference (p. 20) 1. Testing Allyl and 2-phenylisopropyl as orthogonal protecting groups for Asp side chain Peptide sequence AKSADE and CNISR were synthesized on rink amide PEGA resin. Both Allyl and PhiPr groups were used to protect Asp side chain. After the last amino acids building, peptides were cleaved from resin by TFA (without Fmoc deprotection). The crude samples were analyzed by ESI-MS and analytical HPLC to show the quality of the resin-bound peptides. The PhiPr group was removed during TFA treatment for resin cleavage. 2

3 Figure S1. ESI-MS for the synthesis of Fmoc-AKSADE-NH 2. a) Close to complete aspartimide formation by using Allyl protecting group. b) Suppression of aspartimide formation by using PhiPr protecting group. Expected Mass: Fmoc-AKSADE-NH 2 [M+H] + =841.9; Fmoc-AKSAD(O-Allyl)E-NH 2 : [M+H] + =881.9; aspartimide: [M+H] + =

4 Figure S2. Analytical HPLC at 254 nm (0-80% B, 10 min, Beckman SGB 0.46x5 cm Zorbax C8 column, A buffer: Water, 0.1% TFA; B buffer: 90% Acetonitrile 10% Water 0.1% TFA) for the synthesis of for the synthesis of Fmoc-AKSADE-NH 2. a) 100% aspartimide formation by using Allyl protecting group. b) Suppression of aspartimide formation to less than 4% by using PhiPr protecting group. 4

5 Figure S3. ESI-MS for the synthesis of Fmoc-CDISR-NH 2. a) Large amounts of aspartimide formation by using Allyl protecting group; b) Suppression of aspartimide formation by using PhiPr protecting group. Expected Mass: Fmoc-CDISR-NH 2 [M+H] + =814.9; Fmoc-CD(O-Allyl)ISR-NH 2 [M+H] + =855.0; aspartimide: [M+H] + =

6 Figure S4. Analytical HPLC at 254 nm (0-80% B, 10 min, Beckman SGB 0.46x5 cm Zorbax C8 column, A buffer: Water, 0.1% TFA; B buffer: 90% Acetonitrile 10% Water 0.1% TFA) for the synthesis of Fmoc-CDISR-NH 2. a) 40% aspartimide formation by using Allyl protecting group; b) Complete suppression of aspartimide formation by using PhiPr protecting group. 2. Glycosylamine conversions 6

7 Scheme S1. Conversion of free sugar free sugar N-acetyl-D-glucosamine and Man 8 GlcNAc 2 into their corresponding glycosylamines 1 and 2 by the treatment of ammonium hydrogen carbonate. Figure S Hz 1 H-NMR spectra in D 2 O of free reducing end N-acetyl-D-glucosamine after 5 days treatment of ammonium hydrogen carbonate, showing high yield conversion into its corresponding glycosylamine 1. 7

8 Figure S6.. Characterizations of Man 8 GlcNAc 2 NH 2 2 by a) MALDI-TOF-MS, expected mass for C 64 H 109 N 3 O 50 Na, [M+Na] + : ; b) expanded MALDI-TOF-MS; c) expanded 400 Hz 1 H- NMR spectra in D 2 O of c) free reducing end Man 8 GlcNAc 2, and after 5 days treatment with ammonium hydrogen carbonate, showing high yield conversion into its corresponding; d) glycosylamine Recovery of unreacted Man 8 GlcNAc 2 Reaction solutions in DMSO from different Man 8 GlcNAc 2 NH 2 on-resin coupling synthesis trials were pooled together and precipitated by diethyl ether anhydrous. The precipitate was then re-dissolved in a loading buffer (10:3:3 ethyl acetate/methanol/water) and purified by silica gel flash chromatography (ethyl acetate/methanol/ water, 10:3:3 to 5:3:3). Fractions containing glycan were detected positively by phenolsulfuric acid test 1, then pooled together and lyophilized to give Man 8 GlcNAc 2, yield 78% (based on the extra equivalents of Man 8 GlcNAc 2 in reactions). Shown below are the comparison of recovered and freshly 8

9 produced Man 8 GlcNAc 2 and the initial study of reusing recovered Man 8 GlcNAc 2 to couple to rink amide PEGA resin bound Fmoc-Asp and Fmoc-Glu. Figure S Hz 1 H-NMR spectra in D 2 O of a) freshly produced Man 8 GlcNAc 2 ; b) recovered Man 8 GlcNAc 2 from on-resin glycosylation reactions. Recovered Man 8 GlcNAc 2 was converted into glycosylamine 2 again by the treatment of ammonium hydrogen carbonate as described in paper. Fmoc-Asp(O-PhiPr)-OH and Fmoc-Glu(O-PhiPr)-OH were loaded as the first amino acid on rink amide PEGA resin and then PhiPr group was removed by the treatment of 1% TFA. Recovered and reproduced glycosylamine 2 was used to couple to the free acid of resin bound Fmoc-Asp and Fmoc-Glu respectively using the condition, 3 equiv. of glycosylamine 2, 1.5 equiv. of DIEA and 3 equiv. of DEPBT in DMSO, 12 Room Temp. Shown below are the results of the crude samples from these two on-resin glycosylation reactions. 9

10 Figure S8. MALDI-TOF-MS and analytical HPLC for crude sample from on-resin coupling of glycosylamine 2 (produced from recovered Man 8 GlcNAc 2 ) to Rink amide PEGA resin bound a) Fmoc-Asp, expected mass for Fmoc-Asp(Man 8 GlcNAc 2 )-CONH 2, [M+Na] + = ; b) Fmoc- Glu, expected mass for Fmoc-Glu(Man 8 GlcNAc 2 )-CONH 2, [M+Na] + =

11 4. Glycopeptide 3:Fmoc-AKSAN(GlcNAc)E-NH 2 Figure S9. Characterizations of glycopeptide 3 Fmoc-AKSAN(GlcNAc)E-NH 2 by a) ESI-MS and b) analytical HPLC at 214 nm for purified glycopeptide from synthesis entry 5 in Table 1, 2.3 mg, yield (based on Fmoc quantification of the first amino acid loading) 75%. Expected Mass, [M+H] + =

12 5. Glycopeptide 4: Fmoc-AKSAN(Man 8 GlcNAc 2 )E-NH 2 Figure S10. Characterizations of glycopeptide 4 Fmoc-AKSAN(Man 8 GlcNAc 2 )E-NH 2 by a) MALDI- TOF-MS and b) analytical HPLC at 214 nm for purified glycopeptide from synthesis entry 10 in Table 1, 1.2 mg, yield (based on Fmoc quantification of the first amino acid loading), 36%. Expected Mass, [M+Na] + =

13 6. Glycopeptide 5: Fmoc-N(Man 8 GlcNAc 2 )STWFN-NH 2 Figure S11. Characterizations of glycopeptide 5 Fmoc-N(Man 8 GlcNAc 2 )STWFN-NH 2 by a) MALDI- TOF-MS and b) analytical HPLC at 214 nm for purified glycopeptide from synthesis entry 16 in Table 1, 1.3 mg, yield (based on Fmoc quantification of the first amino acid loading), 76%. Expected Mass, [M+Na] + =

14 7. Glycopeptide 6:Fmoc-CN(Man 8 GlcNAc 2 )ISR-NH 2 Figure S12. Characterizations of glycopeptide 6 Fmoc-CN(Man 8 GlcNAc 2 )ISR-NH 2 by a) MALDI-TOF- MS and b) analytical HPLC at 214 nm for purified glycopeptide from synthesis entry 17 in Table 1, 2.4 mg, yield (based on Fmoc quantification of the last amino acid loading), 43%. Expected Mass, [M+H] + =

15 8. C34 peptide 7 Figure S13. Characterizations of C34 peptide, by a) MALDI-TOF-MS and b) analytical HPLC at 214 nm for purified C34 peptide, 2.2 mg, yield (based on Fmoc quantification of the first amino acid loading), 20%. Expected Mass, [M+H] + =

16 9. GlcNAc-C34 glycopeptide 8 The on-resin glycosylamine coupling for the synthesis of GlcNAc-C34 peptide was conducted by using the 3 equivalents of glycosylamine 1, 3 equivalents of DEPBT, 1.5 equivalents of DIEA in DMSO for 12 hours. N-terminal Fmoc was removed before the cleavage of resin. Figure S14. Characterizations of peptide 7, GlcNAc-C34, by a) MALDI-TOF-MS and b) analytical HPLC at 214 nm for purified peptide, 2.1 mg, yield (based on Fmoc quantification of the first amino acid loading), 17%. Expected Mass, [M+H] + = Man 8 GlcNAc 2 -C34 glycopeptide 9 16

17 The on-resin glycosylamine coupling for the synthesis of Man 8 GlcNAc 2 -C34 peptide was conducted by using the 3 equivalents of glycosylamine 2, 3 equivalents of DEPBT, 1.5 equivalents of DIEA in DMSO for 12 hours. N-terminal Fmoc was removed before the cleavage of resin. Figure S15. Characterizations of peptide 8 Man 8 GlcNAc 2 -C34 by a) MALDI-TOF-MS and b) analytical HPLC at 214 nm for purified peptide. 1.3 mg, yield (based on Fmoc quantification of the first amino acid loading), 10%. Expected Mass, [M+H] + =

18 11. High mannose glycan Man 8 GlcNAc 2 High mannose glycan Man 8 GlcNAc 2 was produced in glycosylation deficient yeast in relatively large scale, manuscript in preparation. 1 H-NMR (500 MHz in D 2 O, Varian Inova NMR Spectrometer) ppm: δ (s, 1H), δ (d, J=1.5 Hz, 1H). δ (d, J=2.5Hz, 0.6H), δ (d, J=1.5 Hz, 1H), δ (d, J=1.5Hz, 1H), δ (br, 2H), δ (d, J=1.5Hz, 1H), δ (d, J=8.0 Hz, 0.4H), δ (m, 1H), δ (d, J=2.5Hz, 1H), δ (m, 1H), δ (dd, J=3.5, 2 Hz, 1H), δ (dd, J=3.5, 1.5 Hz, 1H), δ (m, 3H), δ (m, 1H) δ (m, 53H), δ (s, 3H), δ 2.060( s, 3H). HRESI-TOF MS: m/z= , calcd. for C 64 H 108 N 2 O 51 Na 2, [M+2Na] 2+ : Figure S16. HRESI-TOF MS of Man 8 GlcNAc 2 (produced in yeast). 18

19 Figure S17. a) 500 MHz 1 H-NMR spectra of Man 8 GlcNAc 2 (produced in yeast) in D2O, the inset shows the sugar labeling nomenclature. b) Expansion of the 1 H-NMR spectra to show the anomeric fingerprint region with H-1 and H-2 assignments labeled 2. 19

20 References (1) Dubois, M.; Gilles, K. A.; Hamilton, J. K.; Rebers, P. A.; Smith, F. Anal. Chem. 1956, 28, 350. (2) Jongen, S. P.; Gerwig, G. J.; Leeflang, B. R.; Koles, K.; Mannesse, M. L.; van Berkel, P. H.; Pieper, F. R.; Kroos, M. A.; Reuser, A. J.; Zhou, Q.; Jin, X.; Zhang, K.; Edmunds, T.; Kamerling, J. P. Glycobiology 2007, 17,

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