Nature Protocols: doi: /nprot Supplementary Figure 1. HyCoSuL synthesis and quality control exemplified with the P2 sublibrary.
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1 Supplementary Figure 1 HyCoSuL synthesis and quality control exemplified with the P2 sublibrary. P2 HyCoSuL sublibrary contains amino acids mixtures at P3 and P4 positions. To test whether the coupling of isokinetic mixture provided the equal distribution of amino acids in P3 (and P4) position an Edman degradation can be utilized. After coupling and deprotection of P3 position (steps 38-44) several beads are subjected for the analysis in order to determine the molar distribution of amino acids at the N-terminal end of a peptide. The same procedure can be applied to test the equimolar coupling of amino acids mixture to the P4 position.
2 Supplementary Figure 2 HR-MS and RP-HPLC analysis of ACC-labeled legumain substrate containing unnatural amino acids. Substrate was synthesized according to standard solid phase Fmoc/Boc strategy, and purified using reverse phase high performance (pressure) liquid chromatography (RP-HPLC) Waters system with semi-preparative C18 column. The purity of the substrate was confirmed using the analytical HPLC with C18 analytical column (UV detector, 220nm). The molecular mass of the substrate was confirmed using High Resolution Mass Spectrometer WATERS LCT premier XE with Electrospray Ionization (ESI) and Time of Flight (TOF) module.
3 Supplementary Figure 3 HR-MS and RP-HPLC analysis of biotin-6-ahx-dtyr(tbu)-tic-ser(tbu)-cooh. Peptide was synthesized according to the strategy presented in the main protocol (Block A, steps ), and used without further purification. The purity of the peptide was confirmed using analytical HPLC (UV detector, C8 column, 220nm). The molecular mass of the peptide was confirmed using High Resolution Mass Spectrometer WATERS LCT premier XE with Electrospray Ionization (ESI) and Time of Flight (TOF) module.
4 Supplementary Figure 4 HR-MS and RP-HPLC analysis of Boc-Asp(Bzl)-AOMK. AOMK warhead was synthesized according to the strategy presented in the main protocol (Block B, steps ), and purified via extraction. The purity of the product warhead was confirmed using analytical HPLC (UV detector, C8 column, 220nm). The molecular mass of the compound was confirmed using High Resolution Mass Spectrometer WATERS LCT premier XE with Electrospray Ionization (ESI) and Time of Flight (TOF) module.
5 Supplementary Figure 5 HR-MS and RP-HPLC analysis of biotin-labeled legumain activity containing unnatural amino acids. Probe was synthesized according to the strategy presented in the main protocol (Block C, steps ), and purified using reverse phase high performance (pressure) liquid chromatography (RP-HPLC) Waters system with semi-preparative C8 column. The purity of the probe was confirmed using analytical HPLC with C8 column (UV detector, 220nm). The molecular mass of the substrate was confirmed using High Resolution Mass Spectrometer WATERS LCT premier XE with Electrospray Ionization (ESI) and Time of Flight (TOF) module. Since the probe is more hydrophobic than the substrate, we used C8 (instead of C18) column to purify and analyze.
6 No Name and code Structure before synthesis Structure after de-protection 1 L-alanine L-Ala 2 L-arginine L-Arg 3 L-asparagine L-Asn 4 L-aspartic acid L-Asp 5 L-glutamine L-Gln 6 L-glutamic acid L-Glu 7 glycine Gly
7 8 L-histidine L-His 9 L-isoleucine L-Ile 10 L-leucine L-Leu 11 L-lysine L-Lys 12 L-norleucine L-Nle 13 L-phenylalanine L-Phe 14 L-proline L-Pro 15 L-serine L-Ser 16 L-threonine L-Thr
8 17 L-tryptophan L-Trp 18 L-tyrosine L-Tyr 19 L-valine L-Val 20 L-methionine L-Met 21 D-alanine D-Ala 22 D-arginine D-Arg 23 D-asparagine D-Asn 24 D-aspartic acid D-Asp
9 25 D-glutamine D-Gln 26 D-glutamic acid D-Glu 27 D-histidine D-His 28 D-leucine D-Leu 29 D-lysine D-Lys 30 D-phenylalanine D-Phe 31 D-proline D-Pro
10 32 D-serine D-Ser 33 D-phenylglycine D-Phg 34 D-threonine D-Thr 35 D-tryptophan D-Trp 36 D-tyrosine D-Tyr 37 D-valine D-Val 38 D-homophenylalanine D-hPhe 39 beta-alanine -Ala
11 40 L-azetidine L-Aze 41 L-4-hydroxyproline L-Hyp 42 O-benzyl-L-4- hydroxyproline L-Hyp(Bzl) L-thiazolidine L-Thz L-octahydroindole L-Oic L-indoline L-Idc L-piperidine L-Pip L-1,2,3,4- tetrahydroisoquinoline L-Tic 48 dehydrohomoalanine dhabu 49 dehydroleucine dhleu
12 50 amino-l-alanine L-Dap 51 amino-l-homoalanine L-Dab 52 N- - (benzyloxycarbonyl)amino- L-homoalanine L-Dab(Z) or L-Dab(Cbz) 53 L-citrulline L-Cit 54 L-homocitrulline L-hCit 55 L-ornithine L-Orn 56 N,N -dimethyl-l-lysine L-Lys(Me) 2
13 57 N -trifluoroacetyl-l-lysine L-Lys(TFA) 58 N -acetyl-l-lysine L-Lys(Ac) 59 N -2-chlorobenzyloxycarbonyl-L-lysine L-Lys(2-Cl-Z) 60 guanidino-l-alanine L-Agp 61 guanidino-l-homoalanine L-Agb 62 N -nitro-l-arginine L-Arg(NO 2)
14 63 N,N - di(benzyloxycarbonyl)-larginine L-Arg(Cbz) 2 64 L-homoarginine L-hArg 65 N (im)-benzyl-l-histidine L-His(Bzl) 66 L-His(3-Bom) 67 4-amino-L-phenylalanine L-Phe(4-NH 2) 68 N (im)-benzyloxymethyl-lhistidine 4-guanidino-Lphenylalanine L-Phe(4-guan)
15 69 2-methyl-L-tryptophan L-Trp(Me) 70 L-dihydrotryptophan L-Dht 71 L-aspartic acid methyl ester L-Asp(Me) 72 L-aspartic acid cyclohexyl ester L-Asp(Chx) 73 L-aspartic acid benzyl ester L-Asp(Bzl) 74 L-glutamic acid methyl ester L-Glu(Me) 75 L-glutamic acid cyclohexyl ester L-Glu(Chx)
16 76 L-glutamic acid benzyl ester L-Glu(Bzl) 77 L-homoglutamic acid L-Aad or L-hGlu 78 2-fluoro-L-phenylalanine L-Phe(2-F) 79 3-fluoro-L-phenylalanine L-Phe(3-F) 80 4-fluoro-L-phenylalanine L-Phe(4-F) 81 L-Phe(3,4-F 2) 82 3,4-difluoro-Lphenylalanine 2,3,4,5,6-pentafluoro-Lphenylalanine L-Phe(F 5)
17 83 2-chloro-L-phenylalanine L-Phe(2-Cl) 84 3-chloro-L-phenylalanine L-Phe(3-Cl) 85 4-chloro-L-phenylalanine L-Phe(4-Cl) 86 3,4-dichloro-Lphenylalanine L-Phe(3,4-Cl 2) 87 4-bromo-L-phenylalanie L-Phe(4-Br) 88 4-iodo-L-phenylalanine L-Phe(4-I) 89 4-methyl-L-phenylalanine L-Phe(4-Me)
18 90 3-pyridyl-L-alanine L-3-Pal 91 4-pyridyl-L-alanine L-4-Pal 92 2-thienyl-L-alanine L-Ala(2-thienyl) 93 L-Ala(Bth) 94 3-benzothienyl-L-alanine L-Bta 95 L-homoalanine L-Abu 96 3-(benzothiazol-2-yl)-Lalanine 3-(benzothiazol-2-yl)-Lhomoalanine L-Abu(Bth)
19 97 O-acetyl-L-serine L-Ser(Ac) 98 O-benzyl-L-serine L-Ser(Bzl) 99 L-homoserine L-hSer 100 O-benzyl-L-homoserine L-hSer(Bzl) 101 O-benzyl-L-threonine L-Thr(Bzl) 102 S-benzyl-L-cysteine L-Cys(Bzl) 103 S-4-methyl-benzyl-Lcysteine L-Cys(4-MeBzl)
20 104 S-4-methoxy-benzyl-Lcysteine L-Cys(4-MeOBzl) 105 L-methionine sulfoxide L-Met(O) 106 L-methionine sulfone L-Met(O) benzyloxy-L-norleucine L-Nle(O-Bzl) 108 L-phenylglycine L-Phg 109 L-homophenylalanine L-hPhe 110 L-cyclohexylglycine L-Chg 111 L-cyclohexylalanine L-Cha
21 112 L-homocyclohexylalanine L-hCha indanyl-L-glycine L-Igl naphthyl-L-alanine L-1-Nal naphthyl-L-alanine L-2-Nal 116 L-biphenylalanine L-Bip benzoyl-L-phenylalanine L-Bpa 118 L-2-aminooctanoic acid L-2-Aoc 119 L-homoleucine L-hLeu
22 120 L-neopentyl-glycine L-NptGly 121 L-norvaline L-Nva 122 L-hydroxynorvaline L-Hnv 123 L-tert-leucine L-Tle methyl-L-tyrosine L-Tyr(Me) 125 L-Tyr(2,6-Cl 2-Bzl) benzyl-L-tyrosine L-Tyr(Bzl) (2,6-dichlorobenzyl)-Ltyrosine 4-(2bromobenzyl)-Ltyrosine L-Tyr(2-Br-Bzl)
23 128 L-homotyrosine L-hTyr methyl-L-homotyrosine L-hTyr(Me) Table 1 Structure of amino acids used in HyCoSuL synthesis. P1 Asp HyCoSuL contains 129 amino acids (19 natural and 110 unnatural). In the table we present the structures of Fmoc-protected amino acids used in the synthesis (left) and the structures of amino acids after Fmoc de-protection and TFA-assisted cleavage (right). Several protecting groups are TFA labile, thus the amino acids structures in the peptide library differ from the structures used for the synthesis. These groups are: Pbf (Arg), Trt (Asn, Gln, His), tbu (Asp, Glu, Ser, Thr, Trp, Tyr, Hyp, hglu, hser, Hnv, htyr), and Boc (Lys, Dap, Dab, Orn, Agp, Agb, harg, Phe-4- NH 2, Phe-4-guan).
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