Depsidomycins B and C: New Cyclic Peptides from a Ginseng Farm Soil-derived Actinomycete.
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- Ἡρὼ Ευρυδίκη Δασκαλοπούλου
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1 Supporting Information Depsidomycins B and C: ew Cyclic Peptides from a Ginseng Farm Soil-derived Actinomycete. Yun Kwon 1, Woong Sub Byun 1, Byung-Yong Kim 2, Myoung Chong Song 3, Munhyung Bae 1, Yeo Joon Yoon 3, Jongheon Shin 1, Sang Kook Lee 1 and Dong-Chan h 1, * 1 atural Product Research Institute, College of Pharmacy, Seoul ational University, Seoul 8826, Republic of Korea 2 ChunLab, Inc., JW TWER, Seocho-gu, Seoul 6725, Republic of Korea 3 Department of Chemistry and anoscience, Ewha Womans University, Seoul 376, Republic of Korea * Correspondence: dongchanoh@snu.ac.kr; Tel.:
2 Table of Contents Figure S1. 1 MR spectrum (85 Mz) of depsidomycin B (1) in pyridine d5. Figure S2. 13 C MR spectrum (212.5 Mz) of 1 in pyridine d5. Figure S3. CSY spectrum (85 Mz) of 1 in pyridine d5. Figure S4. SQC spectrum (85 Mz) of 1 in pyridine d5. Figure S5. MBC spectrum (85 Mz) of 1 in pyridine d5. Figure S6. RESY spectrum (85 Mz) of 1 in pyridine d5. Figure S7. TCSY spectrum (85 Mz) of 1 in pyridine d5 Figure S8. 1 MR spectrum (85 Mz) of 1 in acetone d6. Figure S9. 13 C MR spectrum (212.5 Mz) of 1 in acetone d6. Figure S1. CSY spectrum (85 Mz) of 1 in acetone d6. Figure S11. SQC spectrum (85 Mz) of 1 in acetone d6. Figure S12. MBC spectrum (85 Mz) of 1 in acetone d6. Figure S13. RESY spectrum (85 Mz) of 1 in acetone d6. Figure S14. TCSY spectrum (85 Mz) of 1 in acetone d6. Figure S15. 1 MR spectrum (85 Mz) of depsidomycin C (2) in acetone d6. Figure S C MR spectrum (212.5 Mz) of 2 in acetone d6. Figure S17. CSY spectrum (85 Mz) of 2 in acetone d6. Figure S18. SQC spectrum (85 Mz) of 2 in acetone d6. Figure S19. MBC spectrum (85 Mz) of 2 in acetone d6. Figure S2. RESY spectrum (85 Mz) of 2 in acetone d6. Figure S21. TCSY spectrum (85 Mz) of 2 in acetone d6. Figure S22. 1 MR spectrum (6 Mz) of methanolysis product (3) of 1 in acetone d6. Figure S C MR spectrum (15 Mz) of 3 in acetone d6. Figure S24. CSY spectrum (6 Mz) of 3 in acetone d6. Figure S25. SQC spectrum (6 Mz) of 3 in acetone d6. Figure S26. MBC spectrum (6 Mz) of 3 in acetone d6.
3 Figure S27. TCSY spectrum (6 Mz) of 3 in acetone d6. Figure S29. LC/MS chromatogram of (a) L- and (b) D-FDAA derivatives of 1. Figure S3. LC/MS chromatogram of (a) L- and (b) D-FDAA derivatives of 2. Figure S31. LC/MS chromatogram of GITC derivatives of (a) 1, (b) authentic D-Ile, (c) D-allo- Ile, (d) coinjection of GITC derivatives of 1 with authentic (d) D-Ile and (e) D-allo-Ile. Figure S32. LC/MS chromatogram of GITC derivatives of (a) 1, (b) authentic D-Thr, (c) L-Thr, (d) D-allo- and L-allo-Thr, and coinjection of GITC derivatives of authentic D-Thr with those of (e) 1 and (f) 2. Figure S33. Positive control data of wound healing assay using sunitinib. Figure S34. Time-course LC/MS analysis of the culture of the strain BYK1371. Depsidomycins B and C (1-2) were detected at 15.4 and 14.6, respectively. Figure S35. Phylogenetic relationships of single strain BYK 1371 and related Streptomyces taxa. Table S1. 1 and 13 C MR data for 1 in pyridine-d5. Table S2. 1 and 13 C MR data for 3 in acetone-d6. Table S3. 1 and 13 C MR data for depsidomycin and B (1) in acetone-d6. Table S4. LC/MS analysis of the FDAA derivatives of 1 and 2. References
4 Figure S1. 1 MR spectrum (85 Mz) of 1 in pyridine d5.
5 Figure S2. 13 C MR spectrum (212.5 Mz) of 1 in pyridine d5.
6 Figure S3. CSY spectrum (85 Mz) of 1 in pyridine d5.
7 Figure S4. SQC spectrum (85 Mz) of 1 in pyridine d5.
8 Figure S5. MBC spectrum (85 Mz) of 1 in pyridine d5.
9 Figure S6. RESY spectrum (85 Mz) of 1 in pyridine d5.
10 Figure S7. TCSY spectrum (85 Mz) of 1 in pyridine d5.
11 Figure S8. 1 MR spectrum (85 Mz) of 1 in acetone d6.
12 Figure S9. 13 C MR spectrum (212.5 Mz) of 1 in acetone d6.
13 Figure S1. CSY spectrum (85 Mz) of 1 in acetone d6.
14 Figure S11. SQC spectrum (85 Mz) of 1 in acetone d6.
15 Figure S12. MBC spectrum (85 Mz) of 1 in acetone d6.
16 Figure S13. RESY spectrum (85 Mz) of 1 in acetone d6.
17 Figure S14. TCSY spectrum (85 Mz) of 1 in acetone d6.
18 Figure S15. 1 MR spectrum (85 Mz) of 2 in acetone d6.
19 Figure S C MR spectrum (212.5 Mz) of 2 in acetone d6.
20 Figure S17. CSY spectrum (85 Mz) of 2 in acetone d6.
21 Figure S18. SQC spectrum (85 Mz) of 2 in acetone d6.
22 Figure S19. MBC spectrum (85 Mz) of 2 in acetone d6.
23 Figure S2. RESY spectrum (85 Mz) of 2 in acetone d6.
24 Figure S21. TCSY spectrum (85 Mz) of 2 in acetone d6.
25 Figure S22. 1 MR spectrum (6 Mz) of 3 in acetone d6.
26 Figure S C MR spectrum (15 Mz) of 3 in acetone d6.
27 Figure S24. CSY spectrum (6 Mz) of 3 in acetone d6.
28 Figure S25. SQC spectrum (6 Mz) of 3 in acetone d6.
29 Figure S26. MBC spectrum (6 Mz) of 3 in acetone d6.
30 Figure S27. TCSY spectrum (6 Mz) of 3 in acetone d6.
31 Figure S28. MS/MS data of 3.
32 Figure S29. LC/MS chromatogram of (a) L- and (b) D-FDAA derivatives of 1. (a) 6 MSD1 383, EIC=382.7:383.7 (:\LCMS\BYK1371\BYK1371_L_MARFEY_791.D) ES-API, Pos, Scan, Frag: 135, "pos scan" Leucine, Isoleucine MSD1 371, EIC=37.7:371.7 (:\LCMS\BYK1371\BYK1371_L_MARFEY_791.D) ES-API, Pos, Scan, Frag: 135, "pos scan" Threonine MSD2 481, EIC=48.7:481.7 (:\LCMS\BYK1371\BYK1371_L_MARFEY_791.D) ES-API, eg, Scan, Frag: 135, "neg scan" Piperazic acid (b) MSD2 368, EIC=367.7:368.7 (:\LCMS\BYK1371\BYK1371_L_MARFEY_791.D) ES-API, eg, Scan, Frag: 135, "neg scan" 8 Valine MSD1 383, EIC=382.7:383.7 (:\LCMS\BYK1371\BYK1371_D_MARFEY_791.D) ES-API, Pos, Scan, Frag: 135, "pos scan" MSD1 371, EIC=37.7:371.7 (:\LCMS\BYK1371\BYK1371_D_MARFEY_791.D) ES-API, Pos, Scan, Frag: 135, "pos scan" Threonine MSD2 481, EIC=48.7:481.7 (:\LCMS\BYK1371\BYK1371_D_MARFEY_791.D) ES-API, eg, Scan, Frag: 135, "neg scan" Leucine, Isoleucine Piperazic acid MSD2 368, EIC=367.7:368.7 (:\LCMS\BYK1371\BYK1371_D_MARFEY_791.D) ES-API, eg, Scan, Frag: 135, "neg scan" Valine
33 Figure S3. LC/MS chromatogram of (a) L- and (b) D-FDAA derivatives of 2. (a) 6 MSD1 383, EIC=382.7:383.7 (:\LCMS\BYK1371\BYK1371_777_L_MARFEY.D) ES-API, Pos, Scan, Frag: 135, "pos scan" Leucine, Isoleucine MSD1 371, EIC=37.7:371.7 (:\LCMS\BYK1371\BYK1371_777_L_MARFEY.D) ES-API, Pos, Scan, Frag: 135, "pos scan" MSD2 481, EIC=48.7:481.7 (:\LCMS\BYK1371\BYK1371_777_L_MARFEY.D) ES-API, eg, Scan, Frag: 135, "neg scan" Threonine Piperazic acid (b) MSD2 368, EIC=367.7:368.7 (:\LCMS\BYK1371\BYK1371_777_L_MARFEY.D) ES-API, eg, Scan, Frag: 135, "neg scan" MSD1 383, EIC=382.7:383.7 (:\LCMS\BYK1371\BYK1371_777_D_MARFEY.D) ES-API, Pos, Scan, Frag: 135, "pos scan" Valine MSD1 371, EIC=37.7:371.7 (:\LCMS\BYK1371\BYK1371_777_D_MARFEY.D) ES-API, Pos, Scan, Frag: 135, "pos scan" MSD2 481, EIC=48.7:481.7 (:\LCMS\BYK1371\BYK1371_777_D_MARFEY.D) ES-API, eg, Scan, Frag: 135, "neg scan" 4 Piperazic acid MSD2 368, EIC=367.7:368.7 (:\LCMS\BYK1371\BYK1371_777_D_MARFEY.D) ES-API, eg, Scan, Frag: 135, "neg scan" Leucine, Isoleucine Threonine Valine
34 Figure S31. LC/MS chromatogram of GITC derivatives of (a) 1, (b) authentic D-Ile, (c) D-allo-Ile, (d) coinjection of GITC derivatives of 1 with authentic (d) D-Ile and (e) D-allo-Ile. MSD1 521, EIC=52.7:521.7 (:\LCMS\BYK1371\GITC\ISLEUCIE\BYK1371_791_GITC.D) ES-API, Pos, Scan, Frag: 135, "pos s (a) Depsidomycin (1) MSD2 MSD , EIC=52.7: (:\LCMS\BYK1371\GITC\ISLEUCIE\D_ISLEUCIE_GITC_35T5.D) \LCMS\BYK1371\GITC\ISLEUCIE\BYK D) ES API ES-API, S Pos, F Scan, 135 " Frag: (b) D-Ile MSD1 MSD2 521, 519 EIC=52.7: (:\LCMS\BYK1371\GITC\ISLEUCIE\D_ALL_ISLEUCIE_GITC_35T5.D) ISLEUCIE 35T5 D) ES API ES-API, S Pos, F Scan, 135 Frag (c) D-allo-Ile MSD2 MSD , EIC=52.7: (:\LCMS\BYK1371\GITC\ISLEUCIE\GITC \LCMS\BYK1371\GITC\ISLEUCIE\D ALL WIT ISLEUCIE 791\791_WIT_D_ISLEUCIE_GITC_35T5_2.D) 35T5 D) ES API S F ES-A (d) Coinjection of 1 with D-Ile MSD2 519, EIC=518.7:519.7 (:\LCMS\BYK1371\GITC\ISLEUCIE\GITC WIT 791\791_WIT_D_ALL_ISLEUCIE_GITC_35T5.D) (e) Coinjection of 1 with D-allo-Ile
35 Figure S32. LC/MS chromatogram of GITC derivatives of (a) 1, (b) authentic D-Thr, (c) L-Thr, (d) D-allo- and L-allo-Thr, and coinjection of GITC derivatives of authentic D-Thr with those of (e) 1 and (f) MSD1 59, EIC=58.7:59.7 (:\LCMS\BYK1371\BYK1371 ALL\BYK1371_791_GITC_REACTI_DC_DEFAULT.D) (a) Depsidomycin (1) ES-API, Pos, Scan, MSD2 MSD1 59, 57 EIC=58.7: (:\LCMS\BYK1371\GITC\TREIE\GITC_D_TREIE_1_T_1_R.D) \LCMS\BYK1371\BYK1371 ALL\BYK REACTI DC DEFAULT ES-API, D) Pos, ES API Scan, Frag: S 1 (b) D-Thr MSD2 MSD , EIC=58.7: (:\LCMS\BYK1371\GITC\TREIE\GITC_L_TREIE.D) D TREIE 1ES-API, T 1 RPos, D) Scan, ES API Frag: 135, S "pos F sc (c) L-Thr MSD2 57, EIC=56.7:57.7 (:\LCMS\BYK1371\GITC\TREIE\GITC_DL_TREIE_8_T_1.D) ES-API, eg, Scan, Frag: 135, (d) D-allo- and L-allo-Thr MSD1 59, EIC=58.7:59.7 (:\LCMS\BYK1371\GITC\TREIE\GITC WIT 791\GITC_D_TREIE_AD_791GITC_2.D) ES-API, P (e) D-Thr + depsidomycin B (1) MSD2 57 EIC ( \LCMS\BYK1371\GITC\TREIE\GITC WIT 791\GITC D TREIE AD 791GITC 2 D) ES API (f) D-Thr + depsidomycin C (2)
36 Figure S33. Positive control data of wound healing assay using sunitinib. Remaining cell free area (%)
37 Figure S34. Time-course LC/MS analysis of the culture of the strain BYK1371. Depsidomycins B and C (1-2) were detected at 15.4 and 14.6, respectively MSD1 TIC, MS File (:\LCMS\BYK1371\BYK1371 ALL\13MAY_D2_YEMEF_BYK1371.D) ES-API, Pos, Scan, Frag: 135, "pos scan" Day MSD1 TIC, MS File (:\LCMS\BYK1371\BYK1371 ALL\13MAY_D2_YEMEF_BYK1371.D) ES-API, Pos, Scan, Frag: 135, "pos scan" MSD2 TIC MS Fil ( \LCMS\BYK1371\BYK1371 ALL\13MAY D2 YEMEF BYK1371 D) ES API S F 135 " " Day MSD1 TIC, MS File (:\LCMS\BYK1371\BYK1371 ALL\17_MAY_YEMEF_D6_BYK1371.D) ES-API, Pos, Scan, Frag: 135, "pos scan" Day MSD1 TIC, MS File (:\LCMS\BYK1371\BYK1371 ALL\16MAY_YEMEF_D5_BYK1371.D) ES-API, Pos, Scan, Frag: 135, "pos scan" Day
![Figure S35. Phylogenetic relationships of single strain BYK 1371 and related Streptomyces taxa. The evolutionary history was inferred using the eighbor-joining method [1].](/docs-images/92/110177390/images/38-1.jpg "The tree based on partial 16S rra gene sequences (about 1,4 nucleotides) showing the relationships between isolate BYK1371 and the closely related type strains of the genus Streptomyces.")
38 Figure S35. Phylogenetic relationships of single strain BYK 1371 and related Streptomyces taxa. The evolutionary history was inferred using the eighbor-joining method [1]. The tree based on partial 16S rra gene sequences (about 1,4 nucleotides) showing the relationships between isolate BYK1371 and the closely related type strains of the genus Streptomyces. umbers at the nodes indicate levels of bootstrap support (%) above 5% based on a neighbour-joining analysis of 1, resampled datasets [2]. Genbank accession numbers are indicated in parentheses. The scale bar indicates the number of substitutions per nucleotide position. The evolutionary distances were computed using the Kimura 2-parameter method [3] and are in the units of the number of base substitutions per site. The analysis involved 33 nucleotide sequences. All positions containing gaps and missing data were eliated. Evolutionary analyses were conducted in MEGA X [4]. S 38
39 Table S1. 1 and 13 C MR data for 1 in pyridine-d5. positon Depsidomycin B (1) δc, type a δ, mult (J in z) a , C , C 5.43, br d (3.5) 3a 21.6, C2 1.3, m 3b 1.88, m 4a 21.3, C2 1.6, m 4b 2.11, m 5a 48.2, C2 2.66, m 5b 3.6, m , br d (12.) , C , C 6.2, dd (1.5, 1.) , br d (1.) 8a 41.7, C2 2.1, m 8b 2.54, br dd (1., 1.) 9 27., C 2.15, m , C3 1.12, d (6.5) , C3 1.24, d (6.5) , C , C 5.77, br d (5.) 14a 25.4, C2 1.65, m 14b 2.91, br d (11.) 15a 23.3, C2 1.48, d (9.) 15b 1.63, m 16a 48.1, C2 3.12, m 16b 2.78, m , br d (13.) , C , C 5.58, m , br d (5.) , C 2.33, m 2 2.2, C3 1.5, m , C3 1.7, m , C , C 5.38, m , br d (1.) 24a 41., C2 2.4, m 24b 2.61, m , C 1.89, m , C3.75, m , C3.79, m , C , C 5.33, m , d (8.) , C 5.21, br s , C3 1.34, d (6.) , C , C 5.35, m , br s , C 2.23, m , C2 1.24, d (6.5) 1.59, m , C3.77, m , C3 1., d (7.) , C 8.77, s a 1 and 13 C MR were recorded at 8 and Mz, respectively S 39
40 Table S2. 1 and 13 C MR data for 3 in Acetone-d6. positon 3 δc, type a δ, mult (J in z) a , C 2 52., C 5.2, d (6.) 3a 26.1, C2 1.87, m 3b 2.21, m , C2 1.57, br s 5a 47.7, C2 3.6, m 5b 2.89, m , br d (12.5) , C , C 5.41, m , brd (8.) 8 41., C2 1.55, m , C 1.75, m 1 2., C3.86, m , C3.92, d (6.5) , C , C 5.11, br d (5.) 14a 26.6, C2 1.74, m 14b 2.33, br d (13.5) 15a 21.4, C2 1.55, m 15b 1.59, br 16a 48.4, C2 3.1, m 16b 2.71, m , br d (13.5) , C , C 5.27, m , br s , C 2.8, m , C3.87, d (6.5) , C3.92, d (6.5) , C , C 4.38, m , br s , C2 1.64, m , C 1.73, m , C3.85, m 27 2., C3.9, m , C , C 4.45, m , d (6.) , C 4.28, m , C3 1.14, d (6.5) , C , C 4.45, m , br s , C 2.5, m , C2 1.28, d (6.5) 1.49, d (6.5) , C3.93, m , C3.95, d (7.) , C 8.29, s , -C3 3.74, s a 1 and 13 C MR were recorded at 6 and 15 Mz, respectively S 4
41 Table S3. 1 and 13 C MR data for depsidomycin and B (1) in Acetone-d6. Positon Depsidomycin Depsidomycin B (1) δc, type δ, mult (J in z) a δc, type δ, mult (J in z) b , C 169.3, C , C 5.16, dd (5., 2.) 51.4, C 5.18, br s 3a 23.4, C2 1.86, m 23.4, C2 1.85, m 3b 2.19, m 2.19, m 4a 21.4, C2 1.55, m 21.3, C2 1.55, m 4b 1.86, m 1.86, m 5a 47.8, C2 3.14, m 47.9, C2 3.12, m 5b 2.85, m 2.85, m , dd (12., 2.5) 4.88, m , C 175.4, C , C 5.4, m 49.7, C 5.4, dd (1.5, 1.5) , d (1.) 7.62, d (1.5) 8a 41.4, C2 1.69, m 41.4, C2 1.68, m 8b 1.95, m 1.95, m , C 1.78, m 26.6, C 1.78, m , C3 1.2, d (6.5) 21., C3 1.2, d (6.5) , C3.93, d (6.5) 23.7, C3.93, d (6.5) , C 167.7, C , C 5.11, dd (5.5, 1.5) 52.8, C 5.12, d (4.5) 14a 25.1, C2 1.55, m 24.9, C2 1.58, m 14b 2.57, m 2.57, br d (13.5) 15a 23., C2 1.4, m 23., C2 1.39, m 15b 1.55, m 1.55, br d (1.5) 16a 48., C2 2.77, m 47.8, C2 2.75, m 16b 3.12, m 3.12, m , dd (13., 2.) 3.95, br d (12.5) , C 175.9, C , C 5.2, dd (1.5, 6.) 56.2, C 5.2, dd (1., 6.) , d (6.) 7.59, d (6.) , C 1.98, m 29,5, C 1.99, m 2 2.1, C3 1.5, d (6.5) 21., C3 1.2, d (6.5) , C3.97, d (6.5) 19.7, C3.97, d (6.5) , C 174.7, C , C 4.97, m 51., C 4.88, m , d (1.) 7.7, br s 24a 24b 41.1, C2 1.68, m 2.17, m 4.8, C 1,68, m 2.17, m , C 1.7, m 25.8, C 1.71, m , C3.89, d (7.) 2.6, C3.89, m , C3.91, d (7.) 24., C3.91, m , C 167.4, C , C 4.5, dd (6.5, 3.5) 55.8, C 4.48, br s , d (6.5) 7.52, br s , C 4.9, dq (6.5, 3.5) 71.4, C 4.91, m , C 1.17, d (6.5) 13.6, C3 1.17, d (6.5) , C 171.7, C , C 4.76, dd (9.5, 4.5) 55.4, C 4.66, m , d (9.5) 7.49, br s , C 1.92, m 38.1, C 1.98, m 35a 27., C2 1.19, m 26.9, C2 1.21, m 35b 1.42, m 1.43, m , C3.89, t (7.5) 11.8, C3.9, m , C3.87, d (7.) 14.6, C3.87, d (7.) , C 8.27, br s 161.8, C 8.27, s a 1 and 13 C MR were cited from the origin paper. b 1 and 13 C MR were recorded at 85 and Mz, respectively S 41
42 Table S4. LC/MS analysis of the FDAA derivatives of 1 and 2. Depsidomycin B (1) Depsidomycin C (2) Ao acid Elution trl () trd () Ao acid Elution trl () trd () order order Val (D) D L Val (D) D L Leu (D) D L Leu (D) D L Ile (D) D L Ile (D) D L Thr (D) D L Thr (D) D L Pip (S) D L Pip (S) D L S 42
43 References. 1. Saitou.; ei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4, Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985, 39, Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 198, 16, Kumar S.; Stecher G.; Li M., Knyaz C.; Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 218 ( S 43
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