CH CN and 0.1% trifluoroacetic acid (TFA) and buffer B (5m ...Microwave assisted peptoid syntheses...
Transcript of CH CN and 0.1% trifluoroacetic acid (TFA) and buffer B (5m ...Microwave assisted peptoid syntheses...
Supplemental Information
Solid-Phase Synthesis of Peptoid-like Oligomers Containing Diverse Diketopiperazine Units
Sujit Suwal and Thomas Kodadek*
Materials and Instruments:Amino acid esters were purchased from either from Aldrich, Acros, Advanced chemtech and Astatech. (S) and (R)-2-bromo-propionic acid were purchased from Aldrich. Mono-N-tboc-ethylenediamine was bought from Astatech Inc. Primay amines were purchased from Advanced Chemtech, Aldrich, Acros, TCI. Rest of the other chemicals and reagents were purchased either from Aldrich or Fisher Scientific. Rink amide MBHA resin (0.5 mmol/g) and Tentagel macrobead-NH2 (160 µg, 0.4 mmol/g) resin were obtained from Chemprep and rapp-polymere, respectively. Disposable fritted columns (5 mL, 50 mL) for peptoid syntheses were bought from Intavis AG. Microwave assisted peptoid syntheses were accomplished utilizing 10% of 1550 W household microwave (GE model JE 1860 BH04). HPLC purification of crude peptoids after acid cleavage from Rink amide resin was carried out in Water 1525 binary HPLC pumps and a 2487 dual absorbance detector, or a 2998 photodiode array detector. Buffer A (H2O with 5% CH3CN and 0.1% trifluoroacetic acid (TFA) and buffer B (5m, 250 x 4.6 mm, Alltech) and Apollo C-18 5µ preparative column. Purities of the compounds were assessed by analytical HPLC under UV (214), otherwise mentioned in description of the spectrum. MS and MS/MS were recorded in MALDI -TOF (4800 Proteomics Analyser, Applied Biosystems) or ESI-MS (Waters). In MS/MS, the signal-to-noise ratio threshold set to 10. Cyano-4-hydroxycinnamic acid (HCCA) or charcoal was used as MALDI matrices (Aldrich). 1H and 13C NMR spectra were recorded in Bruker 400 instrument operating at 400 MHz for 1H and 100 MHz for 13C NMR using Deuterated-methanol (CD3OD) or Deuterated-Dimethylsulfoxide (DMSO) (Cambridge) as a solvent.
Synthesis of 2, 5-DKP (4 a-f)
HN
Br
O
HN
NH
O
O
OR"R
HN
N
O
O
OR"R
O
NH
H2NN
O
O
NR
O
R'
Scheme 1Amino acid esterDMF, 37oC, ON
1. BAA, DIC 37oC, 2x 30 min2. Primary amine DMF, 37oC, 1 h
1. 50 - 60oC, ON
R'
1 2 3
4 a-f
Where,
2. TFA:DCM:TIS (60:38:2)
a. R = (S)-Me, R' = Benzyl
e. R = (S)-Me, R' =OH
b. R = (S)-4-hydroxybenzyl, R'= 2- methoxy ethylamine
R"= CH3 or C2H5
c. R = (S)-Me, R' = Ph
d. R = (R)-Me, R' = Ph f. R = (R)-Me, R' = OH
1
Electronic Supplementary Material (ESI) for Organic & Biomolecular Chemistry.This journal is © The Royal Society of Chemistry 2014
N
N
O
O
H2N
O
4a
Rink amide MBHA resin (1 g, 0.7 mmol) was swelled in DMF. Fmoc group was deprotected with 20% piperidine in DMF (2X, 15 mins). The resultant primary amine was coupled with bromoacetic acid (BAA, 2M) activated with diisopropylcarbodiimide (DIC, 2 M) in N,N’-dimethylformamide (DMF). Subsequently, the bromide was displaced with desired HCl salt of amine acid ester in DMF (2 M) along with DIEA (1.5X with respect to ester). The secondary amine was further coupled with bromoacetic acid (2M), activated with DIC (3M), 37°C (2X, 15 min). The bromide was displaced with a solution of desired primary amine (viz benzyl amine in this case) in DMF at 37oC, 1 h. At this stage, the reaction mixture further incubated at 50oC overnight so that the secondary amine thus generated after SN2 reaction undergo addition elimination at the ester thus generating six-membered 2,5 diketopiperazine. Finally, the solid support was washed with DMF, DCM and ethanol, and subjected to cleave with 50% TFA in DCM along with 2% triisopropylsilane. A crude DKP obtained after the solvent was evaporated under Argon and ether precipitation. A crude dried compound finally was subjected to NMR study without further HPLC purification by dissolving in d-methanol. 1HNMR (400 MHZ, D6-DMSO) δ 7.4-7.3 (m, 5H), 4.7 (d, 1H, J=14.7), 4.5 (d, 1H, J=14.7), 4.3 (d, 1H, J=16.7), 4.12 (q, 1H), 4.0 (d, 1H, J=17.7), 3.9 (d, 1H, J=16.7), 3.82 (d, 1H, J= 17.5), 1.5 (d, 3H, Me, J=7.2); 13CNMR (100 MHz, DMSO) δ 172.3, 169.2, 166.5, 136.8, 129.9, 59.19, 50.3, 49.7, 47.8, 18.1; MALDI-TOF MS (Obs.=MNa+) 298.0681 (298.1270 expected).
Figure S1: 1HNMR of compound 4a
2
Figure S2: COSY of 4a
Figure S3: 13CNMR of 4a
Figure S4: Dept of 4a
3
N
N
O
O
H2N
O
Exact Mass: 275.13
Fig S5: MALDI-MS of compound 4a
N
N
O
O
H2N
O
4bOH
O
Spectral data for compound 4b:A crude dried compound was dissolved in in d-DMSO. 1HNMR (400 MHZ, D6-DMSO) δ 6.83 (d, 2H, J=8.3), 6.66 (d, 2H, J=8.3) 4.35 (d, 1H, J=16.4), 4.15 (t, 1H), 3.6 (d, 1H, J=16.4), 3.32 (m, 1H, J=17.1), 3.5 (d, 1H), 3.35 (m, 1H), 3.3 (m, 1H), 3.2 (s, 3H), 3.15 (m, 1H), 3.0 (dd, 1H, J=14), 2.9 (dd, 1H, J=14), 2.6 (d, 1H, J=17.1); 13CNMR (100 MHz, DMSO) δ 169.2, 165.3, 164.0, 156.5, 130.7, 124.9, 115.0, 69.2, 61.7, 57.8, 49.5, 45.8, 44.9, 35.5; ESI-MS(Obs. MNa+) =358.1398 (Expected=358.1481).
Figure S6: 1HNMR of 4b
4
Figure S7: 13CNMR of compound 4b
Figure S8: 13C-DEPT of compound 4b
Figure S9: COSY of compound 4b
5
N
N
O
O
H2N
O
OH
O
Exact Mass: 335.15
Fig S10: MALDI-MS of compound 4b
Spectral data for compound 4c and 4d:
For compound 4d:
A HPLC purified compound was dissolved in in d-chloroform. 1HNMR (400 MHZ) δ 7.3-7.2 (m, 5H), 4.03-3.97 (m, 2H), 3.90 (d, 1H), 3.60 (d, 1H), 3.35 (d, 1H), 3.23 (m, 1H), 3.02 (m, 1H), 1.45 (d, 3H), 1.29 (d, 3H); 13CNMR (100 MHz, DMSO) δ 172.6,169.6, 166.9, 63.1, 59.2, 52.3, 47.7, 45.5, 17.7, 13.4; MALDI-TOF MS (Obs. MNa+) 326.0962 (Expected = 326.1304 expected).
For compound 4c:
A HPLC purified compound was dissolved in in d-chloroform. 1HNMR (400 MHZ) δ 7.3-7.2 (m, 5H), 4.0 (d, 1H), 3.95-3.84 (m, 3H), 3.83 (d, 1H), 3.61 (d, 1H), 3.40-3.35 (m, 1H), 3.15-310 (m, 1H), 1.3 (d, 3H), 1.2 (d, 3H); MALDI-TOF MS (Obs. MNa+) 326.0962 (Expected = 326.1304 expected).
6
N
N
H2N
O
4d
O
O
Me
Meb
c
N
N
H2N
O
4c
O
O
Me
Meb
a
Figure S11: 1HNMR of compound 4c and 4d
N
N
H2N
O
4d
O
O
Me
Meb
c
N
N
H2N
O
4c
O
O
Me
Meb
a
Figure S12: 13CNMR of compound 4c and 4d
7
N
N
H2N
O
4d
O
O
Me
Meb
c
N
N
H2N
O
4c
O
O
Me
Meb
a
Figure S13: 13CNMR of compound 4c and 4d
N
N
H2N
O
4c
O
O
Me
Meb
a
N
N
H2N
O
4c
O
O
Me
Meb
a
Figure S14: 13CNMR of compound 4c and 4d
8
N
N
H2N
O
4d
O
O
Me
Meb
c
N
N
H2N
O
4c
O
O
Me
Meb
a
Figure S15: HPLC and ESI-MS of compound 4c and 4d
N
N
O
O
H2N
O
4eOH
Spectral data for compound 4e:A crude dried compound was dissolved in in d4-methanol. 1HNMR (400 MHZ, D4- MeOH) 4.6 (m, 1H), 4.3 (d, 1H), 4.14 (d, 1H), 4.06 (q, 1H), 4.02 (d, 1H), 3.9 (d, 1H), 3.64 (m, 1H), 1.49 (d, 1H), 1.18 (d, 1H); 13CNMR (100 MHz, DMSO) δ 172.6,169.6, 166.9, 63.1, 59.2, 52.3, 47.7, 45.5, 17.7, 13.4; MALDI-TOF MS (Obs. MNa+) 266.0499 (Expected =266.1219).
Figure S16: 1HNMR of compound 4e
9
Figure S17: Cosy of compound 4e
Figure S18: 13CNMR of compound 4e
Fig S19: MALDI-MS of compound 4e
10
N
N
O
O
H2N
O
4fOH
Spectral data for compound 4f:A crude dried compound was dissolved in D6-DMSO. 1HNMR (400 MHZ, D6-DMSO) 4.6 (m, 1H), 4.3 (d, 1H), 4.14 (d, 1H), 4.06 (q, 1H), 4.02 (d, 1H), 3.9 (d, 1H), 3.64 (m, 1H), 1.49 (d, 1H), 1.18 (d, 1H); 13CNMR (100 MHz, DMSO) δ 169.3, 166.8, 164.2, 61.6, 59.7, 43.8, 40.0, 45.5, 17.2, 13.1; MALDI-TOF MS (Obs. MNa+) 266.0122 (266.1219 expected).
Figure S20: 1H NMR of compound 4f
11
Figure S21: COSY of compound 4f
Figure S22: 13C NMR of compound 4f
12
Figure S23: DEPT of compound 4f
Figure S24: MALDI-TOF MS of compound 4f
Figure S25: HPLC of compound 4f
13
Solid phase synthesis protocol for 2,5-DKP containing analog utilized for purity test:
R' =
NNH
O
O
O
NH
1. BAA, DIC, DMF, 37oC, O.N.2. Amino acid ester, DMF, 37-50oC
NN
NH
O
O
O
OR'
O
O
NH H2N
NN
NO
O
O
OR'
N
O
O
1. BAA, DIC, DMF 30 min, 37oC
2. 50-60oC, O.N.3. TFA:DCM:TIS (60:38:2), 2 h.
Ph
NH
N
OH
NH
NH2
H , , ,, ,
, , ,
5 6 7
a b c d e
f g h i
Cl
Cl
Cl
Cl
OScheme 2
Cl
Cl
Rink amide MBHA resin (100 mg, 0.07 mmol) was swelled in DMF. After the fmoc group deprotection with 20% piperidine in DMF (2X, 15 mins), a dimer peptoid was synthesized by conventional peptoid synthesis protocol. Onto the resultant dimer additional bromoacetic acid was added and bromide was displaced by amino acid ester. The secondary amine was further coupled with DIC activated bromoacetic acid at 37°C (2X, 15 min). The bromide was displaced primary amine (2 M) in DMF at 37oC, 1 h. To afford DKP, the reaction mixture was further incubated at 50oC overnight. Completion of the reaction was confirmed by Chloranil test. The compound thus obtained was further attempted for chain extension with DIC activated BAA followed by displacement with primary amine. At this stage, the bead was acid-cleaved and subjected for HPLC to test the purity of DKP formation. HPLC fractions were subjected for MALDI-TOF analysis to confirm the presence of desired molecule.
DKP-Gly:
Figure S26: HPLC of 7a showing retention time at 5 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification.
14
DKP-Ala:
Figure S27: HPLC of 7b showing retention time at 5 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification.
DKP-Ileu:
Figure S28: HPLC of 7c showing retention time at 5 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification.
DKP-Leu:
Figure S29: HPLC of 7d showing retention time at 5 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification.
15
DKP-PhGly:
Figure S30: HPLC of 7e showing retention time at 35 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification.
DKP-Tyr:
Figure S31: HPLC of 7f showing retention time at 5 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification.
DKP-His:
Figure S32: HPLC of 7g showing retention time at 26 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification.
16
DKP-Trp
Figure S33: HPLC of 7h showing retention time at 35 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification
DKP-Lys
Figure S34: HPLC of 7i showing retention time at 26 min. with MALDI-TOF (in the middle) showing the molecular mass after the purification.
HPLC and MALD-TOF with MS/MS data of few compounds that are used to test the feasibility and purity for chain extension purpose. In these particular examples alloc group was utilized as a protecting group instead of tboc- group. The alloc-group was deprotected as explained in our previous paper (Org. Biomol. Chem., 2013, 11, 2088-209).
NH
NN
NN
N
O
O
O
O
O N
O
O
HN
O
N
O
NH
O
H2N
O
NH
S
N
N
Exact Mass: 1258.54
HS 378 / 882
531 / 729
857 / 403
1094 / 167
Figure S35: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
17
NH
NN
NN
N
O
O
O
O
O N
O
O
HN
O
N
OHN
O
H2N
HS
O
S
N
N
HN
ONO
HNN
SN
NHO
Exact Mass: 1423.63
378/ 1047
520/ 905
167/ 1259
1106/ 319
319/ 1106
1259/ 167
Figure S36: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NH
NN
NN
O
O
O
OO
H2N
O
Exact Mass: 1301.52
HSO
N
HN
N
O
N
N
O
Cl
ClO
O
O
NH
HN
NH
O
HN O
378 / 925
520 / 783 1049 / 254
873 / 430
1102 / 201
Figure S37: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
18
NH
NN
NN
O
O
O
OO
H2N
O
HSO
N
HN
N
O
N
N
O
O
O
O
NHN
378 / 853
O
OO
Exact Mass: 1229.65
569/ 662
947 / 284 1060/ 171
952 / 279
Figure S38: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
HPLC and MALD-TOF with MS/MS data of few compounds that resembles DKP-hybrid compound library.
H2N
O
N
O
N
N
O
O
Ph
CF3
O
N
O
CF3
N
Exact Mass: 948.33
CF3
583 / 388
368 / 626
254 / 739
Figure S39: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound
19
NH2O
N
O
N
NO
O
O
O
N
NH2
CF3
O
CF3
O
O
N
O
Exact Mass: 1035.36
675 / 384
484 / 598
388 / 693
924 / 135
Figure S40: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
H2N
O
N
O
N
N
O
O
CF3
O
N
N
O
N
CF3
OO
H2N
Exact Mass: 946.38
610/ 384
395/ 599
252/ 709
Figure S41: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
Protocol for peptoid library construction:
DKP-Backbone library:
Tentagel MB NH2 (0.5 g, initial loading 0.4 mmol/g) was soaked in DMF for 30 min, RT. The beads were coupled with fmoc-methionine (5X) activated with N,N,N′,N′-Tetramethyl-O-(1H- benzotriazol-1-yl)uronium hexafluorophosphate (HBTU) (5X), N-Hydroxybenzotriazole (HOBt) (8X) and Diisopropyl ethylamine (DIEA) (10x) in DMF. Mixture was incubated 3 h at room temperature. Fmoc-group was deprotected using 20% piperidine in DMF. Resultant primary amine was treated with BAA/DIC and the bromide was displaced with methoxyethylamine under microwave condition. Likewise, methylamine was added as additional two monomers to represent a linker region. The
20
main chain 2,5-DKP containing peptoid oligomer library (~ 40 K diversity) was created utilizing 12 different commercially available primary amines along with 8 different 2,5-DKP moieties. As a first unit of peptoid library, BAA/DIC was coupled to the secondary amine from the linker. The solid support was split into 12 different fractions after the beads were washed with DMF (5X) and DCM (5X). Each portion of the beads was separately treated with different primary amines (2M) to displace the bromide under microwave condition. The beads were washed as explained above. Resultant secondary amines were pooled and coupled with BAA/DIC. The beads were washed and split into 8 different vessels and treated them separately with amino acid esters. After additional round of BAA/DIC coupling, tboc-protected ethylenediamine was used to displace the bromide. The reaction mixture was incubated 50-60oC, 24h to afford 2,5-DKP formation. T-boc group was deprotected by 50% TFA in DCM. The resultant primary amine was separated into two halves and coupled with DIC-activated BAA or (S)-2-bromopropionic acid separately. The bromides were pooled and split into 12 different fractions and displaced individually by primary amines (R’). Finally a peptoid oligomer library with 2,5-DKP in the main-chain was finally completed by final round to BAA/DIC coupling and bromide displacement with different sets of 12 primary amines (R”, Scheme Sch2).
NN
NNH
O
O
O
O
O
N
R
O HN
O
N
R
O
NH
R"
O
O
A
R'
H2N H2N
O
H2N
NH
O
H2N
H2N
NH2
CF3
H2N
N
O
NH2
O
O
NH2
Ph
H2N
SNH2
O O
SH2N NH2
F
R :
H2N
NH2
H2N
HN
O
H2N
NH2
CF3
H2N
N
O
NH2
O
O
NH2
Ph
H2N
SNH2
O O
SH2N
H2N
NH
N
H2N
OH
H2N
NH
R"
N
N
O
O
N
N
O
O
N
N
O
O
N
N
O
O
N
N
O
O
H2N
N
N
O
O
N
HN
N
N
O
O
NH
N
N
O
O
OH
A
DKP-Side-chain library:
The linker region and the first diversity unit in DKP-side-chain library were created as in the case of DKP-backbone library. After the first diversity element, the chain extension was carried out coupling with BAA/DIC followed by mono-N-tboc-ethylenediamine, as a later point of chain-extension as a side-chain. The secondary amine on the other hand was coupled with BAA and the solid support was split into 5 different reaction vessels. Each vessel was separately treated with amino acid ester. Beads were pooled and split into 8
21
fractions and treated individually with 8 different primary amines. At this stage the reaction mixture was subjected for 2,5-DKP ring formation under basic thermal condition as explained above. Once the cyclization was completed, the t-boc group was deprotected utilizing 50% TFA in DCM. Two additional peptoid monomers were added from the resultant primary amine utilizing conventional peptoid synthesis method via split and pool method.
H2N H2N
O
H2NH2N
NH2
CF3
H2N
N
O
NH2
Ph
H2N
SNH2
O O
SH2N NH2
F
R :
H2N
Cl Cl
O
O
NH2
H2N
Cl Cl
H2N
O
H2N
HN
O
H2N
NH2
CF3
H2N
N
O
H2N
SNH2
O O
SH2N
H2N
NH
N
H2N
OH
H2N
NH
R"
H2N
N
N
O
O
N
N
O
O
N
N
O
O
N
HN
N
N
O
O
N
N
O
O
OH
A
NN
NNH
O
O
O
O
O
N
R
O
AN
HN
O
R'
O
N
R
O
NH
R
HN
S
O
DKP-terminated hybrid peptidomimetic library:The linker region and the first diversity unit in DKP-side-chain library were created as in the case of DKP-backbone library. The solid support was divided into 16 different vessels. In order to incorporate variety of diversity element at the second diversity element, following processes were executed,
1. Out of 16, two of the fractions were separately coupled with DIC activated (S)-2-bromopropionic acid and separately treated with either mono-N-tboc-piperazine or (S)-4-N-Boc-2-methylpiperazine at 50oC, O.N. The t-boc group was deprotected using 50% TFA in DCM prior to third diversity element was incorporated.
2. One portion out of remaining fractions was coupled with BAA/DIC and bromide was displaced with N-mono-t-boc-ethylenediamine. The secondary amine was coupled with DIC activated (S)-2-bromo-3-phenyl-propionic acid. t-boc group was acid-deprotected and the reaction mixture was incubated under 10% DIEA overnight to afford cyclization to afford 2-oxopiperazine unit.
3. Remaining portion of the beads were divided into two fractions after pooling. Each
22
fraction was equilibrated in DCM and treated directly either with 3-chloromethyl benzoyl chloride (10X) or with 4-bromomethyl phenylsulfonyl chloride in DCM (5 mL). A solution of triethylamine (12X) in DCM (5 mL) was slowly added in the acid chloride solution at 0oC. The reaction mixture was brought into the room temperature and allowed to stand for 3 hr. Each vessel was separately washed with DCM several times, pooled together and split into 13 different fractions. The halides were incubated with 13 different amines (R’) separately at 37oC, 3 hr.
After completion of above explained syntheses, all 16 vessels were pooled and coupled with BAA/DIC. The beads were further split into 13 portion and treated with 13 primary amines separately (R’), 37oC, 1 h. Finally, library synthesis was accomplished by incorporating 2,5-DKP as a capping group. The formation of DKP was performed as explained above. At the terminal position, 56 different 2,5-DKPs as capping groups were generated with 7 different amino acid esters and 8 different primary amines.
23
N
N
O
O
RR"
O
DKP:
R= Side-chain from alanine, leucine,lysine, phenylglycine, phenylalanine, histidine, tryptophan
NH
O
DKPN
R'
O
A
Linker
O
NR'
NH
Linker
O
NH
R'
NH
Linker
O
N
R'
O
N
NH
NH
Linker
O
N
R'
O
N
NH
NH
Linker
O
N
R'
O NHR'
NH
Linker
O
N
R'
SO
NH
O
R'
NH
Linker
O
N
R'
O
N
NH
O Ph
1. (S)BPA, DIC, DMF
2. (S)Me-Piperazine, DMF
1. (S)BPA, DIC, DMF
2. Piperazine, DMF
Cl
O
Cl1.
DIEA, DCM, 0oC
2. R'-NH2 , DMF 50oC, 2 h
SCl
O1.
DIEA, DCM, 0oC
2. R'-NH2 , DMF 37oC, 30 min
Br
O1. BAA, DIC, DMF, 37oC, 15 min2. N-tboc-ethylenediamine DMF, 37oC, 30 min
HO
O
Br
Ph
DMF, 37oC, 2 h
3.
4. 50% TFA in DCM, RT, 30 min
5. 10% DIEA in DMF 2 hr, 37oC
a. b. c. d. e.
a.
b.
c.
d.
e.
1. BAA, DIC, DMF
2. R'NH2, DMF
3. DKP formation as shown in Scheme 1
DKP-hybrid library
O
N
O
O
N
O
NLinker =
24
NH2
Cl
NNH2
O
Cl
HN
NH2
O
NH2
SH2N
O O
NH2
F3C
NH2
O
NH2NH2 ONH2
NH2
OO
NH2O
F3C
NH2
NH2
S
R'
NH2
Cl
N
NH2
O
Cl
HN
NH2
O
NH2
SNH2
O
ONH2
CF3
NH2
O
NH2
NH2
O
O
R"
N
N
O
O
RR"
O
DKP:
R= Side-chain from alanine, leucine,lysine, phenylglycine, phenylalanine, histidine, tryptophan
Following are the structures of peptoids from DKP-backbone library, identifed after CNBr mediated cleavage from the resins and subsequent MALDI – MS and MS/MS analyses. Each figure has a peptoid structure showing the mass of corresponding y and b fragments at particular substituent observed during Collision-Induced Dissociation (CID) of the parent peak:
N
N
O
O
O
NN
O
O
HN
O
N
O
NH
NN
O
NH
OO
O
HN O SH2N O
O
O
O
Exact Mass: 1170.5016
501 / 671
712 / 460
966 / 206
359 / 813
O
Figure S42: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound
25
N
N
O
O
O
NN
O
O
HN
O
N
NN
O
NH
OO
O
O
OS
H2NO
O
O
NH
Exact Mass: 1205.5063
OH
564/ 643
775 / 432
1029 / 178
359 / 848
O
Figure S43: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound
N
N
O
O
O
NN
O
O
HN
O
N
NN
O
NH
OO
O
O
NH
Exact Mass: 1011.4348
NH2
Cl
Cl
359 / 656
430 / 583
683 / 330
793 / 230
288 / 727O
Figure S44: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
26
N
N
O
O
O
NN
O
O
HN
O
N
NN
O
NH
OO
O
O
NH
359 / 795
983 / 131
N
O
CF3
NHO
Exact Mass: 1152.5791
501 / 653
754 / 400
O
Figure S45: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
N
N
O
O
O
NN
O
O
HN
O
N
NN
O
NH
OO
O
O
NH
Exact Mass: 1049.4982
HN O
F
359 / 692
456 / 595
729 / 322
885 / 166O
Figure S46: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
27
N
N
O
O
O
N
O
NH
O
N
NN
O
NH
OO
O
O
NH
SO
H2NO
Ph
Exact Mass: 1094.4532
329/ 737
632 / 464
855 / 240
O
Figure S47: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
N
N
O
O
O
NN
O
O
HN
O
N
O
NH
NN
O
NH
OO
O
NHN
F3CS
Exact Mass: 1217.4940
NH
359 / 860
512 / 707
838 / 381
1053 / 166
O
Figure S48: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
28
N
N
O
O
O
NN
O
O
HN
O
N
O
NH
NN
O
NH
OO
O
NHN
Ph
Exact Mass: 1138.5270
S
512 / 628
751 / 389
974 / 167O
Figure S49: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
N
N
O
O
O
NN
O
O
HN
O
N
O
NH
NN
O
NH
OO
O
NHN
CF3
CF3
NH
N
359 / 887
574 / 672
851 / 395
1080 / 166
288 / 958
Exact Mass: 1244.5202
O
Figure S50: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
29
N
N
O
O
O
NN
O
O
HN
O
N
NN
O
NH
OO
O
O
NH
S O
OH2N
OH
NH2
Exact Mass: 1072.4648
359 / 715
599 / 475
902 / 172
1002 / 72
288 / 786O
Figure S51: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound
N
N
O
O
O
NN
O
O
HN
O
N
NN
O
NH
OO
O
O
NH
S
359 / 757
733 / 383
900 / 175
Exact Mass: 1114.4405
CF3OH
430 / 686O
Figure S52: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
\
30
N
N
O
O
O
NN
O
O
HN
O
N
O
NH
NN
O
NH
OO
O
NHN
NH
O
N O
HN
HN
N
S
S
Exact Mass: 1405.6635
O
1074 / 333
1242 / 166
474 / 933
O
Figure S53: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound
N
N
O
O
O
NN
O
O
HN
O
N
O
NH
NN
O
NH
OO
O
NHN
S
NH
O
N O
HN
HN
NS
456 / 933
1223 / 166
1056 / 333
Exact Mass: 1387.6529
O
Figure S54: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
31
NN
NNH
O
O
O
O
O
NO
O
O
N
N
O
O
OH
HN
O
N
O
NH
HN O
O
O
Exact Mass: 1093.51
359 / 736
501 / 594
804 / 291
1023 / 72
288 / 807
Figure S55: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
N
N
O
O
O
NN
O
O
HN
O
N
NN
O
NH
OO
O
O
NH
F
NH
S
524 / 627
359 / 792
795 / 354
950/ / 201
Exact Mass: 1149.4754
O
Figure S56: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
32
N
N
O
O
O
NN
O
O
HN
O
N
O
NH
NN
O
NH
OO
O
NHN
S O
OH2N
NH
O
NO
NH
HN
N
S
OO
NH2
Exact Mass: 1507.6700
O
358 / 1150
428 / 1079
1343 / 166
1102 / 406
Figure S57: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
DKP-side chain library:
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
HN
288 / 1114
359 / 1043
987 / 289
1210 / 192
O
O
O
SOO
H2N
Ph
Exact Mass: 1400.5747
599 / 803
1113 / 289
Figure S58: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
33
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
HN
288 / 1119
359 / 1048
1006 / 401
1230 / 178
588 / 819O
OH
Ph
1088 / 319
Exact Mass: 1405.5553
Cl
Cl
OH
Figure S59: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
HN
288 / 849
359 / 778
849 / 383
989 / 241
Exact Mass: 1230.5452
430 / 802
912 / 320 NH
S
NH2
OO
HN
O
NHN
O
Figure S60: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
34
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
NH
288 / 849
359 / 778
928 / 209
999 / 138
Exact Mass: 1135.5550
922 / 319O
O
O
550 / 587858 / 279
Figure S61: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
NH
OH
288 / 953
359 / 882
428 / 811
848 / 393
1063 / 178F3C
Exact Mass: 1239.5424
O
OH
922 / 319
Figure S62: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
35
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
NH
OH
F
Exact Mass: 1309.5667
O
O
O
OH
288 / 1023
359 / 952
524 / 787
942 / 369
1133/ 178
992 / 319
Figure S63: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
NH
288 / 903
980 / 211
O
1093 / 97
909 / 282
N
O
359/ 832
Exact Mass: 1293.5700
O
SO O
H2N
949 / 344
Figure S64: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
36
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
NH
288 / 903
980 / 211
599 / 592
Exact Mass: 1189.5801
S O
OH2N
1093 / 97
909 / 282N
O
359/ 832
Figure S65: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
NH
288 / 1040
359 / 969
1027 / 301
599 / 729
Exact Mass: 1326.4913
Cl
Cl
S O
OH2N
OH
1256 / 72
329 / 997
Figure S66: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
37
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
O
N
O
NH
HO
S
288 / 809
359 / 738
512 / 585
848 / 249
919 / 178
860 / 237Exact Mass: 1095.5059
Figure S67: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
O
N
O
O
O
OONH
O
N
O
N
NH
O
N
O
O
N
288 / 751NH
HN
O
O
O
N
O
HN
359 / 680
501 / 538
854 / 185
967 / 71 785
254
Exact Mass: 1037.5506
Figure S68: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
38
Hybrid DKP-capped library:
NN
NNH
O
O
O
O
O
NO
O
Exact Mass: 1018.53
O
O
N
N O
NO
O
N
N
O
O
O
474 / 546
614 / 406
729 / 292359 / 661518502
Figure S69: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
NNH
O
O
O
O
O
NO
O
O
N O
N
N
O
O
O
N
N
CF3
OO
Exact Mass: 1112.48456 / 658
596 / 518
789 / 327
359 / 755
288 / 826484 / 630
Figure S70: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
39
NN
NNH
O
O
O
O
O
NO
O
O
N
N
O
O
N O
N
O
N
Exact Mass: 1128.50
NH
OHN
N
SNH2
O O
288 / 842
359 / 771
430 / 700
570 / 560
712 / 418
458 /
672
Figure S71: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
NNH
O
O
O
O
O
NO
O
O
N
N
O
O
O
N
O
Exact Mass: 1267.51 O CF3
N
N
HN
CF3
288 / 981
359 / 910
590 / 679
730 / 539
827 / 442
616 / 653
Figure S72: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
40
NN
N
HN
O
O
O
O
O
N
OO O
N
N
O
O
N
O
N
HN
O
Exact Mass: 1058.52
N
H2N
O
S
288 / 772
359 / 702
456 / 604
596 / 464
749 / 312
482 / 576
Figure S73: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
NNH
O
O
O
O
O
NO
O
O
O
N O
N
N
O
O
Exact Mass: 1067.5651
N
NHO
N
O
359 / 710
456 / 613
572
645 / 424
787 / 282
288/ 781
Figure S74: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
41
NN
N
HN
O
O
O
O
O
N
OO N O
N
N
O
OHN
O
S NH2O
O
OO
O N
Exact Mass: 1441.51
OF3C
OH
O
372 / 893
879 / 588
1117 / 348381 / 1083
288 / 1177
Figure S75: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
SNN
N
HN
O
O
O
O
O
NO
O
O
O
N
O
N
N
O
O
O
Exact Mass: 1138.4753
HN
N
N
O
O
HN O
381 / 781
524 / 637846 / 315
731 / 430
Figure S76: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
42
SNN
N
HN
O
O
O
O
O
NO
O
O
O
N
O
N
N
O
O
Exact Mass: 1258.49
N
O
O
O
O
HOS
NH2
O
O
310 / 993
381 / 921
496 / 809634 / 668
724 / 579
837 / 464
560 / 724
Figure S77: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
NNH
O
O
O
O
O
NO
O
O
O
N
O
N
N
O
O
Exact Mass: 1171.50
N
N
OO
NH
O
S
359 / 814
288 / 885
550 / 623
578 / 595
704 / 469
857 / 316
Figure S78: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
43
NN
NNH
O
O
O
O
O
NO
O
O
N O
N
N
O
O
Exact Mass: 1180.49
S
O
N
N
OH
CF3
288 / 894
359 / 823
512 / 670
666 / 516
763 / 419
642
540
Figure S79: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
N
HN
O
O
O
O
O
N
OO O
N
N
O
O
O
Exact Mass: 1041.56
N
N
O
N
HN
N
HN
O
472 / 571
626 / 417
723 / 320
500 / 543
359 / 684
288 / 755
Figure S80: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
44
NN
NNH
O
O
O
O
O
NO
O
O
N
N
O
O
N O
N
O
SNH2
OO
Exact Mass: 1316.50 (H+) 1338.50 (Na+)
N
O Ph
S
NH2
O
O
HN
N
310 / 1052
381 / 1003
452 / 910 682 / 680
922 / 441
Figure S81: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound
NN
N
HN
O
O
O
O
O
N
OO
O
N
N
O
O
Exact Mass: 1230.48
O
N
NO
PhO
N
NH
N
686 / 546
CF3
S
456 / 546
839 / 393
359 / 874
Figure S82: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
45
NN
N
HN
O
O
O
O
O
N
OO
O
N
O
N
N
O
O
OO
SH2N
O
O
NH
Exact Mass: 1358.56
O
N
NO
Ph
Figure S83: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
NN
N
HN
O
O
O
O
O
N
OO
ON O
N
N
O
O
Exact Mass: 1218.52
F3C
O
O
N
NO
PhO
310 / 954
381 / 883
826 / 437
1017 / 225
Figure S84: Top: MALDI-MS data showing parent peak (left) of peptoid (right). Bottom: MALDI-TOF MS/MS of the compound.
46
47