Supporting Information

Short Helix-Constrained Peptides With Contiguous Hydrophobic and Charged Surface

Patches Are Cell Permeable

Samuel R.Perry,†¶ Timothy A. Hill,†¶ , Aline D. de Araújo ,† Huy N. Hoang,† and David P. Fairlie†*

†Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia

Corresponding author. Tel: (617) 3346 2989. Fax: (617) 3346 2101. d.fairlie@imb.uq.edu.au,

¶ Contributed equally.

Table of Contents

1.1 Supporting Figures 21.1.1 Figure S1: Localisation in cell uptake of cell permeable lactam bridged (A) and hydrocarbon stapled peptides (B). 21.1.2 Figure S2. Representative histogram of HeLa cells after incubation with fluorophore labelled peptide. 31.1.3 Figure S3. Circular dichroism spectra measured in 10 mM phosphate buffer (water)(pH 7.4, 25 °C) (D) in 10 mM SDS (pH 7.4, 25 °C) and (E) in 50 % TFE (pH 7.4, 25 °C) 41.1.4 Figure S4. Circular dichroism spectra measured in 10 mM phosphate buffer (water)(pH 7.4, 25 °C) (D) in 10 mM SDS (pH 7.4, 25 °C) and (E) in 50 % TFE (pH 7.4, 25 °C) 5

1.2 Supporting Tables 61.2.1 Table S1. 61.2.2 Table S2. 71.2.3 Table S3. Peptide UPLC and MS characterization. 81.2.4 Table S4. Calculated Hydrophobic Surface Patches 9

1.3 Experimental 101.3.1 Abbreviations 101.3.2 Compound Synthesis, Purification and Characterization 101.3.3 CD Spectroscopy. 161.3.4 Total Hydrophobic surface area in Å2 171.3.5 Connected Hydrophobic surface area in Å2 171.3.6 Hydrophobic moment (H) 181.3.7 Materials for Biological Studies 191.3.8 Cell culture 191.3.9 Flow Cytometry 191.3.10 Inhibition of endocytosis 201.3.11 Live cell confocal microscopy 211.3.12 Hemolytic activity 21

Electronic Supplementary Material (ESI) for Organic & Biomolecular Chemistry.This journal is © The Royal Society of Chemistry 2017

1.1 Supporting Figures

1.1.1 Figure S1: Localisation in cell uptake of cell permeable lactam bridged (A) and hydrocarbon stapled peptides (B).

Live cell confocal microscopy of HeLa cells. Peptides were incubated at 10 μM for 1h hour at 37 °C in serum free media. Nuclei were counterstained with Hoechst. Scale bar = 30 μm.

1.1.2 Figure S2. Representative histogram of HeLa cells after incubation with fluorophore labelled peptide.

(A) Linear peptides and peptides with KD lactam bridges. (B) Hydrocarbon stapled peptides. Peptides were incubated at 10 μM for 1h hour at 37 °C in serum free media on HeLa cells. Quantitation by flow cytometry with fluorescence intensity calculated from live single cells. Data shown are from a single representative experiment. Experiments were repeated independently atleast three times.

1.1.3 Figure S3. Circular dichroism spectra measured in 10 mM phosphate buffer (water)(pH 7.4, 25 °C) (D) in 10 mM SDS (pH 7.4, 25 °C) and (E) in 50 % TFE (pH 7.4, 25 °C)

1.1.4 Figure S4. Circular dichroism spectra measured in 10 mM phosphate buffer (water)(pH 7.4, 25 °C) (D) in 10 mM SDS (pH 7.4, 25 °C) and (E) in 50 % TFE (pH 7.4, 25 °C)

1.2 Supporting Tables1.2.1 Table S1.

a Peptides were incubated at 10 μM for 1h at 37 °C in serum free media on HeLa cells. Quantitation by flow cytometry with fluorescence intensity calculated from live single cells. Values are relative to 100 % for TAT49-57. Data shown are means ( SD) of three independent repeats. b Human red blood cell (RBC) hemolysis following incubation with peptides at 10 μM b or 30 μM c for 1h at 37 °C relative to 0.1 % Triton X-100 as 100 % hemolysis. Data shown are means ( SD) from three donors. d ƒH calculated based on θ at 222 nm in either B° = 10 mM phosphate buffer ph 7.4 (water), SDS = 10 mM sodium dodecyl sulphate in phosphate buffer pH 7.4, TFE = 50 % 2,2,2-trifluoroethanol in phosphate buffer pH 7.4.* indicates not fully soluble. n/a peptides do not have stable structures for analysing surface properties.

Peptide Sequence θ222/θ208 B°/SDS/TFE

ƒHd

B°/SDS/TFE

Connected hydrophobic surface area

in Å2

Total hydrophobic surface area

in Å2

Hydrophobic

moment (H)

Cell Uptakea

% RBC lysis 10 Mb

% RBC lysis 30 Mc

3 FITC-Ahx-[KAAAD]AA[KAAAD]-NH2 1.08/1.04/0.92 0.46/0.47/0.49 35 65 4.03 1 ± 1 < 1 < 1

3a FITC-Ahx-KAAADAAKAAAD-NH2 0.72/0.71/0.91 0.16/0.19/0.50 n/a

3b FITC-Ahx-K(Nε-Ac)AAANAAK(Nε-Ac)AAAN-NH2

0.81/0.80/0.90 0.21/0.14/0.46 n/a

4 FITC-Ahx-[KAALD]LA[KLALD]-NH2 */3.14/0.82 */0.07*/0.51* 151 259 4.39 18 ± 7 < 1 < 1

5 FITC-Ahx-[KALLD]AL[KAALD]-NH2 */1.04/0.87 */0.70/0.86 282 282 5.13 30 ± 9 2 ± 1 2 ± 1

6 FITC-Ahx-[KAAKD]KA[KKAKD]-NH2 1.02/0.91/0.90 0.39/0.42/0.46 87 87 4.12 6 ±1 < 1 < 1

7 FITC-Ahx-[KKAAD]KA[KKKAD]-NH2 1.03/0.94/0.90 0.51/0.62/0.69 57 92 3.52 8 ±1 < 1 < 1

8 FITC-Ahx-[KKLKD]LK[KLKLD]-NH2 0.90/0.80/0.79 0.46/0.51/0.52 181 258 2.94 4 ± 1 < 1 < 1

9 FITC-Ahx-[KKLLD]KL[KKKLD]-NH2 1.04/0.93/0.81 0.67/0.88/0.86 293 293 5.6 78 ± 19 1 ± 1 7 ± 1

10 FITC-Ahx-[KLKLD]KL[KKLKD]-NH2 0.91/0.75/0.79 0.40/0.39/0.59 215 281 4.75 6 ± 4 < 1 < 1

11 FITC-Ahx-AKLLAKLAKKLA-NH2 0.58/0.82/0.68 0.15/0.64/0.56 n/a 15 ± 4 < 1 3 ± 1

12 FITC-Ahx-K(Nε-Ac)KLLNKLK(Nε-Ac)KKLN-NH2

0.52/0.79/0.76 0.09/0.41/0.38 n/a 2 ± 1 < 1 < 1 %

1.2.2 Table S2.

Peptide Sequence θ222/θ208 B°/SDS/TFE

ƒHd

B°/SDS/TFE

Connected hydrophobic surface area

in Å2

Total hydrophobic surface area

in Å2

Hydrophobic moment (H) Cell

Uptakea

% Hemolysis

10 M b

% Hemolysis

30 M c

13 FITC-Ahx-[XKLKX]LK[XLKLX]-NH2 */0.89/0.84 */0.50/0.60 319 351 3.08 60 ± 7 14 ± 2 44 ± 7

14 FITC-Ahx-[XKLLX]KL[XKKLX]-NH2 1.31/1.02/0.89 0.32/0.70/0.64 370 370 6.06 179 ± 45 30 ± 6 72 ± 11

15 FITC-Ahx-KKLL[XLLLLKKX]-NH2 */0.94/0.85 */0.55/0.57 270 390 0.68 37 ± 8 7 ± 3 41 ± 7

16 FITC-Ahx-LLKL[XLKLLKKX]-NH2 */0.96/0.85 */0.86/0.85 377 389 8.09 97 ± 15 26 ± 4 62 ± 9

17 FITC-Ahx-KL[XKKKX]L-NH2 0.94/0.86/0.91 0.30/0.49/0.54 59 165 3.49 6 ± 2 < 1 < 1

18 FITC-Ahx-KK[XLKKX]L-NH2 3.55/0.93/0.88 0.27/0.51/0.44 122 167 7.28 136 ± 22 7 ± 1 26 ± 1

19 FITC-Ahx-K(Nε-Ac)K(Nε-Ac)[XLK(Nε-Ac)K(Nε-Ac)X]L-NH2

1.10/1.00/0.84 0.67/0.81/0.57 140 198 7.41 5 ± 1 < 1 < 1

a Peptides were incubated at 10 μM for 1h at 37 °C in serum free media on HeLa cells. Quantitation by flow cytometry with fluorescence intensity calculated from live single cells. Values are relative to 100 % for TAT49-57. Data shown are means ( SD) of three independent repeats. b Human red blood cell (RBC) hemolysis following incubation with peptides at 10 μM b or 30 μM c for 1h at 37 °C relative to 0.1 % Triton X-100 as 100 % hemolysis. Data shown are means ( SD) from three donors. d ƒH calculated based on θ at 222 nm in either B° = 10 mM phosphate buffer ph 7.4 (water), SDS = 10 mM sodium dodecyl sulphate in phosphate buffer pH 7.4, TFE = 50 % 2,2,2-trifluoroethanol in phosphate buffer pH 7.4.* indicates not fully soluble

1.2.3 Table S3. Peptide UPLC and MS characterization.

# tR (min) Mol. Weight (Da) Isotopic ions m/z obs [M+nH]+ (n)Purity %

UPLC

3 3.08 1538.7 769.6 (2) >92

4 3.93 1707.0 853.4 (2), 569.6 (3) >95

5 4.25 1707.0 854.1(2), 569.7 (3) >95

6 2.49 1767.1 883.8 (2) 589.7 (3), 443.6 (4) >95

7 2.85 1767.1 883.3 (2) 589.4 (3), 443.6 (4) >90

8 2.68 1935.41 968.5 (2), 645.9 (3), 484.6 (4) >95

9 3.51 1935.41 967.8 (2), 645.7 (3), 484.7 (4) >95

10 2.29 1935.41 968.5 (2), 645.9 (3), 484.9 (4) >95

11 3.09 1769.23 884.9 (2), 590.5 (3), 443.2 (4) >98

12 3.38 2053.5 1026.7 (2), 685.2 (3), 514.2 (4) >98

13 3.67 1985.6 993.2 (2), 662.5 (3), 497.1 (4) >95

14 3.85 1985.6 993.4 (2), 662.2 (3), 497.1 (4) >92

15 3.68 2004.64 1001.7 (2), 668.6 (3), 501.7 (4) >95

16 5.10 2004.64 1001.9 (2), 668.6 (3), 501.8 (4) >95

17 2.86 1508.93 755.2 (2), 503.6 (3), 378.2 (4) >95

18 3.16 1508.93 755.1 (2), 503.6 (3) 377.9 (4) >95

19 3.84 1677.08 1676.1 (1) 838 (2) 830 (-18, 2) 554 (-18, 3) >95

1.2.4 Table S4. Calculated Hydrophobic Surface Patches

Compound Hydrophobic patches (A2)

Patch residues

1 35.5 K12 92.4

26.5X1, A4, X5Ac, A3

3 29.928.335.0

K8Ac, A3K1

4 151.0108.4

K1, L4, K8, L11L6, K9

5 281.6 Ac, K1, L3, L4, L7, K8, L11 6 86.8

28.7K1, K4, K8Ac, A3

7 57.029.729.134.9

K2, K6, K10K8Ac, A3K1

8 76.8180.5

K8, L11Ac, L3, L6, L9

9 292.8 Ac, K1, L3, L4, K6, L9, K8, L11

10 215.066.0

K1, L4, L7, K8, L10, K11L2, K6

13 318.732.3

Ac, L3, X5, L6, X8, L9, L11X1

14 369.5 L3, L7, L4, L11, X1, X5, X8, K9, K2, K6, Ac

15 296.6119.5

L3, L6, L8, L9, X12, X5, AcL7, L4, K1

16 376.6

12.5

L2, L1, L4, L9, L8, L6, X5, X12, K7K3

17 58.247.658.5

L8, K5X3, X7L2

18 121.845.3

L8, L4, K1, K5X3, X7

19 139.559.3

L8, L4, K1, K5X3, X7, K6

Peptide hydrophobic patches calculationed from Protein surface analysis in Biologics (Maestro version 11).

1.3 Experimental

1.3.1 Abbreviations CD, circular dichroism; DCM, dichloromethane; DIPEA, disopropylethylamine;

DMF, N,N-dimethylformamide; HCTU, 2-(6-chloro-1H-benzotriazole-1-yl)-1,1,3,3

tetramethylaminium hexafluorophosphate; MeCN, acetonitrile;; PyBOP,

benzotriazol-1-yl-oxytripyrrolidinophosphonium hexafluorophosphate; TFA,

trifluoroacetic acid; TIPS, triisopropylsilane.

1.3.2 Compound Synthesis, Purification and Characterization

1.3.2.1 Chemicals and Solvents. DCM (Chem-Supply), DMF (RCI Labscan), MeCN (SigmaAldrich), TFA (Halocarbon),

TIPS (Aldrich), DIPEA and pyridine (Auspep) were purchased from commercial

suppliers. PyBOP, HCTU and protected amino acids were purchased from Chem-Impex.

Phosphate buffer solution pH 7.2 was prepared in-house for circular dichroism

measurements. Ultrapure water was obtained by filtration through Elsa PureLab ultra

system.

1.3.2.2 Peptide Synthesis and Purification (3-12). Peptides were synthesized using Fmoc solid support chemistry on Rink amide resin

(low loading 0.38 mmol/g; Novabiochem) at a 50 M scale on a Symphony Multiplex

Synthesizer. Amino acids (4 eq.) were activated using HCTU (4 eq.) and DIPEA (8 eq.)

in DMF (2 10 min) prior to remove N-terminal Fmoc protecting group using 20%

piperidine in DMF (2 5 min). Formation of lactam constraints required a first selective

side-chain deprotection of the phenylisopropyl ester (Opip) on aspartic or glutamic acid

and of the methyl trityl (Mtt) group on lysine from the peptide-resin using 3% TFA in

DCM (2 5 min). Second, cyclization was achieved on peptide-resin with a 6mL

solution of PyBOP / DIPEA (1 g/400 L) in DMF over 10–15 h and under continuous

nitrogen bubbling. The procedure was repeated for multiple cyclizations. Peptides were

cleaved of the resin using a solution of TFA/TIPS/H2O (95/2.5/2.5) over 2 h before being

filtered through original reaction vessels and washed with DCM (3 times). Solutions were

then dried under nitrogen blow; the resulting materials were precipitated with ice-cold

diethyl ether and lyophilized. Crude peptides were dissolved in a solution of H2O/MeCN,

filtered through disposable syringe filter unit (NP045AN, Advantec) before being

purified on reverse-phase Schimadzu HPLC system; Phenomenex C18 10 m, 100 Å,

250 21.2 mm semi-preparative column, 20 mL/min, isocratic 20% solvent B

(H2O/MeCN 10/90 with 0.1% TFA modifier) in solvent A (H2O with 0.1% TFA

modifier) over 5min and gradient 20%–70% solvent B in solvent A over 30 min. HPLC

traces were monitored by UV detectors at 214 and 254 nm. Peptides were >95% purity by

analytical UHPLC-MS method: Schimadzu HPLC system Waters Acquity UPLC HSS

T3 column, 1.8 m, 2.1 mm 50 mm – gradient 0-100% solvent B (H2O/MeCN 10/90

with 0.05% formic acid) in solvent A (H2O with 0.05% formic acid) over 4 min at 0.4

mL/min coupled to LCMS-2020, single quadrupole liquid chromatograph mass

spectrometer (Table S3).

1.3.2.3 Peptide Synthesis and Purification (13-14). Fmoc(S)-2-(4’-pentenyl)alanine(Fmoc-S5-OH) (Okeanos) amino acid was used in the

synthesis the i,i+4 linkers hydrocarbon linkers. Peptides were synthesized using standard

Fmoc solid phase peptide synthesis protocols. Briefly, the chemistry was conducted on

Rink amide resin (low loading 0.38 mmol/g; Novabiochem) at a 50 M scale on a

Symphony Multiplex Synthesizer. Amino acids (4 eq.) were activated using HCTU (4

eq.) and DIPEA (8 eq.) in DMF (2 10 min) prior to remove N-terminal Fmoc protecting

group using 20% piperidine in DMF (2 5 min). On-resin ring closing metathesis

(RCM)[1]: Prior to RCM, the resin was washed with DCM and dried under high vacuum.

The dry resin was then placed in the synthesizer apparatus and swollen in dry DCE under

N2 stream for 10 min and drained. The RCM reaction was performed by treating the resin

with a 10 mM solution of Grubbs catalyst 1st generation in dry DCE (2 mL per 50 µmol

resin) under N2 bubbling for 2h. The catalyst solution was drained and a fresh 10 mM

Grubbs catalyst solution was added to the resin and reacted for 2h. After that, the resin

was washed with DCE, DMF and DCM. The fluorescent marker was incorporated to the

N-terminus by treating the free amine resin with FITC (2 equiv) and DIPEA (4 equiv) in

DMF overnight. Peptides were cleaved of the resin using a solution of TFA/TIPS/H2O

(95/2.5/2.5) over 2 h before being filtered through original reaction vessels and

washed with DCM (3 times). Solutions were then dried under nitrogen blow; the

resulting materials were precipitated with ice-cold diethyl ether and lyophilized.

Crude peptides were dissolved in a solution of H2O/MeCN, filtered through

disposable syringe filter unit (NP045AN, Advantec) before being purified on

reverse-phase Schimadzu HPLC system; Phenomenex C18 10 m, 100 Å, 250 21.2

mm semi-preparative column, 20 mL/min, isocratic 20% solvent B (H2O/MeCN

10/90 with 0.1% TFA modifier) in solvent A (H2O with 0.1% TFA modifier) over

5min and gradient 20%–70% solvent B in solvent A over 30 min. HPLC traces were

monitored by UV detectors at 214 and 254 nm. Peptides were >95% purity by

analytical UHPLC-MS method: Schimadzu HPLC system Waters Acquity UPLC HSS

T3 column, 1.8 m, 2.1 mm 50 mm – gradient 0-100% solvent B (H2O/MeCN 10/90

with 0.05% formic acid) in solvent A (H2O with 0.05% formic acid) over 4 min at 0.4

mL/min coupled to LCMS-2020, single quadrupole liquid chromatograph mass

spectrometer (Table S3).

1.3.2.4 Peptide Synthesis and Purification (15-16). Fmoc(R)-N-Fmoc-2-(7'-octenyl)alanine(Fmoc-R8-OH) and Fmoc-(S)-2-(4’-

pentenyl)alanine( Fmoc-S5-OH) (Okeanos) was used in the synthesis of i,i+7

hydrocarbonlinkers. Peptides were synthesized using standard Fmoc solid phase peptide

synthesis protocols. Briefly, the chemistry was conducted on Rink amide resin (low

loading 0.38 mmol/g; Novabiochem) at a 50 M scale on a Symphony Multiplex

Synthesizer. Amino acids (4 eq.) were activated using HCTU (4 eq.) and DIPEA (8 eq.)

in DMF (2 10 min) prior to remove N-terminal Fmoc protecting group using 20%

piperidine in DMF (2 5 min). On-resin ring closing metathesis (RCM):The ring-

closing- metathesis was performed by treating the resin with Hoveyda-Grubbs 2nd

generation catalyst in 2 mL dry DCE in a sealed vessel under Argon atmosphere and

under microwave heating (10 min at 1000C) in a Biotage Initiator Microwave system. The

fluorescent marker was incorporated to the N-terminus by treating the free amine resin

with FITC (2 equiv) and DIPEA (4 equiv) in DMF overnight. Peptides were cleaved of

the resin using a solution of TFA/TIPS/H2O (95/2.5/2.5) over 2 h before being

filtered through original reaction vessels and washed with DCM (3 times). Solutions

were then dried under nitrogen blow; the resulting materials were precipitated with

ice-cold diethyl ether and lyophilized. Crude peptides were dissolved in a solution of

H2O/MeCN, filtered through disposable syringe filter unit (NP045AN, Advantec)

before being purified on reverse-phase Schimadzu HPLC system; Phenomenex C18

10 m, 100 Å, 250 21.2 mm semi-preparative column, 20 mL/min, isocratic 20%

solvent B (H2O/MeCN 10/90 with 0.1% TFA modifier) in solvent A (H2O with 0.1%

TFA modifier) over 5min and gradient 20%–70% solvent B in solvent A over 30 min.

HPLC traces were monitored by UV detectors at 214 and 254 nm. Peptides were

>95% purity by analytical UHPLC-MS method: Schimadzu HPLC system Waters

Acquity UPLC HSS T3 column, 1.8 m, 2.1 mm 50 mm – gradient 0-100% solvent B

(H2O/MeCN 10/90 with 0.05% formic acid) in solvent A (H2O with 0.05% formic acid)

over 4 min at 0.4 mL/min coupled to LCMS-2020, single quadrupole liquid

chromatograph mass spectrometer. (Table S3)

1.3.2.5 Peptide Synthesis and Purification (17-19). Peptides were synthesized using standard Fmoc solid phase peptide synthesis protocols.

Briefly, the chemistry was conducted on Rink amide resin (low loading 0.38 mmol/g;

Novabiochem) at a 50 M scale on a Symphony Multiplex Synthesizer. Amino acids (4

eq.) were activated using HCTU (4 eq.) and DIPEA (8 eq.) in DMF (2 10 min) prior to

remove N-terminal Fmoc protecting group using 20% piperidine in DMF (2 5 min).

On-resin ring closing metathesis (RCM)24:Prior to RCM, the resin was washed with

DCM and dried under high vacuum. The dry resin was then placed in the synthesizer

apparatus and swollen in dry DCE under N2 stream for 10 min and drained. The RCM

reaction was performed by treating the resin with a 10 mM solution of Grubbs catalyst 1st

generation in dry DCE (2 mL per 50 µmol resin) under N2 bubbling for 2h. The catalyst

solution was drained and a fresh 10 mM Grubbs catalyst solution was added to the resin

and reacted for 2h. After that, the resin was washed with DCE, DMF and DCM. The

fluorescent marker was incorporated to the N-terminus by treating the free amine resin

with FITC (2 equiv) and DIPEA (4 equiv) in DMF overnight. Peptides were cleaved of

the resin using a solution of TFA/TIPS/H2O (95/2.5/2.5) over 2 h before being

filtered through original reaction vessels and washed with DCM (3 times). Solutions

were then dried under nitrogen blow; the resulting materials were precipitated with

ice-cold diethyl ether and lyophilized. Crude peptides were dissolved in a solution of

H2O/MeCN, filtered through disposable syringe filter unit (NP045AN, Advantec)

before being purified on reverse-phase Schimadzu HPLC system; Phenomenex C18

10 m, 100 Å, 250 21.2 mm semi-preparative column, 20 mL/min, isocratic 20%

solvent B (H2O/MeCN 10/90 with 0.1% TFA modifier) in solvent A (H2O with 0.1%

TFA modifier) over 5min and gradient 20%–70% solvent B in solvent A over 30 min.

HPLC traces were monitored by UV detectors at 214 and 254 nm. Peptides were

>95% purity by analytical UHPLC-MS method: Schimadzu HPLC system Waters

Acquity UPLC HSS T3 column, 1.8 m, 2.1 mm 50 mm – gradient 0-100% solvent B

(H2O/MeCN 10/90 with 0.05% formic acid) in solvent A (H2O with 0.05% formic acid)

over 4 min at 0.4 mL/min coupled to LCMS-2020, single quadrupole liquid

chromatograph mass spectrometer. (Table S3)

(1) Verdine, G. L.; Hilinski, G. J. Stapled Peptides for Intracellular Drug Targets. In Methods in Enzymology, Wittrup, K. D.; Gregory, L. V., Eds. Academic Press: 2012; Vol. 503, pp 3-33.

1.3.3 CD Spectroscopy. Circular dichroism (CD) spectroscopy was conducted with a Jasco model J-710

spectropolarimeter using 400 L sample in a 0.1 cm Jasco quartz cell (routinely

calibrated with (1S)-(+)-10-camphorsulfonic acid). Peptide solutions were prepared

from aqueous peptide stock solutions of accurate molecular concentrations

determined by fluorescence detection. The final concentration of the peptide samples

was 50 μM in 10mM phosphate buffer pH 7.2. Spectra were recorded at room

temperature (298K) over the wavelength range 260-185 nm at 50 nm/min, with a

bandwidth of 1.0 nm, response time of 1 s, resolution step width of 1 nm and

sensitivity of 20-50 millidegrees. Each spectrum represents the average of 5 scans.

Spectra were analysed using the spectral analysis software and smoothed using

‘adaptive smoothing’ function. All data were converted from raw ellipticity to molar

residue ellipticity MRE or [θ] according to the equation:

(Equation 1)𝑀𝑅𝐸 =

𝜃10 × 𝑙 × 𝑟 × 𝑐

where θ is the CD signal of the sample in millidegrees, l is the path length of the cell in

centimetres, r is the number of residues in the peptide, and c is the total peptide molar

concentration of the sample. CD Spectra for constrained peptides 7–28 are shown in

Figure S1. Percentage helicity fhelix of peptides were calculated from molar residue

ellipticity at 222 nm using the following equation:

(Equation 2)𝑓ℎ𝑒𝑙𝑖𝑥 =

[𝜃]222 ‒ [𝜃]0

[𝜃]𝑚𝑎𝑥 ‒ [𝜃]0

where [θ]max ([θ]max = [θ]∞(n – x)/n) is the maximum theoretical mean residue

ellipticity for a helix of n residues, [θ]∞ is the mean residue ellipticity of an infinite

helix, and x is an empirical constant that can be interpreted as the effective number

of amides missing as a result of end effects, usually about 2.4-4 (we used x=3) and

[θ]∞ = (−44000 + 250T) (T is temperature of the peptide solution in ˚C). [θ]0 is the

mean residue ellipticity of the peptide in random coil conformation and equals to

(2220 − 53T).

1.3.4 Total Hydrophobic surface area in Å2

Calculations were performed using Maestro Biologics simulation package version 11.

The force field topologies for all cyclic peptides were derived from the OPSL3 parameter

set. Cyclic peptide structures were modelled in an alpha-helix conformations using 3D

builder module and energy minimizations were applied to these structures before carrying

out surface calculations. Total Hydrophobic surface area was calculated using Protein

Surface Analysis module with surface size cutoff positive = 15.0 Å2, negative = 15.0 Å2,

hydrophobic = 30.0 and 50.0 Å2 (Alanine and Leucine containing peptides respectively)

and value cutoff 0.05 eV (positive), -0.05 eV (negative) and slogP = 0.04 and 0.08

(Alanine and Leucine containing peptides respectively). Total hydrophobic surface areas

(tHSA) is the total of all hydrophobic patches oon a peptide determined from the from

the calculation.

1.3.5 Connected Hydrophobic surface area in Å2

Calculations were performed using Maestro Biologics simulation package version 11.

The force field topologies for all cyclic peptides were derived from the OPSL3 parameter

set. Cyclic peptide structures were modelled in an alpha-helix conformations using 3D

builder module and energy minimizations were applied to these structures before carrying

out surface calculations. Connected hydrophobic surface area was calculated using

Protein Surface Analysis module with surface size cutoff positive = 15.0 Å2, negative =

15.0 Å2, hydrophobic = 30.0 and 50.0 Å2 (Alanine and Leucine containing peptides

respectively) and value cutoff 0.05 eV (positive), -0.05 eV (negative) and slogP = 0.04

and 0.08 (Alanine and Leucine containing peptides respectively). Connected hydrophobic

surface areas (cHSA) is determined as the largest hydrophobic patch/region present in the

calculation.

1.3.6 Hydrophobic moment (H)

Calculations were performed using Maestro Biologics simulation package version 11.

The force field topologies for all cyclic peptides were derived from the OPSL3 parameter

set. Cyclic peptide structures were modelled in an alpha-helix conformations using 3D

builder module and energy minimizations were applied to these structures before carrying

out surface calculations. Amphipathic moment were calculated using Protein Surface

Analysis module with surface size cutoff positive = 15.0 Å2, negative = 15.0 Å2,

hydrophobic = 30.0 and 50.0 Å2 (Alanine and Leucine containing peptides respectively)

and value cutoff 0.05 eV (positive), -0.05 eV (negative) and slogP = 0.04 and 0.08

(Alanine and Leucine containing peptides respectively). Hydrophobic moment (H) is

the measurement of amphipathicity for a peptide, per residue and in the unit of kcal.mol-

1.resd-1.

1.3.7 Materials for Biological StudiesNunc Lab-Tek II chambered coverglass (8 well) were purchased from Thermo

Fisher Scientific (Newstead, QLD, Australia). The 7-aminoactinomycin D was purchased

from Biolegend (San Diego, CA, USA). Fetal calf serum (FCS) was obtained from

Bovogen (East Keilor, VIC, Australia). All cell culture reagents were sourced from

Invitrogen (Mulgrave, VIC, Australia). The 384 well non-binding surface black wall

black bottom plates were purchased from Corning Incorporated (New York, USA). All

other reagents were purchased from Sigma Aldrich (Castle Hill, NSW, Australia) or

prepared in-house.

1.3.8 Cell cultureHeLa cervical adenocarcinoma cells were obtained from the American Type Culture

Collection. HeLa cells were cultured in DMEM supplemented with 10 % fetal bovine

serum, penicillin (50 U/mL) and streptomycin (50 μg/mL) in a humidified chamber at

37°C with 5 % CO2.

1.3.9 Flow CytometryHeLa cells were seeded overnight into 12 well plates at a density of 1.5 x 105 cells/well in

full medium. On the day of the experiment, medium was removed and the cells were

washed once with phosphate buffered saline (PBS) and the peptides were incubated in

500 µL of serum free media at 10 µM for 1 hour at 37°C. The cells were then washed

twice with PBS and incubated with 1 mg/ml heparin for 2 x 5 mins. Cells were washed

with PBS and de-adhered with 0.25% trypsin EDTA for 10 mins. De-adhered cells were

diluted in cold medium without serum and centrifuged at 500g at 4°C. Cell were re-

suspended in cold PBS and centrifuged at 500g at 4°C. Cells were re-suspended in cold

PBS before addition of 7-aminoactinomycin D and trypan blue (160 µg/mL) followed by

measuring fluorescence (excitation λ = 488 nm and emission detection at 525 nm) on a

Gallios flow cytometer (Beckman Coulter, Lane Cove NSW). Single live cells were used

to calculate mean fluorescence intensity using Kaluza software (Beckman Coulter). Data

shown are means (+ SD) of at least three independent repeats.

1.3.10 Inhibition of endocytosisHeLa cells were seeded overnight into 12 well plates at a density of 1.25 x 105 cells/well

in full medium. On the day of the experiment, medium was removed and the cells were

washed once with phosphate buffered saline (PBS) and the cells were incubated with

endocytosis inhibitors (10 µM 5-(N-Ethyl-N-isopropyl)amiloride, 20 µM Cytochalasin D,

5 µg/mL Filipin or 10 µg/mL Chlorpromazine hydrochloride) or ATP depleting media

(0.1 % sodium azide and 50 mM 2-Deoxy-D-Glucose) or heparin (Heparin sodium salt

from porcine intestinal mucosa, either 18 or 180U/mL) in 300 µL of serum free DMEM

at 37°C for 1h. Peptides were prepared at 4x concentration in serum free media with

endocytosis inhibitors in 100 µL and added at a final concentration of 10 µM and

incubated at 37°C for 1h. For the 4°C incubations, cells were placed in a cold room at

4°C for 1h before addition of cold peptides and also incubated for 1h at 4°C. The cells

were then washed twice with PBS and incubated with 1 mg/ml heparin for 2 x 5 mins.

Cells were washed with PBS and de-adhered with 0.25% trypsin EDTA for 10 mins. De-

adhered cells were diluted in cold medium without serum and centrifuged at 500g at 4°C.

Cell were re-suspended in cold PBS and centrifuged at 500g at 4°C. Cells were re-

suspended in cold PBS before addition of 7-aminoactinomycin D and trypan blue (160

µg/mL) followed by measuring fluorescence (excitation λ = 488 nm and emission

detection at 525 nm) on a Gallios flow cytometer (Beckman Coulter, Lane Cove NSW).

Single live cells were used to calculate mean fluorescence intensity using Kaluza

software (Beckman Coulter). Data shown are means (+ SD) of at least three independent

repeats.

1.3.11 Live cell confocal microscopyHeLa cells were seeded overnight into 8 well Nunc Lab-Tek II chambered coverglass at a

density of 1 x 104 cells/well in complete medium. On the day of the experiment, medium

was replaced with 300 µL of serum free DMEM containing peptides at 10 µM and

incubated for 1 hour at 37°C. Nuclei were counterstained with Hoechst for 10 min at 2.5

µg/mL. Cells were washed twice with PBS. Serum and phenol red free DMEM was

added and cells were placed into a humidified, temperature and atmosphere controlled

microscope stage at 37°C with CO2. Imaging was performed on a Zeiss LSM 710 FCCS

confocal microscope (Carl Zeiss, Munich, Germany) using a LD C-Apochromat 63x/1.15

W objective. Acquired images were adjusted using ImageJ 1.47i (National Institutes of

Health, Bethesda) and Photoshop CS6 (Adobe Systems, San Jose). Representative cells

are shown from three independent experiments.

1.3.12 Hemolytic activityHuman primary red blood cells (hRBC) were obtained from anonymous human donors

(Australian Red Cross Blood Service, Brisbane, QLD, Australia). Cells were washed with

PBS and centrifuged until the supernatant was clear. hRBC were resuspended at 6 % v/v

in PBS in 75 μL followed by addition of 2x concentrated peptides in another 75 μL and

incubated at 37°C for 1h. hRBC were pelleted by centrifugation and supernatant removed

and absorbance was measured at 560 nm. Data are normalised against 0.1 % triton X-100

as 100 % lysis. Data shown are means ( SD) of experiments with hRBC from four

donors.