Supporting information Antibacterial peptide nucleic acid - antimicrobial peptide (PNA-AMP) conjugates: Antisense targeting of bacterial fatty acid biosynthesis Anna Mette Hansen, Gitte Bonke, Camilla Josephine Larsen, Niloofar Yavari, Peter E. Nielsen, and Henrik Franzyk * Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark *To whom reprint requests should be addressed. Email: henrik.franzyk@sund.ku.dk Contents: S2-S4: Experimental procedures S4: Table S1: Amino acid sequences, molecular masses, retention times, and purity of tested AMP S5: Figure S1. E. coli growth curves in the presence of AMP 1 and 2, of anti-acpp-pna-amp conjugates 1a and 2a, and mismatch-acpp-pna-amp conjugates 1c and 2c S6-S21: HRMS characterization data and analytical HPLC chromatograms for compounds 1-16. S22-S49: MALDI-TOF characterization data and analytical HPLC chromatograms for conjugates based on peptides 1-16. S1
Experimental procedures Starting materials and solvents were purchased from commercial suppliers (ABCR GmbH, Alfa Aesar, AppliChem, CHEMsolute, Fluka, Iris Biotech, LabScan, Merck, Sigma Aldrich and VWR and used without further purification. Deionized water was filtered (0.22 µm) in-house by use of a Milli-Q plus system (Millipore, Billerica, MA). For peptides preparative reversed-phase high pressure liquid chromatography (RP-HPLC) was performed by using a Phenomenex Luna C 18 (2) column (250 21.2 mm, 5 µm particle size) on an Agilent 1100 LC system with a multiplewavelength UV detector or on a Shimadzu system consisting of a CBM-20A Prominence communication bus module, an LC-20AP Prominence pump, an SPD-M20A Prominence diode array detector, and an SIL-20A HT Prominence autosampler. Elution was performed by using an aqueous MeCN gradient with 0.1% TFA (eluent A: 5:95 MeCN H 2 O + 0.1% TFA, eluent B: 95:5 MeCN H 2 O + 0.1% TFA). Analytical RP-HPLC was performed on a Shimadzu system consisting of an SCL-10A VP controller, a SIL-10AD VP autosampler, an LC-10AT VP pump, an SPD-M10A VP diode array detector, and a CTO-10AC VP column oven, using a Phenomenex Luna C 18 (2) column (150 4.6 mm, 3 µm particle size) by using same eluents as for preparative RP-HPLC. High-resolution mass spectra were obtained on a Bruker MicroTOF-Q LC mass spectrometer equipped with an electrospray ionization source and a Quadropol MS detector. The analyses were performed as ESI-MS (m/z): [M + nh] n+ for all compounds. MALDI-TOF: Acquisition of MS spectra was performed on MALDI-TOF instruments, AXIMA Assurance (Shimadzu Bioitech), Voyager-DE (Applied Biosystems, Foster City, CA, USA) operating at an accelerating voltage of 20 kv in the linear mode, or Bruker Autoflex (Bruker Daltonik GmbH, Bremen, Germany). Peptide synthesis. All peptides listed in Table 1 were synthesized on a CEM Liberty TM microwave peptide synthesizer by using microwave-assisted Fmoc-based solid-phase peptide synthesis (SPPS) on an H-Rink-Amide ChemMatrix resin (loading 0.52 mmol/g, 0.1 mmol) or on an Fmoc-Rink- Amide AM resin (loading 0.7 mmol/g, 0.1 mmol). Chain elongation was performed by using 0.2 M N α -Fmoc-protected and side chain protected amino acid building blocks in DMF (5.0 equiv) in combination with 0.5 M HBTU (5.0 equiv) as coupling reagent or by using 0.2 M N α -Fmoc-protected and side chain protected amino acid building blocks in DMF (5.0 equiv) together with 0.2 M HOBt (5.0 equiv) and 0.5 M DIC (5.0 equiv) as coupling reagent. When using HBTU couplings, 2 M DIPEA in NMP was used as activator base. Acetic S2
anhydride DIPEA NMP (1:2:3) was used as capping reagent. Fmoc deprotection was performed with 20% piperidine in DMF. Different microwave methods were used depending on the coupling procedure. Fmoc deprotections were conducted at 75 C (37 W for 30 sec followed by 40 W for 180 sec). When using HBTU as coupling reagent single amino acid couplings were conducted at 75 C (25 W for 300 sec followed by 25 W for 300 sec for double couplings). Difficult couplings involving hindered amino acid building blocks (Arg, Val, Pro, Ile, Thr) or peptoid building blocks as well as subsequent couplings were performed as double couplings. When using HOBt/DIC couplings amino acid building blocks were coupled at 75 C (25 W for 900 sec for single coupling and followed by 900 sec, 75 C, 25 W for double couplings). C-terminal Cys and His were coupled at 50 C (25 W for 900 sec) regardless of coupling reagents. After assembly of the delivery peptide sequence, the final tagging with a cysteine residue was carried out by manual coupling (2 h) of Boc-Cys(Trt)-OH (5 equiv) to the deprotected N-terminus in the presence of HBTU (5 equiv), 1-hydroxybenzotriazole (HOBt) (5 equiv) and DIPEA (10 equiv) or HOBt (5 equiv) and DIC (5 equiv) using half of the resin. All peptides were cleaved by using TFA TIS H 2 O (95:2.5:2.5; 4 ml, 1 h), TFA CH 2 Cl 2 (95:5; 2 ml, 1 h) or TFA CH 2 Cl 2 TIS (95:2.5:2.5; 2 ml, 1 h) eluting the resin with additional CH 2 Cl 2 and TFA. The combined eluates were co-evaporated with toluene under vacuum. The residue was then triturated twice with Et 2 O giving crude peptides with C-terminal amides. Peptides were purified by preparative RP-HPLC, purity (>95% with the presence of 2-3% dimer) was confirmed by analytical RP-HPLC (see Table S1 in supporting information), while the molecular mass of the peptides was confirmed by HRMS. PNA synthesis and conjugation of PNA and AMP. PNAs were synthesized using Boc-based SPPS and PNA-AMPs were conjugated as previously described. 1,2 All conjugates were more than 95% pure, and identity established by MALDI-TOF. Growth curve assay. MG1655 and MG1655 sbma (frozen stock) was inoculated in LB at 37 C, with shaking under aerobic conditions, overnight (Innova 4400 Incubator Shaker). The overnight culture was diluted to contain approx. 10 5 CFU/mL in Müeller-Hinton Broth II (MHB). AMPs were dissolved in water to give a known concentration and UV absorbance of aqueous solutions of AMP- PNA conjugates were measured on a NanoDrop spectrophotometer (ND1000, Thermo Fisher Scientific), and then the concentration was calculated by using Lambert-Beer s law. A three-fold S3
dilution row was made in a low-binding 96 well microtiter plate (Nunc TM ), and to each well was added approx. 8 10 4 CFU/mL to give a total volume of 100 µl. The plate was incubated at 37 C with shaking (220 rpm) in a GENios microplate reader (Tecan) with continuous OD 595 measurement for 15 h. From the growth curves the MIC was determined as the lowest concentration of the antimicrobial compound that did not show any growth after 15 h at 37 C. (1) Good, L., Awasthi, S. K., Dryselius, R., Larsson, O., and Nielsen, P. E. (2001) Bactericidal antisense effects of peptide-pna conjugates, Nat Biotechnol 19, 360-364. (2) Nielsen, P., (Ed.) (2002) Peptide Nucleic Acids Methods and Protocols, Vol. 208, Humana Press Inc., Totowa, New Jersey. Table S1. Amino acid sequences, molecular masses, retention times, and purity of tested AMP No. AMP Amino acid sequence Calculated m/z Net charge Retention time (min) a 1 BF2-A RAGLQFPVGRVHRLLRK-NH 2 2001.2337 +7 15.83 a 100 2 Drosocin GKPRPYSPRPTSHPRPIRV-NH 2 2197.2538 +7 11.40 a 95.7 3 Apidaecin (1a) GNNRPVYIPQPRPPHPRI-NH 2 2107.1745 +5 13.59 a 97.8 4 Pyrrhocoricin VDKGSYLPRPTPPRPIYNRN-NH 2 2339.2692 +4 13.29 a 98.1 5 Oncocin 10 VDKPPYLPRPRPPRRIYNR-NH 2 2389.3801 +6 12.95 a 100 6 Bac 1-15 RRIRPRPPRLPRPRP-NH 2 1918.2190 +8 12.92 a 97.8 7 IsCT-p ILKKIWKpIKKLF-NH 2 1653.1222 +6 17.74 a 99.7 8 Pep-1-K KKTWWKTWWTKWSQPKKKRKV-NH 2 2843.6421 +10 17.79 a 98.8 9 TPk VRRFkWWWkFLRR-NH 2 1963.1515 +7 18.15 a 96.5 10 SA-3 IKWAGKWWKLFK-NH 2 1588.9395 +5 20.33 a 98.9 11 K 6 L 2 W 3 KLWKKWKKWLK-NH 2 1570.0024 +7 15.68 a 100 12 KLW-L9,13-a KWKKLLKKaLKLaKKLLK-NH 2 2177.5425 +10 15.04 a 99.3 13 NLS-Gb3 WHWTWLRIRKKLR-NH 2 1877.1165 +7 18.17 a 99.0 14 (P59 W59)-Tat 48-60 GRKKRRQRRRPWQ-NH 2 1806.0938 +9 20.68 b 100 15 BF2-A-RXR RAGLQFPVGRVHRLLRXR-NH 2 2143.3273 +7 25.86 b 100 16 Drosocin-RXR GKPRPYSPRPTSHPRPIRXR-NH 2 2367.3706 +8 20.70 b 100 p = D -proline, k = NLys, a = NAla, a The AMP was eluted over 30 min by using a linear gradient of 10-60% B. b The AMP was eluted over 35 min starting with 5 min 0% eluent B followed by a linear gradient of 0-60% eluent B over 30 min. Purity (%) S4
Figure S2. E. coli growth curves in the presence of AMP 1 and 2, of anti-acpp-pna-amp conjugates 1a and 2a, and mismatch-acpp-pna-amp conjugates 1c and 2c. S5
Compound 1: BF2-A. Sequence: RAGLQFPVGRVHRLLRK-NH 2. Charge: 7+. Rt = 15.83 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+4H] 4+ 501.3163, found 501.3168; M = 0.9 ppm. S6
Compound 2: Drosocin. Sequence: GKPRPYSPRPTSHPRPIRV-NH 2. Charge: 7+. Rt = 11.40 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+5H] 5+ 440.4586, found 440.4584; M = 0.43 ppm. S7
Compound 3: Apidaecin (1a). Sequence: GNNRPVYIPQPRPPHPRI-NH 2. Charge: 5+. Rt = 13.59 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+5H] 5+ 422.4427, found 422.4420; M = 1.73 ppm. S8
Compound 4: Pyrrhocoricin. Sequence: VDKGSYLPRPTPPRPIYNRN-NH 2. Charge: 4+. Rt = 13.29 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+5H] 5+ 468.8617, found 468.8610; M = 1.43 ppm. S9
Compound 5: Oncocin 10. Sequence: VDKPPYLPRPRPPRRIYNR-NH 2. Charge: 6+. Rt = 12.95 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+6H] 6+ 399.2378, found 399.2370; M = 2.12 ppm. S10
Compound 6: Bac 1-15. Sequence: RRIRPRPPRLPRPRP-NH 2. Charge: 8+. Rt = 12.92 min. Gradient: 10-60B over 0-30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+5H] 5+ 384.6516, found 384.6520; M = 1.0 ppm. S11
Compound 7: IsCT-p. Sequence: ILKKIWKpIKKLF-NH 2. p = D -proline. Charge: 6+. Rt = 17.74 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+4H] 4+ 414.2884, found 414.2888; M = 0.9 ppm. S12
Compound 8: Pep-1-K. Sequence: KKTWWKTWWTKWSQPKKKRKV-NH 2. Charge: 10+. Rt = 17.79 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+6H] 6+ 474.9482, found 474.9476; M = 1.22 ppm. S13
Compound 9: TPk. Sequence: VRRFkWWWkFLRR-NH 2. Charge: 7+. Rt = 18.15 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+5H] 5+ 393.6381, found 393.6370; M = 2.87 ppm. S14
Compound 10: SA-3. Sequence: IKWAGKWWKLFK-NH 2. Charge: 5+. Rt = 20.33 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+3] 3+ 530.6543 found 530.6549; M = 1.1 ppm. S15
Compound 11: K 6 L 2 W 3. Sequence: KLWKKWKKWLK-NH 2. Charge: 7+. Rt = 15.68 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+3H] 3+ 524.3420, found 524.3426; M = 1.1 ppm. S16
Compound 12: KLW-L9, 13-a. Sequence: KWKKLLKKaLKLaKKLLK-NH 2. a = NAla. Charge: 10+. Rt = 15.04 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+5H] 5+ 436.5163, found 436. 5168; M = 1.1 ppm. S17
Compound 13: NLS-Gb3. Sequence: WHWTWLRIRKKLR-NH 2. Charge: 7+. Rt = 18.17 min. Gradient: 10-60B over 30 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+4H] 4+ 470.2897, found 470.2875; M = 4.6 ppm. S18
Compound 14: (P59 W59)-Tat 48-60 earlier reported in reference (19) Zhu, W. L., and Shin, S. Y. (2009) Effects of dimerization of the cell-penetrating peptide Tat analog on antimicrobial activity and mechanism of bactericidal action, J. Pept. Sci. 15, 345-352. Sequence: GRKKRRQRRRPWQ- NH 2. Charge: 9+. Rt = 20.68 min. Gradient: 0-0-60B over 0-5-35 min. B = 95% MeCN + 0.1% TFA. MALDI: calcd for [M+H] + 1807.10, found 1808.52. S19
Compound 15: BF2-A-RXR. Sequence: RAGLQFPVGRVHRLLRXR-NH 2. Charge: 7+. Rt = 25.86 min. Gradient: 0-0-60B over 0-5-35 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+4H] 4+ 536.8397, found 536.8376; M = 3.9 ppm. S20
Compound 16: Drosocin-RXR. Sequence: GKPRPYSPRPTSHPRPIRXR-NH 2. Charge: 8+. Rt = 20.70 min. Gradient: 0-0-60B over 0-5-35 min. B = 95% MeCN + 0.1% TFA. HRMS: calcd for [M+4H] 4+ 592.8505, found 592.8457; M = 8.0 ppm. S21
Conjugate 1a. MALDI-TOF: m/z calcd for [M+H] + : 4962.41 S22
Conjugate 1b. MALDI-TOF: m/z calcd for [M+H] + : 4962.41 S23
Conjugate 1c. MALDI-TOF: m/z calcd for [M+H] + : 4962.41 S24
Conjugate 2a. MALDI-TOF: m/z calcd for [M+H] + : 5157.43 S25
Conjugate 2b. MALDI-TOF: m/z calcd for [M+H] + : 5157.43 S26
Conjugate 2c. MALDI-TOF: m/z calcd for [M+H] + : 5157.43 S27
Conjugate 3a. MALDI-TOF: m/z calcd for [M+H] + : 5067.35 S28
Conjugate 4a. MALDI-TOF: m/z calcd for [M+H] + : 5299.45 S29
Conjugate 5a. MALDI-TOF: m/z calcd for [M+H] + : 5349.56 S30
Conjugate 5b. MALDI-TOF: m/z calcd for [M+H] + : 5349.56 S31
Conjugate 5c. MALDI-TOF: m/z calcd for [M+H] + : 5349.56 S32
Conjugate 6a. MALDI-TOF: m/z calcd for [M+H] + : 4879.40 S33
Conjugate 7a. MALDI-TOF: m/z calcd for [M+H] + : 4614.30 S34
Conjugate 8a. MALDI-TOF: m/z calcd for [M+H] + : 5803.82 S35
Conjugate 8b. MALDI-TOF: m/z calcd for [M+H] + : 5803.82 S36
Conjugate 8c. MALDI-TOF: m/z calcd for [M+H] + : 5803.82 S37
Conjugate 8d. MALDI-TOF: m/z calcd for [M+H] + : 5803.82 S38
Conjugate 9a. MALDI-TOF: m/z calcd for [M+H] + : 4923.33 S39
Conjugate 10a. MALDI-TOF: m/z calcd for [M+H] + : 4550.12 S40
Conjugate 11a. MALDI-TOF: m/z calcd for [M+H] + : 4531.18 S41
Conjugate 12a. MALDI-TOF: m/z calcd for [M+H] + : 5137.72 S42
Conjugate 12c. MALDI-TOF: m/z calcd for [M+H] + : 5137.72 S43
Conjugate 13a. MALDI-TOF: m/z calcd for [M+H] + : 4838.30 S44
Conjugate 14a. MALDI-TOF: m/z calcd for [M+H] + : 4767.27) S45
Conjugate 15a. (m/z calcd for [M+H] + : 5101.52) S46
Conjugate 15c. (m/z calcd for [M+H] + : 5101.52) S47
Conjugate 16a. MALDI-TOF: m/z calcd for [M+H] + : 5327.55 S48
Conjugate 16c. MALDI-TOF: m/z calcd for [M+H] + : 5327.55 S49