Supporting Information for

Supporting Information for Ligand-directed chemistry of AMPA receptors confers live-cell fluorescent biosensors under natural habitat Shigeki Kiyonaka*, Seiji Sakamoto, Sho Wakayama, Yuma Morikawa, Muneo Tsujikawa and Itaru amachi*, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, ishikyo-ku, Kyoto 615-8510, Japan CREST(Core Research for Evolutional Science and Technology, JST), Chiyodaku, Tokyo, 102-0075, JAPA *Correspondence : kiyonaka@sbchem.kyoto-u.ac.jp ihamachi@sbchem.kyoto-u.ac.jp Table of Contents 1. Supporting Table (Table S1) 2. Supporting Figures (Figures S1 S14) 3. Supporting otes 4. Supporting Reference S1

1. Supporting Table Table S1 K d values of glutamate for Alexa488-AMPARs (GluA2) in live cells or for Alexa488-S1S2 in live cells or the test tubes 1). AMPAR K d values (µm) 1) Protein labeling was performed using CAM2(Ax488-5S). 2) Targeting Alexa488-S1S2 to the cell surface was conducted using avidin-biotin interaction. 3) Condition: 20 mm EPES, 107 mm acl, 6 mm KCl, 2 mm CaCl 2, 1.2 mm MgS 4, 11.5 mm glucose (p7.4). 4) Condition: 50 mm Tris Cl, 100 mm KSC, 2.5 mm CaCl 2 (p7.4). S1S2 2) Test tube Live cell Live cell in BS 3) Test tube in radioisotope-ligand binding buffer 4) Glu 252 ± 14 13.4 ± 0.7 11.9 ± 0.4 1.67 ± 0.01 S2

2. Supporting Figures Figure S1 Confocal live imaging of labeled AMPARs by CAM2(Ax488-5S) in EK293T cells. EK293T cells transfected with GluA2 or its control vector were treated with 2 µm CAM2(Ax488-5S) in the presence or absence of 50 µm BQX in serum free DMEM. mcherry was utilized as a transfection marker. Scale bars, 10 µm. S3

Figure S2 Confocal live imaging of labeled AMPARs by a series of CAM2(Ax488) derivatives in EK293T cells. EK293T cells transfected with GluA2 were treated with 2 µm CAM2 reagents in the presence or absence of 50 µm BQX in serum free DMEM. mcherry was utilized as a transfection marker. Confocal images after addition of 1 mm glutamate are also shown. Scale bars, 10 µm. S4

Figure S3 Effects of the orientation of the labeled Alexa488 on AMPARs upon the glutamate-induced fluorescence responses. a,b) Effects of linker length and substitution position (5-isomer or 6-isomer) on glutamate-induced fluorescent changes. Averaged time courses of the fluorescent changes (F/F 0 ) are shown for 5-isomers in a and 6-isomers in b. The bar indicates a period of 1 mm L-glutamate addition. (n = 14 24). Maximum of F/F 0 value after addition of 1 mm L-glutamate are shown in Figure 3b. S5

Figure S4 Glutamate-induced fluorescent responses of S1S2 labeled with CAM2(Ax488-5S) in test tubes. a) Cartoon of a recombinant S1S2 protein and chemical labeling of S1S2 using CAM2. b) Chemical labeling of S1S2 of GluA2 with CAM2(Ax488-5S). ne µm of S1S2 was incubated with 3 µm of CAM2(Ax488-5S) in the buffer (20 mm EPES, 100 mm acl (p 7.4)). The fluorescent gel image of the SDS-PAGE shows chemical labeling of S1S2 by CAM2(Ax488-5S), which was inhibited in the presence of 50 µm of BQX. CBB indicates Coomassie brilliant blue stained gel image. c) Fluorescent spectra of Alexa488-labeled S1S2 before and after addition 10 µm L-glutamate in cuvettes. Excitation wavelength is 480 nm. S6

Figure S5 Fluorescent responses of full-length AMPARs in live cells or S1S2 in test tubes after adding DQX. a) Epifluorescence imaging of DQX-induced responses for Alexa488-labeled AMPARs in live cells. The bar indicates a period of 1 mm glutamate or 30 µm DQX addition. An averaged time course of the fluorescent changes (F/F 0 ) is shown. (n = 8). b) Fluorescent spectra of Alexa488-labeled S1S2 before and after addition 30 µm DQX. [Alexa488-S1S2] = 0.1 µm. S7

Figure S6 Effects of the fluorophore structure of the labeled AMPARs upon the ligand-induced fluorescence changes. a,b) Averaged time course of glutamate- or BQX-induced the fluorescent changes (F/F 0 ). The bar indicates a period of 1 mm L-glutamate (in a) or 10 µm BQX addition (in b). (n =8 10). Maximum of F/F 0 value after addition of ligands are shown in Figure 3c. S8

Figure S7 Fluorescent responses of Alexa488-AMPARs or Alexa488-S1S2 for AMPA. a) Fluorescence responses of Alexa488-AMPARs in live cells after adding AMPA. The bar indicates a period of adding each concentration of AMPA. An averaged time course of the fluorescent changes (F/F 0 ) is shown. (n = 15). b) Fluorescent spectra of Alexa488-S1S2 after titrating AMPA in radioisotope-labeled ligand binding buffer. [Alexa488-S1S2] = 20 nm. Excitation wavelength is 480 nm. c) Concentration-dependency of fluorescence responses for AMPA for AMPAR in live cells (closed circle) or S1S2 in cuvettes (open circle). S9

Figure S8 Fluorescent responses of Alexa488-AMPARs or Alexa488-S1S2 for DQX. a) Fluorescence responses of Alexa488-AMPARs in live cells after adding DQX. The bar indicates a period of adding each concentration of DQX. An averaged time course of the fluorescent changes (F/F 0 ) is shown. (n = 13). b) Fluorescent spectra of Alexa488-S1S2 after titrating DQX in radioisotope-labeled ligand binding buffer. [Alexa488-S1S2] = 0.1 µm. Excitation wavelength is 480 nm. S10

Figure S9 Fluorescent responses of Alexa488-AMPARs or Alexa488-S1S2 for BQX. a) Fluorescence responses of Alexa488-AMPARs in live cells after adding BQX. The bar indicates a period of adding each concentration of BQX. An averaged time course of the fluorescent changes (F/F 0 ) is shown. (n = 10). b) Fluorescent spectra of Alexa488-S1S2 after titrating BQX in radioisotope-labeled ligand binding buffer. [Alexa488-S1S2] = 0.1 µm. Excitation wavelength is 480 nm. c) Concentration-dependency of fluorescence responses for BQX for AMPAR in live cells (closed circle) or S1S2 in cuvettes (open circle). S11

Figure S10 Fluorescent responses of S1S2 labeled with CAM2(Ax488-5S), CAM2(Ax488-5L), or CAM2(Ax488-6S) for glutamate in cuvettes. a,b,c) Fluorescent spectra of Alexa488-5S-S1S2 (in a), Alexa488-5L-S1S2 (in b), and Alexa488-6S-S1S2 (in c) after titrating L-glutamate. [Alexa488-5S-S1S2, Alexa488-5L-S1S2 or Alexa488-6S-S1S2] = 0.1 µm. Excitation wavelength is 480 nm. c) Concentration-dependency of fluorescence responses for L-glutamate for Alex488-5S-S1S2 (closed circle). Alexa488-5L-S1S2 (open circle), and Alexa488-6S-S1S2 (open triangle) in cuvettes. These measurements were examined in EPES buffer (20 mm EPES, 100 mm acl (p7.4)). S12

Figure S11 Comparison of fluorescent responses of Alexa488-S1S2 for glutamate between on live cell surface and in test tubes. a) Cartoon of immobilization scheme of Alexa488-S1S2 on EK293T cells. b) Fluorescence responses of Alexa488-S1S2 on live cells after adding glutamate. The bar indicates a period of adding each concentration of glutamate. An averaged time course of the fluorescent changes (F/F 0 ) is shown. (n = 12). c) Fluorescent spectra of Alexa488-S1S2 after titrating glutamate in BS. [Alexa488-S1S2] = 0.1 µm. Excitation wavelength is 480 nm. d) Concentration-dependency of fluorescence responses for glutamate for Alexa488-S1S2 on live cells (closed circle) or S1S2 in cuvettes (open circle). S13

Figure S12 Chemical structure of various glutamate receptor ligands. S14

Figure S13 Concentration-dependency of fluorescence responses for AMPA in the presence of 100 µm CTZ for AMPARs in live cells. Left, averaged time course. The bar indicates a period of adding 100 µm CTZ or each concentration of AMPA. (n = 10). Right, a concentration dependent curve for AMPA in the presence or absence of 100 µm CTZ. S15

Figure S14 Chemical labeling of GluA4 with CAM2(Ax488-5S) under live cell condition. Western blotting of GluA4 labeled with CAM2(Ax488-5S) in EK293T cells. EK293T cells transfected with GluA4 or its control vector were treated with 1 µm CAM2(Ax488-5S) in the presence or absence of 50 µm BQX in serum free DMEM. S16

3. Supporting otes Synthesis and Characterization General materials and methods for organic synthesis All chemical reagents and solvents were obtained from commercial suppliers (Aldrich, Tokyo Chemical Industry (TCI), Wako Pure Chemical Industries, Acros rganics, Sasaki Chemical, or Watanabe Chemical Industries) and used without further purification. Thin layer chromatography (TLC) was performed on silica gel 60 F 254 precoated aluminum sheets (Merck) and visualized by fluorescence quenching or ninhydrin staining. Chromatographic purification was conducted by flash column chromatography on silica gel 60 (neutral, 40 50 µm, Kanto Chemical). 1 -MR spectra were recorded in deuterated solvents on a Varian Mercury 400 (400 Mz). Chemical shifts were referenced to residual solvent peaks or tetramethylsilane (δ = 0 ppm). Multiplicities are abbreviated as follows: s = singlet, d = doublet, t = triplet, m = multiplet. MALDI-TF Mass spectra were measured on Autoflex II (Bruker Daltonics). igh resolution mass spectra were measured on an Exactive (Thermo Scientific) equipped with electron spray ionization (ESI). Reversed-phase PLC (RP-PLC) was carried out on a itachi Chromaster system equipped with a diode array and a YMC-Pack DS-A column. Synthesis of CAM2(Ax488-5S) and CAM2(Ax488-6S) 10 TFA 2 Alexa488-S DIEA dry DMF S 3 C 1 (CAM2(Ax488-5S)) S 3 2 + 2 (CAM2(Ax488-6S)) C + 2 S - 3 S - 3 2 A solution of 10 (0.60 mg, 0.74 µmol) S1, Alexa488-S (5,6-isomer) (1.0 mg, 1.6 µmol) and DIEA (2.80 µl, 16 µmol) in dry DMF (1.0 ml) was stirred for 5 hr at r.t. under 2 atmosphere. After removal of the solvent, the residue was purified by RP-PLC (column; YMC-pack DS-A, 250 x 25 mm, mobile phase; C 3 C : 10 mm Ac 4 aq. = 5 : 95 S17

50 : 50 (linear gradient over 50 min), flow rate; 10 ml/min, detection; UV (220 nm)) to give CAM2(Ax488-5S) (0.04 µmol, 5.4%) and CAM2(Ax488-6S) (0.09 µmol, 12.1%) as orange solids. CAM2(Ax488-5S): R-ESI MS m/z calcd for C 51 46 F 3 10 19 S 2 [M+] + 1223.2329, found 1223.2329. 1 -MR and 13 -MR were shown in our previous report S1. CAM2(Ax488-6S): R-ESI MS m/z calcd for C 51 46 F 3 10 19 S 2 [M+] + 1223.2329, found 1223.2326, respectively. Synthesis of CAM2(Ax488-5M) and CAM2(Ax488-6M) Boc TEA C 3 C Boc 11 pyridine dry DMF 12 13 Boc TFA DCM + 2 S 3 14 Alexa488-S DIEA dry DMF 3 (CAM2(Ax488-5M)) C S 3 2 + 4 (CAM2(Ax488-6M)) C + 2 S - 3 S - 3 2 Synthesis of compound 11 A solution of tert-butyl (2-(2-(2-(2-hydroxyethoxy)ethoxy)ethoxy)ethyl)carbamate (120 mg, 0.41 mmol), DSC (515 mg, 2.01 mmol) and TEA (170 µl, 1.23 mmol) in dry MeC (2.5 ml) was stirred for 7 hr at 40 C under 2 atmosphere. After removal of the solvent, the residue was diluted with CCl 3 (30 ml) and washed with water (30 ml 2) and brine (40 ml). The orgnic layer was dried over MgS 4, and filterd. The crude was purified by column chromatography (silica, CCl 3 / Me = 30 / 1 to 15 / 1) to give an oil 11 (152 mg, 85%). 1 -MR (400 Mz, CDCl 3 ) δ 4.47 (t, J = 4.0 z, 2), 3.81 3.31 (m, 14), 2.84 (s, 4), 1.44 (s, 9). Synthesis of compound 13 A solution of 11 (16 mg, 37 µmol), 12 (15 mg, 25 µmol) S1 and dry pyridine (16.3 µl, 196 S18

µmol) in dry DMF (2.0 ml) was stirred for 9 hr at r.t. under 2 atmosphere. The crude solution was purified by RP-PLC (column; YMC-pack DS-A, 250 x 25 mm, mobile phase; C 3 C : 10 mm Ac 4 aq. = 5 : 95 60 : 40 (linear gradient over 50 min), flow rate; 10 ml/min, detection; UV (220 nm)) to give 13 as an amorphous film (3.0 mg, 13%). MALDI-TF MS m/z calcd for C 39 50 F 3 8 13 [M+] + 895.34, found 896.52. Synthesis of CAM2(Ax488-5M) and CAM2(AX488-6M) A mixture of 13 (3.0 mg, 3.4 µmol) and TFA (0.3 ml) in dry dichloromethane (0.6 ml) was stirred at r.t. for 2 hr under 2 atmosphere. After removal of the solvent and the residual TFA was further removed azeotropically with toluene (three times) to give 14. The product was carried forward with no further purification. A solution of 14 (2.7 mg, 3.4 µmol), Alexa488-S (5,6-isomer) (2.0 mg, 3.2 µmol) and DIEA (3.92 µl, 22.4 µmol) in dry DMF (1.5 ml) was stirred for 7 hr at r.t. under 2 atmosphere. The crude solution was purified by RP-PLC (column; YMC-pack DS-A, 250 x 25 mm, mobile phase; C 3 C : 10 mm Ac 4 aq. = 0 : 100 30 : 70 (linear gradient over 45 min), flow rate; 10 ml/min, detection; UV (220 nm)) to give CAM2(Ax488-5M) (0.02 µmol, 0.58%) and CAM2(Ax488-6M) (0.07 µmol, 2.1%) as orange solids. CAM2(Ax488-5M): R-ESI MS m/z calcd for C 55 54 F 3 10 21 S 2 [M+] + 1311.2853, found 1311.2859 CAM2(Ax488-6M): R-ESI MS m/z calcd for C 55 54 F 3 10 21 S 2 [M+] + 1311.2853, found 1311.2857. Synthesis of CAM2(Ax488-5L) and CAM2(Ax488-6L) Boc DIEA BTU dry DMF 2 15 Boc TEA C 3 C 12 pyridine Boc dry DMF 16 17 Boc S19

TFA DCM 18 Alexa488-S DIEA dry DMF 2 + S 3-5 CAM2(Ax488-5L) C S 3-2 + 6 CAM2(Ax488-6L) C S 3-2 + S 3-2 Synthesis of compound 15 A solution of tert-butyloxycarbonylamino-3,6-dioxaoctanoic acid (222 mg, 0.50 mmol), 8-amino-3,6-dioxa-1-octanol (75 µl, 0.50 mmol), BTU (284 mg, 0.75 mmol) and DIEA (434 µl, 2.50 mmol) in dry DMF (7.0 ml) was stirred for 5 hr at r.t. under 2 atmosphere. After removal of the solvent, the crude was purified by column chromatography (silica, CCl 3 / Me = 20 / 1 to 10 / 1) to give brown oil 15 (188 mg, 95 %). 1 -MR (400 Mz, CDCl 3 ) δ 7.34 (s, 1), 5.39 (s, 1), 4.01 (s, 2), 3.74-3.33 (m, 20), 1.44 (s, 9) Synthesis of compound 16 A solution of 15 (188 mg, 0.48 mmol), DSC (610 mg, 2.38 mmol,) and TEA (198 µl, 1.43 mmol,) in dry C 3 C (3.0 ml) was stirred for 6 hr at 40 C under 2 atmosphere. After removal of the solvent, the residue was diluted with CCl 3 (30 ml) and washed with water (30 ml 2) and brine (30 ml). The orgnic layer was dried over MgS 4, and filterd. The crude was purified by column chromatography (silica, CCl 3 / Me = 20 / 1) to give colorless oil 16 (177 mg, 69%). 1 -MR (400 Mz, CDCl 3 ) δ 4.46 (t, J = 2.8 z, 2), 4.00 (s, 2), 3.78 3.49 (m, 16), 3.32 (d, J = 4.4 z, 2), 1.44 (s, 9) Synthesis of compound 17 A solution of 16 (25 mg, 25 µmol), 12 (15 mg, 25 µmol) and dry pyridine (16.6 µl, 200 µmol) in dry DMF (2.0 ml) was stirred for 6 hr at r.t. under 2 atmosphere. The crude solution was purified by RP-PLC (column; YMC-pack DS-A, 250 x 25 mm, mobile phase; C 3 C : 10 mm Ac 4 aq. = 5 : 95 60 : 40 (linear gradient over 50 min), flow rate; 10 ml/min, detection; UV (220 nm)) to give 17 as an amorphous film (9.0 mg, 36 %). MALDI-TF MS m/z calcd for C 43 57 F 3 9 15 [M+] + 996.39, found 995.79. Synthesis of compound CAM2(Ax488-5L) and CAM2(Ax488-6L) S20

A mixture of 17 (1.4 mg, 1.4 µmol) and TFA (0.3 ml) in dry dichloromethane (0.6 ml) was stirred at r.t. for 3 hr under 2 atmosphere. After removal of the solvent, the residual TFA was further removed azeotropically with toluene (three times) to give 18. The product was carried forward with no further purification. A mixture of 18 (1.3 mg, 1.44 µmol), Alexa488-S (5,6-isomer) (1.0 mg, 1.60 µmol) and DIEA (2.80 µl, 16.0 µmol) in dry DMF (1.0 ml) was stirred for 5 hr at r.t. under 2 atmosphere. The crude solution was purified by RP-PLC (column; YMC-pack DS-A, 250 x 25 mm, mobile phase; C 3 C : 10 mm Ac 4 aq. = 5 : 95 50 : 50 (linear gradient over 50 min), flow rate; 10 ml/min, detection; UV (220 nm)) to give CAM2(Ax488-5L) (0.08 µmol, 5.6%) and CAM2(Ax488-6L) (0.10 µmol, 6.9 %) as orange solids. CAM2(Ax488-5M): R-ESI MS m/z calcd for C 59 69 F 3 11 23 S 2 [M+] + 1412.3330, found 1412.3320. CAM2(Ax488-6M): R-ESI MS m/z calcd for C 55 54 F 3 10 21 S 2 [M+] + 1412.3330, found 1412.3327. Synthesis of CAM2(Ax488-5LL) and CAM2(Ax488-6LL) Boc DIEA BTU dry DMF 2 19 Boc TEA C 3 C 20 Boc 12 pyridine dry DMF 21 Boc TFA DCM 22 Alexa488-S DIEA dry DMF 7 CAM2(Ax488-5LL) C + 2 S - 3 S - 3 + 2 + 2 S - 3 8 CAM2(Ax488-6LL) C S 3-2 S21

Synthesis of compound 19 A solution of -(tert-butyloxycarbonyl)-15-amino-4,7,10,13-tetraoxapentanedecanoic acid (163 µl, 0.50 mmol), 8-amino-3,6-dioxa-1-octanol (75 µl, 0.50 mmol), BTU (284 mg, 0.75 mmol) and DIEA (434 µl, 2.50 mmol) in dry DMF (7.0 ml) was stirred for 5 hr at r.t. under 2 atmosphere. After removal of the solvent, the crude was purified by column chromatography (silica, CCl 3 / Me = 20 / 1 to 10 / 1) to give 19 (208 mg, 84 %) as brown oil. 1 -MR (400 Mz, CDCl 3 ) δ 6.82 (s, 1), 5.17 (s, 1), 3.76-3.43 (m, 30), 2.47 (t, 2), 1.44 (s, 9). Synthesis of compound 20 A solution of 19 (208 mg, 0.42 mmol), DSC (538 mg, 2.10 mmol) and TEA (174 µl, 1.26 mmol) in dry C 3 C (2.5 ml) was stirred for 5 hr at 40 C under 2 atmosphere. After removal of the solvent, the residue was diluted with CCl 3 (30 ml) and washed with water (30 ml 2) and brine (40 ml). The orgnic layer was dried over MgS 4, and filtered. The crude was purified by column chromatography (silica, CCl 3 / Me = 20 / 1) to give 20 (217 mg, 81%) as colorless oil. 1 -MR (400 Mz, CDCl 3 ) δ 4.48 (t, J = 4.4 z, 2), 3.80 3.30 (m, 28), 2.84 (s, 4), 2.46 (t, 2), 1.44 (s, 9) Synthesis of compound 21 A solution of 20 (16 mg, 25 µmol), 12 (14 mg, 25 µmol) and dry pyridine (16.6 µl, 200 µmol) in dry DMF (2.0 ml) was stirred for 5.5 hr at r.t. under 2 atmosphere. The crude solution was purified by RP-PLC (column; YMC-pack DS-A, 250 x 25 mm, mobile phase; C 3 C : 10 mm Ac 4 aq. = 5 : 95 60 : 40 (linear gradient over 50 min), flow rate; 10 ml/min, detection; UV (220 nm)) to give 21 (19 mg, 69 %) as an amorphous film. MALDI-TF MS m/z calcd for C 48 66 F 3 9 17 [M+] + 1098.46, found 1100.26. Synthesis of compound CAM2(Ax488-5LL) and CAM2(Ax488-6LL) A mixture of 21 (1.6 mg, 1.46 µmol) and TFA (0.3 ml) in dry dichloromethane (0.6 ml) was stirred at r.t. for 2 hr under 2 atmosphere. After removal of the solvent, the residual TFA was further removed azeotropically with toluene (three times) to give 22. The product was carried forward with no further purification. A solution of 22 (1.5 mg, 1.44 µmol), Alexa488-S (5,6-isomer) (1.0 mg, 1.60 µmol) and DIEA (2.80 µl, 16.0 µmol) in dry DMF (1.0 ml) was stirred for 5 hr at r.t. under 2 atmosphere. The crude solution was purified by RP-PLC (column; YMC-pack DS-A, 250 x 25 mm, mobile phase; C 3 C : 10 mm Ac 4 aq. = 5 : 95 50 : 50 (linear gradient S22

over 50 min), flow rate; 10 ml/min, detection; UV (220 nm)) to give CAM2(Ax488-5LL) (0.06 µmol, 4.2%) and CAM2(Ax488-6LL) (0.006 µmol, 4.2%) as orange solids. CAM2(Ax488-5LL): R-ESI MS m/z calcd for C 64 70 F 3 11 25 S 2 [M+] + 1514.4011, found 1514.4041. CAM2(Ax488-6LL): R-ESI MS m/z calcd for C 64 70 F 3 11 25 S 2 [M+] + 1514.4011, found 1514.4004. Synthesis of compound CAM2(Ax568) 10 TFA 2 Alexa568-S DIEA dry DMF + 3 S C 9 (CAM2(Ax568)) S 3 A solution of 10 (0.88 mg, 1.24 µmol), Alexa568-S-ester (0.98 mg, 1.24 µmol, 1.0 eq) and DIEA (0.65 µl, 3.72 µmol) in dry DMF (0.5 ml) was stirred at r.t. for 5 hr under 2 atmosphere. The crude solution was purified by RP-PLC (column; YMC-pack DS-A, 250 x 25 mm, mobile phase; C3C : 10 mm Ac 4 aq. = 5 : 95 40 : 60 (linear gradient over 50 min), flow rate; 10 ml/min, detection; UV (220 nm)) to give CAM2(Alexa568) (0.065 µmol, 5.2%) as a purple solid. R-ESI MS m/z calcd for C 63 59 F 3 10 19 S 2 [M 2] 2 690.1681, found 690.1686. 4. Supporting Reference S1. Wakayama, S., Kiyonaka, S., Arai, I., Kakegawa, W., Matsuda, S., Ibata, K., emoto, Y. L., Kusumi, A., Yuzaki, M., and amachi, I. (2017) Chemical labelling for visualizing native AMPA receptors in live neurons. at. Commun. 8, 14850. S23