Electronic Supplementary Material (ESI) for ChemComm. This journal is © The Royal Society of Chemistry 2018 Supporting Information Live-Cell Imaging and Profiling of c-Jun N-Terminal Kinases with Covalent Inhibitor-Derived Probes Linghui Qian,a,b* Sijun Pan,a Jun-Seok Lee,c Jingyan Ge,d Lin Li,e* Shao Q. Yaoa* aDepartment of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore), E-mail: [email protected] (S.Q.Y.). bInstitute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China), E-mail: [email protected] (L.Q.) cMolecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792 (South Korea) dKey Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014 (China) eKey Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211800 (China), E-mail: [email protected] (L.L.) S1_1 List of contents: 1 General Information 2 Chemical Synthesis and Characterizations 3 Experimental Methods 4 Results and Discussions 5 Appendix (1H and 13C NMR spectra & HRMS Data) 6 LC-MS/MS Data for Chemoproteomic Studies 7 Summary of performance of the probes and reporters Fig. S1 8 LC-MS characterization of QT1/QT2 + trans-cyclooctenol (TCO) ligation Fig. S2 9 Characterization of AAN-N3 + propargyl alcohol ligation Fig. S3 Photophysical properties of two-photon reporters before and after click 10 Fig. S4 reaction 11 Bioactivity of parental inhibitors and probes derived from them Fig. S5 Concentration-dependent in situ reactivity profiles of JP3/JP2-TCO in 12 Fig. S6 JNK1-GFP-transfected HeLa cells 13 Cellular imaging using small-molecule probes/two-photon reporters for JNKs Fig. S7 In situ profiling of endogenous JNKs in HeLa/HEK293T/SH-SY5Y cells upon 14 Fig. S8 labeling by JP3/JP2-TCO 15 Summary of probes and reporters used in the current study Table S1 Photophysical properties of fluorogenic reporters (QT1, QT2 and AAN-N3) 16 Table S2 before and after click reaction Summary of putative hits identified from standard PD/LC-MS by using 1 μM 17 of JP3/JP2-TCO/JP2-CP for 1 h in anisomycin-induced (2 μM, 0.5 h) HeLa Table S3 cells Design of bioorthogonal small-molecule probes for JNKs 18 (JP2-TCO/JP2-CP/JP3) based on the irreversible inhibitor selective for JNKs Scheme S1 (JNK-IN-8) 19 Synthesis of small-molecule probes and reporters for JNKs Scheme S2 S1_2 1. General Information All chemicals were purchased from commercial vendors and used without further purification, unless otherwise noted. All non-aqueous reactions were carried out under a nitrogen/argon atmosphere in oven-dried glassware. Reaction progress was monitored by TLC on pre-coated silica plates (Merck 60 F254 nm, 250 μm thickness) and spots were visualized by UV light or appropriate staining (e.g., ceric ammonium molybdate (CAM), basic KMnO4). Flash column 1 13 chromatography was carried out using silica gel (Merck 60 F254 nm 0.040-0.063 μm). All H NMR and C NMR spectra were taken on a Bruker AFC 300 (300 MHz) or AMX500 (500 MHz) spectrometer. Chemical shifts were reported in parts per million (ppm) relative to residual solvent peaks (CDCl3 = 7.26 ppm, DMSO-d6 = 2.50 ppm, CD3OD = 3.31 ppm, 1 Acetone-d6 = 2.05 ppm). H NMR coupling constants (J) are reported in Hertz (Hz) and multiplicity is indicated as follows: s (singlet), d (doublet), t (triplet), q (quartet), m (multiplet), br s (broad singlet), br d (broad doublet), dd (doublet of doublet), dt (doublet of triplet), dq (doublet of quartet), tq (triplet of quartet). Analytical HPLC and Mass spectra were recorded on a Shimadzu LC-IT-TOF spectrometer or LC-ESI spectrometer equipped with an autosampler, using reverse-phase Phenomenex Luna 5 μm C18 100 Å 50 × 3.0 mm columns. UV-vis absorption and fluorescence spectra were measured by using a Shimadzu UV-vis spectrophotometer and a Perkin Elmer LS50 spectrofluorometer, respectively. The two-photon excited fluorescence measurements were performed using a Spectra Physics femtosecond Ti:sapphire oscillator (Tsunami) as the excitation source. The output laser pulses have a tunable center wavelength at 760 nm with pulse duration of 40 fs and a repetition rate of 76 MHz. The laser beam was focused onto the sample that was contained in a cuvette with path length of 1 cm. The emission from the sample was collected at 90° angle by a pair of lenses and an optical fiber that was connected to a monochromator (Acton, Spectra Pro 2300i) coupled with CCD system (Princeton Instruments, Pixis 100B). A short pass filter with cut-off wavelength at 700 nm was placed before the spectrometer to minimize the scattering from the pump beam. All optical measurements were performed at room temperature. All 2D images were acquired on Leica TCS SP5X Confocal Microscope System equipped with Leica HCX PL APO 63x/1.20 W CORR CS, 405 nm Diode laser, Argon ion laser, white laser (470 nm to 670 nm, with 1 nm increments, with 8 channels AOTF for simultaneous control of 8 laser lines, each excitation wavelength provides 1.5 mV), and Ti-Sapphire laser (~4 W at 800 nm) which corresponded to approximately 1% (~40 mW at 800 nm) average power in the focal plane. A PMT detector ranging from 420 nm to 700 nm for steady-state fluorescence was used with Leica and images were processed with Leica Application Suite Advanced Fluorescence (LAS AF). Human recombinant JNK1 (M33-10G-10) and its substrate ATF2 (A10-55G-20) were purchased from SignalChem. JNK-IN-8 was a gift from Prof. Nathanael S. Gray (Harvard Medical School). Anisomycin (2222S), antibodies against Phospho-JNK (9255S), total JNK (9252S) and Phospho-c-Jun (9261S) were obtained from Cell Signaling Technology. Human JNK1 plasmid (transcript variant JNK1-b2 Gene ORF cDNA clone expression plasmid, C-GFPSpark tag; HG10795-ACG) was purchased from Sino Biological Inc. FITC-conjugated Goat anti-rabbit IgG (H+L) secondary antibody (A16097), Lipofectamine® 2000 Transfection Reagent (11668027) and Opti-MEM® (Reduced Serum Medium; 31985070) were bought from Thermo Fisher Scientfic. Cell lines (HeLa, HEK293T, SH-SY5Y) were purchased from ATCC. S1_3 Table S1. Summary of probes and reporters used in the current study. *The following reporters were prepared based [1] [2] [1] [3] [4] on reported literature: TER-Tz1; TMR-Tz; Biotin-Tz2; TER-N3; Biotin-N3 . Scheme S1. Design of bioorthogonal small-molecule probes for JNKs (JP2-TCO/JP2-CP/JP3) based on the irreversible inhibitor selective for JNKs (JNK-IN-8). With proper tags, they can either be clicked with (left) conventional reporters containing rhodamine/biotin for in situ proteomic studies or (right) two-photon fluorogenic reporters (QT1/QT2/AAN-N3) for no-wash live-cell imaging. S1_4 2. Chemical Synthesis and Characterizations Scheme S2. Synthesis of small-molecule probes and reporters for JNKs. (A) Synthesis scheme of covalent ABPs derived from JNK-specific irreversible inhibitor JNK-IN-8. (B) Synthesis of various two-photon fluorogenic reporters derived from acedan. (J1) J1 was synthesized according to published procedures.[5] 3-(dimethylamino)-1-(pyridin-3-yl) prop-2-en-1-one (2.64 S1_5 g, 15.0 mmol, obtained according to a previously published procedure)[5] and guanidinium hydrochloride (1.50 g, 15.7 mmol) were mixed in 25 mL of 2-propanol. To the suspension was added NaOH (0.70 g, 17.5 mmol) and the mixture was refluxed for 24 h. The reaction was then cooled to 0 oC and the precipitate was filtered off, suspended in water, filtered off once more and washed with 2-propanol and diethyl ether. The residue was dried in oven at 60 to 70 oC and the desired 1 product was obtained as a white powder (1.876 g, 72.6%). H NMR (300 MHz, CDCl3) δ 9.20 (d, J = 2.2 Hz, 1H), 8.70 (dd, J = 4.7, 1.3 Hz, 1H), 8.39 (d, J = 5.2 Hz, 1H), 8.31 (dt, J = 8.0, 1.6 Hz, 1H), 7.41 (dd, J = 8.0, 4.8 Hz, 1H), 7.07 (d, J = 5.2 Hz, 1H), 5.20 (s, 2H). (J2) J2 was synthesized according to published procedures.[5] J1 (2.4776 g, 14.39 mmol), CuI (0.6228 g, 3.27 mmol) and anhydrous K2CO3 (3.6157 g, 26.16 mmol) were added to a dry RBF. The RBF was filled with N2 gas and subsequently added a mixture of 2-bromo-5-nitrotoluene (2.8254 g, 13.08 mmol) and N,N'-dimethylethylenediamine (DMEDA, 0.35 mL, 3.25 mmol) in anhydrous dioxane (110 mL) at room temperature. The reaction mixture was stirred at 120 oC for 24 h, before being cooled to room temperature. Subsequently, concentrated ammonia (55 mL) and brine (220 mL) were added and the resulting mixture was extracted with EtOAc (5 × 220 mL). The organic layers were dried over Na2SO4, concentrated under reduced pressure and the residue was purified by flash chromatography (DCM/MeOH = 50/1) to give 1 J2 as a yellow powder (1.60 g, 39.8%). H NMR (300 MHz, CDCl3) δ 9.29 (s, 1H), 8.76 (s, 1H), 8.71 (d, J = 9.1 Hz, 1H), 8.61 (d, J = 5.2 Hz, 1H), 8.43-8.27 (m, 1H), 8.19 (dd, J = 9.1, 2.7 Hz, 1H), 8.13 (d, J = 2.5 Hz, 1H), 7.48 (dd, J = 7.9, 4.8 Hz, 1H), 7.34 (t, J = 4.9 Hz, 2H), 2.48 (s, 3H).