Quantitative measurement of cytosolic penetration using the chloroalkane penetration assay

Methods in Enzymology - Tập 641 - Trang 277-309 - 2020
Kirsten Deprey1, Joshua A. Kritzer1
1Department of Chemistry, Tufts University, Medford, MA, United States

Tài liệu tham khảo

Appelbaum, 2012, Arginine topology controls escape of minimally cationic proteins from early endosomes to the cytoplasm, Chemistry & Biology, 19, 819, 10.1016/j.chembiol.2012.05.022 Aubry, 2010, MALDI-TOF mass spectrometry: A powerful tool to study the internalization of cell-penetrating peptides, Biochimica et Biophysica Acta-Biomembranes, 1798, 2182, 10.1016/j.bbamem.2009.11.011 Augustijns, 2000, Hydration changes implicated in the remarkable temperature-dependent membrane permeation of cyclosporin A, Biochemistry, 39, 7621, 10.1021/bi9929709 Ballister, 2014, Localized light-induced protein dimerization in living cells using a photocaged dimerizer, Nature Communications, 5, 5475, 10.1038/ncomms6475 Birch, 2017, Fluorophore labeling of a cell-penetrating peptide induces differential effects on its cellular distribution and affects cell viability, Biochimica et Biophysica Acta-Biomembranes, 1859, 2483, 10.1016/j.bbamem.2017.09.015 Bird, 2016, Biophysical determinants for cellular uptake of hydrocarbon-stapled peptide helices, Nature Chemical Biology, 12, 845, 10.1038/nchembio.2153 Burlina, 2005, Quantification of the cellular uptake of cell-penetrating peptides by MALDI-TOF mass spectrometry, Angewandte Chemie International Edition, 44, 4244, 10.1002/anie.200500477 Burlina, 2006, A direct approach to quantification of the cellular uptake of cell-penetrating peptides using MALDI-TOF mass spectrometry, Nature Protocols, 1, 200, 10.1038/nprot.2006.30 Cai, 2019, Selection of DNA-encoded libraries to protein targets within and on living cells, Journal of the American Chemical Society, 141, 54, 10.1021/jacs.9b08085 Chan, 2000 Chang, 2013, Stapled α−helical peptide drug development: A potent dual inhibitor of MDM2 and MDMX for p53-dependent cancer therapy, Proceedings of the National Academy of Sciences of the United States of America, 110, E3445, 10.1073/pnas.1303002110 Chu, 2015, Towards understanding cell penetration by stapled peptides, Medicinal Chemistry Communications, 6, 111, 10.1039/C4MD00131A de Menorva, 2012, Effects of dimethyl sulfoxide in cholesterol-containing lipid membranes: A comparative study of experiments in silico and with cells, PLoS One, 7 Deprey, 2019, Trapped! A critical evaluation of methods for measuring total cellular uptake versus cytosolic localization, Bioconjugate Chemistry, 30, 1006, 10.1021/acs.bioconjchem.9b00112 Dougherty, 2019, Understanding cell penetration of cyclic peptides, Chemical Reviews, 119, 10241, 10.1021/acs.chemrev.9b00008 Dowdy, 2017, Perspective overcoming cellular barriers for RNA therapeutics, Nature Biotechnology, 35, 222, 10.1038/nbt.3802 Encell, 2012, Development of a dehalogenase-based protein fusion tag capable of rapid, selective and covalent attachment to customizable ligands, Current Chemical Genomics, 6, 55, 10.2174/1875397301206010055 Fischer, 2004, A stepwise dissection of the intracellular fate of cationic cell-penetrating peptides, The Journal of Biological Chemistry, 279, 12625, 10.1074/jbc.M311461200 Foley, 2019, Assessing the cell permeability of bivalent chemical degraders using the chloroalkane penetration assay, ACS Chemical Biology, 15, 290, 10.1021/acschembio.9b00972 Fretz, 2007, Temperature-, concentration-and cholesterol-dependent translocation of L-and D-octa-arginine across the plasma and nuclear membrane of CD34 + leukaemia cells, The Biochemical Journal, 403, 335, 10.1042/BJ20061808 Futaki, 2001, Arginine-rich peptides. An abundant source of membrane-permeable peptides having potential as carriers for intracellular protein delivery, The Journal of Biological Chemistry, 276, 5836, 10.1074/jbc.M007540200 Gadagkar, 2015, Computational tools for fitting the Hill equation to dose-response curves, Journal of Pharmacological and Toxicological Methods, 71, 68, 10.1016/j.vascn.2014.08.006 Hedegaard, 2018, Fluorophore labeling of a cell-penetrating peptide significantly alters the mode and degree of biomembrane interaction, Scientific Reports, 8, 6327, 10.1038/s41598-018-24154-z Hill, 1910, The possible effects of the aggregation of the molecules of hemoglobin on its dissociation curves, The Journal of Physiology, 40, 4 Holub, 2013, Improved assays for determining the cytosolic access of peptides, proteins, and their mimetics, Biochemistry, 52, 9036, 10.1021/bi401069g Jiao, 2009, Translocation and endocytosis for cell-penetrating peptide internalization, Journal of Biological Chemistry, 284, 33957, 10.1074/jbc.M109.056309 Kang, 1998, Up-regulation of luciferase gene expression with antisense oligonucleotides: Implications and applications in functional assay development, Biochemistry, 37, 6235, 10.1021/bi980300h Kato, 2010, The split luciferase complementation assay, 359 Kauffman, 2015, Mechanism matters: A taxonomy of cell penetrating peptides, Trends in Biochemical Sciences, 40, 749, 10.1016/j.tibs.2015.10.004 Keppler, 2003, A general method for the covalent labeling of fusion proteins with small molecules in vivo, Nature Biotechnology, 21, 86, 10.1038/nbt765 Kim, 2015, Quantitative assessment of cellular uptake and cytosolic access of antibody in living cells by an enhanced split GFP complementation assay, Biochemical and Biophysical Research Communications, 467, 771, 10.1016/j.bbrc.2015.10.066 Lamb, 2019, Discovery and characterization of a cellular potent positive allosteric modulator of the polycomb repressive complex 1 chromodomain, CBX7, Cell Chemical Biology, 26, 10.1016/j.chembiol.2019.07.013 Larochelle, 2015, Fluorescence correlation spectroscopy reveals highly efficient cytosolic delivery of certain penta-arg proteins and stapled peptides, Journal of the American Chemical Society, 137, 2536, 10.1021/ja510391n Lau, 2018, Therapeutic peptides: Historical perspectives, current development trends, and future directions, Bioorganic & Medicinal Chemistry, 26, 2700, 10.1016/j.bmc.2017.06.052 Liu, 2017, The cation−π interaction enables a halo-tag fluorogenic probe for fast no-wash live cell imaging and gel-free protein quantification, Biochemistry, 56, 1585, 10.1021/acs.biochem.7b00056 López-Andarias, 2020, Cell-penetrating streptavidin: A general tool for bifunctional delivery with spatiotemporal control, mediated by transport systems such as adaptive benzopolysulfance networks, Journal of the American Chemical Society, 142, 4784, 10.1021/jacs.9b13621 Los, 2008, HaloTag: A novel protein labeling technology for cell imaging and protein analysis, ACS Chemical Biology, 3, 373, 10.1021/cb800025k Madani, 2011, Mechanisms of cellular uptake of cell-penetrating peptides, Journal of Biophysics, 2011, 414729, 10.1155/2011/414729 Matsson, 2016, Cell permeability beyond the rule of 5, Advanced Drug Delivery Reviews, 101, 42, 10.1016/j.addr.2016.03.013 Mayor, 2007, Pathways of clathrin-independent endocytosis, Nature Reviews Molecular Cell Biology, 8, 603, 10.1038/nrm2216 Méndez-Ardoy, 2019, Where in the cell is our cargo? Methods currently used to study intracellular cytosolic localisation, ChemBioChem, 20, 488, 10.1002/cbic.201800390 Milech, 2015, GFP-complementation assay to detect functional CPP and protein delivery into living cells, Scientific Reports, 5, 18329, 10.1038/srep18329 Murrey, 2015, Systematic evaluation of bioorthogonal reactions in live cells with clickable HaloTag ligands: Implications for intracellular imaging, Journal of the American Chemical Society, 137, 11461, 10.1021/jacs.5b06847 Pei, 2019, Overcoming endosomal entrapment in drug delivery, Bioconjugate Chemistry, 30, 273, 10.1021/acs.bioconjchem.8b00778 Peraro, 2018, Cell penetration profiling using the chloroalkane penetration assay, Journal of the American Chemical Society, 140, 11360, 10.1021/jacs.8b06144 Peraro, 2018, Emerging methods and design principles for cell-penetrant peptides, Angewandte Chemie International Edition, 57, 2, 10.1002/anie.201801361 Peraro, 2017, Diversity-oriented stapling yields intrinsically cell-penetrant inducers of autophagy, Journal of the American Chemical Society, 139, 7792, 10.1021/jacs.7b01698 Puckett, 2009, Fluorescein redirects a ruthenium-octaarginine conjugate to the nucleus, Journal of the American Chemical Society, 131, 8738, 10.1021/ja9025165 Pye, 2017, Nonclassical size dependence of permeation defines bounds for passive adsorption of large drug molecules, Journal of Medicinal Chemistry, 60, 1665, 10.1021/acs.jmedchem.6b01483 Qian, 2015, Monitoring the cytosolic entry of cell-penetrating peptides using a pH-sensitive fluorophore, Chemical Communications, 51, 2162, 10.1039/C4CC09441G Richard, 2003, Cell-penetrating peptides. A reevaluation of the mechanism of cellular uptake, The Journal of Biological Chemistry, 278, 585, 10.1074/jbc.M209548200 Shin, 2018, Comparison of cell permeability of cyclic peptoids and linear peptoids, ACS Combinatorial Science, 20, 237, 10.1021/acscombsci.7b00194 Tomat, 2008, Organelle-specific zinc detection using zinpyr-labeled fusion proteins in live cells, Journal of the American Chemical Society, 130, 15776, 10.1021/ja806634e Torchilin, 2008, Intracellular delivery of protein and peptide therapeutics, Drug Discovery Today: Technologies, 5, e95, 10.1016/j.ddtec.2009.01.002 Verdine, 2012, Stapled peptides for intracellular drug targets, Methods in Enzymology, 503, 3, 10.1016/B978-0-12-396962-0.00001-X Verdurmen, 2015, Efficient cell-specific uptake of binding proteins into the cytoplasm through engineered modular transport systems, Journal of Controlled Release, 200, 13, 10.1016/j.jconrel.2014.12.019 Wadia, 2004, Transducible TAT-HA fusogenic peptide enhances escape of TAT-fusion proteins after lipid raft macropinocytosis, Nature Medicine, 10, 310, 10.1038/nm996 Wang, 2015, Organelle-specific nitric oxide detection in living cells via HaloTag protein labeling, PLoS One, 10, 10.1371/journal.pone.0123986 Wang, 2009, Enhancement of TAT cell membrane penetration efficiency by dimethyl sulphoxide, Journal of Controlled Release, 143, 64, 10.1016/j.jconrel.2009.12.003 Yang, 2015, Getting across the cell membrane: An overview for small molecules, peptides, and proteins, Methods in Molecular Biology, 1266, 29, 10.1007/978-1-4939-2272-7_3 Yin, H., Huang, Y., Deprey, K., Condon, N., Kritzer, J. A., Craik, D., et al. (2020). submitted. Yin, 2019, Targeting RNA: A transformative therapeutic strategy, Clinical and Translational Science, 12, 98, 10.1111/cts.12624 Yu, 2005, A high-throughput assay for assessing the cell permeability of combinatorial libraries, Nature Biotechnology, 23, 746, 10.1038/nbt1099 Zhao, 2008, Intracellular water specific MR of microbead-adherent cells: The HeLa cell intracellular water exchange lifetime, NMR Biomedicine, 21, 159, 10.1002/nbm.1173 Zhu, 2016, Fluorescent probes for sensing and imaging within specific cellular organelles, Accounts of Chemical Research, 49, 2115, 10.1021/acs.accounts.6b00292