Labelled Chemical Probes for Demonstrating Direct Target Engagement in Living Systems

References

• Bunnage ME , CheklerEL, JonesLH. Target validation using chemical probes. Nat. Chem. Biol.9(4), 195–199 (2013).
   PubMed Web of Science ®Google Scholar
• Morgan P , VanDer Graaf PH, ArrowsmithJet al. Can the flow of medicines be improved? Fundamental pharmacokinetic and pharmacological principles toward improving Phase II survival. Drug Discov. Today17(9-10), 419–424 (2012).
   PubMed Web of Science ®Google Scholar
• Hann MM , SimpsonGL. Intracellular drug concentration and disposition – the missing link?Methods68(2), 283–285 (2014).
   PubMed Web of Science ®Google Scholar
• Smyth LA , CollinsI. Measuring and interpreting the selectivity of protein kinase inhibitors. J. Chem. Biol.2(3), 131–151 (2009).
   PubMedGoogle Scholar
• Simon GM , NiphakisMJ, CravattBF. Determining target engagement in living systems. Nat. Chem. Biol.9(4), 200–205 (2013).
   PubMed Web of Science ®Google Scholar
• Schürmann M , JanningP, ZieglerS, WaldmannH. Small-molecule target engagement in cells. Cell Chem. Biol.23(4), 435–441 (2016).
   PubMed Web of Science ®Google Scholar
• Martinez Molina D , JafariR, IgnatushchenkoMet al. Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay. Science341(6141), 84–87 (2013).
   PubMed Web of Science ®Google Scholar
• Cimmperman P , BaranauskieneL, JachimoviciūteSet al. A quantitative model of thermal stabilization and destabilization of proteins by ligands. Biophys. J.95(7), 3222–3231 (2008).
   PubMed Web of Science ®Google Scholar
• Blagg J , WorkmanP. Choose and use your chemical probe wisely to explore cancer biology. Cancer Cell32(1), 9–25 (2017).
   PubMed Web of Science ®Google Scholar
• Frye SV . The art of the chemical probe. Nat. Chem. Biol.6(3), 159–161 (2010).
   PubMed Web of Science ®Google Scholar
• Workman P , CollinsI. Probing the probes: fitness factors for small molecule tools. Chem. Biol.17(6), 561–577 (2010).
   PubMedGoogle Scholar
• Arrowsmith CH , AudiaJE, AustinCet al. The promise and peril of chemical probes. Nat. Chem. Biol.11(8), 536–541 (2015).
   PubMed Web of Science ®Google Scholar
• Antolin AA , TymJE, KomianouA, CollinsI, WorkmanP, Al-LazikaniB. Objective, quantitative, data-driven assessment of chemical probes. Cell Chem. Biol.25(2), 194–205.e195 (2018).
   PubMed Web of Science ®Google Scholar
• Lang K , ChinJW. Bioorthogonal reactions for labeling proteins. ACS Chem. Biol.9(1), 16–20 (2014).
   PubMed Web of Science ®Google Scholar
• Chen X , WuYW. Selective chemical labeling of proteins. Org. Biomol. Chem.14, 5417–5439 (2016).
   PubMed Web of Science ®Google Scholar
• Sletten EM , BertozziCR. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew. Chem. Int. Ed. Engl.48(38), 6974–6998 (2009).
   PubMed Web of Science ®Google Scholar
• Ramil CP , LinQ. Bioorthogonal chemistry: strategies and recent developments. Chem. Commun. (Camb.)49(94), 11007–11022 (2013).
   PubMed Web of Science ®Google Scholar
• Shieh P , BertozziCR. Design strategies for bioorthogonal smart probes. Org. Biomol. Chem.12(46), 9307–9320 (2014).
   PubMed Web of Science ®Google Scholar
• Patterson DM , NazarovaLA, PrescherJA. Finding the right (bioorthogonal) chemistry. ACS Chem. Biol.9(3), 592–605 (2014).
   PubMed Web of Science ®Google Scholar
• Row RD , PrescherJA. Constructing new bioorthogonal reagents and reactions. Acc. Chem. Res.51(5), 1073–1081 (2018).
   PubMed Web of Science ®Google Scholar
• Wu H , DevarajNK. Advances in tetrazine bioorthogonal chemistry driven by the synthesis of novel tetrzines and dienophiles. Acc. Chem. Res.51(5), 1249–1259 (2018).
   PubMed Web of Science ®Google Scholar
• Kang K , ParkJ, KimE. Tetrazine ligation for chemical proteomics. Proteome Sci.15, 15 (2016).
   PubMed Web of Science ®Google Scholar
• McFedries A , SchwaidA, SaghatelianA. Methods for the elucidation of protein–small molecule interactions. Chem. Biol.20(5), 667–673 (2013).
   PubMedGoogle Scholar
• Devaraj NK , HilderbrandS, UpadhyayR, MazitschekR, WeisslederR. Bioorthogonal turn-on probes for imaging small molecules inside living cells. Angew. Chem. Int. Ed. Engl.49(16), 2869–2872 (2010).
   PubMed Web of Science ®Google Scholar
• Carlson JC , MeimetisLG, HilderbrandSA, WeisslederR. BODIPY-tetrazine derivatives as superbright bioorthogonal turn-on probes. Angew. Chem. Int. Ed. Engl.52(27), 6917–6920 (2013).
   PubMed Web of Science ®Google Scholar
• Meimetis LG , CarlsonJC, GiedtRJ, KohlerRH, WeisslederR. Ultrafluorogenic coumarin-tetrazine probes for real-time biological imaging. Angew. Chem. Int. Ed. Engl.53(29), 7531–7534 (2014).
   PubMed Web of Science ®Google Scholar
• Wieczorek A , WertherP, EuchnerJ, WombacherR. Green- to far-red-emitting fluorogenic tetrazine probes – synthetic access and no-wash protein imaging inside living cells. Chem. Sci.8(2), 1506–1510 (2017).
   PubMed Web of Science ®Google Scholar
• Lapinsky DJ . Tandem photoaffinity labeling-bioorthogonal conjugation in medicinal chemistry. Bio. Org. Med. Chem.20(21), 6237–6247 (2012).
   PubMed Web of Science ®Google Scholar
• Dubach JM , KimE, YangKet al. Quantitating drug-target engagement in single cells in vitro and in vivo. Nat. Chem. Biol.13(2), 168–173 (2017).
   PubMed Web of Science ®Google Scholar
• Tanaka Y , BondMR, KohlerJJ. Photocrosslinkers illuminate interactions in living cells. Mol. Biosyst.4(6), 473–480 (2008).
   PubMedGoogle Scholar
• Geurink PP , PrelyLM, VanDer Marel GA, BischoffR, OverkleeftHS. Photoaffinity labeling in activity-based protein profiling. Top Curr. Chem.324, 85–113 (2012).
   PubMed Web of Science ®Google Scholar
• Schülke JP , McAllisterLA, GeogheganKFet al. Chemoproteomics demonstrates target engagement and exquisite selectivity of the clinical phosphodiesterase 10A inhibitor MP-10 in its native environment. ACS Chem. Biol.9(12), 2823–2832 (2014).
   PubMed Web of Science ®Google Scholar
• Crump CJ , MurreyHE, BallardTEet al. Development of sulfonamide photoaffinity inhibitors for probing cellular γ-secretase. ACS Chem. Neurosci.7(8), 1166–1173 (2016).
   PubMed Web of Science ®Google Scholar
• Soethoudt M , StolzeSC, WestphalMVet al. Selective photoaffinity probe that enables assessment of cannabinoid CB2 receptor expression and ligand engagement in human cells. J. Am. Chem. Soc.140(19), 6067–6075 (2018).
   PubMed Web of Science ®Google Scholar
• Parker CG , GalmozziA, WangYet al. Ligand and target discovery by fragment-based screening in human cells. Cell168(3), 527–541.e529 (2017).
   PubMed Web of Science ®Google Scholar
• Gertsik N , AmEnde CW, GeogheganKFet al. Mapping the binding site of BMS-708163 on γ-secretase with cleavable photoprobes. Cell Chem. Biol.24(1), 3–8 (2017).
   PubMed Web of Science ®Google Scholar
• Smith E , CollinsI. Photoaffinity labeling in target- and binding-site identification. Future Med. Chem.7(2), 159–183 (2015).
   PubMed Web of Science ®Google Scholar
• Sipthorp J , LebraudH, GilleyRet al. Visualization of endogenous ERK1/2 in cells with a bioorthogonal covalent probe. Bioconjug. Chem.28(6), 1677–1683 (2017).
   PubMed Web of Science ®Google Scholar
• Lebraud H , WrightDJ, EastCE, HoldingFP, O’ReillyM, HeightmanTD. In-gel activity-based protein profiling of a clickable covalent ERK1/2 inhibitor. Mol. Biosyst.12, 2867–2874 (2016).
   PubMedGoogle Scholar
• Chen YC , ZhangC. A Chemoproteomic method for identifying cellular targets of covalent kinase inhibitors. Genes Cancer7(5-6), 148–153 (2016).
   PubMedGoogle Scholar
• Rutkowska A , ThomsonDW, VappianiJet al. A modular probe strategy for drug localization, target identification and target occupancy measurement on single cell level. ACS Chem. Biol.11(9), 2541–2550 (2016).
   PubMed Web of Science ®Google Scholar
• Yang KS , BudinG, ReinerT, VinegoniC, WeisslederR. Bioorthogonal imaging of aurora kinase A in live cells. Angew. Chem. Int. Ed. Engl.51(27), 6598–6603 (2012).
   PubMed Web of Science ®Google Scholar
• Budin G , YangKS, ReinerT, WeisslederR. Bioorthogonal probes for polo-like kinase 1 imaging and quantification. Angew. Chem. Int. Ed. Engl.50(40), 9378–9381 (2011).
   PubMed Web of Science ®Google Scholar
• Kim E , YangKS, WeisslederR. Bioorthogonal small molecule imaging agents allow single-cell imaging of MET. PLoS ONE8(11), e81275 (2013).
   PubMed Web of Science ®Google Scholar
• D’Alessandro PL , BuschmannN, KaufmannMet al. Bioorthogonal probes for the study of MDM2-p53 inhibitors in cells and development of high-content screening assays for drug discovery. Angew. Chem. Int. Ed. Engl.55(52), 16026–16030 (2016).
   PubMed Web of Science ®Google Scholar
• Lebraud H , NobleRA, PhillipsNet al. Highly potent clickable probe for cellular imaging of MDM2 and assessing dynamic responses to MDM2-p53 inhibition. Bioconjug. Chem.29(6), 2100–2106 (2018).
   PubMed Web of Science ®Google Scholar
• Tyler DS , VappianiJ, CañequeTet al. Click chemistry enables preclinical evaluation of targeted epigenetic therapies. Science356(6345), 1397–1401 (2017).
   PubMed Web of Science ®Google Scholar
• Matthews PM , RabinerI, GunnR. Non-invasive imaging in experimental medicine for drug development. Curr. Opin. Pharmacol.11(5), 501–507 (2011).
   PubMed Web of Science ®Google Scholar
• Croteau E , RenaudJM, RichardMA, RuddyTD, BénardF, DekempRA. PET metabolic biomarkers for cancer. Biomark. Cancer8(Suppl. 2), 61–69 (2016).
   PubMedGoogle Scholar
• Nicastro N , GaribottoV, BurkhardPR. The role of molecular imaging in assessing degenerative Parkinsonism – an updated review.Swiss Med. Wkly148, w14621 (2018).
   PubMed Web of Science ®Google Scholar
• Rice L , BisdasS. The diagnostic value of FDG and amyloid PET in Alzheimer’s disease: a systematic review. Eur. J. Radiol.94, 16–24 (2017).
   PubMed Web of Science ®Google Scholar
• Sathekge MM , AnkrahAO, LawalI, VorsterM. Monitoring response to therapy. Semin. Nucl. Med.48(2), 166–181 (2018).
   PubMed Web of Science ®Google Scholar
• Dupont AC , LargeauB, GuilloteauD, SantiagoRibeiro MJ, ArlicotN. The place of PET to assess new therapeutic effectiveness in neurodegenerative diseases. Contrast Media Mol. Imaging2018, 7043578 (2018).
   PubMedGoogle Scholar
• Knight JC , KoustoulidouS, CornelissenB. Imaging the DNA damage response with PET and SPECT. Eur. J. Nucl. Med. Mol. Imaging44(6), 1065–1078 (2017).
   PubMed Web of Science ®Google Scholar
• Matthews PM , RabinerEA, PasschierJ, GunnRN. Positron emission tomography molecular imaging for drug development. Br. J. Clin. Pharmacol.73(2), 175–186 (2012).
   PubMed Web of Science ®Google Scholar
• Hargreaves RJ , RabinerEA. Translational PET imaging research. Neurobiol. Dis.61, 32–38 (2014).
   PubMed Web of Science ®Google Scholar
• Carney B , KossatzS, ReinerT. Molecular Imaging of PARP. J. Nucl. Med.58(7), 1025–1030 (2017).
   PubMed Web of Science ®Google Scholar
• Carney B , CarlucciG, SalinasBet al. Non-invasive PET imaging of PARP1 expression in glioblastoma models. Mol. Imaging Biol.18(3), 386–392 (2016).
   PubMed Web of Science ®Google Scholar
• Carney B , KossatzS, LokBHet al. Target engagement imaging of PARP inhibitors in small-cell lung cancer. Nat. Commun.9(1), 176 (2018).
   PubMedGoogle Scholar
• Michel LS , DyroffS, BrooksFJet al. PET of poly (ADP-ribose) polymerase activity in cancer: preclinical assessment and first in-human studies. Radiology282(2), 453–463 (2017).
   PubMed Web of Science ®Google Scholar
• Kaufman B , Shapira-FrommerR, SchmutzlerRKet al. Olaparib monotherapy in patients with advanced cancer and a germline BRCA1/2 mutation. J. Clin. Oncol.33(3), 244–250 (2015).
   PubMed Web of Science ®Google Scholar
• Quiles-Perez R , Muñoz-GámezJA, Ruiz-ExtremeraAet al. Inhibition of poly adenosine diphosphate-ribose polymerase decreases hepatocellular carcinoma growth by modulation of tumor-related gene expression. Hepatology51(1), 255–266 (2010).
   PubMed Web of Science ®Google Scholar
• Takano A , StenkronaP, StepanovVet al. A human [(11)C]T-773 PET study of PDE10A binding after oral administration of TAK-063, a PDE10A inhibitor. Neuroimage141, 10–17 (2016).
   PubMed Web of Science ®Google Scholar
• Naganawa M , DickinsonGL, ZhengMQet al. Receptor occupancy of the κ-opioid antagonist LY2456302 measured with positron emission tomography and the novel radiotracer 11C-LY2795050. J. Pharmacol. Exp. Ther.356(2), 260–266 (2016).
   PubMed Web of Science ®Google Scholar
• Gallezot JD , PlanetaB, NabulsiNet al. Determination of receptor occupancy in the presence of mass dose. J. Cereb. Blood Flow Metab.37(3), 1095–1107 (2017).
   PubMed Web of Science ®Google Scholar
• Patel AG , DeLorenzo SB, FlattenKS, PoirierGG, KaufmannSH. Failure of iniparib to inhibit poly(ADP-ribose) polymerase in vitro. Clin. Cancer Res.18(6), 1655–1662 (2012).
   PubMed Web of Science ®Google Scholar
• Aljakouch K , LechtonenT, YosefHKet al. Raman microspectroscopic evidence for the metabolism of a tyrosine kinase inhibitor, neratinib, in cancer cells. Angew. Chem. Int. Ed. Engl.57(24), 7250–7254 (2018).
   PubMed Web of Science ®Google Scholar
• Gao M , YuF, LvC, ChooJ, ChenL. Fluorescent chemical probes for accurate tumor diagnosis and targeting therapy. Chem. Soc. Rev.46, 2237–2271 (2017).
   PubMed Web of Science ®Google Scholar
• Han X , WangR, SongX, YuF, LvC, ChenL. A mitochondrial-targeting near-infrared fluorescent probe for bioimaging and evaluating endogenous superoxide anion changes during is chemia/reperfusion injury. Biomaterials156, 134–146 (2018).
   PubMed Web of Science ®Google Scholar
• Gao M , WangR, YuF, ChenL. Evaluation of sulfane sulfur bioeffects via a mitochondria-targeting selenium-containing near-infrared fluorescent probe. Biomaterials160, 1–14 (2018).
   PubMed Web of Science ®Google Scholar
• Wang R , HanX, YouJ, YuF, ChenL. Ratiometric near-infrared fluorescent probe for synergetic detection of monoamine oxidase b and its contribution to oxidative stress in cell and mice aging models. Anal. Chem.90(6), 4054–4061 (2018).
   PubMed Web of Science ®Google Scholar
• Song X , HanX, YuF, ZhangX, ChenL, LvC. Polyamine-targeting gefitinib prodrug and ots near-infrared fluorescent theranostic derivative for monitoring drug delivery and lung cancer therapy. Theranostics8(8), 2217–2228 (2018).
   PubMed Web of Science ®Google Scholar
• Collins I , WangH, CaldwellJJ, ChopraR. Chemical approaches to targeted protein degradation through modulation of the ubiquitin-proteasome pathway. Bio. Chem. J.474(7), 1127–1147 (2017).
   PubMed Web of Science ®Google Scholar
• Chessum NEA , SharpSY, CaldwellJJet al. Demonstrating in-cell target engagement using a pirin protein degradation probe (CCT367766). J. Med. Chem.61(3), 918–933 (2018).
   PubMed Web of Science ®Google Scholar
• Lebraud H , WrightDJ, JohnsonCN, HeightmanTD. Protein degradation by in-cell self-assembly of proteolysis targeting chimeras. ACS Cent. Sci.2(12), 927–934 (2016).
   PubMed Web of Science ®Google Scholar
• Mateus A , GordonLJ, WayneGJet al. Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery. Proc. Natl Acad. Sci. USA114(30), E6231–E6239 (2017).
   PubMed Web of Science ®Google Scholar