Recent Developments and Applications of Clickable Photoprobes in Medicinal Chemistry and Chemical Biology

References

• 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
• He B , VelaparthiS, PieffetGet al. Binding ensemble profiling with photoaffinity labeling (BEProFL) approach: mapping the binding poses of HDAC8 inhibitors. J. Med. Chem.52 (22), 7003–7013 (2009).
   PubMed Web of Science ®Google Scholar
• Sadaghiani AM , VerhelstSH, BogyoM. Tagging and detection strategies for activity-based proteomics. Curr. Opin. Chem. Biol.11 (1), 20–28 (2007).
   PubMed Web of Science ®Google Scholar
• Geurink PP , PrelyLM, van der MarelGA, BischoffR, OverkleeftHS. Photoaffinity labeling in activity-based protein profiling. Top. Curr. Chem.324, 85–113 (2012).
   PubMed Web of Science ®Google Scholar
• Lapinsky DJ . Tandem photoaffinity labeling-bioorthogonal conjugation in medicinal chemistry. Bioorg. Med. Chem.20 (21), 6237–6247 (2012).
   PubMed Web of Science ®Google Scholar
• Lallana E , RigueraR, Fernandez-MegiaE. Reliable and efficient procedures for the conjugation of biomolecules through Huisgen azide-alkyne cycloadditions. Angew. Chem. Int. Ed. Engl.50 (38), 8794–8804 (2011).
   PubMed Web of Science ®Google Scholar
• van Berkel SS , van EldijkMB, van HestJC. Staudinger ligation as a method for bioconjugation. Angew. Chem. Int. Ed. Engl.50 (38), 8806–8827 (2011).
   PubMed Web of Science ®Google Scholar
• Speers AE , AdamGC, CravattBF. Activity-based protein profiling in vivo using a copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition. J. Am. Chem. Soc.125 (16), 4686–4687 (2003).
   PubMed Web of Science ®Google Scholar
• Wigglesworth MJ , MurrayDC, BlackettCJ, KossenjansM, NissinkJW. Increasing the delivery of next generation therapeutics from high throughput screening libraries. Curr. Opin. Chem. Biol.26, 104–110 (2015).
   PubMed Web of Science ®Google Scholar
• Wassermann AM , CamargoLM, AuldDS. Composition and applications of focus libraries to phenotypic assays. Front. Pharmacol.5, 164 (2014).
   PubMed Web of Science ®Google Scholar
• Eggert US . The why and how of phenotypic small-molecule screens. Nat. Chem. Biol.9 (4), 206–209 (2013).
   PubMed Web of Science ®Google Scholar
• Schreiber SL , KotzJD, LiMet al. Advancing biological understanding and therapeutics discovery with small-molecule probes. Cell161 (6), 1252–1265 (2015).
   PubMed Web of Science ®Google Scholar
• Côté M , MisasiJ, RenTet al. Small molecule inhibitors reveal Niemann- Pick C1 is essential for Ebola virus infection. Nature477 (7364), 344–348 (2011).
   PubMed Web of Science ®Google Scholar
• Lee K , RenT, CôtéMet al. Inhibition of Ebola Virus Infection: Identification of Niemann-Pick C1 as the target by optimization of a chemical probe. ACS Med. Chem. Lett.4 (2), 239–243 (2013).
   PubMed Web of Science ®Google Scholar
• Gillespie EJ , HoCL, BalajiKet al. Selective inhibitor of endosomal trafficking pathways exploited by multiple toxins and viruses. Proc. Natl Acad. Sci. USA110 (50), E4904–E4912 (2013).
   PubMed Web of Science ®Google Scholar
• Jung ME , ChamberlainBT, HoCL, GillespieEJ, BradleyKA. Structure-activity relationship of semicarbazone EGA furnishes photoaffinity inhibitors of anthrax toxin cellular entry. ACS Med. Chem. Lett.5 (4), 363–367 (2014).
   PubMed Web of Science ®Google Scholar
• Eirich J , BraigS, SchyschkaLet al. A small molecule inhibits protein disulfide isomerase and triggers the chemosensitization of cancer cells. Angew. Chem. Int. Ed. Engl.53 (47), 12960–12965 (2014).
   PubMed Web of Science ®Google Scholar
• Koh M , ParkJ, KooJYet al. Phenotypic screening to identify small-molecule enhancers for glucose uptake: target identification and rational optimization of their efficacy. Angew. Chem. Int. Ed. Engl.53 (20), 5102–5106 (2014).
   PubMed Web of Science ®Google Scholar
• Pieper AA , XieS, CapotaEet al. Discovery of a proneurogenic, neuroprotective chemical. Cell142 (1), 39–51 (2010).
   PubMed Web of Science ®Google Scholar
• Wang G , HanT, NijhawanDet al. P7C3 neuroprotective chemicals function by activating the rate-limiting enzyme in NAD salvage. Cell158 (6), 1324–1334 (2014).
   PubMed Web of Science ®Google Scholar
• Warashina M , MinKH, KuwabaraTet al. A synthetic small molecule that induces neuronal differentiation of adult hippocampal neural progenitor cells. Angew. Chem. Int. Ed. Engl.45 (4), 591–593 (2006).
   PubMed Web of Science ®Google Scholar
• Wurdak H , ZhuS, MinKHet al. A small molecule accelerates neuronal differentiation in the adult rat. Proc. Natl Acad. Sci. USA107 (38), 16542–16547 (2010).
   PubMed Web of Science ®Google Scholar
• Lee S , NamY, KooJYet al. A small molecule binding HMGB1 and HMGB2 inhibits microglia-mediated neuroinflammation. Nat. Chem. Biol.10 (12), 1055–1060 (2014).
   PubMed Web of Science ®Google Scholar
• Park J , OhS, ParkSB. Discovery and target identification of an antiproliferative agent in live cells using fluorescence difference in two-dimensional gel electrophoresis. Angew. Chem. Int. Ed. Engl.51 (22), 5447–5451 (2012).
   PubMed Web of Science ®Google Scholar
• Sun H , XuY, SitkiewiczIet al. Inhibitor of streptokinase gene expression improves survival after group A streptococcus infection in mice. Proc. Natl Acad. Sci. USA109 (9), 3469–3474 (2012).
   PubMed Web of Science ®Google Scholar
• Yestrepsky BD , KretzCA, XuYet al. Development of tag-free photoprobes for studies aimed at identifying the target of novel Group A Streptococcus antivirulence agents. Bioorg. Med. Chem. Lett.24 (6), 1538–1544 (2014).
   PubMed Web of Science ®Google Scholar
• Kambe T , CorreiaBE, NiphakisMJ, CravattBF. Mapping the protein interaction landscape for fully functionalized small-molecule probes in human cells. J. Am. Chem. Soc.136 (30), 10777–10782 (2014).
   PubMed Web of Science ®Google Scholar
• Yang P , LiuK. Activity-based protein profiling: recent advances in probe development and applications. ChemBioChem16 (5), 712–724 (2015).
   PubMed Web of Science ®Google 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
• van der Meijden B , RobinsonJA. Synthesis of a polymyxin derivative for photolabeling studies in the Gram-negative bacterium Escherichia coli. J. Pept. Sci.21 (3), 231–235 (2015).
   PubMed Web of Science ®Google Scholar
• Eirich J , OrthR, SieberSA. Unraveling the protein targets of vancomycin in living S. aureus and E. faecalis cells. J. Am. Chem. Soc.133 (31), 12144–12153 (2011).
   PubMed Web of Science ®Google Scholar
• Lapinski L , RostkowskaH, KhvorostovA, FaustoR, NowackMJ. Photochemical ring-opening reaction in 2(1H)-pyrimidinones: a matrix isolation study. J. Phys. Chem. A107 (31), 5913–5919 (2003).
   Web of Science ®Google Scholar
• Nishio T . Photochemical reactions of 1-aryl-2(1H)-pyrimidinones in alcohol. Liebigs Ann. Chem.1, 71–73 (1992).
   Google Scholar
• Battenberg OA , NodwellMB, SieberSA. Evaluation of α-pyrones and pyrimidones as photoaffinity probes for affinity-based protein profiling. J. Org. Chem.76 (15), 6075–6087 (2011).
   PubMed Web of Science ®Google Scholar
• Dubinsky L , DelagoA, AmaraNet al. Species selective diazirine positioning in tag-free photoactive quorum sensing probes. Chem. Commun.49 (52), 5826–5828 (2013).
   PubMed Web of Science ®Google Scholar
• Kita M , HirayamaY, YamagishiK, YonedaK, FujisawaR, KigoshiH. Interactions of the antitumor macrolide aplyronine A with actin and actin-related proteins established by its versatile photoaffinity derivatives. J. Am. Chem. Soc.134 (50), 20314–20317 (2012).
   PubMed Web of Science ®Google Scholar
• Kempf K , RajaA, SasseF, SchobertR. Synthesis of penicillenol C1 and of a bis-azide analogue for photoaffinity labeling. J. Org. Chem.78 (6), 2455–2461 (2013).
   PubMed Web of Science ®Google Scholar
• Sharma LK , CupitPM, GorongaT, WebbTR, CunninghamC. Design and synthesis of molecular probes for the determination of the target of the anthelmintic drug praziquantel. Bioorg. Med. Chem. Lett.24 (11), 2469–2472 (2014).
   PubMed Web of Science ®Google Scholar
• Penarete-Vargas DM , BoissonA, UrbachSet al. A chemical proteomics approach for the search of pharmacological targets of the antimalarial clinical candidate albitiazolium in Plasmodium falciparum using photocrosslinking and click chemistry. PLoS ONE9 (12), e113918 (2014).
   PubMed Web of Science ®Google Scholar
• Mizuhara T , OishiS, OhnoH, ShimuraK, MatsuokaM, FujiiN. Design and synthesis of biotin- or alkyne-conjugated photoaffinity probes for studying the target molecules of PD 404182. Bioorg. Med. Chem.21 (7), 2079–2087 (2013).
   PubMed Web of Science ®Google Scholar
• Duckworth BP , WilsonDJ, NelsonKM, BoshoffHI, BarryCE3rd, AldrichCC. Development of a selective activity-based probe for adenylating enzymes: profiling MbtA involved in siderophore biosynthesis from Mycobacterium tuberculosis. ACS Chem. Biol.7 (10), 1653–1658 (2012).
   PubMed Web of Science ®Google Scholar
• Kiyonaka S , KatoK, NishidaMet al. Selective and direct inhibition of TRPC3 channels underlies biological activities of a pyrazole compound. Proc. Natl Acad. Sci. USA106 (13), 5400–5405 (2009).
   PubMed Web of Science ®Google Scholar
• Schülke JP , McAllisterLA, GeogheganKFet al. Chemoproteomics demonstrates target engagement and exquisite selectivity of the clinical phosphodiesterase10A inhibitor MP-10 in its native environment. ACS Chem. Biol.9 (12), 2823–2832 (2014).
   PubMed Web of Science ®Google Scholar
• Li Z , HaoP, LiLet al. Design and synthesis of minimalist terminal alkyne-containing diazirine photo-crosslinkers and their incorporation into kinase inhibitors for cell- and tissue-based proteome profiling. Angew. Chem. Int. Ed. Engl.52 (33), 8551–8556 (2013).
   PubMed Web of Science ®Google Scholar
• Su Y , PanS, LiZet al. Multiplex imaging and cellular target identification of kinase inhibitors via an affinity-based proteome profiling approach. Sci. Rep.5, 7724 (2015).
   PubMed Web of Science ®Google Scholar
• Ranjitkar P , PereraBG, SwaneyDLet al. Affinity-based probes based on type II kinase inhibitors. J. Am. Chem. Soc.134 (46), 19017–19025 (2012).
   PubMed Web of Science ®Google Scholar
• Andrews SS , HillZB, PereraBG, MalyDJ. Label transfer reagents to probe p38 MAPK binding partners. ChemBioChem14 (2), 209–216 (2013).
   PubMed Web of Science ®Google Scholar
• Bell JL , HaakAJ, WadeSM, SunY, NeubigRR, LarsenSD. Design and synthesis of tag-free photoprobes for the identification of the molecular target for CCG-1423, a novel inhibitor of the Rho/MKL1/SRF signaling pathway. Beilstein J. Org. Chem.9, 966–973 (2013).
   PubMed Web of Science ®Google Scholar
• Sherratt AR , NasheriN, McKayCSet al. A new chemical probe for phosphatidylinositol kinase activity. ChemBioChem15 (9), 1253–1256 (2014).
   PubMed Web of Science ®Google Scholar
• Naik R , WonM, BanHSet al. Synthesis and structure-activity relationship study of chemical probes as hypoxia induced factor-1α/malate dehydrogenase 2 inhibitors. J. Med. Chem.57 (22), 9522–9538 (2014).
   PubMed Web of Science ®Google Scholar
• Lee K , BanHS, NaikRet al. Identification of malate dehydrogenase 2 as a target protein of the HIF-1 inhibitor LW6 using chemical probes. Angew. Chem. Int. Ed. Engl.52 (39), 10286–10289 (2013).
   PubMed Web of Science ®Google Scholar
• Kim BS , LeeK, JungHJ, BhattaraiD, KwonHJ. HIF-1α suppressing small molecule, LW6, inhibits cancer cell growth by binding to calcineurin B homologous protein 1. Biochem. Biophys. Res. Commun.458 (1), 14–20 (2015).
   PubMed Web of Science ®Google Scholar
• Hiroyuki N , HyunSB, KazukiS, HidemitsuM, ShinichiS. Design of photoaffinity probe molecules for identification and modification of target proteins. J. Photopolymer Sci. Tech.27 (4), 453–458 (2014).
   Web of Science ®Google Scholar
• Crump CJ , FishBA, CastroSVet al. Piperidine acetic acid based γ-secretase modulators directly bind to Presenilin-1. ACS Chem. Neurosci.2 (12), 705–710 (2011).
   PubMed Web of Science ®Google Scholar
• Pozdnyakov N , MurreyHE, CrumpCJet al. γ-Secretase modulator (GSM) photoaffinity probes reveal distinct allosteric binding sites on presenilin. J. Biol. Chem.288 (14), 9710–9720 (2013).
   PubMed Web of Science ®Google Scholar
• Crump CJ , CastroSV, WangFet al. BMS-708,163 targets presenilin and lacks notch-sparing activity. Biochemistry51 (37), 7209–7211 (2012).
   PubMed Web of Science ®Google Scholar
• Pettersson M , JohnsonDS, SubramanyamCet al. Design, synthesis, and pharmacological evaluation of a novel series of pyridopyrazine-1,6-dione γ-secretase modulators. J. Med. Chem.57 (3), 1046–1062 (2014).
   PubMed Web of Science ®Google Scholar
• Pettersson M , JohnsonDS, HumphreyJMet al. Discovery of indole-derived pyridopyrazine-1,6-dione γ-secretase modulators that target presenilin. Bioorg. Med. Chem. Lett.25 (4), 908–913 (2015).
   PubMed Web of Science ®Google Scholar
• Ballard TE , MurreyHE, GeogheganKF, am EndeCW, JohnsonDS. Investigating γ-secretase protein interactions in live cells using active site-directed clickable dual-photoaffinity probes. Med. Chem. Commun.5 (3), 321–327 (2014).
   Google Scholar
• Gertsik N , BallardTE, Am EndeCW, JohnsonDS, LiYM. Development of CBAP-BPyne, a probe for γ-secretase and presenilinase. Med. Chem. Commun.5 (3), 338–341 (2014).
   Google Scholar
• Vaidya AS , NeelarapuR, MadriagaAet al. Novel histone deacetylase 8 ligands without a zinc chelating group: exploring an ‘upside-down’ binding pose. Bioorg. Med. Chem. Lett.22 (21), 6621–6627 (2012).
   PubMed Web of Science ®Google Scholar
• Abdelkarim H , BrunsteinerM, NeelarapuRet al. Photoreactive “nanorulers” detect a novel conformation of full length HDAC3-SMRT complex in solution. ACS Chem. Biol.8 (11), 2538–2549 (2013).
   PubMed Web of Science ®Google Scholar
• Montgomery DC , SorumAW, MeierJL. Chemoproteomic profiling of lysine acetyltransferases highlights an expanded landscape of catalytic acetylation. J. Am. Chem. Soc.136 (24), 8669–8676 (2014).
   PubMed Web of Science ®Google Scholar
• Tam EK , LiZ, GohYLet al. Cell-based proteome profiling using an affinity-based probe (AfBP) derived from 3-deazaneplanocin A (DzNep). Chem. Asian J.8 (8), 1818–1828 (2013).
   PubMed Web of Science ®Google Scholar
• Li Z , WangD, LiLet al. “Minimalist” cyclopropene-containing photo-cross-linkers suitable for live-cell imaging and affinity-based protein labeling. J. Am. Chem. Soc.136 (28), 9990–9998 (2014).
   PubMed Web of Science ®Google Scholar
• Harbut MB , VelmourouganeG, ReissG, ChandramohanadasR, GreenbaumDC. Development of bestatin-based activity-based probes for metallo-aminopeptidases. Bioorg. Med. Chem. Lett.18 (22), 5932–5936 (2008).
   PubMed Web of Science ®Google Scholar
• Zhou Y , GuoT, LiXet al. Discovery of selective 2,4-diaminopyrimidine-based photoaffinity probes for glyoxalase I. Med. Chem. Commun.5, 352–357 (2014).
   Google Scholar
• Guo LW , HajipourAR, KaraogluK, MavlyutovTA, RuohoAE. Development of benzophenone-alkyne bifunctional sigma receptor ligands. ChemBioChem13 (15), 2277–2289 (2012).
   PubMed Web of Science ®Google Scholar
• George Cisar EA , NguyenN, RosenH. A GTP affinity probe for proteomics highlights flexibility in purine nucleotide selectivity. J. Am. Chem. Soc.135 (12), 4676–4679 (2013).
   PubMed Web of Science ®Google Scholar
• Zhang L , ZhangY, DongJ, LiuJ, ZhangL, SunH. Design and synthesis of novel photoaffinity probes for study of the target proteins of oleanolic acid. Bioorg. Med. Chem. Lett.22 (2), 1036–1039 (2012).
   PubMed Web of Science ®Google Scholar
• Hulce JJ , CognettaAB, NiphakisMJ, TullySE, CravattBF. Proteome-wide mapping of cholesterol-interacting proteins in mammalian cells. Nat. Methods10 (3), 259–264 (2013).
   PubMed Web of Science ®Google Scholar
• Li L , TangW, ZhaoZ. Synthesis and application of prenyl-derived photoaffinity probes. Chin. J. Chem.27, 1391–1396 (2009).
   Web of Science ®Google Scholar
• Haberkant P , RaijmakersR, WildwaterMet al. In vivo profiling and visualization of cellular protein-lipid interactions using bifunctional fatty acids. Angew. Chem. Int. Ed. Engl.52 (14), 4033–4038 (2013).
   PubMed Web of Science ®Google Scholar
• Peng T , HangHC. Bifunctional fatty acid chemical reporter for analyzing S-palmitoylated membrane protein-protein interactions in mammalian cells. J. Am. Chem. Soc.137 (2), 556–559 (2015).
   PubMed Web of Science ®Google Scholar
• Abe M , NakanoM, KosakaA, MiyoshiH. Syntheses of photoreactive cardiolipins for a photoaffinity labeling study. Tetrahedron Lett.56, 2258–2261 (2015).
   Web of Science ®Google Scholar
• Khan AA , KamenaF, TimmerMS, StockerBL. Development of a benzophenone and alkyne functionalised trehalose probe to study trehalose dimycolate binding proteins. Org. Biomol. Chem.11 (6), 881–885 (2013).
   PubMed Web of Science ®Google Scholar
• Murai M , MatsunobuK, KudoS, IfukuK, KawamukaiM, MiyoshiH. Identification of the binding site of the quinone-head group in mitochondrial Coq10 by photoaffinity labeling. Biochemistry53 (24), 3995–4003 (2014).
   PubMed Web of Science ®Google Scholar
• Murai M , MurakamiS, ItoT, MiyoshiH. Amilorides bind to the quinone binding pocket of bovine mitochondrial complex I. Biochemistry54 (17), 2739–2746 (2015).
   PubMed Web of Science ®Google Scholar
• Singh A , ThortonER, WestheimerFH. The photolysis of diazoacetylchymotrypsin. J. Biol. Chem.237, 3006–3008 (1962).
   PubMed Web of Science ®Google Scholar
• Wittelsberger A , ThomasBE, MierkeDF, RosenblattM. Methionine acts as a “magnet” in photoaffinity crosslinking experiments. FEBS Lett.580 (7), 1872–1876 (2006).
   PubMed Web of Science ®Google Scholar
• Pettersson MY , JohnsonDS, SubramanyamCet al. WO 2015049616 A1 20150409 (2015).
   Google Scholar
• Tae HS , HinesJ, SchneeklothAR, CrewsCM. Total synthesis and biological evaluation of tyroscherin. Org. Lett.12 (19), 4308–4311.
   PubMed Web of Science ®Google Scholar
• Yoshida S , MisawaY, HosoyaT. Formal C-H-azidation-based shortcut to diazido building blocks for the versatile preparation of photoaffinity labeling probes. Eur. J. Org. Chem. (19), 3991–3995 (2014).
   Web of Science ®Google Scholar
• Klein LL , PetukhovaV. Synthesis of trifunctional bis-azide photoaffinity probe. Synthetic Commun.43 (16), 2242–2245 (2013).
   Web of Science ®Google Scholar
• Xu H , HettEC, GopalsamyA, ParikhMDet al. A library approach to rapidly discover photoaffinity probes of the mRNA decapping scavenger enzyme DcpS. Mol. BioSyst. doi:10.1039/c5mb00288e (2015) ( Epub ahead of print).
   Google Scholar
• Swinney DC , AnthonyJ. How were new medicines discovered?Nat. Rev. Drug Discov.10 (7), 507–519 (2011).
   PubMed Web of Science ®Google Scholar