17,551
Views
0
CrossRef citations to date
0
Altmetric
Review

Photoaffinity Labeling in Target- and Binding-Site Identification

&
Pages 159-183 | Published online: 16 Feb 2015

References

  • Lapinsky DJ . Tandem photoaffinity labeling-bioorthogonal conjugation in medicinal chemistry. Bioorg. Med. Chem.20, 6237–6247 (2012).
  • Hashimoto M , HatanakaY. Recent progress in diazirine-based photoaffinity labeling. Eur. J. Org. Chem.15, 2513–2523 (2008).
  • Sadakane Y , HatanakaY. Photochemical fishing approaches for identifying target proteins and elucidating the structure of a ligand-binding region using carbene-generated photoreactive probes. Anal. Sci.22, 209–218 (2006).
  • Singh A , ThorntonER, WestheimerFH. The photolysis of diazoacetylchymotrypsin. J. Biochem.237, 3006–3008 (1962).
  • Das J . Aliphatic diazirines as photoaffinity probes for proteins: recent developments. Chem. Rev.111, 4405–4417 (2011).
  • Hughes JP , ReesS, KalinjianSB, PhilpottKL. Principles of early drug discovery. Br. J. Pharmacol.162, 1239–1249 (2011).
  • Han SY , ChoiSH, KimMHet al. Design and synthesis of novel photoaffinity reagents for labeling VEGF receptor tyrosine kinases. Tetrahedron Lett.47, 2915–1919 (2006).
  • Shi H , ZhangCJ, ChenGYJ, YaoSQ. Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes. J. Am. Chem. Soc.134, 3001–3014 (2012).
  • MacKinnon AL , TauntonJ. Target identification by diazirine photo-cross-linking and click chemistry. Curr. Protoc. Chem. Biol.1, 55–73 (2009).
  • Kolb HC , SharplessKB. The growing impact of click chemistry on drug discovery. Drug Discov. Today8, 1128–1137 (2003).
  • Ghosh B , JonesLH. Target validation using in-cell small molecule clickable imaging probes. Med. Chem. Commun.5, 247–254 (2013).
  • Fleming SA . Chemical reagents in photoaffinity labelling. Tetrahedron51, 12479–12520 (1995).
  • Sakurai K , OzawaS, YamadaR, YasuiT, MizunoS. Comparison of the reactivity of carbohydrate photoaffinity probes with different photoreactive groups. Chem. Bio. Chem.15, 1399–1403 (2014).
  • Dubinsky L , KromBP, MeijlerMM. Diazirine based photoaffinity labelling. Bioorg. Med. Chem.20, 554–570 (2012).
  • Geurink PP , PrelyML, van der MarelAG, BischoffR, OverkleeftHS. Photoaffinity labeling in activity-based protein profiling. Top. Curr. Chem.324, 85–114 (2012).
  • Staros JV , BayleyH, StandringDN, KnowlesJR. Reduction of aryl azides by thiols: implications for the use of photoaffinity reagents. Biochem. Biophys. Res. Commun.80, 568–572 (1978).
  • Terstappen GC , SchlüpenC, RaggiaschiR, GaviraghiG. Target deconvolution strategies in drug discovery. Nat. Rev. Drug Discov.6, 891–903 (2007).
  • Sadaghiani AM , VerhelstSHL, BogyoM. Tagging and detection strategies for activity-based proteomics. Curr. Opin. Chem. Biol.11, 20–28 (2007).
  • Liu J , LiuC, HeW. Fluorophores and their applications as molecular probes in living cells. Curr. Org. Chem.17, 564–579 (2013).
  • Lamos SM , KrusemarkCJ, McGeeCJet al. Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry. Angew. Chem. Int. Ed.45, 4329–4333 (2006).
  • Song Z , HuangW, ZhangQ. Isotope-coded, fluorous photoaffinity labelling reagents. Chem. Commun.48, 3339–3341 (2012).
  • Rix U , Superti-FurgaG. Target profiling of small molecules by chemical proteomics. Nat. Chem. Biol.5, 616–624 (2009).
  • Cong F , CheungAK, HuangSMA. Chemical genetics-based target identification in drug discovery. Annu. Rev. Pharmacol. Toxicol.52, 57–78 (2012).
  • Kawatani M , OsadaH. Affinity-based target identification for bioactive small molecules. Med. Chem. Commun.5, 277–287 (2013).
  • Sleno L , EmiliA. Proteomic methods for drug target discovery. Curr. Opin. Chem. Biol.12, 46–54 (2008).
  • Lomenick B , OlsenRW, HuangJ. Identification of direct protein targets of small molecules. ACS Chem. Biol.6, 34–46 (2011).
  • Dzubak P , HajduchM, VydraDet al. Pharmacological activities of natural triterpenoids and their therapeutic implications. Nat. Prod. Rep.22, 394–411 (2006).
  • Zhang L , ZhangY, DongJ, LiuJ, ZhangL, SunS. Design and synthesis of novel photoaffinity probes for study of the target proteins of oleanolic acid. Bioorg. Med. Chem. Lett.22, 1036–1039 (2012).
  • Kotake Y , SaganeK, OwaTet al. Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat. Chem. Biol.3, 570–575 (2007).
  • Xu C , SoragniE, ChouJCet al. Chemical probes identify a role for histone deacetylase 3 in Friedrich's ataxia gene silencing. Chem. Biol.16, 980–989 (2009).
  • Jessen KA , EnglishNM, WangJYet al. The discovery and mechanism of action of novel tumor-selective and apoptosis-inducing 3,5-diaryl-1,2,4-oxadiazole series using a chemical genetics approach. Mol. Cancer Ther.4, 761–771 (2005).
  • 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.52, 10286–10289 (2013).
  • 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).
  • Kotoku N , NakataC, KawachiTet al. Synthesis and evaluation of effective photoaffinity probe molecule of furospinosulin-1, a hypoxia-selective growth inhibitor. Bioorg. Med. Chem.22, 2102–2112 (2014).
  • Mackinnon AL , GarrisonJL, HegdeR, TauntonJ. Photo-leucine incorporation reveals target of cyclodepsipeptide inhibitor of cotranslational translocation. J. Am. Chem. Soc.129, 14560–14561 (2007).
  • Colca JR , McDonaldWG, CaveyGSet al. Identification of a mitochondrial target of thiazolidinedione insulin sensitizers (mTOT) – relationship to newly identified mitochondrial pyruvate carrier proteins. PLoS ONE8, e61551 (2013).
  • Webb Y , ZhouX, NgoLet al. Photoaffinity labeling and mass spectrometry identify ribosomal protein S3 as a potential target for hybrid polar cytodifferentiation agents. J. Biol. Chem.274, 14280–14287 (1999).
  • Mésange F , SebbarM, CapedevielleJet al. Identification of two tamoxifen target proteins by photolabeling with 4-(2-morpholinoethoxy) benzophenone. Bioconjugate Chem.13, 766–772 (2002).
  • Kambe T , CorreiaBE, NiphakisMJ, CravattBF. Mapping the protein interaction landscape for fully functionalised small-molecule probes in human cells. J. Am. Chem. Soc.136, 10777–10782 (2014).
  • Kashiwayama Y , TomohiroT, NaritaKet al. Identification of a substrate-binding site in a peroxisomal β-oxidation enzyme by photoaffinity labeling with a novel palmitoyl derivative. J. Biol. Chem.285, 26315–26325 (2010).
  • Misu R , OishiS, SetsudaSet al. Characterization of the receptor binding residues of kisspeptins by positional scanning using peptide photoaffinity probes. Bioorg. Med. Chem. Lett.23, 2628–2631 (2013).
  • Kyro K , ManandharSP, MullenD, SchmidtWK, DistefanoMD. Photoaffinity labelling of Ras converting enzyme using peptide substrates that incorporate benzoylphenylalanine (Bpa) residues: improved labeling and structural implications. Bioorg. Med. Chem.19, 7559–7569 (2011).
  • Pozdnyakov N , MurreyHE, CrumpCJet al. γ-Secretasemodulator (GSM) photoaffinity probes reveal distinct allosteric binding sites on presenilin. J. Biol. Chem.288, 9710–9720 (2013).
  • Li YM , XuM, LaiMTet al. Photoactivated-γ-secretase inhibitors directed to the active site covalently label presenilin 1. Nature.405, 689–694 (2004).
  • Hamouda AK , StewartDS, ChiaraDC, SavechenkovPY, BruzikKS, CohenJC. Identifying barbiturate binding sites in a nicotinic acetylcholine receptor with [3H] m-trifluoromethyldiazirinemephobarbital a photoreactive barbiturate. Mol. Pharmacol.85, 735–746 (2014).
  • Yamazaki Y , SumikuraM, HidakaKet al. Anti-microtubule ‘plinabulin’ chemical probe KPU-244 labeled both α- and β- tubulin. Bioorg. Med. Chem.18, 3169–3174 (2010).
  • Montgomery DC , SorumAW, MeierJL. Chemoproteomic profiling of lysine acetyltransferases highlights an expanded landscape of catalytic acetylation. J. Am. Chem. Soc.136, 8669–8676 (2014).
  • Thomas EA , CoppolaG, DesplatsPAet al. The HDAC inhibitor 4b ameliorates the disease phenotype and transcriptional abnormalities in Huntington's disease transgenic mice. Proc. Natl Acad. Sci. USA105, 15564–15569 (2008).
  • Herman D , JenssenK, BurnettR, SoragniE, PerlmanSL, GottesfeldJM. Histone deacetylase inhibitors reverse gene splicing in Friedrich's ataxia. Nat. Chem. Biol.2, 551–558 (2006).
  • Marks PA , BreslowR. Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug. Nat. Biotechnol.25, 84–90 (2007).
  • Chen QJ , MassaquéJ. Molecular pathways: VCAM-1 as a potential therapeutic target in metastasis. Clin. Cancer Res.18, 5520–5525 (2012).
  • Carter RA , CampbellIK, O'DonnelKL, WicksIP. Vascular cell adhesion molecule-1 (VCAM-1) blockade in collagen-induced arthritis reduces joint involvement and alters B cell trafficking. Clin. Exp. Immunol.128, 44–51 (2002).
  • Besemer J , HarantH, WangSet al. Selective inhibition of cotranslational translocation of vascular cell adhesion molecule 1. Nature436, 290–293 (2005).
  • Nury C , CzarnyB, Cassar-LajeunesseE, GeorgiadisD, BregantS, DiveV. A pan photoaffinity probe for detecting active forms of matrix metalloproteinases. Chembiochem14, 107–114 (2013).
  • Diamant M , HeineRJ. Thiazolidinediones in type 2 diabetes mellitus: current clinical evidence. Drugs63, 1373–1405 (2003).
  • Mansour M , SchwartzD, JuddRet al. Thiazolidinediones/PPARγ agonists and fatty acid synthase inhibitors as an experimental combination therapy for prostate cancer. Int. J. Oncol.38, 537–546 (2011).
  • Chen Z , VigueiraPA, ChambersKTet al. Insulin resistance and metabolic derangements in obese mice are ameliorated by a novel peroxisome proliferator activated receptor γ-sparing thiazolidinedione. J. Biol. Chem.287, 235237–23548 (2012).
  • Colca JR , McDonaldWG, WaldonDet al. Identification of a novel mitochondrial protein (“mitoNEET”) cross-linked specifically by a thiazolidinedione photoprobe. Am. J. Physiol. Endocrinol. Metab.286, E252–E260 (2004).
  • Divakaruni AS , WileySE, RogersGWet al. Thiazolidinediones are acute, specific inhibitors of the mitochondrial pyruvate carrier. Proc. Natl Acad. Sci. USA110, 5422–5427 (2013).
  • Richon VM , EmililaniS, VerdinEet al. A class of hybrid polar inducers of transformed cell differentiation inhibits histone deacetylases. Proc. Natl Acad. Sci. USA95, 3003–3007 (1998).
  • Grant S , EasleyC, KirkpatrickP. Vorinostat. Nat. Rev. Drug Discov.6, 21–22 (2007).
  • Richon VM , RussoP, Venta-PerezG, Cordon-CardoC, RifkindRA, MarksPA. Two cytodifferentiation agent-induced pathways, differentiation and apoptosis, are distinguished by the expression of human papillomavirus 16 E7 in human bladder carcinoma cells. Cancer Res.57, 2789–2798 (1997).
  • Shenoy N , KesselR, BhagatTDet al. Alterations in the ribosomal machinery in cancer and hematologic disorders. J. Hematol. Oncol.5, 32 (2012).
  • Riggs BL , HartmannLC. Selective estrogen-receptor modulators – mechanism of action and application to clinical practice. N. Engl. J. Med.348, 618–629 (2003).
  • Mésange F , SebbarM, CapedevielleJet al. Microsomal epoxide hydrolase of rat liver is a subunit of the anti-oestrogen binding site. Biochem. J.334, 107–112 (1998).
  • Chiara DC , JayakarSS, ZhouXet al. Specificity of intersubunit general anesthetic-binding sites in the transmembrane domain of the human a1b3g2 g-aminobutyric acid type A (GABAA) receptor. J. Biol. Chem.288, 19343–19357 (2013).
  • Hamouda AK , StewartDS, HusainSS, CohenJB. Multiple transmembrane binding sites for p-trifluoromethyldiazirinyl-etomidate, a photoreactive Torpedo nicotinic acetylcholine receptor allosteric inhibitor. J. Biol. Chem.286, 20466–20477 (2011).
  • McKernan RM , FarrarS, CollinsIet al. Photoaffinity labeling of the benzodiazepine binding site of α1β3γ2 γ-aminobutyric acidA receptors with flunitrazepam identifies a subset of ligands that interact directly with His102 of the α subunit and predicts orientation of these within the benzodiazepine pharmacophore. Mol. Pharmacol.54, 33–43 (1998).
  • Hamouda AK , JayakarSS. Photoaffinity labeling of nicotinic receptors: diversity of drug binding sites. J. Mol. Neurosci.53, 480–486 (2014).
  • Downward J . Targeting RAS signalling pathways in cancer therapy. Nat. Rev. Cancer.3, 11–22 (2003).
  • Deng Y , CouchBA, KoleskeAJ, TurkBE. A peptide photoaffinity probe specific for the active conformation of the Abl tyrosine kinase. Chem. Bio. Chem.13, 2510–2512 (2012).
  • Murphy MP , LeVineIIIH. Alzheimer's disease and the β-amyloid peptide. J. Alzheimers. Dis.19, 311–323 (2010).
  • De Strooper B , IwatsuboT, WolfeMS. Presenilins and γ-secretase: structure, function and role in Alzheimer disease. Cold Spring Harb. Perspect. Med.2, a006304 (2012).
  • Tate B , McKeeTD, LoureiroRMBet al. Modulation of gamma-secretase for the treatment of Alzheimer's disease. Int. J. Alzheimers. Dis.2012, 210756 (2012).
  • Arias HR , McCardyEA, GallagherMJ, BlantonMP. Interaction of barbiturate analogs with the Torpedo californica nicotinic acetylcholine receptor ion channel. Mol. Pharmacol.60, 497–506 (2001).
  • Jayakar SS , DaileyWP, EckenhoffRG, CohenJB. Identification of propofol binding sites in a nicotinic acetylcholine receptor allosteric inhibitor. J. Biol. Chem.288, 6178–6189 (2013).
  • Singh AV , BandiM, RajeNet al. A novel vascular disrupting agent plinabulin triggers JNK-mediated apoptosis and inhibits angiogenesis in multiple myeloma cells. Blood117, 5692–5700 (2011).
  • Yang XJ . The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic Acid Res.32, 959–976 (2004).
  • Lau OD , KunduTK, SoccioREet al. HATs off: selective synthetic inhibitors of the histone acetyltransferases p300 and PCAF. Mol. Cell.5, 589–595 (2000).
  • Li G , LiuY, LiuY, ChenL, WuS, LiuY, LiX. Photoaffinity labeling of small-molecule-binding proteins by DNA-templated chemistry. Angew. Chem., Intl. Ed.52, 9544–9549 (2013).
  • Li G , LiuY, YuX, LiX. Multivalent photoaffinity probe for labeling small molecule binding proteins. Bioconj. Chem.25, 1172–1180 (2014).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.