Photoaffinity labeling in target- and binding-site identification.

Photoaffinity labeling (PAL) using a chemical probe to covalently bind its target in response to activation by light has become a frequently used tool in drug discovery for identifying new drug targets and molecular interactions, and for probing the location and structure of binding sites. Methods to identify the specific target proteins of hit molecules from phenotypic screens are highly valuable in early drug discovery. In this review, we summarize the principles of PAL including probe design and experimental techniques for in vitro and live cell investigations. We emphasize the need to optimize and validate probes and highlight examples of the successful application of PAL across multiple disease areas.

[1]  David J. Lapinsky,et al.  Tandem photoaffinity labeling-bioorthogonal conjugation in medicinal chemistry. , 2012, Bioorganic & medicinal chemistry.

[2]  J. Downward.  Targeting RAS signalling pathways in cancer therapy , 2003, Nature Reviews Cancer.

[3]  S. Rees,et al.  Principles of early drug discovery , 2011, British journal of pharmacology.

[4]  J. Hiltunen,et al.  Identification of a Substrate-binding Site in a Peroxisomal β-Oxidation Enzyme by Photoaffinity Labeling with a Novel Palmitoyl Derivative* , 2010, The Journal of Biological Chemistry.

[5]  R. Eckenhoff,et al.  Identification of Propofol Binding Sites in a Nicotinic Acetylcholine Receptor with a Photoreactive Propofol Analog* , 2013, The Journal of Biological Chemistry.

[6]  C. Bannow,et al.  Identification of a novel mitochondrial protein ("mitoNEET") cross-linked specifically by a thiazolidinedione photoprobe. , 2004, American journal of physiology. Endocrinology and metabolism.

[7]  Shao Q Yao,et al.  Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes. , 2012, Journal of the American Chemical Society.

[8]  H. Kolb,et al.  The growing impact of click chemistry on drug discovery. , 2003, Drug discovery today.

[9]  R. Heine,et al.  Thiazolidinediones in type 2 diabetes mellitus: current clinical evidence. , 2003, Drugs.

[10]  Brahma Ghosh,et al.  Target validation using in-cell small molecule clickable imaging probes , 2014 .

[11]  A. Verma,et al.  Alterations in the ribosomal machinery in cancer and hematologic disorders , 2012, Journal of Hematology & Oncology.

[12]  L. Hartmann,et al.  Selective estrogen-receptor modulators -- mechanisms of action and application to clinical practice. , 2003, The New England journal of medicine.

[13]  Mahmoud Mansour,et al.  Thiazolidinediones/PPARγ agonists and fatty acid synthase inhibitors as an experimental combination therapy for prostate cancer. , 2011, International journal of oncology.

[14]  F. Westheimer,et al.  The photolysis of diazoacetylchymotrypsin. , 1962, The Journal of biological chemistry.

[15]  M. Bogyo,et al.  Tagging and detection strategies for activity-based proteomics. , 2007, Current opinion in chemical biology.

[16]  B. Cravatt,et al.  Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells , 2014, Journal of the American Chemical Society.

[17]  M. Distefano,et al.  Photoaffinity labeling of Ras converting enzyme using peptide substrates that incorporate benzoylphenylalanine (Bpa) residues: improved labeling and structural implications. , 2011, Bioorganic & medicinal chemistry.

[18]  Jonathan B. Cohen,et al.  Multiple Transmembrane Binding Sites for p-Trifluoromethyldiazirinyl-etomidate, a Photoreactive Torpedo Nicotinic Acetylcholine Receptor Allosteric Inhibitor* , 2011, The Journal of Biological Chemistry.

[19]  Giovanni Coppola,et al.  The HDAC inhibitor 4b ameliorates the disease phenotype and transcriptional abnormalities in Huntington's disease transgenic mice , 2008, Proceedings of the National Academy of Sciences.

[20]  V. Dive,et al.  A Pan Photoaffinity Probe for Detecting Active Forms of Matrix Metalloproteinases , 2013, Chembiochem : a European journal of chemical biology.

[21]  W. Xia,et al.  Modulation of Gamma-Secretase for the Treatment of Alzheimer's Disease , 2012, International journal of Alzheimer's disease.

[22]  Andrew Emili,et al.  Proteomic methods for drug target discovery. , 2008, Current opinion in chemical biology.

[23]  M. Hashimoto,et al.  Recent Progress in Diazirine-Based Photoaffinity Labeling , 2008 .

[24]  Wei He,et al.  Fluorophores and Their Applications as Molecular Probes in Living Cells , 2013 .

[25]  G. Terstappen,et al.  Target deconvolution strategies in drug discovery , 2007, Nature Reviews Drug Discovery.

[26]  M. Meijler,et al.  Diazirine based photoaffinity labeling. , 2012, Bioorganic & medicinal chemistry.

[27]  G. Superti-Furga,et al.  Target profiling of small molecules by chemical proteomics. , 2009, Nature chemical biology.

[28]  P. Ferrara,et al.  Microsomal epoxide hydrolase of rat liver is a subunit of theanti-oestrogen-binding site. , 1998, The Biochemical journal.

[29]  J. Massagué,et al.  Molecular Pathways Molecular Pathways : VCAM-1 as a Potential Therapeutic Target in Metastasis , 2012 .

[30]  H. Overkleeft,et al.  Photoaffinity labeling in activity-based protein profiling. , 2012, Topics in current chemistry.

[31]  S. Fleming.  Chemical reagents in photoaffinity labeling , 1995 .

[32]  L. Ngo,et al.  Photoaffinity Labeling and Mass Spectrometry Identify Ribosomal Protein S3 as a Potential Target for Hybrid Polar Cytodifferentiation Agents* , 1999, The Journal of Biological Chemistry.

[33]  Jack Taunton,et al.  Target Identification by Diazirine Photo‐Cross‐Linking and Click Chemistry , 2009, Current protocols in chemical biology.

[34]  H. Arias,et al.  Interaction of barbiturate analogs with the Torpedo californica nicotinic acetylcholine receptor ion channel. , 2001, Molecular pharmacology.

[35]  M. Hashimoto,et al.  Recent Progress in Diazirine‐Based Photoaffinity Labeling , 2008 .

[36]  J. Taunton,et al.  Photo-leucine incorporation reveals the target of a cyclodepsipeptide inhibitor of cotranslational translocation. , 2007, Journal of the American Chemical Society.

[37]  Affinity-Based Target Identification for Bioactive Small Molecules , 2014 .

[38]  J. Knowles,et al.  Reduction of aryl azides by thiols: implications for the use of photoaffinity reagents. , 1978, Biochemical and biophysical research communications.

[39]  R. Roeder,et al.  HATs off: selective synthetic inhibitors of the histone acetyltransferases p300 and PCAF. , 2000, Molecular cell.

[40]  P. Džubák,et al.  Pharmacological activities of natural triterpenoids and their therapeutic implications. , 2006, Natural product reports.

[41]  E. Schreiner,et al.  Selective inhibition of cotranslational translocation of vascular cell adhesion molecule 1 , 2005, Nature.

[42]  Y. Liu,et al.  Photoaffinity labeling of small-molecule-binding proteins by DNA-templated chemistry. , 2013, Angewandte Chemie.

[43]  R. Olsen,et al.  Identification of Direct Protein Targets of Small Molecules , 2010, ACS chemical biology.

[44]  P. Marks,et al.  A class of hybrid polar inducers of transformed cell differentiation inhibits histone deacetylases. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Heather L. Plasterer,et al.  Chemical probes identify a role for histone deacetylase 3 in Friedreich's ataxia gene silencing. , 2009, Chemistry & biology.

[46]  Jun O. Liu,et al.  Design and synthesis of novel photoaffinity probes for study of the target proteins of oleanolic acid. , 2012, Bioorganic & medicinal chemistry letters.

[47]  R. Mckernan,et al.  Photoaffinity labeling of the benzodiazepine binding site of alpha1beta3gamma2 gamma-aminobutyric acidA receptors with flunitrazepam identifies a subset of ligands that interact directly with His102 of the alpha subunit and predicts orientation of these within the benzodiazepine pharmacophore. , 1998, Molecular pharmacology.

[48]  N. Fujii,et al.  Characterization of the receptor binding residues of kisspeptins by positional scanning using peptide photoaffinity probes. , 2013, Bioorganic & medicinal chemistry letters.

[49]  K. Bales,et al.  γ-Secretase Modulator (GSM) Photoaffinity Probes Reveal Distinct Allosteric Binding Sites on Presenilin* , 2013, The Journal of Biological Chemistry.

[50]  S. Son,et al.  Identification of malate dehydrogenase 2 as a target protein of the HIF-1 inhibitor LW6 using chemical probes. , 2013, Angewandte Chemie.

[51]  P. Richardson,et al.  A novel vascular disrupting agent plinabulin triggers JNK-mediated apoptosis and inhibits angiogenesis in multiple myeloma cells. , 2011, Blood.

[52]  J. Das.  Aliphatic diazirines as photoaffinity probes for proteins: recent developments. , 2011, Chemical reviews.

[53]  Kambe Tohru,et al.  Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells , 2015 .

[54]  S. Perlman,et al.  Histone deacetylase inhibitors reverse gene silencing in Friedreich's ataxia , 2006, Nature chemical biology.

[55]  Qisheng Zhang,et al.  Isotope-coded, fluorous photoaffinity labeling reagents. , 2012, Chemical communications.

[56]  B. Turk,et al.  A Peptide Photoaffinity Probe Specific for the Active Conformation of the Abl Tyrosine Kinase , 2012, Chembiochem : a European journal of chemical biology.

[57]  Photoaffinity Labeling of Nicotinic Receptors: Diversity of Drug Binding Sites! , 2014, Journal of Molecular Neuroscience.

[58]  Identifying Barbiturate Binding Sites in a Nicotinic Acetylcholine Receptor with [3H]Allyl m-Trifluoromethyldiazirine Mephobarbital, a Photoreactive Barbiturate , 2014, Molecular Pharmacology.

[59]  A. Salajegheh.  Vascular Cell Adhesion Molecule-1 (VCAM-1) , 2016 .

[60]  Lloyd M Smith,et al.  Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry. , 2006, Angewandte Chemie.

[61]  R. Neubig,et al.  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 , 2013, Beilstein journal of organic chemistry.

[62]  Motomasa Kobayashi,et al.  Synthesis and evaluation of effective photoaffinity probe molecule of furospinosulin-1, a hypoxia-selective growth inhibitor. , 2014, Bioorganic & medicinal chemistry.

[63]  Gang Li,et al.  Multivalent photoaffinity probe for labeling small molecule binding proteins. , 2014, Bioconjugate chemistry.

[64]  D. C. Chiara,et al.  Specificity of Intersubunit General Anesthetic-binding Sites in the Transmembrane Domain of the Human α1β3γ2 γ-Aminobutyric Acid Type A (GABAA) Receptor*♦ , 2013, The Journal of Biological Chemistry.

[65]  J. Meier,et al.  Chemoproteomic Profiling of Lysine Acetyltransferases Highlights an Expanded Landscape of Catalytic Acetylation , 2014, Journal of the American Chemical Society.

[66]  Ronald Breslow,et al.  Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug , 2007, Nature Biotechnology.

[67]  B. de Strooper,et al.  Presenilins and γ-secretase: structure, function, and role in Alzheimer Disease. , 2012, Cold Spring Harbor perspectives in medicine.

[68]  Y. Kiso,et al.  Anti-microtubule 'plinabulin' chemical probe KPU-244-B3 labeled both alpha- and beta-tubulin. , 2010, Bioorganic & medicinal chemistry.

[69]  Min Xu,et al.  Photoactivated γ-secretase inhibitors directed to the active site covalently label presenilin 1 , 2000, Nature.

[70]  R. Yamada,et al.  Comparison of the Reactivity of Carbohydrate Photoaffinity Probes with Different Photoreactive Groups , 2014, Chembiochem : a European journal of chemical biology.

[71]  Y. Sadakane,et al.  Photochemical Fishing Approaches for Identifying Target Proteins and Elucidating the Structure of a Ligand-binding Region Using Carbene-generating Photoreactive Probes , 2006, Analytical sciences : the international journal of the Japan Society for Analytical Chemistry.

[72]  Ajit S. Divakaruni,et al.  Thiazolidinediones are acute, specific inhibitors of the mitochondrial pyruvate carrier , 2013, Proceedings of the National Academy of Sciences.

[73]  Seo-Hyun Choi,et al.  Design and synthesis of novel photoaffinity reagents for labeling VEGF receptor tyrosine kinases , 2006 .

[74]  Ajit S. Divakaruni,et al.  Identification of a Mitochondrial Target of Thiazolidinedione Insulin Sensitizers (mTOT)—Relationship to Newly Identified Mitochondrial Pyruvate Carrier Proteins , 2013, PloS one.

[75]  L. Qiu,et 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 , 2005, Molecular Cancer Therapeutics.

[76]  M. Murphy,et al.  Alzheimer's disease and the amyloid-beta peptide. , 2010, Journal of Alzheimer's disease : JAD.

[77]  P. Ferrara,et al.  Identification of two tamoxifen target proteins by photolabeling with 4-(2-morpholinoethoxy)benzophenone. , 2002, Bioconjugate chemistry.

[78]  Xiang-Jiao Yang.  The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. , 2004, Nucleic acids research.

[79]  Feng Cong,et al.  Chemical genetics-based target identification in drug discovery. , 2012, Annual review of pharmacology and toxicology.

[80]  C. Cordon-Cardo,et al.  Two cytodifferentiation agent-induced pathways, differentiation and apoptosis, are distinguished by the expression of human papillomavirus 16 E7 in human bladder carcinoma cells. , 1997, Cancer research.

[81]  Nathan R. Qi,et al.  Insulin Resistance and Metabolic Derangements in Obese Mice Are Ameliorated by a Novel Peroxisome Proliferator-activated Receptor γ-sparing Thiazolidinedione* , 2012, The Journal of Biological Chemistry.

[82]  T. Owa,et al.  Splicing factor SF3b as a target of the antitumor natural product pladienolide , 2007, Nature Chemical Biology.