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Soundarya Vaithianathan Graduate Student Department of Medicinal Chemistry, School of Pharmacy, VCU. email: [email protected] February 12th, 2010. 1 WHAT ARE BIOMOLECULES ? Biomolecules: Organic compounds that are involved in the maintenance and metabolic processes of living organisms. AMINO ACIDS DNA&RNA BIO MOLECULES PEPTIDES PROTEINS http://www.biobasics.gc.ca/english/View.asp?mid=411&x=696 2 BIOMOLECULES Implicated in various disease conditions such as those with impaired amino acid metabolism. E.g. Phenylketonuria Peptide based pharmaceuticals, important class of therapeutic agent. Used to treat many diseases. E.g. Interferon used in treat Multiple Sclerosis. NEED TO BE DETECTED !! Gatti, M.; Gioia, M. G.; Andreatta, P.; Pentassuglia, G. J. Pharm. Biomed. Anal. 2004, 35, 339-348. Bennett, F. A.; Barlow, D. J.; Dodoo, A. N. O.; Hider, R. C.; Lansley, A. B.; Lawrence, M. J.; Marriott, C.; Bansal, S. S. Anal. Biochem. 1999, 270, 15-23. 3 BIOMOLECULES Problems in detection: 1. Structural similarity between Analyte Degradation product Endogenous component Impurities 2. Lack of selectivity 3. Sensitivity requirements not met 4. Lack of an effective method for detection in biological matrices Bennett, F. A.; Barlow, D. J.; Dodoo, A. N. O.; Hider, R. C..; Lansley, A. B.; Lawrence, M. J.; Marriott, C.; Bansal, S. S. Anal. Biochem. 1999, 270, 15-23. Wang, W.; Li, H. Tetrahedron Lett. 2004, 45, 8479-8481. 4 LABELING OF BIOMOLECULES LABELING COMPOUNDS WITH FLUORESCENCE INORGANIC RADIOACTIVE COMPOUNDS ORGANIC Goncalves, S. Chem Rev. 2009, 109, 190-212. Toyo’oka, T. Anal. Chim. Acta 2002, 465, 111. 5 FLUORESCENCE ν ν Absorption Fluorescence 6 ORGANIC FLUOROPHORES Organic Fluorophore: component of a molecule which causes it to be fluorescent Form covalent or non covalent linkage with sample to be analyzed Production of conjugates or complexes Fluorescence from short to very long wavelength Detection of biomolecules Goncalves, S. Chem Rev. 2009, 109, 190-212. 7 ELECTROMAGNETIC SPECTRUM VISIBLE LIGHT INFRARED UV X-RAY MICROWAVE nan RADIO GAMMA Wavelength: 5,000,000,000 1,000 500 250 Energy: 0.000000248 0.124 2.48 4.96 0.5 0.0005 nanometers 2480 2,480,000 electron volts 1cm = 10,000,000 nm Image taken from: http://lot.astro.utoronto.ca/images/spectrum.png 8 CLASSIFICATION Organic Labels Emission up to 500 nm 1. 2. 3. 4. OXYGEN heterocycle SULFUR heterocycle NITROGEN heterocycle NAPHTHALENE fluorophores Goncalves, S. Chem Rev. 2009, 109, 190-212 Emission beyond 500 nm 1. 2. 3. 4. 5. Fluoresceins Rhodamines BODIPY fluorophores Squarines Cyanines 9 CLASSIFICATION Organic Labels Emission up to 500 nm 1. 2. 3. 4. OXYGEN heterocycle SULFUR heterocycle NITROGEN heterocycle NAPHTHALENE fluorophores Goncalves, S. Chem Rev. 2009, 109, 190-212 Emission beyond 500 nm 1. 2. 3. 4. 5. Fluoresceins Rhodamines BODIPY fluorophores Squarines Cyanines 10 OXYGEN HETEROCYCLE Fluorescent Quantum Yield φF = Photons emitted Photons absorbed φF : 0.0 to 1.0 Molar absorptivity ε : measure of how strongly a chemical species absorbs Units: M-1 cm-1 11 OXYGEN HETEROCYCLE Two main classes of compounds: 1. COUMARINS : 2. FURANS : a) BENZOFURAN b) NAPHTHOFURAN Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 12 Gikas, E.; Parissi-Poulou, M.; Kazanis, M.; Vavagianis, A. Anal. Chim. Acta 2003, 57,259. COUMARINS 1. COUMARINS Characteristics: λ ex: 345 nm λ em: 440 nm ɸF: 0.52 ε : 10,900 M-1 cm-1 Wang, W.; Li, H. Tetrahedron Lett. 2004, 45, 8479-8481. Bennett, F. A,; Barlow, D. J.; Dodoo, A. N. O.; Hider, R. C.; Lansley, A. B.; Lawrence, M. J.; Marriott, 13 C.; Bansal, S. S. Anal. Biochem. 1999, 270, 15-23. SYNTHESIS OF Dmca 91% 6,7-Dimethoxy-4-methylcoumarin 77% Z/E : 95/5 Buchi, G.; Foulkes, D. M.; Kurono, M.; Mitchell, G. F.; Schneider, R. S. J. Am. Chem. Soc. 1967, 89, 6745-6753 . 14 Wadsworth Jr., W.S.; Emmons, W.D. J. Am. Chem. Soc., 1961, 83, 1733. SYNTHESIS OF Dmca S 96% 95% ee 1,2-bis-((2R,5R)-2,5- diethylphospholano)benzene(cyclooctadiene)rhodium(I) trifluoromethane sulfonate High Yield : 96% Lactone not reduced Wang, W.; Li, H. Tetrahedron Lett. 2004, 45, 8479-8481. 15 ADVANTAGES OF Dmca Coumarin side chain is fluorescent. Selective determination. High detection sensitivity. Easy incorporation into peptide sequence. Treatment with HBr/TFA does not alter stability. Bennett, F. A,; Barlow, D. J.; Dodoo, A. N. O.; Hider, R. C.; Lansley, A. B.; Lawrence, M. J.; Marriott, 16 C.; Bansal, S. S. Anal. Biochem. 1999, 270, 15-23. OXYGEN HETEROCYCLE Two main classes of compounds: 1. COUMARINS : 2. FURANS : a) BENZOFURAN b) NAPHTHOFURAN Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 17 Gikas, E.; Parissi-Poulou, M.; Kazanis, M.; Vavagianis, A. Anal. Chim. Acta 2003, 57,259. BENZOFURANS & NAPHTHOFURANS Polycyclic Oxygen Heterocycles Fluorescent pre column derivatization agent in HPLC analysis of amino acids Piloto, A.M.; Costa, S. P. G.; Goncalves, M. S. T. Tetrahedron Lett. 2005, 46, 4757. Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 18 SYNTHESIS OF BENZOFURAN 92% Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 19 SYNTHESIS OF NAPHTHOFURAN Piloto, A.M.; Costa, S. P. G.; Goncalves, M. S. T. Tetrahedron Lett. 2005, 46, 4757-4760. 20 APPLICATION OF BENZOFURAN Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 21 APPLICATION OF NAPHTHOFURAN Piloto, A.M.; Costa, S. P. G.; Goncalves, M. S. T. Tetrahedron Lett. 2005, 46, 4757-4760. 22 NAPHTHOFURAN IS BETTER FLUOROPHORE STRUCTURE λex λem φF 298 349 0.20 285 315 0.020 (nm) (nm) NAPHTHOFURAN ( R= OCH3) BENZOFURAN Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 23 NAPHTHOFURAN IS BETTER FLUOROPHORE STRUCTURE λex λem (nm) (nm) 298 349 0.32 288 315 0.064 φF NAPHTHOFURAN LINKED TO PHENYLALANINE BENZOFURAN LINKED TO PHENYLALANINE Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 24 NAPHTHOFURAN IS BETTER FLUOROPHORE STRUCTURE λex λem (nm) (nm) 298 346 0.37 288 315 0.070 φF NAPHTHOFURAN LINKED TO VALINE BENZOFURAN LINKED TO VALINE Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 25 EFFECT OF SUBSTITUENTS 1. ɸF λex λem 0.20 298 341 0.062 301 349 0.076 293 340 R = OCH3 2. 3. R = OH R=H Piloto, A.M.; Fonseca, A.S.C.; Costa,S.P.G.; Goncalves, M.S.T. Tetrahedron 2006, 62,9258-9267. 26 CLASSIFICATION Organic Labels Emission up to 500 nm 1. 2. 3. 4. OXYGEN heterocycle SULFUR heterocycle NITROGEN heterocycle NAPHTHALENE fluorophores Goncalves, S. Chem Rev. 2009, 109, 190-212 Emission beyond 500 nm 1. 2. 3. 4. 5. Fluoresceins Rhodamines BODIPY fluorophores Squarines Cyanines 27 SULFUR HETEROCYCLE Oligothiophenes are sulfur containing compounds Intrinsic Fluorescence E.g. Terthiophene λex = 356 nm λex = 441 nm 5-(2-Hydroxyethyl)-2,2’:5’,2”-terthiophene Used as a fluorescent tag for oligonucleotides via phosphoramidite coupling Capobianco, M.L.; Naldi, M.; Zambianchi, M.; Barbarella, G. Tetrahedron Lett. 2005, 46, 8181-8184. 28 PHOSPHORAMIDITE OF TERTHIOPHENE Capobianco, M.L.; Naldi, M.; Zambianchi, M.; Barbarella, G. Tetrahedron Lett. 2005, 46, 8181-8184. 29 TERTHIOPHENE – T4 CONJUGATE λex = 360nm λex = 454 nm Probes for detecting DNA & RNA Capobianco, M.L.; Naldi, M.; Zambianchi, M.; Barbarella, G. Tetrahedron Lett. 2005, 46, 8181-8184. 30 APPLICATION Oligothiophene N-succinimidyl ester Conjugated to oligonucleotides with free –NH2 terminal at 3’ position FRET (Fluorescence Resonance Energy Transfer) experiments are carried out Barbarella, G.; Zambianchi, M,; Sotgiu, G.; Ventola, A.;Galeotti, M.;Gigli, G.;Cazzato, A.;Capobianco, M.L. J.Non-Cryst. Solids 2006, 352,2465-2467. 31 FRET – MOLECULAR BEACON Barbarella, G.; Zambianchi, M,; Sotgiu, G.; Ventola, A.;Galeotti, M.;Gigli, G.;Cazzato, A.;Capobianco, M.L. J.Non-Cryst. Solids 2006, 352,2465-2467. 32 CLASSIFICATION Organic Labels Emission up to 500 nm 1. 2. 3. 4. OXYGEN heterocycle SULFUR heterocycle NITROGEN heterocycle NAPHTHALENE fluorophores Goncalves, S. Chem Rev. 2009, 109, 190-212 Emission beyond 500 nm 1. 2. 3. 4. 5. Fluoresceins Rhodamines BODIPY fluorophores Squarines Cyanines 33 NITROGEN HETEROCYCLE Used as pre or post column chemical derivatization reagent. Efficient tool for analysis of amino acid. Gatti, M.; Gioia, M. G.; Andreatta, P.; Pentassuglia, G. J. Pharm. Biomed. Anal. 2004, 35, 339-348. Dafau, I.; Mazerguil, H. Tetrahedron Lett. 2000, 41, 6063-6066. 34 PHANQUINONES 4,7-Phenanthroline-5,6-dione Produces highly fluorescent iminoquinols separated by reverse phase HPLC. λ ex : 400 nm λ em :460 nm Gatti, M.; Gioia, M. G.; Andreatta, P.; Pentassuglia, G. J. Pharm. Biomed. Anal. 2004, 35, 339-348. 35 Gatti, R.;Gioia, M.G.; Di Pietra, A.M. Anal. Chim. Acta 2002, 474,11-20. BENZOOXADIAZOLE λ ex : 470 nm λ em: 530 nm Uchiyama, S.; Takehira, K.; Kohtani, S.; Imai, K.; Nagasaki, R.; Tobita, S.; Santa, T. Org. Biomol. 2003,H.1,Tetrahedron 1067-1072. Lett. 2000, 41, 6063-6066. Dafau, I.;Chem. Mazerguil, 36 INTRINSIC PROBES Tryptophan , tyrosine and phenylalanine. Disadvantages of Tryptophan (W): Quenched by neighboring protonated acidic groups. More than 1 residue Interpretation of spectral changes is difficult. λ ex : 280 nm λ em :348 nm Chen, Y.; Gai, F.; Petrich, J. W. J. Phys. Chem. 1994, 98, 2203 Fillipis, V.; Boni, S.; Dea, E.; Dalzoppo, D.; Grandi, C.; Fontana, A. Protein Sci. 2004,13, 14891502. 37 NON-CODED ANALOG Non-coded analogs used instead of Tryptophan Tryptophan λ ex : 280 nm λ ex : 290 nm λ em :348 nm λ em :394 nm Chen, Y.; Gai, F.; Petrich, J. W. J. Phys. Chem. 1994, 98, 2203 Fillipis, V.; Boni, S.; Dea, E.; Dalzoppo, D.; Grandi, C.; Fontana, A. Protein Sci. 2004,13, 14891502. 38 HIRUDIN To investigate disulfide-coupled folding of Hirudin fragment 1- 47: Anticoagulant : potent inhibitor of thrombin N terminal: 1-47 amino acids; C terminal: 48-64 amino acids 3 disulfide linkages (Cys6-Cys14, Cys16-Cys28, Cys22-Cys37) Image: http://en.wikipedia.org/wiki/File:Hirudin in complex with thrombin.png Fillips, V.; Russo, I.; Vindigni, A.; DiCera, E.; Salmaso, S.; Fontana, A.; Protein Sci. 1999, 8, 2213-2217. 39 CHANGES IN HIRUDIN 1 Tyrosine Tyrosine 3 13 47 N – Terminal of Hirudin Tryptophan Tyrosine 3 13 1 N – Terminal of Hirudin 7-Azatryptophan 1 3 47 Y3W Tyrosine 13 N – Terminal of Hirudin 47 Y3AW Fillips, V.; Boni, S.; Dea, E.; Dalzoppo, D.; Grandi, C.; Fontana, A. Protein Sci. 2004, 13, 14891502. 40 UV & FLUORESCENCE SPECTRUM Absorptivity M-1 cm-1 x 10-3 UV-absorption spectrum: Tryptophan (W) 7-Azatryptophan (AW) Fluorescence spectra: Tyrosine (Y) Red shift in absorption of AW compared to W Wavelength (nm) Fillips, V.; Boni, S.; Dea, E.; Dalzoppo, D.; Grandi, C.; Fontana, A. Protein Sci. 2004, 13, 14891502. 41 FLUOROSENCE EMISSION OF Y3AW 7-Azatryptophan 1 Tyrosine 3 13 47 N – Terminal of Hirudin Y3AW Relative Fluorosence Reduced Form: Tyr 13305 nm AW 3 397 nm Oxidized Form: Tyr band disappears AW 3 390 nm Reduced form solid line Disulfide oxidized dashed line Wavelength (nm) Fillips, V.; Boni, S.; Dea, E.; Dalzoppo, D.; Grandi, C.; Fontana, A. Protein Sci. 2004, 13, 14891502. 42 FLUOROSENCE EMISSION OF Y3W Tryptophan Tyrosine 3 13 1 47 N – Terminal of Hirudin Y3W Relative Fluorosence Reduced Form: Trp 3 355 nm Tyr 13 303 nm Oxidized Form: Trp 3 350 nm Wavelength (nm) Reduced form solid line Disulfide oxidized dashed line Fillips, V.; Boni, S.; Dea, E.; Dalzoppo, D.; Grandi, C.; Fontana, A. Protein Sci. 2004, 13, 14891502. 43 CLASSIFICATION Organic Labels Emission up to 500 nm 1. 2. 3. 4. OXYGEN heterocycle SULFUR heterocycle NITROGEN heterocycle NAPHTHALENE fluorophores Goncalves, S. Chem Rev. 2009, 109, 190-212. Emission beyond 500 nm 1. 2. 3. 4. 5. Fluoresceins Rhodamines BODIPY fluorophores Squarines Cyanines 44 NAPHTHALENE FLUOROPHORES Extensively used as labels for amino acids, peptides and proteins. Dansyl chloride Non fluorescent. Pre column derivatization agent for detection of amino acids in biological samples. Kang, X.; Xiao, J.; Huang, X.; Gu, Z. Cli. Chim. Acta 2006, 366, 352-356. 45 “IN-SYNTHESIS” LABELING OF PEPTIDES Peptides synthesized by solid-phase method Coupling of Boc-Lys( Fmoc )-COOH to the growing peptide chain Chersi, A.; Modugno, F.; Rosano, L. Biochim Biophys. Acta 1997, 1336, 83-88. 46 “IN-SYNTHESIS” LABELING OF PEPTIDES 8ml of 20% solution of piperidine in DMF cleave Fmoc group 20 fold molar excess of Dansyl Chloride in solvent mixture ( Sodium carbonate +ethanol +DMF +acetone ) Chersi, A.; Modugno, F.; Rosano, L. Biochim Biophys. Acta 1997, 1336, 83-88. 47 “IN-SYNTHESIS” LABELING OF PEPTIDES 45% Trifluoroacetic Acid Cleaves Boc New coupling step Treatment of resin particles with TFMSA Filtered through Gelman Acrodisc and precipitated with cold ether Advantages: Extensive modification of proteins avoided. Peptides are better fluorescent labeled entities. Alpha amino group is spared. Chersi, A.; Modugno, F.; Rosano, L. Biochim Biophys. Acta 1997, 1336, 83-88. 48 PRODAN 6-Propionyl-2-(dimethylamino)naphthalene Environmentally sensitive fluorophore: Red shift with increasing polarity of solvent. Cyclohexane: λ ex = 342 nm ; λ em = 401 nm Water: λ ex = 364 nm ; λ em = 531 nm Electron donor group Electron acceptor group Maximum effects 2 groups far apart Weber, G.; Farris, F. J. J. Biochem. 1979, 18, 3075-3078. Nitz, M.; Mezo, A. R.; Ali, M. H.; Imperiali, B. Chem. Commun. 2002, 1912-1913. 49 DANA PROBLEM WITH PRODAN: Various degrees of freedom and distances develop on labeling amino acids reduces environment sensitivity. DANA was synthesized 6-(2-Dimethylaminonaphthoyl)alanine Cohen, B.E.; McAnaney, T.B.; Park, E.S.; Jan, Y.N.; Boxer, S.G.; Jan, L.Y. Science 2002, 296, 17001703. 50 Nitz, M.; Mezo, A. R.; Ali, M. H.; Imperiali, B. Chem. Commun. 2002, 1912-1913. APPLICATION OF DANA To monitor phosphorylation dependent binding of peptides to proteins: AcHN-Arg-Leu-ɸ-Arg-X-Leu-Pro-Ala-CONH2 ɸ = DANA Rothman, D. M.; Vazquez, M. E.; Vogel, E. M.; Imperali, B. Org. Lett. 2002, 4, 2865-2868. Vazquez, M. E.; Nitz, M.; Stehn, J.; Yaffee, M. B.; Imperiali, B. J. Am. Chem. Soc.2003, 125, 10150. 51 APPLICATION OF DANA X = SERINE 1. Unmodified serine 2. Phosphoserine 3. Caged phosphoserine 14-3-3 Proteins: Highly conserved family of proteins. Essential intermediates in cell cycle regulation. Phosphorylation dependent protein-protein interaction. Rothman, D. M.; Vazquez, M. E.; Vogel, E. M.; Imperali, B. Org. Lett. 2002, 4, 2865-2868. Vazquez, M. E.; Nitz, M.; Stehn, J.; Yaffee, M. B.; Imperiali, B. J. Am. Chem. Soc.2003, 125, 10150. 52 PHOSPHORYLATION DEPENDENT BINDING hν λ em1 = 522 nm 14-3-3 λ em2 = 501 nm 14-3-3 Rothman, D. M.; Vazquez, M. E.; Vogel, E. M.; Imperiali, B. Org. Lett. 2002, 4, 2865-2868. Vazquez, M. E.; Nitz, M.; Stehn, J.; Yaffee, M. B.; Imperiali, B. J. Am. Chem. Soc.2003, 125, 10150. 53 NDA Naphthalene-2,3-dicarboxaldehyde: Non fluorescent. Fluorescent derivatizing agent . Used for detection of primary amines in HPLC. Yang , Q.; Zhang, X-L.; Ma, M.; Huang, K-J.; Zhang, J-X.; Ni, W-Z.; Fang, C-X.; Zheng, C-Y. J.Chromatogr. A 2007, 1146,23-31. 54 DETECTION OF DEGRADATION PRODUCTS OF MELANIN Melanin: Color of skin, eye and hair in mammals is due to melanin. Uses: Powerful antioxidant. Photo protective pigment. Free radical scavengers. Yang , Q.; Zhang, X-L.; Ma, M.; Huang, K-J.; Zhang, J-X.; Ni, W-Z.; Fang, C-X.; Zheng, C-Y. J.Chromatogr. A 2007, 1146,23-31. 55 DEGRADATION PRODUCTS OF PHEOMELANIN 2 main degradation products 3-Amino-4-hydroxyphenylalanine hydroxyphenylalanine 4-Amino-3- Melanoma: melanocytes become malignant. Skin: cutaneous melanoma. Eyes: ocular melanoma. Yang , Q.; Zhang, X-L.; Ma, M.; Huang, K-J.; Zhang, J-X.; Ni, W-Z.; Fang, C-X.; Zheng, C-Y. J.Chromatogr. A 2007, 1146, 23-31. 56 DETECTION λ ex = 420 nm λ em = 490 nm Yang , Q.; Zhang, X-L.; Ma, M.; Huang, K-J.; Zhang, J-X.; Ni, W-Z.; Fang, C-X.; Zheng, C-Y. J.Chromatogr. A 2007, 1146,23-31. 57 SUMMARY Biomolecules important mediators of various physiological processes Number of short comings in the methods to detect biomolecules, fluorescent labels were used. Compounds with Oxygen heterocycle, Sulfur heterocycle, Nitrogen heterocycle and Naphthalene were used as organic fluorescent labels. Fluorophore + Biomolecules = Fluorescent derivative Use: Pre-column derivatization agent Metabolic products Degradation products 58 ACKNOWLEDGEMENTS Dr. Yan Zhang The Zhang Group Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University. 59