Crossing borders to bind proteins-a new concept in protein recognition based on the conjugation of small organic molecules or short peptides to polypeptides from a designed set

Analytical and Bioanalytical Chemistry

Volumn 400, Issue 6, 2011, Pages 1653-1664

  Baltzer, Lars ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Affinity; Binder technology; Diagnostics; Molecular recognition; Polypeptide; Protein; Specificity

Indexed keywords

, INHIBITOR; ACETYLCHOLINE ESTERASE; AFFINITY; BINDER CONCEPTS; C-REACTIVE PROTEINS; DIAGNOSTICS; DRUG DEVELOPMENT; ENZYME SUBSTRATES; FOUR-ORDER; HIGH AFFINITY; HIGH-AFFINITY BINDERS; HUMAN CARBONIC ANHYDRASE II; HUMAN SERUM; MRNA-DISPLAY; PHAGE DISPLAY; PHOSPHORYLATED PROTEINS; PROTEIN RECOGNITION; PROTEIN SEPARATIONS; PROTEIN TARGETS; SMALL MOLECULES; SMALL ORGANIC MOLECULES; SMALL-MOLECULE LIBRARY; SPECIFICITY; THREE-DIMENSIONAL STRUCTURE; THYMIDINE KINASE;

ANTIBODIES; BINDERS; CARBONIC ANHYDRASE; HIGH ENERGY PHYSICS; LAKES; LIBRARIES; MEDICAL IMAGING; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; MOLECULES; PEPTIDES; PHOSPHORYLATION; POLYPEPTIDES;

DIMERS;

ORGANIC COMPOUND; PEPTIDE; PROTEIN;

CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; ISOLATION AND PURIFICATION; REVIEW;

HUMANS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; ORGANIC CHEMICALS; PEPTIDES; PROTEINS;

EID: 79956267309     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-011-4905-7     Document Type: Review

References (51)

1. CAK Borrebaeck 2000 Antibodies in diagnostics - from immunoassays to protein chips Immunol Today 21 379 382 10.1016/S0167-5699(00)01683-2 1:CAS:528:DC%2BD3cXlsVOqsL8%3D (Pubitemid 30612298)
2. Dübel S (2007) Handbook of Therapeutic Antibodies. Wiley-VCH, Weinheim
3. JS Huston AJ George 2001 Engineered antibodies take center stage Hum Antibodies 10 127 142 1:CAS:528:DC%2BD38XislCitLY%3D (Pubitemid 34258592)
4. CE Hagemeyer MC von Zur D von Elverfeldt K Peter 2009 Single-chain antibodies as diagnostic tools and therapeutic agents Thromb Haemost 101 1012 1019 1:CAS:528:DC%2BD1MXos1aktLY%3D
5. MT Stumpp P Amstutz 2007 DARPins: a true alternative to antibodies Curr Opin Drug Discov Dev 10 153 159 1:CAS:528:DC%2BD2sXktVOntr4%3D (Pubitemid 46438644)
6. J Feldwisch V Tolmachev C Lendel N Herne A Sjöberg B Larsson D Rosik E Lindqvist G Fant I Höjden-Guthenberg J Galli P Jonasson L Abrahmsen 2010 Design of an optimized scaffold for affibody molecules J Mol Biol 398 232 247 10.1016/j.jmb.2010.03.002 1:CAS:528:DC%2BC3cXkvFeksbw%3D
7. D Schönfeld G Matschiner L Chatwell S Trentmann H Gille M Hulsmeyer N Brown PM Kaye S Schlehuber AM Hohlbaum A Skerra 2009 An engineered lipocalin specific for CTLA-4 reveals a combining site with structural and conformational features similar to antibodies Proc Natl Acad Sci USA 106 8198 8203 10.1073/pnas.0813399106
8. DHJ Bunka PG Stockley 2006 Aptamers come of age - at last Nat Rev Microbiol 4 588 596 10.1038/nrmicro1458 1:CAS:528:DC%2BD28XmvFamtbw%3D (Pubitemid 44317021)
9. CA Lipinski F Lombardo BW Dominy PJ Feeney 1997 Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings Adv Drug Deliv Rev 23 3 25 10.1016/S0169-409X(96)00423-1 1:CAS:528:DyaK2sXktlKlsQ%3D%3D (Pubitemid 27046991)
10. EM Driggers SP Hale J Lee NK Terrett 2008 The exploration of macrocycles for drug discovery-an underexploited structural class Nat Rev Drug Discov 7 608 624 10.1038/nrd2590 1:CAS:528:DC%2BD1cXnvFShsbc%3D (Pubitemid 351927725)
11. VJ Hruby 2002 Designing peptide receptor agonists and antagonists Nature Rev Drug Disc 1 847 858 10.1038/nrd939 1:CAS:528:DC%2BD38XotleqtLg%3D (Pubitemid 37361580)
12. LT Tegler G Nonglaton F Büttner K Caldwell T Christopeit UH Danielson K Fromell T Gossas A Larsson P Longati T Norberg R Ramapanicker J Rydberg L Baltzer 2011 Powerful protein binders from designed polypeptides and small organic molecules-a general concept for protein recognition Angew Chem Int Ed 50 1823 1827 10.1002/anie.201005059 1:CAS:528:DC%2BC3MXitVOht7g%3D
13. L Baltzer 2007 Polypeptide conjugate binders for protein recognition Top Curr Chem 277 89 106 10.1007/128-2007-129 1:CAS:528:DC%2BD2sXhtVSrurrF
14. LT Tegler K Fromell B-H Jonsson J Viljanen C Winander J Carlsson L Baltzer 2011 Polypeptide conjugate binders that discriminate between two isoforms of human Carbonic Anhydrase in human blood Chembiochem 12 559 566 10.1002/cbic.201000556 1:CAS:528:DC%2BC3MXisVemsL4%3D
15. T Andersson M Lundquist GT Dolphin K Enander B-H Jonsson JW Nilsson L Baltzer 2005 Cooperative binding of human Carbonic Anhydrase II by functionalized folded polypeptide receptors Chem Biol 12 1245 1252 10.1016/j.chembiol.2005.08.018 1:CAS:528:DC%2BD2MXht1aqu73L (Pubitemid 41628260)
16. Fersht A (1999) A Guide to Enzyme Catalysis and Protein Folding, W. H. Freeman and Company, New York, chap 11
17. S Olofsson G Johansson L Baltzer 1995 Design, Synthesis and Solution Structure of a Helix-Loop-Helix Dimer-a Template for the Rational Design of Catalytically Active Polypeptides J Chem Soc Perkin Trans 2 21047 2056
18. L Baltzer H Nilsson J Nilsson 2001 De novo design of proteins - What are the rules? Chem Rev 101 3153 3163 10.1021/cr0000473 1:CAS:528: DC%2BD3MXmvVKjtrg%3D (Pubitemid 35377815)
19. AK Dunker I Silman VN Uversky JL Sussman 2008 Function and structure of inherently disordered proteins Curr Opin Struct Biol 18 756 764 10.1016/j.sbi.2008.10.002 1:CAS:528:DC%2BD1cXhsVOisr%2FK
20. PJ Hajduk 2006 SAR by NMR: putting the pieces together Mol Interv 6 266 272 10.1124/mi.6.5.8 1:CAS:528:DC%2BD28Xht1ehs7vE (Pubitemid 44556047)
21. C Dalvit M Fasolini M Flocco S Knapp P Pevarello M Veronesi 2002 NMR-Based Screening with Competition Water∈-∈Ligand Observed via Gradient Spectroscopy Experiments: Detection of High-Affinity Ligands J Med Chem 45 2610 2614 10.1021/jm011122k 1:CAS:528:DC%2BD38XjsVygtL4%3D (Pubitemid 34595231)
22. L Gold 2001 mRNA display: Diversity matters during in vitro selection Proc Nat Acad Sci USA 98 4825 4826 10.1073/pnas.091101698 1:CAS:528: DC%2BD3MXjt1Ogt7Y%3D (Pubitemid 32397039)
23. GP Smith VA Petrenko 1997 Phage Display Chem Rev 97 391 410 10.1021/cr960065d 1:CAS:528:DyaK2sXhslamtb8%3D (Pubitemid 127659250)
24. AP Laudano RF Doolittle 1980 Studies on synthetic peptides that bind to fibrinogen and prevent fibrin polymerization. Structural requirements, number of binding sites, and species differences Biochemistry 19 1013 1019 10.1021/bi00546a028 1:CAS:528:DyaL3cXht1Gqs7w%3D (Pubitemid 10112241)
25. K Enander GT Dolphin LK Andersson I Lundström B Liedberg L Baltzer 2002 Designed, folded polypeptide scaffolds that combine key biosensing events of recognition and reporting J Org Chem 67 3120 3123 10.1021/jo010954n 1:CAS:528:DC%2BD38XisVeks74%3D (Pubitemid 34457275)
26. K Enander GT Dolphin L Baltzer 2004 Designed, functionalized helix-loop-helix motifs that bind human Carbonic Anhydrase II - a new class of synthetic receptor molecules J Am Chem Soc 126 4464 4465 10.1021/ja038799c 1:CAS:528:DC%2BD2cXitFekt7g%3D (Pubitemid 38469064)
27. K Enander GT Dolphin B Liedberg I Lundström L Baltzer 2004 A versatile polypeptide platform for integrated recognition and reporting-affinity arrays for protein-ligand interaction analysis Chem Eur J 10 2375 2385 10.1002/chem.200305391 1:CAS:528:DC%2BD2cXksFCrsbk%3D
28. J Westhuyzen H Healy 2000 Biology and relevance of C-reactive protein in cardiovascular and renal disease Ann Clin Lab Sci 30 133 143 1:CAS:528:DC%2BD3cXjt1CqtLc%3D
29. S Verma PE Szmitko PM Ridker 2005 C-reactive protein comes of age Nat Clin Pract Cardiovasc Med 2 29 36 10.1038/ncpcardio0074 1:CAS:528: DC%2BD2MXlslGmt7o%3D (Pubitemid 40823207)
30. D Thompson MB Pepys SP Wood 1999 The physiological structure of human C-reactive protein and its complex with phosphocholine Structure 7 169 177 10.1016/S0969-2126(99)80023-9 1:CAS:528:DyaK1MXhsFeltLk%3D (Pubitemid 29159702)
31. T Christopeit T Gossas UH Danielson 2009 Characterization of Ca2+ and phosphocholine interactions with C-reactive protein Anal Biochem 391 39 44 10.1016/j.ab.2009.04.037 1:CAS:528:DC%2BD1MXntVSisL0%3D
32. RC Renauld H Xuereb 2003 Vision impairment therapies Nat Rev Drug Discov 2 425 426 10.1038/nrd1113 (Pubitemid 37361722)
33. S Parkkila J Lasota JA Fletcher W Ou AJ Kivelä K Nuorva A-K Parkkila J Ollikainen WS Sly A Waheed S Pastorekova J Pastorek J Isola M Miettinen 2010 Carbonic anhydrase II. A novel biomarker for gastrointestinal stromal tumors Mod Path 23 743 750 10.1038/modpathol.2009.189 1:CAS:528:DC%2BC3cXlsFSjtLw%3D
34. PW Taylor RW King ASV Burgen 1970 Kinetics of complex formation between human carbonic anhydrases and aromatic sulfonamides Biochemistry 9 2638 2645 10.1021/bi00815a012 1:CAS:528:DyaE3cXks1aku7Y%3D
35. HA Krebs 1948 Inhibition of carbonic anhydrase by sulphonamides Biochem J 43 525 528 1:CAS:528:DyaH1MXitVWjsg%3D%3D
36. J-Y Winum D Vullo A Casini J-L Montero A Scozzafava CT Supuran 2003 Carbonic Anhydrase Inhibitors. Inhibition of Cytosolic Isozymes I and II and Transmembrane, Tumor-Associated Isozyme IX with Sulfamates Including EMATE Also Acting as Steroid Sulfatase Inhibitors J Med Chem 46 2197 2204 10.1021/jm021124k 1:CAS:528:DC%2BD3sXjtFagtrk%3D (Pubitemid 36583498)
37. MC Jeckling S Schauer CE Dumelin R Zenobi 2009 Label-free determination of protein-ligand binding constants using mass spectrometry and validation using surface plasmon resonance and isothermal titration calorimetry J Mol Recog 22 319 329 10.1002/jmr.951
38. S Holdenrieder J von Pawel T Duell K Feldmann H Raith A Schollen D Nagel P Stieber 2010 Clinical Relevance of Thymidine Kinase for the Diagnosis, Therapy Monitoring and Prognosis of Non-οperable Lung Cancer Anticancer Res 30 1855 1862 1:CAS:528:DC%2BC3cXhtVWmu73P
39. SS Adam NS Key CS Greenberg 2009 D-dimer antigen: current concepts and future prospects Blood 113 2878 2887 10.1182/blood-2008-06-165845 1:CAS:528:DC%2BD1MXktFWnsLk%3D
40. Ramapanicker R, Sun X, Viljanen J, Baltzer L (2011) Boosting the affinity of a tetrapeptide by polypeptide conjugation in the molecular recognition of the D-dimer. submitted for publication
41. Marks F (1996) Protein Phosphorylation. Wiley-VCH, New York
42. Ślósarczyk AT, Baltzer L (2011) The molecular recognition of phosphorylated proteins by designed polypeptides conjugated to a small molecule that binds phosphate. Submitted for publication
43. A Mangalum RC Smith 2009 Label-free determination of protein-ligand binding constants using mass spectrometry and validation using surface plasmon resonance and isothermal titration calorimetry Tetrahedron 65 4298 4303 10.1016/j.tet.2009.03.051 1:CAS:528:DC%2BD1MXltl2htbc%3D
44. K Fromell G Hulting A Ilichev A Larsson KC Caldwell 2007 Particulate platform for bioluminescent immunosensing Anal Chem 79 8601 8607 10.1021/ac0715118 1:CAS:528:DC%2BD2sXhtVKgtbvN (Pubitemid 350171369)
45. Fromell K, Karlsson M, Forsberg P, Nikolajeff F, Baltzer L (2011) Designed protein binders in combination with nano crystalline diamond for use in high-sensitivity biosensors. Submitted for publication
46. W Leung CPY Chan M Leung K Lehmann I Renneberg M Lehmann A Hempel JFC Glatz R Renneberg 2005 Novel.,digital-style" rapid test simultaneously detecting heart attack and predicting cardiovascular disease risk Anal Lett 38 423 439 1:CAS:528:DC%2BD2MXis1ylsbc%3D (Pubitemid 40470179)
47. D Aili R Selegard L Baltzer K Enander B Liedberg 2009 Colorimetric Protein Sensing by Controlled Assembly of Gold Nanoparticles Functionalized with Synthetic Receptors Small 5 2445 2452 10.1002/smll.200900530 1:CAS:528:DC%2BD1MXhtlGhsrfP
48. Schmitt HM, Brecht A, Piehler J, Gauglitz G (1997) An integrated system for optical biomolecular interaction analysis. Elsevier Advanced Technology, 809- 816
49. C Albrecht P Fechner D Honcharenko L Baltzer G Gauglitz 2010 A new assay design for clinical diagnostics based on alternative recognition elements Biosens Bioelectron 25 2302 2308 10.1016/j.bios.2010.03.022 1:CAS:528: DC%2BC3cXlvVegs7o%3D
50. Q Zhang T Norberg J Bergquist L Baltzer 2010 Synthesis of C-11 linked active ester derivatives of vitamin D-3 and their conjugations to 42-residue helix loop helix peptides Tetrahedron 19 4577 4586 10.1016/j.tet.2010.04.051
51. D Seebach M Overhand FNM Kühnle B Martinoni L Oberer U Hommel H Widmer 1996 β-Peptides: Synthesis by Arndt-Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X-ray crystallography. Helical secondary structure of a β-hexapeptide in solution and its stability towards pepsin Helv Chim Acta 79 913 941 10.1002/hlca.19960790402 1:CAS:528:DyaK28XktlOlt78%3D (Pubitemid 26200956)