Fragment screening by SPR and advanced application to GPCRs

Progress in Biophysics and Molecular Biology

Volumn 116, Issue 2-3, 2014, Pages 113-123

  Shepherd, Claire A ^a   Hopkins, Andrew L ^a   Navratilova, Iva ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Biophysical screening; Fragment screening; G protein coupled receptors; GPCRs; Membrane proteins; SPR; Surface plasmon resonance

Indexed keywords

G PROTEIN COUPLED RECEPTOR;

ANIMAL; CHEMISTRY; DRUG SCREENING; HUMAN; METABOLISM; PROCEDURES; PROTEIN STABILITY; SURFACE PLASMON RESONANCE;

ANIMALS; DRUG EVALUATION, PRECLINICAL; HUMANS; PROTEIN STABILITY; RECEPTORS, G-PROTEIN-COUPLED; SURFACE PLASMON RESONANCE;

EID: 84923922485     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2014.09.008     Document Type: Article

References (60)

1. Andrews G., Jones C., Wreggett K.A. An intracellular allosteric site for a specific class of antagonists of the CC chemokine G protein-coupled receptors CCR4 and CCR5. Mol. Pharmacol. 2008, 73:855-867.
2. Aristotelous T., Ahn S., Shukla A.K., Gawron S., Sassano M.F., Kahsai A.W., Wingler L.M., Zhu X., Tripathi-Shukla P., Huang X.P., Riley J., Besnard J., Read K.D., Roth B.L., Gilbert I.H., Hopkins A.L., Lefkowitz R.J., Navratilova I. Discovery of beta 2 adrenergic receptor ligands using biosensor fragment screening of tagged wild-type receptor. ACS Med. Chem. Lett. 2013, 4:1005-1010.
3. Blundell T.L. Structure-based drug design. Nature 1996, 384:23-26.
4. Chen D., Errey J.C., Heitman L.H., Marshall F.H., Ijzerman A.P., Siegal G. Fragment screening of GPCRs using biophysical Methods: Identification of ligands of the adenosine A(2A) receptor with novel biological activity. ACS Chem. Biol. 2012, 7:2064-2073.
5. Chessari G., Woodhead A.J. From fragment to clinical candidate-a historical perspective. Drug Discov. Today 2009, 14:668-675.
6. Christopher J.A., Brown J., Doré A.S., Errey J.C., Koglin M., Marshall F.H., Myszka D.G., Rich R.L., Tate C.G., Tehan B., Warne T., Congreve M. Biophysical fragment screening of the β1-adrenergic receptor: identification of high affinity arylpiperazine leads using structure-based drug design. J.Med. Chem. 2013, 56:3446-3455.
7. Cole D.C., Olland A.M., Jacob J., Brooks J., Bursavich M.G., Czerwinski R., DeClercq C., Johnson M., Joseph-McCarthy D., Ellingboe J.W., Lin L., Nowak P., Presman E., Strand J., Tam A., Williams C.M., Yao S., Tsao D.H., Fitz L.J. Identification and characterization of acidic mammalian chitinase inhibitors. J.Med. Chem. 2010, 53(16):6122-6128.
8. Congreve M.S., Davis D.J., Devine L., Granata C., O'Reilly M., Wyatt P.G., Jhoti H. Detection of ligands from a dynamic combinatorial library by X-ray crystallography. Angew. Chem. Int. Ed. Engl. 2003, 42:4479-4482.
9. Congreve M., Chessari G., Tisi D., Woodhead A.J. Recent developments in fragment-based drug discovery. J.Med. Chem. 2008, 51:3661-3680.
10. Congreve M., Langmead C.L., Mason J.S., Marshall F.H. Progress in structure based drug design for G protein-coupled receptors. J.Med. Chem. 2011, 54:4283-42311.
11. Congreve M., Rich R.L., Myszka D.G., Figaroa F., Siegal G., Marshall F.H. Fragment screening of stabilized G-protein-coupled receptors using biophysical methods. Methods Enzymol. 2011, 493:115-136.
12. Dalvit C., Pevarello P., Tatò M., Veronesi M., Vulpetti A., Sundström M. Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J.Biomol. NMR. 2000, 18:65-68.
13. Danielson U.H. Fragment library screening and Lead characterization using SPR biosensors. Curr. Top. Med. Chem. 2009, 9(18):1725-1735.
14. Duong-Thi M.D., Meiby E., Bergström M., Fex T., Isaksson R., Ohlson S. Weak affinity chromatography as a new approach for fragment screening in drug discovery. Anal. Biochem. 2011, 414:138-146.
15. English A.C., Done S.H., Caves L.S., Groom C.R., Hubbard R.E. Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol. Proteins 1999, 37:628-640.
16. Fejzo J., Lepre C.A., Peng J.W., Bemis G.W., Ajay, Murcko M.A., Moore J.M. The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Chem. Biol. 1999, 6:755-769.
17. Freire E. Do enthalpy and entropy distinguish first in class from best in class?. Drug Discov. Today 2008, 13:869-874.
18. Geschwindner S., Olsson L.-L., Albert J.-S., Deinum J., Edwards P.D., de Beer T., Folmer R.H.A. Discovery of a novel warhead against β-secretase through fragment-based Lead generation. J.Med. Chem. 2007, 2007:24.
19. Giannetti A.M. From experimental design to validated hits a comprehensive walk-through of fragment lead identification using surface plasmon resonance. Methods Enzymol. 2011, 493:169.
20. Godemann R., Madden J., Krämer J., Smith M., Fritz U., Hesterkamp T., Barker J., Höppner S., Hallett D., Cesura A., Ebneth A., Kemp J. Fragment-based discovery of BACE1 inhibitors using functional assays. Biochemistry 2009, 48:10743-10751.
21. Hajduk P., Greer J. Adecade of fragment-based drug design: strategic advances and lessons learned. Nat. Rev. Drug Discov. 2007, 6:211-219.
22. Hann M.M., Leach A.R., Harper G. Molecular complexity and its impact on the probability of finding leads for drug discovery. J.Chem. Inf. Comput. Sci. 2001, 41:856-864.
23. Hopkins A.L., Groom C.R., Alex A. Ligand efficiency: a useful metric for lead selection. Drug Discov. Today. 2004, 9:430-431.
24. Hopkins A.L., Mason J.S., Overington J.P. Can we rationally design promiscuous drugs?. Curr. Opin. Struct. Biol. 2006, 16:127-136.
25. Houston J., Banks M., Binnie M., Brenner S., O'Connell J., Petrillo E. Case study: impact of technology investment on lead discovery at Bristol-Myers Squibb, 1998-2006. Drug Discov. Today 2008, 13:44-51.
26. Huber W. Anew strategy for improved secondary screening and lead optimization using high-resolution SPR characterization of compound-target interactions. J.Mol. Recognit. 2005, 19:273-281.
27. Huber W., Mueller F. Biomolecular interaction analysis in drug discovery using surface plasmon resonance technology. Curr. Pharm. Des. 2006, 12:3999-4021.
28. January B., Seibold A., Whaley B., Hipkin R.W., Lin D., Schonbrunn A., Barber R., Clark R.B. Beta2-adrenergic receptor desensitization, internalization, and phosphorylation in response to full and partial agonists. J.Biol. Chem. 1997, 272:23871-23879.
29. Kranz J.K., Schalk-Hihi C. Protein Thermal shifts to identify low molecular weight fragments. Fragment-based Drug Design - Tools, Practical Approaches, and Examples 2011, vol. 493:277-298. L.C. Kuo (Ed.).
30. Ladbury J.E., Klebe G., Freire E. Adding calorimetric data to decision making in lead discovery: a hot tip. Nat. Rev. Drug Discov. 2010, 9:23-27.
31. Lewis L.M., Engle L.J., Pierceall W.E., Hughes D.E., Shaw K.J. Affinity capillary electrophoresis for the screening of novel antimicrobial targets. J.Biomol. Screen. 2004, 9:303-308.
32. Magnani F., Shibata Y., Serrano-Vega M.J., Tate C.G. Co-evolving stability and conformational homogeneity of the human adenosine A2a receptor. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:10744-10749.
33. Mansfield R., Able S., Griffin P., Irvine B., James I., Macartney M., Miller K., Mills J., Napier C., Navratilova I., Perros M., Rickett G., Root H., van der Ryst E., Westby M., Dorr P. CCR5 pharmacology methodologies and associated applications. Methods Enzymol. 2009, 460:17-55.
34. Mayer M., Meyer B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chem. Int. Ed. 1999, 38:1784-1788.
35. Myszka D.G. Kinetic, equilibrium, and thermodynamic analysis of macromolecular interactions with BIACORE. Meth. Enzy. 2000, 323:325-332.
36. Navratilova I., Hopkins A.L. Fragment screening by surface plasmon resonance. ACS Med. Chem. Letts. 2010, 1:44-48.
37. Navratilova I., Sodroski J., Myszka D.G. Solubilization, stabilization, and purification of chemokine receptors using biosensor technology. Anal. Biochem. 2005, 339:271-281.
38. Navratilova I., Papalia G.A., Rich R.L., Bedinger D., Brophy S., Condon B., Deng T., Emerick A.W., Guan H.W., Hayden T., Heutmekers T., Hoorelbeke B., McCroskey M.C., Murphy M.M., Nakagawa T., Parmeggiani F., Qin X., Rebe S., Tomasevic N., Tsang T., Waddell M.B., Zhang F.F., Leavitt S., Myszka D.G. Thermodynamic benchmark study using Biacore technology. Anal. Biochem. 2007, 364:67-77.
39. Navratilova I., Besnard J., Hopkins A.L. Screening for GPCR ligands using surface plasmon resonance. ACS Med. Chem. Letts. 2011, 2:549-554.
40. Overington J.P., Al-Lazikani B., Hopkins A.L. How many drug targets are there?. Nat. Rev. Drug Discov. 2006, 5:993-996.
41. Papalia G.A., Leavitt S., Bynum M.A., Katsamba P.S., Wilton R., Qiu H., Steukers M., Wang S., Bindu L., Phogat S., Giannetti A.M., Ryan T.E., Pudlak V.A., Matusiewicz K., Michelson K.M., Nowakowski A., Pham-Baginski A., Brooks J., Tieman B.C., Bruce B.D., Vaughn M., Baksh M., Cho Y.H., Wit M.D., Smets A., Vandersmissen J., Michiels L., Myszka D.G. Comparative analysis of 10 small molecules binding to carbonic anhydrase II by different investigators using Biacore technology. Anal. Biochem. 2006, 359:94-105.
42. Papalia G.A., Giannetti A.M., Arora N., Myszka D.G. Thermodynamic characterization of pyrazole and azaindole derivatives binding to p38 mitogen-activated protein kinase using Biacore T100 technology and van't Hoff analysis. Anal. Biochem. 2008, 383:255-264.
43. Pereira D.A., Williams J.A. Origin and evolution of high throughput screening. Br. J. Pharmacol. 2007, 161:53-61.
44. Pollack S.J., Beyer K.S., Lock C., Müller I., Sheppard D., Lipkin M., Hardick D., Blurton P., Leonard P.M., Hubbard P.A., Todd D., Richardson C.M., Ahrens T., Baader M., Hafenbradl D.O., Hilyard K., Bürli R.W. Acomparative study of fragment screening methods on the p38a kinase: new methods, new insights. J.Comput. Aided Mol. Des. 2011, 10.1007/s10822-011-9454-9.
45. Pröll F., Fechner P., Günther Proll G. Direct optical detection in fragment-based screening. Anal. Bioanal. Chem. 2009, 393:1557-1562.
46. Rawlins P. Current trends in label-free technologies. Drug Discov. World 2010, 17-26.
47. Rich R.L., Errey J., Marshall F., Myszka D.G. Biacore analysis with stabilized G-protein-coupled receptors. Anal. Biochem. 2011, 409:267-272.
48. Robertson N., Jazayeri A., Errey J., Baig A., Hurrell E., Zhukov A., Langmead C.J., Weir M., Marshall F.H. The properties of thermostabilised G protein-coupled receptors (StaRs) and their use in drug discovery. Neuropharmacology 2011, 60:36-44.
49. Schulz M.N., Hubbard R.E. Recent progress in fragment-based lead discovery. Curr. Opin. Pharmacol. 2009, 9:615-621.
50. Serrano-Vega M.J., Magnani F., Shibata Y., Tate C.G. Conformational thermostabilization of the beta1-adrenergic receptor in a detergent-resistant form. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:877-882.
51. Shibata Y., White J., Serrano-Vega M., Magnani F., Aloia A., Grisshammer R., Tate C.G. Thermostabilization of the Neurotensin receptor NTS1. J.Mol. Biol. 2009, 390:262-277.
52. Shuker S.B., Hajduk P.J., Meadows R.P., Fesik S.W. Discovering high-affinity ligands for proteins: SAR by NMR. Science 1996, 274:1531-1534.
53. Spencer R. High-throughput screening of historic collections: observations on file size, biological targets, and file diversity. Biotechnol. Bioeng. Com. Chem.) 1998, 61:61-67.
54. Stoddart L.A., Vernall A.J., Denman J.L., Briddon S.J., Kellam B., Hill S.J. Fragment screening at adenosine-a(3) receptors in living cells using a fluorescence-based binding assay. Chem. Biol. 2012, 19:1105-1115.
55. Swinney D.C. Applications of binding kinetics to drug discovery: translation of binding mechanisms to clinically differentiated therapeutic responses. Pharm. Med. 2008, 22:23-34.
56. Vanwetswinkel S., Heetebrij R.J., van Duynhoven J., Hollander J.G., Filippov D.V., Hajduk P.J., Siegal G. TINS, target immobilized NMR screening: an efficient and sensitive method for ligand discovery. Chem. Biol. 2005, 12:2.
57. 3A. Bioorg. Med. Chem. Lett. 2011, 21:5460-5464.
58. Warne T., Moukhametzianov R., Baker J., Nehme R., Edwards P., Leslie A., Schertler G., Tate C. The structural basis for agonist and partial agonist action on a beta(1)-adrenergic receptor. Nature 2011, 469:241-244.
59. Warne T., Edwards P., Leslie A., Tate C. Crystal structures of a stabilized beta(1)-adrenoceptor bound to the Biased agonists Bucindolol and Carvedilol. Structure. 2012, 20:841-849.
60. Wermuth C.G. Analogues as means of discovering new drugs. Analog Based Drug Discovery 2006, John Wiley-VCH. J. Fischer, C.R. Ganellin (Eds.).