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21Tetko, IV, Tanchuk, VY, Kasheva, TN, Viaal, AEP. J. Chem. Inf. Comput. Sci., 2001, 41, 1488-1493. 22 Baurin, N, Aboul-Ela, F, Barril, X, Davis, B, Drysdale, M, Dymock, B, Finch, H, Fromont, C, Richardson, C, Simmonite, H, Hubbard, R. J. Chem. Inf. Comput. Sci., 2004, 44, 2157-2166. 23 Gianti, E, Sartori, L. J. Chem. Inform. Mod., 2008, 48, 2129-2139. 24 Siegal, G, AB, E, Schultz, J. Drug Dis. Today, 2007, 12, 1032-1039. 25 Akritopoulou-Zanze, I, Hajduk, PJ. Drug Discov. Today, 2009, 14, 291-297. 26 Fink, T, Reymond, JL. J. Chem. Inf. Model., 2007, 47, 342-353. 27 Roughley, SD, Hubbard, RH. J. Med Chem. 2011, 54, 3989-4005. 28 Schuffenhauer, A. Curr. Top. Med. Chem. 2005, 5, 751-762. 29 Hubbard, RE, Davis, B, Chen, I, Drysdale, MJ. Curr. Top. Med. Chem., 2007, 7, 1568. 30Tounge, BA, Parker, MH. Meth. in Enzym., 2011, 493, 3-20. 31 Shemetulskis, NE, Weininger, D, Blankley, CJ, Yang, JJ, Humblet, C. J. Chem. Inf. Comput. Sci., 1996, 36, 826-871. 32 Rogers, D, Hahn, M. J. Chem Inf. Model, 2010, 50, 742-754. 33 Darko, B. J. Chem. Inf. Comput. Sci. 1999, 39, 747-750. 34 Stoichet, BK et al. J. Med. Chem., 2002, 45, 8, 1712-1722. 35 Roeschlaub, CA, Redwood, CJ, Cross, DJ, Bridge, E, Green, S, Overfield, D, Evans, D. High- throughput technique for rapid measurement of fragment solubility, poster available at
www.maybridge.com. 36 Congreve, M, Rich, RL, Myszka, DG, Siegal, G, Marshall, F. Methods Enzymol., 2011, 493, 115-136. 37 Rich, RL, Myszka, DG. Anal. Biochem., 2010, 402, 170-178. 38 Rich, RL, Myszka, DG. Anal. Biochem., 2007, 361, 1-6. 39 Rich, RL, Quinn, JG, Morton, T, Stepp, JD, Myszka, DG. Anal. Biochem. 2010, 407, 270-277.
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target surface (Figure 4C). The data for many of the apparent binders actually lie along a diagonal indicating they bind similarly to both proteins. Compounds in this region are not worth following up on, as they do not show specificity. The most interesting compounds will lie off the diagonal. The closer to the axis they are, the more specific they will be (note the positions of the highly selec- tive positive-control compounds). The number of binders to choose for follow-up analyses will of course vary depending on the library and the tar- get, but it is the quality not the quantity of poten- tial hits that really matter at this stage. Often proj- ect teams find that the hits identified in SPR screens do not show up as reliable binders in struc- tural analyses. This is a result of poor hit selection in the screen. Too often investigators flag all com- pounds that show target binding as hits, but only later find that most of their hits are non-specific binders. By including an off-target or secondary target in the analysis, and plotting the responses in a versus plot, it is easy to identify fragments that bind specifically to one target and to disregard those fragments that are not selective.
Follow-up concentration-dependent studies. Follow- up assays of the selected hits are typically run in full concentration series to demonstrate the binding is stoichiometric and establish affinity of the fragment. While ranking hits by their relative affinities may be useful at this point in the discovery process, frag- ments that bind stoichiometrically provide the high- est likelihood for success in structural analysis.
Follow-up competition studies. It is possible to carry out competition studies using the biosensor to identify potential binding sites for hits from a screen. In these blocking experiments, the hits are tested for binding in the presence of a saturating concentration of a known binder. This added infor- mation about whether a fragment is competitive or non-competitive for known site binders can further help identify which compounds to pursue in struc- tural analyses and hit optimisation programmes.
Fragment-based SAR. Often structural analogues of potential hits may be present in the library or available as part of a larger compound collection. Given the speed of the biosensor methodology, typ- ically an analysis of existing analogues can provide additional insight into the structure activity rela- tionship for a particular framework to aid in the selection process. It is also not uncommon to find more potent fragments even within a small collec- tion of analogues.
After choosing a well-behaved library and estab- lishing the activity and stability of a target and control protein, SPR-based fragment screening and follow-up studies are relatively straightforward. The most significant challenge is hit selection. Wisely choosing which fragments are indeed worth pursuing in downstream analyses requires careful evaluation of the responses obtained for the entire library from the target, control protein and refer- ence surfaces.
Conclusions
The pharmaceutical industry faces unprecedented challenges in small molecule drug discovery. Low hit rates from HTS screens and high attrition of subse- quent lead candidates have lead Medicinal Chemists to seek other ways of identifying progressable hit compounds. Fragment screening permits a much larger chemical space to be probed by screening a relatively low number of diverse fragments and yields hits that can be readily optimised into potent leads, while still maintaining ‘drug-likeness’. The success of the screen ultimately depends on the design of the fragment library. Aqueous solu- bility is a key consideration, as compounds are screened at very high concentrations in order to detect weak binding. Fragment libraries are being actively enhanced to support recent advancements in biosensor screening technologies that have now increased the feasibility of higher sensitivity screen- ing of larger numbers of compounds against multi- ple targets.
DDW
Dr David Myszka is the Director of Biosensor Tools LLC, a contract services and consulting firm with a focus on biosensor-based drug discovery. Over the past 18 years he has published more than 150 research articles and reviews on biosensor technology. Further information can be obtained at
www.biosensortools.com.
Dr Jane Paul is the Maybridge Value Stream Manager and overseas the development of the Maybridge Ro3 Library. Previously she was a Chemistry Team Leader responsible for generating New Building Blocks and screening compounds for the Maybridge portfolio. Prior to joining Thermo Fisher Scientific in 1999, Jane spent four years at Chiroscience Ltd and carried out post- doctoral research at The Novartis Institute of Medical Sciences.
Drug Discovery World Winter 2011/12
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