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4 - NMR in fragment-based drug discovery

from PART I - STRUCTURAL BIOLOGY

Published online by Cambridge University Press:  06 July 2010

By
Christopher A. Lepre ,
Peter J. Connolly  and
Jonathan M. Moore
Edited by
Kenneth M. Merz, Jr ,
Dagmar Ringe  and
Charles H. Reynolds
Kenneth M. Merz, Jr
Affiliation:
University of Florida
Dagmar Ringe
Affiliation:
Brandeis University, Massachusetts
Charles H. Reynolds
Affiliation:
Johnson & Johnson Pharmaceutical Research & Development
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Summary

AN INTRODUCTION TO FRAGMENT-BASED LEAD DISCOVERY

For decades, molecular starting points for drug discovery have been found by screening large numbers of natural and synthetic compounds for biological activity in phenotypic and biochemical assays. Then, beginning in the mid to late 1990s, several pharmaceutical groups developed new approaches [such as structure/activity relationship by nuclear magnetic resonance (SAR by NMR), the SHAPES strategy, and needle screening] in which simple, low-molecular-weight compounds were screened for binding to the target of interest, and these relatively weak binding molecules were then used to systematically construct larger, more potent, drug leads. Such small screening molecules are now commonly called fragments and the related processes collectively called fragment-based lead discovery (FBLD).

NMR was the first experimental method used to screen fragments, and although a variety of other techniques (including x-ray crystallography, surface plasmon resonance, high concentration bioassays, and mass spectroscopy) have also been applied, NMR is still the most widely used. This chapter reviews the use of NMR for FBLD, beginning with an explanation of the principles behind fragment screening. NMR screening methods are then described, followed by a series of examples that illustrate the process through which fragment screening hits are converted into leads.

Type
Chapter
Information
Drug Design
Structure- and Ligand-Based Approaches
 , pp. 41 - 58
Publisher: Cambridge University Press
Print publication year: 2010

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References

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.Google Scholar
Fejzo, J.; et al. The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Chem. Biol. 1999, 6, 755–769.Google Scholar
Boehm, H. J.; et al. Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. J. Med. Chem. 2000, 43, 2664–2674.Google Scholar
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeny, P. J.Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 1997, 23, 3–25.Google Scholar
Teague, S. J.; Davis, A. M.; Leeson, P.D.; Oprea, T.The design of leadlike combinatorial libraries. Angew. Chem. Int. Ed. 1999, 38, 3743–3747.Google Scholar
Oprea, T. I.; Davis, A. M.; Teague, S. J.; Leeson, P. D.Is there a difference between leads and drugs? A historical perspective. J. Chem. Inf. Comput. Sci. 2001, 41, 1308–1315.Google Scholar
Bemis, G. W.; Murcko, M. A.The properties of known drugs. 1. Molecular frameworks. J. Med. Chem. 1996, 39, 2887–2893.Google Scholar
Lewell, X. Q.; Judd, D. B.; Watson, S. P.; Hann, M. M.RECAP – retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J. Chem. Inf. Comput. Sci. 1998, 38, 511–522.Google Scholar
Congreve, M.; Carr, R.; Murray, C.; Jhoti, H.A ‘rule of three’ for fragment-based lead discovery?Drug Discov. Today 2003, 8, 876–877.Google Scholar
Hann, M. M.; Oprea, T. I.Pursuing the leadlikeness concept in pharmaceutical research. Curr. Opin. Chem. Biol. 2004, 8, 255–263.Google Scholar
Lepre, C. A.; Moore, J. M.; Peng, J. W.Theory and applications of NMR-based screening in pharmaceutical research. Chem. Rev. 2004, 104, 3641–3676.Google Scholar
Schuffenhauer, A.; et al. Library design for fragment based screening. Curr. Top. Med. Chem. 2005, 5, 751–762.Google Scholar
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.Google Scholar
Shoichet, B. K.Interpreting steep dose-response curves in early inhibitor discovery. J. Med. Chem. 2006, 49, 7274–7277.Google Scholar
Siegal, G.; Ab, E.; Schultz, J.Integration of fragment screening and library design. Drug Discov. Today 2007, 12, 1032–1039.Google Scholar
Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J.Recent developments in fragment-based drug discovery. J. Med. Chem. 2008, 51, 3661–3680.Google Scholar
Leeson, P. D.; Springthorpe, B.The influence of drug-like concepts on decision-making in medicinal chemistry. Nat. Rev. Drug Discov. 2007, 6, 881–890.Google Scholar
Bohacek, R. S.; McMartin, C.; Guida, W. C.The art and practice of structure-based drug design: a molecular modeling perspective. Med. Res. Rev. 1996, 16, 3–50.Google Scholar
Lipinski, C. A.Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods 2000, 44, 235–249.Google Scholar
Fink, T.; Reymond, J. L.Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery. J. Chem. Inf. Model 2007, 47, 342–353.Google Scholar
Lepre, C. A.Library design for NMR-based screening. Drug. Discov. Today 2001, 6, 133–140.Google Scholar
Lepre, C. A.Strategies for NMR screening and library design. In: BioNMR Techniques in Drug Research, Zerbe, O.; Ed. Weinheim: Wiley-VCH; 2002, 1349–1364.
Jacoby, E.; Davies, J.; Blommers, M. J.Design of small molecule libraries for NMR screening and other applications in drug discovery. Curr. Top. Med. Chem. 2003, 3, 11–23.Google Scholar
Baurin, N., et al. Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets. J. Chem. Inf. Comput. Sci. 2004, 44, 2157–2166.Google Scholar
Hubbard, R. E.; Davis, B.; Chen, I.; Drysdale, M. J.The SeeDs approach: integrating fragments into drug discovery. Curr. Top. Med. Chem. 2007, 7, 1568–1581.Google Scholar
Hartshorn, M. J.; et al. Fragment-based lead discovery using X-ray crystallography. J. Med. Chem. 2005, 48, 403–413.Google Scholar
Blaney, J.; Nienaber, V.; Burley, S.Fragment-based lead discovery and optimisation using X-ray crystallography, computational chemistry, and high-throughput organic synthesis. In: Fragment-Based Approaches in Drug Discovery: Methods and Principles in Medicinal Chemistry, Vol. 34, Jahnke, W.; Erlanson, D.; Eds. Wennheim: Wiley–VCH; 2006, 215–248.
Albert, J. S.; et al. An integrated approach to fragment-based lead generation: philosophy, strategy and case studies from AstraZeneca's drug discovery programmes. Curr. Top. Med. Chem. 2007, 7, 1600–1629.Google Scholar
Bogan, A. A.; Thorn, K. S.Anatomy of hot spots in protein interfaces. J. Mol. Biol. 1998, 280, 1–9.Google Scholar
Clackson, T.; Wells, J. A.A hot spot of binding energy in a hormone-receptor interface. Science 1995, 267, 383–386.Google Scholar
Moreira, I. S.; Fernandes, P. A.; Ramos, M. J.Hot spots–a review of the protein-protein interface determinant amino-acid residues. Proteins 2007, 68, 803–812.Google Scholar
Reichmann, D.; et al. Binding hot spots in the TEM1-BLIP interface in light of its modular architecture. J. Mol. Biol. 2007, 365, 663–679.Google Scholar
Rejto, P. A.; Verkhivker, G. M.Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8945–8950.Google Scholar
Ciulli, A.; Williams, G.; Smith, A. G.; Blundell, T. L.; Abell, C.Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods. J. Med. Chem. 2006, 49, 4992–5000.Google Scholar
Hajduk, P. J.; Huth, J. R.; Fesik, S. W.Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem. 2005, 48, 2518–2525.Google Scholar
Lobley, C. M.; et al. The crystal structure of Escherichia coli ketopantoate reductase with NADP+ bound. Biochemistry 2005, 44, 8930–8939.Google Scholar
Murray, C. W.; Verdonk, M. L.The consequences of translational and rotational entropy lost by small molecules on binding to proteins. J. Comput. Aided Mol. Des. 2002, 16, 741–753.Google Scholar
Page, M. I.; Jencks, W. P.Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. Proc. Natl. Acad. Sci. U.S.A. 1971, 68, 1678–1683.Google Scholar
Hajduk, P. J.; Greer, J.A decade of fragment-based drug design: strategic advances and lessons learned. Nat. Rev. Drug Discov. 2007, 6, 211–219.Google Scholar
Hopkins, A. L.; Groom, C. R.; Alex, A.Ligand efficiency: a useful metric for lead selection. Drug Discov. Today 2004, 9, 430–431.Google Scholar
Abad-Zapatero, C.; Metz, J. T.Ligand efficiency indices as guideposts for drug discovery. Drug Discov. Today 2005, 10, 464–469.Google Scholar
Hajduk, P. J.Fragment-based drug design: how big is too big?J. Med. Chem. 2006, 49, 6972–6976.Google Scholar
Reynolds, C. H.; Tounge, B. A.; Bembenek, S. D.Ligand binding efficiency: trends, physical basis, and implications. J. Med. Chem. 2008, 51, 2432–243.Google Scholar
Vieth, M.; et al. Characteristic physical properties and structural fragments of marketed oral drugs. J. Med. Chem. 2004, 47, 224–232.Google Scholar
Wenlock, M. C.; Austin, R. P.; Barton, P.; Davis, A. M.; Leeson, P. D.A comparison of physiochemical property profiles of development and marketed oral drugs. J. Med. Chem. 2003, 46, 1250–1256.Google Scholar
Dill, K. A.Additivity principles in biochemistry. J. Biol. Chem. 1997, 272, 701–704.Google Scholar
Jencks, W. P.On the attribution and additivity of binding energies. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 4046–4050.Google Scholar
Hajduk, P. J.; Huth, J. R.; Sun, C.SAR by NMR: an analysis of potency gains realized through fragment-linking and fragment elaboration strategies for lead generation. In: Fragment-Based Approaches in Drug Discovery, Jahnke, W.; Erlanson, D. A.; Eds. Wennheim: Wiley-VCH; 2006, 181–192.
Hajduk, P. J.; Meadows, R. P.; Fesik, S. J.NMR-based screening in drug discovery. Q. Rev. Biophys. 1999, 32, 211–240.Google Scholar
Moore, J. M.NMR screening in drug discovery. Curr. Opin. Biotechnol. 1999, 10, 54–58.Google Scholar
Pellecchia, M.; Sem, D. S.; Wuthrich, K.NMR in drug discovery. Nat. Rev. Drug Discov. 2002, 1, 211–219.Google Scholar
Peng, J. W.; Moore, J. M.; Abdul-Manan, N.NMR experiments for lead generation in drug discovery. Prog. Nucl. Mag. Reson. Spectrosc. 2004, 44, 225–256.Google Scholar
Roberts, G. C.Applications of NMR in drug discovery. Drug Discov. Today 2000, 5, 230–240.Google Scholar
Stockman, B.; Dalvit, C.NMR screening techniques in drug discovery and drug design. Prog. Nucl. Mag. Reson. Spectrosc. 2002, 41, 187–231.Google Scholar
Dongen, M.; Weigelt, J.; Uppenberg, J.; Schultz, J.; Wikstrom, M.Structure-based screening and design in drug discovery. Drug Discov. Today 2002, 7, 471–478.Google Scholar
Wyss, D. F.; McCoy, M. A.; Senior, M. M.NMR-based approaches for lead discovery. Curr. Opin. Drug Discov. Devel. 5, 630–647.
Ross, A.; Schlotterbeck, G.; Klaus, W.; Senn, H.Automation of NMR measurements and data evaluation for systematically screening interactions of small molecules with target proteins. J. Biomol. NMR 2000, 16, 139–146.Google Scholar
Salzmann, M.; Pervushin, K.; Wider, G.; Senn, H.; Wuthrich, K.TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 13585–13590.Google Scholar
Weigelt, J.; Dongen, M.; Uppenberg, J.; Schultz, J.; Wikström, M.Site-selective screening by NMR spectroscopy with labeled amino acid pairs. J. Am. Chem. Soc. 2002, 124, 2446–2447.Google Scholar
Grzesiek, S.; Bax, A.Improved 3D triple-resonance NMR techniques applied to a 31 kDa protein. J. Magn. Reson. 1992, 96, 432–440.Google Scholar
Ikura, M.; Kay, L.E.; Bax, A.A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry 1990, 29, 4659–4667.Google Scholar
Hohwy, M.; et al. Novel prostaglandin D synthase inhibitors generated by fragment-based drug design. J. Med. Chem. 2008, 51, 2178–2186.Google Scholar
Mayer, M.; Meyer, B.Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chem. Int. Ed. 1999, 38, 1784–1788.Google Scholar
Claasen, B.; Axmann, M.; Meinecke, R.; Meyer, B.Direct observation of ligand binding to membrane proteins in living cells by a saturation transfer double difference (STDD) NMR spectroscopy method shows a significantly higher affinity of integrin alpha(IIb)beta3 in native platelets than in liposomes. J. Am. Chem. Soc. 2005, 127, 916–919.Google Scholar
Meinecke, R.; Meyer, B.Determination of the binding specificity of an integral membrane protein by saturation transfer difference NMR: RGD peptide ligands binding to integrin αIIbβ. J. Am. Chem. Soc. 2001, 44, 3059–3065.Google Scholar
Dalvit, C.; Fogliatto, G.; Stewart, A.; Veronesi, M.; Stockman, B.WaterLOGSY as a method for primary NMR screening: practical aspects and range of applicability. J. Biomol. NMR 2001, 21, 349–359.Google Scholar
Dalvit, C.; et al. Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J. Biomol. NMR 2000, 18, 65–68.Google Scholar
Johnson, E. C.; Feher, V. A.; Peng, J. W.; Moore, J. M.; Williamson, J. R.Application of NMR SHAPES screening to an RNA target. J. Am. Chem. Soc. 2003, 125, 15724–15725.Google Scholar
Lepre, C. A.; et al. Applications of SHAPES screening in drug discovery. Comb. Chem. High Throughput Screen. 2002, 5, 583–590.Google Scholar
Lin, M. L.; Shapiro, M. J.; Wareing, J. R.Diffusion-edited NMR: affinity NMR for direct observation of molecular interactions. J. Am. Chem. Soc. 1997, 119, 5349–5250.Google Scholar
Bleicher, K.; Lin, M.; Shapiro, M.; Wareing, J.Diffusion edited NMR: screening compound mixtures by affinity NMR to detect binding ligands to vancomycin. J. Org. Chem. 1998, 63, 8486–8490.Google Scholar
Hajduk, P. J.; Olejniczak, E. T.; Fesik, S. W.One-dimensional relaxation- and diffusion-edited NMR methods for screening compounds that bind to macromolecules. J. Am. Chem. Soc. 1997, 119, 12257–12261.Google Scholar
Jahnke, W.; et al. Second-site NMR screening with a spin-labeled first ligand. J. Am. Chem. Soc. 2000, 122, 7394–7395.Google Scholar
Jahnke, W.; Rudisser, S.; Zurini, M.Spin label enhanced NMR screening. J. Am. Chem. Soc. 2001, 123, 3149–3150.Google Scholar
Murali, N.; Jarori, G. K.; Landy, S. B.; Rao, B. D.Two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) studies of nucleotide conformations in creatine kinase complexes: effects due to weak nonspecific binding. Biochemistry 1993, 32, 12941–12948.Google Scholar
Dalvit, C.; et al. High-throughput NMR-based screening with competition binding experiments. J. Am. Chem. Soc. 2002, 124, 7702–7709.Google Scholar
Wang, Y.-S.; Liu, D.; Wyss, D. F.Competition STD NMR for the detection of high-affinity ligands and NMR-based screening. Magn. Reson. Chem. 2004, 42, 485–489.Google Scholar
Huth, J. R.; et al. Discovery and design of novel HSP90 inhibitors using multiple fragment-based design strategies. Chem. Biol. Drug Des. 2007, 70, 1–12.Google Scholar
Li, D.; DeRose, E. F.; London, R. E.The inter-ligand Overhauser effect: a powerful new NMR approach for mapping structural relationships of macromolecular ligands. J. Biomol. NMR 1999, 15, 71–76.Google Scholar
Lugovskoy, A. A.; et al. A novel approach for characterizing protein ligand complexes: molecular basis for specificity of small-molecule Bcl-2 inhibitors. J. Am. Chem. Soc. 2002, 124, 1234–1240.Google Scholar
Pellecchia, M.; et al. NMR-based structural characterization of large protein-ligand interactions. J. Biomol. NMR 2002, 22, 165–173.Google Scholar
Medek, A.; Hajduk, P. J.; Mack, J.; Fesik, S. W.The use of differential chemical shifts for determining the binding site location and orientation of protein-bound ligands. J. Am. Chem. Soc. 2000, 122, 1241–124.Google Scholar
McCoy, M. A.; Wyss, D. F.Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations. J. Biomol. NMR 2000, 18, 189–198.Google Scholar
McCoy, M. A.; Wyss, D. F.Spatial localization of ligand binding sites from electron current density surfaces calculated from NMR chemical shift perturbations. J. Am. Chem. Soc. 2002, 124, 11758–11763.Google Scholar
Klaus, W.; Senn, H.Strategies for hit finding using NMR. In: BioNMR in Drug Research, Zerbe, O.; Ed. Weinheim: Wiley-VCH; 2003, 417–437.
Liepinsh, E.; Otting, G.Organic solvents identify specific ligand binding sites on protein surfaces. Nat. Biotechnol. 1997, 15, 264–268.Google Scholar
Fejzo, J.; Lepre, C.; Xie, X.Applications of NMR screening in drug discovery. Curr. Top. Med. Chem. 2002, 2, 1349–1364.Google Scholar
Hajduk, P. J.; et al. Identification of novel inhibitors of urokinase via NMR-based screening. J. Med. Chem. 2000, 43, 3862–3866.Google Scholar
Nienaber, V. L.; et al. Discovering novel ligands for macromolecules using x-ray crystallographic screening. Nat. Biotechnol. 2000, 18, 1105–1108.Google Scholar
Carr, R.; Jhoti, H.Structure-based screening of low-affinity compounds. Drug Discov. Today 2002, 7, 522–527.Google Scholar
Lesuisse, D.; et al. SAR and X-ray. A new approach combining fragment-based screening and rational drug design: application to the discovery of nanomolar inhibitors of Src SH2. J. Med. Chem. 2002, 45, 2379–2387.Google Scholar
Oltersdorf, T.; et al. An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature 2005, 435, 677–681.Google Scholar
Petros, A. M.; et al. Discovery of a potent inhibitor of the antiapoptotic protein Bcl-xL from NMR and parallel synthesis. J. Med. Chem. 2006, 49, 656–663.Google Scholar
Bruncko, M.; et al. Studies leading to potent, dual inhibitors of Bcl-2 and Bcl-xL. J. Med. Chem. 2007, 50, 641–662.Google Scholar
Hajduk, P. J.; et al. Novel inhibitors of Erm methyltransferases from NMR and parallel synthesis. J. Med. Chem. 1999, 42, 3852–3859.Google Scholar
Park, C. M.; et al. Non-peptidic small molecule inhibitors of XIAP. Bioorg. Med. Chem. Lett. 2005, 15, 771–775.Google Scholar
Hochgurtel, M.; Lehn, J.-M.Dynamic combinatorial diversity in drug discovery. In: Fragment-Based Approaches in Drug Discovery, Vol. 34, Jahnke, W.; Ed. Wennheim: Wiley-VCH; 2006, 341–364.
Roper, S.; Kolb, H.Click chemistry for drug discovery. In: Fragment-Based Approaches in Drug Discovery, Vol. 34, Jahnke, W.; Ed. Wennheim: Wiley-VCH; 2006, 313–339.
Huth, J. R.; Sun, C.Utility of NMR in lead optimization: fragment-based approaches. Comb. Chem. High Throughput Screen. 2002, 5, 631–643.Google Scholar
Edwards, P. D.; et al. Application of fragment-based lead generation to the discovery of novel, cyclic amidine beta-secretase inhibitors with nanomolar potency, cellular activity, and high ligand efficiency. J. Med. Chem. 2007, 50, 5912–5925.Google Scholar
Geschwindner, S.; et al. Discovery of a novel warhead against beta-secretase through fragment-based lead generation. J. Med. Chem. 2007, 50, 5903–5911.Google Scholar
Congreve, M.; et al. Application of fragment screening by x-ray crystallography to the discovery of aminopyridines as inhibitors of beta-secretase. J. Med. Chem. 2007, 50, 1124–1132.Google Scholar
Murray, C. W.; et al. Application of fragment screening by x-ray crystallography to beta-secretase. J. Med. Chem. 2007, 50, 1116–1123.Google Scholar

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