NMR in Fragment Based Lead Discovery

Abstract

Abstract:

The fragment based drug screening and design emerged in the past decade, and has gained important applications. Many fragmentderived drugs have entered clinical trials. Probing the weak interactions between the target protein and small molecule fragments Modern NMR techniques play a vital role in fragment based lead discovery. In this article, the basic procedures of NMR fragment screening and the relevant key concepts (i.e., target validation, fragment library design, quality control and prevailing NMR fragment screening techniques) were first introduced. The theoretical framework of the NMR techniques commonly used in fragment based lead discovery stage, including chemical shift perturbation, intermolecular NOE, residual dipolar coupling and paramagnetic spin label etc., were also reviewed. Examples were given to show how these techniques can be used to resolve the structure of target/ligand complexs. Strategies of fragment growth, linking and merging were also discussed.

Key words: NMR, fragment based lead discovery, fragment growth, fragment linking, STD, water-LOGSY

CLC Number:

O482.53

RUAN Ke, GAO Jia, MA Rong-Sheng. NMR in Fragment Based Lead Discovery[J]. Chinese Journal of Magnetic Resonance, 2012, 29(2): 163-181.

References

[1] Paul S M, Mytelka D S, Dunwiddie C T, et al. How to improve R&D productivity: the pharmaceutical industry's grand challenge[J]. Nat Rev Drug Discovery, 2010, 9: 203-214.

[2] Murray C W, Rees D C. The rise of fragment-based drug discovery[J]. Nature Chem, 2009, 1: 187-192.

[3] Lipinski C A. Drug-like properties and the causes of poor solubility and poor permeability[J]. J Pharmacol Toxicol Methods, 2000, 44: 235-249.

[4] Hajduk P J, Greer J. A decade of fragment-based drug design: strategic advances and lessons learned[J]. Nat Rev Drug Discovery, 2007, 6: 211-219.

[5] Clackson T, Wells J A. A hot spot of binding energy in a hormone-receptor interface[J]. Science, 1995, 267: 383-386.

[6] Aggarwal S. Targeted cancer therapies[J]. Nat Rev Drug Discovery, 2010, 9: 427-428.

[7] Schade M, Oschkinat H. NMR fragment screening: Tackling protein-protein interaction targets[J]. Curr Opin Drug Discovery & Development, 2005, 8: 365-373.

[8] Alex A A, Flocco M M. Fragment-based drug discovery: what has it achieved so far?[J]. Curr Top Med Chem (Sharjah, United Arab Emirates), 2007, 7: 1 544-1 567.

[9] Huth J R, Park C, Petros A M, et al. Discovery and design of novel HSP90 inhibitors using multiple fragment-based design strategies[J]. Chem Biol & Drug Design, 2007, 70: 1-12.

[10] Stockman B J, Kothe M, Kohls D, et al. Identification of allosteric PIF-pocket ligands for PDK1 using NMR-based fragment screening and H-1-N-15 TROSY experiments[J]. Chem Biol & Drug Design, 2009, 73: 179-188.

[11] Rees D C, Congreve M, Murray C W, et al. Fragment-based lead discovery[J]. Nat Rev Drug Discovery, 2004, 3: 660-672.

[12] Hajduk P J. Puzzling through fragment-based drug design[J]. Nat Chem Biol, 2006, 2: 658-659.

[13] Pellecchia M. Fragment-based drug discovery takes a virtual turn[J]. Nat Chem Biol, 2009, 5: 274-275.

[14] Zartler E R, Shapiro M J. Fragonomics: fragment-based drug discovery[J]. Curr Opin Chem Biol, 2005, 9: 366-370.

[15] Zartler E R, Mo H. Practical aspects of NMR-based fragment discovery[J]. Curr Top Med Chem, 2007, 7: 1 592-1 599.

[16] Schulz M N, Hubbard R E. Recent progress in fragment-based lead discovery[J]. Curr Opin Pharm, 2009, 9: 615-621.

[17] Congreve M, Carr R, Murray C, et al. A 'rule of three' for fragment-based lead discovery?[J]. Drug Discov Today, 2003, 8: 876-877.

[18] Hajduk P J. Fragment-based drug design: How big is too big?[J]. J Med Chem, 2006, 49: 6 972-6 976.

[19] Hesterkamp T, Whittaker M. Fragment-based activity space: smaller is better[J]. Curr Opin Chem Biol, 2008, 12: 260-268.

[20] Bembenek S D, Tounge B A, Reynolds C H. Ligand efficiency and fragment-based drug discovery[J]. Drug Discov Today, 2009, 14: 278-283.

[21] Abad-Zapatero C. Ligand efficiency indices for effective drug discovery[J]. Expert Opin Drug Discovery, 2007, 2: 469-488.

[22] Murray C W, Carr M G, Callaghan O, et al. Fragment-based drug discovery applied to Hsp90. Discovery of two lead series with high ligand efficiency[J]. J Med Chem, 2010, 53: 5 942-5 955.

[23] Tanaka D, Tsuda Y, Shiyama T, et al. A practical use of ligand efficiency indices out of the fragment-based approach: ligand efficiencyguided lead identification of soluble epoxide hydrolase inhibitors[J]. J Med Chem, 2011, 54: 851-857.

[24] Orita M, Warizaya M, Amano Y, et al. Advances in fragment-based drug discovery platforms[J]. Exp Opin Drug Discovery, 2009, 4: 1 125-1 144.

[25] Kojima K, Konopleva M, McQueen T, et al. Mdm2 inhibitor Nutlin-3a induces p53-mediated apoptosis by transcription-dependent and transcription-independent mechanisms and may overcome Atm-mediated resistance to fludarabine in chronic lymphocytic leukemia[J]. Blood, 2006, 108: 993-1 000.

[26] Morselli E, Galluzzi L, Kepp O, et al. Nutlin kills cancer cells via mitochondrial p53[J]. Cell Cycle, 2009, 8: 1 647-1 648.

[27] Frearson J A, Wyatt P G, Gilbert I H, et al. Target assessment for antiparasitic drug discovery[J]. Trends in Parasitology, 2007, 23: 589-595.

[28] Hann M M, Leach A R, Harper G. Molecular complexity and its impact on the probability of finding leads for drug discovery[J]. J Chem Inf Comput Sci, 2001, 41: 856-864.

[29] Erlanson D A, McDowell R S, O'Brien T. Fragment-based drug discovery[J]. J Med Chem, 2004, 47: 3 463-3 482.

[30] Dalvit C. NMR methods in fragment screening: theory and a comparison with other biophysical techniques[J]. Drug Discovery Today, 2009, 14: 1 051-1 057.

[31] Zhou Qiu-ju（周秋菊）, Xiang Jun-feng（向俊峰）, Tang Ya-lin（唐亚林）. Applications of nuclear magnetic resonance spectroscopy in drug discovery(核磁共振波谱在药物发现中的应用)[J]. Chinese J Magn Reson(波谱学杂志), 2010, 27（1）: 68-79.

[32] Hubbard R E, Davis B, Chen I, et al. The SeeDs approach: Integrating fragments into drug discovery[J]. Curr Top Med Chem, 2007, 7: 1 568-1 581.

[33] Shuker S B, Hajduk P J, Meadows R P, et al. Discovering high-affinity ligands for proteins: SAR by NMR[J]. Science, 1996, 274: 1 531-1 534.

[34] Hajduk P J, Gerfin T, Boehlen J M, et al. High-throughput nuclear magnetic resonance-based screening[J]. J Med Chem, 1999, 42: 2 315-2 317.

[35] Tu K C, Gochin M,Kollman P. Structural studies on a paramagnetic drug-DNA complex using pseudocontact shift constraints in NMR spectroscopy[J]. Faseb J, 1997, 11: M27.

[36] Dalvit C, Stockman B J, Flocco M, et al. Use of fluorine-19 NMR for high throughput screening: US, 2003-US177292004051214[P]. 2004.

[37] Lucas L H, Price K E, Larive C K. Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion measurements[J]. J Am Chem Soc, 2004, 126: 14 258-14 266.

[38] Angulo J, Enriquez-Navas P M, Nieto P M. Ligand-receptor binding affinities from Saturation transfer difference (STD) NMR spectroscopy: the binding isotherm of STD initial growth rates[J]. Chem-a Eur J, 2010, 16: 7 803-7 812.

[39] Di Micco S, Bassarello C, Bifulco G, et al. Differential-frequency saturation transfer difference NMR spectroscopy allows the detection of different ligand-DNA binding mods[J]. Angew Chem Int Ed Engl, 2005, 45: 224-228.

[40] Mari S, Serrano-Gomez D, Canada F J, et al. 1D saturation transfer difference NMR experiments on living cells: the DCSIGN/oligomannose interaction[J]. Angew Chem Int Ed Engl, 2004, 44: 296-298.

[41] Claasen B, Axmann M, Meinecke R, et al. 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)beta(3) in native platelets than in liposomes[J]. J Am Chem Soc, 2005, 127: 916-919.

[42] Mayer M, Meyer B. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor[J]. J Amer Chem Soc, 2001, 123: 6 108-6 117.

[43] Dalvit C, Fogliatto G, Stewart A, et al. WaterLOGSY as a method for primary NMR screening: Practical aspects and range of applicability[J]. J Biom NMR, 2001, 21: 349-359.

[44] Jayalakshmi V, Krishna N R. Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes[J]. J Magn Reson, 2002, 155: 106-118.

[45] Gossert A D, Henry C, Blommers M J J, et al. Time efficient detection of protein-ligand interactions with the polarization optimized POWaterLOGSY NMR experiment[J]. J Biom NMR, 2009, 43: 211-217.

[46] Chen I J,Hubbard R E. Lessons for fragment library design: analysis of output from multiple screening campaigns[J]. J Comput-Aid Mol Des, 2009, 23: 603-620.

[47] Jhoti H, Cleasby A, Verdonk M, et al. Fragment-based screening using X-ray crystallography and NMR spectroscopy[J]. Curr Opin Chem Biol, 2007, 11: 485-493.

[48] Hopkins A L, Groom C R,Alex A. Ligand efficiency: a useful metric for lead selection[J]. Drug Discovery Today, 2004, 9: 430-431.

[49] Howard S, Berdini V, Boulstridge J A, et al. Fragment-based discovery of the pyrazol-4-yl urea (AT9283), a multitargeted kinase inhibitor with potent aurora kinase activity[J]. J Med Chem, 2009, 52: 379-388.

[50] Petros A M, Huth J R, Oost T, et al. Discovery of a potent and selective Bcl-2 inhibitor using SAR by NMR[J]. Bioorg Med Chem Lett, 2010, 20: 6 587-6 591.

[51] Brough P A, Barril X, Borgognoni J, et al. Combining hit identification strategies: Fragment-based and in silico approaches to orally active 2-aminothieno[2,3-d]pyrimidine inhibitors of the Hsp90 molecular chaperone[J]. J Med Chem, 2009, 52: 4 794-4 809.

[52] Jahnke W, Florsheimer A, Blommers M J J, et al. Second-site NMR screening and linker design[J]. Curr Top Med Chem, 2003, 3: 69-80.

[53] Antonyuk S, Strange R W, Hasnain S S. Structural discovery of small molecule binding sites in Cu-Zn human superoxide dismutase familial amyotrophic lateral sclerosis mutants provides insights for lead optimization[J]. J Med Chem, 2010, 53: 1 402-1 406.

[54] Chung F, Tisne C, Lecourt T, et al. NMR-Guided fragment-based approach for the design of tRNA(Lys3) ligands[J]. Angew Chem Int Edit, 2007, 46: 4 489-4 491.

[55] Scheich C, Puetter V, Schade M. Novel small molecule inhibitors of MDR mycobacterium tuberculosis by NMR fragment screening of antigen 85C[J]. J Med Chem, 2010, 53: 8 362-8 367.

[56] Szczepankiewicz B G, Liu G, Hajduk P J, et al. Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy[J]. J Am Chem Soc, 2003, 125: 4 087-4 096.

[57] Petros A M, Dinges J, Augeri D J, et al. Discovery of a potent inhibitor of the antiapoptotic protein Bcl-x(L) from NMR and parallel synthesis[J]. J Med Chem, 2006, 49: 656-663.

[58] Pellecchia M, Becattini B, Crowell K J, et al. NMR-based techniques in the hit identification and optimisation processes[J]. Expert Opin Therapeutic Targets, 2004, 8: 597-611.

[59] Becattini B, Culmsee C, Leone M, et al. Structure-activity relationships by interligand NOE-based design and synthesis of antiapoptotic compounds targeting Bid[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103: 12 602-12 606.
[60] Sanchez-Pedregal V M, Reese M, Meiler J, et al. The INPHARMA method: Protein-mediated interligand NOEs for pharmacophore mapping[J]. Angewa Chem Int Edit, 2005, 44: 4 172-4 175.

[61] Macnaughtan M A, Kamar M, AlvarezManilla G, et al. NMR structural characterization of substrates bound to N-scetylglucosaminyltransferase V[J]. J Mol Biol, 2007, 366: 1 266-1 281.

[62] Orts J, Griesinger C, Carlomagno T. The INPHARMA technique for pharmacophore mapping: A theoretical guide to the method[J]. J Magn Reson, 2009, 200: 64-73.

[63] Bi Yun-chen(毕允晨), Wang Yu-juan(王玉娟), Wang Jun-feng(王俊峰). The Nanodics: A novel tool to study membrane protein structure and function (Nanodisc体系在膜蛋白结构与功能研究中的应用)[J]. Chinese J Magn Reson(波谱学杂志), 2011, 28(2): 177-189.

[64] Tolman J R, Ruan K. NMR residual dipolar couplings as probes of biomolecular dynamics[J]. Chemical Reviews, 2006, 106: 1 720-1 736.

[65] Losonczi J A, Andrec M, Fischer M W F, et al. Order matrix analysis of residual dipolar couplings using singular value decomposition[J]. J Magn Reson, 1999, 138: 334-342.

[66] Ruan K, Tolman J R. Composite alignment media for the measurement of independent sets of NMR residual dipolar couplings[J]. J Am Chem Soc, 2005, 127: 15 032-15 033.

[67] Ruan K, Briggman K B, Tolman J R. De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media[J]. J Biomol NMR, 2008, 41: 61-76.

[68] Yao L, Voegeli B, Torchia D A, et al.Simultaneous NMR study of protein structure and dynamics using conservative mutagenesis[J]. J Phys Chem B, 2008, 112: 6 045-6 056.

[69] Seidel R D, 3rd, Zhuang T, Prestegard J H. Bound-state residual dipolar couplings for rapidly exchanging ligands of His-tagged proteins[J]. J Am Chem Soc, 2007, 129: 4 834-4 839.

[70] Zhuang T, Leffler H, Prestegard J H. Enhancement of bound-state residual dipolar couplings: conformational analysis of lactose bound to Galectin-3[J]. Protein Sci, 2006, 15: 1 780-1 790.

[71] Clore G M, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient lowpopulation states of biological macromolecules and their complexes[J]. Chem Rev, 2009, 109: 4 108-4 139.

[72] Chun T, Schwieters C D, Clore G M. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR[J]. Nature, 2007: 1 078-1 082.

[73] Morgado L, Saraiva I H, Louro R O, et al. Orientation of the axial ligands and magnetic properties of the hemes in the triheme ferricytochrome PpcA from G. sulfurreducens determined by paramagnetic NMR[J]. Febs Lett, 2010, 584: 3 442-3 445.

[74] Gochin M, Zhou G, Phillips A H. Paramagnetic relaxation assisted docking of a small indole compound in the HIV-1 gp41 hydrophobic pocket[J]. Acs Chem Biol, 2011, 6: 267-274.

[75] Otting G. Protein NMR using paramagnetic ions[J]. Annu Rev Biophysics, 2010, 39: 387-405.