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NMR spectroscopy: the swiss army knife of drug discovery

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Abstract

Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool within drug discovery over the last two decades. While traditionally being used by medicinal chemists for small molecule structure elucidation, it can also be a valuable tool for the identification of small molecules that bind to drug targets, for the characterization of target–ligand interactions and for hit-to-lead optimization. Here, we describe how NMR spectroscopy is integrated into the Pfizer drug discovery pipeline and how we utilize this approach to identify and validate initial hits and generate leads.

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References

  • Akaike H (1974) A new look at the statistical model identification. IEEE T Automat Contr 19:716–723

    ADS  MathSciNet  MATH  Google Scholar 

  • Balazs AYS, Carbajo RJ, Davies NL, Dong Y, Hird AW, Johannes JW, Lamb ML, McCoull W, Raubo P, Robb GR, Packer MJ, Chiarparin E (2019) Free ligand 1D NMR conformational signatures to enhance structure based drug design of a Mcl-1 inhibitor (AZD5991) and other synthetic macrocycles. J Med Chem 62:9418–9437

    Google Scholar 

  • Bartels C, Xia TH, Billeter M, Güntert P, Wüthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1–10

    Google Scholar 

  • Basit S, Ashraf Z, Lee K, Latif M (2017) First macrocyclic 3(rd)-generation ALK inhibitor for treatment of ALK/ROS1 cancer: Clinical and designing strategy update of lorlatinib. Eur J Med Chem 134:348–356

    Google Scholar 

  • Blum LC, Reymond J-L (2009) 970 Million druglike small molecules for virtual screening in the chemical universe database GDB-13. J Am Chem Soc 131:8732–8733

    Google Scholar 

  • Blundell CD, Nowak T, Watson MJ (2016) Measurement, interpretation and use of free ligand solution conformations in drug discovery. Prog Med Chem 55:45–147

    Google Scholar 

  • Butts CP, Jones CR, Towers EC, Flynn JL, Appleby L, Barron NJ (2011) Interproton distance determinations by NOE–surprising accuracy and precision in a rigid organic molecule. Org Biomol Chem 9:177–184

    Google Scholar 

  • Cai TQ, Ren N, Jin L, Cheng K, Kash S, Chen R, Wright SD, Taggart AK, Waters MG (2008) Role of GPR81 in lactate-mediated reduction of adipose lipolysis. Biochem Biophys Res Commun 377:987–991

    Google Scholar 

  • Calabrese, M.F., Rajamohan, F., Harris .M.S, Caspers N.L., Magyar R., Withka J.M., Wang H., Borzilleri K.A., Sahasrabudhe P.V., Hoth L.R., Geoghegan K.F., Han S., Brown J., Subashi T.A., Reyes A.R., Frisbie R.K., Ward J., Miller R.A., Landro J.A., Londregan A.T., Carpino P.A., Cabral S., Smith A.C., Conn E.L., Cameron K.O., Qiu X., Kurumbail R.G. Structural basis for AMPK activation: Natural and synthetic ligands regulate kinase activity from opposite poles by different molecular mechanisms. Structure 22, 1161–1172 (2014).

  • Chiarparin E, Packer MJ, Wilson DM (2019) Experimental free ligand conformations: a missing link in structure-based drug discovery. Future Med Chem 11:79–82

    Google Scholar 

  • Cho LT, Alexandrou AJ, Torella R, Knafels J, Hobbs J, Taylor T, Loucif A, Konopacka A, Bell S, Stevens EB, Pandit J, Horst R, Withka JM, Pryde DC, Liu S, Young GT (2018) An intracellular allosteric modulator binding pocket in SK2 ion channels is shared by multiple chemotypes. Structure 26:533–544

    Google Scholar 

  • Cobas JC, Sardina FJ (2003) Nuclear magnetic resonance data processing. MestRe-C: a software package for desktop computers. Concepts Magn Reson A 19:80–96

    Google Scholar 

  • Dalvit C, Vulpetti A (2019) Ligand-Based Fluorine NMR Screening: Principles and applications in drug discovery projects. J Med Chem 62:2218–2244

    Google Scholar 

  • Dalvit C, Fogliatto G, Stewart A, Veronesi M, Stockman B (2001) WaterLOGSY as a method for primary NMR screening: practical aspects and range of applicability. J Biomol NMR 21:349–359

    Google Scholar 

  • Davidsson O, Nilsson K, Branalt J, Andersson T, Berggren K, Chen Y, Fjellstrom O, Graden H, Gustafsson L, Hermansson NO, Jansen F, Johannesson P, Ohlsson B, Tyrchan C, Wellner A, Wellner E, Olwegard-Halvarsson M (2020) Identification of novel GPR81 agonist lead series for target biology evaluation. Bioorg Med Chem Lett 30:126953

    Google Scholar 

  • Doak BC, Norton RS, Scanlon MJ (2016) The ways and means of fragment-based drug design. Pharmacol Ther 167:28–37

    Google Scholar 

  • Erlanson DA, Jahnke W (2016) Fragment-based drug discovery: lessons and outlook. Wiley, Weinheim

    Google Scholar 

  • Erlanson DA, Fesik SW, Hubbard RE, Jahnke W, Jhoti H (2016) Twenty years on: the impact of fragments on drug discovery. Nat Rev Drug Discov 15:605–619

    Google Scholar 

  • Farley KA, Reilly U, Anderson DP, Boscoe BP, Bundesmann MW, Foley DA, Lall MS, Li C, Reese MR, Yan J (2017) Utilizing on- and off-line monitoring tools to follow a kinetic resolution step during flow synthesis. Magn Reson Chem 55:348–354

    Google Scholar 

  • Farley KA, Che Y, Navarro-Vazquez A, Limberakis C, Anderson D, Yan J, Shapiro M, Shanmugasundaram V, Gil RR (2019) Cyclic Peptide design guided by residual dipolar couplings, J-couplings, and intramolecular hydrogen bond analysis. J Org Chem 84:4803–4813

    Google Scholar 

  • Garcia ME, Woodruff SR, Hellemann E, Tsarevsky NV, Gil RR (2017) Di(ethylene glycol) methyl ether methacrylate (DEGMEMA)-derived gels align small organic molecules in methanol. Magn Reson Chem 55:206–209

    Google Scholar 

  • Gayathri C, Tsarevsky NV, Gil RR (2010) Residual dipolar couplings (RDCs) analysis of small molecules made easy: fast and tuneable alignment by reversible compression/relaxation of reusable PMMA Gels. Chemistry 16:3622–3626

    Google Scholar 

  • Gil-Silva LF, Santamaría-Fernández R, Navarro-Vázquez A, Gil RR (2016) Collection of NMR scalar and residual dipolar couplings using a single experiment. Chem Eur J 22:472–476

    Google Scholar 

  • Gossert AD, Jahnke W (2016) NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules. Prog Nucl Magn Reson Spectrosc 97:82–125

    Google Scholar 

  • Goto NK, Gardner KH, Mueller GA, Willis RC, Kay LE (1999) A robust and cost-effective method for the production of Val, Leu, Ile (δ1) methyl-protonated 15N-, 13C-, 2H-labeled proteins. J Biomol NMR 13:369–374

    Google Scholar 

  • Hajduk PJ, Sheppard G, Nettesheim DG, Olejniczak ET, Shuker SB, Meadows RP, Steinman DH, Carrera GM, Marcotte PA, Severin J, Walter K, Smith H, Gubbins E, Simmer R, Holzman TF, Morgan DW, Davidsen SK, Summers JB, Fesik SW (1997a) Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR. J Am Chem Soc 119:5818–5827

    Google Scholar 

  • Hajduk PJ, Olejniczak ET, Fesik SW (1997b) One-dimensional relaxation- and diffusion-edited NMR methods for screening compounds that bind to macromolecules. J Am Chem Soc 119:12257–12261

    Google Scholar 

  • Hall RJ, Mortenson PN, Murray CW (2014) Efficient exploration of chemical space by fragment-based screening. Progr Biophys Mol Biol 116:82–91

    Google Scholar 

  • Hann MM, Leach AR, Harper G (2001) Molecular complexity and Its impact on the probability of finding leads for drug discovery. J Chem Inform Comput Sci 41:856–864

    Google Scholar 

  • Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA (2016) OPLS3: A force field providing broad coverage of drug-like small molecules and proteins. J Chem Theory Comput 12:281–296

    Google Scholar 

  • Harner MJ, Frank AO, Fesik SW (2013) Fragment-based drug discovery using NMR spectroscopy. J Biomol NMR 56:65–75

    Google Scholar 

  • Horst R, Wüthrich K (2015) Micro-scale NMR experiments for monitoring the optimization of membrane protein solutions for structural biology. Bio-protocol 5:e1539

    Google Scholar 

  • Horst R, Stanczak P, Stevens RC, Wüthrich K (2013) beta2-Adrenergic receptor solutions for structural biology analyzed with microscale NMR diffusion measurements. Angew Chem 52:331–335

    Google Scholar 

  • Hu H, Krishnamurthy K (2006) Revisiting the initial rate approximation in kinetic NOE measurements. J Magn Reson 182:173–177

    ADS  Google Scholar 

  • Huard K, Ahn K, Amor P, Beebe DA, Borzilleri KA, Chrunyk BA, Coffey SB, Cong Y, Conn EL, Culp JS, Dowling MS, Gorgoglione MF, Gutierrez JA, Knafels JD, Lachapelle EA, Pandit J, Parris KD, Perez S, Pfefferkorn JA, Price DA, Raymer B, Ross TT, Shavnya A, Smith AC, Subashi TA, Tesz GJ, Thuma BA, Tu M, Weaver JD, Weng Y, Withka JM, Xing G, Magee TV (2017) Discovery of fragment-derived small molecules for in vivo inhibition of Ketohexokinase (KHK). J Med Chem 60:7835–7849

    Google Scholar 

  • Huben K, Jewginski M, Pabis A, Paluch P, Luy B, Jankowski S (2014) The structure of cyclolinopeptide A in chloroform refined by RDC measurements. J Pept Sci 20:901–907

    Google Scholar 

  • Jencks WP (1981) On the attribution and additivity of binding energies. Proc Natl Acad Sci USA 78:4046–4050

    ADS  Google Scholar 

  • Jorgensen WL, Tirado-Rives J (1988) The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657–1666

    Google Scholar 

  • Judge TM, Phillips G, Morris JK, Lovasz KD, Romines KR, Luke GP, Tulinsky J, Tustin JM, Chrusciel RA, Dolak LA, Mizsak SA, Watt W, Morris J, Vander Velde SL, Strohbach JW, Gammill RB (1997) Asymmetric syntheses and absolute stereochemistry of 5,6-Dihydro-α-pyrones, a new class of potent HIV protease inhibitors. J Am Chem Soc 119:3627–3628

    Google Scholar 

  • Kessler H, Gehrke M, Lautz J, Kock M, Seebach D, Thaler A (1990) Complexation and medium effects on the conformation of cyclosporin A studied by NMR spectroscopy and molecular dynamics calculations. Biochem Pharmacol 40:169–173

    Google Scholar 

  • Klages J, Neubauer C, Coles M, Kessler H, Luy B (2005) Structure refinement of cyclosporin A in chloroform by using RDCs measured in a stretched PDMS-gel. ChemBioChem 6:1672–1678

    Google Scholar 

  • LaPlante SR, Nar H, Lemke CT, Jakalian A, Aubry N, Kawai SH (2014) Ligand bioactive conformation plays a critical role in the design of drugs that target the hepatitis C virus NS3 protease. J Med Chem 57:1777–1789

    Google Scholar 

  • Lau WF, Withka JM, Hepworth D, Magee TV, Du YJ, Bakken GA, Miller MD, Hendsch ZS, Thanabal V, Kolodziej SA, Xing L, Hu Q, Narasimhan LS, Love R, Charlton ME, Hughes S, van Hoorn WP, Mills JE (2011) Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics. J Comput Aided Mol Des 25:621–636

    ADS  Google Scholar 

  • Leach AR, Hann MM (2011) Molecular complexity and fragment-based drug discovery: ten years on. Curr Opin Chem Biol 15:489–496

    Google Scholar 

  • Lee KL, Ambler CM, Anderson DR, Boscoe BP, Bree AG, Brodfuehrer JI, Chang JS, Choi C, Chung S, Curran KJ, Day JE, Dehnhardt CM, Dower K, Drozda SE, Frisbie RK, Gavrin LK, Goldberg JA, Han S, Hegen M, Hepworth D, Hope HR, Kamtekar S, Kilty IC, Lee A, Lin L-L, Lovering FE, Lowe MD, Mathias JP, Morgan HM, Murphy EA, Papaioannou N, Patny A, Pierce BS, Rao VR, Saiah E, Samardjiev IJ, Samas BM, Shen MWH, Shin JH, Soutter HH, Strohbach JW, Symanowicz PT, Thomason JR, Trzupek JD, Vargas R, Vincent F, Yan J, Zapf CW, Wright SW (2017) Discovery of clinical candidate 1-{[(2S,3S,4S)-3-ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (PF-06650833), a potent, selective inhibitor of interleukin-1 receptor associated kinase 4 (IRAK4), by fragment-based drug design. J Med Chem 60:5521–5542

    Google Scholar 

  • Marcó N, Souza AA, Nolis P, Gil RR, Parella T (2017) Perfect 1JCH-resolved HSQC: efficient measurement of one-bond proton-carbon coupling constants along the indirect dimension. J Magn Reson 276:37–42

    ADS  Google Scholar 

  • Mayer M, Meyer B (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem 38:1784–1788

    Google Scholar 

  • Murray CW, Newell DR, Angibaud P (2019) A successful collaboration between academia, biotech and pharma led to discovery of erdafitinib, a selective FGFR inhibitor recently approved by the FDA. MedChemComm 10:1509–1511

    Google Scholar 

  • Navarro-Vázquez A, Gil RR, Blinov K (2018) Computer-assisted 3D structure elucidation (CASE-3D) of natural products combining isotropic and anisotropic NMR parameters. J Nat Prod 81:203–210

    Google Scholar 

  • Pauli GF, Chen SN, Simmler C, Lankin DC, Godecke T, Jaki BU, Friesen JB, McAlpine JB, Napolitano JG (2014) Importance of purity evaluation and the potential of quantitative 1H NMR as a purity assay. J Med Chem 57:9220–9231

    Google Scholar 

  • Pellecchia M, Bertini I, Cowburn D, Dalvit C, Giralt E, Jahnke W, James TL, Homans SW, Kessler H, Luchinat C, Meyer B, Oschkinat H, Peng J, Schwalbe H, Siegal G (2008) Perspectives on NMR in drug discovery: a technique comes of age. Nat Rev Drug Discov 7:738–745

    Google Scholar 

  • Poppe L, Brown GS, Philo JS, Nikrad PV, Shah BH (1997) Conformation of sLex tetrasaccharide, free in solution and bound to E-, P-, and L-selectin. J Am Chem Soc 119:1727–1736

    Google Scholar 

  • Proudfoot A, Frank AO, Ruggiu F, Mamo M, Lingel A (2016) Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids. J Biomol NMR 65:15–27

    Google Scholar 

  • Rezai T, Yu B, Millhauser GL, Jacobson MP, Lokey RS (2006) Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers. J Am Chem Soc 128:2510–2511

    Google Scholar 

  • Riek R, Wider G, Pervushin K, Wüthrich K (1999) Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules. Proc Natl Acad Sci USA 96:4918–4923

    ADS  Google Scholar 

  • Rigling C, Ebert MO (2017) RDC-enhanced structure calculation of a beta-heptapeptide in methanol. Magn Reson Chem 55:655–661

    Google Scholar 

  • Rossi P, Swapna GV, Huang YJ, Aramini JM, Anklin C, Conover K, Hamilton K, Xiao R, Acton TB, Ertekin A, Everett JK, Montelione GT (2010) A microscale protein NMR sample screening pipeline. J Biomol NMR 46:11–22

    Google Scholar 

  • Sahasrabudhe P, Shanmugasundaram V, Flanagan M, Borzilleri KA, Heaslet H, Rane A, McColl A, Subashi T, Karam G, Sarver R, Harris M, Chrunyk BA, Subramanyam C, Magee TV, Fahnoe K, Lacey B, Putz H, Miller JR, Cho J, Palmer III A, Withka JM (2017) Driving drug discovery with biophysical information. Appl Biophys Drug Discov 241–261

  • Shepherd NE, Hoang HN, Abbenante G, Fairlie DP (2005) Single turn peptide alpha helices with exceptional stability in water. J Am Chem Soc 127:2974–2983

    Google Scholar 

  • Shuker SB, Hajduk PJ, Meadows RP, Fesik SW (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274:1531–1534

    ADS  Google Scholar 

  • Trigo-Mourino P, Merle C, Koos MR, Luy B, Gil RR (2013) Probing spatial distribution of alignment by deuterium NMR imaging. Chemistry 19:7013–7019

    Google Scholar 

  • Uccello DP, Miller SM, Dieterich NA, Stepan AF, Chung S, Farley KA, Samas B, Chen J, Montgomery JI (2011) The synthesis of C-13 functionalized pleuromutilins via C-H amidation and subsequent novel rearrangement product. Tetrahedron Lett 52:4247–4251

    Google Scholar 

  • Walker GS, Ryder TF, Sharma R, Smith EB, Freund A (2011) Validation of isolated metabolites from drug metabolism studies as analytical standards by quantitative NMR. Drug Metab Dispos 39:433–440

    Google Scholar 

  • Weber C, Wider G, von Freyberg B, Traber R, Braun W, Widmer H, Wüthrich K (1991) The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Biochemistry 30:6563–6574

    Google Scholar 

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Acknowledgements

The authors would like to acknowledge the Pfizer SK2 and AMPK teams for providing protein NMR samples used in this work. R.H. and J.M.W. would like to thank the Pfizer Structural and Molecular Sciences group for support with the SK2 and AMPK FBDD campaigns. All work presented here was funded by Pfizer R&D.

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All research presented here was funded by Pfizer R&D.

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  1. Reto Horst and Kathleen A. Farley have contributed equally to this work.

Authors and Affiliations

  1. Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA

    Reto Horst & Kathleen A. Farley

  2. Medicinal Sciences, Pfizer, 610 Main St., Cambridge, MA, 02139, USA

    Bethany L. Kormos & Jane M. Withka

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  1. Reto Horst
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  2. Kathleen A. Farley
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Correspondence to Reto Horst.

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R.H., K.A.F., B.L.K. and J.M.W. were full-time employees and shareholders of Pfizer R&D at the time the research presented here was conducted.

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Horst, R., Farley, K.A., Kormos, B.L. et al. NMR spectroscopy: the swiss army knife of drug discovery. J Biomol NMR 74, 509–519 (2020). https://doi.org/10.1007/s10858-020-00330-0

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