References
- Folmer RHA. Integrating biophysics with HTS-driven drug discovery projects. Drug Discov Today. 2016;21:491–498.
- Ciulli A. Biophysical screening for the discovery of small-molecule ligands. In: Williams MA, Daviter T, editors. Protein-ligand interactions: methods and applications. Totowa (NJ): Humana Press; 2013. p. 357–388.
- Genick CC, Barlier D, Monna D, et al. Applications of biophysics in high-throughput screening hit validation. J Biomol Screen. 2014;19:707–714.
- Baell JB, Holloway GA. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem. 2010;53:2719–2740.
- Renaud J-P, Chung C-W, Danielson UH, et al. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov. 2016;15:679–698.
- Erlanson DA, Fesik SW, Hubbard RE, et al. Twenty years on: the impact of fragments on drug discovery. Nat Rev Drug Discov. 2016;15:605–619.
- Davis BJ, Erlanson DA. Learning from our mistakes: the ‘unknown knowns’ in fragment screening. Bioorgan & Med Chem Lett. 2013;23:2844–2852.
- Silvestre HL, Blundell TL, Abell C, et al. Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Proc Natl Acad Sci. 2013;110:12984–12989.
- Jahnke W, Erlanson DA. Fragment-based approaches in drug discovery. Weinheim, Germany:John Wiley & Sons; 2006.
- Wan Z, Hu D, Li P, et al. Synthesis, antiviral bioactivity of novel 4-thioquinazoline derivatives containing chalcone moiety. Molecules. 2015;20:11861–11874.
- Sheffield K, Rahul Vohra R, Scott J, et al. Using surface plasmon resonance spectroscopy to characterize the inhibition of NGF-p75NTRand proNGF-p75NTR interactions by small molecule inhibitors. Pharmacolog Res. 2016;103:292–299.
- Gutmann S, Hinniger A, Fendrich G, et al. The crystal structure of cancer osaka thyroid kinase reveals an unexpected kinase domain fold. J Biol Chem. 2015;290(24):15210–15218.
- Sahin E, Roberts CJ. Size-exclusion chromatography with multi-angle light scattering for elucidating protein aggregation mechanisms. In: Voynov V, Caravella JA, editors. Therapeutic proteins: methods and protocols. Clifton (NJ): Humana Press; 2012. p. 403–423.
- Vedadi M, Niesen F, Abdellah Allali-Hassani A, et al. Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc Natl Acad Sci. 2006;103(43):15835–15840.
- Branigan E, Pliotas C, Hagelueken G, et al. Quantification of free cysteines in membrane and soluble proteins using a fluorescent dye and thermal unfolding. 2090–2097. Published online 3 October 2013. DOI:10.1038/nprot.2013.128
- Furusawa H, Komatsu M, Okahata Y. In situ monitoring of conformational changes of and peptide bindings to calmodulin on a 27 MHz quartz-crystal microbalance. Anal Chem. 2009;81:1841–1847.
- Schlichtiger A, Baier C, Yin M, et al. Covalent attachment of functionalized cardiolipin on a biosensor gold surface allows repetitive measurements of anticardiolipin antibodies in serum. Anal Bioanal Chem. 2013;405:275–285.
- Moree B, Connell K, Mortensen RB, et al. Protein conformational changes are detected and resolved site specifically by second-harmonic generation. Biophys J. 2015;109:806–815.
- Pantoliano MW, Petrella EC, Kwasnoski JD, et al. High-density miniaturized thermal shift assays as a general strategy for drug discovery. J Biomol Screen. 2001;6:429–440.
- Mullard A. DNA tags help the hunt for drugs. Nature. 2016;530:367–369.
- Ai C, McGregor LM, Liu DR. Novel selection methods for DNA-encoded chemical libraries. Curr Opin Chem Biol. 2015;26:55–61.
- Buller F, Mannocci L, Scheuermann J, et al. Drug discovery with DNA-encoded chemical libraries. Biocon Chem. 2010;21:1571–1580.
- Franzini RM, Randolph C. Chemical space of DNA-encoded libraries. J Med Chem. 2016;59:6629–6644.
- Mannocci L, Leimbacher M, Wichert M, et al. 20 years of DNA-encoded chemical libraries. Chem Commun. 2011;47:12747–12753.
- McDonnell PA, Yanchunas J, Newitt JA, et al. Assessing compound binding to the Eg5 motor domain using a thermal shift assay. Anal Biochem. 2009;392:59–69.
- Zehender H, Mayr LM. Application of mass spectrometry technologies for the discovery of low-molecular weight modulators of enzymes and protein–protein interactions. Curr Opin Chem Biol. 2007;11:511–517.
- Annis DA, Nickbarg E, Yang X, et al. Affinity selection-mass spectrometry screening techniques for small molecule drug discovery. Curr Opin Chem Biol. 2007;11:518–526.
- O’Connell TN, Ramsay J, Rieth SF, et al. Solution-based indirect affinity selection mass spectrometry—a general tool for high-throughput screening of pharmaceutical compound libraries. Anal Chem. 2014;86:7413–7420.
- Senisterra G, Chau I, Vedadi M. Thermal denaturation assays in chemical biology. Assay Drug Dev Technol. 2011;10:128–136.
- Niesen FH, Berglund H, Vedadi M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc. 2007;2:2212–2221.
- Senisterra GA, Finerty JPJ. High throughput methods of assessing protein stability and aggregation. Mol BioSyst. 2009;5:217–223.
- Simeonov A. Recent developments in the use of differential scanning fluorometry in protein and small molecule discovery and characterization. Expert Opin Drug Discov. 2013;8:1071–1082.
- Erlanson DA, Jahnke W. Fragment-based drug discovery: lessons and outlook. Weinheim, Germany:John Wiley & Sons; 2015.DOI: 10.1002/cmdc.201600256
- Wagner B. The resurgence of phenotypic screening in drugdiscovery and development. Expert Opin Drug Discov. 2016;11(2):121–125.
- Vincent F, Loria P, Pregel M, et al. Developing predictive assays: the phenotypic screening “rule of 3”. Sci Transl Med. 2015;7:293ps15.
- Savitski M, Reinhard F, Franken H, et al. Tracking cancer drugs in living cells by thermal profiling of the proteome. Science. 2014;346(6205): 1255784-1 – 10.
- Jafari R, Almqvist H, Axelsson H, et al. The cellular thermal shift assay for evaluating drug target interactions in cells. Nat Protocols. 2014;9(9):2100–2122.
- Schürmann M, Janning P, Ziegler S, et al. Small-molecule target engagement in cells. Cell Chem Biol. 2016. DOI:10.1016/j.chembiol.2016.03.008.
- Almqvist H, Axelsson H, Jafari R. CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil. Nat Comm. 2016. DOI:10.1038/ncomms11040
- Kurien BT, Scofield RH. Valerie M. Harris. Protein Detection by Simple Western (TM) Analysis. In: Kurien BT, Scofield RH, editors. Methods in molecular biology: Western blotting methods and protocols. New York: Humana Press; 2015. p. 465–468.
- Erik G, Thayer W, John P. Peggy™: size or charge-based Western blotting at the push of a button. Nat Methods. 2013;10:i–ii.
- Liang C, Hao H, Wu X, et al. Design and synthesis of N-(5-chloro-2,4-dihydroxybenzoyl)-(R)-1,2,3,4-tetrahydroisoquinoline-3-carboxamides as novel Hsp90 inhibitors. Euro J Med Chem. 2016;121:272–282.
- Cowan-Jacob SW, Jahnke W, Knapp S. Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med Chem. 2014;6:541–561.
- Wenthur CJ, Gentry PR, Mathews TP, et al. Drugs for allosteric sites on receptors. Annu Rev Pharmacol Tox. 2014;54:165–184.
- Laskowski RA, Gerick F, Thornton JM. The structural basis of allosteric regulation in proteins. FEBS Lett. 2009;583:1692–1698.
- Cornish-Bowden A. Understanding allosteric and cooperative interactions in enzymes. FEBS J. 2014;281:621–632.
- Goodey NM, Benkovic SJ. Allosteric regulation and catalysis emerge via a common route. Nat Chem Biol. 2008;4:474–482.
- Hardy JA, Wells JA. Searching for new allosteric sites in enzymes. Curr Opin Struct Biol. 2004;14:706–715.
- Zhang J, Yang PL, Gray NS. Targeting cancer with small molecule kinase inhibitors. Nat Rev Cancer. 2009;9:28–39.
- Drag M, Salvesen GS. Emerging principles in protease-based drug discovery. Nat Rev Drug Discov. 2010;9:690–701.
- Chen Y-NP, LaMarche MJ, Chan HM, et al. Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases. Nature. 2016;535:148–152.
- Jahnke W, Widmer H. Protein NMR in biomedical research. Cell Mol Life Sci CMLS. 2004;61:580–599.
- Coan KED, Maltby DA, Burlingame AL, et al. Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem. 2009;52:2067–2075.
- Feng BY, Simeonov A, Jadhav A, et al. A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem. 2007;50:2385–2390.
- Cook P, Cleland WW. Enzyme kinetics and mechanism. London, UK:Garland Science; 2007.
- Walsh C. Enzymatic reaction mechanisms. New york:WH Freeman; 1979.
- Ericsson UB, Hallberg BM, DeTitta GT, et al. Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal Biochem. 2006;357:289–298.
- Lea WA, Simeonov A. Differential scanning fluorometry signatures as indicators of enzyme inhibitor mode of action: case study of glutathione S-transferase. PLoS One. 2012;7:e36219.
- Yamada K, Zhang J-H, Xie X, et al. Discovery and characterization of allosteric WNK kinase inhibitors. ACS Chem Biol. 2016.
- Spurny R, Debaveye S, Farinha A, et al. Molecular blueprint of allosteric binding sites in a homologue of the agonist-binding domain of the α7 nicotinic acetylcholine receptor. Proc Natl Acad Sci. 2015;112:E2543–E2552.
- Huber W, Francis M. Biomolecular interaction analysis in drug discovery using surface plasmon resonance technology. Curr Pharm Des. 2006;12:3999–4021 .
- Huber W, Sinopoli A, Kohler J, et al. Elucidation of direct competition and allosteric modulation of small-molecular-weight protein ligands using surface plasmon resonance methods. J Mol Recognit. 2015;28:480–491.
- GE Healthcare UK LTD. Direct measurement of challenging target-ligand interactions; 2016. Available from: http://www.europeanpharmaceuticalreview.com
- Bradrick TD, Beechem JM, Howell EE. Unusual binding stoichiometries and cooperativity are observed during binary and ternary complex formation in the single active pore of R67 dihydrofolate reductase, a D2 symmetric protein. Biochemistry. 1996;35:11414–11424.
- Smith CK, Windsor WT. Thermodynamics of nucleotide and non-atp-competitive inhibitor binding to MEK1 by circular dichroism and isothermal titration calorimetry. Biochemistry. 2007;46:1358–1367.
- Velazquez-Campoy A, Freire E. Isothermal titration calorimetry to determine association constants for high-affinity ligands. Nat Protoc. 2006;1:186–191.
- Velázquez Campoy A, Freire E. ITC in the post-genomic era…? Priceless. Biophys Chem. 2005;115:115–124.
- Boulton S, Melacini G. Advances in NMR methods to map allosteric sites: from models to translation. Chem Rev. 2016;116:6267–6304.
- Lisi GP, Loria JP. Solution NMR spectroscopy for the study of enzyme allostery. Chem Rev. 2016;116:6323–6369.
- Manley G, Loria JP. NMR insights into protein allostery. Arch Biochem Biophys. 2012;519:223–231.
- Jahnke W, Grotzfeld RM, Pellé X, et al. Binding or bending: distinction of allosteric Abl kinase agonists from antagonists by an NMR-based conformational assay. J Am Chem Soc. 2010;132:7043–7048.
- Wylie A, Schoepfer J, Jahnke W, et al. The allosteric inhibitor ABL001 enables dual targeting of BCR-ABL1. Nature. 2017;543(7647):733–737.
- Moree B, Yin G, Lázaro DF, et al. Small molecules detected by second-harmonic generation modulate the conformation of monomeric α-synuclein and reduce its aggregation in cells. J Biol Chem. 2015;290:27582–27593.
- Salafsky JS. Second-harmonic generation as a probe of conformational change in molecules. Chem Phys Lett. 2003;381:705–709.
- Adeniyi A, Muthusamy R, Soliman M. New drug design with covalent modifiers. Expert Opin Drug Discov. 2016;11(1):79–90.
- Moghaddam M, Tang Y, O’Brien Z, et al. A proposed screening paradigm for discovery of covalent inhibitor drugs. Drug Metab Lett. 2014;8:19–30.
- Singh J, Petter R, Baillie T. The resurgence of covalent drugs. Nat Rev Drug Discov. 2011;10:307–317.
- Liu Q, Sabnis Y, Zhao Z, et al. Developing irreversible inhibitors of the protein kinase cysteinome. Chem Biol. 2013;20(2):146–159.
- Lanning B, Landon R, Whitby L, et al. A roadmap to evaluate the proteome-wide selectivity of covalent kinase inhibitors. Nat Chem Biol. 2014;10(9):760–767.
- Kathman S, Statsyuk A. Covalent tethering of fragments for covalent probe discovery. Med Chem Commun. 2016;7:576–585.s.
- Xu D, Xu Z, Li C, et al. Identification of new ATG4B inhibitors based on a novel high-throughput screening platform. J Biomol Screen. 2016;22:1–10.
- Bligh S, Haley T, Lowe P. Measurement of dissociation constants of inhibitors binding to Src SH2 domain protein by non-covalent electrospray ionization mass spectrometry. J Mol Recognit. 2003;16:139–147.
- Kathman S, Xu Z, Statsyuk A. A fragment-based method to discover irreversible covalent inhibitors of cysteine proteases. J Med Chem. 2014;57:4969−4974.
- Schön A, Brown RK, Hutchins BM, et al. Ligand binding analysis and screening by chemical denaturation shift. Anal Biochem. 2013;443:52–57.
- Jones AM, Westwood IM, Osborne JD, et al. A fragment-based approach applied to a highly flexible target: insights and challenges towards the inhibition of HSP70 isoforms. Sci Rep. 2016;6:34701.
- Shepherd CA, Hopkins AL, Navratilova I. Fragment screening by SPR and advanced application to GPCRs. Prog Biophys Mol Biol. 2014;116:113–123.
- GE Healthcare Life Sciences. Fragment library screening and characterization with Biacore™ 4000. 2011. Available from: www.Biacore.com.2011; Application note 28-9796-95 AA
- Krainer G, Keller S. Single-experiment displacement assay for quantifying high-affinity binding by isothermal titration calorimetry. Methods. 2015;76:116–123.
- Vega S, Abian O, Velazquez-Campoy A. A unified framework based on the binding polynomial for characterizing biological systems by isothermal titration calorimetry. Methods. 2015;76:99–115.
- Ferenczy G, Keseru G. Physico-chemical and computational approaches to drug discovery Royal Society of Chemistry. Cambridge; 2012. Chapter 2. Thermodynamics of ligand binding. RSC Publishing. p. 23–79.
- Schiebel J, Radeva N, Krimmer SG, et al. Six biophysical screening methods miss a large proportion of crystallographically discovered fragment hits: a case study. ACS Chem Biol. 2016;11:1693–1701.
- Meiby E, Simmonite H, le Strat L, et al. Fragment screening by weak affinity chromatography: comparison of established techniques for screening against HSP90. Anal Chem. 2013;85(14):6756–6766.
- Kobayashi M, Retra K, Figaroa F, et al. Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification. J Biomol Screen. 2010;15:978–989.
- Wielens J, Headey SJ, Rhodes DI, et al. Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? J Biomol Screen. 2013;18:147–159.
- Lipinski CA. Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Tox Methods. 2000;44:235–249.
- Stegemann S, Leveiller F, Franchi D, et al. When poor solubility becomes an issue: from early stage to proof of concept. Eur J Pharma Sci. 2007;31:249–261.s.
- McGovern SL, Helfand BT, Feng B, et al. A specific mechanism of nonspecific inhibition. J Med Chem. 2003;46:4265–4272.