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Combining 'dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography.

Gelin M, Delfosse V, Allemand F, Hoh F, Sallaz-Damaz Y, Pirocchi M, Bourguet W, Ferrer JL, Labesse G, Guichou JF
Acta Crystallogr D Biol Crystallogr 71 1777-87 (2015)
Related entries: 3rdc, 4xn6, 4xnc, 4xne, 4xoy, 4xoz, 4xp0, 4xp2, 4xp3, 4xrj, 4xrl, 4zsc, 4zsd

Cited: 25 times
EuropePMC logo PMID: 26249358

Abstract

X-ray crystallography is an established technique for ligand screening in fragment-based drug-design projects, but the required manual handling steps - soaking crystals with ligand and the subsequent harvesting - are tedious and limit the throughput of the process. Here, an alternative approach is reported: crystallization plates are pre-coated with potential binders prior to protein crystallization and X-ray diffraction is performed directly 'in situ' (or in-plate). Its performance is demonstrated on distinct and relevant therapeutic targets currently being studied for ligand screening by X-ray crystallography using either a bending-magnet beamline or a rotating-anode generator. The possibility of using DMSO stock solutions of the ligands to be coated opens up a route to screening most chemical libraries.

Articles - 4xld mentioned but not cited (5)

  1. Madecassic acid, the contributor to the anti-colitis effect of madecassoside, enhances the shift of Th17 toward Treg cells via the PPARγ/AMPK/ACC1 pathway. Xu X, Wang Y, Wei Z, Wei W, Zhao P, Tong B, Xia Y, Dai Y. Cell Death Dis 8 e2723 (2017)
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  4. Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPARγ Drug Pioglitazone. Mosure SA, Shang J, Eberhardt J, Brust R, Zheng J, Griffin PR, Forli S, Kojetin DJ. J Med Chem 62 2008-2023 (2019)
  5. Structural dataset for the PPARγ V290M mutant. Puhl AC, Webb P, Polikarpov I. Data Brief 7 1430-1437 (2016)


Reviews citing this publication (3)

  1. Peptidyl-Proline Isomerases (PPIases): Targets for Natural Products and Natural Product-Inspired Compounds. Dunyak BM, Gestwicki JE. J Med Chem 59 9622-9644 (2016)
  2. Protein X-ray Crystallography and Drug Discovery. Maveyraud L, Mourey L. Molecules 25 E1030 (2020)
  3. Guidelines for the successful generation of protein-ligand complex crystals. Müller I. Acta Crystallogr D Struct Biol 73 79-92 (2017)

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  1. Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter. Martinez Molledo M, Quistgaard EM, Flayhan A, Pieprzyk J, Löw C. Structure 26 467-476.e4 (2018)
  2. High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Broecker J, Morizumi T, Ou WL, Klingel V, Kuo A, Kissick DJ, Ishchenko A, Lee MY, Xu S, Makarov O, Cherezov V, Ogata CM, Ernst OP. Nat Protoc 13 260-292 (2018)
  3. PPARγ in Complex with an Antagonist and Inverse Agonist: a Tumble and Trap Mechanism of the Activation Helix. Frkic RL, Marshall AC, Blayo AL, Pukala TL, Kamenecka TM, Griffin PR, Bruning JB. iScience 5 69-79 (2018)
  4. Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor. Schwartz M, Perrot T, Aubert E, Dumarçay S, Favier F, Gérardin P, Morel-Rouhier M, Mulliert G, Saiag F, Didierjean C, Gelhaye E. Sci Rep 8 8472 (2018)
  5. Non-Carbohydrate Glycomimetics as Inhibitors of Calcium(II)-Binding Lectins. Kuhaudomlarp S, Siebs E, Shanina E, Topin J, Joachim I, da Silva Figueiredo Celestino Gomes P, Varrot A, Rognan D, Rademacher C, Imberty A, Titz A. Angew Chem Int Ed Engl 60 8104-8114 (2021)
  6. Discovery of non-peptidic small molecule inhibitors of cyclophilin D as neuroprotective agents in Aβ-induced mitochondrial dysfunction. Park I, Londhe AM, Lim JW, Park BG, Jung SY, Lee JY, Lim SM, No KT, Lee J, Pae AN. J Comput Aided Mol Des 31 929-941 (2017)
  7. Pushing the Limits of Detection of Weak Binding Using Fragment-Based Drug Discovery: Identification of New Cyclophilin Binders. Georgiou C, McNae I, Wear M, Ioannidis H, Michel J, Walkinshaw M. J Mol Biol 429 2556-2570 (2017)
  8. Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B. Skaist Mehlman T, Biel JT, Azeem SM, Nelson ER, Hossain S, Dunnett L, Paterson NG, Douangamath A, Talon R, Axford D, Orins H, von Delft F, Keedy DA. Elife 12 e84632 (2023)
  9. Aminoglycoside binding and catalysis specificity of aminoglycoside 2″-phosphotransferase IVa: A thermodynamic, structural and kinetic study. Kaplan E, Guichou JF, Chaloin L, Kunzelmann S, Leban N, Serpersu EH, Lionne C. Biochim Biophys Acta 1860 802-813 (2016)
  10. Binding of thiazolidinediones to the endoplasmic reticulum protein nutrient-deprivation autophagy factor-1. Geldenhuys WJ, Skolik R, Konkle ME, Menze MA, Long TE, Robart AR. Bioorg Med Chem Lett 29 901-904 (2019)
  11. Structural and Dynamic Elucidation of a Non-acid PPARγ Partial Agonist: SR1988. Frkic RL, Chua BS, Shin Y, Pascal BD, Novick SJ, Kamenecka TM, Griffin PR, Bruning JB. Nucl Receptor Res 5 101350 (2018)
  12. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening. Sui S, Mulichak A, Kulathila R, McGee J, Filiatreault D, Saha S, Cohen A, Song J, Hung H, Selway J, Kirby C, Shrestha OK, Weihofen W, Fodor M, Xu M, Chopra R, Perry SL. J Appl Crystallogr 54 1034-1046 (2021)
  13. High-throughput in situ experimental phasing. Lawrence JM, Orlans J, Evans G, Orville AM, Foadi J, Aller P. Acta Crystallogr D Struct Biol 76 790-801 (2020)
  14. Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design. Loeffler JR, Ehmki ES, Fuchs JE, Liedl KR. J Comput Aided Mol Des 30 391-400 (2016)
  15. Phosphopantetheinyl transferase binding and inhibition by amidino-urea and hydroxypyrimidinethione compounds. Carivenc C, Maveyraud L, Blanger C, Ballereau S, Roy-Camille C, Nguyen MC, Génisson Y, Guilhot C, Chalut C, Pedelacq JD, Mourey L. Sci Rep 11 18042 (2021)
  16. BioisoIdentifier: an online free tool to investigate local structural replacements from PDB. Zhang T, Sun S, Wang R, Li T, Gan B, Zhang Y. J Cheminform 16 7 (2024)
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