Ralf Flaig

Structural characterisation and drug design of epigenetic regulators

Epigenetic modifications (reversible, heritable genetic changes that occur without changes in DNA sequence) lead to chromatin remodelling, altered gene expression and changes in the cellular phenotype and therefore have been linked to a number of pathologies, including cancer, cardiac disease, neurological disorders, infections and inflammatory diseases. One epigenetic process is histone modification. This is important since gene regulation in eukaryotes requires the coordinate interaction of chromatin-modulating proteins with specific transcription factors. Gene activation and repression is specifically regulated by histone modification at distinct residues. Understanding these mechanisms can therefore provide new and specific theraphies for pathologies caused by these processes.

Currently, my research projects focus on two protein families which have been identified as potential therapeutic targets. One aim is to investigate the structure and function of proteins binding to histone modifying proteins and another aim is to structurally characterise potential inhibitors of lysine demethylases and histone acetylases and elucidate the structural and functional relationships between these proteins and potential small molecule inhibitors, therefore aiding the process of finding potential drug molecules by structure-based optimisation that could possibly enter the step of pre-clinical assessment. The project involves the use of established biochemistry and molecular biology techniques and structure determination by X-ray crystallography.

Beamline development

I am responsible for the overall development of the beamline. This includes the implementation of competitive upgrades to the instrument with a view to fully exploit the capabilities of a future storage ring.

In particular I am developing the implementation of multi-axis goniometry in conjunction with suitable beam diagnostics, new beam delivery optics, development of the experimental end station, including state of the art detectors, in order to enable reliable and sophisticated data collection strategies for macromolecular crystals with the aim to push the limits of structure solution.

My role entails the responsibility of the operation and development of the macromolecular crystallography beamline (MX) I04, contributions to shaping the future of the MX group, user support and research projects in the area of structural biology and beamline technique development, in particular multi-axis goniometry, beam diagnostics and beam delivery implementation, and project management.

Dr. Erika Mancini, University of Sussex, Brighton
Structural studies of chromatin remodellers
 

Prof. David Heery, University of Nottingham
Histone modification and epigenetic regulation
 

Prof. Roland Schuele, University Medical Centre Freiburg (Germany)
Epigenetic modifications
 

Prof. Manfred Jung, Institute of Pharmaceutical Sciences, University of Freiburg (Germany)
Drug development of epigenetic regulators
 

Prof. Ray Owens, PPUK, University of Oxford
Drug development of epigenetic regulators and histone-modifying proteins

Dr. Danilo Belviso, IC-CNR, Bari (Italy)
Structural studies on peroxidases
 

Winter G, Gildea RJ, Paterson NG, Beale J, Gerstel M, Axford D, Vollmar M, McAuley KE, Owen RL, Flaig R, Ashton AW, Hall DR
How best to use photons
Acta Crystallogr D Struct Biol. (2019) Mar 1;75(Pt 3):242-261. doi: 10.1107/S2059798319003528

Dittrich, B., Lübben, J., Mebs, S., Wagner, A., Luger, P., Flaig, R.
Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks.
Chemistry – a European Journal 23(19), 4605-4614 (2017)

Woińska M, Jayatilaka D, Dittrich B, Flaig R, Luger P, Woźniak K, Dominiak PM, Grabowsky S
Validation of X-ray wavefunction refinement
Chemphyschem. (2017) Dec 6;18(23):3334-3351. doi: 10.1002/cphc.201700810

Robaa, D., Wagner, T., Luise, C., Carlino, L., McMillan, J., Flaig, R., Schüle, R., Jung, M., Sippl, W.
Identification and Structure-Activity Relationship Studies of Small-Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1
ChemMedChem, 11, 2327-2338 (2016)
doi: 10.1002/cmdc.201600362

Roatsch, M., Robaa, D., Pippel, M., Nettleship, JE., Reddivari, Y., Bird, LE., Hoffmann, I., Franz, H., Owens, RJ., Schüle, R., Flaig, R., Sippl, W., & Jung, M.
Substituted 2-(2-aminopyrimidin-4-yl)pyridine-4-carboxylates as potent inhibitors of JumonjiC domain-containing histone demethylases
Future Medicinal Chemistry, 8, 1553-1571 (2016)
doi: 10.4155/fmc.15.188

Metzger, E., Willmann, D., McMillan, J., Forne, I., Metzger, P., Gerhardt, S., Petroll, K., von Maessenhausen, A., Urban, S., Schott, A-K., Espejo, A., Eberlin,A., Wohlwend, D., Schüle, KM., Schleicher, M., Perner, S., Bedford,MT., Jung, M., Dengjel, J., Flaig, R., Imhof, A.,Einsle, O. & Schüle, R.
Assembly of methylated KDM1A and CHD1 drives androgen receptor–dependent transcription and translocation
Nature Structural & Molecular Biology, 23, 132–139 (2016)
doi: 10.1038/nsmb.3153

Aller, P., Sanchez-Weatherby, J., Foadi, J., Winter, G., Lobley, C.M., Axford, D., Ashton, A.W., Bellini, D., Brandao-Neto, J., Culurgioni, S., Douangamath, A., Duman, R., Evans, G., Fisher, S., Flaig, R., Hall, D.R., Lukacik, P., Mazzorana, M., McAuley, K.E., Mykhaylyk, V., Owen, R.L., Paterson, N.G., Romano, P., Sandy, J., Sorensen, T., von Delft, F., Wagner, A., Warren, A., Williams, M., Stuart, D.I., Walsh, M.A.
Application of in situ diffraction in high-throughput structure determination platforms
Methods Mol Biol., 1261, 233-53 (2015). doi: 10.1007/978-1-4939-2230-7_13

Duke, E.H.M., Evans, G., Flaig, R., Hall, D.R., Latchem, M., McAuley, K.E., Sandy, D.J., Sorensen, T.L-M., Waterman, D., Johnson, L.N.
The Phase I MX Beam lines at Diamond Light Source.
AIP Conference Proceedings 1234, 165-168 (2010)

Drew, D., Klebsch, M.M., Newstead, S., Flaig, R., De Gier, J-W., Iwata, S., Beis, K.
The structure of the efflux pump AcrB in complex with bile acid.
Molecular Membrane Biology 25 677-682 (2008)
doi: 10.1080/09687680802552257

Greschik, H., Althage, M., Flaig, R., Sato, Y., Chavant, V., Peluso-Iltis, C., Choulier, L., Cronet, P., Rochel, N., Schüle, R., Strömstedt, P-E., Moras, D.
Communication between the ERR-alpha homodimer interface and the PGC-1-alpha
binding surface via the helix 8-9 loop.
J. Biol. Chem. 283 20220-20230 (2008)

Sorensen, T.L-M., McAuley, K.E., Flaig, R., Duke, E.H.M.
New light for science: synchrotron radiation in structural medicine.
Trends in Biotechnology 24(11) 500-508 (2006)
doi:10.1016/j.tibtech.2006.09.006

Flaig, R., Greschik, H., Peluso-Iltis, C., Moras, D.
Structural Basis for the Cell-specific Activities of the NGFI-B and the Nurr1 Ligand-binding Domain.
J. Biol. Chem. 280 19250-19258 (2005)
doi: 10.1074/jbc.M413175200

Kammerer, S., Germain, P., Flaig, R., Peluso-Iltis, C., Mitschler, A., Rochel, N., Gronemeyer, H., Moras, D.
RAR-beta ligand-binding domain bound to an SRC-1 co-activator peptide: purification, crystallization and preliminary X-ray diffraction analysis.
Acta Crystallogr. D60 2048-2050 (2004)

Greschik, H., Flaig, R., Renaud, J-P., Moras, D.
Structural basis for the Deactivation of the Estrogen-related Receptor gamma by Diethylstilbestrol or 4-Hydroxytamoxifen and Determinants of Selectivity
J. Biol. Chem. 279, 33639-33646 (2004)

Wagner, A., Flaig, R., Dittrich, B., Schmidt, H., Koritsanszky, T., Luger, P.
Charge Density and Electrostatic Potentials of two Penicillin Derivatives
Chem. Eur. J. 10, 2977-2982 (2004)

Wagner, A., Flaig, R., Zobel, D., Dittrich, B., Bombicz, P., Strumpel, M., Luger, P., Koritsanszky, T., Krane, H.G.
Structure and Charge Density of a C₆₀-Fullerene Derivative Based on a High Resolution Synchrotron Diffraction Experiment at 100 K
J. Phys. Chem. A106, 6581-6590 (2002)

Kingsford-Adaboh, R., Dittrich, B., Wagner, A., Messerschmidt, M., Flaig, R., Luger, P.
Topological Analysis of D,L-Argininine Monohydrate at 100K
Z. Kristallogr. 217, 168-173 (2002)

Dittrich, B., Koritsanszky, T., Grosche, M., Scherer, W., Flaig, R., Wagner, A., Krane, H.G., Kessler, H., Riemer, C., Schreurs, A.M.M., Luger, P.
Reproducibility and Transferability of Topological Properties: Experimental Charge Density of the Hexapeptide cyclo-(D,L-Pro)₂-(L-Ala)₄ Monohydrate
Acta Crystallogr. B58, 721-727 (2002)

Flaig, R., Koritsanszky, T., Dittrich, B., Wagner, A., Luger, P.
Intra and Intermolecular Topological Properties of Amino Acids - A Comparative Study of Experimental and Theoretical Results
J. Am. Chem. Soc. 124, 3407-3417 (2002)

Flaig, R., Koritsanszky, T., Soyka, R., Häming, L., Luger, P.
Electronic Insight into an AntiThrombotic Agent by High-resolution X-ray Crystallography
Einblick in die elektronische Struktur eines antithrombotischen Wirkstoffs durch hochaufgelöste Röntgenbeugung
Angew. Chem. Int. Ed. 40, 355-359 (2001), Angew. Chem. 113, 368-371 (2001)

Dittrich, B., Flaig, R., Koritsanszky, T., Krane, H.G., Morgenroth, W., Luger, P.
Topological Properties of the Peptide Bond in Glycyl-L-threonine Dihydrate Based on a Fast Synchrotron/CCD-Diffraction Experiment at 100K
Chem. Eur. J. 6, 2582-2589 (2000)

Flaig, R., Koritsanszky, T., Janczak, J., Krane, H.G., Morgenroth, W., Luger, P.
Fast Experiments for Charge Density Determination: Topological Analysis and Electrostatic Potential of the Amino Acids L-Asn, DL-Glu, DL-Ser, and L-Thr
Schnelle Experimente zur Ladungsdichtebestimmung: topologische Analyse und elektrostatisches Potential der Aminosäuren L-Asn, DL-Glu, DL-Ser und L-Thr
Angew. Chem. Int. Ed. 38, 1397-1400 (1999), Angew. Chem. 111, 1494-1497 (1999)

Flaig, R., Koritsanszky, T., Zobel, D., Luger, P.
Topological Analysis of the Experimental Electron Densities of Amino Acids. 1. DL-Aspartic Acid at 20K
J. Am. Chem. Soc. 120, 2227-2238 (1998)

Koritsanszky, T., Flaig, R., Zobel, D., Krane, H.G., Morgenroth, W., Luger, P.
Accurate Experimental Electronic Properties of DL-Proline Monohydrate Obtained Within 1 Day
Science 279, 356-358 (1998)
 

Dissertation/Thesis

Neue experimentelle Methoden der Ladungsdichtebestimmung - New experimental methods of charge density determination, FU Berlin (Germany) (2000)