Publications

  • Fluorescence polarization-based assays for detecting compounds binding to inactive JNK3 and p38alpha MAP kinase
    Francesco Ansideri, Andreas Lange, Ahmed El-Gokha, Frank M. Boeckler & Pierre Koch
    Analytical Biochemistry, 2016, in press
    (doi: 10.1016/j.ab.2016.02.018)

  • Targeting the Protein Backbone with Aryl Halides: Systematic Comparison of Halogen Bonding and pi···pi Interactions using N-methylacetamide
    Markus O. Zimmermann and Frank M. Boeckler
    Med. Chem. Commun., 2015 (doi: 10.1039/C5MD00499C)

  • Exploiting Transient Protein States for the Design of Small-Molecule Stabilizers of Mutant p53
    Andreas C. Joerger, Matthias R. Bauer, Rainer Wilcken, Matthias G.J. Baud, Hannes Harbrecht, Thomas E. Exner, Frank M. Boeckler, John Spencer,  and Alan R. Fersht
    Structure. 2015 Dec 1; 23(12): 2246–2255.
    (doi:  10.1016/j.str.2015.10.016)

  • Targeting the Gatekeeper MET146 of C-Jun N-terminal Kinase 3 (JNK3) Induces a Bivalent Halogen / Chalcogen Bond
    Andreas Lange, Marcel B. Guenther, Felix M. Büttner, Markus O. Zimmermann ,Johannes Heidrich, Susanne Hennig, Stefan Zahn, Christoph Schall, Adrian Sievers-Engler, Francesco Ansideri, Pierre Koch, Michael Laemmerhofer, Thilo Stehle, Stefan A. Laufer & Frank M. Boeckler
    J. Am. Chem. Soc., 2015, 137 (46), pp 14640–14652
    (doi: 10.1021/jacs.5b07090)

  • pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening
    Tamer M. Ibrahim, Matthias R. Bauer, Alexander Dörr, Erdem Veyisoglu, and Frank M. Boeckler
    J. Chem. Inf. Model., 2015, 55 (11), pp 2297–2307
    doi: (10.1021/acs.jcim.5b00475)

  • Data quality in drug discovery: the role of analytical performance in ligand binding assays
    Hermann Wätzig, Imke Oltmann-Norden, Franziska Steinicke, Hassan A. Alhazmi, Markus Nachbar, Deia Abd El-Hady, Hassan M. Albishri, Knut Baumann, Thomas Exner, Frank M. Boeckler, Sami El Deeb
    J Comput Aided Mol Des, (2015), 29:847–865 (doi: 10.1007/s10822-015-9851-6)

  • Experimental and Theoretical Evaluation of the Ethynyl Moiety as a Halogen Bioisostere
    Rainer Wilcken, Markus O. Zimmermann, Matthias R. Bauer, Trevor J. Rutherford, Alan R. Fersht, Andreas C. Joerger, and Frank M. Boeckler
    ACS Chem. Biol., 2015, 10 (12), pp 2725–2732 (doi: 10.1021/acschembio.5b00515)

  • Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization
    Tamer M. Ibrahim, Matthias R. Bauer, and Frank M. Boeckler
    J Cheminform. 2015; 7: 21
    doi: (10.1186/s13321-015-0074-6)

  • Evaluating the Potential of Halogen Bonding in Molecular Design: Automated Scaffold Decoration Using the New Scoring Function XBScore
    Markus O. Zimmermann , Andreas Lange , and Frank Michael Boeckler
    J. Chem. Inf. Model, 2015, 55 (3), pp 687–699
    (doi: 10.1021/ci5007118)

  • Halogen-enriched fragment libraries as chemical probes for harnessing halogen bonding in fragment-based lead discovery
    Markus O Zimmermann, Andreas Lange, Rainer Wilcken, Markus B Cieslik, Thomas E Exner, Andreas C Joerger, Pierre Koch & Frank M Boeckler
    Future Medicinal Chemistry, April 2014, Vol. 6, No. 6, Pages 617-639.
    (Perspective, Link)

  • Machine Learning Estimates of Natural Product Conformational Energies
    Matthias Rupp, Matthias R. Bauer, Rainer Wilcken, Andreas Lange, Michael Reutlinger, Frank M. Boeckler, Gisbert Schneider
    PLOS Computational Biology, 2014, 10 (1)
    (doi: 10.1371/journal.pcbi.1003400)

  • Trisubstituted and tetrasubstituted pyrazolines as a novel class of cell-growth inhibitors in tumor cells with wild type p53
    Mohammad Abdel-Halim,  Adam B. Keeton, Evrim Gurpinar, Bernard D. Gary, Simon M. Vogel, Matthias Engel, Gary A. Piazza, Frank M. Boeckler, Rolf W. Hartmann, Ashraf H. Abadi
    Bioorganic & Medicinal Chemistry, 2013, 21 (23),  7343–7356
    doi: (10.1016/j.bmc.2013.09.055)

  • Hitting a Moving Target: TargetingTransient Protein States
    Matthias R. Bauer, and Frank M. Boeckler
    Structure. 2013; 21 (12), p2095–2097
    doi: (10.1016/j.str.2013.11.003)

  • Targeting histidine sidechains in molecular design through nitrogen-halogen bonds
    Andreas Lange, Markus O. Zimmermann, Rainer Wilcken, Stefan Zahn and Frank M. Boeckler
    J. Chem. Inf. Model., 2013, 53 (12), pp 3178–3189
    (doi: 10.1021/ci4004305)

  • Inferring multi-target QSAR models with taxonomy-based multi-task learning
    Lars Rosenbaum,  Alexander Dörr,  Matthias R Bauer, Frank M Boeckler, and Andreas Zell
    J Cheminform. 2013; 5: 33
    doi: (10.1186/1758-2946-5-33)

  • Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets
    Matthias R. Bauer, Tamer M. Ibrahim, Simon M. Vogel and Frank M. Boeckler
    Journal of Chemical Information and Modeling (2013). (doi: 10.1021/ci400115b)

  • Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology
    Rainer Wilcken, Markus O. Zimmermann, Andreas Lange, Andreas C. Joerger, and Frank M. Boeckler
    Journal of Medicinal Chemistry, 2013
    (Perspective, Link)

  • Dibenzosuberones as p38 Mitogen-Activated Protein Kinase Inhibitors with Low ATP Competitiveness and Outstanding Whole Blood Activity
    Stefan Fischer, Heike K. Wentsch, Svenja C. Mayer-Wrangowski, Markus Zimmermann, Silke M. Bauer, Kirsten Storch, Raimund Niess, Solveigh C. Koeberle, Christian Grütter, Frank M. Boeckler, Daniel Rauh, and Stefan A. Laufer
    J Med Chem, 2012 (Link)

  • Lithocholic Acid is an Endogenous inhibitor for MDM4 and MDM2
    Simon M. Vogel, Matthias R. Bauer, Andreas C. Joerger, Rainer Wilcken, Tobias Brandt, Dmitry B. Veprintsev, Trevor J. Rutherford, Alan R. Fersht, and Frank M. Boeckler
    Proc. Natl. Acad. Sci. USA, 2012, 109 (34), 13584-13589.
    (doi: 10.1073/pnas.1215060109)

  • Using halogen bonds to address the protein backbone: a systematic evaluation
    Rainer Wilcken, Markus O. Zimmermann, Andreas Lange, Stefan Zahn, and Frank M. Boeckler
    J. Comput. Aided Mol. Des. 2012, 26 (8), 935-945.
    (doi: 10.1007/s10822-012-9592-8)

  • Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant p53
    Rainer Wilcken, Xiangrui Liu, Markus O. Zimmermann, Trevor J. Rutherford, Alan R. Fersht, Andreas C. Joerger, and Frank M. Boeckler
    J. Am. Chem. Soc., 2012, 134 (15), 6810-6818.
    (doi: 10.1021/ja301056a)

  • Kinetic mechanism of p53 oncogenic mutant aggregation and its inhibition
    Rainer Wilcken, GuoZhen Wang, Frank M. Boeckler, and Alan R. Fersht

    Proc. Natl. Acad. Sci. USA, 2012,  109 (34), 13584-13589.
    (doi:10.1073/pnas.1211550109)

  • Tri- and Tetrasubstituted Pyrazole Derivates: Regioisomerism Switches Activity from p38MAP Kinase to Important Cancer Kinases
    Bassam Abu Thaher, Martina Arnsmann, Frank Totzke, Jan E. Ehlert, Michael H. G. Kubbutat, Christoph Schächtele, Markus O. Zimmermann, Pierre Koch, Frank M. Boeckler, and Stefan A. Laufer
    Journal of Medicinal Chemistry 2012, 55 (2), 961-965.
    (doi: 10.1021/jm201391u)

  • Intramolecular signaling in tandem-GAF domains from PDE5 and PDE10 studied with a cyanobacterial adenylyl cyclase reporter
    Ana Banjac, Markus O. Zimmermann, Frank M. Boeckler, Ursula Kurz, Anita Schultz, Joachim E. Schultz, Cellular Signalling, 2012, 24 (3), 629–634.
    (doi: 10.1016/j.cellsig.2011.10.013)

  • DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions.
    Simon M. Vogel, Matthias R. Bauer, and Frank M. Boeckler
    Journal of Chemical Information and Modeling, 2011, 51 (10), 2650-2665.
    (doi: 10.1021/ci2001549)

  • Addressing Methionine in Molecular Design through Directed Sulfur–Halogen Bonds
    Rainer Wilcken, Markus O. Zimmermann, Andreas Lange, Stefan Zahn, Barbara Kirchner, Frank M. Boeckler, Journal of Chemical Theory and Computation, 2011, 7 (7), 2307-2315. (doi: 10.1021/ct200245e)

  • Synthesis and Molecular Modeling of Novel Tetrahydro-β-carboline Derivatives with Phosphodiesterase 5 Inhibitory and Anticancer Properties.
    Heba A. Mohamed, Nancy M. R. Girgis, Rainer Wilcken, Matthias R. Bauer, Heather N. Tinsley, Bernard D. Gary, Gary A. Piazza, Frank M. Boeckler, and Ashraf H. Abadi
    Journal of Medicinal Chemistry, 2011, 54 (2), 495–509. (doi: 10.1021/jm100842v)

  • Targeted rescue of a destabilized mutant of p53 by an in silico screened drug
    Frank M. Boeckler, Andreas C. Joerger, Gaurav Jaggi, Trevor J. Rutherford, Dmitry B. Veprintsev, and Alan R. Fersht,
    Proc. Natl. Acad. Sci. USA, 2008, 105 (10), 10360-10365.
    (doi: 10.1073/pnas.0805326105)