Synthesis of Amino Acids Bearing Halodifluoromethyl Moieties and Their Application to p53-Derived Peptides Binding to Mdm2/Mdm4 Sebastian Vaas, Markus O Zimmermann, Theresa Klett, Frank M Boeckler Drug Des. Devel. Ther., 2023, 17:, 1247-1274, 10.2147/DDDT.S406703
Screening of a Halogen-Enriched Fragment Library Leads to Unconventional Binding Modes Marcel Dammann, Jason Stahlecker, Markus O Zimmermann, Theresa Klett, Kilian Rotzinger, Markus Kramer, Murray Coles, Thilo Stehle, Frank M Boeckler J. Med. Chem. 2022, 65, 21, 14539–14552, https://doi.org/10.1021/acs.jmedchem.2c00951
Discovery of Ircinianin Lactones B and C—Two New Cyclic Sesterterpenes from the Marine Sponge Ircinia wistarii Thomas Majer, Keshab Bhattarai, Jan Straetener, Justus Pohlmann, Patrick Cahill, Markus O Zimmermann, Marc P Hübner, Marcel Kaiser, Johan Svenson, Michael Schindler, Heike Brötz-Oesterhelt, Frank M Boeckler, Harald Gross Mar. Drugs2022, 20, 532. https://doi.org/10.3390/md20080532
Revisiting a challenging p53 binding site: A diversity-optimized HEFLib reveals diverse binding modes in T-p53C-Y220C Jason Stahlecker, Theresa Klett, Martin Schwer, Simon Jaag, Marcel Dammann, Larissa N Ernst, Michael B Braun, Markus O Zimmermann, Markus Kramer, Michael Lämmerhofer, Thilo Stehle, Murray Coles, Frank M Boeckler RSC Med. Chem., 2022, 13, 1575-1586, 10.1039/D2MD00246A
Quadruple Target Evaluation of Diversity-Optimized Halogen-Enriched Fragments (HEFLibs) Reveals Substantial Ligand Efficiency for AP2-Associated Protein Kinase 1 (AAK1) Marcel Dammann, Markus Kramer, Markus O. Zimmermann, Frank M. Boeckler Front. Chem., 9, 2022, (https://doi.org/10.3389/fchem.2021.815567)
Identification of N,N-arylalkyl-picolinamide derivatives targeting the RNA- binding protein HuR, by combining biophysical fragment-screening and molecular hybridization Serena Della Volpe, Pasquale Linciano, Roberta Listro, Elisabetta Tumminelli, Marialaura Amadio, Isabelle Bonomo, Walid AM Elgaher, Sebastian Adam, Anna KH Hirsch, Franck M Boeckler, Francesca Vasile, Daniela Rossi, Simona Collina Bioorg. Chem., 116, 2021 https://doi.org/10.1016/j.bioorg.2021.105305
Embracing the Diversity of Halogen Bonding Motifs in Fragment-Based Drug Discovery - Construction of a Diversity-Optimized Halogen-Enriched Fragment Library Johannes Heidrich, Laura E. Sperl, Frank M. Boeckler Front. Chem., 7, 2019 https://doi.org/10.3389/fchem.2019.00009
Scaffold Effects on Halogen Bonding Strength Andreas Lange, Johannes Heidrich, Markus O. Zimmermann, Thomas E. Exner, and Frank M. Boeckler J. Chem. Inf. Model., 2019, 59 (2), pp 885–894 (doi: 10.1021/acs.jcim.8b00621)
Predicting the Magnitude of σ-Holes Using VmaxPred, a Fast and Efficient Tool Supporting the Application of Halogen Bonds in Drug Discovery Johannes Heidrich, Thomas E. Exner, and Frank M. Boeckler J. Chem. Inf. Model., 2019, 59 (2), pp 636–643 (doi: 10.1021/acs.jcim.8b00622)
The Symmetric Tetravalent Sulfhydryl-Specific Linker NATBA Facilitates a Combinatorial “Tool Kit” Strategy for Phage Display-Based Selection of Functionalized Bicyclic Peptides Christoph Ernst, Julia Sindlinger, Dirk Schwarzer, Pierre Koch , and Frank M. Boeckler ACS Omega, 2018, 3 (10), pp 12361–12368 (doi: 10.1021/acsomega.8b01814)
Switching Between Bicyclic and Linear Peptides — The Sulfhydryl-Specific Linker TPSMB Enables Reversible Cyclization of Peptides Christoph Ernst, Johannes Heidrich, Catharina Sessler, Julia Sindlinger, Dirk Schwarzer, Pierre Koch and Frank M. Boeckler Frontiers in Chemistry, 2018, 6, 484 (doi: https://doi.org/10.3389/fchem.2018.00484)
Structural Optimization of a Pyridinylimidazole Scaffold: Shifting the Selectivity from p38α Mitogen-Activated Protein Kinase to c-Jun N-Terminal Kinase 3 Francesco Ansideri, Joana T. Macedo, Michael Eitel, Ahmed El-Gokha, Dhafer S. Zinad, Camilla Scarpellini, Mark Kudolo, Dieter Schollmeyer, Frank M. Boeckler, Bärbel S. Blaum, Stefan A. Laufer , and Pierre Koch ACS Omega, 2018, 3 (7), pp 7809–7831 (doi: 10.1021/acsomega.8b00668)
Tri- and Tetrasubstituted Pyridinylimidazoles as Covalent Inhibitors of c-Jun N-Terminal Kinase 3
Felix Muth, Ahmed El-Gokha, Francesco Ansideri, Michael Eitel, Eva Döring, Adrian Sievers-Engler, Andreas Lange, Frank M. Boeckler, Michael Lämmerhofer, Pierre Koch, and Stefan A. Laufer J. Med. Chem., 2017, 60 (2), pp 594–607 (doi: 10.1021/acs.jmedchem.6b01180)
Fluorescence polarization-based competition binding assay for c-Jun N-terminal kinases 1 and 2 Francesco Ansideri, Marcel Dammann, Frank M. Boeckler, Pierre Koch Analytical Biochemistry, 2017, 532, pp 26-28 (doi: https://doi.org/10.1016/j.ab.2017.05.022)
Arylpiperidines as a new class of oxidosqualene cyclase inhibitors Marco Keller, Annette Wolfgardt, Christoph Müller, Rainer Wilcken, Frank M. Boeckler, Simonetta Oliaro-Bosso, Terenzio Ferrante, Gianni Balliano, Franz Bracher European Journal of Medicinal Chemistry, 2016, 109, pp 13-22 (doi: https://doi.org/10.1016/j.ejmech.2015.12.025)
Harnessing Fluorine–Sulfur Contacts and Multipolar Interactions for the Design of p53 Mutant Y220C Rescue Drugs Matthias R. Bauer, Rhiannon N. Jones, Matthias G. J. Baud, Rainer Wilcken, Frank M. Boeckler, Alan R. Fersht, Andreas C. Joerger, and John Spencer ACS Chem. Biol., 2016, 11 (8), pp 2265–2274 (doi: 10.1021/acschembio.6b00315)
Using Surface Scans for the Evaluation of Halogen Bonds toward the Side Chains of Aspartate, Asparagine, Glutamate, and Glutamine Markus O. Zimmermann, Andreas Lange, Stefan Zahn, Thomas E. Exner, and Frank M. Boeckler J. Chem. Inf. Model., 2016, 56 (7), pp 1373–1383 (doi: 10.1021/acs.jcim.6b00075)
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, 503, pp 28-40 (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
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)
