Publications
- 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. Drugs 2022, 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 - 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)