Pharmazeutische Chemie

Dr. Markus Zimmermann

Postdoctoral Research Associate
Computational Biologist (Dipl.-Bioinformatiker)

Lab for Molecular Design & Pharmaceutical Biophysics
Institute of Pharmaceutical Sciences
Eberhard Karls University Tuebingen
Auf der Morgenstelle 8
72076 Tuebingen, Germany
Phone (29-)78792 (only within the university)
E-Mail m.zimmermannspam prevention@uni-tuebingen.de

Curriculum Vitae

Publications

  1. 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)
  2. 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, Volume 24, Issue 3, March 2012, Pages 629–634 (doi: 10.1016/j.cellsig.2011.10.013)

  3. 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)
  4. 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 Joerger, and Frank Michael Boeckler
    J. Am. Chem. Soc. 2012, 134 (15), pp 6810–6818 (doi: 10.1021/ja301056a)
  5. Using halogen bonds to address the protein backbone: a systematic evaluation
    Rainer Wilcken, Markus O. Zimmermann, Andreas Lange, Stefan Zahn, Frank M. Boeckler
    J Comput Aided Mol Des 2012, (doi: 10.1007/s10822-012-9592-8)
  6. 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)
  7. Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology
    Rainer Wilcken, Markus O. Zimmermann, Andreas Lange, Andreas Christian Joerger and Frank M. Boeckler
    J Med Chem, 2012, (Perspective, Link)
  8. 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)
  9. 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)
  10. 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)
  11. 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, Article ASAP, Link
  12. 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)
  13. 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., 2016, Accepted Manuscript
    (doi: 10.1039/C5MD00499C)

Prizes

  1. Poster Prize, Frontiers in Medicinal Chemistry, Munich, 2013
  2. "CIC-Förderpreis für Computational Chemistry" (PhD prize) of the GDCh, GCC Fulda, 2015

Posters

  1. Utilizing Halogen Bonds in Rational Molecular Design - QM investigation of interaction strengths and geometric variablity
    Rainer Wilcken, Markus Zimmermann, Andreas Lange & Frank M. Boeckler
    Celebrating Computational Biology - A tribute to Frank Blaney, Oxford, United Kingdom. September 2010.
  2. QM-Based Evalutation of Nitrogen-Ligand Contacts Driven by Halogen Bonding: Applications for Drug Design
    Andreas Lange, Rainer Wilcken, Markus O. Zimmermann & Frank M. Boeckler
    EFMC-ISMC 2012, XXIInd International Symposium Medicinal Chemistry
  3. Automated Molecular Design of Halogen Bonds by Scaffold Decoration
    Markus O. Zimmermann, Rainer Wilcken, Andreas Lange & Frank M. Boeckler
    EFMC-ISMC 2012, XXIInd International Symposium Medicinal Chemistry
  4. Exploring New Binding Modes Based on Halogen Bonding Using HEFLibs (Halogen-enriched fragment libraries)
    Frank M. Boeckler, Rainer Wilcken, Andreas Lange & Markus O. Zimmermann
    Fragments 2013: 4th RSC-BMSC fragment-based drug discovery symposium
  5. Halogen bonding-based scaffold decoration: Data mining the PDB
    M.O. Zimmermann, A. Lange, R. Wilcken, F.M. Boeckler
    245th ACS National Meeting, New Orleans, 2013
  6. Halogen Bonding in rational drug design: Targeting Histidine
    A. Lange, M.O. Zimmermann, R. Wilcken, F.M. Boeckler
    245th ACS National Meeting, New Orleans, 2013
  7. Designing Halogen Bonds in Protein-Ligand Complexes - Automated Scaffold Decoration
    Markus O. Zimmermann, Andreas Lange & Frank M. Boeckler
    Frontiers in Medicinal Chemistry 2013, Poster Prize Winner
  8. Scaffold Dependency of Halogen Bonding - Quantum Mechanical Investigation of Different Aromatic Ring Systems
    Andreas Lange, Markus O. Zimmermann & Frank M. Boeckler
    Frontiers in Medicinal Chemistry 2013
  9. Aspartate and Glutamate Residues as New Targets for Halogen Bonding
    Andreas Lange, Markus O. Zimmermann & Frank M. Boeckler
    DPhG Jahrestagung 2013
  10. Halogen Bonding: From Scaffold Decoration to Scoring Functions
    Markus O. Zimmermann, Andreas Lange, & Frank M. Boeckler
    DPhG Jahrestagung 2013
  11. Scaffold Dependencies for Halogen-Bonding: Quantum Mechanical Investigation of Nitrogen-Bearing Heterocycles
    Andreas Lange, Markus O. Zimmermann, Thomas E. Exner & Frank M. Boeckler
    GCC 2013
  12. Targetability of Binding Sites by Halogen Bonding
    Markus O. Zimmermann, Andreas Lange, Frank M. Boeckler
    Frontiers in Medicinal Chemistry 2014
  13. Correlation between Vmax of Nitrogen-bearing Heterocycles and their adduct formation energy with N-methylacetamide using Halogen Bonds
    Andreas Lange, Markus O. Zimmermann, Frank M. Boeckler
    Frontiers in Medicinal Chemistry 2014
  14. Addressing Aromatic Residues through Halogen Bonding - Development of an Empirical Scoring Function
    Erdem Veyisoglu, Markus O. Zimmermann, Frank M. Boeckler
    Frontiers in Medicinal Chemistry 2014
  15. Dibenzosuberones as p38 MAP kinase inhibitors with excellent enzyme and whole blood activity - Introduction of amides and esters targeting the hydrophobic region II
    H.K. Wentsch, S. Fischer, M. Zimmermann, S.M. Bauer, S.A. Laufer
    Frontiers in Medicinal Chemistry 2014
  16. Scaffold Effects on Halogen Bond Strength
    Andreas Lange, Markus O. Zimmermann, Thomas E. Exner, Frank M. Boeckler
    1st International Symposium on Halogen Bonding, Lecce, Italy
  17. Application of Halogen Bonding in Molecular Design
    Markus O. Zimmermann, Andreas Lange, Frank M. Boeckler
    1st International Symposium on Halogen Bonding, Lecce, Italy
  18. Development of an Empirical Scoring Function for Halogen-pi Interactions
    Erdem Veyisoglu, Markus O. Zimmermann, Frank M. Boeckler
    1st International Symposium on Halogen Bonding, Lecce, Italy
  19. Quantum Mechanical Investigation of Scaffold Effects on Halogen Bond Strength
    Andreas Lange, Markus O. Zimmermann, Thomas E. Exner, Frank M. Boecker
    248th ACS National Meeting & Exposition, San Francisco, USA
  20. Towards a QM-based Scoring Function for the Recognition and Assessment of Halogen Bonds
    Markus O. Zimmermann, Andreas Lange, Frank M. Boeckler
    248th ACS National Meeting & Exposition, San Francisco, USA

Conference Lectures

  1. Research Telegram: Validated Scoring of Halogen Bonding in Molecular Design
    9th German Conference on Chemoinformatics (GdCh), Fulda, 2013
    Link
  2. Research Telegram: ChemPLPXB: Implementation of QM-based terms for the recognition of halogen bonding in drug design
    11th German Conference of Chemoinformatics (GDCh), Fulda, 2015

Teaching

1. Semester:

2. Semester: