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

• Since 11/2019 Postdoctoral reasearch associate in the group of Prof. Dr. Frank Böckler
• 10/2017-10/2019 Industry collaboration (External Postdoc)
• 12/2018 Teaching Prize awarded by the Pharmacy Department, University of Tuebingen
• 10/2016 Merckle Promotionspreis
• November 2015: CIC-Förderpreis für Computational Chemistry (PhD prize) of the GDCh
• 2009-2015: PhD student in the group of Prof. Dr. Frank Böckler
• April 2009: Graduation (Bioinformatik-Diplom)
  Group of Prof. Dr. Oliver Kohlbacher
  Group of Prof. Dr. Stefan Laufer
  Thesis: "Strukturelle Analyse von Kinaseinhibitoren und Selektivitätsbestimmung unter Anwendung von Entscheidungsbäumen"
• 2004: Final examination of undergraduate studies in Bioinformatics (Vordiplom)
• 2000-2001: Mandatory civillian service at Deutsches Institut für Ärztliche Mission eV (Difäm, Tropenklinik Paul-Lechler-Krankenhaus), Tübingen
• 2000: Allgemeine Hochschulreife, Geschwister-Scholl-Gymnasium Tübingen

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)
14. 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)
15. 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)
16. 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)
17. Screening of a Halogen-Enriched Fragment Library Leads to Unconventional Binding Modes
    Stahlecker, J.; Klett, T.; Schwer, M.; Jaag, S.; Dammann, M.; Ernst, L.N.; Braun, M.B.; Zimmermann, M.O.; Kramer, M.; Lämmerhofer, M.; Stehle, T.; Coles, M.; Boeckler, F.M.
    J. Med. Chem. 2022 65 (21), 14539-14552 (DOI: 10.1021/acs.jmedchem.2c00951)
18. Revisiting a challenging p53 binding site: a diversity-optimized HEFLib reveals diverse binding modes in T-p53C-Y220C
    Stahlecker, J.; Klett, T.; Schwer, M.; Jaag, S.; Dammann, M.; Ernst, L.N.; Braun, M.B.; Zimmermann, M.O.; Kramer, M.; Lämmerhofer, M.; Stehle, T.; Coles, M.; Boeckler, F.M.
    RSC Med. Chem. 2022,13, 1575-1586 (https://doi.org/10.1039/D2MD00246A)
19. Discovery of Ircinianin Lactones B and C-Two New Cyclic Sesterterpenes from the Marine Sponge Ircinia wistarii
    Majer, T.; Bhattarai, K.; Straetener, J.; Pohlmann, J.; Cahill, P.; Zimmermann, M.O.; Hübner, M.P.; Kaiser, M.; Svenson, J.; Schindler, M.; Brötz-Oesterhelt, H.; Boeckler, F.M., Gross, H.
    Mar. Drugs 2022, 20(8), 532 (https://doi.org/10.3390/md20080532)
20. 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

Prizes

1. Poster Prize, Frontiers in Medicinal Chemistry, Munich, 2013
2. "CIC-Förderpreis für Computational Chemistry" for the PhD thesis of the GDCh, GCC Fulda, 2015
3. Merckle Promotionspreis, Tübingen, 2016
4. Lehrpreis der Eberhard-Karls-Universität Tübingen, Tübingen, 2018

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
21. Systematic Evaluation of Halogenated Heterocyclic Compounds regarding σ-hole Strength and Shape
    M. O. Zimmermann, M. U. Engelhardt, F. M. Boeckler
    4th International Symposium  on Halogen Bonding, Stellenbosch, South Africa 
22. Employing Machine Learning to establish QM-derived Scoring Functions for the Assessment of Halogen-π-Interactions
    M. U. Engelhardt, M. O. Zimmermann, F.-M. Siemers, M. Dammann, S. Vaas, F. M. Boeckler
    4th International Symposium  on Halogen Bonding, Stellenbosch, South Africa 
23. HEFLibs (Halogen Enriched Fragment Library): Screening and Hit Validation 
    M. Dammann, M. U. Engelhardt, S. Vaas, M. O. Zimmermann, F. M. Boeckler
    4th International Symposium  on Halogen Bonding, Stellenbosch, South Africa 
24. Synthesis and Evaluation of Fragments containing Halodifluoro Methyl Groups as Novel XB Donors
    S. Vaas, M. O. Zimmermann, T. Klett, M. U. Engelhardt, M. Dammann, B. Drotleff, M. Lämmerhofer, F. M. Boeckler
    4th International Symposium  on Halogen Bonding, Stellenbosch, South Africa 

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: ChemPLP^XB: 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:

• Übungen zum Praktikum Allgemeine und analytische Chemie der anorganischen Arznei-, Hilfs- und Schadstoffe
• Praktikum "Chemie zum Anfassen"

2. Semester:

• Praktikum "Qualitative und Quantitative Analytik"
• Übungen zum Praktikum "Qualitative und Quantitative Analytik"