Dr. Marcel Bermúdez


Institut für Pharmazie

Postdoctoral researcher


Mechanistic models for transmembrane proteins

Adresse Königin-Luisestr. 2+4
Raum 277
14195 Berlin
Telefon +49 30 838 59870
Fax +49 30 545 4 52686

- Instrumentelle Analytik (3. Semester Pharmazie)

- Molecular Modeling (8. Semester Pharmazie)

- Drug Development (Master Pharmaceutical Sciences)

My research focuses on in silico pharmacology, following the interdisciplinary approach to connect computational methods and molecular pharmacology. I am particularly interested in mechanistic investigations of G protein-coupled receptors (GPCRs) as an important class of drug targets. This includes the investigation of multidimensional receptor functions like selectivity profiles, partial agonism, allosteric modulation, dimerization, and functional selectivity. I believe that a deeper understanding of specific receptor mechanisms can allow drug design to be more rational and goal-oriented. Besides my research on GPCRs, I am also studying other protein classes like bacterial toxins, toll-like receptors, and ion channels.

Peer-reviewed journal articles

  1. M. Bermudez*, A. Bock*, F. Krebs, U. Holzgrabe, K. Mohr, M. J. Lohse and G. Wolber. Ligand-Specific Restriction of Extracellular Conformational Dynamics Constrains Signaling of the M2 Muscarinic Receptor, ACS Chem Biol, 2017. 12(7). [doi:10.1021/acschembio.7b00275]
  2. D. Schaller, S. Hagenow, G. Alpert, A. Naß, R. Schulz, M. Bermudez, H. Stark and G. Wolber. Systematic Data Mining Reveals Synergistic H3R/MCHR1 Ligands, ACS Med. Chem. Lett., 2017. 8 [doi:10.1021/acsmedchemlett.7b00118]
  3. E. Guerrieri*, M. Bermudez*, G. Wolber, I. Berzetei-Gurske, H. Schmidhammer, M. Spetea. Structural determinants of diphenethylamines for interaction with the κ opioid receptor: Synthesis, pharmacology and molecular modeling studies, Bioorg Med Chem Lett, 2016. 26(19). [doi:10.1016/j.bmcl.2016.08.031]
  4. M. Bermudez, J. Mortier, C. Rakers, D. Sydow and G. Wolber. More than a look into a crystal ball - protein structure elucidation guided by molecular dynamics simulations, Drug Discov Today, 2016. 21(11). [doi:10.1016/j.drudis.2016.07.001]
  5. A. Bock*, M. Bermudez*, F. Krebs, C. Matera, B. Chirinda, D. Sydow, C. Dallanoce, U. Holzgrabe, M. De Amici, M. J. Lohse, G. Wolber and K. Mohr. Ligand binding ensembles determine graded agonist efficacies at a G protein-coupled receptor, J Biol Chem, 2016. 291(31). [doi:10.1074/jbc.M116.735431]
  6. S. Köhling, G. Künze, K. Lemmnitzer, M. Bermudez, G. Wolber, J. Schiller, D. Huster and J. Rademann. Chemoenzymatic synthesis of nonasulfated tetrahyaluronan with a paramagnetic tag for studying its complex with interleukin-10, Chem Eur J, 2016. 22(16). [doi:10.1002/chem.201504459]
  7. M. Bermudez, C. Rakers, and G. Wolber. Structural characteristics of the allosteric binding site represent a key to subtype selective modulators of muscarinic acetylcholine receptors, Mol Inf, 2015. 34(8). [doi:10.1002/minf.201500025]
  8. C. Rakers, M. Bermudez, B. G. Keller, J. Mortier, and G. Wolber. Computational close up on protein–protein interactions: how to unravel the invisible using molecular dynamics simulations?, WIREs Comput Mol Sci, 2015. 5(5). [doi:10.1002/wcms.1222]
  9. M. Bermudez and G. Wolber, Structure versus function - the impact of computational methods on the discovery of specific GPCR–ligands, Bioorg Med Chem, 2015. 23(14). [doi:10.1016/j.bmc.2015.03.026]
  10. J. Mortier, C. Rakers, M. Bermudez, M. S. Murgueitio, S. Riniker, and G. Wolber. The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes, Drug Discov Today, 2015. 120(6). [doi:10.1016/j.drudis.2015.01.003]
  11. J. Schmitz, D. van der Mey, M. Bermudez, J. Klöckner, R. Schrage, E. Kostenis, C. Tränkle, G. Wolber, K. Mohr, and U. Holzgrabe, Dualsteric muscarinic antagonists - orthosteric binding pose controls allosteric subtype selectivity, J Med Chem, 2014. 57(15). [doi:10.1021/jm500790x]
  12. M. Levay, K. A. Krobert, K. Wittig, N. Voigt, M. Bermudez, G. Wolber, D. Dobrev, F. O. Levy, and T. Wieland, NSC23766, a widely used inhibitor of Rac1 activation, additionally acts as a competitive antagonist at muscarinic acetylcholine receptors, J Pharmacol Exp Ther, 2013. 347(1). [doi:10.1124/Jpet.113.207266]
  13. J. Leschner, G. Wennerberg, J. Feierler, M. Bermudez, B. Welte, I. Kalatskaya, G. Wolber, and A. Faussner, Interruption of the ionic lock in the bradykinin B-2 receptor results in constitutive internalization and turns several antagonists into strong agonists, J Pharmacol Exp Ther, 2013. 344(1). [doi:10.1124/Jpet.112.199190]
  14. A. Faussner, S. Schussler, J. Feierler, M. Bermudez, J. Pfeifer, K. Schnatbaum, T. Tradler, M. Jochum, G. Wolber, and C. Gibson, Binding characteristics of 3H -JSM10292: a new cell membrane-permeant non-peptide bradykinin B2 receptor antagonist, Br J Pharmacol, 2012. 167(4). [doi:10.1111/J.1476-5381.2012.02054.X]
  15. M. S. Murgueitio, M. Bermudez, J. Mortier, and G. Wolber, In silico virtual screening approaches for anti-viral drug discovery, Drug Discov Today Technol, 2012. 9(3). [doi:10.1016/j.ddtec.2012.07.009]