CRC 1093 Publications Project A8

Area A: Chemical Ligands and Method

Publications by Dr. Elsa Sánchez-García

Project A8:
Exploring protein-recognition by supramolecular binders with MD and QM/MM methods

G. König, P. Sokkar, N. Pryk, S. Heinrich, D. Möller, G. Cimicata, D. Matzov, P. Dietze, W. Thiel, A. Bashan, J. E. Bandow, J. Zuegg, A. Yonath, F. Schulz, E. Sanchez-Garcia: Rational prioritization strategy allows the design of macrolide derivatives that overcome antibiotic resistance. PNAS November 16, 2021 118 (46) e2113632118; doi: 10.1073/pnas.2113632118

R. Malishev, N. Salinas, J. Gibson, A. B. Eden, J. Mieres-Perez, Y. B. Ruiz-Blanco, O. Malka, S. Kolusheva, F. G. Klärner, T. Schrader , E. Sanchez-Garcia, C. Wang, M. Landau, G. Bitan, R. Jelinek: Inhibition of Staphylococcus aureus biofilm-forming functional amyloid by molecular tweezers. Cell Chem Biol 2021 Apr 2:S2451-9456(21)00152-5. doi: 10.1016/j.chembiol.2021.03.013.

A. Meiners, S. Bäcker, I. Hadrovic, C. Heid, C. Beuck, Y. B. Ruiz-Blanco, J. Mieres-Perez, M. Pörschke, J.-N. Grad, C. Vallet, D. Hoffmann, P. Bayer, E. Sanchez-Garcia *, T. Schrader*, S. K. Knauer*: Targeting a protein epitope: Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. *corresponding authors Nat. Comm. 2021, doi 10.1038/s41467-021-21753-9.

D. Schütz, Y. B. Ruiz-Blanco, J. Münch, F. Kirchhoff, E. Sanchez-Garcia, J. A. Müller: Peptide and peptide-based inhibitors of SARS-CoV-2 entry. Adv Drug Deliv Rev 2020 Dec;167:47-65. doi: 10.1016/j.addr.2020.11.007.

T. Weil, R. Groß, A. Röcker, K. Bravo-Rodriguez, C. Heid, A. Sowislok, M.-H. Le, N. Erwin, M. Dwivedi, S. Bart, P. Bates, L. Wettstein, J. Müller, M. Harms, K. Sparrer, Y. B. Ruiz-Blanco, C. Stuerzel, J. von Einem, S. Lippold, C. Read, P. Walther, M. Hebel, F. Kreppel, F.-G. Klärner, G. Bitan, M. Ehrmann, T. Weil, R. Winter, T. Schrader*, J. Shorter*, E. Sanchez-Garcia*, J. Muench*: Supramolecular Mechanism of Viral Envelope Disruption by Molecular Tweezers. J Am Chem Soc. 2020 Sep 14.doi: 10.1021/jacs.0c06400.*corresponding authors

Y. B. Ruiz-Blanco and E. Sanchez-Garcia: CL-FEP: An End-State Free Energy Perturbation Approach. J Chem Theory Comput. 2020, Mar 10;16(3):1396-1410. doi: 10.1021/acs.jctc.9b00725.

N. Berger, L. J. B Wollny, P. Sokkar, S. Mittal, J. Mieres-Perez, R. Stoll, W. Sander, E. Sanchez-Garcia: Solvent-Enhanced Conformational Flexibility of Cyclic Tetrapeptides. Chemphyschem. 2019 Jul 2;20(13):1664-1670. doi: 10.1002/cphc.201900345.

S. Wagner, A. Z. Politi, A. Ast, K. Bravo-Rodriguez, K. Baum, A. Buntru, N. U. Strempel, L. Brusendorf, C. Hänig, A. Boeddrich, S. Plassmann, K. Klockmeier, J. M. Ramirez-Anguita, E. Sanchez-Garcia, J. Wolf and E Wanker: Self -assembly of Mutant Huntingtin Exon-1 Fragments into Large Complex Fibrillar Structures Involves Nucleated Branching. J Mol Biol 2018. 430:1725-1744. doi: 10.1016/j.jmb.2018.03.017

S. Mittal, K. Bravo-Rodriguez, E. Sanchez-Garcia: Mechanism of Inhibition of Beta Amyloid Toxicity by Supramolecular Tweezers. J. Phys. Chem. B. 2018 Apr 19;122(15):4196-4205. doi: 10.1021/acs.jpcb.7b10530. Epub 2018 Apr 9.

T. Vöpel, K. Bravo-Rodriguez, S. Mittal, S. Vachharajani, D. Gnutt, A. Sharma, A. Steinhof, O. Fatoba, G. Ellrichmann, M. Nshanian, C. Heid, J. A. Loo, F. G. Klärner, T. Schrader, G. Bitan, E. E. Wanker, S. Ebbinghaus E. Sanchez-Garcia: Inhibition of Huntingtin Exon-1 Aggregation by the Molecular Tweezer CLR01. J. Am. Chem. Soc. 2017 Apr 26;139(16):5640-5643. doi: 10.1021/jacs.6b11039.

E. Lump, L. M. Castellano, C. Meier, J. Seeliger, N. Erwin, B. Sperlich, C. M. Stürzel, S. Usmani, R. M. Hammond, J. von Einem, G. Gerold, F. Kreppel, K. Bravo-Rodriguez, T. Pietschmann, V. M. Holmes, D. Palesch, O. Zirafi, D. Weissman, A. Sowislok, B. Wettig, C. Heid, F. Kirchhoff, T. Weil, F.-G. Klärner, T. Schrader, G. Bitan, E. Sanchez-Garcia, R. Winter, J. Shorter, J. Münch: Molecular Tweezers Inhibit Islet Amyloid Polypeptide Assembly and Toxicity by a New Mechanism. eLife. 2015; 4:e05397. DOI: 10.7554/eLife.05397

D.H. Lopes, A. Attar, G. Nair, E.Y. Hayden, Z. Du, K. McDaniel, S. Dutt, K. Bravo-Rodriguez, .S Mittal, F.G. Klärner, C. Wang, E. Sanchez-Garcia, T. Schrader, G. Bitan: Molecular Tweezers Inhibit Islet Amyloid Polypeptide Assembly and Toxicity by a New Mechanism. ACS Chem Biol . 2015 Apr 16.

P. Costa, I. Trosien, M. Fernandez-Oliva, E. Sanchez-Garcia, W. Sander: The Fluorenyl Cation Angewandte Chemie . 2015 54, 2656-2660. (VIP publication and Journal Cover)

P. Sokkar, E. Boulanger, W. Thiel, E. Sanchez-Garcia: Hybrid Quantum Mechanics/Molecular Mechanics/Coarse-Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems”. Journal of Chemical Theory and Computation. 2015 DOI: 10.1021/ct500956u (Journal Cover)

P. Costa, M. Fernandez Oliva, E. Sanchez-Garcia, W. Sander: The Highly Reactive Benzhydryl Cation Isolated and Stabilized in Water Ice Journal of the American Chemical Society . ), 136, 15625−15630. Featured in JACS Spotlights and Journal Cover).

K. Bravo-Rodriguez, Kenny, A. F. Ismail-Ali, S. Klopries, S. Kushnir, S. Ismail, E. K. Fansa, A. Wittinghofer, F. Schulz and E. Sanchez-Garcia: Predicted Incorporation of Non-Native Substrates by a Polyketide Synthase Yields Bioactive Natural Product Derivatives. Chembiochem. 2014 15, 1991–1997.

U. Sundermann, K. Bravo-Rodriguez, S. Klopries, S. Kushnir, H. Gomez, E. Sánchez-Garcia, F. Schulz: Enzyme-Directed Mutasynthesis: A Combined Experimental and Theoretical Approach to Substrate Recognition of a Polyketide Synthase. ACS Chem. Biol. 2013, 8, 443−450.

S. Dutt, C. Wilch, T. Gersthagen, P. Talbiersky, K. Bravo-Rodriguez, M. Hanni, E. Sanchez-Garcia,C. Ochsenfeld, F.G. Klärner, T. Schrader: Molecular tweezers with varying anions: a comparative study. J Org Chem 2013, Jul 5;78(13): 6721-34.

D. Bier, R. Rose, K. Bravo-Rodriguez, M. Bartel, J. M. Ramirez-Anguita, S. Dutt, C. Wilch, F.-G. Klärner, E. Sánchez-Garcia, T. Schrader, C. Ottmann: Molecular tweezers modulate 14-3-3 protein-protein interactions. Nat. Chem. 2013, 5, 234-239.

E. W. Hernández-Rodríguez, E. Sánchez-García, R. Crespo-Otero, A. L. Montero Alejo, L. A. Montero, W. Thiel: Understanding Rhodopsin Mutations Linked to the Retinitis Pigmentosa Disease: A QM/MM and DFT/MRCI Study. J. Phys. Chem. B. 2012, 116, 1060-76.

Y-W Hsiao, E. Sánchez-Garcia, M. Doerr, W. Thiel: Quantum Refinement of Protein Structures: Implementation and Application to the Red Fluorescent Protein DsRed.M1. J. Phys. Chem. B. 2010, 114, 15413-15423.

E. Sánchez-Garcia, M. Doerr, W. Thiel: QM/MM Study of the Absorption Spectra of DsRed.M1 Chromophores, J. Comp. Chem. 2009, 31, 1603-1612.

E. Sánchez-Garcia, M. Doerr; W. Thiel: QM/MM Study of the Monomeric Red Fluorescent Protein DsRed.M1. J. Phys. Chem. B. 2009, 113, 16622-16631.

More Publications Area A

  • Project A1
    Protein-recognition by supramolecular ligands from focused combinatorial libraries (Carsten Schmuck)
  • Project A2
    Natural products as starting structures for the development of supramolecular ligands (Markus Kaiser)
  • Project A3
    Designed copolymers and molecular tweezers for protein surface recognition (Thomas Schrader)
  • Project A5
    Protein-specific nanoparticles for cellular uptake (Matthias Epple)
  • Project A6
    DNA-based nanocontainers for predesigned spatial confinement of proteins (Barbara Saccà)
  • Project A7
    Pareto-optimization of protein-surface targeting supramolecular binders with hetero-avidity (Daniel Hoffmann)
  • Project A8
  • Project A9
    Raman spectroscopic monitoring of protein recognition by supramolecular ligands (Sebastian Schlücker)

Biological Targets Publications Area B

  • Project B1
    Supramolecular ligands modulate assembly and function of HtrA proteases (Michael Ehrmann)
  • Project B2
    Probing mechanisms of the Cdc48/p97 segregase with designed supramolecular ligands (Hemmo Meyer)
  • Project B3
    Supramolecular specific inhibitors of intestinal proteases against ischemia/reperfusion injury (Herbert de Groot)
  • Project B4
    Modulation of 14-3-3 protein-protein interactions by supramolecular chemistry (Christian Ottmann)
  • Project B5
    Dissection and modulation of (patho)biological Survivin functions by supramolecular ligands (Shirley Knauer)
  • Project B6
    Targeting centromer recruitment of mitotic regulators by supramolecular ligands (Andrea Musacchio)