Zhang Group - Publications | B CUBE Center for Molecular Bioengineering

2020

Arranging Small Molecules with Sub-Nanometer Precision on DNA Origami Substrates for the Single-Molecule Investigation of Protein-Ligand Interactions

Jingyuan Huang, Antonio Suma, Meiying Cui, Guido Grundmeier, Vincenzo Carnevale, Yixin Zhang,* Charlotte Kielar, and Adrian Keller*

Small structures (accepted)

A Novel Synthetic, Xeno-free Biomimetic Surface for Serum-free Expansion of Human Mesenchymal Stromal Cells

Kristina Thamm, Kristin Möbus, Russell Towers, Sandra Segeletz, Richard Wetzel, Martin Bornhäuser, Yixin Zhang, Manja Wobus*

Advanced Biosystems

Influence of the Geometry of Fluorescently Labelled DNA Constructs on Fluorescence Anisotropy Assay

Tomas Brom, Francesco V. Reddavide, Stephan Heiden, Michael Thompson*, Yixin Zhang*

Biochemical and Biophysical Research Communications

Advancing DNA Steganography with Incorporation of Randomness

Meiying Cui, Yixin Zhang

ChemBioChem

Screening a Chemically Defined Extracellular Matrix Mimetic Substrate Library to Identify Substrates That Enhance Substrate-Mediated Transfection

Andrew Hamann, Alvin K Thomas, Tyler Kozisek, Eric Farris, Steffen Lück, Yixin Zhang*, Angela K. Pannier*

Exp. Biol. Med., 2020 Apr;245(7):606-619.

2019

DNA-Encoded Fragment Libraries: Dynamic Assembly, Single-Molecule Detection, and High-Throughput Hit Validation

F. V. Reddavide, M. Thompson, L. Mannocci, Y. Zhang

Aldrichimica Acta Vol. 52, No. 3, 2019 p63

Neuron-glia interaction through Serotonin-BDNF-NGFR axis underlies the regenerative neurogenesis after Amyloid toxicity in zebrafish brain

Prabesh Bhattarai; Mehmet Ilyas Cosacak; Violeta Mashkaryan; Sevgican Yilmaz; Stanislava Dimitrova Popova; Nambirajan Govindarajan; Kerstin Brandt; Yixin Zhang; Caghan Kizil

PLOS Biology, 2019

Multivalent electrostatic microtubule-interactions of synthetic peptides are sufficient to mimic advanced MAP-like behaviour

H. Drechsler, Y. Xu, V. F. Geyer, Y. Zhang, S. Diez

Mol Biol Cell 30(24), 2953-2968, 2019

Analysis and Modelling of Large and Heterogeneous Populations of DNA Using a PCR-Based Method

Helena Andrade, Alvin K. Thomas, Weilin Lin, Francesco V- Reddavide, Yixin Zhang

ChemBioChem, 2019

Blockchain of Signature Material Combining Cryptographic Hash Function and DNA Steganography

Yixin Zhang

arXiv, 2019

Cytocompatible, Injectable, and Electroconductive Soft Adhesives with Hybrid Covalent/Noncovalent Dynamic Network

Y. Xu, P. A. Patsis, S. Hauser, D. Voigt, R. Rothe, M. Günther, M. Cui, X. Yang, R. Wieduwild, K. Eckert, C. Neinhuis, T. F. Akbar, I. R. Minev, J. Pietzsch*, Y. Zhang*

Advanced Science, 2019

Single-Cell Transcriptomics Analyses of Neural Stem Cell Heterogeneity and Contextual Plasticity in a Zebrafish Brain Model of Amyloid Toxicity

M. I. Cosacak, P. Bhattarai, S. Reinhardt, A. Petzold, A. Dahl, Y. Zhang, C. Kizil*

Cell Reports, 2019, 1307–1318

Engineering Hydrogels beyond a Hydrated Network.

Wieduwild R., Xu Y., Ostrovidov S., Khademhosseini A., Zhang Y.*, Orive G.*

Adv. Healthc. Mater. 2019 Apr 16:e1900038.

Highly Conductive, Stretchable and Cell Adhesive Hydrogel by Nanoclay Doping

C. Tondera, T. F. Akbar, A. K. Thomas, C. Werner, V. Busskamp, Y. Zhang and I. R. Minev*

Small. 2019 Apr 26:e1901406.

Second Generation DNA-Encoded Dynamic Combinatorial Chemical Libraries

Reddavide F. V., Cui M., Lin W., Fu N., Heiden S., Andrade H., Thompson M., Zhang Y.

Chem Commun (Camb). 2019 Mar 26;55(26):3753-3756.

Specificity from Non-Specific Interaction: Regulation of TNF-alpha Activity by DNA

Andrade H., Lin W., Zhang Y.

J Biol Chem. 2019 Apr 19;294(16):6397-6404.

Reversibly Assembled Electroconductive Hydrogel via a Host-Guest Interaction for 3D Cell Culture.

Xu Y., Cui M., Patsis P. A., Günther M., Yang X., Eckert K., Zhang Y.

ACS Appl Mater Interfaces. 2019 Feb 15. doi: 10.1021/acsami.8b19482.

Peptidyl prolyl cis/trans isomerase activity on the cell surface correlates with extracellular matrix development.

Lin W., Bonin M., Boden A., Wieduwild R., Murawala P., Wermke M., Andrade H., Bornhäuser M., Zhang Y.

Commun Biol. 2019 Feb 11;2:58. doi: 10.1038/s42003-019-0315-8.

The Effect of Terminal Modifications on the Adsorption and Assembly of hIAPP(20-29)

Hajiraissi R., Hanke M., Gonzalez O. A. Duderija B., Hofmann U., Zhang Y., Grundmeier G., Keller A.

ACS Omega, 2019, 42, 2649-2660

2018

Pharmacophore Nanoarrays on DNA Origami Substrates as a Single-Molecule Assay for Fragment-based Drug Discovery.

Kielar C., Reddavide F., Tubbenhauer S., Cui M., Xu X., Grundmeier G., Zhang Y.*, Keller A.*

Angew Chem Int Ed Engl. 2018 Sep 14. doi: 10.1002/anie.201806778.

Donor-acceptor Stenhouse adduct-grafted polycarbonate surfaces: selectivity of the reaction for secondary amine on surface.

Singh S.*, Mai P., Borowiec J., Zhang Y., Lei Y., Schober A.

R. Soc. Open. Sci. 2018 Jul 25;5(7):180207. doi: 10.1098/rsos.180207.

3D Culture Method for Alzheimer's Disease Modeling Reveals Interleukin-4 Rescues A?42-Induced Loss of Human Neural Stem Cell Plasticity.

Papadimitriou C., Celikkaya H., Cosacak M. I., Mashkaryan V., Bray L., Bhattarai P., Brandt K., Hollak H., Chen X., He S., Antos C. L., Lin W., Thomas A. K., Dahl A., Kurth T., Friedrichs J., Zhang Y., Freudenberg U., Werner C., Kizil C.*

Dev. Cell. 2018 Jul 2;46(1):85-101.e8. doi: 10.1016/j.devcel.2018.06.005.

Layer-by-Layer assembly of heparin and peptide-polyethylene glycol conjugates to form hybrid nanothin films of biomatrices

A. K. Thomas, R. Wieduwild, R. Zimmermann, W. Lin, J. Friedrichs, M. Bickle, K. Fahmy, C. Werner, Y. Zhang*

ACS Applied Materials & Interfaces, 2018 May 2;10(17):14264-14270.

Non-covalently Assembled Electroconductive Hydrogel

Y. Xu, X. Yang, A. K. Thomas, P. Patsis, T. Kurth, M. Kräter, K. Eckert, M. Bornhäuser, Y. Zhang*

ACS Applied Materials & Interfaces, 2018 May 2;10(17):14418-14425.

Coacervation-Mediated Combinatorial Synthesis of Biomatrices for Stem Cell Culture and Directed Differentiation

R. Wieduwild, R. Wetzel, D. Husman, S. Bauer, I. El-Sayed, S. Duin, P. Murawala, A. K. Thomas, M. Wobus, M. Bornhäuser, Y. Zhang*

Advanced Materials, 2018 May;30(22):e1706100

Modelling Large, Dynamic, and Heterogeneous Populations Using DNA Libraries

H. Andrade, A. K. Thomas, W. Lin, F. V. Reddavide, Y. Zhang*

bioRxiv 276873; doi: https://doi.org/10.1101/276873

2017

From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns.

S. Salentin,M. F. Adasme, J. C, Heinrich, V. J. Haup, S. Daminelli, Y. Zhang, M. Schroeder*

Sci Rep. 2017 Sep 12;7(1):11401. doi: 10.1038/s41598-017-11924-4.

Modeling Amyloid-beta42 Toxicity and Neurodegeneration in Adult Zebrafish Brain

P. Bhattarai, A. K. Thomas, M. I. Cosacak, C. Papadimitriou, V. Mashkaryan, Y. Zhang, C. Kizil*

Journal of Visualized Experiments, 2017

The effects of aging on Amyloid-beta42-induced neurodegeneration and regeneration in adult zebrafish brain.

P. Bhattarai, A. K. Thomas, Y. Zhang, C. Kizil*

Neurogenesis. 2017 May 2;4(1):e1322666.

In Vivo Examination of an Injectable Hydrogel System Crosslinked by Peptide–Oligosaccharide Interaction in Immunocompetent Nude Mice.

C. Tondera, R. Wieduwild, E. Röder, C. Werner, Y. Zhang*, J. Pietzsch*

Advanced Functional Materials, 2017 DOI: 10.1002/adfm.201605189

Lab-on-a-chip platform for high throughput drug discovery with DNA-encoded chemical libraries.

S. Grünzner; F. V. Reddavide; C. Steinfelder; M. Cui; M. Busek; U. Klotzbach; Y. Zhang; F. Sonntag

Proc. SPIE 10061, Microfluidics, BioMEMS, and Medical Microsystems XV, 1006111 (28 February 2017); doi: 10.1117/12.2253840

2016

Augmented Reversible Photoswitching of Drug-Target Interaction through “Surface Borrowing”

F. Erdmann, W. Lin, C. Platzer, M. Schmidt, W. Sippl, G. Fischer, Y. Zhang

Biochemical Pharmacology, 2016, 125, 84-92

Thioxylated cyclosporin A for studying protein-drug interactions.

W. Lin, F. Erdmann, A. Quintero, G. Fischer, Y. Zhang

Bioorg Med Chem Lett. 2016, 26(23), 5754-5756

IL4/STAT6 Signaling Activates Neural Stem Cell Proliferation and Neurogenesis upon Amyloid-?42 Aggregation in Adult Zebrafish Brain.

P. Bhattarai, A.K. Thomas, M.I. Cosacak, C. Papadimitriou, V. Mashkaryan, C. Froc, S. Reinhardt, T. Kurth, A. Dahl, Y. Zhang, C. Kizil

Cell Rep. 2016 Oct 18;17(4):941-948. doi: 10.1016/j.celrep.2016.09.075.

New HSP27 inhibitors efficiently suppress drug resistance development in cancer cells

J. Heinrich, S. Donakonda, J. Haupt, P. Lennig, Y. Zhang, M. Schroeder*

Oncotarget, 2016, 7(42):68156-68169.

The pivotal role of reactivity in the design of novel biotinylation reagents for the chemical-proteomics-based identification of vascular accessible biomarkers

S. Hanke, A. Kerner, W. Nadler, A. Trumpp, Y. Zhang, C. Rösli*

Journal of Proteomics 2016, 141, 57

Conformational Heterogeneity of Cyclosporin A in Cyclophilin 18 Binding

W. Lin, A. Quintero, Y. Zhang*

PLOS ONE 2016 Apr 15;11(4):e0153669

Designing an Antibody-based Chaperoning System through Pro-gramming the Binding and Release of Folding Intermediate

T. Liu, C. Sun, C. Li, J. Lee, Y. Park, Y. Zhang*, S. Li*

ACS Chemical Biology 2016 Apr 15;11(4):1090-7

Automated screening for small organic ligands using DNA-encoded chemical libraries

W. Decurtins, M. Wichert, R. Franzini, F. Buller, M. Stravs, Y. Zhang, D. Neri*, J. Scheuermann*

Nature Protocol 2016 Apr;11(4):764-80.

2015

Rational design of dual peptides targeting ghrelin and Y2 receptors to regulate food intake and body

T. Kilian, N. Klöting, R. Bergmann, S. Els-Heindl, S. Babilon, M. Clément-Ziza, Y. Zhang, A. G. Beck-Sickinger, C. Chollet

J. Med. Chem. 2015, 58(10), 4180-93.

Amphipathic DNA origami nanoparticles can scaffold and deform lipid membrane vesicles

A. Czogalla, D. J. Kauert, H. G. Franquelim, V. Uzunova, Y. Zhang, R. Seidel, P. Schwille

Angew. Chem. Int. Ed. Engl. 2015, 54(22), 6501-5

DNA-Encoded Dynamic Combinatorial Chemical Libraries

F. Reddavide, W. Lin, S. Lehnert, Y. Zhang

Angew. Chem. Int. Ed. Engl. 2015, 54(27), 7924-8

Efficient cargo delivery to parenchymal cells of the brain using a short cell-penetrating peptide.

C. Kizil, A. Iltzsche, A. K. Thomas, P. Bhattarai, Y. Zhang, M. Brand

PLoS one 2015, e0124073

Photopatterning of Multifunctional Hydrogels to Direct Adult Neural Precursor Cells

M. Tsurkan, R. Wetzel, H. Pe?rez-Herna?ndez, K. Chwalek, A. Kozlova, U. Freudenberg, G. Kempermann, Y. Zhang, A. Lasagni, C. Werner

Advanced Healthcare Materials 2015, 4(4), 516-21.

Noncovalent hydrogel beads as microcarriers for cell culture.

R. Wieduwild, S. Krishnan, K. Chwalek, A. Boden, M. Nowak, D. Drechsel, C. Werner, Y. Zhang

Angew. Chem. Int. Ed. Engl. 2015, 54(13), 3962-6.

Self-Assembling Hydrogels Crosslinked Solely by Receptor-Ligand Interactions: Tunability, Rationalization of Physical Properties and 3D Cell Culture.

M. Thompson, M. Tsurkan, K. Chwalek, M. Bornhauser, M. Schlierf, C. Werner, Y. Zhang

Chem. Eur. J. 2015, 21(8), 3178

Characterization of DNA-conjugated compounds using a regenerable chip.

W. Lin, F. Reddavide, V. Uzunova, F. Gür, Y. Zhang

Analytical Chemistry, 2015, 87(2):864-8

Open-access and Structured Data in Drug Discovery

Y. Zhang

Biomed Data J, Volume 1, Issue 1, p.39-41 (2015)

2014

Encoding Method for Fast Deconvolution of DNA-encoded Chemical Library.

Y. Zhang, J. Herrmann, R. Wieduwild, A. Boden

(German patent 102014200446.2 approved)

Light Induced Inhibition of Protein Phosphatase Calcineurin

A. Quintero, W. Lin, S. Hermanna, Y. Zhang

Chin. J. Chem. 2014, 32, 1011

Chapter 16. Hit Identification and Hit Follow-up

Zhang Y.

A Handbook for DNA-Encoded Chemistry: Theory and Applications for Exploring Chemical Space and Drug Discovery. 2014, p357-376 (Wiley)

A Repertoire of Peptide Tags for Controlled Drug Release from Injectable Non-covalent Hydrogel.

Wieduwild R., Lin W., Boden A., Kretschmer K., Zhang Y.

Biomacromolecules. 2014, 15(6), 2058-66.

Calcineurin regulates coordinated outgrowth of zebrafish regenerating fins.

Kujawski S., Lin W., Kitte F., Börmel M., Fuchs S., Arulmozhivarman G., Vogt S., Theil D., Zhang Y., Antos C. L.

Developmental Cell. 2014, 28(5), 573-87

2013

Chaperone-like effects of a scFv antibody on the folding of human muscle creatine kinase.

Li S., Sun C., Teng N., Yang W., Zhou L., Zhang Y..

Protein Eng. Des. Sel. 2013, 26(8), p523-31

Minimal Peptide Motif for Non-covalent Peptide-Heparin Hydrogels

Wieduwild R, Tsurkan M, Chwalek K, Murawala P, Nowak M, Freudenberg U, Neinhuis C, Werner C, Zhang Y.

J. Am. Chem. Soc. 2013 Feb 27;135(8):2919-22.

Switchable domain partitioning and diffusion of DNA origami rods on membranes

A. Czogalla, E. P. Petrov, D. J. Kauert, V. Uzunova, Y. Zhang, R. Seidel and P. Schwille

Faraday Discussion, 2013, 161, 31

2012

Discovery of small-molecule interleukin-2 inhibitors from a DNA-encoded chemical library.

Leimbacher M, Zhang Y, Mannocci L, Stravs M, Geppert T, Scheuermann J, Schneider G, Neri D.

Chemistry - A European Journal 2012 Jun 18;18(25):7729-37

2010

Reversible photoswitching of protein function.

F. Erdmann, Y. Zhang

Mol. Biosyst. 2010 Nov;6(11):2103-9.

2009

Discovery of TNF inhibitors from a DNA-encoded chemical library based on diels-alder cycloaddition

Buller F, Zhang Y, Scheuermann J, Schäfer J, Bühlmann P, Neri D.

Chem Biol. 2009 16(10):1075-86.

Augmented photoswitching modulates immune signaling.

Zhang Y, Erdmann F, Fischer G

Nature Chem. Biol. 2009 5(10):724-6.

2008

High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries.

Mannocci L, Zhang Y, Scheuermann J, Leimbacher M, De Bellis G, Rizzi E, Dumelin C, Melkko S, Neri D.

Proc. Natl. Acad. Sci. 2008 105(46):17670-5.

2007

Isolation of high-affinity trypsin inhibitors from a DNA-encoded chemical library.

Melkko S, Zhang Y, Dumelin CE, Scheuermann J, Neri D.

Angew. Chem. Int. Ed. Engl. 2007 46(25):4671-4.

2005

Unexpected side chain effects at residue 8 of cyclosporin a derivatives allow photoswitching of immunosuppression.

Zhang Y, Erdmann F, Baumgrass R, Schutkowski M, Fischer G.

J. Biol. Chem. 2005 280(6):4842-50

2004

Branches on the alpha-C atom of cyclosporin A residue 3 result in direct calcineurin inhibition and rapid cyclophilin 18 binding.

Zhang Y, Baumgrass R, Schutkowski M, Fischer G.

Chembiochem. 2004 5(7):1006-9

Substitution in position 3 of cyclosporin A abolishes the cyclophilin-mediated gain-of-function mechanism but not immunosuppression.

Baumgrass R, Zhang Y, Erdmann F, Thiel A, Weiwad M, Radbruch A, Fischer G.

J. Biol. Chem. 2004 279(4):2470-9

2002

Substrate-based design of reversible Pin1 inhibitors.

Zhang Y, Füssel S, Reimer U, Schutkowski M, Fischer G.

Biochemistry. 2002 41(39):11868-77.

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