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Pritzlaff A, Ferré G, Mulry E, Lin L, Pour NG, Savin DA, Harris M, Eddy MT. Atomic-Scale View of Protein-PEG Interactions that Redirect the Thermal Unfolding Pathway of PEGylated Human Galectin-3. Angew Chem Int Ed Engl 2022; 61:e202203784. [PMID: 35922375 PMCID: PMC9529833 DOI: 10.1002/anie.202203784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 07/28/2023]
Abstract
PEGylation is a promising approach to address the central challenge of applying biologics, i.e., lack of protein stability in the demanding environment of the human body. Wider application is hindered by lack of atomic level understanding of protein-PEG interactions, preventing design of conjugates with predicted properties. We deployed an integrative structural and biophysical approach to address this critical challenge with the PEGylated carbohydrate recognition domain of human galectin-3 (Gal3C), a lectin essential for cell adhesion and potential biologic. PEGylation dramatically increased Gal3C thermal stability, forming a stable intermediate and redirecting its unfolding pathway. Structural details revealed by NMR pointed to a potential role of PEG localization facilitated by charged residues. Replacing these residues subtly altered the protein-PEG interface and thermal unfolding behavior, providing insight into rationally designing conjugates while preserving PEGylation benefits.
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Affiliation(s)
- Amanda Pritzlaff
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Guillaume Ferré
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Emma Mulry
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Ling Lin
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | | | - Daniel A. Savin
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Michael Harris
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Matthew T. Eddy
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
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2
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Pritzlaff A, Ferré G, Mulry E, Lin L, Pour NG, Eddy M, Savin DA, Harris M. Atomic‐Scale View of Protein–PEG Interactions that Redirect the Thermal Unfolding Pathway of PEGylated Human Galectin‐3. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Emma Mulry
- University of Florida Department of Chemistry UNITED STATES
| | - Ling Lin
- University of Florida Department of Chemistry UNITED STATES
| | | | - Matthew Eddy
- University of Florida Chemistry 126 Sisler Hall 32611 Gainesville UNITED STATES
| | | | - Michael Harris
- University of Florida Department of Chemistry UNITED STATES
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3
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Kallen J, Izaac A, Chau S, Wirth E, Schoepfer J, Mah R, Schlapbach A, Stutz S, Vaupel A, Guagnano V, Masuya K, Stachyra TM, Salem B, Chene P, Gessier F, Holzer P, Furet P. Structural States of Hdm2 and HdmX: X-ray Elucidation of Adaptations and Binding Interactions for Different Chemical Compound Classes. ChemMedChem 2019; 14:1305-1314. [PMID: 31066983 DOI: 10.1002/cmdc.201900201] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Indexed: 01/02/2023]
Abstract
Hdm2 (human MDM2, human double minute 2 homologue) counteracts p53 function by direct binding to p53 and by ubiquitin-dependent p53 protein degradation. Activation of p53 by inhibitors of the p53-Hdm2 interaction is being pursued as a therapeutic strategy in p53 wild-type cancers. In addition, HdmX (human MDMX, human MDM4) was also identified as an important therapeutic target to efficiently reactivate p53, and it is likely that dual inhibition of Hdm2 and HdmX is beneficial. Herein we report four new X-ray structures for Hdm2 and five new X-ray structures for HdmX complexes, involving different classes of synthetic compounds (including the worldwide highest resolutions for Hdm2 and HdmX, at 1.13 and 1.20 Å, respectively). We also reveal the key additive 18-crown-ether, which we discovered to enable HdmX crystallization and show its stabilization of various Lys residues. In addition, we report the previously unpublished details of X-ray structure determinations for eight further Hdm2 complexes, including the clinical trial compounds NVP-CGM097 and NVP-HDM201. An analysis of all compound binding modes reveals new and deepened insight into the possible adaptations and structural states of Hdm2 (e.g., flip of F55, flip of Y67, reorientation of H96) and HdmX (e.g., flip of H55, dimer induction), enabling key binding interactions for different compound classes. To facilitate comparisons, we used the same numbering for Hdm2 (as in Q00987) and HdmX (as in O15151, but minus 1). Taken together, these structural insights should prove useful for the design and optimization of further selective and/or dual Hdm2/HdmX inhibitors.
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Affiliation(s)
- Joerg Kallen
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Aude Izaac
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Suzanne Chau
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Emmanuelle Wirth
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Joseph Schoepfer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Robert Mah
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Achim Schlapbach
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Stefan Stutz
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Andrea Vaupel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Vito Guagnano
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | | | - Therese-Marie Stachyra
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Bahaa Salem
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Patrick Chene
- Disease Area Oncology, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Francois Gessier
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Philipp Holzer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Pascal Furet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
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4
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Lee CC, Ko TP, Chen CT, Chan YT, Lo SY, Chang JY, Chen YW, Chung TF, Hsieh HJ, Hsiao CD, Wang AHJ. Crystal Structure of PigA: A Prolyl Thioester-Oxidizing Enzyme in Prodigiosin Biosynthesis. Chembiochem 2018; 20:193-202. [DOI: 10.1002/cbic.201800409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Cheng-Chung Lee
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Chun-Ting Chen
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Yueh-Te Chan
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Shin-Yi Lo
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Jen-Yu Chang
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Ya-Wen Chen
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Ting-Fang Chung
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Hsin-Ju Hsieh
- Industrial Technology Research Institute; 195 Chung Hsing Road Section 4, Chutung Hsinchu 31057 Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry; Academia Sinica; 128 Academia Road Section 2 Taipei 11529 Taiwan
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5
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Yilmaz E, Bier D, Guillory X, Briels J, Ruiz-Blanco YB, Sanchez-Garcia E, Ottmann C, Kaiser M. Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins. Chemistry 2018; 24:13807-13814. [PMID: 29924885 DOI: 10.1002/chem.201801074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/15/2018] [Indexed: 12/26/2022]
Abstract
Previous studies have indicated the presence of defined interactions between oligo or poly(ethylene glycol) (OEG or PEG) and lysine residues. In these interactions, the OEG or PEG residues "wrap around" the lysine amino group, thereby enabling complexation of the amino group by the ether oxygen residues. The resulting biochemical binding affinity and thus biological relevance of this supramolecular interaction however remains unclear so far. Here, we report that OEG-containing phosphophenol ether inhibitors of 14-3-3 proteins also display such a "lysine-wrapping" binding mode. For better investigating the biochemical relevance of this binding mode, we made use of the dimeric nature of 14-3-3 proteins and designed as well as synthesized a set of bivalent 14-3-3 inhibitors for biochemical and X-ray crystallography-based structural studies. We found that all synthesized derivatives adapted the "lysine-wrapping" binding mode in the crystal structures; in solution, a different binding mode is however observed, most probably as the "lysine-wrapping" binding mode turned out to be a rather weak interaction. Accordingly, our studies demonstrate that structural studies of OEG-lysine interactions are difficult to interpret and their presence in structural studies may not automatically be correlated with a relevant interaction also in solution but requires further biochemical studies.
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Affiliation(s)
- Elvan Yilmaz
- Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - David Bier
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Xavier Guillory
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Jeroen Briels
- Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christian Ottmann
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Markus Kaiser
- Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
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6
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Liu T, Zhang G, Evans RE, Trindle CO, Altun Z, DeRosa CA, Wang F, Zhuang M, Fraser CL. Phosphorescence Tuning through Heavy Atom Placement in Unsymmetrical Difluoroboron β‐Diketonate Materials. Chemistry 2018; 24:1859-1869. [DOI: 10.1002/chem.201703513] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Tiandong Liu
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22904 USA
| | - Guoqing Zhang
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22904 USA
- Hefei National Laboratory for Physical Sciences at the Microscale University of Science and Technology of China Hefei, Anhui 230026 P. R. China
| | - Ruffin E. Evans
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22904 USA
- Department of Physics Harvard University Cambridge MA 02138 USA
| | - Carl O. Trindle
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22904 USA
| | - Zikri Altun
- Department of Physics Marmara University Göztepe Kampus Istanbul 34772 Turkey
| | - Christopher A. DeRosa
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22904 USA
| | - Fang Wang
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22904 USA
| | - Meng Zhuang
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22904 USA
| | - Cassandra L. Fraser
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22904 USA
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7
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Doolan AM, Rennie ML, Crowley PB. Protein Recognition by Functionalized Sulfonatocalix[4]arenes. Chemistry 2017; 24:984-991. [PMID: 29125201 DOI: 10.1002/chem.201704931] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 12/31/2022]
Abstract
The interactions of two mono-functionalized sulfonatocalix[4]arenes with cytochrome c were investigated by structural and thermodynamic methods. The replacement of a single sulfonate with either a bromo or a phenyl substituent resulted in altered recognition of cytochrome c as evidenced by X-ray crystallography. The bromo-substituted ligand yielded a new binding mode in which a self-encapsulated calixarene dimer contributed to crystal packing. This ligand also formed a weak halogen bond with the protein. The phenyl-substituted ligand was bound to Lys4 of cytochrome c, in a 1.7 Å resolution crystal structure. A dimeric packing arrangement mediated by ligand-ligand contacts in the crystal suggested a possible assembly mechanism. The different protein recognition properties of these calixarenes are discussed.
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Affiliation(s)
- Aishling M Doolan
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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8
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Mallon M, Dutt S, Schrader T, Crowley PB. Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin. Chembiochem 2016; 17:774-83. [PMID: 26818656 DOI: 10.1002/cbic.201500477] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 11/11/2022]
Abstract
Progress in the field of bio-supramolecular chemistry, the bottom-up assembly of protein-ligand systems, relies on a detailed knowledge of molecular recognition. To address this issue, we have characterised complex formation between human ubiquitin (HUb) and four supramolecular anions. The ligands were: pyrenetetrasulfonic acid (4PSA), p-sulfonato-calix[4]arene (SCLX4), bisphosphate tweezers (CLR01) and meso-tetrakis (4-sulfonatophenyl)porphyrin (TPPS), which vary in net charge, size, shape and hydrophobicity. All four ligands induced significant changes in the HSQC spectrum of HUb. Chemical shift perturbations and line-broadening effects were used to identify binding sites and to quantify affinities. Supporting data were obtained from docking simulations. It was found that these weakly interacting ligands bind to extensive surface patches on HUb. A comparison of the data suggests some general indicators for the protein-binding specificity of supramolecular anions. Differences in binding were observed between the cavity-containing and planar ligands. The former had a preference for the arginine-rich, flexible C terminus of HUb.
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Affiliation(s)
- Madeleine Mallon
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Som Dutt
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.
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9
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Kuo TY, Tseng WH, Chen CH. Force Spectroscopy of Metal-Crown Ether Multivalency: Effect of Local Environments on Energy Landscape and Sensing Kinetics. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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10
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Kuo TY, Tseng WH, Chen CH. Force Spectroscopy of Metal-Crown Ether Multivalency: Effect of Local Environments on Energy Landscape and Sensing Kinetics. Angew Chem Int Ed Engl 2015; 54:9213-7. [DOI: 10.1002/anie.201503948] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/09/2022]
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