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Pedroso CC, Mann VR, Zuberbühler K, Bohn MF, Yu J, Altoe V, Craik CS, Cohen BE. Immunotargeting of Nanocrystals by SpyCatcher Conjugation of Engineered Antibodies. ACS NANO 2021; 15:18374-18384. [PMID: 34694776 PMCID: PMC9035480 DOI: 10.1021/acsnano.1c07856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Inorganic nanocrystals such as quantum dots (QDs) and upconverting nanoparticles (UCNPs) are uniquely suited for quantitative live-cell imaging and are typically functionalized with ligands to study specific receptors or cellular targets. Antibodies (Ab) are among the most useful targeting reagents owing to their high affinities and specificities, but common nanocrystal labeling methods may orient Ab incorrectly, be reversible or denaturing, or lead to Ab-NP complexes too large for some applications. Here, we show that SpyCatcher proteins, which bind and spontaneously form covalent isopeptide bonds with cognate SpyTag peptides, can conjugate engineered Ab to nanoparticle surfaces with control over stability, orientation, and stoichiometry. Compact SpyCatcher-functionalized QDs and UCNPs may be labeled with short-chain variable fragment Ab (scFv) engineered to bind urokinase-type plasminogen activator receptors (uPAR) that are overexpressed in many human cancers. Confocal imaging of anti-uPAR scFv-QD conjugates shows the antibody mediates specific binding and internalization by breast cancer cells expressing uPAR. Time-lapse imaging of photostable scFv-UCNP conjugates shows that Ab binding causes uPAR internalization with a ∼20 min half-life on the cell surface, and uPAR is internalized to endolysosomal compartments distinct from general membrane stains and without significant recycling to the cell surface. The controlled and stable conjugation of engineered Ab to NPs enables targeting of diverse receptors for live-cell study of their distribution, trafficking, and physiology.
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Affiliation(s)
- Cassio C.S. Pedroso
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Victor R. Mann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Kathrin Zuberbühler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Markus-Frederik Bohn
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Jessica Yu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Virginia Altoe
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Bruce E. Cohen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Division of Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Corresponding Author:
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Dolgikh V, Tsarev A, Timofeev S, Zhuravlyov V, Senderskiy I, Lovegrove A, Konarev A. Antibodies raised against a Sunn bug ( Eurygaster integriceps Put.) recombinant protease, rGHP3p2, can inhibit gluten-hydrolyzing activity. Food Sci Nutr 2020; 8:703-708. [PMID: 31993194 PMCID: PMC6977494 DOI: 10.1002/fsn3.1361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/24/2019] [Accepted: 11/25/2019] [Indexed: 11/12/2022] Open
Abstract
Sunn pest or Sunn bug, Eurygaster integriceps Put., salivary gland proteases are responsible for the deterioration of wheat flour quality during dough mixing, resulting from gluten hydrolysis. These proteases are highly heterogeneous and show low sensitivity to most types of proteinaceous inhibitors, meaning that such inhibitors cannot be used to prevent gluten damage. The present study describes the generation of a specific peptide antibody, raised against the active center of the recombinant gluten-hydrolyzing protease (GHP3). The recombinant protein, encoding two repeats of the GHP3 sequence element involved in forming the S4 pocket and binding of substrate at position P4, was designed and expressed in Escherichia coli. The antibodies raised to this recombinant protein showed inhibitory activity against the GHP3 protease. The results indicate that it is possible to design specific antibodies to inhibit wheat-bug gluten-hydrolyzing proteases.
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Affiliation(s)
- Vyacheslav Dolgikh
- Department of Molecular Plant ProtectionAll‐Russian Research Institute of Plant Protection (VIZR)Pushkin, St. PetersburgRussia
| | - Alexander Tsarev
- Department of Molecular Plant ProtectionAll‐Russian Research Institute of Plant Protection (VIZR)Pushkin, St. PetersburgRussia
| | - Sergey Timofeev
- Department of Molecular Plant ProtectionAll‐Russian Research Institute of Plant Protection (VIZR)Pushkin, St. PetersburgRussia
| | - Vladimir Zhuravlyov
- Department of Molecular Plant ProtectionAll‐Russian Research Institute of Plant Protection (VIZR)Pushkin, St. PetersburgRussia
| | - Igor Senderskiy
- Department of Molecular Plant ProtectionAll‐Russian Research Institute of Plant Protection (VIZR)Pushkin, St. PetersburgRussia
| | - Alison Lovegrove
- Plant Biology and Crop Science DepartmentRothamsted ResearchHarpendenUK
| | - Alexander Konarev
- Department of Agicultural EntomologyAll‐Russian Research Institute of Plant Protection (VIZR)Pushkin, St. PetersburgRussia
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Dupont DM, Bjerregaard N, Verpaalen B, Andreasen PA, Jensen JK. Building a Molecular Trap for a Serine Protease from Aptamer and Peptide Modules. Bioconjug Chem 2016; 27:918-26. [PMID: 26926041 DOI: 10.1021/acs.bioconjchem.6b00007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In drug development, molecular intervention strategies are usually based on interference with a single protein function, such as enzyme activity or receptor binding. However, in many cases, protein drug targets are multifunctional, with several molecular functions contributing to their pathophysiological actions. Aptamers and peptides are interesting synthetic building blocks for the design of multivalent molecules capable of modulating multiple functions of a target protein. Here, we report a molecular trap with the ability to interfere with the activation, catalytic activity, receptor binding, etc. of the serine protease urokinase-type plasminogen activator (uPA) by a rational combination of two RNA aptamers and a peptide with different inhibitory properties. The assembly of these artificial inhibitors into one molecule enhanced the inhibitory activity between 10- and 10,000-fold toward several functions of uPA. The study highlights the potential of multivalent designs and illustrates how they can easily be constructed from aptamers and peptides using nucleic acid engineering, chemical synthesis, and bioconjugation chemistry. By aptamer to aptamer and aptamer to peptide conjugation, we created, to the best of our knowledge, the first trivalent molecule which combines three artificial inhibitors binding to three different sites in a protein target. We hypothesize that by simultaneously preventing all of the functional interactions and activities of the target protein, this approach may represent an alternative to siRNA technology for a functional knockout.
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Affiliation(s)
- Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Nils Bjerregaard
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Ben Verpaalen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Jan K Jensen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
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4
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Kaczmarek JZ, Skottrup PD. Selection and characterization of camelid nanobodies towards urokinase-type plasminogen activator. Mol Immunol 2015; 65:384-90. [DOI: 10.1016/j.molimm.2015.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 01/17/2023]
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5
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LeBeau AM, Sevillano N, Markham K, Winter MB, Murphy ST, Hostetter DR, West J, Lowman H, Craik CS, VanBrocklin HF. Imaging active urokinase plasminogen activator in prostate cancer. Cancer Res 2015; 75:1225-35. [PMID: 25672980 DOI: 10.1158/0008-5472.can-14-2185] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022]
Abstract
The increased proteolytic activity of membrane-bound and secreted proteases on the surface of cancer cells and in the transformed stroma is a common characteristic of aggressive metastatic prostate cancer. We describe here the development of an active site-specific probe for detecting a secreted peritumoral protease expressed by cancer cells and the surrounding tumor microenvironment. Using a human fragment antigen-binding phage display library, we identified a human antibody termed U33 that selectively inhibited the active form of the protease urokinase plasminogen activator (uPA, PLAU). In the full-length immunoglobulin form, U33 IgG labeled with near-infrared fluorophores or radionuclides allowed us to noninvasively detect active uPA in prostate cancer xenograft models using optical and single-photon emission computed tomography imaging modalities. U33 IgG labeled with (111)In had a remarkable tumor uptake of 43.2% injected dose per gram (%ID/g) 72 hours after tail vein injection of the radiolabeled probe in subcutaneous xenografts. In addition, U33 was able to image active uPA in small soft-tissue and osseous metastatic lesions using a cardiac dissemination prostate cancer model that recapitulated metastatic human cancer. The favorable imaging properties were the direct result of U33 IgG internalization through an uPA receptor-mediated mechanism in which U33 mimicked the function of the endogenous inhibitor of uPA to gain entry into the cancer cell. Overall, our imaging probe targets a prostate cancer-associated protease, through a unique mechanism, allowing for the noninvasive preclinical imaging of prostate cancer lesions.
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Affiliation(s)
- Aaron M LeBeau
- Center for Molecular and Functional Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California.
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Kate Markham
- CytomX Therapeutics, Inc., South San Francisco, California
| | - Michael B Winter
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Stephanie T Murphy
- Center for Molecular and Functional Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California
| | | | - James West
- CytomX Therapeutics, Inc., South San Francisco, California
| | - Henry Lowman
- CytomX Therapeutics, Inc., South San Francisco, California
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Henry F VanBrocklin
- Center for Molecular and Functional Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California.
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Mengele K, Napieralski R, Magdolen V, Reuning U, Gkazepis A, Sweep F, Brünner N, Foekens J, Harbeck N, Schmitt M. Characteristics of the level-of-evidence-1 disease forecast cancer biomarkers uPA and its inhibitor PAI-1. Expert Rev Mol Diagn 2014; 10:947-62. [DOI: 10.1586/erm.10.73] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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7
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Angelini A, Cendron L, Chen S, Touati J, Winter G, Zanotti G, Heinis C. Bicyclic peptide inhibitor reveals large contact interface with a protease target. ACS Chem Biol 2012; 7:817-21. [PMID: 22304751 DOI: 10.1021/cb200478t] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
From a large combinatorial library of chemically constrained bicyclic peptides we isolated a selective and potent (K(i) = 53 nM) inhibitor of human urokinase-type plasminogen activator (uPA) and crystallized the complex. This revealed an extended structure of the peptide with both peptide loops engaging the target to form a large interaction surface of 701 Å(2) with multiple hydrogen bonds and complementary charge interactions, explaining the high affinity and specificity of the inhibitor. The interface resembles that between two proteins and suggests that these constrained peptides have the potential to act as small protein mimics.
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Affiliation(s)
- Alessandro Angelini
- Institute
of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Laura Cendron
- Department of Biological Chemistry, University of Padua, Viale G. Colombo 3, 35131 Padua,
Italy
- Venetian Institute of Molecular Medicine (VIMM), Via Giuseppe Orus 2, 35129
Padua, Italy
| | - Shiyu Chen
- Institute
of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jeremy Touati
- Institute
of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Greg Winter
- Laboratory of
Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2
0QH, U.K
| | - Giuseppe Zanotti
- Department of Biological Chemistry, University of Padua, Viale G. Colombo 3, 35131 Padua,
Italy
- Venetian Institute of Molecular Medicine (VIMM), Via Giuseppe Orus 2, 35129
Padua, Italy
| | - Christian Heinis
- Institute
of Chemical Sciences
and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Cyranka-Czaja A, Wulhfard S, Neri D, Otlewski J. Selection and characterization of human antibody fragments specific for psoriasin - a cancer associated protein. Biochem Biophys Res Commun 2012; 419:250-5. [PMID: 22342672 DOI: 10.1016/j.bbrc.2012.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 02/01/2012] [Indexed: 10/14/2022]
Abstract
S100A7 (psoriasin) is a calcium-binding protein that is upregulated in many types of cancer and often associated with poor prognosis. Its role in carcinogenesis has been associated with the stimulation of VEGF and EGF activity. The recent research showed that psoriasin directly interacts with αvβ6 integrin, a protein related to the invasive phenotype of cancer. Moreover, this interaction promotes the αvβ6-dependent invasive activity. The important function of S100A7 in carcinoma development determines a great need for valuable tools enabling its detection, quantification and also activity inhibition. Here, we show the selection of S100A7 specific antibody fragments from the human scFv phage library ETH-2 Gold. We have selected antibody fragments specific for psoriasin, purified them and analyzed by BIAcore affinity measurements. The best clone was subjected to affinity maturation procedure yielding molecule with a subnanomolar affinity towards human S100A7 protein. Selected clone was expressed in a bivalent format and applied for immunostaining analysis, which confirmed the ability of the antigen recognition in physiological conditions. We therefore propose that obtained antibody, that is the first phage display-derived human antibody against psoriasin, can serve as a useful psoriasin binding platform in research, diagnostics and therapy of cancer.
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Affiliation(s)
- Anna Cyranka-Czaja
- Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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Schmitt M, Mengele K, Napieralski R, Magdolen V, Reuning U, Gkazepis A, Sweep F, Brünner N, Foekens J, Harbeck N. Clinical utility of level-of-evidence-1 disease forecast cancer biomarkers uPA and its inhibitor PAI-1. Expert Rev Mol Diagn 2011; 10:1051-67. [PMID: 21080821 DOI: 10.1586/erm.10.71] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The prognostic and/or predictive value of the cancer biomarkers, urokinase-type plasminogen activator (uPA) and its inhibitor (plasminogen activator inhibitor [PAI]-1), determined by ELISA in tumor-tissue extracts, was demonstrated for several cancer types in numerous clinically relevant retrospective or prospective studies, including a multicenter breast cancer therapy trial (Chemo-N0). Consequently, for the first time ever for any cancer biomarker for breast cancer, uPA and PAI-1 have reached the highest level of evidence, level-of-evidence-1. At present, two other breast cancer therapy trials, NNBC-3 and Plan B, also incorporating uPA and PAI-1 as treatment-assignment tools are in effect. Furthermore, small synthetic molecules targeting uPA are currently in Phase II clinical trials in patients afflicted with advanced cancer of the ovary, breast or pancreas.
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Affiliation(s)
- Manfred Schmitt
- Frauenklinik der Technischen Universitaet Muenchen, Germany.
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Villa A, Lovato V, Bujak E, Wulhfard S, Pasche N, Neri D. A novel synthetic naïve human antibody library allows the isolation of antibodies against a new epitope of oncofetal fibronectin. MAbs 2011; 3:264-72. [PMID: 21487243 DOI: 10.4161/mabs.3.3.15616] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Human monoclonal antibodies (mAbs) can routinely be isolated from phage display libraries against virtually any protein available in sufficient purity and quantity, but library design can influence epitope coverage on the target antigen. Here we describe the construction of a novel synthetic human antibody phage display library that incorporates hydrophilic or charged residues at position 52 of the CDR2 loop of the variable heavy chain domain, instead of the serine residue found in the corresponding germline gene. The novel library was used to isolate human mAbs to various antigens, including the alternatively-spliced EDA domain of fibronectin, a marker of tumor angiogenesis. In particular, the mAb 2H7 was proven to bind to a novel epitope on EDA, which does not overlap with the one recognized by the clinical-stage F8 antibody. F8 and 2H7 were used for the construction of chelating recombinant antibodies (CRAbs), whose tumor-targeting properties were assessed in vivo in biodistribution studies in mice bearing F9 teratocarcinoma, revealing a preferential accumulation at the tumor site.
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Abstract
Antibodies display great versatility in protein interactions and have become important therapeutic agents for a variety of human diseases. Their ability to discriminate between highly conserved sequences could be of great use for therapeutic approaches that target proteases, for which structural features are conserved among family members. Recent crystal structures of antibody-protease complexes provide exciting insight into the variety of ways antibodies can interfere with the catalytic machinery of serine proteases. The studies revealed the molecular details of two fundamental mechanisms by which antibodies inhibit catalysis of trypsin-like serine proteases, exemplified by hepatocyte growth factor activator and MT-SP1 (matriptase). Enzyme kinetics defines both mechanisms as competitive inhibition systems, yet, on the molecular level, they involve distinct structural elements of the active-site region. In the steric hindrance mechanism, the antibody binds to protruding surface loops and inserts one or two CDR (complementarity-determining region) loops into the enzyme's substrate-binding cleft, which results in obstruction of substrate access. In the allosteric inhibition mechanism the antibody binds outside the active site at the periphery of the substrate-binding cleft and, mediated through a conformational change of a surface loop, imposes structural changes at important substrate interaction sites resulting in impaired catalysis. At the centre of this allosteric mechanism is the 99-loop, which is sandwiched between the substrate and the antibody-binding sites and serves as a mobile conduit between these sites. These findings provide comprehensive structural and functional insight into the molecular versatility of antibodies for interfering with the catalytic machinery of proteases.
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Roesli C, Neri D. Methods for the identification of vascular markers in health and disease: from the bench to the clinic. J Proteomics 2010; 73:2219-29. [PMID: 20541635 DOI: 10.1016/j.jprot.2010.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 05/25/2010] [Accepted: 05/30/2010] [Indexed: 02/07/2023]
Abstract
Several diseases are characterized by changes in the molecular composition of vascular structures, thus offering the opportunity to use specific ligands (e.g., monoclonal antibodies) for imaging and therapy application. This novel pharmaceutical strategy, often referred to as "vascular targeting", promises to facilitate the discovery and development of selective biopharmaceuticals for the management of angiogenesis-related diseases. This article reviews novel biomedical applications based on vascular targeting strategies, as well as methodologies which have been used for the discovery of vascular markers of pathology.
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Affiliation(s)
- Christoph Roesli
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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