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How Do Molecular Tweezers Bind to Proteins? Lessons from X-ray Crystallography. Molecules 2024; 29:1764. [PMID: 38675584 PMCID: PMC11051928 DOI: 10.3390/molecules29081764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
To understand the biological relevance and mode of action of artificial protein ligands, crystal structures with their protein targets are essential. Here, we describe and investigate all known crystal structures that contain a so-called "molecular tweezer" or one of its derivatives with an attached natural ligand on the respective target protein. The aromatic ring system of these compounds is able to include lysine and arginine side chains, supported by one or two phosphate groups that are attached to the half-moon-shaped molecule. Due to their marked preference for basic amino acids and the fully reversible binding mode, molecular tweezers are able to counteract pathologic protein aggregation and are currently being developed as disease-modifying therapies against neurodegenerative diseases such as Alzheimer's and Parkinson's disease. We analyzed the corresponding crystal structures with 14-3-3 proteins in complex with mono- and diphosphate tweezers. Furthermore, we solved crystal structures of two different tweezer variants in complex with the enzyme Δ1-Pyrroline-5-carboxyl-dehydrogenase (P5CDH) and found that the tweezers are bound to a lysine and methionine side chain, respectively. The different binding modes and their implications for affinity and specificity are discussed, as well as the general problems in crystallizing protein complexes with artificial ligands.
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Günter Wulff (1935 -2023): Father of Molecular Imprinting. Angew Chem Int Ed Engl 2024; 63:e202402244. [PMID: 38372496 DOI: 10.1002/anie.202402244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Günter Wulff, internationally well known for his invention of Molecular Imprinting, passed away on December 11, 2023 in Erkrath-Hochdahl, Germany, not far from the University of Düsseldorf, where he made his greatest discoveries. A passionate researcher and deep conceptual thinker, he greatly advanced our understanding of polymer chemistry.
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Characterization of Molecular Tweezer Binding on α-Synuclein with Native Top-Down Mass Spectrometry and Ion Mobility-Mass Spectrometry Reveals a Mechanism for Aggregation Inhibition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2739-2747. [PMID: 37936057 PMCID: PMC10959575 DOI: 10.1021/jasms.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Parkinson's disease, a neurodegenerative disease that affects 15 million people worldwide, is characterized by deposition of α-synuclein into Lewy Bodies in brain neurons. Although this disease is prevalent worldwide, a therapy or cure has yet to be found. Several small compounds have been reported to disrupt fibril formation. Among these compounds is a molecular tweezer known as CLR01 that targets lysine and arginine residues. This study aims to characterize how CLR01 interacts with various proteoforms of α-synuclein and how the structure of α-synuclein is subsequently altered. Native mass spectrometry (nMS) measurements of α-synuclein/CLR01 complexes reveal that multiple CLR01 molecules can bind to α-synuclein proteoforms such as α-synuclein phosphorylated at Ser-129 and α-synuclein bound with copper and manganese ions. The binding of one CLR01 molecule shifts the ability for α-synuclein to bind other ligands. Electron capture dissociation (ECD) with Fourier transform-ion cyclotron resonance (FT-ICR) top-down (TD) mass spectrometry of α-synuclein/CLR01 complexes pinpoints the locations of the modifications on each proteoform and reveals that CLR01 binds to the N-terminal region of α-synuclein. CLR01 binding compacts the gas-phase structure of α-synuclein, as shown by ion mobility-mass spectrometry (IM-MS). These data suggest that when multiple CLR01 molecules bind, the N-terminus of α-synuclein shifts toward a more compact state. This compaction suggests a mechanism for CLR01 halting the formation of oligomers and fibrils involved in many neurodegenerative diseases.
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Design and Synthesis of Artificial Nucleobases for Sequence-Selective DNA Recognition within the Major Groove. Chem Asian J 2023; 18:e202300637. [PMID: 37616375 DOI: 10.1002/asia.202300637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 08/26/2023]
Abstract
We present the design and synthesis of artificial specific nucleobases, each one recognizing a single base pair within the major groove of duplex DNA. Computational calculations indicate that PNAs modified with these nucleobases enable the formation of highly stable triple helices with no sequence restrictions through multiple hydrogen bonding and π⋅⋅⋅π stacking interactions, without significantly widening the DNA double helix. New synthetic routes were developed to the structures of these fused heterocycles which have rarely been described in the literature. NMR titration experiments indicate specific hydrogen bonding at the Hoogsteen sites. The new building blocks allow the construction of four PNA monomers for each canonic base pair and their covalent connection to PNA oligomers. These can be designed complementary to any given DNA sequence. With high efficiency and relative simplicity of operation, the described methodologies and strategies hence form the basis for a new supramolecular ligand system targeting double-stranded DNA without strand invasion.
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Evaluating Interoperability in German Critical Incident Reporting Systems. Stud Health Technol Inform 2023; 307:249-257. [PMID: 37697860 DOI: 10.3233/shti230722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
INTRODUCTION In industrialised countries, one in ten patients suffers harm during hospitalization. Critical Incident Reporting Systems (CIRS) aim to minimize this by learning from errors and identifying potential risks. However, a lack of interoperability among the 16 CIRS in Germany hampers their effectiveness. METHODS This study investigates reports' syntactic and semantic interoperability across seven different reporting systems. Syntactic interoperability was examined using WHO's Minimal Information Models (MIM), while semantic interoperability was evaluated with SNOMED concepts. RESULTS The findings reveal a low structural overlap, with only two terms correctly represented in the SNOMED CT terminology. In addition, most systems showed no syntactic interoperability. CONCLUSION Improving interoperability is essential for increasing the effectiveness and usability of CIRS. The study suggests a unified data model such as MIM or using Health Level 7 Fast Healthcare Interoperability Resources (HL7 FHIR) resources and expanding SNOMED CT with patient safety-relevant terms for semantic interoperability. Given the current lack of both syntactic and semantic interoperability in CIRS, developing a patient safety ontology is recommended for efficient critical incident analysis too.
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Potentiating Tweezer Affinity to a Protein Interface with Sequence-Defined Macromolecules on Nanoparticles. Biomacromolecules 2023; 24:3666-3679. [PMID: 37507377 DOI: 10.1021/acs.biomac.3c00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Survivin, a well-known member of the inhibitor of apoptosis protein family, is upregulated in many cancer cells, which is associated with resistance to chemotherapy. To circumvent this, inhibitors are currently being developed to interfere with the nuclear export of survivin by targeting its protein-protein interaction (PPI) with the export receptor CRM1. Here, we combine for the first time a supramolecular tweezer motif, sequence-defined macromolecular scaffolds, and ultrasmall Au nanoparticles (us-AuNPs) to tailor a high avidity inhibitor targeting the survivin-CRM1 interaction. A series of biophysical and biochemical experiments, including surface plasmon resonance measurements and their multivalent evaluation by EVILFIT, reveal that for divalent macromolecular constructs with increasing linker distance, the longest linkers show superior affinity, slower dissociation, as well as more efficient PPI inhibition. As a drawback, these macromolecular tweezer conjugates do not enter cells, a critical feature for potential applications. The problem is solved by immobilizing the tweezer conjugates onto us-AuNPs, which enables efficient transport into HeLa cells. On the nanoparticles, the tweezer valency rises from 2 to 16 and produces a 100-fold avidity increase. The hierarchical combination of different scaffolds and controlled multivalent presentation of supramolecular binders was the key to the development of highly efficient survivin-CRM1 competitors. This concept may also be useful for other PPIs.
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Multivalent Molecular Tweezers Disrupt the Essential NDC80 Interaction with Microtubules. J Am Chem Soc 2023. [PMID: 37392180 DOI: 10.1021/jacs.3c02186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
Binding of microtubule filaments by the conserved Ndc80 protein is required for kinetochore-microtubule attachments in cells and the successful distribution of the genetic material during cell division. The reversible inhibition of microtubule binding is an important aspect of the physiological error correction process. Small molecule inhibitors of protein-protein interactions involving Ndc80 are therefore highly desirable, both for mechanistic studies of chromosome segregation and also for their potential therapeutic value. Here, we report on a novel strategy to develop rationally designed inhibitors of the Ndc80 Calponin-homology domain using Supramolecular Chemistry. With a multiple-click approach, lysine-specific molecular tweezers were assembled to form covalently fused dimers to pentamers with a different overall size and preorganization/stiffness. We identified two dimers and a trimer as efficient Ndc80 CH-domain binders and have shown that they disrupt the interaction between Ndc80 and microtubules at low micromolar concentrations without affecting microtubule dynamics. NMR spectroscopy allowed us to identify the biologically important lysine residues 160 and 204 as preferred tweezer interaction sites. Enhanced sampling molecular dynamics simulations provided a rationale for the binding mode of multivalent tweezers and the role of pre-organization and secondary interactions in targeting multiple lysine residues across a protein surface.
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Molecular Tweezers: Supramolecular Hosts with Broad-Spectrum Biological Applications. Pharmacol Rev 2023; 75:263-308. [PMID: 36549866 PMCID: PMC9976797 DOI: 10.1124/pharmrev.122.000654] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Lysine-selective molecular tweezers (MTs) are supramolecular host molecules displaying a remarkably broad spectrum of biologic activities. MTs act as inhibitors of the self-assembly and toxicity of amyloidogenic proteins using a unique mechanism. They destroy viral membranes and inhibit infection by enveloped viruses, such as HIV-1 and SARS-CoV-2, by mechanisms unrelated to their action on protein self-assembly. They also disrupt biofilm of Gram-positive bacteria. The efficacy and safety of MTs have been demonstrated in vitro, in cell culture, and in vivo, suggesting that these versatile compounds are attractive therapeutic candidates for various diseases, infections, and injuries. A lead compound called CLR01 has been shown to inhibit the aggregation of various amyloidogenic proteins, facilitate their clearance in vivo, prevent infection by multiple viruses, display potent anti-biofilm activity, and have a high safety margin in animal models. The inhibitory effect of CLR01 against amyloidogenic proteins is highly specific to abnormal self-assembly of amyloidogenic proteins with no disruption of normal mammalian biologic processes at the doses needed for inhibition. Therapeutic effects of CLR01 have been demonstrated in animal models of proteinopathies, lysosomal-storage diseases, and spinal-cord injury. Here we review the activity and mechanisms of action of these intriguing compounds and discuss future research directions. SIGNIFICANCE STATEMENT: Molecular tweezers are supramolecular host molecules with broad biological applications, including inhibition of abnormal protein aggregation, facilitation of lysosomal clearance of toxic aggregates, disruption of viral membranes, and interference of biofilm formation by Gram-positive bacteria. This review discusses the molecular and cellular mechanisms of action of the molecular tweezers, including the discovery of distinct mechanisms acting in vitro and in vivo, and the application of these compounds in multiple preclinical disease models.
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Modulation of Aβ42 Aggregation Kinetics and Pathway by Low-Molecular-Weight Inhibitors. Chembiochem 2023; 24:e202200760. [PMID: 36652672 DOI: 10.1002/cbic.202200760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
The aggregation of amyloid-β 42 (Aβ42) is directly related to the pathogenesis of Alzheimer's disease. Here, we have investigated the early stages of the aggregation process, during which most of the cytotoxic species are formed. Aβ42 aggregation kinetics, characterized by the quantification of Aβ42 monomer consumption, were tracked by real-time solution NMR spectroscopy (RT-NMR) allowing the impact that low-molecular-weight (LMW) inhibitors and modulators exert on the aggregation process to be analysed. Distinct differences in the Aβ42 kinetic profiles were apparent and were further investigated kinetically and structurally by using thioflavin T (ThT) and transmission electron microscopy (TEM), respectively. LMW inhibitors were shown to have a differential impact on early-state aggregation. Insight provided here could direct future therapeutic design based on kinetic profiling of the process of fibril formation.
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The Amyloid Inhibitor CLR01 Relieves Autophagy and Ameliorates Neuropathology in a Severe Lysosomal Storage Disease. Mol Ther 2022; 30:3499. [PMID: 36261045 PMCID: PMC9637752 DOI: 10.1016/j.ymthe.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Recognition of a Flexible Protein Loop in Taspase 1 by Multivalent Supramolecular Tweezers. Biomacromolecules 2022; 23:4504-4518. [PMID: 36200481 DOI: 10.1021/acs.biomac.2c00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many natural proteins contain flexible loops utilizing well-defined complementary surface regions of their interacting partners and usually undergo major structural rearrangements to allow perfect binding. The molecular recognition of such flexible structures is still highly challenging due to the inherent conformational dynamics. Notably, protein-protein interactions are on the other hand characterized by a multivalent display of complementary binding partners to enhance molecular affinity and specificity. Imitating this natural concept, we here report the rational design of advanced multivalent supramolecular tweezers that allow addressing two lysine and arginine clusters on a flexible protein surface loop. The protease Taspase 1, which is involved in cancer development, carries a basic bipartite nuclear localization signal (NLS) and thus interacts with Importin α, a prerequisite for proteolytic activation. Newly established synthesis routes enabled us to covalently fuse several tweezer molecules into multivalent NLS ligands. The resulting bi- up to pentavalent constructs were then systematically compared in comprehensive biochemical assays. In this series, the stepwise increase in valency was robustly reflected by the ligands' gradually enhanced potency to disrupt the interaction of Taspase 1 with Importin α, correlated with both higher binding affinity and inhibition of proteolytic activity.
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Advanced Molecular Tweezers with Lipid Anchors against SARS-CoV-2 and Other Respiratory Viruses. JACS AU 2022; 2:2187-2202. [PMID: 36186568 PMCID: PMC9516563 DOI: 10.1021/jacsau.2c00220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/16/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 presents a global health emergency. Therapeutic options against SARS-CoV-2 are still very limited but urgently required. Molecular tweezers are supramolecular agents that destabilize the envelope of viruses resulting in a loss of viral infectivity. Here, we show that first-generation tweezers, CLR01 and CLR05, disrupt the SARS-CoV-2 envelope and abrogate viral infectivity. To increase the antiviral activity, a series of 34 advanced molecular tweezers were synthesized by insertion of aliphatic or aromatic ester groups on the phosphate moieties of the parent molecule CLR01. A structure-activity relationship study enabled the identification of tweezers with a markedly enhanced ability to destroy lipid bilayers and to suppress SARS-CoV-2 infection. Selected tweezer derivatives retain activity in airway mucus and inactivate the SARS-CoV-2 wildtype and variants of concern as well as respiratory syncytial, influenza, and measles viruses. Moreover, inhibitory activity of advanced tweezers against respiratory syncytial virus and SARS-CoV-2 was confirmed in mice. Thus, potentiated tweezers are broad-spectrum antiviral agents with great prospects for clinical development to combat highly pathogenic viruses.
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Correction for "Comparison of Three Amyloid Assembly Inhibitors: The Sugar scyllo-Inositol, the Polyphenol Epigallocatechin Gallate, and the Molecular Tweezer CLR01". ACS Chem Neurosci 2022; 13:2666. [PMID: 36001876 DOI: 10.1021/acschemneuro.2c00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Iron binding and photoreduction in the ABC transporter subunit FutA. ACTA CRYSTALLOGRAPHICA SECTION A FOUNDATIONS AND ADVANCES 2022. [DOI: 10.1107/s2053273322093378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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[The analysis of CIRSmedical.de using Natural Language Processing]. ZEITSCHRIFT FUR EVIDENZ, FORTBILDUNG UND QUALITAT IM GESUNDHEITSWESEN 2022; 169:1-11. [PMID: 35184999 DOI: 10.1016/j.zefq.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/17/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND CIRSmedical.de is a publicly accessible, cross-institutional reporting and learning system, which is organized by the German Agency for Quality in Medicine (ÄZQ). CIRSmedical.de has existed since 2005 and has published more than 6,000 event reports. Up to now it has been common practice to analyse these reports in detail or carry out systematic evaluations focusing on specific topics. A systematic evaluation of all case reports has not yet been conducted. Natural Language Processing (NLP) is an analysis strategy from the field of Artificial Intelligence for indexing texts. The examination of case reports using NLP was carried out to describe the characteristics of event reports and comments. MATERIALS AND METHODS For this analysis 6,480 case reports from CIRSmedical.de (as of December 10, 2019) were provided by the ÄZQ as Excel files. Several free text fields were included in the analysis as well as the feedback of the CIRS team (expert commentary). Text lengths, reporting behaviour, sentiment values and keywords were examined. The algorithms for the analysis were developed with the programming language Python and the corresponding libraries NLTK and SpaCy. RESULTS The comparison of report lengths depending on the different subject groups presented a heterogeneous picture, in terms of both the number of reports and the number of words. There are more than 4,000 reports from the field of anaesthesiology, whereby text lengths vary particularly strongly with a right-skewed distribution. There are only a few reports from the field of psychotherapy, and these are also very short. The different professional groups (nurses, doctors, other staff) write reports of about the same length. Reports and expert commentaries also differ in terms of sentiment values. Due to the length of the comments, they are more negative in terms of sentiment. Keywords can be identified but show a high heterogeneity. DISCUSSION Systematic analysis using NLP allows for the description of text properties in event reports and comments. It is now possible to draw a conclusion about the reporters' intention, focus and mood when they report in CIRS. The sentiment analysis is an indication of the mood which the texts convey, both as a report and as a commentary. Text length analysis draws attention to different problems and tendencies: event reports are usually much shorter. Texts that are too short, however, run the risk that the information will not be readily usable for analysis. Comments are often longer, but here one faces the opposite problem: texts that are too long may not be read. The examination of texts by means of NLP helps to rethink the reason for and the form of input, both when reporting and when commenting. It is a first step in the automatic, supportive classification of texts and an improvement of the interaction between reporters and the system.
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Molecular Tweezers – a new class of potent broad-spectrum antivirals against enveloped viruses. Chem Commun (Camb) 2022; 58:2954-2966. [DOI: 10.1039/d1cc06737k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new supramolecular approach to broad spectrum antivirals utilizes host guest chemistry between molecular tweezers and lysine/arginine as well as choline. Basic amino acids in amyloid-forming SEVI peptides (semen-derived enhancers...
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A tribute to Carsten Schmuck. Beilstein J Org Chem 2021; 17:2795-2798. [PMID: 34925618 PMCID: PMC8649200 DOI: 10.3762/bjoc.17.190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/02/2021] [Indexed: 11/23/2022] Open
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Binding Methylarginines and Methyllysines as Free Amino Acids: A Comparative Study of Multiple Host Classes*. Chembiochem 2021; 23:e202100502. [PMID: 34758178 PMCID: PMC9299052 DOI: 10.1002/cbic.202100502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/09/2021] [Indexed: 01/18/2023]
Abstract
Methylated free amino acids are an important class of targets for host‐guest chemistry that have recognition properties distinct from those of methylated peptides and proteins. We present comparative binding studies for three different host classes that are each studied with multiple methylated arginines and lysines to determine fundamental structure‐function relationships. The hosts studied are all anionic and include three calixarenes, two acyclic cucurbiturils, and two other cleft‐like hosts, a clip and a tweezer. We determined the binding association constants for a panel of methylated amino acids using indicator displacement assays. The acyclic cucurbiturils display stronger binding to the methylated amino acids, and some unique patterns of selectivity. The two other cleft‐like hosts follow two different trends, shallow host (clip) following similar trends to the calixarenes, and the other more closed host (tweezer) binding certain less‐methylated amino acids stronger than their methylated counterparts. Molecular modelling sheds some light on the different preferences of the various hosts. The results identify hosts with new selectivities and with affinities in a range that could be useful for biomedical applications. The overall selectivity patterns are explained by a common framework that considers the geometry, depth of binding pockets, and functional group participation across all host classes.
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Lysine-selective molecular tweezers are cell penetrant and concentrate in lysosomes. Commun Biol 2021; 4:1076. [PMID: 34521989 PMCID: PMC8440717 DOI: 10.1038/s42003-021-02603-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/24/2021] [Indexed: 11/09/2022] Open
Abstract
Lysine-selective molecular tweezers are promising drug candidates against proteinopathies, viral infection, and bacterial biofilm. Despite demonstration of their efficacy in multiple cellular and animal models, important questions regarding their mechanism of action, including cell penetrance and intracellular distribution, have not been answered to date. The main impediment to answering these questions has been the low intrinsic fluorescence of the main compound tested to date, called CLR01. Here, we address these questions using new fluorescently labeled molecular tweezers derivatives. We show that these compounds are internalized in neurons and astrocytes, at least partially through dynamin-dependent endocytosis. In addition, we demonstrate that the molecular tweezers concentrate rapidly in acidic compartments, primarily lysosomes. Accumulation of molecular tweezers in lysosomes may occur both through the endosomal-lysosomal pathway and via the autophagy-lysosome pathway. Moreover, by visualizing colocalization of molecular tweezers, lysosomes, and tau aggregates we show that lysosomes likely are the main site for the intracellular anti-amyloid activity of molecular tweezers. These findings have important implications for the mechanism of action of molecular tweezers in vivo, explaining how administration of low doses of the compounds achieves high effective concentrations where they are needed, and supporting the development of these compounds as drugs for currently cureless proteinopathies.
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Abstract
Rational design of protein-protein interaction (PPI) inhibitors is challenging. Connecting a general supramolecular protein binder with a specific peptidic ligand provides a novel conceptual approach. Thus, lysine-specific molecular tweezers were conjugated to a peptide-based 14-3-3 ligand and produced a strong PPI inhibitor with 100-fold elevated protein affinity. X-ray crystal structure elucidation of this supramolecular directed assembly provides unique molecular insight into the binding mode and fully aligns with Molecular Dynamics (MD) simulations. This new supramolecular chemical biology concept opens the path to novel chemical tools for studying PPIs.
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The Molecular Tweezer CLR01 Inhibits Antibody-Resistant Cell-to-Cell Spread of Human Cytomegalovirus. Viruses 2021; 13:v13091685. [PMID: 34578265 PMCID: PMC8472163 DOI: 10.3390/v13091685] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
Human cytomegalovirus (HCMV) uses two major ways for virus dissemination: infection by cell-free virus and direct cell-to-cell spread. Neutralizing antibodies can efficiently inhibit infection by cell-free virus but mostly fail to prevent cell-to-cell transmission. Here, we show that the ‘molecular tweezer’ CLR01, a broad-spectrum antiviral agent, is not only highly active against infection with cell-free virus but most remarkably inhibits antibody-resistant direct cell-to-cell spread of HCMV. The inhibition of cell-to-cell spread by CLR01 was not limited to HCMV but was also shown for the alphaherpesviruses herpes simplex viruses 1 and 2 (HSV-1, -2). CLR01 is a rapid acting small molecule that inhibits HCMV entry at the attachment and penetration steps. Electron microscopy of extracellular virus particles indicated damage of the viral envelope by CLR01, which likely impairs the infectivity of virus particles. The rapid inactivation of viral particles by CLR01, the viral envelope as the main target, and the inhibition of virus entry at different stages are presumably the key to inhibition of cell-free virus infection and cell-to-cell spread by CLR01. Importance: While cell-free spread enables the human cytomegalovirus (HCMV) and other herpesviruses to transmit between hosts, direct cell-to-cell spread is thought to be more relevant for in vivo dissemination within infected tissues. Cell-to-cell spread is resistant to neutralizing antibodies, thus contributing to the maintenance of virus infection and virus dissemination in the presence of an intact immune system. Therefore, it would be therapeutically interesting to target this mode of spread in order to treat severe HCMV infections and to prevent dissemination of virus within the infected host. The molecular tweezer CLR01 exhibits broad-spectrum antiviral activity against a number of enveloped viruses and efficiently blocks antibody-resistant cell-to-cell spread of HCMV, thus representing a novel class of small molecules with promising antiviral activity.
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Prospects of ultraviolet resonance Raman spectroscopy in supramolecular chemistry on proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119622. [PMID: 33743304 DOI: 10.1016/j.saa.2021.119622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Ultraviolet resonance Raman scattering (UVRR) has been frequently used for studying peptide and protein structure and dynamics, while applications in supramolecular chemistry are quite rare. Since UVRR offers the additional advantages of chromophore selectivity and high sensitivity compared with conventional non-resonant Raman scattering, it is ideally suited for label-free probing of relatively small artificial/supramolecular ligands exhibiting electronic resonances in the UV. In this perspective article, we first summarize results of UVRR spectroscopy in supramolecular chemistry in the context of peptide/protein recognition. We focus on selected artificial ligands which were rationally designed as selective carboxylate binders (guanidiniocarbonyl pyrrole, GCP, and guanidiniocarbonyl indole, GCI) and selective lysine binder (molecular tweezer, CLR01), respectively, via a combination of non-covalent interactions involving electrostatics, hydrogen bonding, and hydrophobic effects/van der Waals forces. Current limitations of applying UVRR as a universally applicable method for label-free and site-specific probing of molecular recognition between supramolecular ligands and proteins are highlighted. We then propose solutions to overcome these limitations for transforming UVRR spectroscopy into a generic tool in supramolecular chemistry on proteins, with an emphasis on mono- and multivalent GCP- and GCI-based ligands. Finally, we outline specific cases of supramolecular ligands such as molecular tweezers where alternative approaches such as laser-based mid-IR spectroscopy are required since UVRR can intrinsically not provide the required molecular information.
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Correction to: The molecular tweezer CLR01 improves behavioral deficits and reduces tau pathology in P301S-tau transgenic mice. ALZHEIMERS RESEARCH & THERAPY 2021; 13:88. [PMID: 33888156 PMCID: PMC8063374 DOI: 10.1186/s13195-021-00823-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Inhibition of Staphylococcus aureus biofilm-forming functional amyloid by molecular tweezers. Cell Chem Biol 2021; 28:1310-1320.e5. [PMID: 33852903 DOI: 10.1016/j.chembiol.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Biofilms are rigid and largely impenetrable three-dimensional matrices constituting virulence determinants of various pathogenic bacteria. Here, we demonstrate that molecular tweezers, unique supramolecular artificial receptors, modulate biofilm formation of Staphylococcus aureus. In particular, the tweezers affect the structural and assembly properties of phenol-soluble modulin α1 (PSMα1), a biofilm-scaffolding functional amyloid peptide secreted by S. aureus. The data reveal that CLR01, a diphosphate tweezer, exhibits significant S. aureus biofilm inhibition and disrupts PSMα1 self-assembly and fibrillation, likely through inclusion of lysine side chains of the peptide. In comparison, different peptide binding occurs in the case of CLR05, a tweezer containing methylenecarboxylate units, which exhibits lower affinity for the lysine residues yet disrupts S. aureus biofilm more strongly than CLR01. Our study points to a possible role for molecular tweezers as potent biofilm inhibitors and antibacterial agents, particularly against untreatable biofilm-forming and PSM-producing bacteria, such as methicillin-resistant S. aureus.
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Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. Nat Commun 2021; 12:1505. [PMID: 33686072 PMCID: PMC7940618 DOI: 10.1038/s41467-021-21753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.
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The molecular tweezer CLR01 improves behavioral deficits and reduces tau pathology in P301S-tau transgenic mice. ALZHEIMERS RESEARCH & THERAPY 2021; 13:6. [PMID: 33397489 PMCID: PMC7784007 DOI: 10.1186/s13195-020-00743-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Molecular tweezers (MTs) are broad-spectrum inhibitors of abnormal protein aggregation. A lead MT, called CLR01, has been demonstrated to inhibit the aggregation and toxicity of multiple amyloidogenic proteins in vitro and in vivo. Previously, we evaluated the effect of CLR01 in the 3 × Tg mouse model of Alzheimer's disease, which overexpresses mutant human presenilin 1, amyloid β-protein precursor, and tau and found that subcutaneous administration of the compound for 1 month led to a robust reduction of amyloid plaques, neurofibrillary tangles, and microgliosis. CLR01 also has been demonstrated to inhibit tau aggregation in vitro and tau seeding in cell culture, yet because in Alzheimer's disease (AD) and in the 3 × Tg model, tau hyperphosphorylation and aggregation are thought to be downstream of Aβ insults, the study in this model left open the question whether CLR01 affected tau in vivo directly or indirectly. METHODS To determine if CLR01 could ameliorate tau pathology directly in vivo, we tested the compound similarly using the P301S-tau (line PS19) mouse model. Mice were administered 0.3 or 1.0 mg/kg per day CLR01 and tested for muscle strength and behavioral deficits, including anxiety- and disinhibition-like behavior. Their brains then were analyzed by immunohistochemical and biochemical assays for pathological forms of tau, neurodegeneration, and glial pathology. RESULTS CLR01 treatment ameliorated muscle-strength deterioration, anxiety-, and disinhibition-like behavior. Improved phenotype was associated with decreased levels of pathologic tau forms, suggesting that CLR01 exerts a direct effect on tau in vivo. Limitations of the study included a relatively short treatment period of the mice at an age in which full pathology is not yet developed. In addition, high variability in this model lowered the statistical significance of the findings of some outcome measures. CONCLUSIONS The findings suggest that CLR01 is a particularly attractive candidate for the treatment of AD because it targets simultaneously the two major pathogenic proteins instigating and propagating the disease, amyloid β-protein (Aβ), and tau, respectively. In addition, our study suggests that CLR01 can be used for the treatment of other tauopathies in the absence of amyloid pathology.
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New Tools to Probe the Protein Surface: Ultrasmall Gold Nanoparticles Carry Amino Acid Binders. J Phys Chem B 2020; 125:115-127. [DOI: 10.1021/acs.jpcb.0c09846] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Structural rearrangement of amyloid-β upon inhibitor binding suppresses formation of Alzheimer's disease related oligomers. eLife 2020; 9:59306. [PMID: 33095161 PMCID: PMC7682991 DOI: 10.7554/elife.59306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/22/2020] [Indexed: 01/24/2023] Open
Abstract
The formation of oligomers of the amyloid-β peptide plays a key role in the onset of Alzheimer's disease. We describe herein the investigation of disease-relevant small amyloid-β oligomers by mass spectrometry and ion mobility spectrometry, revealing functionally relevant structural attributes. In particular, we can show that amyloid-β oligomers develop in two distinct arrangements leading to either neurotoxic oligomers and fibrils or non-toxic amorphous aggregates. Comprehending the key-attributes responsible for those pathways on a molecular level is a pre-requisite to specifically target the peptide's tertiary structure with the aim to promote the emergence of non-toxic aggregates. Here, we show for two fibril inhibiting ligands, an ionic molecular tweezer and a hydrophobic peptide that despite their different interaction mechanisms, the suppression of the fibril pathway can be deduced from the disappearance of the corresponding structure of the first amyloid-β oligomers.
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Abstract
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Broad-spectrum
antivirals are powerful weapons against dangerous
viruses where no specific therapy exists, as in the case of the ongoing
SARS-CoV-2 pandemic. We discovered that a lysine- and arginine-specific
supramolecular ligand (CLR01) destroys enveloped viruses, including
HIV, Ebola, and Zika virus, and remodels amyloid fibrils in semen
that promote viral infection. Yet, it is unknown how CLR01 exerts
these two distinct therapeutic activities. Here, we delineate a novel
mechanism of antiviral activity by studying the activity of tweezer
variants: the “phosphate tweezer” CLR01, a “carboxylate
tweezer” CLR05, and a “phosphate clip” PC. Lysine
complexation inside the tweezer cavity is needed to antagonize amyloidogenesis
and is only achieved by CLR01. Importantly, CLR01 and CLR05 but not
PC form closed inclusion complexes with lipid head groups of viral
membranes, thereby altering lipid orientation and increasing surface
tension. This process disrupts viral envelopes and diminishes infectivity
but leaves cellular membranes intact. Consequently, CLR01 and CLR05
display broad antiviral activity against all enveloped viruses tested,
including herpesviruses, Measles virus, influenza, and SARS-CoV-2.
Based on our mechanistic insights, we potentiated the antiviral, membrane-disrupting
activity of CLR01 by introducing aliphatic ester arms into each phosphate
group to act as lipid anchors that promote membrane targeting. The
most potent ester modifications harbored unbranched C4 units, which
engendered tweezers that were approximately one order of magnitude
more effective than CLR01 and nontoxic. Thus, we establish the mechanistic
basis of viral envelope disruption by specific tweezers and establish
a new class of potential broad-spectrum antivirals with enhanced activity.
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Abstract
Oligomers of amyloid β-protein (Aβ) are thought to be the proximal toxic agents initiating the neuropathologic process in Alzheimer's disease (AD). Therefore, targeting the self-assembly and oligomerization of Aβ has been an important strategy for designing AD therapeutics. In parallel, research into the metallobiology of AD has shown that Zn2+ can strongly modulate the aggregation of Aβ in vitro and both promote and inhibit the neurotoxicity of Aβ, depending on the experimental conditions. Thus, successful inhibitors of Aβ self-assembly may have to inhibit the toxicity not only of Aβ oligomers themselves but also of Aβ-Zn2+ complexes. However, there has been relatively little research investigating the effects of Aβ self-assembly and toxicity inhibitors in the presence of Zn2+. Our group has characterized previously a series of Aβ42 C-terminal fragments (CTFs), some of which have been shown to inhibit Aβ oligomerization and neurotoxicity. Here, we asked whether three CTFs shown to be potent inhibitors of Aβ42 toxicity maintained their activity in the presence of Zn2+. Biophysical analysis showed that the CTFs had different effects on oligomer, β-sheet, and fibril formation by Aβ42-Zn2+ complexes. However, cell viability experiments in differentiated PC-12 cells incubated with Aβ42-Zn2+ complexes in the absence or presence of these CTFs showed that the CTFs completely lost their inhibitory activity in the presence of Zn2+ even when applied at 10-fold excess relative to Aβ42. In light of these results, we tested another inhibitor, the molecular tweezer CLR01, which coincidentally had been shown to have a high affinity for Zn2+, suggesting that it could disrupt both Aβ42 oligomerization and Aβ42-Zn2+ complexation. Indeed, we found that CLR01 effectively inhibited the toxicity of Aβ42-Zn2+ complexes. Moreover, it did so at a lower concentration than needed for inhibiting the toxicity of Aβ42 alone. In agreement with these results, CLR01 inhibited β-sheet and fibril formation in Aβ42-Zn2+ complexes. Our data suggest that, for the development of efficient therapeutic agents, inhibitors of Aβ self-assembly and toxicity should be examined in the presence of relevant metal ions and that molecular tweezers may be particularly attractive candidates for therapy development.
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Abstract
Communication between and inside cells as well as their response to external stimuli relies on elaborated systems of signal transduction. They all require a directional transmission across membranes, often realized by primary messenger docking onto external receptor units and subsequent internalization of the signal in form of a released second messenger. This in turn starts a cascade of events which ultimately control all functions of the living cell. Although signal transduction is a fundamental biological process realized by supramolecular recognition and multiplication events with small molecules, chemists have just begun to invent artificial models which allow to study the underlying rules, and one day perhaps to rescue damaged transduction systems in nature. This review summarizes the exciting pioneering efforts of chemists to create simple models for the basic principles of signal transduction across a membrane. It starts with first attempts to establish molecular recognition events on liposomes with embedded receptor amphiphiles and moves on to simple transmembrane signaling across lipid bilayers. More elaborated systems step by step incorporate more elements of cell signaling, such as primary and secondary messenger or a useful cellular response such as cargo release.
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[The similarity of drug names as a possible cause of confusion: Analysis of data from outpatient care]. ZEITSCHRIFT FUR EVIDENZ FORTBILDUNG UND QUALITAET IM GESUNDHEITSWESEN 2020; 150-152:29-37. [PMID: 32279980 DOI: 10.1016/j.zefq.2020.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND The incidence of adverse drug events (ADE) described in the literature varies between 6.5 and 20 %. Furthermore, it is assumed that up to 29 % of ADE are due to medication errors as a result of confusion because of similarities in spelling (sound alike) or in name, physical appearance or packaging (look alike). Studies dealing with the so-called "LASA" issue were mostly carried out in inpatient care. As far as we know, no systematic investigations into this subject have been carried out for the outpatient sector where patients themselves take care of the application of their medication. In addition, there is no documentation about medication errors in the home setting. The aim of the present study is to describe the importance of the LASA issue in the home setting where medication errors are likely to occur due to similarity of drug names. METHODS In this context, the similarity of names of prescription drugs was systematically analyzed. We examined in detail how often prescription drug pairings showing orthographic and phonetic similarity were dispensed in the investigation period to an individual patient at the same time. Orthographic similarity was defined as relevant at a Levenshtein index value of ≤ 0.4. This corresponds to the similarity measures of the drugs listed in the LASA public lists and means that the similarity in the lettering of two drug names amounts to at least 60 %. Phonetic similarity was analysed using the Cologne Phonetic ("Kölner Phonetik") for the German language. RESULTS A total of 255,770 prescriptions were included in the analysis. In 11.4 %, drug pairings were detected that fall below the critical orthographic similarity threshold (Levenshtein index value ≤ 0.4), which represents an increased likelihood of medication error due to the critical similarity of drug names in this fraction. Within this group of "LASA drugs" different degrees of similarity were identified. Even drug pairings with very high orthographic similarity (Levenshtein index value from ≤ 0.1 and 0.1 to ≤ 0.2, 12.4 % and 3.6 % of the drug pairings, respectively) were detected. These drug pairings were mostly different in strength while active ingredients, manufacturer name and pharmaceutical form were the same. For the majority of drug pairings (84 %), the orthographic similarity was lower and showed a Levenshtein index value of ≥ 0.2 to 0.4. Despite different active ingredients, there is a degree of similarity resulting from both identical manufacturer name and pharmaceutical form appearing as part of the drug name. At the phonetic level, the analysis shows comparable frequency of similarity of drug pairings that are subject to potential medication error. DISCUSSION For the first time, a study was carried out in the outpatient setting recording the incidence of drug pairings that carry a risk for medication errors resulting from patients' confusion over too similar drug names. In the light of the age structure of the patients to whom these look- or sound-alike drugs are prescribed, we can assume that there is a considerable risk of ADE. The conceivable consequences of such medication errors on a pharmacological level range from relatively harmless to potentially highly dangerous. CONCLUSION There is a major need to fully inform patients about this risk of confusion and subsequent medication errors with certain drug combinations. The similarity structures of drug pairings identified in this study could serve as a basis for developing an appropriate information routine.
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Chirality sensing of terpenes, steroids, amino acids, peptides and drugs with acyclic cucurbit[n]urils and molecular tweezers. Chem Commun (Camb) 2020; 56:4652-4655. [PMID: 32253396 DOI: 10.1039/d0cc00707b] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Achiral chromophoric hosts, i.e. acyclic cucurbit[n]urils and molecular tweezers, were found to respond with characteristic Circular Dichroism (CD) spectra to the presence of micromolar concentrations of chiral hydrocarbons, terpenes, steroids, amino acids and their derivates, and drugs in water. In favourable cases, this allows for analyte identification or for reaction monitoring.
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Accelerated trypsin autolysis by affinity polymer templates. RSC Adv 2020; 10:28711-28719. [PMID: 35520047 PMCID: PMC9055874 DOI: 10.1039/d0ra05827k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 11/21/2022] Open
Abstract
Affinity copolymers specifically recognize the trypsin surface and act as templates for multiple protease molecules, leading to drastically accelerated autolysis – an unusual way for highly efficient enzyme inhibition at physiological conditions.
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Molecular Lysine Tweezers Counteract Aberrant Protein Aggregation. Front Chem 2019; 7:657. [PMID: 31632951 PMCID: PMC6779714 DOI: 10.3389/fchem.2019.00657] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/13/2019] [Indexed: 01/10/2023] Open
Abstract
Molecular tweezers (MTs) are supramolecular host molecules equipped with two aromatic pincers linked together by a spacer (Gakh, 2018). They are endowed with fascinating properties originating from their ability to hold guests between their aromatic pincers (Chen and Whitlock, 1978; Zimmerman, 1991; Harmata, 2004). MTs are finding an increasing number of medicinal applications, e.g., as bis-intercalators for DNA such as the anticancer drug Ditercalinium (Gao et al., 1991), drug activity reverters such as the bisglycoluril tweezers Calabadion 1 (Ma et al., 2012) as well as radioimmuno detectors such as Venus flytrap clusters (Paxton et al., 1991). We recently embarked on a program to create water-soluble tweezers which selectively bind the side chains of lysine and arginine inside their cavity. This unique recognition mode is enabled by a torus-shaped, polycyclic framework, which is equipped with two hydrophilic phosphate groups. Cationic amino acid residues are bound by the synergistic effect of disperse, hydrophobic, and electrostatic interactions in a kinetically fast reversible process. Interactions of the same kind play a key role in numerous protein-protein interactions, as well as in pathologic protein aggregation. Therefore, these particular MTs show a high potential to disrupt such events, and indeed inhibit misfolding and self-assembly of amyloidogenic polypeptides without toxic side effects. The mini-review provides insight into the unique binding mode of MTs both toward peptides and aggregating proteins. It presents the synthesis of the lead compound CLR01 and its control, CLR03. Different biophysical experiments are explained which elucidate and help to better understand their mechanism of action. Specifically, we show how toxic aggregates of oligomeric and fibrillar protein species are dissolved and redirected to form amorphous, benign assemblies. Importantly, these new chemical tools are shown to be essentially non-toxic in vivo. Due to their reversible moderately tight binding, these agents are not protein-, but rather process-specific, which suggests a broad range of applications in protein misfolding events. Thus, MTs are highly promising candidates for disease-modifying therapy in early stages of neurodegenerative diseases. This is an outstanding example in the evolution of supramolecular concepts toward biological application.
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The molecular tweezer CLR01 reduces aggregated, pathologic, and seeding-competent α-synuclein in experimental multiple system atrophy. Biochim Biophys Acta Mol Basis Dis 2019; 1865:165513. [PMID: 31319154 DOI: 10.1016/j.bbadis.2019.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 11/26/2022]
Abstract
Multiple system atrophy (MSA) is a fatal, adult-onset neurodegenerative disorder that has no cure and very limited treatment options. MSA is characterized by deposition of fibrillar α-synuclein (α-syn) in glial cytoplasmic inclusions in oligodendrocytes. Similar to other synucleinopathies, α-syn self-assembly is thought to be a key pathologic event and a prominent target for disease modification in MSA. Molecular tweezers are broad-spectrum nanochaperones that prevent formation of toxic protein assemblies and enhance their clearance. The current lead compound, CLR01, has been shown to inhibit α-syn aggregation but has not yet been tested in the context of MSA. To fill this gap, here, we conducted a proof-of-concept study to assess the efficacy of CLR01 in remodeling MSA-like α-syn pathology in the PLP-α-syn mouse model of MSA. Six-month-old mice received intracerebroventricular CLR01 (0.3 or 1 mg/kg per day) or vehicle for 32 days. Open-field test revealed a significant, dose-dependent amelioration of an anxiety-like phenotype. Subsequently, immunohistochemical and biochemical analyses showed dose-dependent reduction of pathological and seeding-competent forms of α-syn, which correlated with the behavioral phenotype. CLR01 treatment also promoted dopaminergic neuron survival in the substantia nigra. To our knowledge, this is the first demonstration of an agent that reduces formation of putative high-molecular-weight oligomers and seeding-competent α-syn in a mouse model of MSA, supporting the view that these species are key to the neurodegenerative process and its cell-to-cell progression in MSA. Our study suggests that CLR01 is an attractive therapeutic candidate for disease modification in MSA and related synucleinopathies, supporting further preclinical development.
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F2-06-01: MAJOR DIFFERENCES BETWEEN THE SELF-ASSEMBLY, SEEDING BEHAVIOR, AND INTERACTION WITH MODULATORS OF HEPARIN-INDUCED VERSUS IN-VITRO PHOSPHORYLATED TAU. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.4436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dissociation of the Signaling Protein K‐Ras4B from Lipid Membranes Induced by a Molecular Tweezer. Chemistry 2019; 25:9827-9833. [DOI: 10.1002/chem.201901861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/29/2019] [Indexed: 12/21/2022]
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Major Differences between the Self-Assembly and Seeding Behavior of Heparin-Induced and in Vitro Phosphorylated Tau and Their Modulation by Potential Inhibitors. ACS Chem Biol 2019; 14:1363-1379. [PMID: 31046227 PMCID: PMC6636790 DOI: 10.1021/acschembio.9b00325] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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Self-assembly of
the microtubule-associated protein tau into neurotoxic
oligomers, fibrils, and paired helical filaments, and cell-to-cell
spreading of these pathological tau species are critical processes
underlying the pathogenesis of Alzheimer’s disease and other
tauopathies. Modulating the self-assembly process and inhibiting formation
and spreading of such toxic species are promising strategies for therapy
development. A challenge in investigating tau self-assembly in vitro
is that, unlike most amyloidogenic proteins, tau does not aggregate
in the absence of posttranslational modifications (PTM), aggregation
inducers, or preformed seeds. The most common induction method is
addition of polyanions, such as heparin; yet, this artificial system
may not represent adequately tau self-assembly in vivo, which is driven
by aberrant phosphorylation and other PTMs, potentially leading to
in vitro data that do not reflect the behavior of tau and its interaction
with modulators in vivo. To tackle these challenges, methods for in
vitro phosphorylation of tau to produce aggregation-competent forms
recently have been introduced (Despres
et al. (2017) , 114, 9080−908528784767). However, the oligomerization, seeding, and interaction
with assembly modulators of the different forms of tau have not been
studied to date. To address these knowledge gaps, we compared here
side-by-side the self-assembly and seeding activity of heparin-induced
tau with two forms of in vitro phosphorylated tau and tested how the
molecular tweezer CLR01, a negatively charged compound, affected these
processes. Tau was phosphorylated by incubation either with activated
extracellular signal-regulated kinase 2 or with a whole rat brain
extract. Seeding activity was measured using a fluorescence-resonance
energy transfer-based biosensor-cell method. We also used solution-state
NMR to investigate the binding sites of CLR01 on tau and how they
were impacted by phosphorylation. Our systematic structure–activity
relationship study demonstrates that heparin-induced tau behaves differently
from in vitro phosphorylated tau. The aggregation rates of the different
forms are distinct as is the intracellular localization of the induced
aggregates, which resemble brain-derived tau strains suggesting that
heparin-induced tau and in vitro phosphorylated tau have different
conformations, properties, and activities. CLR01 inhibits aggregation
and seeding of both heparin-induced and in vitro phosphorylated tau
dose-dependently, although heparin induction interferes with the interaction
between CLR01 and tau.
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The molecular tweezer CLR01 inhibits aberrant superoxide dismutase 1 (SOD1) self-assembly in vitro and in the G93A-SOD1 mouse model of ALS. J Biol Chem 2019; 294:3501-3513. [PMID: 30602569 DOI: 10.1074/jbc.ra118.005940] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/01/2019] [Indexed: 12/13/2022] Open
Abstract
Mutations in superoxide dismutase 1 (SOD1) cause 15-20% of familial amyotrophic lateral sclerosis (fALS) cases. The resulting amino acid substitutions destabilize SOD1's protein structure, leading to its self-assembly into neurotoxic oligomers and aggregates, a process hypothesized to cause the characteristic motor-neuron degeneration in affected individuals. Currently, effective disease-modifying therapy is not available for ALS. Molecular tweezers prevent formation of toxic protein assemblies, yet their protective action has not been tested previously on SOD1 or in the context of ALS. Here, we tested the molecular tweezer CLR01-a broad-spectrum inhibitor of the self-assembly and toxicity of amyloid proteins-as a potential therapeutic agent for ALS. Using recombinant WT and mutant SOD1, we found that CLR01 inhibited the aggregation of all tested SOD1 forms in vitro Next, we examined whether CLR01 could prevent the formation of misfolded SOD1 in the G93A-SOD1 mouse model of ALS and whether such inhibition would have a beneficial therapeutic effect. CLR01 treatment decreased misfolded SOD1 in the spinal cord significantly. However, these histological findings did not correlate with improvement of the disease phenotype. A small, dose-dependent decrease in disease duration was found in CLR01-treated mice, relative to vehicle-treated animals, yet motor function did not improve in any of the treatment groups. These results demonstrate that CLR01 can inhibit SOD1 misfolding and aggregation both in vitro and in vivo, but raise the question whether such inhibition is sufficient for achieving a therapeutic effect. Additional studies in other less aggressive ALS models may be needed to determine the therapeutic potential of this approach.
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Bisphosphonate ligand mediated ultrasensitive capacitive protein sensor: complementary match of supramolecular and dynamic chemistry. NEW J CHEM 2019. [DOI: 10.1039/c8nj05238g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A powerful polymeric protein sensor was constructed by microcontact imprinting taking advantage of the specific interaction between a bisphosphonate binding monomer and lysine/arginine residues on the surface of trypsin.
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Native Top-Down Mass Spectrometry and Ion Mobility Spectrometry of the Interaction of Tau Protein with a Molecular Tweezer Assembly Modulator. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:16-23. [PMID: 30062477 PMCID: PMC6320309 DOI: 10.1007/s13361-018-2027-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 05/19/2023]
Abstract
Native top-down mass spectrometry (MS) and ion mobility spectrometry (IMS) were applied to characterize the interaction of a molecular tweezer assembly modulator, CLR01, with tau, a protein believed to be involved in a number of neurodegenerative disorders, including Alzheimer's disease. The tweezer CLR01 has been shown to inhibit aggregation of amyloidogenic polypeptides without toxic side effects. ESI-MS spectra for different forms of tau protein (full-length, fragments, phosphorylated, etc.) in the presence of CLR01 indicate a primary binding stoichiometry of 1:1. The relatively high charging of the protein measured from non-denaturing solutions is typical of intrinsically disordered proteins, such as tau. Top-down mass spectrometry using electron capture dissociation (ECD) is a tool used to determine not only the sites of post-translational modifications but also the binding site(s) of non-covalent interacting ligands to biomolecules. The intact protein and the protein-modulator complex were subjected to ECD-MS to obtain sequence information, map phosphorylation sites, and pinpoint the sites of inhibitor binding. The ESI-MS study of intact tau proteins indicates that top-down MS is amenable to the study of various tau isoforms and their post-translational modifications (PTMs). The ECD-MS data point to a CLR01 binding site in the microtubule-binding region of tau, spanning residues K294-K331, which includes a six-residue nucleating segment PHF6 (VQIVYK) implicated in aggregation. Furthermore, ion mobility experiments on the tau fragment in the presence of CLR01 and phosphorylated tau reveal a shift towards a more compact structure. The mass spectrometry study suggests a picture for the molecular mechanism of the modulation of protein-protein interactions in tau by CLR01. Graphical Abstract ᅟ.
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A Synthetic Methodology Toward Pyrrolo[2,3-b]pyridones for GC Base Pair Recognition. Org Lett 2018; 20:6961-6964. [DOI: 10.1021/acs.orglett.8b03111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Abstract
PURPOSE Open reduction and internal fixation with a tension band construct is the standard treatment for displaced transverse intra-articular olecranon fractures. The purpose of this study is to describe the outcomes of tension band fixation of olecranon fractures in children, specifically assessing the need for revision fixation and hardware removal. METHODS Patients less than 18 years of age diagnosed with a displaced transverse intra-articular olecranon fracture and treated with tension band fixation between 2008 and 2017 were retrospectively enrolled. Operative treatment was with tension band wire (TBW) or tension band suture (TBS) constructs. RESULTS A total of 46 patients, 36 male and ten female with a mean age of 12.3 years (6 to 17), were included. Surgical fixation was with TBW in 17 patients and TBS in 29 patients. Revision fixation due to failure and fracture displacement was required in 6% of the TBW group and 14% of the TBS group (p = 0.19). The patients who required revision fixation in the TBS group were older (14.7 years versus 11.6 years, p = 0.05) and heavier (70.5 kg versus 48.5 kg, p = 0.05) than those in the same group who did not require revision fixation. CONCLUSION Paediatric olecranon fractures treated with TBW or TBS fixation unite in the majority of patients with similar need for hardware removal due to prominence and/or pain between fixation techniques. In a select group of older patients weighing greater than 50 kg, TBS constructs demonstrate increased failure rates, requiring revision fixation, and should be avoided in this population group. LEVEL OF EVIDENCE IV.
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Cover Feature: Molecular Tweezers with Additional Recognition Sites (Chem. Eur. J. 44/2018). Chemistry 2018. [DOI: 10.1002/chem.201803759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
The animal-pathogenic oomycete Saprolegnia parasitica causes serious losses in aquaculture by infecting and killing freshwater fish. Like plant-pathogenic oomycetes, S. parasitica employs similar infection structures and secretes effector proteins that translocate into host cells to manipulate the host. Here, we show that the host-targeting protein SpHtp3 enters fish cells in a pathogen-independent manner. This uptake process is guided by a gp96-like receptor and can be inhibited by supramolecular tweezers. The C-terminus of SpHtp3 (containing the amino acid sequence YKARK), and not the N-terminal RxLR motif, is responsible for the uptake into host cells. Following translocation, SpHtp3 is released from vesicles into the cytoplasm by another host-targeting protein where it degrades nucleic acids. The effector translocation mechanism described here, is potentially also relevant for other pathogen-host interactions as gp96 is found in both animals and plants.
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Grants
- BB/E007120/1 Biotechnology and Biological Sciences Research Council
- BB/G012075/1 Biotechnology and Biological Sciences Research Council
- Biotechnology and Biological Sciences Research Council (BBSRC)
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- Our work is supported by the [European Community's] Seventh Framework Programme [FP7/2007-2013] under grant agreement no [238550] (LL, JDU, CJS, PvW); BBSRC [BBE007120/1, BB/J018333/1 and BB/G012075/1] (FT, IdB, CJS, SW, PvW); Newton Global partnership Award [BB/N005058/1] (FT, PvW), the University of Aberdeen (ADT, TR, CJS, PvW) and Deutsche Forschungsgemeinschaft [CRC1093] (PB, TS). We would like to acknowledge the Ministry of Higher Education Malaysia for funding INA. We would like to thank Brian Haas for his bioinformatics support. We would like to acknowledge Neil Gow and Johannes van den Boom for critical reading of the manuscript. We would like to acknowledge Svetlana Rezinciuc for technical help with pH-studies.
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Metabolic shift toward oxidative phosphorylation in docetaxel resistant prostate cancer cells. Oncotarget 2018; 7:61890-61904. [PMID: 27542265 PMCID: PMC5308698 DOI: 10.18632/oncotarget.11301] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/27/2016] [Indexed: 01/24/2023] Open
Abstract
Drug resistance of cancer cells is recognized as the primary cause of failure of chemotherapeutic treatment in most human cancers. Growing evidences support the idea that deregulated cellular metabolism is linked to such resistance. Indeed, both components of the glycolytic and mitochondrial pathways are involved in altered metabolism linked to chemoresistance of several cancers. Here we investigated the drug-induced metabolic adaptations able to confer advantages to docetaxel resistant prostate cancer (PCa) cells. We found that docetaxel-resistant PC3 cells (PC3-DR) acquire a pro-invasive behavior undergoing epithelial-to-mesenchymal-transition (EMT) and a decrease of both intracellular ROS and cell growth. Metabolic analyses revealed that PC3-DR cells have a more efficient respiratory phenotype than sensitive cells, involving utilization of glucose, glutamine and lactate by the mitochondrial oxidative phosphorylation (OXPHOS). Consequently, targeting mitochondrial complex I by metformin administration, impairs proliferation and invasiveness of PC3-DR cells without effects on parental cells. Furthermore, stromal fibroblasts, which cause a "reverse Warburg" phenotype in PCa cells, reduce docetaxel toxicity in both sensitive and resistant PCa cells. However, re-expression of miR-205, a microRNA strongly down-regulated in EMT and associated to docetaxel resistance, is able to shift OXPHOS to a Warburg metabolism, thereby resulting in an elevated docetaxel toxicity in PCa cells. Taken together, these findings suggest that resistance to docetaxel induces a shift from Warburg to OXPHOS, mandatory for conferring a survival advantage to resistant cells, suggesting that impairing such metabolic reprogramming could be a successful therapeutic approach.
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The molecular tweezer CLR01 inhibits Ebola and Zika virus infection. Antiviral Res 2018; 152:26-35. [PMID: 29428508 PMCID: PMC7113745 DOI: 10.1016/j.antiviral.2018.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 01/13/2023]
Abstract
Ebola (EBOV) and Zika viruses (ZIKV) are responsible for recent global health threats. As no preventive vaccines or antiviral drugs against these two re-emerging pathogens are available, we evaluated whether the molecular tweezer CLR01 may inhibit EBOV and ZIKV infection. This small molecule has previously been shown to inactivate HIV-1 and herpes viruses through a selective interaction with lipid-raft-rich regions in the viral envelope, which results in membrane disruption and loss of infectivity. We found that CLR01 indeed blocked infection of EBOV and ZIKV in a dose-dependent manner. The tweezer inhibited infection of epidemic ZIKV strains in cells derived from the anogenital tract and the central nervous system, and remained antivirally active in the presence of semen, saliva, urine and cerebrospinal fluid. Our findings show that CLR01 is a broad-spectrum inhibitor of enveloped viruses with prospects as a preventative microbicide or antiviral agent.
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[A structured case analysis from the Critical Incident Reporting System of the German Medical Association and the National Association of Statutory Health Insurance Physicians]. ZEITSCHRIFT FUR EVIDENZ FORTBILDUNG UND QUALITAET IM GESUNDHEITSWESEN 2018; 133:24-29. [PMID: 29567385 DOI: 10.1016/j.zefq.2018.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND Reporting systems for near misses are necessary to improve patient safety. In Germany, different systems are publicly available on both a national and regional level or as systems related to various medical domains. In contrast with the British Registry, our reporting systems still lack systematic evaluation. Using the Open-Task-Process Model (OPT model) one case of CIRSmedical (www.cirsmedical.de) was selected for a systematic analysis. METHOD Case 148384 reports on a patient with a tentative diagnosis of pulmonary embolism with an oxygen saturation of 71 %. The attending physician was ordered to leave the patient to participate in the daily team meeting. After 40minutes, the nurses transferred the patient from the emergency department to the ICU. The OPT model systematically checks the properties of all tasks in a given process and matches them to requirements or solving capacities of the task. RESULTS The analysis manifests some structural problems: Although the case was not very difficult (high priority, but a frequent problem), the solving capacities were not adequate in order to avoid errors. Since the physician left the patient, the loyalty toward medical standards and the team error correction activity were low. The team did not intervene to prevent the doctor from leaving his patient. CONCLUSION The OPT model allows for the analysis of both single cases and complete data sets of CIR systems and is able to disclose structural problems of clinical management.
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