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Fang L, Laakso J, Rinke P, Chen X. Machine-learning accelerated structure search for ligand-protected clusters. J Chem Phys 2024; 160:094106. [PMID: 38426517 DOI: 10.1063/5.0180529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Finding low-energy structures of ligand-protected clusters is challenging due to the enormous conformational space and the high computational cost of accurate quantum chemical methods for determining the structures and energies of conformers. Here, we adopted and utilized a kernel rigid regression based machine learning method to accelerate the search for low-energy structures of ligand-protected clusters. We chose the Au25(Cys)18 (Cys: cysteine) cluster as a model system to test and demonstrate our method. We found that the low-energy structures of the cluster are characterized by a specific hydrogen bond type in the cysteine. The different configurations of the ligand layer influence the structural and electronic properties of clusters.
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Affiliation(s)
- Lincan Fang
- Department of Applied Physics, Aalto University, 00076 AALTO, Espoo, Finland
| | - Jarno Laakso
- Department of Applied Physics, Aalto University, 00076 AALTO, Espoo, Finland
| | - Patrick Rinke
- Department of Applied Physics, Aalto University, 00076 AALTO, Espoo, Finland
| | - Xi Chen
- Department of Applied Physics, Aalto University, 00076 AALTO, Espoo, Finland
- School of Physical Science and Technology, Lanzhou University, Lanzhou, Gansu 730000, China
- Lanzhou Center for Theoretical Physics and Key Laboratory for Quantum Theory and Applications of the Ministry of Education, Lanzhou University, Lanzhou, Gansu 730000, China
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Wang S, Pang Z, Fan H, Tong Y. Advances in anti-EV-A71 drug development research. J Adv Res 2024; 56:137-156. [PMID: 37001813 PMCID: PMC10834817 DOI: 10.1016/j.jare.2023.03.007] [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] [Received: 01/17/2023] [Revised: 03/05/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Enterovirus A71 (EV-A71) is capable of causing hand, foot and mouth disease (HFMD), which may lead to neurological sequelae and even death. As EV-A71 is resistant to environmental changes and mutates easily, there is still a lack of effective treatments or globally available vaccines. AIM OF REVIEW For more than 50 years since the HFMD epidemic, related drug research has been conducted. Progress in this area can promote the further application of existing potential drugs and develop more efficient and safe antiviral drugs, and provide useful reference for protecting the younger generation and maintaining public health security. KEY SCIENTIFIC CONCEPTS OF REVIEW At present, researchers have identified hundreds of EV-A71 inhibitors based on screening repurposed drugs, targeted structural design, and rational modification of previously effective drugs as the main development strategies. This review systematically introduces the current potential drugs to inhibit EV-A71 infection, including viral inhibitors targeting key sites such as the viral capsid, RNA-dependent RNA polymerase (RdRp), 2C protein, internal ribosome entry site (IRES), 3C proteinase (3Cpro), and 2A proteinase (2Apro), starting from each stage of the viral life cycle. Meanwhile, the progress of host-targeting antiviral drugs and their development are summarized in terms of regulating host immunity, inhibiting autophagy or apoptosis, and regulating the cellular redox environment. In addition, the current clinical methods for the prevention and treatment of HFMD are summarized and discussed with the aim of providing support and recommendations for the treatment of enterovirus infections including EV-A71.
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Affiliation(s)
- Shuqi Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.
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Reshamwala D, Shroff S, Liimatainen J, Tienaho J, Laajala M, Kilpeläinen P, Viherä-Aarnio A, Karonen M, Jyske T, Marjomäki V. Willow ( Salix spp.) bark hot water extracts inhibit both enveloped and non-enveloped viruses: study on its anti-coronavirus and anti-enterovirus activities. Front Microbiol 2023; 14:1249794. [PMID: 38029113 PMCID: PMC10663278 DOI: 10.3389/fmicb.2023.1249794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/18/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Recurring viral outbreaks have a significant negative impact on society. This creates a need to develop novel strategies to complement the existing antiviral approaches. There is a need for safe and sustainable antiviral solutions derived from nature. Objective This study aimed to investigate the antiviral potential of willow (Salix spp.) bark hot water extracts against coronaviruses and enteroviruses. Willow bark has long been recognized for its medicinal properties and has been used in traditional medicines. However, its potential as a broad-spectrum antiviral agent remains relatively unexplored. Methods Cytopathic effect inhibition assay and virucidal and qPCR-based assays were used to evaluate the antiviral potential of the bark extracts. The mechanism of action was investigated using time-of-addition assay, confocal microscopy, TEM, thermal, and binding assays. Extracts were fractionated and screened for their chemical composition using high-resolution LC-MS. Results The native Salix samples demonstrated their excellent antiviral potential against the non-enveloped enteroviruses even at room temperature and after 45 s. They were equally effective against the seasonal and pandemic coronaviruses. Confocal microscopy verified the loss of infection capacity by negligible staining of the newly synthesized capsid or spike proteins. Time-of-addition studies demonstrated that Salix bark extract had a direct effect on the virus particles but not through cellular targets. Negative stain TEM and thermal assay showed that antiviral action on enteroviruses was based on the added stability of the virions. In contrast, Salix bark extract caused visible changes in the coronavirus structure, which was demonstrated by the negative stain TEM. However, the binding to the cells was not affected, as verified by the qPCR study. Furthermore, coronavirus accumulated in the cellular endosomes and did not proceed after this stage, based on the confocal studies. None of the tested commercial reference samples, such as salicin, salicylic acid, picein, and triandrin, had any antiviral activity. Fractionation of the extract and subsequent MS analysis revealed that most of the separated fractions were very effective against enteroviruses and contained several different chemical groups such as hydroxycinnamic acid derivatives, flavonoids, and procyanidins. Conclusion Salix spp. bark extracts contain several virucidal agents that are likely to act synergistically and directly on the viruses.
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Affiliation(s)
- Dhanik Reshamwala
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Sailee Shroff
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | | | - Jenni Tienaho
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Mira Laajala
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | | | | | - Maarit Karonen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, Turku, Finland
| | - Tuula Jyske
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Varpu Marjomäki
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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Groysbeck N, Hanss V, Donzeau M, Strub JM, Cianférani S, Spehner D, Bahri M, Ersen O, Eltsov M, Schultz P, Zuber G. Bioactivated and PEG-Protected Circa 2 nm Gold Nanoparticles for in Cell Labelling and Cryo-Electron Microscopy. SMALL METHODS 2023; 7:e2300098. [PMID: 37035956 DOI: 10.1002/smtd.202300098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/09/2023] [Indexed: 06/09/2023]
Abstract
Advances in cryo-electron microscopy (EM) enable imaging of protein assemblies within mammalian cells in a near native state when samples are preserved by cryogenic vitrification. To accompany this progress, specialized EM labelling protocols must be developed. Gold nanoparticles (AuNPs) of 2 nm are synthesized and functionalized to bind selected intracellular targets inside living human cells and to be detected in vitreous sections. As a proof of concept, thioaminobenzoate-, thionitrobenzoate-coordinated gold nanoparticles are functionalized on their surface with SV40 Nuclear Localization Signal (NLS)-containing peptides and 2 kDa polyethyleneglycols (PEG) by thiolate exchange to target the importin-mediated nuclear machinery and facilitate cytosolic diffusion by shielding the AuNP surface from non-specific binding to cell components, respectively. After delivery by electroporation into the cytoplasm of living human cells, the PEG-coated AuNPs diffuse freely in the cytoplasm but do not enter the nucleus. Incorporation of NLS within the PEG coverage promotes a quick nuclear import of the nanoparticles in relation to the density of NLS onto the AuNPs. Cryo-EM of vitreous cell sections demonstrate the presence of 2 nm AuNPs as single entities in the nucleus. Biofunctionalized AuNPs combined with live-cell electroporation procedures are thus potent labeling tools for the identification of macromolecules in cellular cryo-EM.
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Affiliation(s)
- Nadja Groysbeck
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
| | - Victor Hanss
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Mariel Donzeau
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, F-67000, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, F-67000, France
| | - Danièle Spehner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Mounib Bahri
- Albert Crewe Centre, University of Liverpool, 4. Waterhouse Building, Block C, 1-3 Brownlow Street, London, L69 3GL, UK
| | - Ovidiu Ersen
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), 23 rue de Loess, Strasbourg, 67034, France
| | - Mikhael Eltsov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Patrick Schultz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Guy Zuber
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
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Obstarczyk P, Pniakowska A, Nonappa, Grzelczak MP, Olesiak-Bańska J. Crown Ether-Capped Gold Nanoclusters as a Multimodal Platform for Bioimaging. ACS OMEGA 2023; 8:11503-11511. [PMID: 37008092 PMCID: PMC10061685 DOI: 10.1021/acsomega.3c00426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 12/01/2023]
Abstract
The distinct polarity of biomolecule surfaces plays a pivotal role in their biochemistry and functions as it is involved in numerous processes, such as folding, aggregation, or denaturation. Therefore, there is a need to image both hydrophilic and hydrophobic bio-interfaces with markers of distinct responses to hydrophobic and hydrophilic environments. In this work, we present a synthesis, characterization, and application of ultrasmall gold nanoclusters capped with a 12-crown-4 ligand. The nanoclusters present an amphiphilic character and can be successfully transferred between aqueous and organic solvents and have their physicochemical integrity retained. They can serve as probes for multimodal bioimaging with light (as they emit near-infrared luminescence) and electron microscopy (due to the high electron density of gold). In this work, we used protein superstructures, namely, amyloid spherulites, as a hydrophobic surface model and individual amyloid fibrils with a mixed hydrophobicity profile. Our nanoclusters spontaneously stained densely packed amyloid spherulites as observed under fluorescence microscopy, which is limited for hydrophilic markers. Moreover, our clusters revealed structural features of individual amyloid fibrils at a nanoscale as observed under a transmission electron microscope. We show the potential of crown ether-capped gold nanoclusters in multimodal structural characterization of bio-interfaces where the amphiphilic character of the supramolecular ligand is required.
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Affiliation(s)
- Patryk Obstarczyk
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Anna Pniakowska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Nonappa
- Faculty
of Engineering and Natural Sciences, Tampere
University, FI-33720 Tampere, Finland
| | - Marcin P. Grzelczak
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Johansson E, Caraballo R, Zocher G, Mistry N, Arnberg N, Stehle T, Elofsson M. Exploring divalent conjugates of 5- N-acetyl-neuraminic acid as inhibitors of coxsackievirus A24 variant (CVA24v) transduction. RSC Adv 2022; 12:2319-2331. [PMID: 35425270 PMCID: PMC8979015 DOI: 10.1039/d1ra08968d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022] Open
Abstract
Coxsackievirus A24 variant (CVA24v) is responsible for several outbreaks and two pandemics of the highly contagious eye infection acute hemorrhagic conjunctivitis (AHC). Currently, neither prevention (vaccines) nor treatments (antivirals) are available for combating this disease. CVA24v attaches to cells by binding Neu5Ac-containing glycans on the surface of cells which facilitates entry. Previously, we have demonstrated that pentavalent Neu5Ac conjugates attenuate CVA24v infection of human corneal epithelial (HCE) cells. In this study, we report on the structure-based design of three classes of divalent Neu5Ac conjugates, with varying spacer lengths, and their effect on CVA24v transduction in HCE cells. In relative terms, the most efficient class of divalent Neu5Ac conjugates are more efficient than the pentavalent Neu5Ac conjugates previously reported.
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Affiliation(s)
- Emil Johansson
- Department of Chemistry, Umeå University SE90187 Umeå Sweden
| | - Rémi Caraballo
- Department of Chemistry, Umeå University SE90187 Umeå Sweden
| | - Georg Zocher
- Interfaculty Institute of Biochemistry, University of Tübingen 72076 Tübingen Germany
| | - Nitesh Mistry
- Department of Clinical Microbiology, Umeå University SE90185 Umeå Sweden
| | - Niklas Arnberg
- Department of Clinical Microbiology, Umeå University SE90185 Umeå Sweden
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen 72076 Tübingen Germany
- Vanderbilt University School of Medicine Nashville Tennessee 37232 USA
| | - Mikael Elofsson
- Department of Chemistry, Umeå University SE90187 Umeå Sweden
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Hulkko E, Lahtinen T, Marjomäki V, Pohjolainen E, Saarnio V, Sokolowska K, Ajitha A, Kuisma M, Lehtovaara L, Groenhof G, Häkkinen H, Pettersson M. Covalent and non-covalent coupling of a Au 102 nanocluster with a fluorophore: energy transfer, quenching and intracellular pH sensing. NANOSCALE ADVANCES 2021; 3:6649-6658. [PMID: 36132657 PMCID: PMC9417352 DOI: 10.1039/d1na00368b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/22/2021] [Indexed: 05/08/2023]
Abstract
Interactions between an atomically precise gold nanocluster Au102(p-MBA)44 (p-MBA = para mercaptobenzoic acid) and a fluorescent organic dye molecule (KU, azadioxatriangulenium) are studied. In solution, the constituents form spontaneously a weakly bound complex leading to quenching of fluorescence of the KU dye via energy transfer. The KU can be separated from the complex by lowering pH, leading to recovery of fluorescence, which forms a basis for an optical reversible pH sensor. However, the sensor is not a stable entity, which could be delivered inside cells. For this purpose, a covalently bound hybrid is synthesized by linking the KU dye to the ligand layer of the cluster via an ester bond. Covalent linking facilitates entry of the cluster-dye hybrids into cells via endocytosis. Inside cells, the hybrids accumulate in endosomes where Au102 releases its cargo via hydrolysis of the ester bond. Changes of the local pH inside endosomes regulate reversible fluorescence due to variations in the interactions between the Au102 cluster and the dye. This work presents a concept for delivering reporter molecules into cells by using atomically precise gold nanoclusters as carriers and paves the way for future developments of cluster-reporter sensors for in vivo measurements of e.g. absolute pH values or ion concentrations.
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Affiliation(s)
- Eero Hulkko
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Tanja Lahtinen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Varpu Marjomäki
- Department of Biology and Environmental Science, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Emmi Pohjolainen
- Department of Physics, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Ville Saarnio
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Karolina Sokolowska
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Ardra Ajitha
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Mikael Kuisma
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Lauri Lehtovaara
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Gerrit Groenhof
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Hannu Häkkinen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
- Department of Physics, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
| | - Mika Pettersson
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P.O. Box 35 FI-40014 Finland
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Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses. Pharmaceutics 2021; 13:pharmaceutics13081182. [PMID: 34452144 PMCID: PMC8398301 DOI: 10.3390/pharmaceutics13081182] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 01/10/2023] Open
Abstract
To efficiently lower virus infectivity and combat virus epidemics or pandemics, it is important to discover broadly acting antivirals. Here, we investigated two naturally occurring polyphenols, Epigallocatechin gallate (EGCG) and Resveratrol (RES), and polyphenol-functionalized nanoparticles for their antiviral efficacy. Concentrations in the low micromolar range permanently inhibited the infectivity of high doses of enteroviruses (107 PFU/mL). Sucrose gradient separation of radiolabeled viruses, dynamic light scattering, transmission electron microscopic imaging and an in-house developed real-time fluorescence assay revealed that polyphenols prevented infection mainly through clustering of the virions into very stable assemblies. Clustering and stabilization were not compromised even in dilute virus solutions or after diluting the polyphenols-clustered virions by 50-fold. In addition, the polyphenols lowered virus binding on cells. In silico docking experiments of these molecules against 2- and 3-fold symmetry axes of the capsid, using an algorithm developed for this study, discovered five binding sites for polyphenols, out of which three were novel binding sites. Our results altogether suggest that polyphenols exert their antiviral effect through binding to multiple sites on the virion surface, leading to aggregation of the virions and preventing RNA release and reducing cell surface binding.
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Matus MF, Häkkinen H. Atomically Precise Gold Nanoclusters: Towards an Optimal Biocompatible System from a Theoretical-Experimental Strategy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005499. [PMID: 33533179 DOI: 10.1002/smll.202005499] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Potential biomedical applications of gold nanoparticles have increasingly been reported with great promise for diagnosis and therapy of several diseases. However, for such a versatile nanomaterial, the advantages and potential health risks need to be addressed carefully, as the available information about their toxicity is limited and inconsistent. Atomically precise gold nanoclusters (AuNCs) have emerged to overcome this challenge due to their unique features, such as superior stability, excellent biocompatibility, and efficient renal clearance. Remarkably, the elucidation of their structural and physicochemical properties provided by theory-experiment investigations offers exciting opportunities for site-specific biofunctionalization of the nanoparticle surface, which remains a significant concern for most of the materials in the biomedical field. This concept highlights the advantages conferred by atomically precise AuNCs for biomedical applications and the powerful strategy combining computational and experimental studies towards finding an optimal biocompatible AuNCs-based nanosystem.
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Affiliation(s)
- María Francisca Matus
- Department of Physics, Nanoscience Center (NSC), University of Jyväskylä, Jyväskylä, FI-40014, Finland
| | - Hannu Häkkinen
- Departments of Physics and Chemistry, Nanoscience Center (NSC), University of Jyväskylä, Jyväskylä, FI-40014, Finland
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Pap N, Reshamwala D, Korpinen R, Kilpeläinen P, Fidelis M, Furtado MM, Sant'Ana AS, Wen M, Zhang L, Hellström J, Marnilla P, Mattila P, Sarjala T, Yang B, Lima ADS, Azevedo L, Marjomäki V, Granato D. Toxicological and bioactivity evaluation of blackcurrant press cake, sea buckthorn leaves and bark from Scots pine and Norway spruce extracts under a green integrated approach. Food Chem Toxicol 2021; 153:112284. [PMID: 34044082 DOI: 10.1016/j.fct.2021.112284] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022]
Abstract
Aqueous extracts from blackcurrant press cake (BC), Norway spruce bark (NS), Scots pine bark (SP), and sea buckthorn leaves (SB) were obtained using maceration and pressurized hot water and tested for their bioactivities. Maceration provided the extraction of higher dry matter contents, including total phenolics (TPC), anthocyanins, and condensed tannins, which also impacted higher antioxidant activity. NS and SB extracts presented the highest mean values of TPC and antioxidant activity. Individually, NS extract presented high contents of proanthocyanidins, resveratrol, and some phenolic acids. In contrast, SB contained a high concentration of ellagitannins, ellagic acid, and quercetin, explaining the antioxidant activity and antibacterial effects. SP and BC extracts had the lowest TPC and antioxidant activity. However, BC had strong antiviral efficacy, whereas SP can be considered a potential ingredient to inhibit α-amylase. Except for BC, the other extracts decreased reactive oxygen species (ROS) generation in HCT8 and A549 cells. Extracts did not inhibit the production of TNF-alpha in lipopolysaccharide-stimulated THP-1 macrophages but inhibited the ROS generation during the THP-1 cell respiratory burst. The recovery of antioxidant compounds from these by-products is incentivized for high value-added applications.
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Affiliation(s)
- Nora Pap
- Biorefinery and Bioproducts, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland.
| | - Dhanik Reshamwala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Risto Korpinen
- Biorefinery and Bioproducts, Natural Resources Institute Finland (Luke), FI-02150, Espoo, Finland
| | - Petri Kilpeläinen
- Biorefinery and Bioproducts, Natural Resources Institute Finland (Luke), FI-02150, Espoo, Finland
| | - Marina Fidelis
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI-02150, Espoo, Finland
| | - Marianna M Furtado
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Mingchun Wen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Liang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jarkko Hellström
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland
| | - Pertti Marnilla
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland
| | - Pirjo Mattila
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI- 20520, Turku, Finland
| | - Tytti Sarjala
- Biomass Characterization and Properties, Natural Resources Institute Finland (Luke), FI-39700, Parkano, Finland
| | - Baoru Yang
- Food Chemistry and Food Development, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Amanda Dos Santos Lima
- Department of Food, Faculty of Nutrition, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 714, 37130-000, Alfenas, Brazil
| | - Luciana Azevedo
- Department of Food, Faculty of Nutrition, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 714, 37130-000, Alfenas, Brazil
| | - Varpu Marjomäki
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Daniel Granato
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI-02150, Espoo, Finland.
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12
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Prospects and challenges for computer simulations of monolayer-protected metal clusters. Nat Commun 2021; 12:2197. [PMID: 33850156 PMCID: PMC8044087 DOI: 10.1038/s41467-021-22545-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 11/16/2022] Open
Abstract
Precise knowledge of chemical composition and atomic structure of functional nanosized systems, such as metal clusters stabilized by an organic molecular layer, allows for detailed computational work to investigate structure-property relations. Here, we discuss selected recent examples of computational work that has advanced understanding of how these clusters work in catalysis, how they interact with biological systems, and how they can make self-assembled, macroscopic materials. A growing challenge is to develop effective new simulation methods that take into account the cluster-environment interactions. These new hybrid methods are likely to contain components from electronic structure theory combined with machine learning algorithms for accelerated evaluations of atom-atom interactions.
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13
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Mammen N, Malola S, Honkala K, Häkkinen H. Dynamics of weak interactions in the ligand layer of meta-mercaptobenzoic acid protected gold nanoclusters Au 68( m-MBA) 32 and Au 144( m-MBA) 40. NANOSCALE 2020; 12:23859-23868. [PMID: 33237092 DOI: 10.1039/d0nr07366k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Atomically precise metal nanoclusters, stabilized and functionalized by organic ligands, are emerging nanomaterials with potential applications in plasmonics, nano-electronics, bio-imaging, nanocatalysis, and as therapeutic agents or drug carriers in nanomedicine. The ligand layer has an important role in modifying the physico-chemical properties of the clusters and in defining the interactions between the clusters and the environment. While this role is well recognized from a great deal of experimental studies, there is very little theoretical information on dynamical processes within the layer itself. Here, we have performed extensive molecular dynamics simulations, with forces calculated from the density functional theory, to investigate thermal stability and dynamics of the ligand layer of the meta-mercaptobenzoic acid (m-MBA) protected Au68 and Au144 nanoclusters, which are the first two gold nanoclusters structurally solved to atomic precision by electron microscopy [Azubel et al., Science, 2014, 345, 909 and ACS Nano, 2017, 11, 11866]. We visualize and analyze dynamics of three distinct non-covalent interactions, viz., ligand-ligand hydrogen bonding, metal-ligand O[double bond, length as m-dash]C-OHAu interaction, and metal-ligand Ph(π)Au interaction. We discuss their relevance for defining, at the same time, the dynamic stability and reactivity of the cluster. These interactions promote the possibility of ligand addition reactions for bio-functionalization or allow the protected cluster to act as a catalyst where active sites are dynamically accessible inside the ligand layer.
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Affiliation(s)
- Nisha Mammen
- Department of Physics, Nanoscience Center, University of Jyväskylä, Jyväskylä-40014, Finland
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14
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Johansson E, Caraballo R, Mistry N, Zocher G, Qian W, Andersson CD, Hurdiss DL, Chandra N, Thompson R, Frängsmyr L, Stehle T, Arnberg N, Elofsson M. Pentavalent Sialic Acid Conjugates Block Coxsackievirus A24 Variant and Human Adenovirus Type 37-Viruses That Cause Highly Contagious Eye Infections. ACS Chem Biol 2020; 15:2683-2691. [PMID: 32845119 PMCID: PMC7586296 DOI: 10.1021/acschembio.0c00446] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
Coxsackievirus A24
variant (CVA24v) and human adenovirus 37 (HAdV-37)
are leading causative agents of the severe and highly contagious ocular
infections acute hemorrhagic conjunctivitis and epidemic keratoconjunctivitis,
respectively. Currently, neither vaccines nor antiviral agents are
available for treating these diseases, which affect millions of individuals
worldwide. CVA24v and HAdV-37 utilize sialic acid as attachment receptors
facilitating entry into host cells. Previously, we and others have
shown that derivatives based on sialic acid are effective in preventing
HAdV-37 binding and infection of cells. Here, we designed and synthesized
novel pentavalent sialic acid conjugates and studied their inhibitory
effect against CVA24v and HAdV-37 binding and infection of human corneal
epithelial cells. The pentavalent conjugates are the first reported
inhibitors of CVA24v infection and proved efficient in blocking HAdV-37
binding. Taken together, the pentavalent conjugates presented here
form a basis for the development of general inhibitors of these highly
contagious ocular pathogens.
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Affiliation(s)
- Emil Johansson
- Department of Chemistry, Umeå University, SE90187 Umeå, Sweden
| | - Rémi Caraballo
- Department of Chemistry, Umeå University, SE90187 Umeå, Sweden
| | - Nitesh Mistry
- Section of Virology, Department of Clinical Microbiology, Umeå University, SE90185 Umeå, Sweden
| | - Georg Zocher
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Weixing Qian
- Department of Chemistry, Umeå University, SE90187 Umeå, Sweden
| | | | - Daniel L. Hurdiss
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, The Netherlands
| | - Naresh Chandra
- Section of Virology, Department of Clinical Microbiology, Umeå University, SE90185 Umeå, Sweden
| | - Rebecca Thompson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lars Frängsmyr
- Section of Virology, Department of Clinical Microbiology, Umeå University, SE90185 Umeå, Sweden
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
- Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Niklas Arnberg
- Section of Virology, Department of Clinical Microbiology, Umeå University, SE90185 Umeå, Sweden
| | - Mikael Elofsson
- Department of Chemistry, Umeå University, SE90187 Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, SE90187 Umeå, Sweden
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15
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Laajala M, Reshamwala D, Marjomäki V. Therapeutic targets for enterovirus infections. Expert Opin Ther Targets 2020; 24:745-757. [DOI: 10.1080/14728222.2020.1784141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mira Laajala
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Dhanik Reshamwala
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Varpu Marjomäki
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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16
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Pihlajamäki A, Hämäläinen J, Linja J, Nieminen P, Malola S, Kärkkäinen T, Häkkinen H. Monte Carlo Simulations of Au 38(SCH 3) 24 Nanocluster Using Distance-Based Machine Learning Methods. J Phys Chem A 2020; 124:4827-4836. [PMID: 32412747 DOI: 10.1021/acs.jpca.0c01512] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present an implementation of distance-based machine learning (ML) methods to create a realistic atomistic interaction potential to be used in Monte Carlo simulations of thermal dynamics of thiolate (SR) protected gold nanoclusters. The ML potential is trained for Au38(SR)24 by using previously published, density functional theory (DFT) based, molecular dynamics (MD) simulation data on two experimentally characterized structural isomers of the cluster and validated against independent DFT MD simulations. This method opens a door to efficient probing of the configuration space for further investigations of thermal-dependent electronic and optical properties of Au38(SR)24. Our ML implementation strategy allows for generalization and accuracy control of distance-based ML models for complex nanostructures having several chemical elements and interactions of varying strength.
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Affiliation(s)
- Antti Pihlajamäki
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Joonas Hämäläinen
- Faculty of Information Technology, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Joakim Linja
- Faculty of Information Technology, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Paavo Nieminen
- Faculty of Information Technology, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Sami Malola
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Tommi Kärkkäinen
- Faculty of Information Technology, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Hannu Häkkinen
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
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17
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Zuber G, Weiss E, Chiper M. Biocompatible gold nanoclusters: synthetic strategies and biomedical prospects. NANOTECHNOLOGY 2019; 30:352001. [PMID: 31071693 DOI: 10.1088/1361-6528/ab2088] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The latest advances concerning ultra-small gold nanoparticles (≤2 nm) commonly known as gold nanoclusters (AuNCs) are reviewed and discussed in the context of biological and biomedical applications (labeling, delivery, imaging and therapy). A great diversity of synthetic methods has been developed and optimized aiming to improve the chemical structures and physicochemical properties of the resulting AuNCs. The main synthetic approaches were surveyed with emphasis on methods leading to water-soluble AuNCs since aqueous solutions are the preferred media for biological applications. The most representative and recent experimental results are discussed in relationship to their potential for biomedical applications.
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Affiliation(s)
- Guy Zuber
- Molecular and Pharmaceutical Engineering of Biologics, CNRS-Université de Strasbourg UMR 7242, Boulevard Sebastien Brant, F-67412, Illkirch, France
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18
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Extracellular Albumin and Endosomal Ions Prime Enterovirus Particles for Uncoating That Can Be Prevented by Fatty Acid Saturation. J Virol 2019; 93:JVI.00599-19. [PMID: 31189702 DOI: 10.1128/jvi.00599-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
There is limited information about the molecular triggers leading to the uncoating of enteroviruses under physiological conditions. Using real-time spectroscopy and sucrose gradients with radioactively labeled virus, we show at 37°C, the formation of albumin-triggered, metastable uncoating intermediate of echovirus 1 without receptor engagement. This conversion was blocked by saturating the albumin with fatty acids. High potassium but low sodium and calcium concentrations, mimicking the endosomal environment, also induced the formation of a metastable uncoating intermediate of echovirus 1. Together, these factors boosted the formation of the uncoating intermediate, and the infectivity of this intermediate was retained, as judged by end-point titration. Cryo-electron microscopy reconstruction of the virions treated with albumin and high potassium, low sodium, and low calcium concentrations resulted in a 3.6-Å resolution model revealing a fenestrated capsid showing 4% expansion and loss of the pocket factor, similarly to altered (A) particles described for other enteroviruses. The dimer interface between VP2 molecules was opened, the VP1 N termini disordered and most likely externalized. The RNA was clearly visible, anchored to the capsid. The results presented here suggest that extracellular albumin, partially saturated with fatty acids, likely leads to the formation of the infectious uncoating intermediate prior to the engagement with the cellular receptor. In addition, changes in mono- and divalent cations, likely occurring in endosomes, promote capsid opening and genome release.IMPORTANCE There is limited information about the uncoating of enteroviruses under physiological conditions. Here, we focused on physiologically relevant factors that likely contribute to opening of echovirus 1 and other B-group enteroviruses. By combining biochemical and structural data, we show that, before entering cells, extracellular albumin is capable of priming the virus into a metastable yet infectious intermediate state. The ionic changes that are suggested to occur in endosomes can further contribute to uncoating and promote genome release, once the viral particle is endocytosed. Importantly, we provide a detailed high-resolution structure of a virion after treatment with albumin and a preset ion composition, showing pocket factor release, capsid expansion, and fenestration and the clearly visible genome still anchored to the capsid. This study provides valuable information about the physiological factors that contribute to the opening of B group enteroviruses.
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19
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Linnakoski R, Reshamwala D, Veteli P, Cortina-Escribano M, Vanhanen H, Marjomäki V. Antiviral Agents From Fungi: Diversity, Mechanisms and Potential Applications. Front Microbiol 2018; 9:2325. [PMID: 30333807 PMCID: PMC6176074 DOI: 10.3389/fmicb.2018.02325] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/11/2018] [Indexed: 01/14/2023] Open
Abstract
Viral infections are amongst the most common diseases affecting people worldwide. New viruses emerge all the time and presently we have limited number of vaccines and only few antivirals to combat viral diseases. Fungi represent a vast source of bioactive molecules, which could potentially be used as antivirals in the future. Here, we have summarized the current knowledge of fungi as producers of antiviral compounds and discuss their potential applications. In particular, we have investigated how the antiviral action has been assessed and what is known about the molecular mechanisms and actual targets. Furthermore, we highlight the importance of accurate fungal species identification on antiviral and other natural products studies.
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Affiliation(s)
| | - Dhanik Reshamwala
- Division of Cell and Molecular Biology, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Pyry Veteli
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | | | - Henri Vanhanen
- Natural Resources Institute Finland (Luke), Joensuu, Finland
| | - Varpu Marjomäki
- Division of Cell and Molecular Biology, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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20
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Nasaruddin RR, Chen T, Yan N, Xie J. Roles of thiolate ligands in the synthesis, properties and catalytic application of gold nanoclusters. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.016] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Linnakoski R, Reshamwala D, Veteli P, Cortina-Escribano M, Vanhanen H, Marjomäki V. Antiviral Agents From Fungi: Diversity, Mechanisms and Potential Applications. Front Microbiol 2018. [PMID: 30333807 DOI: 10.3389/fmicb.2018.02325/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023] Open
Abstract
Viral infections are amongst the most common diseases affecting people worldwide. New viruses emerge all the time and presently we have limited number of vaccines and only few antivirals to combat viral diseases. Fungi represent a vast source of bioactive molecules, which could potentially be used as antivirals in the future. Here, we have summarized the current knowledge of fungi as producers of antiviral compounds and discuss their potential applications. In particular, we have investigated how the antiviral action has been assessed and what is known about the molecular mechanisms and actual targets. Furthermore, we highlight the importance of accurate fungal species identification on antiviral and other natural products studies.
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Affiliation(s)
| | - Dhanik Reshamwala
- Division of Cell and Molecular Biology, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Pyry Veteli
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | | | - Henri Vanhanen
- Natural Resources Institute Finland (Luke), Joensuu, Finland
| | - Varpu Marjomäki
- Division of Cell and Molecular Biology, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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22
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Pohjolainen E, Malola S, Groenhof G, Häkkinen H. Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations. Bioconjug Chem 2017; 28:2327-2339. [DOI: 10.1021/acs.bioconjchem.7b00367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emmi Pohjolainen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Sami Malola
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Gerrit Groenhof
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Hannu Häkkinen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
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23
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Ross C, Knox C, Tastan Bishop Ö. Interacting motif networks located in hotspots associated with RNA release are conserved in Enterovirus capsids. FEBS Lett 2017; 591:1687-1701. [PMID: 28471477 DOI: 10.1002/1873-3468.12663] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/23/2017] [Accepted: 04/27/2017] [Indexed: 12/20/2022]
Abstract
Enteroviruses are responsible for a multitude of human diseases. Expansion of the virus capsid is associated with a cascade of conformational changes that allow the subsequent release of RNA. For the first time, this study presents a comprehensive bioinformatic screen for the prediction of interacting motifs within intraprotomer interfaces and across respective interfaces surrounding the fivefold and twofold axes. The results identify a network of conserved motif residues involved in interactions in enteroviruses that may be critical to capsid stabilisation, providing guidelines towards developing antivirals that interfere with viral expansion during RNA release.
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Affiliation(s)
- Caroline Ross
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Caroline Knox
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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24
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Lahtinen T, Haataja JS, Tero TR, Häkkinen H, Ikkala O. Template-Free Supracolloidal Self-Assembly of Atomically Precise Gold Nanoclusters: From 2D Colloidal Crystals to Spherical Capsids. Angew Chem Int Ed Engl 2016; 55:16035-16038. [PMID: 27879034 DOI: 10.1002/anie.201609036] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/15/2016] [Indexed: 01/03/2023]
Abstract
We report supracolloidal self-assembly of atomically precise and strictly monodisperse gold nanoclusters involving p-mercaptobenzoic acid ligands (Au102 -pMBA44 ) under aqueous conditions into hexagonally packed monolayer-thick two-dimensional facetted colloidal crystals (thickness 2.7 nm) and their bending to closed shells leading to spherical capsids (d ca. 200 nm), as controlled by solvent conditions. The 2D colloidal assembly is driven in template-free manner by the spontaneous patchiness of the pMBA ligands around the Au102 -pMBA44 nanoclusters preferably towards equatorial plane, thus promoting inter-nanocluster hydrogen bonds and high packing to planar sheets. More generally, the findings encourage to explore atomically precise nanoclusters towards highly controlled colloidal self-assemblies.
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Affiliation(s)
- Tanja Lahtinen
- Departments of Chemistry and Physics, Nanoscience centre, University of Jyväskylä, Survontie 9, 40014, Jyväskylä, Finland
| | - Johannes S Haataja
- Department of Applied Physics, Molecular Materials Group, Aalto University School of Science, Puumiehenkuja 2, Espoo, 02150, Finland
| | - Tiia-Riikka Tero
- Departments of Chemistry and Physics, Nanoscience centre, University of Jyväskylä, Survontie 9, 40014, Jyväskylä, Finland
| | - Hannu Häkkinen
- Departments of Chemistry and Physics, Nanoscience centre, University of Jyväskylä, Survontie 9, 40014, Jyväskylä, Finland
| | - Olli Ikkala
- Department of Applied Physics, Molecular Materials Group, Aalto University School of Science, Puumiehenkuja 2, Espoo, 02150, Finland
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25
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Nonappa, Lahtinen T, Haataja JS, Tero TR, Häkkinen H, Ikkala O. Template-Free Supracolloidal Self-Assembly of Atomically Precise Gold Nanoclusters: From 2D Colloidal Crystals to Spherical Capsids. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Nonappa
- Department of Applied Physics, Molecular Materials Group; Aalto University School of Science; Puumiehenkuja 2 Espoo 02150 Finland
| | - Tanja Lahtinen
- Departments of Chemistry and Physics, Nanoscience centre; University of Jyväskylä; Survontie 9 40014 Jyväskylä Finland
| | - Johannes. S. Haataja
- Department of Applied Physics, Molecular Materials Group; Aalto University School of Science; Puumiehenkuja 2 Espoo 02150 Finland
| | - Tiia-Riikka Tero
- Departments of Chemistry and Physics, Nanoscience centre; University of Jyväskylä; Survontie 9 40014 Jyväskylä Finland
| | - Hannu Häkkinen
- Departments of Chemistry and Physics, Nanoscience centre; University of Jyväskylä; Survontie 9 40014 Jyväskylä Finland
| | - Olli Ikkala
- Department of Applied Physics, Molecular Materials Group; Aalto University School of Science; Puumiehenkuja 2 Espoo 02150 Finland
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26
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Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle. Nat Commun 2016; 7:10401. [PMID: 26791253 PMCID: PMC4736050 DOI: 10.1038/ncomms10401] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/08/2015] [Indexed: 11/20/2022] Open
Abstract
Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications. The core structure of inorganic nanoparticles, stabilized by a passivating layer of organic molecules, is often known but information about the organic layer is tougher to derive. Here, the authors use NMR and computational methods to probe the ligand disorder and visualize possible ligand conformations.
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