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EXaSCale smArt pLatform Against paThogEns for Corona Virus

Deliverables

Setup and Maintenance of Website & Social Media

This task provides the coordination of dissemination activities (E4C project webpage, workshops, conferences, articles, and book) and communication activities. WP10 will take care of the overall coordination of the dissemination and communication activities to be run in parallel to other activities throughout the whole project duration to ensure a prompt communication and publication of project results on several dissemination media channels. The project webpage will be set up at the beginning of the project and regularly updated and maintained. Communication activities will ensure the spreading out of the project’s outcome outside the Consortium so that the methodologies developed and the results obtained can be widely spread out in the scientific community. Communication objectives will be achieved by using multiple different strategies including the use of social networks such as Linkedin, Facebook, Twitter and YouTube to spread out the project knowledge to a larger audience. Given the wide social impact of this research, actions towards the general press will be given through press releases, newsletters and through local press. The dissemination of the results will be realized through a number of training activities and publications in top-level scientific journals. The project results will be presented to the scientific community at a number of prestigious international venues such as top-level conferences and exhibitions.The main dissemination and communication activities to be carried out in the project are described in Section 2.2.1.

Publications

Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities

Author(s): Rolando Cannalire, Carmen Cerchia, Andrea R. Beccari, Francesco Saverio Di Leva, Vincenzo Summa
Published in: Journal of Medicinal Chemistry, 11/2020, 2020, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.0c01140

Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples

Author(s): Flora Marzia Liotti, Giulia Menchinelli, Eleonora Lalle, Ivana Palucci, Simona Marchetti, Francesca Colavita, Marilena La Sorda, Giuseppe Sberna, Licia Bordi, Maurizio Sanguinetti, Paola Cattani, Maria Rosaria Capobianchi, Brunella Posteraro
Published in: Clinical Microbiology and Infection, 27/3, 2021, Page(s) 487-488, ISSN 1198-743X
Publisher: Blackwell Publishing Inc.
DOI: 10.1016/j.cmi.2020.09.030

Virological Characterization of the First 2 COVID-19 Patients Diagnosed in Italy: Phylogenetic Analysis, Virus Shedding Profile From Different Body Sites, and Antibody Response Kinetics

Author(s): Francesca Colavita, Daniele Lapa, Fabrizio Carletti, Eleonora Lalle, Francesco Messina, Martina Rueca, Giulia Matusali, Silvia Meschi, Licia Bordi, Patrizia Marsella, Emanuele Nicastri, Luisa Marchioni, Andrea Mariano, Laura Scorzolini, Tommaso Ascoli Bartoli, Antonino Di Caro, Giuseppe Ippolito, Maria Rosaria Capobianchi, Concetta Castilletti, Isabella Abbate, Chiara Agrati, Loredana Aleo, Tonino
Published in: Open Forum Infectious Diseases, 7/10, 2020, ISSN 2328-8957
Publisher: Infectious Diseases Society of America
DOI: 10.1093/ofid/ofaa403

A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization

Author(s): Bruce Schultz, Andrea Zaliani, Christian Ebeling, Jeanette Reinshagen, Denisa Bojkova, Vanessa Lage-Rupprecht, Reagon Karki, Sören Lukassen, Yojana Gadiya, Neal G. Ravindra, Sayoni Das, Shounak Baksi, Daniel Domingo-Fernández, Manuel Lentzen, Mark Strivens, Tamara Raschka, Jindrich Cinatl, Lauren Nicole DeLong, Phil Gribbon, Gerd Geisslinger, Sandra Ciesek, David van Dijk, Steve Gardner, Alpha T
Published in: Scientific Reports, 11/1, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-90296-2

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease

Author(s): Sebastian Günther, Patrick Y. A. Reinke, Yaiza Fernández-García, Julia Lieske, Thomas J. Lane, Helen M. Ginn, Faisal H. M. Koua, Christiane Ehrt, Wiebke Ewert, Dominik Oberthuer, Oleksandr Yefanov, Susanne Meier, Kristina Lorenzen, Boris Krichel, Janine-Denise Kopicki, Luca Gelisio, Wolfgang Brehm, Ilona Dunkel, Brandon Seychell, Henry Gieseler, Brenna Norton-Baker, Beatriz Escudero-Pérez, Mar
Published in: Science, 2021, Page(s) eabf7945, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abf7945

Natural and Nature-Derived Products Targeting Human Coronaviruses

Author(s): Konstantina Vougogiannopoulou, Angela Corona, Enzo Tramontano, Michael N. Alexis, Alexios-Leandros Skaltsounis
Published in: Molecules, 26/2, 2021, Page(s) 448, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26020448

Saliva Is a Valid Alternative to Nasopharyngeal Swab in Chemiluminescence-Based Assay for Detection of SARS-CoV-2 Antigen

Author(s): Alessandra Amendola, Giuseppe Sberna, Eleonora Lalle, Francesca Colavita, Concetta Castilletti, Giulia Menchinelli, Brunella Posteraro, Maurizio Sanguinetti, Giuseppe Ippolito, Licia Bordi, Maria Capobianchi
Published in: Journal of Clinical Medicine, 10/7, 2021, Page(s) 1471, ISSN 2077-0383
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/jcm10071471

Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

Author(s): Candida Manelfi, Jonas Gossen, Silvia Gervasoni, Carmine Talarico, Simone Albani, Benjamin Joseph Philipp, Francesco Musiani, Giulio Vistoli, Giulia Rossetti, Andrea Rosario Beccari, Alessandro Pedretti
Published in: Molecules, 26/4, 2021, Page(s) 797, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26040797

Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen

Author(s): Maria Kuzikov, Elisa Costanzi, Jeanette Reinshagen, Francesca Esposito, Laura Vangeel, Markus Wolf, Bernhard Ellinger, Carsten Claussen, Gerd Geisslinger, Angela Corona, Daniela Iaconis, Carmine Talarico, Candida Manelfi, Rolando Cannalire, Giulia Rossetti, Jonas Gossen, Simone Albani, Francesco Musiani, Katja Herzog, Yang Ye, Barbara Giabbai, Nicola Demitri, Dirk Jochmans, Steven De Jonghe, Jaspe
Published in: ACS Pharmacology & Translational Science, 3/2021, 2021, ISSN 2575-9108
Publisher: American Chemical Society
DOI: 10.1021/acsptsci.0c00216

Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay

Author(s): Licia Bordi, Giuseppe Sberna, Eleonora Lalle, Pierluca Piselli, Francesca Colavita, Emanuele Nicastri, Andrea Antinori, Evangelo Boumis, Nicola Petrosillo, Luisa Marchioni, Giulia Minnucci, Elena D’Agostini, Concetta Castilletti, Franco Locatelli, Alimuddin Zumla, Giuseppe Ippolito, Maria Capobianchi
Published in: Viruses, 12/10, 2020, Page(s) 1184, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12101184

Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs

Author(s): Camila Pontes, Victoria Ruiz-Serra, Rosalba Lepore, Alfonso Valencia
Published in: Computational and Structural Biotechnology Journal, 19, 2021, Page(s) 759-766, ISSN 2001-0370
Publisher: Computational and Structural Biotechnology Journal
DOI: 10.1016/j.csbj.2021.01.006

Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis

Author(s): Martina Rueca, Barbara Bartolini, Cesare Ernesto Maria Gruber, Antonio Piralla, Fausto Baldanti, Emanuela Giombini, Francesco Messina, Luisa Marchioni, Giuseppe Ippolito, Antonino Di Caro, Maria Rosaria Capobianchi
Published in: Microorganisms, 8/9, 2020, Page(s) 1302, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms8091302

Comparison of Allplex™ SARS-CoV-2 Assay, Easy SARS-CoV-2 WE and Lumipulse quantitative SARS-CoV-2 antigen test performance using automated systems for the diagnosis of COVID-19

Author(s): Giuseppe Sberna, Flavia Basile, Maria Luisa Guarino, Maria Rosaria Capobianchi, Licia Bordi, Gabriella Parisi
Published in: International Journal of Infectious Diseases, 113, 2021, Page(s) 113-115, ISSN 1201-9712
Publisher: Elsevier BV
DOI: 10.1016/j.ijid.2021.09.069

SARS-CoV-2 Phylogenetic Analysis, Lazio Region, Italy, February–March 2020

Author(s): Barbara Bartolini, Martina Rueca, Cesare Ernesto Maria Gruber, Francesco Messina, Fabrizio Carletti, Emanuela Giombini, Eleonora Lalle, Licia Bordi, Giulia Matusali, Francesca Colavita, Concetta Castilletti, Francesco Vairo, Giuseppe Ippolito, Maria Rosaria Capobianchi, Antonino Di Caro
Published in: Emerging Infectious Diseases, 26/8, 2020, Page(s) 1842-1845, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2608.201525

A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0

Author(s): Silvia Gervasoni, Giulio Vistoli, Carmine Talarico, Candida Manelfi, Andrea R. Beccari, Gabriel Studer, Gerardo Tauriello, Andrew Mark Waterhouse, Torsten Schwede, Alessandro Pedretti
Published in: International Journal of Molecular Sciences, 21/14, 2020, Page(s) 5152, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21145152

A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics

Author(s): Jonas Gossen, Simone Albani, Anton Hanke, Benjamin P. Joseph, Cathrine Bergh, Maria Kuzikov, Elisa Costanzi, Candida Manelfi, Paola Storici, Philip Gribbon, Andrea R. Beccari, Carmine Talarico, Francesca Spyrakis, Erik Lindahl, Andrea Zaliani, Paolo Carloni, Rebecca C. Wade, Francesco Musiani, Daria B. Kokh, Giulia Rossetti
Published in: ACS Pharmacology & Translational Science, 3/2021, 2020, Page(s) -, ISSN 2575-9108
Publisher: American Chemical Society
DOI: 10.1021/acsptsci.0c00215

Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations

Author(s): Alessandro Grottesi, Neva Bešker, Andrew Emerson, Candida Manelfi, Andrea R. Beccari, Francesco Frigerio, Erik Lindahl, Carmen Cerchia, Carmine Talarico
Published in: International Journal of Molecular Sciences, 21/15, 2020, Page(s) 5346, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21155346

Medical treatment options for COVID-19

Author(s): Leen Delang, Johan Neyts
Published in: European Heart Journal: Acute Cardiovascular Care, 9/3, 2020, Page(s) 209-214, ISSN 2048-8726
Publisher: SAGE Publications Ltd
DOI: 10.1177/2048872620922790

SARS-CoV-2 Entry Inhibitors: Small Molecules and Peptides Targeting Virus or Host Cells

Author(s): Rolando Cannalire, Irina Stefanelli, Carmen Cerchia, Andrea R. Beccari, Sveva Pelliccia, Vincenzo Summa
Published in: International Journal of Molecular Sciences, 21/16, 2020, Page(s) 5707, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21165707

Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing

Author(s): Martina Rueca, Andrea Fontana, Barbara Bartolini, Pierluca Piselli, Antonio Mazzarelli, Massimiliano Copetti, Elena Binda, Francesco Perri, Cesare Ernesto Maria Gruber, Emanuele Nicastri, Luisa Marchioni, Giuseppe Ippolito, Maria Rosaria Capobianchi, Antonino Di Caro, Valerio Pazienza
Published in: International Journal of Environmental Research and Public Health, 18/4, 2021, Page(s) 2174, ISSN 1660-4601
Publisher: MDPI
DOI: 10.3390/ijerph18042174

Proteomic analysis identifies the RNA helicase DDX3X as a host target against SARS-CoV-2 infection

Author(s): Fabiola Ciccosanti, Martina Di Rienzo, Alessandra Romagnoli, Francesca Colavita, Giulia Refolo, Concetta Castilletti, Chiara Agrati, Annalaura Brai, Fabrizio Manetti, Lorenzo Botta, Maria Rosaria Capobianchi, Giuseppe Ippolito, Mauro Piacentini, Gian Maria Fimia
Published in: Antiviral Research, 190, 2021, Page(s) 105064, ISSN 0166-3542
Publisher: Elsevier BV
DOI: 10.1016/j.antiviral.2021.105064

16S rRNA gene sequencing of rectal swab in patients affected by COVID-19

Author(s): Antonio Mazzarelli, Maria Letizia Giancola, Anna Farina, Luisa Marchioni, Martina Rueca, Cesare Ernesto Maria Gruber, Barbara Bartolini, Tommaso Ascoli Bartoli, Gaetano Maffongelli, Maria Rosaria Capobianchi, Giuseppe Ippolito, Antonino Di Caro, Emanuele Nicastri, Valerio Pazienza
Published in: PLOS ONE, 16/2, 2021, Page(s) e0247041, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0247041

In Vitro Models for Studying Entry, Tissue Tropism, and Therapeutic Approaches of Highly Pathogenic Coronaviruses

Author(s): Saeid Najafi Fard, Linda Petrone, Elisa Petruccioli, Tonino Alonzi, Giulia Matusali, Francesca Colavita, Concetta Castilletti, Maria Rosaria Capobianchi, Delia Goletti
Published in: BioMed Research International, 2021, 2021, Page(s) 1-21, ISSN 2314-6133
Publisher: Hindawi Publishing Corporation
DOI: 10.1155/2021/8856018

Evidences for lipid involvement in SARS-CoV-2 cytopathogenesis

Author(s): Roberta Nardacci, Francesca Colavita, Concetta Castilletti, Daniele Lapa, Giulia Matusali, Silvia Meschi, Franca Del Nonno, Daniele Colombo, Maria Rosaria Capobianchi, Alimuddin Zumla, Giuseppe Ippolito, Mauro Piacentini, Laura Falasca
Published in: Cell Death & Disease, 12/3, 2021, ISSN 2041-4889
Publisher: Nature Publishing Group
DOI: 10.1038/s41419-021-03527-9

Repurposing the estrogen receptor modulator raloxifene to treat SARS-CoV-2 infection

Author(s): Marcello Allegretti, Maria Candida Cesta, Mara Zippoli, Andrea Beccari, Carmine Talarico, Flavio Mantelli, Enrico M. Bucci, Laura Scorzolini, Emanuele Nicastri
Published in: Cell Death & Differentiation, 2021, ISSN 1350-9047
Publisher: Nature Publishing Group
DOI: 10.1038/s41418-021-00844-6

Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L

Author(s): Elisa Costanzi, Maria Kuzikov, Francesca Esposito, Simone Albani, Nicola Demitri, Barbara Giabbai, Marianna Camasta, Enzo Tramontano, Giulia Rossetti, Andrea Zaliani, Paola Storici
Published in: International Journal of Molecular Sciences, 22/21, 2021, Page(s) 11779, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222111779

Altered Local Interactions and Long-Range Communications in UK Variant (B.1.1.7) Spike Glycoprotein

Author(s): Stefano Borocci, Carmen Cerchia, Alessandro Grottesi, Nico Sanna, Ingrid Guarnetti Prandi, Nabil Abid, Andrea R. Beccari, Giovanni Chillemi, Carmine Talarico
Published in: International Journal of Molecular Sciences, 22/11, 2021, Page(s) 5464, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22115464