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Computational Prediction of Potential Inhibitors of the Main Protease of SARS-CoV-2.
Abel, Renata; Paredes Ramos, María; Chen, Qiaofeng; Pérez-Sánchez, Horacio; Coluzzi, Flaminia; Rocco, Monica; Marchetti, Paolo; Mura, Cameron; Simmaco, Maurizio; Bourne, Philip E; Preissner, Robert; Banerjee, Priyanka.
  • Abel R; Institute of Physiology, Charité-University Medicine Berlin, Berlin, Germany.
  • Paredes Ramos M; METMED Research Group, Physical Chemistry Department, Universidade da Coruña (UDC), A Coruña, Spain.
  • Chen Q; Institute of Physiology, Charité-University Medicine Berlin, Berlin, Germany.
  • Pérez-Sánchez H; Structural Bioinformatics and High-Performance Computing (BIO-HPC) Research Group, Universidad Católica de Murcia (UCAM), Murcia, Spain.
  • Coluzzi F; Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.
  • Rocco M; Unit of Anesthesia and Intensive Care Medicine, Sant' Andrea University Hospital, Rome, Italy.
  • Marchetti P; Unit of Anesthesia and Intensive Care Medicine, Sant' Andrea University Hospital, Rome, Italy.
  • Mura C; Department of Clinical and Surgical Translational Medicine, Sapienza University of Rome, Rome, Italy.
  • Simmaco M; Department of Clinical and Surgical Translational Medicine, Sapienza University of Rome, Rome, Italy.
  • Bourne PE; Department of Biomedical Engineering and School of Data Science, University of Virginia, Charlottesville, VA, United States.
  • Preissner R; Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy.
  • Banerjee P; Advanced Molecular Diagnostic Unit, Sant' Andrea University Hospital, Rome, Italy.
Front Chem ; 8: 590263, 2020.
Article in English | MEDLINE | ID: covidwho-1021883
ABSTRACT
The rapidly developing pandemic, known as coronavirus disease 2019 (COVID-19) and caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently spread across 213 countries and territories. This pandemic is a dire public health threat-particularly for those suffering from hypertension, cardiovascular diseases, pulmonary diseases, or diabetes; without approved treatments, it is likely to persist or recur. To facilitate the rapid discovery of inhibitors with clinical potential, we have applied ligand- and structure-based computational approaches to develop a virtual screening methodology that allows us to predict potential inhibitors. In this work, virtual screening was performed against two natural products databases, Super Natural II and Traditional Chinese Medicine. Additionally, we have used an integrated drug repurposing approach to computationally identify potential inhibitors of the main protease of SARS-CoV-2 in databases of drugs (both approved and withdrawn). Roughly 360,000 compounds were screened using various molecular fingerprints and molecular docking methods; of these, 80 docked compounds were evaluated in detail, and the 12 best hits from four datasets were further inspected via molecular dynamics simulations. Finally, toxicity and cytochrome inhibition profiles were computationally analyzed for the selected candidate compounds.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Topics: Traditional medicine Language: English Journal: Front Chem Year: 2020 Document Type: Article Affiliation country: Fchem.2020.590263

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Topics: Traditional medicine Language: English Journal: Front Chem Year: 2020 Document Type: Article Affiliation country: Fchem.2020.590263