Journal article

Interaction of the prototypical alpha-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex

Julia Liang, Eleni Pitsillou, Chris Karagiannis, Kevion K Darmawan, Ken Ng, Andrew Hung, Tom C Karagiannis

Computational Biology and Chemistry | ELSEVIER SCI LTD | Published : 2020

Abstract

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes an illness known as COVID-19, which has been declared a global pandemic with over 2 million confirmed cases and 137,000 deaths in 185 countries and regions at the time of writing (16 April 2020), over a quarter of these cases being in the United States. In the absence of a vaccine, or an approved effective therapeutic, there is an intense interest in repositioning available drugs or designing small molecule antivirals. In this context, in silico modelling has proven to be an invaluable tool. An important target is the SARS-CoV-2 main protease (Mpro), involved in processing translated viral proteins. Peptidomimetic α-keto..

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University of Melbourne Researchers

Grants

Funding Acknowledgements

We would like to acknowledge intellectual and financial support by McCord Research (Iowa, USA). JL and KKD are supported by Australian Government Research Training Program Scholarships. We are indebted to Alfonso Perez Escuredo (crowdfightcovid) for enabling access to supercomputing facilities and to Matthew Gasperetti (Hypernet Labs; Galileo), for enabling cloud computing for this project. We thank the National Computing Infrastructure (NCI), and the Pawsey Supercomputing Centre in Australia (funded by the Australian Government). Further, we thank the Spartan High Performance Computing service (University of Melbourne), and the Partnership for Advanced Computing in Europe (PRACE) for awarding the access to Piz Daint, hosted at the Swiss National Supercomputing Centre (CSCS), Switzerland.