A Computational Approach to Identify Potential Novel Inhibitors against the Coronavirus SARS‐CoV‐2

The current pandemic threat of COVID‐19, caused by the novel coronavirus SARS‐CoV‐2, not only gives rise to a high number of deaths around the world but also has immense consequences for the worldwide health systems and global economy. Given the fact that this pandemic is still ongoing and there are currently no drugs or vaccines against this novel coronavirus available, this in silico study was conducted to identify a potential novel SARS‐CoV‐2‐inhibitor. Two different approaches were pursued: 1) The Docking Consensus Approach (DCA) is a novel approach, which combines molecular dynamics simulations with molecular docking. 2) The Common Hits Approach (CHA) in contrast focuses on the combination of the feature information of pharmacophore modeling and the flexibility of molecular dynamics simulations. The application of both methods resulted in the identification of 10 compounds with high coronavirus inhibition potential.

[1]  G. Gao,et al.  A Novel Coronavirus from Patients with Pneumonia in China, 2019 , 2020, The New England journal of medicine.

[2]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[3]  Richard E. Baldwin,et al.  Economics in the time of COVID-19 , 2020 .

[4]  N. Wilson,et al.  Case-Fatality Risk Estimates for COVID-19 Calculated by Using a Lag Time for Fatality , 2020, Emerging infectious diseases.

[5]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[6]  P. Strevens Iii , 1985 .

[7]  Kai Liu,et al.  Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations , 2017, Journal of Computer-Aided Molecular Design.

[8]  Hideaki Fujitani,et al.  Molecular dynamics analysis to evaluate docking pose prediction , 2016, Biophysics and physicobiology.

[9]  Asher Mullard,et al.  Drug repurposing programmes get lift off , 2012, Nature Reviews Drug Discovery.

[10]  Thierry Langer,et al.  LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters , 2005, J. Chem. Inf. Model..

[11]  E. Tobinick The value of drug repositioning in the current pharmaceutical market. , 2009, Drug news & perspectives.

[12]  Jean-Charles Carvaillo,et al.  TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries , 2018, J. Chem. Inf. Model..

[13]  L. M. Espinoza-Fonseca,et al.  The benefits of the multi-target approach in drug design and discovery. , 2006, Bioorganic & medicinal chemistry.

[14]  Thierry Langer,et al.  Evaluating the stability of pharmacophore features using molecular dynamics simulations. , 2016, Biochemical and biophysical research communications.

[15]  Taehoon Kim,et al.  CHARMM‐GUI: A web‐based graphical user interface for CHARMM , 2008, J. Comput. Chem..

[16]  A. M. Leontovich,et al.  The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 , 2020, Nature Microbiology.

[17]  Alexandre Varnek,et al.  Chemoinformatics approaches to virtual screening , 2008 .

[18]  Natalia Novac,et al.  Challenges and opportunities of drug repositioning. , 2013, Trends in pharmacological sciences.

[19]  Thierry Langer,et al.  Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations , 2017, J. Chem. Inf. Model..

[20]  Cynthia Liu,et al.  Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases , 2020, ACS central science.

[21]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..