Inhibitory activity of hydroxychloroquine on COVID-19 main protease: An insight from MD-simulation studies

Liu, 2020, Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases, ACS Cent. Sci., 6, 315, 10.1021/acscentsci.0c00272 Tyrrell, 1966, Cultivation of viruses from a high proportion of patients with colds, Lancet, 1, 76, 10.1016/S0140-6736(66)92364-6 Khan, 2005, History and recent advances in coronavirus discovery, Pediatr. Infect. Dis. J., 24, S223, 10.1097/01.inf.0000188166.17324.60 Drosten, 2003, Identification of a novel coronavirus in patients with severe acute respiratory syndrome, N. Engl. J. Med., 348, 1967, 10.1056/NEJMoa030747 Ksiazek, 2003, A novel coronavirus associated with severe acute respiratory syndrome, N. Engl. J. Med., 348, 1953, 10.1056/NEJMoa030781 Peiris, 2003, Coronavirus as a possible cause of severe acute respiratory syndrome, Lancet, 361, 1319, 10.1016/S0140-6736(03)13077-2 Lai, 2020, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges, Int. J. Atnimicrob. Agent, 10.1016/j.ijantimicag.2020.105924 Wang, 2020, A review of the 2019 Novel Coronavirus (COVID-19) based on current evidence, Int. J. Antimicrob. Agents, 10.1016/j.ijantimicag.2020.106137 Retallack, 2016, Zika virus cell tropism in the developing human brain and inhibition by azithromycin, Proc. Natl. Acad. Sci. Unit. States Am., 113, 14408, 10.1073/pnas.1618029113 Bosseboeuf, 2018, Azithromycin inhibits the replication of Zika virus, J. Antivir. Antiretrovir., 10, 6 Gautret, 2020, Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial, Int. J. Antimicrob. Agents, 105949, 10.1016/j.ijantimicag.2020.105949 Biot, 2006, Design and synthesis of hydroxyferroquine derivatives with antimalarial and antiviral activities, J. Med. Chem., 49, 2845, 10.1021/jm0601856 Colson, 2020, Chloroquine and hydroxychloroquine as available weapons to fight COVID-19, Int. J. Antimicrob. Agents, 105932, 10.1016/j.ijantimicag.2020.105932 Philippe, 2020, Chloroquine for the 2019 novel coronavirus, Int. J. Antimicrob. Agents Gao, 2020, Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies, Biosci. Trends, 10.5582/bst.2020.01047 Marmor, 2016, Recommendations on screening for chloroquine and hydroxychloroquine retinopathy (2016 revision), Ophthalmology, 123, 1386, 10.1016/j.ophtha.2016.01.058 Pettersen, 2004, UCSF Chimera - a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 Trott, 2010, Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, J. Comput. Chem., 31, 455 Berendsen, 1995, GROMACS: a message-passing parallel molecular dynamics implementation, Comput. Phys. Commun., 91, 43, 10.1016/0010-4655(95)00042-E Lee, 2014, CHARMM36 united atom chain model for lipids and surfactants, J. Phys. Chem. B, 118, 547, 10.1021/jp410344g Boonstra, 2016, CHARMM TIP3P water model suppresses peptide folding by solvating the unfolded state, J. Phys. Chem. B, 120, 3692, 10.1021/acs.jpcb.6b01316 Abraham, 2011, Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5, J. Comput. Chem., 32, 2031, 10.1002/jcc.21773