Non-competitive interactions between hydroxychloroquine and azithromycin: Systematic density functional, molecular dynamics, and docking calculations.
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ABSTRACT:
SUBMITTER: Khalafalla MAH
PROVIDER: S-EPMC8129801 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Millions of people are affected by COVID-19 since the last quarter of 2019. Treatment using hydroxychloroquine (HCQ) as monotherapy in combination with azithromycin (HCQ-AZ) were administered at several clinical centres to patients tested positive to the virus across continents. Therefore, it is of interest to document the molecular docking analysis data of azithromycin and hydroxychloroquine drug with the spike surface glycoprotein of novel COVID-19. Thus, we report the molecular modelling docking based structural binding features of HCQ-AZ with the spike surface glycoprotein of COVID-19 for further evaluation in this regard.
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Project description:The emergence of SARS-coronavirus-2 (SARS-CoV-2) has led to a global pandemic disease referred to as coronavirus disease 19 (COVID-19). Hydroxychloroquine (CLQ-OH)/azithromycin (ATM) combination therapy is currently being tested for the treatment of COVID-19, with promising results. However, the molecular mechanism of action of this combination is not yet established. Using molecular dynamics (MD) simulations, this study shows that the drugs act in synergy to prevent any close contact between the virus and the plasma membrane of host cells. Unexpected molecular similarity is shown between ATM and the sugar moiety of GM1, a lipid raft ganglioside acting as a host attachment cofactor for respiratory viruses. Due to this mimicry, ATM interacts with the ganglioside-binding domain of SARS-CoV-2 spike protein. This binding site shared by ATM and GM1 displays a conserved amino acid triad Q-134/F-135/N-137 located at the tip of the spike protein. CLQ-OH molecules are shown to saturate virus attachment sites on gangliosides in the vicinity of the primary coronavirus receptor, angiotensin-converting enzyme-2 (ACE-2). Taken together, these data show that ATM is directed against the virus, whereas CLQ-OH is directed against cellular attachment cofactors. We conclude that both drugs act as competitive inhibitors of SARS-CoV-2 attachment to the host-cell membrane. This is consistent with a synergistic antiviral mechanism at the plasma membrane level, where therapeutic intervention is likely to be most efficient. This molecular mechanism may explain the beneficial effects of CLQ-OH/ATM combination therapy in patients with COVID-19. Incidentally, the data also indicate that the conserved Q-134/F-135/N-137 triad could be considered as a target for vaccine strategies.
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Project description:Correlations of the shear viscosity of quartz nanofluids with particle concentration, particle size, and temperature were investigated with molecular dynamics simulations and density functional theory (DFT) calculations. A new understanding to the experimentally concluded correlations was addressed in terms of microscopic particle–water interfacial interaction in three aspects. First, the viscosity of quartz nanofluids at different particle concentrations, particle sizes, and temperatures were simulated using the equilibrium molecular dynamics simulations method to reproduce the experimental observations. At the same particle size, the nanofluid viscosity decreases significantly with temperature and increases with nanoparticle volume concentration, and at the same volume concentration, the nanofluid viscosity increases with the decrease of particle size. Second, DFT calculations confirm a stronger particle–water interaction than that among water molecules. The important role of particle–water interaction in the viscosity determination of nanofluids was revealed. Finally, a correlation was proposed to fit the simulated results and compared with earlier two-parameter correlations. One parameter in the correlation is indeed a constant, while the other is a function of SiO2–water interaction energy. Our study proposes a physical basis for the experimentally concluded correlations on the viscosity of nanofluids. Supplementary Information The online version contains supplementary material available at 10.1007/s00894-022-05177-w.
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2014-10-16 | E-GEOD-61210 | biostudies-arrayexpress