Structural Deformability Induced in Proteins of Potential Interest Associated with COVID-19 by binding of Homologues present in Ivermectin: Comparative Study Based in Elastic Networks Models
et al., Journal of Molecular Liquids, doi:10.1016/j.molliq.2021.117284, Aug 2021
Ivermectin for COVID-19
4th treatment shown to reduce risk in
August 2020, now with p < 0.00000000001 from 106 studies, recognized in 24 countries.
No treatment is 100% effective. Protocols
combine treatments.
6,300+ studies for
210+ treatments. c19early.org
|
In silico elastic network model analysis of ivermectin components (avermectin-B1a and avermectin-B1b) providing a biophysical and computational perspective of proposed multi-target activity of ivermectin for COVID-19.
74 preclinical studies support the efficacy of ivermectin for COVID-19:
Ivermectin, better known for antiparasitic activity, is a broad spectrum antiviral with activity against many viruses including H7N771, Dengue37,72,73 , HIV-173, Simian virus 4074, Zika37,75,76 , West Nile76, Yellow Fever77,78, Japanese encephalitis77, Chikungunya78, Semliki Forest virus78, Human papillomavirus57, Epstein-Barr57, BK Polyomavirus79, and Sindbis virus78.
Ivermectin inhibits importin-α/β-dependent nuclear import of viral proteins71,73,74,80 , shows spike-ACE2 disruption at 1nM with microfluidic diffusional sizing38, binds to glycan sites on the SARS-CoV-2 spike protein preventing interaction with blood and epithelial cells and inhibiting hemagglutination41,81, shows dose-dependent inhibition of wildtype and omicron variants36, exhibits dose-dependent inhibition of lung injury61,66, may inhibit SARS-CoV-2 via IMPase inhibition37, may inhibit SARS-CoV-2 induced formation of fibrin clots resistant to degradation9, inhibits SARS-CoV-2 3CLpro54, may inhibit SARS-CoV-2 RdRp activity28, may minimize viral myocarditis by inhibiting NF-κB/p65-mediated inflammation in macrophages60, may be beneficial for COVID-19 ARDS by blocking GSDMD and NET formation82, may interfere with SARS-CoV-2's immune evasion via ORF8 binding4, may inhibit SARS-CoV-2 by disrupting CD147 interaction83-86, shows protection against inflammation, cytokine storm, and mortality in an LPS mouse model sharing key pathological features of severe COVID-1959,87, may be beneficial in severe COVID-19 by binding IGF1 to inhibit the promotion of inflammation, fibrosis, and cell proliferation that leads to lung damage8, may minimize SARS-CoV-2 induced cardiac damage40,48, may counter immune evasion by inhibiting NSP15-TBK1/KPNA1 interaction and restoring IRF3 activation88, may disrupt SARS-CoV-2 N and ORF6 protein nuclear transport and their suppression of host interferon responses1, reduces TAZ/YAP nuclear import, relieving SARS-CoV-2-driven suppression of IRF3 and NF-κB antiviral pathways35, increases Bifidobacteria which play a key role in the immune system89, has immunomodulatory51 and anti-inflammatory70,90 properties, and has an extensive and very positive safety profile91.
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González-Paz et al., 17 Aug 2021, peer-reviewed, 9 authors.
In silico studies are an important part of preclinical research, however results may be very different in vivo.
Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models
Journal of Molecular Liquids, doi:10.1016/j.molliq.2021.117284
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The Z-Score showed conformational fluctuations between free protein and lowenergy ligand-protein complexes. Starting from this model, it was observed that all the Avermectins-Protein complexes presented differences in the distances of their Cα atoms, as well as in their energetics at 100 ns of simulation and with respect to their corresponding free protein subjected to the same dynamic conditions. In ProSA-web, the most extreme Z-Score values were related to more dynamic and distant conformations of the free protein. This applies both for very negative values and for values very close to 0, since they tend to fall outside the Z-Score obtained from all the protein chains determined experimentally in the Protein Data Bank (PDB). In fact, the Z-Score for proteins such as the Multidrug ABC transporter (PDB: 2HYD) has been reported to be -8.29, which is in the range of native conformations. Whereas according to the ProSA-web results obtained for the homologous ABC transporter protein of multiple drugs (PDB: 1JSQ), the Z-Score of this model is −0.60, a value too high for a typical native structure [52] . In IMPα1, the complexes with the homologues presented the most distant conformational fluctuation from the free protein one with a Z-Score more negative than that obtained for the ligand-free protein, which suggests unfolding of this protein with both stereoisomers. On the contrary, although a similar trend towards unfolding against Mpro was predicted, especially with compound..
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