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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

González-Paz et al., Journal of Molecular Liquids, doi:10.1016/j.molliq.2021.117284
Aug 2021  
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Ivermectin for COVID-19
4th treatment shown to reduce risk in August 2020
 
*, now with p < 0.00000000001 from 104 studies, recognized in 22 countries.
No treatment is 100% effective. Protocols combine treatments. * >10% efficacy, ≥3 studies.
4,300+ studies for 75 treatments. c19ivm.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.
68 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 H7N766, Dengue32,67,68, HIV-168, Simian virus 4069, Zika32,70,71, West Nile71, Yellow Fever72,73, Japanese encephalitis72, Chikungunya73, Semliki Forest virus73, Human papillomavirus52, Epstein-Barr52, BK Polyomavirus74, and Sindbis virus73.
Ivermectin inhibits importin-α/β-dependent nuclear import of viral proteins66,68,69,75, shows spike-ACE2 disruption at 1nM with microfluidic diffusional sizing33, binds to glycan sites on the SARS-CoV-2 spike protein preventing interaction with blood and epithelial cells and inhibiting hemagglutination36,76, shows dose-dependent inhibition of wildtype and omicron variants31, exhibits dose-dependent inhibition of lung injury56,61, may inhibit SARS-CoV-2 via IMPase inhibition32, may inhibit SARS-CoV-2 induced formation of fibrin clots resistant to degradation5, inhibits SARS-CoV-2 3CLpro49, may inhibit SARS-CoV-2 RdRp activity24, may minimize viral myocarditis by inhibiting NF-κB/p65-mediated inflammation in macrophages55, may be beneficial for COVID-19 ARDS by blocking GSDMD and NET formation77, shows protection against inflammation, cytokine storm, and mortality in an LPS mouse model sharing key pathological features of severe COVID-1954,78, may be beneficial in severe COVID-19 by binding IGF1 to inhibit the promotion of inflammation, fibrosis, and cell proliferation that leads to lung damage4, may minimize SARS-CoV-2 induced cardiac damage35,43, increases Bifidobacteria which play a key role in the immune system79, has immunomodulatory46 and anti-inflammatory65,80 properties, and has an extensive and very positive safety profile81.
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.
This PaperIvermectinAll
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
María Lenin González-Paz, María Laura Hurtado-León, Carla Lossada, Francelys V Fernández-Materán, Joan Vera-Villalobos, Marcos Loroño, J L Paz, Laura Jeffreys, Instituto Ysaias J Alvarado
Journal of Molecular Liquids, doi:10.1016/j.molliq.2021.117284
This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
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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