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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
González-Paz et al., Structural Deformability Induced in Proteins of Potential Interest Associated with COVID-19 by binding of.., Journal of Molecular Liquids, doi:10.1016/j.molliq.2021.117284
Aug 2021   Source   PDF  
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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.
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.
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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
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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