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Interaction of the New Inhibitor Paxlovid (PF-07321332) and Ivermectin With the Monomer of the Main Protease SARS-CoV-2: A Volumetric Study Based on Molecular Dynamics, Elastic Networks, Classical Thermodynamics and SPT

Alvarado et al., Computational Biology and Chemistry, doi:10.1016/j.compbiolchem.2022.107692
May 2022  
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Ivermectin for COVID-19
4th treatment shown to reduce risk in August 2020, now with p < 0.00000000001 from 105 studies, recognized in 23 countries.
No treatment is 100% effective. Protocols combine treatments.
5,100+ studies for 110 treatments. c19ivm.org
In Silico study comparing ivermectin and paxlovid Mpro interaction, showing similar interaction for paxlovid and the ivermectin B1a homologue, a different mechanism for ivermectin B1b, and interaction at different sites for paxlovid.
70 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 H7N768, Dengue34,69,70, HIV-170, Simian virus 4071, Zika34,72,73, West Nile73, Yellow Fever74,75, Japanese encephalitis74, Chikungunya75, Semliki Forest virus75, Human papillomavirus54, Epstein-Barr54, BK Polyomavirus76, and Sindbis virus75.
Ivermectin inhibits importin-α/β-dependent nuclear import of viral proteins68,70,71,77, shows spike-ACE2 disruption at 1nM with microfluidic diffusional sizing35, binds to glycan sites on the SARS-CoV-2 spike protein preventing interaction with blood and epithelial cells and inhibiting hemagglutination38,78, shows dose-dependent inhibition of wildtype and omicron variants33, exhibits dose-dependent inhibition of lung injury58,63, may inhibit SARS-CoV-2 via IMPase inhibition34, may inhibit SARS-CoV-2 induced formation of fibrin clots resistant to degradation7, inhibits SARS-CoV-2 3CLpro51, may inhibit SARS-CoV-2 RdRp activity26, may minimize viral myocarditis by inhibiting NF-κB/p65-mediated inflammation in macrophages57, may be beneficial for COVID-19 ARDS by blocking GSDMD and NET formation79, may interfere with SARS-CoV-2's immune evasion via ORF8 binding2, may inhibit SARS-CoV-2 by disrupting CD147 interaction80-83, shows protection against inflammation, cytokine storm, and mortality in an LPS mouse model sharing key pathological features of severe COVID-1956,84, may be beneficial in severe COVID-19 by binding IGF1 to inhibit the promotion of inflammation, fibrosis, and cell proliferation that leads to lung damage6, may minimize SARS-CoV-2 induced cardiac damage37,45, increases Bifidobacteria which play a key role in the immune system85, has immunomodulatory48 and anti-inflammatory67,86 properties, and has an extensive and very positive safety profile87.
Alvarado et al., 14 May 2022, peer-reviewed, 12 authors. Contact: alvaradoysaias@gmail.com, lgonzalezpaz@gmail.com.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperIvermectinAll
Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT
Ysaias José Alvarado, Yosmari Olivarez, Carla Lossada, Joan Vera-Villalobos, José Luis Paz, Eddy Vera, Marcos Loroño, Alejandro Vivas, Fernando Javier Torres, María Laura N Jeffreys, María Laura Hurtado-León, Lenin González-Paz
Computational Biology and Chemistry, doi:10.1016/j.compbiolchem.2022.107692
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.
Under this same study strategy, it was found that PF-07321332 can also covalently bind to another region of the monomer (a drug multi-site for M pro ), but both complexes have similar structural flexibility and volumetric properties. Finally, we consider that this type of study can help to understand the mechanism by which a ligand can block the homodimerization of this important monomer to form the dimeric protease dM pro and in turn help in studies of activity-structure relationships for the design of new drugs. Declaration of competing interest. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Highlights
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