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Insights from a computational analysis of the SARS-CoV-2 Omicron variant: Host–pathogen interaction, pathogenicity, and possible drug therapeutics

Parvez et al., Immunity, Inflammation and Disease, doi:10.1002/iid3.639 (date from preprint)
Jan 2022  
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Ivermectin for COVID-19
4th treatment shown to reduce risk in August 2020
 
*, now known with p < 0.00000000001 from 100 studies, recognized in 22 countries.
No treatment is 100% effective. Protocols combine complementary and synergistic treatments. * >10% efficacy in meta analysis with ≥3 clinical studies.
3,800+ studies for 60+ treatments. c19ivm.org
In Silico analysis of the omicron variant and 10 treatments reported effective for previous variants, predicting that all will be effective for omicron, with ivermectin showing the best results.
Ivermectin, better known for antiparasitic activity, is a broad spectrum antiviral with activity against many viruses including H7N7 Götz, Dengue Tay, Wagstaff, HIV-1 Wagstaff, Simian virus 40 Wagstaff (B), Zika Barrows, Yang, West Nile Yang, Yellow Fever Mastrangelo, Varghese, Japanese encephalitis Mastrangelo, Chikungunya Varghese, Semliki Forest virus Varghese, Human papillomavirus Li, Epstein-Barr Li, BK Polyomavirus Bennett, and Sindbis virus Varghese.
Ivermectin inhibits importin-α/β-dependent nuclear import of viral proteins Götz, Kosyna, Wagstaff, Wagstaff (B), inhibits SARS-CoV-2 3CLpro Mody, shows spike-ACE2 disruption at 1nM with microfluidic diffusional sizing Fauquet, binds to glycan sites on the SARS-CoV-2 spike protein preventing interaction with blood and epithelial cells and inhibiting hemagglutination Boschi, Scheim, exhibits dose-dependent inhibition of lung injury Abd-Elmawla, Ma, may inhibit SARS-CoV-2 induced formation of fibrin clots resistant to degradation Vottero, may be beneficial for COVID-19 ARDS by blocking GSDMD and NET formation Liu (C), shows protection against inflammation, cytokine storm, and mortality in an LPS mouse model sharing key pathological features of severe COVID-19 DiNicolantonio, Zhang, may be beneficial in severe COVID-19 by binding IGF1 to inhibit the promotion of inflammation, fibrosis, and cell proliferation that leads to lung damage Zhao, may minimize SARS-CoV-2 induced cardiac damage Liu, Liu (B), increases Bifidobacterium which plays a key role in the immune system Hazan, has immunomodulatory Munson and anti-inflammatory DiNicolantonio (B), Yan properties, and has an extensive and very positive safety profile Descotes.
Parvez et al., 20 Jan 2022, preprint, 7 authors. Contact: ohtsuki.gen.7w@kyoto-u.ac.jp, jakir-gen@sust.edu.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperIvermectinAll
Insights from a computational analysis of the SARS‐CoV‐2 Omicron variant: Host–pathogen interaction, pathogenicity, and possible drug therapeutics
Md Sorwer Alam Parvez, Manash Kumar Saha, Md D Ibrahim, Yusha Araf, Md. Taufiqul Islam, Gen Ohtsuki, Mohammad Jakir Hosen
Immunity, Inflammation and Disease, doi:10.1002/iid3.639
Introduction: Prominently accountable for the upsurge of COVID-19 cases as the world attempts to recover from the previous two waves, Omicron has further threatened the conventional therapeutic approaches. The lack of extensive research regarding Omicron has raised the need to establish correlations to understand this variant by structural comparisons. Here, we evaluate, correlate, and compare its genomic sequences through an immunoinformatic approach to understand its epidemiological characteristics and responses to existing drugs. Methods: We reconstructed the phylogenetic tree and compared the mutational spectrum. We analyzed the mutations that occurred in the Omicron variant and correlated how these mutations affect infectivity and pathogenicity. Then, we studied how mutations in the receptor-binding domain affect its interaction with host factors through molecular docking. Finally, we evaluated the drug efficacy against the main protease of the Omicron through molecular docking and validated the docking results with molecular dynamics simulation. Results: Phylogenetic and mutational analysis revealed the Omicron variant is similar to the highly infectious B.1.620 variant, while mutations within the prominent proteins are hypothesized to alter its pathogenicity. Moreover, docking evaluations revealed significant differences in binding affinity with human receptors, angiotensin-converting enzyme 2 and NRP1. Surprisingly, most of the tested drugs were proven to be effective. Nirmatrelvir, 13b, and Lopinavir displayed increased effectiveness against Omicron. Conclusion: Omicron variant may be originated from the highly infectious B.1.620 variant, while it was less pathogenic due to the mutations in the prominent proteins. Nirmatrelvir, 13b, and Lopinavir would be the most effective, compared to other promising drugs that were proven effective.
AUTHOR CONTRIBUTIONS Md Sorwer Alam Parvez: Conceptualization; methodology; formal analysis; data interpretation; validation; visualization; original draft preparation. Manash Kumar Saha: Methodology; software; visualization. Md Ibrahim: Formal analysis. Yusha Araf: Formal analysis; original draft preparation and editing. Md Taufiqul Islam: Validation. Gen Ohtsuki: Supervision, writing-review & editing. Mohammad Jakir Hosen: Supervision, writing-review & editing. ACKNOWLEDGMENT This study was supported by grants from the Mitsubishi Foundation, the Takeda Science Foundation (to G. O.). CONFLICTS OF INTEREST The authors declare no conflicts of interest. ETHICS STATEMENT This study did not deal with human subjects and biological materials. All open-source data were analyzed, in which all personal information was anonymized, and no data allowing individual identification was retained. Therefore, no ethics approval and no informed consent were required.
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