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Validation of the binding affinities and stabilities of ivermectin and moxidectin against SARS-CoV-2 receptors using molecular docking and molecular dynamics simulation

Oranu et al., GSC Biological and Pharmaceutical Sciences, doi:10.30574/gscbps.2024.26.1.0030
Jan 2024  
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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 study showing that ivermectin and moxidectin bind strongly to SARS-CoV-2 viral targets including the main protease, helicase, and RNA polymerase. Binding was further validated through molecular dynamics simulations indicating stability of ivermectin and moxidectin complexes over 10ns. Authors suggest inhibition of viral replication and transcription by binding to the main protease, a key enzyme for these processes.
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.
Oranu et al., 30 Jan 2024, peer-reviewed, 7 authors.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperIvermectinAll
Validation of the binding affinities and stabilities of ivermectin and moxidectin against Sars-CoV-2 receptors using molecular docking and molecular dynamics simulation
Emmanuel Chuks Oranu, Esther Oluchukwu Eze, Adanna Ijeawele, Chisom George Obidimma, Belinda Chinecherem Umeh, Perpetua Chinonyelum Ejezie, Ic Uzochukwu
GSC Biological and Pharmaceutical Sciences, doi:10.30574/gscbps.2024.26.1.0030
Corona-viruses (CoVs), a large family of single-stranded RNA viruses, can infect animals and also humans, causing respiratory, gastrointestinal, hepatic, and neurologic disease. As the largest known RNA viruses, they are further divided into four genera: alpha-coronavirus, beta-corona-virus, gamma-corona virus and delta-coronavirus. SARS-CoV-2 belong to genus betacoronavirus. The viral genome of SARS-CoV-2 codes 4 major structural proteins: the nucleocapsid (N) protein, the transmembrane (M) protein, the envelope (E) protein, and the spike (S) protein. It also encodes 16 nonstructural proteins (NSPs) and 9 accessory proteins required for replication and pathogenesis. The Molecular docking simulations was used to determine the binding affinities of Ivermectin, Moxidectin and Molnupiravir against NSP13 receptor of SARS-CoV-2. The experimental crystal structures of the receptor was obtained from the protein data bank (PDB). The receptor was prepared using Chimera-1.10.1 and AutoDock tools-1.5.6. The 3D structure of the selected approved drugs and the reference ligand was obtained from PDB and Drugbank and prepared using AutoDock tools-1.5.6. Validation of docking protocol was done by reproducing the PDB crystal structures insilico. Molecular docking simulations were performed using AutoDockVina-4.2.6 on the Linux operating system (ubuntu) 20.04. Then the docking results were analysed and visualized using Pymol-2.3.0. Molecular dynamics of the frontrunners with the reference ligand and protein was done in 10000 ps. Moxidectin, molnupiravir and Ivermectin showed high binding affinities to the receptors. Moxidectin and Ivermectin showed stability after molecular dynamics simulation to further validate the claim. These drugs are predicted as possible antivirals in the treatment of Covid-19.
Flexibility Profile analysis Figure 6 RMSF Plot of the molecular dynamics simulation of the drug target and ligands Root Mean Square Fluctuation is a measure of the displacement of a particular atom or group of atoms, relative to the reference structure, averaged over the number of atoms. It is used for the analysis of time-dependent motions of the structures [14] . From the results in 7JIT, In the RMS fluctuation plot, the system was reasonably stable between 1500 atoms and 2000 atoms which indicates that above 2000 atoms, some amino acid residues caused fluctuation within the system with the least fluctuations between 800 atoms and 1800 atoms From the results in 7JKV,from point 1 atom to 2700 atoms the system was more stable than from point 2800 atoms to 3100 atoms. It can also be seen that Moxidectin exhibited better stability than Ivermectin. From the results in 5rlj,in the graph above, it can be deduced that there were a lot of fluctuations which might be due to the presence of amino acid residues in the system. However, there was still stability at points 3600 pico seconds to 4600 pico seconds. Compliance with ethical standards Disclosure of conflict of interest The authors have no conflicts of interest to declare. All co-authors have seen and agree with the contents of the manuscript. We certify that the submission is original work and is not under review at any other publication.
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Hwa, Chaudhary, Mishra, (n.D, A Review on Molecular Docking : Novel Tool for Drug Discovery Related papers A Review on Molecular Docking : Novel Tool for Drug Discovery
López-Vallejo, Caulfield, Martínez-Mayorga, Giulianotti, Houghten et al., Integrating virtual screening and combinatorial chemistry for accelerated drug discovery, Comb. Chem. High Throughput Screen
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