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Non-spike protein inhibition of SARS-CoV-2 by natural products through the key mediator protein ORF8

Bagheri-Far et al., Molecular Biology Research Communications, doi:10.22099/mbrc.2024.50245.2001
Oct 2024  
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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 109 treatments. c19ivm.org
In Silico study showing that ivermectin, artemisinin, and DEG-168 may inhibit SARS-CoV-2 by targeting the ORF8 protein's binding sites. Ivermectin showed the highest binding affinity. Authors identified two key binding regions on ORF8 - a deep groove between monomers (DGBM) and a galectin-1-like site. Docking studies found the natural products, especially in combination, effectively bound these sites with high affinity. Inhibiting ORF8 could reduce SARS-CoV-2's immune evasion and pathogenic functions.
69 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 H7N767, Dengue33,68,69, HIV-169, Simian virus 4070, Zika33,71,72, West Nile72, Yellow Fever73,74, Japanese encephalitis73, Chikungunya74, Semliki Forest virus74, Human papillomavirus53, Epstein-Barr53, BK Polyomavirus75, and Sindbis virus74.
Ivermectin inhibits importin-α/β-dependent nuclear import of viral proteins67,69,70,76, shows spike-ACE2 disruption at 1nM with microfluidic diffusional sizing34, binds to glycan sites on the SARS-CoV-2 spike protein preventing interaction with blood and epithelial cells and inhibiting hemagglutination37,77, shows dose-dependent inhibition of wildtype and omicron variants32, exhibits dose-dependent inhibition of lung injury57,62, may inhibit SARS-CoV-2 via IMPase inhibition33, may inhibit SARS-CoV-2 induced formation of fibrin clots resistant to degradation6, inhibits SARS-CoV-2 3CLpro50, may inhibit SARS-CoV-2 RdRp activity25, may minimize viral myocarditis by inhibiting NF-κB/p65-mediated inflammation in macrophages56, may be beneficial for COVID-19 ARDS by blocking GSDMD and NET formation78, may interfere with SARS-CoV-2's immune evasion via ORF8 binding1, may inhibit SARS-CoV-2 by disrupting CD147 interaction79-82, shows protection against inflammation, cytokine storm, and mortality in an LPS mouse model sharing key pathological features of severe COVID-1955,83, may be beneficial in severe COVID-19 by binding IGF1 to inhibit the promotion of inflammation, fibrosis, and cell proliferation that leads to lung damage5, may minimize SARS-CoV-2 induced cardiac damage36,44, increases Bifidobacteria which play a key role in the immune system84, has immunomodulatory47 and anti-inflammatory66,85 properties, and has an extensive and very positive safety profile86.
Bagheri-Far et al., 26 Oct 2024, peer-reviewed, 5 authors. Contact: m_azimzadeh@sbu.ac.ir, ma_hosseini@sbu.ac.ir.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperIvermectinAll
Non-spike protein inhibition of SARS-CoV-2 by natural products through the key mediator protein ORF8
Mostafa Bagheri-Far, Mohammad Assadizadeh, Maryam Azimzadeh-Irani, Mohammad Yaghoubi-Avini, Seyed Massoud Hosseini
doi:10.22099/mbrc.2024.50245.2001
The recent pernicious COVID-19 pandemic is caused by SARS-CoV-2. While most therapeutic strategies have focused on the viral spike protein, Open Reading Frame 8 (ORF8) plays a critical role in causing the severity of the disease. Nonetheless, there still needs to be more information on the ORF8 binding epitopes and their appropriate safe inhibitors. Herein, the protein binding sites were detected through comprehensive structural analyses. The validation of the binding sites was investigated through protein conservation analysis and blind docking. The potential natural product (NP) inhibitors were selected based on a structurefunction approach. The solo and combined inhibition functions of these NPs were examined through molecular docking studies. Two binding epitopes were identified, one between the ORF8 monomers (DGBM) and the other on the surface (Gal1-Like). E92 was predicted to be pivotal for DGBM, and R101 for Gal1-like, which was then confirmed through molecular dockings. The inhibitory effects of selected phytochemical (Artemisinin), bacterial (Ivermectin), and native-liken (DEG-168) NPs were compared with the Remdesivir. Selected NPs showed solo-and co-functionality against Remdesivir to inhibit functional regions of the ORF8 structure. The DGBM is highly engaged in capturing the NPs. Additionally, the co-functionality study of NPs showed that the Ivermectin-DEG168 combination has the strongest mechanism for inhibiting all the predicted binding sites. Ivermectin can interfere with ORF8-MHC-I interaction through inhibition of A51 and F120. Two new binding sites on this non-infusion protein structure were introduced using a combination of approaches. Additionally, three safe and effective were found to inhibit these binding sites.
Conflict of Interest: The authors have no relevant financial or non-financial interests to disclose. Authors' Contribution: MBF carried out the analyses and provided all figures and tables and wrote the initial draft. MA re-wrote the manuscript text and citations and revised the manuscript. MAI designed and supervised the project, edited the text, figures and plots, interpreted the data and outlined the manuscript. SMH contributed in interpretation of the results and co-supervised the project. MYA contributed in interpretation of the results.
References
Adasme, Linnemann, Bolz, Kaiser, Salentin et al., PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA, Nucleic Acids Res
Ahmed, Karim, Ross, Hossain, Clemens et al., A fiveday course of ivermectin for the treatment of COVID-19 may reduce the duration of illness, Int J Infect Dis
Alkhansa, Lakkis, El Zein, Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic, Gene Rep
Assadizadeh, Irani, Oligomer formation of SARS-CoV-2 ORF8 through 73YIDI76 motifs regulates immune response and non-infusion antiviral interactions, Front Mol Biosci
Atanasov, Zotchev, Dirsch, International, Product et al., Natural products in drug discovery: advances and opportunities, Nat Rev Drug Discov
Benson, Cavanaugh, Clark, Karsch-Mizrachi, Lipman et al., GenBank, Nucleic Acids Res
Berman, Battistuz, Bhat, Bluhm, Bourne et al., The Protein Data Bank, Acta Crystallogr D Biol Crystallogr
Biber, Harmelin, Ram, Shaham, Nemet et al., The effect of ivermectin on the viral load and culture viability in early treatment of nonhospitalized patients with mild COVID-19 -a double-blind, randomized placebo-controlled trial, Int J Infect Dis
Bryant, Lawrie, Dowswell, Fordham, Mitchell et al., Ivermectin for Prevention and Treatment of COVID-19 Infection: A Systematic Review, Metaanalysis, and Trial Sequential Analysis to Inform Clinical Guidelines, Am J Ther
Camby, Mercier, Lefranc, Kiss, Galectin-1: a small protein with major functions, Glycobiology
Campbell, History of Avermectin and Ivermectin, with Notes on the History of Other Macrocyclic Lactone Antiparasitic Agents, Curr Pharm Biotechnol
Cavezzi, Troiani, Corrao, COVID-19: hemoglobin, iron, and hypoxia beyond inflammation. A narrative review, Clin Pract
Chaccour, Hammann, Rabinovich, Ivermectin to reduce malaria transmission I. Pharmacokinetic and pharmacodynamic considerations regarding efficacy and safety, Malar J
Chakravarti, Singh, Ghosh, Dey, Sharma et al., A review on potential of natural products in the management of COVID-19, RSC Adv
Chaudhari, Singh, Joshi, Patel, Joshi, Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8-MHC1 interaction, Mol Divers
Chaudhari, Singh, Joshi, Patel, Joshi, Defective ORF8 dimerization in delta variant of SARS CoV2 leads to abrogation of ORF8 MHC-I interaction and overcome suppression of adaptive immune response, bioRxiv
Chen, Zhou, Huang, Zhou, Kang et al., Crystal Structures of Bat and Human Coronavirus ORF8 Protein Ig-Like Domain Provide Insights Into the Diversity of Immune Responses, Front Immunol
Christy, Uekusa, Gerwick, Gerwick, Natural Products with Potential to Treat RNA Virus Pathogens Including SARS-CoV-2, J Nat Prod
Clamp, Cuff, Searle, Barton, The Jalview Java alignment editor, Bioinformatics
Consortium, Pan, Peto, Henao-Restrepo, Preziosi et al., Repurposed Antiviral Drugs for Covid-19 -Interim WHO Solidarity Trial Results, N Engl J Med
Doak, Kihlberg, Drug discovery beyond the rule of 5 -Opportunities and challenges, Expert Opin Drug Discov
Dyshlovenko, Adaptive numerical method for Poisson-Boltzmann equation and its application, Comput Phys Commun
Díaz, SARS-CoV-2 Molecular Network Structure, Front Physiol
Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res
Egbert, Whitty, Keserű, Vajda, Why Some Targets Benefit from beyond Rule of Five Drugs, J Med Chem
Elfiky, Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study, Life Sci
Fahmi, Kitagawa, Yasui, Kubota, Ito, The Functional Classification of ORF8 in SARS-CoV-2 Replication, Immune Evasion, and Viral Pathogenesis Inferred through Phylogenetic Profiling, Evol Bioinform Online
Fiser, Sali, ModLoop: automated modeling of loops in protein structures, Bioinformatics
Flower, Buffalo, Hooy, Allaire, Ren et al., Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein, Proc Natl Acad Sci U S A
Fourmont, Revest, Polard, Lederlin, Delaval et al., Acute eosinophilic pneumonia following artenimol-piperaquine exposure, J Travel Med
Gandhi, Klein, Robertson, Peña-Hernández, Lin et al., De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report, Nat Commun
Giguère, Bonin, Cloutier, Patnam, St-Pierre et al., Synthesis of stable and selective inhibitors of human galectins-1 and -3, Bioorg Med Chem
Gong, Tsao, Hsiao, Huang, Huang et al., SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East, Emerg Microbes Infect
Gordon, Jang, Bouhaddou, Xu, Obernier et al., A SARS-CoV-2 protein interaction map reveals targets for drug repurposing, Nature
Hachim, Kavian, Cohen, Chin, Chu et al., ORF8 and ORF3b antibodies are accurate serological markers of early and late SARS-CoV-2 infection, Nat Immunol
Hamdorf, Imhof, Bailey-Elkin, Betz, Theobald et al., The unique ORF8 protein from SARS-CoV-2 binds to human dendritic cells and induces a hyper-inflammatory cytokine storm, J Mol Cell Biol
Hetényi, Van Der Spoel, Toward prediction of functional protein pockets using blind docking and pocket search algorithms, Protein Sci
Hsia, Respiratory function of hemoglobin, N Engl J Med
Huey, Morris, Forli, Others, Using AutoDock 4 and AutoDock vina with AutoDockTools: a tutorial, The Scripps Research Institute Molecular Graphics Laboratory
Humeniuk, Mathias, Kirby, Lutz, Cao et al., Pharmacokinetic, Pharmacodynamic, and Drug-Interaction Profile of Remdesivir, a SARS-CoV-2 Replication Inhibitor, Clin Pharmacokinet
Islam, Parves, Islam, Ali, Efaz et al., Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study, J Biomol Struct Dyn
Jungreis, Sealfon, Kellis, SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes, Nat Commun
Kandeel, Fayez, Al-Nazawi, From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes, J Med Virol
Kerwin, ChemBioOffice Ultra 2010 Suite, J Am Chem Soc
Kim, Chen, Cheng, Gindulyte, He et al., PubChem 2019 update: improved access to chemical data, Nucleic Acids Res
Krieger, Smeilus, Kaiser, Seo, Efferth et al., Total synthesis and biological investigation of (-)-artemisinin: The antimalarial activity of artemisinin is not stereospecific, Angew Chem Int Ed Engl
Kriplani, Clohisey, Fonseca, Fletcher, Lee et al., Secreted SARS-CoV-2 ORF8 modulates the cytokine expression profile of human macrophages, bioRxiv
Kumar, Nyodu, Maurya, Saxena, Host Immune Response and Immunobiology of Human SARS-CoV-2 Infection, Coronavirus Disease
Lai, Shih, Ko, Tang, Hsueh, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges, Int J Antimicrob Agents
Laing, Devaney, Ivermectin -Old Drug, New Tricks?, Trends Parasitol
Lawrence, Meyerowitz-Katz, Heathers, Brown, Sheldrick, The lesson of ivermectin: meta-analyses based on summary data alone are inherently unreliable, Nat Med
Li, Liao, Wang, Tan, Luo et al., The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway, Virus Res
Li, Weina, Milhous, Pharmacokinetic and Pharmacodynamic Profiles of Rapid-Acting Artemisinins in the Antimalarial Therapy, Curr Drug ther
Lin, Fu, Xiong, Xing, Xue et al., Unconventional secretion of unglycosylated ORF8 is critical for the cytokine storm during SARS-CoV-2 infection, PLoS Pathog
Lin, Fu, Yin, Li, Liu et al., ORF8 contributes to cytokine storm during SARS-CoV-2 infection by activating IL-17 pathway, iScience
Llivisaca-Contreras, Naranjo-Morán, Pino-Acosta, Pieters, Berghe et al., Plants and Natural Products with Activity against Various Types of Coronaviruses: A Review with Focus on SARS-CoV-2, Molecules
Mannan, Ahmed, Arshad, Asim, Qureshi et al., Survey of artemisinin production by diverse Artemisia species in northern Pakistan, Malar J
Matsuoka, Imahashi, Ohno, Ode, Nakata et al., SARS-CoV-2 accessory protein ORF8 is secreted extracellularly as a glycoprotein homodimer, J Biol Chem
Mcchesney, Natural products in drug discovery--organizing for success, P R Health Sci J
Motlagh, Irani, Nomandan, Assadizadeh, Computational design and investigation of the monomeric spike SARS-CoV-2-ferritin nanocage vaccine stability and interactions, Front Mol Biosci
Nagy, Pongor, Győrffy, Different mutations in SARS-CoV-2 associate with severe and mild outcome, Int J Antimicrob Agents
Nitsure, Sarangi, Shankar, Reddy, Walimbe et al., Mechanisms of Hypoxia in COVID-19 Patients: A Pathophysiologic Reflection, Indian J Crit Care Med
Oostra, De Haan, Rottier, The 29-nucleotide deletion present in human but not in animal severe acute respiratory syndrome coronaviruses disrupts the functional expression of open reading frame 8, J Virol
Patridge, Gareiss, Kinch, Hoyer, An analysis of FDA-approved drugs: natural products and their derivatives, Drug Discov Today
Pereira, Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene, Infect Genet Evol
Pettersen, Goddard, Huang, Couch, Greenblatt et al., UCSF Chimera--a visualization system for exploratory research and analysis, J Comput Chem
Peña-Silva, Duffull, Steer, Jaramillo-Rincon, Gwee et al., Pharmacokinetic considerations on the repurposing of ivermectin for treatment of COVID-19, Br J Clin Pharmacol
Rashid, Dzakah, Wang, Tang, The ORF8 protein of SARS-CoV-2 induced endoplasmic reticulum stress and mediated immune evasion by antagonizing production of interferon beta, Virus Res
Roman, Burela, Pasupuleti, Piscoya, Vidal et al., Ivermectin for the Treatment of Coronavirus Disease 2019: A Systematic Review and Meta-analysis of Randomized Controlled Trials, Clin Infect Dis
Roy, Kucukural, Zhang, I-TASSER: a unified platform for automated protein structure and function prediction, Nat Protoc
Saha, Patgaonkar, Shroff, Ayyar, Bashir et al., Hemoglobin expression in nonerythroid cells: novel or ubiquitous?, Int J Inflam
Salentin, Schreiber, Haupt, Adasme, Schroeder, PLIP: fully automated protein-ligand interaction profiler, Nucleic Acids Res
Schlick, Molecular modeling and simulation: an interdisciplinary guide, doi:10.1007/978-0-387-22464-0
Shandilya, Chacko, Jayaram, Ghosh, A plausible mechanism for the antimalarial activity of artemisinin: A computational approach, Sci Rep
Shoop, Soll, Chemistry, pharmacology and safety of the macrocyclic lactones: ivermectin, abamectin and eprinomectin. Macrocyclic lactones in antiparasitic therapy
Siadat, Direkvand-Moghadam, Study of phytochemical characteristics Artemisia persica Boiss in Ilam Province, Future Natural Products
Sll, The PyMOL molecular graphics system, Version
Sohrabi, Alsafi, Neill, Khan, Kerwan et al., World Health Organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19), Int J Surg
St-Pierre, Ouellet, Giguère, Ohtake, Roy et al., Galectin-1specific inhibitors as a new class of compounds to treat HIV-1 infection, Antimicrob Agents Chemother
Su, Young, Linster, Zhu, Jayakumar et al., Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2, MBio
Surade, Blundell, Structural biology and drug discovery of difficult targets: the limits of ligandability, Chem Biol
Tilley, Straimer, Gnädig, Ralph, Fidock, Artemisinin Action and Resistance in Plasmodium falciparum, Trends Parasitol
Trott, Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J Comput Chem
Valcarcel, Bensussen, Álvarez-Buylla, Díaz, Structural Analysis of SARS-CoV-2 ORF8 Protein: Pathogenic and Therapeutic Implications, Front Genet
Villar, Beglov, Chennamadhavuni, Jr, Kozakov et al., How proteins bind macrocycles, Nat Chem Biol
Vinjamuri, Li, Bouvier, SARS-CoV-2 ORF8: One protein, seemingly one structure, and many functions, Front Immunol
Wang, Cao, Zhang, Yang, Liu et al., Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro, Cell Res
Wang, Wang, Wang, Jiang, Wang et al., SARS-CoV-2 ORF8 Protein Induces Endoplasmic Reticulum Stress-like Responses and Facilitates Virus Replication by Triggering Calnexin: an Unbiased Study, J Virol
Wang, Xu, Wong, Li, Liao et al., Artemisinin, the Magic Drug Discovered from Traditional Chinese Medicine, Proc Est Acad Sci Eng
Waterhouse, Procter, Martin, Clamp, Barton, Jalview Version 2--a multiple sequence alignment editor and analysis workbench, Bioinformatics
Wenzhong, Hualan, COVID-19: ORF8 Synthesizes Nitric Oxide to Break the Blood-Brain/Testi Barrier and Damage the Reproductive System, ChemRxiv
White, Clinical pharmacokinetics and pharmacodynamics of artemisinin and derivatives, Trans R Soc Trop Med Hyg
Wunsch, Mechanical Ventilation in COVID-19: Interpreting the Current Epidemiology, Am J Respir Crit Care Med
Yang, Shen, Hou, Is Ivermectin Effective in Treating COVID-19?, Front Pharmacol
Yang, Zhang, Protein structure and function prediction using I-TASSER, Curr Protoc Bioinformatics
Young, Fong, Chan, Mak, Ang et al., Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study, Lancet
Zhang, Chen, Li, Huang, Luo et al., The ORF8 protein of SARS-CoV-2 mediates immune evasion through downregulating MHC-Ι, Proc Natl Acad Sci
Zhang, I-TASSER server for protein 3D structure prediction, BMC Bioinformatics
Zhou, Gilmore, Ramirez, Settels, Gammeltoft et al., In vitro efficacy of artemisinin-based treatments against SARS-CoV-2, Sci Rep
Ziegel, Berk, Carey, Data Analysis with Microsoft® Excel, Technometrics
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