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Active-site Molecular docking of Nigellidine to nucleocapsid/Nsp2/Nsp3/MPro of COVID-19 and to human IL1R and TNFR1/2 may stop viral-growth/cytokine-flood, and the drug source Nigella sativa (black cumin) seeds show potent antioxidant role in experimental rats

Maiti et al., Research Square, doi:10.21203/rs.3.rs-26464/v1
May 2021  
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11th treatment shown to reduce risk in January 2021
 
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In Silico and animal study of nigella sativa and component nigellidine, showing nigellidine binding activity for several important SARS-CoV-2 proteins and for relevant host receptors; and that black cumin seed extract was antioxidative, hepato- and reno-protective in rats.
20 preclinical studies support the efficacy of nigella sativa for COVID-19:
Maiti et al., 5 May 2021, preprint, 5 authors.
This PaperNigella SativaAll
Active-site Molecular docking of Nigellidine to nucleocapsid/Nsp2/Nsp3/MPro of COVID-19 and to human IL1R and TNFR1/2 may stop viral-growth/cytokine-flood, and the drug source Nigella sativa (black cumin) seeds show potent antioxidant role in experimental rats.
Smarajit Maiti, Amrita Banerjee, Aarifa Nazmeen, Mehak Kanwar, Shilpa Das
doi:10.21203/rs.3.rs-26464/v1
The recent outbreak of SARS CoV-2 has changed the global scenario of human lives and economy. In this pandemic-outbreak the ratio of infected person is much higher than the death encountered. Most of the dead patients were observed with dysfunction/failure of cardiac and renal systems. Beside this a 'cytokine storm' namely TNF-α/IL1 receptors i.e. TNFR1/TNFR2/IL1R over-functioning was reported in the infected-persons. Here, nigellidine, an indazole-alkaloid and key-component of Nigella Sativa L. (NS); black-cumin-seed, has been analyzed for COVID-19 different protein and TNFα receptors TNFR1/TNFR2 and IL1R inhibition through molecular-docking study and biochemical-study of cuminseed extract exposure to experimental-rat. The NMR, X-ray-crystallographic or Electron-microscopic structures of COVID-19 Main-protease(6LU7), Spike-glycoprotein(6vsb), NSP2(QHD43415_2), Nterminus-protenase (QHD43415_3), Nucleocapsid(QHD43423) and Human IL1R (1itb), TNFR1 (1ncf), TNFR2 (3alq) from PDB were retrieved/analyzed for receptor-ligand interaction in normal condition. Then those structures were docked with nigellidine using Autodock-software and Patchdock-server. Where nigellidine showed highest binding-energy of -7.61 (kcal/mol) and ligand-efficiency value of (-0.35) forming bonds with amino acids THR943/LYS945/MET1556/ALA1557/PRO1558/ILE1559. Highest ACE-value of -356.72 was also observed for nigellidine N-terminal-protease interaction. Nigellidine also showed strong interaction with NSP2 (-6.28) and Mpro/3CLpro_Q (-6.38s). Nigellidine showed affinity to TNFR1 (-6.81), IL1R (-6.23) and TNFR2 (-5.16). In rat experiment 2-groups (vehicle and NS treated) of female Wistar-rats were taken for experiments. The NS treated tissue showed marked decline in ALP/SGPT/ SGOT/MDA level then the basal-levels. From the Western-blot or activity analysis it was observed that Nigellidine, the sulfuryl-group containing drug showed no impact on Phenol-catalyzing ASTIV or Steroid-catalyzing EST expressions/activities and thus have no influence in sulfation-mediated adverse metabolic-processes. Current-results concluded that Nigellidine has hepato/reno-protective; immunomodulatory/anti-inflammatory and antioxidant activities as well as it inhibits important proteins of COVID-19. With steps to further validation/checking nigellidine can be used in COVID-19 infection.
Conflict Of Interest
References
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Where nigellidine showed highest binding-energy of ' '-7.61 (kcal/mol) and ligand-efficiency value of (-0.35) forming bonds with amino acids ' 'THR943/LYS945/MET1556/ALA1557/PRO1558/ILE1559. Highest ACE-value of -356.72 was also observed ' 'for nigellidine N-terminal-protease interaction. Nigellidine also showed strong interaction ' 'with NSP2 (-6.28) and Mpro/3CLpro_Q (-6.38s). Nigellidine showed affinity to TNFR1 (-6.81), ' 'IL1R (-6.23) and TNFR2 (-5.16). In rat experiment 2-groups (vehicle and NS treated) of female ' 'Wistar-rats were taken for experiments. The NS treated tissue showed marked decline in ' 'ALP/SGPT/ SGOT/MDA level then the basal-levels. From the Western-blot or activity ' 'analysis<jats:italic> </jats:italic>it was observed that Nigellidine, the sulfuryl-group ' 'containing drug showed no impact on Phenol-catalyzing ASTIV or Steroid-catalyzing EST ' 'expressions/activities and thus have no influence in sulfation-mediated adverse ' 'metabolic-processes. 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