Results
Cytoscape v3.7.2 was used to create master network, which comprised of total 2693 nodes and 3736 edges. The master network had clustering coefficient of 0.562 and was divided into clusters using k-means clustering and the most tightly knit cluster around ACE2 was chosen (Figure 1(a)). Network Analysis revealed various hub nodes in the network. Hub nodes are those proteins which control the disperse of signaling in the network (Figure 1(a)). Major hub nodes obtained from the protein-protein interaction network was ACE2, INS, AKT1, VEGFA, IL-6, NOS3, JUN, IL-10, HIF1A etc. (Table 1).
Figure 1.  (a) Hub nodes in ACE2 protein related protein interaction network (b) Second line receptors to be used for targeting SARS-CoV2.
Table 1.  Top 10 hub nodes in ACE2 network with their affected pathways.
Human Readable Labels  Degree  Betweenness Centrality  Closeness Centrality  AverageShortestPathLength  Affected Pathways (Predicted by BiNGO)
ACE2 (Angiotensin converting enzyme II)  70  0.245142  0.666667  1.5  Angiotensin maturation, active regulation of amino acid transport, active regulation of cardiac muscle contraction, positive regulation of reactive oxygen species metabolic process, regulation of blood vessel diameter, regulation of cytokine production, regulation of inflammatory response and regulation of systemic arterial blood pressure by renin angiotensin
INS (Insulin)  67  0.085781  0.651163  1.535714  Protein kinase B activity, T cell activation, endoplasmic reticulum to Golgi vesicle-mediated transport, insulin receptor signaling pathway, glucose homeostasis, regulation of protein secretion and regulation of synaptic plasticity
AKT1(RACalpha serine/threonine-protein kinase)  65  0.08418  0.614035  1.628571  Activation-induced cell death of T cells, activation of protein kinase B activity, cellular response to hypoxia, cellular response to insulin stimulus, cellular response to tumour necrosis factor, cellular response to vascular endothelial growth factor stimulus, I-kappaB kinase/NF-kappaBsignaling, interleukin-18-mediated signaling pathway, regulation of apoptotic process
VEGFA (Vascular endothelial growth factor A)  57  0.043122  0.598291  1.671429  Activation of protein kinase activity, cellular response to hypoxia, cytokine-mediated signaling pathway, dopaminergic neuron differentiation, lung development, response to hypoxia
IL6 (Interleukin-6)  56  0.055244  0.619469  1.614286  Acute-phase response, cellular response to hydrogen peroxide, cellular response to lipopolysaccharide, cytokine-mediated signaling pathway, defence response to Gram-negative bacterium, defence response to Gram-positive bacterium, defence response to virus, glucagon secretion, humoral immune response, inflammatory response
ALB(Serum albumin)  56  0.039049  0.598291  1.671429  Cellular protein metabolic process, cellular response to starvation, high-density lipoprotein particle remodeling, maintenance of mitochondrion location negative regulation of apoptotic process, negative regulation of programmed cell death, platelet degranulation, post-translational protein modification, receptor-mediated endocytosis
ACE (Angiotensin converting enzyme)  50  0.037446  0.557769  1.792857  angiotensin maturation, antigen processing and presentation of peptide antigen via MHC class I, kidney development, positive regulation of blood pressure, regulation of angiotensin metabolic process, regulation of blood pressure, regulation of renal output by angiotensin
AGT (Angiotensinogen)  45  0.031026  0.585774  1.707143  Activation of MAPK activity, activation of phospholipase C activity, aging, angiotensin-activated signaling pathway, cell-cell signaling, cell growth involved in cardiac muscle cell development, cell surface receptor signaling pathway, cytokine secretion, ERK1 and ERK2 cascade, phospholipase C-activating G protein-coupled receptor signaling pathway, stress-activated MAPK cascade, renin-angiotensin regulation of aldosterone production
KNG1 (Kininogen-1)  43  0.019695  0.56  1.785714  Antimicrobial humoral immune response mediated by antimicrobial peptide, blood coagulation, intrinsic pathway, cellular protein metabolic process, G protein-coupled receptor signaling pathway, inflammatory response, killing of cells of other organism, platelet degranulation, positive regulation of apoptotic process, positive regulation of cytosolic calcium ion concentration, post-translational protein modification, vasodilation
REN (Renin)  42  0.021562  0.56  1.785714  angiotensin maturation, hormone-mediated signaling pathway, kidney development, regulation of blood pressure, regulation of MAPK cascade, renin-angiotensin regulation of aldosterone production, response to cAMP, response to cGMP ACE2 alone has various functions related to blood-vessel dilation, controlling blood pressure, cytokine production, inflammatory response, and protein transport. The initial symptoms of breathlessness, dysregulated blood pressure and inflammation are the ones which are reported initially in COVID-19 diagnosis. The next receptors downstream in this signaling event are IL6, AKT1, VEGFA, INS, IGF1, etc. (Figure 1(b)).
IL-6, IL-8, IL-10 and TNF-α were present in similar concentrations in SARS infected patients and may potentially cause SARS-associated ARDS. Similarly, VEGFA is the key regulator of vascular permeability, hence called as “vascular permeability factor”. High VEGF expression allows the pulmonary vascular albumin extravasation which leads to the vascular permeability, causing pulmonary oedema. Furthermore, Nitric Oxide (NO) (NOS3) has been observed to inhibit the viral replication during early stages which reduces the chances of spread of virus giving ample time to the immune system for recovery. KNG has a role in contact activation of blood coagulation. The histidine rich domain of high molecular weight KNG (HMW-KNG) releases bradykinin which helps in the release of anti-microbial peptides.
Therefore, these protein receptors are interconnected and have a cascade effect in overall pathology of COVID-19. It is hypothesized that combination of medications for VEGFA (Bevacizumab), IL6 (Tocilizumab), AKT1 (BAY 1125976), IGF1 (Increlex), etc. might be useful to manage the disease. Therefore, when SARS-CoV-2 binds to human ACE2 receptor, the above-mentioned protein receptors and their cascading interactions to other proteins will be affected. This interaction is further seen as pathology in human system.
We have investigated the potential of N. sativa as a phytotherapy against COVID-19. Therefore, computational studies were carried out to further add to this data and validate whether N. sativa bioactive constituents can be effective for management of COVID-19 symptoms. For this, the structures of constituents of N. sativa were retrieved from PubChem (Figure 2).
Figure 2.  2 D structures of the constituents of N. sativa obtained from PubChem. (a) 2719 (Chloroquine), (b) 6654 (Alpha-pinene), (c) 7463 (P-cymene), (d) 3652 (Hydroxychloroquine), (e) 10281 (Thymoquinone), (f) 10364 (Carvacrol), (g) 11230 (Terpinen-4-ol), (h) 398941 (Dithymoquinone), (i) 95779 (Thymohydroquinone), (j) 1796220 (Longifolene), (k) 73296 (alpha-Hederin), (l) 637563 (trans-Anethole), (m) 11402337 (Nigellicine), (n) 136828302(Nigellidine) A total of 12 bioactive constituents were retrieved namely thymoquinone, thymohydroquinone, dithymoquinone, p-cymene, carvacrol, 4-terpineol, t-anethol, longifolene, α-pinene, thymol, nigellidine, nigellicine and α-hederin (Figure 3). The computational ADME of N. sativa bioactive constituents is shown in Table 2. Along with these compounds Remdesivir was also retrieved as it is the upcoming medication in COVID-19 and is in clinical trials and it was used in this study to compare its efficacy to N. sativa bioactive constitutents in human system.
Figure 3.  (a) α-hederin(b) Thymohydroquinone(c) Thymoquinonein in ACE2 receptor binding site.
Table 2.  Computational ADME analysis of N. sativa constituents by QikProp v3.1.
Compound Name and PubChem ID  SMW  D  QPlogP  LogKhsa  Log BB  PM  Caco  Rule of 5  OA  Similar compounds and similarity index (%)
Alpha-Pinene(6654)  136.236  0.048  3.618  0.343  0.865  3  9906  0  100  Pempidine 78.80Clomethiazole 76.61Tranylcypromine 74.79Levamisole 72.26Mecamylamine 70.18
P-CYMENE (7463)  134.221  0.063  3.657  0.344  0.699  2  9906  0  100  Clomethiazole 89.85Phenylpropanol 84.91Isaxonine 84.31Mephentermine 82.16Pempidine 81.71
Thymoquinone (10281)  164.204  0.146  0.754  −0.635  −0.322  2  1091  0  86  Ethadione 91.24Paramethadione 91.07Acipimox 90.18Metacetamol 90.04Menadione 88.99
CARVACROL(10364)  150.220  1.514  3.298  0.056  0.073  3  3697  0  100  Mephentermine 91.54Phenylpropanol 91.35Isaxonine 90.81Paroxypropione 88.74Etilamfetamine 88.69
Terpinen-4-ol (11230)  154.252  1.902  2.950  0.101  0.224  4  5373  0  100  Sobrerol 88.09Aptrol 85.79Mephentermine 85.24Pempidine 84.79Phenylpropanol 84.79
alpha-Hederin (73296)  750.965  13.055  2.210  −0.287  −3.032  8  7M  3  16M  Azithromycin 68.93Flurithromycin 67.56Metildigoxin 66.53Clarithromycin 64.48beta 61.13
Thymohydroquinone (95779)  166.219  2.985  1.919  −0.171  −0.357  4  1396  0  94  Aptrol 95.09Sobrerol 93.88Prothionamide 93.02Bethanidine 91.64Mexiletine 91.28
Dithymoquinone (398941)  328.407  0.713  1.531  −0.527  −0.598  4  714  0  87  Nitisinone 81.63Trimetozine 80.19Fropenem 78.15Carboquone 78.13Emorfazone 77.37
trans-Anethole (637563)  148.204  1.354  3.167  0.120  0.284  2  9906  0  100  Clomethiazole 91.29Mephentermine 89.60Phenylpropanol 89.55Isaxonine 89.01Fenipentol 87.70
LONGIFOLENE (1796220)  204.355  0.434  4.846  0.857  1.028  1  9906  0  100  Chlornaphazine 79.84Levamisole 78.13Medazepam 78.10Pyrantel 77.74Methsuximide 77.61
Nigellidine (136828302)  294.352  7.916  3.728  0.666  −0.379  3  1219  0  100  Mesterolone 90.40Ondansetron 89.21Mazindol 88.92Metandienone 88.84Methandrostenolone 88.77
Nigellicine (11402337)  246.265  0.873  2.748  −0.597  −0.053  2  1794  0  88  Flumequine 91.32Ketorolac 88.64Oxolinic 86.54Anagrelide 85.98Glutethimide 85.82
SMW-Solute Molecular weight, D- Solute dipole moment, QPlog P- QP log P for octanol/water, QPlog S - QP log S for aqueous solubility, LogKhsa -QP log K hsa Serum Protein Binding, Log BB - QP log BB for brain/blood, PM: No of primary metabolites, Caco- Apparent Caco-2 Permeability (nm/sec), Rule of 5 - Lipinski Rule of 5 Violations, Rule of 3- Jorgensen Rule of 3 Violations, OA- % Human Oral Absorption in GI. Receptor prediction was carried out for all the constituents and then receptors were utilized to find out the biological pathways and processes in which these constituents will be useful. Separate networks were created for each constituent and hub nodes were identified. Hub nodes provide the information about the genes which will be majorly targeted by these constituents and the type of biological processes involved. Remdesivir was formulated for RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 virus but in current study we have proposed its probable targets in human system as well (Table 3) so that we can compare its therapeutic capability to N. sativa bioactive constituents.
Table 3.  Pathways targeted by Remdesivir and constituents of N. sativa.
PubChem ID  Compound Name  Hub Nodes  Pathways targeted
121304016  Remdesivir  CDK2, SRC, AURKA, ABL1, CDK1, MAPK1, MAPK14, TOP1, MTOR, CASP8, AURKB, CCNB1, PRKCA, PTK2, CDK5, SYK, MET, IGF1R, CASP3, PDGFRB, EIF4A1, PIK3CA, MAP3K5, CDK2, SRC  Pathways in cancer, Relaxin signaling pathway, PI3K-Akt signaling pathway, Endocrine resistance, Phospholipase D signaling pathway, AGE-RAGE signaling pathway in diabetic complications, HIF-1 signaling pathway, IL-17 signaling pathway, VEGF signaling pathway, MAPK pathway,Platelet activation, Chemokine signaling pathway, mTOR signaling pathway,FoxO signaling pathway,EGFR tyrosine kinase inhibitor resistance.
6654  Alpha-pinene  ESR1, AR, MAPK1, PTPN11, MAPK14, PTPN1, RARA, RXRA, NR3C1, PPARG, PTPN6, MAPK3, TOP1, ESR2, CDC25A, CD81, NCOA1, NOS2, TERT  Th17 cell differentiation, VEGF signaling pathway, cAMP signaling pathway, Type 2 diabetes, Fat digestion and absorption, Neuroactive ligand-receptor interaction, Calcium signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, HIF-1 signaling pathway, IL-17 signaling pathway, Ras signaling pathway, Pathways in cancer
7463  P-Cymene  ESR1, HDAC1, AR, KDM1A, GSK3B, ESR2, ALB, KIF11, IGF1R, HTR3A, HTR2C, ALOX5, SHBG, CHRM3, AHR, PPARA  Amphetamine addiction, Neuroactive ligand-receptor interaction, Calcium signaling pathway, Cocaine addiction, Alcoholism, Regulation of lipolysis in adipocytes, AGE-RAGE signaling pathway in diabetic complications, Inflammatory mediator regulation of TRP channels, c-GMP PkGsignaling pathway, NF-Κbsignaling pathway, IL-17 signaling pathway, cAMP signaling pathway
10281  Thymoquinone  GSK3B, PLK1, PARP1, PABPC1, NR3C1, MTNR1A, PTPN1, SOAT1, MTNR1B, XIAP, BRD4, PPARG, TOP2A, SYK, MAP2K1, IMPDH2, PTPN2, PGR, GLI1, MCL1, ALOX5  Neuroactive ligand-receptor interaction, Calcium signaling pathway, c-GMP PkGsignaling pathway, Alcoholism, Apoptosis, cAMP signaling pathway, lysosome, Influenza A, PI3K-AkT TNF signaling pathway, Pathways in cancer, NF-Κbsignaling pathway
10364  Carvacrol  ESR1, CDK2, HDAC1, AR, AURKA, AKT1, HDAC6, HDAC3, ADRB2, GAPDH, ESR2, ALB, MAPK8, CLK1,LDHA, PRKCA, LDHB, HDAC11, CCNA2, MAPK9, IGF1R  Neuroactive ligand-receptor interaction, MAPK signaling pathway, Calcium signaling pathway, Relaxinsignaling pathway, Pathways in cancer, Alcoholism, PI3K-AkT TNF signaling pathway, Ras signaling pathway, Th17 cell differentiation, Influenza, Regulation of lipolysis in adipocytes, Endocrine and other factor- regulated calcium reabsorption, Adrenergic signaling in cardiomyocytes, Amphetamine addiction, VEGF signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, Apoptosis, c-GMP PkGsignaling pathway, FOXO signaling pathway, Cocaine addiction
11230  Terpinen-4-ol  MAPK8, AR, JAK1, ESR1, JAK2, PTPN6, NR3C1, MAPK10, PPARA, PPARG, PTPN1, CHRM2, HTR2C, ESR2, CHRM4, HTR2A, DRD2, OPRK1, OPRD1, PGR, OPRM1, PARP1, MTNR1A  Neuroactive ligand-receptor interaction, Calcium signaling pathway, Inflammatory mediator regulation of TRP channels, Th17 cell differentiation, Pathways in cancer, AGE-RAGE signaling pathway in diabetic complications, cAMP signaling pathway, Tuberculosis, AMPK signaling pathway, Influenza, c-GMP PkGsignaling pathway, JAK-STAT pathway, Circadian rhythm, Relaxinsignaling pathway, Apoptosis- multiple species
73296  alpha-Hederin  GRB2, ITGA4, PPP1CA, SRC, AR, AURKA, PPP2CA, STAT3, CDK1, LGALS3, PTPN1, CASP8, XIAP, NCSTN, ATP1A1, ITGB1, PRKCD, IGF1R, CASP3, LGALS8, BCL2L1, MME, PSEN1, IMPDH2, HTR2C, IMPDH1, GLI1, HLA-A, ITGAV, ITGB3, PTPRA  Neuroactive ligand-receptor interaction, Calcium signaling pathway, AGE-RAGE signaling pathway in diabetic complications, Rennin- angiotensin system, c-GMP PkGsignaling pathway, Pathways in cancer, PI3K-AkT TNF signaling pathway, Apoptosis, Autophagy, Complement and coagulation cascades, P53 signaling pathway, T-cell receptor signaling pathway, NF-Κbsignaling pathway, JAK-STAT pathway, Alcoholism, Chemokine signaling pathway, Tuberculosis, HIF-1 signaling pathway, MAPK signaling pathway
95779  Thymohydroquinone  HSP90AA1, HDAC1, AURKA, AKT1, PARP1, ERBB2, ABL1, HDAC6, CDK1, HDAC3, ADRB2, GAPDH, MTNR1A, MAPK14, ALB, PTPN1, MTNR1B, PRKCA, LDHA, NOS2, LDHB, BRAF  Neuroactive ligand-receptor interaction, Calcium signaling pathway, AGE-RAGE signaling pathway in diabetic complications, Relaxinsignaling pathway, MAPK signaling pathway, Regulation of lipolysis in adipocytes, Oxytocin , Alcoholism, mTOR signaling pathway, PI3K-AkT TNF signaling pathway, FOXO signaling pathway, Inflammatory mediator regulation of TRP channels, VEGF signaling pathway, HIF-1 signaling pathway, Pathways in cancer, Natural killer cell mediated cytotoxicity, Tuberculosis, Colorectal cancer, Influenza A, Apoptosis, Amphetamine addiction, TNF signaling pathway, Hepatocellular carcinoma
398941  Dithymoquinone  HSP90AA1, SRC, AR, PRKDC, STAT3, NR3C1, MTNR1A, GAPDH, ESR2, ATM, MAPK8, TGFBR1, PTPN11, MTNR1B, EZR, NOS2, NCSTN, BRAF, CAPN1, PSEN1, CDC25A, PGR, PTK2B, ALOX5, PSEN2, OPRM1  Neuroactive ligand-receptor interaction, Calcium signaling pathway, AGE-RAGE signaling pathway in diabetic complications, Relaxinsignaling pathway, GABAergic synapse, Fluid shear stress and atherosclerosis, Apoptosis, Antigen processing and presentation, Chemokine signaling pathway, Morphine addiction, FOXO signaling pathway, Inflammatory mediator regulation of TRP channels, Cocaine addiction, Th17 cell differentiation, IL-17 signaling pathway, Alcoholism, c-GMP PkGsignaling pathway, Tuberculosis, Amphetamine addiction, Natural killer cell mediated cytotoxicity, TNF signaling pathway
637563  trans-Anethole  APP, EGF, RXPO1, ESR1 LRRK2 AR AURKA, RELA, PARP1, PRKDC, TUBB3, STAT3 MAPK14 KAT2B, PRKCA, NOS2, CDK5 KIF11, MAPT, JAK1, JAK2, CDC25B, TYK2  Nitrogen metabolism, Calcium signaling pathway, Primary immunodeficiency, TNF signaling pathway, T-cell receptor signaling pathway, Proximal tubule bicarbonate reclamation, Morphine addiction, IL-17 signaling pathway, NF-Κbsignaling pathway, Tuberculosis, VEGF signaling pathway, PI3K-AkT TNF signaling pathway, JAK-STAT pathway, Cocaine addiction, HIF-1 signaling pathway, Th17 cell differentiation, Pathways in cancer, Viral carcinogenesis
11402337  Nigellicine  HDAC1, EP300, AR, PPP1CA, CSNK2A1, RPA1, MAPK1, HDAC6, HSPA1A, CSNK2A2, MAP2K1, MCL1, TP53, NR4A1, ICAM1, TERT, EPRS, SORT1, FEN1, PGR  Neuroactive ligand-receptor interaction, cAMP signaling pathway, Nitrogen metabolism, Apoptosis, Lysosome, TNF signaling pathway, NF-Κbsignaling pathway, Influenza A, Autophagy, Alcoholism, Rheumatoid arthritis, HIF-1 signaling pathway, IL-17 signaling pathway, VEGF signaling pathway, Renin- angiotensin system, FOXO signaling pathway, Transcriptional misregulation in cancer, c-GMP PkGsignaling pathway, Oxytocin signaling pathway, Viral carcinogenesis, Nitrogen metabolism
136828302  Nigellidine  ESR1, CDK2, VCP, AKT1, ERBB2, HTT, GSK3B, RAF1, PLK1, CDK1, CFTR, KIT, MTNR1A, ILK, PPARG, CCNA2, CCNB1, MTNR1B, PDGFRB, CCNE1, PRKACA, FGFR1, CDK5, PSEN1, OPRM1  Pathways in cancer, Neuroactive ligand-receptor interaction, Calcium signaling pathway, MAPK signaling pathway, Chemokine signaling pathway, c-GMP PkGsignaling pathway, Ras signaling pathway, HIF-1 signaling pathway, VEGF signaling pathway, Arachidonic acid metabolism, Autophagy, Apoptosis, FOXO signaling pathway, Tuberculosis, AGE-RAGE signaling pathway in diabetic complications, Morphine addiction, Cocaine addiction, T-cell receptor signaling pathway
1796220  Longifolene  ESR1, AR, ESR2, PTPN1, UBA2, NR1H3, SAE1, SHBG, PPARA, POLB, NR1I3, NR1H4, BCHE, AKR1B10, HSD11B1, SLC6A4, NCOA3, EP300, NCOA1, ACTB, ACHE, MED1, NCOR1  Steroid hormone mediated signaling pathway, response to oxygen- containing compound, lipid metabolic process, regulation of inflammatory response, regulation of cytokine mediated signaling pathway, regulation of innate immune process, blood circulation, regulation of insulin receptor signaling pathway, regulation of toll- like receptor signaling pathway Protein interaction network created for remdesivir was analysed and it was observed to be targeting certain families of proteins and pathways such as Cancer, Relaxin signaling pathway, PI3K-Akt signaling pathway, IL-17, chemokine, HIF-1 signaling pathway, AGE-RAGE, VEGF pathway, Foxo pathway etc. On the other end, N. sativa constituents collectively were also targeting these as well other families such as Nuclear receptors, Cytochrome P450, Oxidoreductases, Erasers, Lyases, Enzymes, Family A G protein coupled receptors, calcium signaling pathways, Circadian pathways, Foxo pathway etc. These results reveal that there is clearly a lot of protection which can be contributed by this wonder herb (Figure 5).
Glide Standard-Precision (SP) docking was performed and the best binding ligand to ACE2 was observed to be α-hederin (-6.265 kcal/mol), Thymohydroquinone (-5.466 kcal/mol) and Thymoquinone (-5.048 kcal/mol) (Table 4). Their binding energies were good and therefore, these compounds can be looked further to use them as future therapeutics. The docking poses of best binding compounds are displayed in Figure 3(a–c).
Table 4.  Docking analysis of N sativa constituents with ACE2 receptor.
Title  glide gscore  glide evdw  glide ecoul  glide energy  glide einternal  glide lipo  glide hbond
73296 (α-hederin)  −6.265  −25.96  −19.94  −50.00  0.783  −0.478  −1.487
95779 (Thymohydroquinone)  −5.466  −21.445  −7.586  −29.031  0.791  −0.417  −0.59
10281 (Thymoquinone)  −5.048  −24.979  −3.678  −28.657  0.028  −0.518  −0.32
10364 (Carvacrol)  −4.704  −20.361  −3.907  −24.268  0.064  −0.403  −0.446
11230 (Terpinen-4-ol)  −4.458  −15.737  −7.84  −23.577  0.884  −0.086  −0.16
637563 (trans-Anethole)  −4.287  −20.901  −0.824  −21.725  0.067  −1.433  0
7463 (P-Cymene)  −4.114  −19.554  −0.782  −20.336  0.044  −0.769  0
6654 (Alpha-Pinene)  −3.798  −17.04  −0.792  −17.832  0  −0.577  0 Remdesivir, which is the current most suited therapeutic drug for COVID-19 along with α-hederin, Thymohydroquinone and Thymoquinone were further explored more for their mode of action (Figure 4(a–c)). Since the initial diagnosis of COVID-19 is compromised immunity and it is always associated with inflammation and oxidative stress therefore it is suggested that N. sativa bioactive constituents can be very useful for boosting our immunity and helping patients to overcome the symptoms of COVID-19. While Remdesivir was observed to be targeting proteins involved in growth and proliferation (Figure 4(a)), α-hederin was observed to be engaged in regulation of blood pressure, regulation of cell communication, regulation of vascular processes, negative regulation of cell death, response to stress and immune effector processes. The genes identified for regulating immune response via α-hederin are ACE2, F2, SRC etc (Figure 4(b)). Thymohydroquinone was observed to be targeting proteins involved in response to oxidative stress, negative regulation of cell death, regulation of blood pressure, positive regulation of kinase activity, regulation of immune response etc. Regulation of immune response by thymohydroquinone was through genes like HSP90AA1, PRKCA, VEGFA, ADORA1 etc. (Figure 4(c)) and Thymoquinone was seen to be targeting kinases, heat shock proteins and oxidoreductases (Figure 4(d)).
Figure 4.  Mechanism of action (a) Remdesivir (b) α-hederin (c) Thymohydroquinone (d) Thymoquinone. Both α-hederin and thymoquinone have ACE as their predicted receptor in human system and therefore can be explored further for targeted therapies. The plant extract of N. sativa with the above-mentioned bioactive constituents is proposed to excel and outweigh any other treatment proposed so far for COVID-19 (Figure 5).
Figure 5.  Comparison of Remdesivir and N. sativa extract with their genes and pathways. The best docking compound among all the N. sativa constituents is α-hederin and it is a saponin which possesses multiple properties like antioxidant, anti-inflammatory, antitumor and is also known to be affective against fungi and parasites. Many studies have been conducted at cell lines and in-vivo models and it was shown to impressively working in conditions like cancer, asthma, and inflammation (51). We need more wet-lab studies to explore its effectiveness in viral infections.
Numerous ACE2 medications are already tried on COVID-19 patients but they are also not exhibiting the good results. This might be because chemical-based compounds are targeted to single receptor and therefore have a limited mode of action to work in the body, other than their accompanied side effects. On the contrary, natural compounds derived from herbs and medicinal plants have proven to work in body in an all-round manner.