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Research Article
Identification of Dietary Molecules as Therapeutic Agents to Combat COVID-19 Using Molecular Docking Studies
Mohammad Faheem Khan
Era' Lucknow medical College, Era University, Lucknow-226003, India
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1943-7160
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Recently, a new and fatal strain of coronavirus named as SARS-CoV-2 (Disease: COVID-19) appeared in Wuhan, China in December of 2019. Due to its fast growing human to human transmission and confirmed cases in nearly every country, it has been declared as pandemic by World Health Organisation (WHO) on 11 March 2020. Till now, there is no therapy such as vaccines and specific therapeutic agents available globally. Inspite of this, some protease inhibitors and antiviral agents namely lopinavir, ritonavir, remdisivir and chloroquine are under investigation and also implemented in several countries as therapeutic agents for the treatment of COVID-19. Seeing the health crisis across the world, it was our aim to find out a suitable drug candidate which could target SARS-CoV-2. For this purpose, molecular docking of 7 proteinsof SARS-CoV-2 was done with 18active constituents that have previously been reported to be antiviral or anti-SARS-CoV agents. The docking results of these 18 compounds were compared with 2 FDA approved drugs that have are currently being used in COVID 19, namely Remdesivir and Chloroquine. Our result revealed that among all, epigallocatechin gallate (EGCG), a major constituent of green tea, is the lead compound that could fit well into the binding sites of docked proteins of SARS-CoV-2. EGCG showed very strong molecular interactions with binding energies -9.30, -8.66, -8.38, -7.57, -7.26, -6.99 and -4.90 kcal/mole for6y2e, 6vw1, 6vww, 6lxt,6vsb, 6lu7 and 6lvnproteins of SARS-CoV-2, respectively.Therefore, EGCG as per our results, should be explored as a drug candidate for the treatment of COVID-19.
Keywords
SARS-CoV-2, EGCG, COVID-19, Dietary Molecules, Molecular Docking
Figure 1
Figure 2
Figure 3
In the light of recent pandemic situation, there are two questions raised: first of which protein molecule of SARS-CoV–2 is responsible for their high virulence and replication processeswhile second is that which therapeutic agent can prevent or kill the SARS-CoV–2. For the answer of the first question, we searched the literatureand found out recently released structural and non-structural proteins of SARS-CoV–2 which are structured and repositioned on Protein Data Bank (PDB) site (https://www.rcsb.org/). Thus, based on database of PDB, we have selected seven different types of protein macromolecules which play a pivotal role in propagating the SARS-CoV–2 (table 1). Our intriguing protein targets include main protease covid–19 (6lu7), structure of the 2019-nCoV HR2 Domain (6lvn), structure of post fusion core of 2019-nCoV S2 subunit (6lxt), prefusion 2019-nCoV spike glycoprotein (6vsb), structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2 (6vw1), crystal structure of NSP15 endoribonuclease from SARS CoV–2 (6vww) and crystal structure of the free enzyme of the SARS-CoV–2 (2019-nCoV) main protease (6y2e).
Due to technical limitations, Table 1 is provided in the Supplementary Files section.
In search of the answer for the second question, we selected 18 dietary molecules namely allicin, alliin, apigenin, beta-glucan, curcumin, diadzein, EGCG, ferullic acid, genistein, gingerol-[6], glucosamine, alpha-lipoic acid, myricetin, phycocyanobillin, piperine, quercetin, resveratrol andsulphoraphanethat are abundantly present in commonly used herbs, spices, fruits and vegetables. All the dietary moleculesexhibited either antiviral or anti-SARS-CoV activities as reported in previous studies (table 2).Recent studies revealed that some drugs like remdisivir, chloroquine, lopinavir and ritonavir could be repurposed and studied to treat COVID–19. All these dietary molecules as well as selected drugs remdisivir and chloroquine as control to verify and compare our results were docked against SARS-CoV–2 3CL homology model. Based on our docking analysis, we recommend that theligands with the highest binding affinity and lowest inhibition constant be considered for further investigation.
Due to technical limitations, Table2 is provided in the Supplementary Files section.
Among these dietary molecules, epigallocatechin gallate (EGCG) which is found abundantly in green tea, was found as most active agent against COVID–19. EGCG showed highest binding affinity (–9.30kcal/mole) and lowest inhibition constant (0.152µM) for 6y2e protein. Moreover, EGCG exhibited a strong molecular interaction with 6vw1 which is an important target of this new CoV. It showed highest binding affinity and lowest inhibition constant with –8.66 kcal/mole and 0.152µM values respectively. Further, EGCG displayed excellent interactions with 6vww wherein it showed highest binding affinity (–8.38 kcal/mole) with lowest inhibition constant at 0.724 µM concentration. Additionally, EGCG also exhibited good molecular interactions with SARS-CoV–2 proteins 6lu7, 6lvn, 6lxt, and 6vsb with the values of binding energies and inhibition constant as –6.99, –4.90, –7.57, –7.26 kcal/mole and 7.57, 255.95, 2.84, 4.75 µM concentrations. The computed activity of EGCG was found to be higher than that of both reference drugs, Remdesivir and Chloroquine. All docked poses are depicted in figure 1 and 2 which showstrong interactions of EGCG with selected protein residues.
It has been established that the molecules having hydroxyl (-OH) and carbonyl (C = O) functionalities showed strong intermolecular interactions with amino acid residues at active sites of proteins through physical forces such as hydrogen bonds and hydrophobic bonds. Due to amount and types of these intermolecular interactions, they show druggable and druglikeness properties. In this study, we also identified eight more active phytochemicals namely curcumin, apigenin, beta-glucan, myricetin, piperine, genistein, diadzein and quercetin. Apigenin, myricetin, and quercetin are flavonoids while genistein and diadzein are isoflavonoids. On the other hand curcumin and piperineare phenolic compounds whereas beta-glucan is a polymer of sugar. They all have hydroxyl (-OH) and carbonyl (C = O) functionalitiesin their core structures and hence exhibited strong molecular interaction with all protein macromolecules chosen under this study. All values of binding affinities and inhibition constant of these dietary molecules are listed in table 3.
Table 3: Molecular docking values of phytochemicals against target protein macromolecules
|
Phytochemicals |
Targets Proteins; binding energy in kcal/mole (inhibition constant in µM) |
|
|
|
||||
|
|
|
6lu7 |
6lvn |
6lxt |
6vsb |
6vw1 |
6vww |
6y2e |
|
1 |
EGCG |
-6.99 (7.57) |
-4.90 (255.95) |
-7.57 (2.84) |
-7.26 (4.75) |
-8.66 (0.451) |
-8.38 (0.724) |
-9.30 (0.152) |
|
2 |
Curcumin |
-6.04 (37.57) |
-4.73 (340.89) |
-5.50 (92.90) |
-5.05 (197.96) |
-7.13 (5.91) |
-7.37 (3.96) |
-7.39 (3.83) |
|
3 |
Apigenin |
-5.96 (43.03) |
-3.71 (1.9x10-5) |
-5.13 (1.74x10-5) |
-5.98 (4.1x10-5) |
-6.02 (38.69) |
-6.48 (17.86) |
-7.05 (6.76) |
|
4 |
Beta Glucan |
-5.96 (42.79) |
-4.16 (889.95) |
-5.06 (195.39) |
-3.20 (4.4x10-5) |
-6.44 (19.09) |
-6.72 (11.86) |
-7.05 (6.83) |
|
5 |
Myricetin |
-5.38 (114.10) |
-3.70 (1.96x10-5) |
-5.74 (62.01) |
-6.14 (31.32) |
-6.50 (17.16) |
-6.57 (15.20) |
-7.15 (5.79) |
|
6 |
Quercetin |
-5.29 (132.27) |
-3.68 (2.02x10-5) |
-5.73 (63.52) |
-6.14 (31.32) |
-6.59 (14.73) |
-6.53 (16.36) |
-6.77 (10.86) |
|
7 |
Piperine |
-5.16 (165.72) |
-4.08 (1.02x10-5) |
-5.40 (109.87) |
-6.05 (36.85) |
-5.64 (73.80) |
-6.18 (29.44) |
-6.40 (20.37) |
|
8 |
Genistein |
-5.03 (204.91) |
-3.97 (1.24x10-5) |
-5.68 (69.09) |
-6.54 (16.04) |
-6.35 (22.18) |
-6.73 (11.70 ) |
-6.80 (10.32) |
|
9 |
Diadzein |
-4.86 (275.53) |
-3.72 (1.89x10-5) |
-5.21 (151.77) |
-6.16 (30.34) |
-5.96 (42.54) |
-6.43 (19.50) |
-6.05 (36.86) |
|
10 |
Ferulic acid |
-4.76 (322.26) |
-2.79 (9.00x10-5) |
-3.75 (1.80 x10-5) |
-5.44 (103.05) |
-3.74 (1.8x10-5) |
-3.90 (1.3 x10-5) |
-4.71 (355.68) |
|
11 |
Alliin |
-4.66 (385.74) |
-3.90 (1.37x10-5) |
-5.02 (210.26) |
-4.57 (447.67) |
-5.15 (168.32) |
-4.07 (1.0 x10-5) |
-5.68 (68.09) |
|
12 |
Lipoic acid |
-4.58 (439.80) |
-1.90 (40.6x10-5) |
-3.25 (4.16x10-5) |
-4.93 (243.60) |
-2.73 (9.9x10-5) |
-3.38 (3.3 x10-5) |
-3.59 (2.3x10-5) |
|
13 |
Resveratrol |
-4.20 (832.91) |
-3.58 (2.38x10-5) |
-4.32 (685.04) |
-5.57 (82.09) |
-5.26 (138.32) |
-5.57 (83.02) |
-5.54 (86.98) |
|
14 |
Glucosamine |
-4.06 (1.06x10-5) |
-3.59 (2.32x10-5) |
-5.26 (138.93) |
-4.89 (262.36) |
-6.77 (10.89) |
-4.18 (862.43) |
-4.70 (359.49) |
|
15 |
Gingerol-[6] |
-4.00 (1.16) |
-2.23 (23.38) |
-3.08 (50.56) |
-4.46 (537.58) |
-4.60 (425.87) |
-4.57 (449.30) |
-5.30 (130.87) |
|
16 |
Sulforaphane |
-3.74 (1.81x10-5) |
-2.25 (22.3x10-5) |
-3.11 (5.22x10-5) |
-3.43 (3.0x10-5) |
-3.46 (2.9x10-5) |
-3.21 (4.4x10-5) |
-4.21 (815.35) |
|
17 |
Allicin |
-3.46 (2.89x10-5) |
-2.09 (29.4x10-5) |
-3.20 (4.49x10-5) |
-3.46 (2.92) |
-3.07 (5.6x10-5) |
-3.14 (5.0x10-5) |
-3.63 (2.1x10-5) |
|
18 |
PCB |
+0.16, (Nil) |
-3.12 (5.14x10-5) |
-4.63 (4.05x10-5) |
+11.3 (Nil) |
-3.59 (2.3x10-5) |
-6.14 (3.1x10-5) |
-5.15 (1.6x10-5) |
|
19 |
Remdesvir |
-2.47 (15.4x10-5) |
-2.68 (10.7x10-5) |
-4.84 (281.48) |
-4.27 (745.64) |
-5.27 (136.97) |
-5.10 (183.96) |
-5.47 (97.23) |
|
20 |
Chloroquine |
-3.62 (2.2x10-5) |
-3.26 (4.0x10-5) |
-4.35 (651.5) |
-4.79 (309.3) |
-6.41 (19.9) |
-4.85 (277.5) |
-6.10 (33.5) |
6lu7: Main protease of covid-19; 6lvn: Structure of the 2019-nCoV-HR2 Domain; 6lxt: Structure of post fusion core of 2019-nCoV S2 subunit; 6vsb: Prefusion 2019-nCoV spike glycoprotein; 6vw1: Structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2; 6vww: Crystal structure of NSP15 endoribonuclease from SARS CoV-2; 6y2e: Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease. Remdesvir and Chloroquine are used as standard drugs to compare our results; EGCG: Epigallocatechin gallate; PCB: Phycocyanobillin
From docking results as well as analysis of binding affinity with binding pockets within active sites of proteins, we prepared a decreasing order of their potency against SARS-CoV–2.
- Orderof activityagainst main protease (6lu7) of SARS-CoV–2is EGCG > curcumin > apigenin > beta-glucan > myricetin
- Order of activity against HR2 domain of spike glycoprotein (6lvn) of SARS-CoV–2is EGCG > curcumin > beta-glucan > piperine > genistein.
- Order of activity against chimeric receptor-binding domain of spike glycoprotein (6vw1) of SARS-CoV–2 is EGCG > curcumin > glucosamine > quercetin > myricetin.
- Order of activity against single receptor binding domain of spike glycoprotein (6vsb) of SARS-CoV–2 is EGCG > genistein > myricetin > quercetin > curcumin > diadzein
- Order of activity against NSP15 endoribonuclease (6vww) of SARS-CoV–2 is EGCG > curcumin > genistein > beta-glucan > myricetin
- Order of activity against post fusion core S2 subunit (6lxt) of SARS-CoV–2is EGCG > myricetin > quercetin > genistein > curcumin
- Order of activity against free enzyme of (6y2e) of SARS-CoV–2 main protease is EGCG > curcumin > apigenin > myricetin > beta-glucan
We, thus, found EGCG, curcumin, myricetin, genistein, myricetin, beta-glucan, quercetin and diadzein as recommended compounds for the treatment of COVID–19 (figure 3). Finally, as a result of our study, we have discovered EGCG as potent SARS-CoV–2 inhibitor which might be a drug candidate in future to treat this dreadful disease
Diet Suggestions
In light of current findings, intake of the suggested foods (Table 4) as supplements in adequate doses could be helpful to prevent and control COVID–19 infection by suppression of propagation and pathogenesis of SARS-CoV–2.Since green tea is a rich source of EGCG, it may have a major role in combating the SARS-CoV–2. Our careful and extensive analysis revealed that other promising molecules that can be easily available to us, might also be expected to suppress the pathogenicity of this coronavirus. It might be helpful to include the suggested food substances in the diet of COVID 19 patients and healthcare workers to control and avoid the infection. Doing so may also prevent secondary infections, since these compounds have previously been reported to have antimicrobial activity. Hence, these dietary suggestions may also be implemented in case of influenza and common flu.
Table 4: Daily dose based diet suggestion for prevention and treatment of COVID-19
|
Dietary Molecules (DM) |
Recommen- dedDaily Intake |
Amount of DM present in Food Source (per 100g) |
Suggested Dose of Food Source Per Day (gm) |
t1/2(h) |
Suggested Frequency |
Suggested Preparation |
|
EGCG |
800 mg |
7.38 gin Green Tea |
16.67* |
4.5 |
3-4 times a day after every 4.5 h |
Brewed for 3 minutes in boiling water |
|
Curcumin |
500 mg |
3.2 gin Turmeric |
15.625 |
6-7 |
3 times a day every 6.5 h |
Mix with lukewarm milk |
|
Apigenin |
3-10 mg |
1.2 gin Chamomile Tea |
1.08** |
12 |
2 times a day every 12 h |
Brewed for 5-10 minutes in boiling water |
|
300 mg in Parsley |
2.16 |
|||||
|
Beta Glucan |
3-10 g |
5.5 g in Whole Grain Oats# |
118.18 |
19.5- 27.3 |
Once a day |
Boil in water or milk |
|
11 g in Whole Grain Barley## |
59 |
#average based on range 3-8%; ##average based on range 2-20%; *assuming 65% yield; **assuming 50% yield. All values of dietary molecules are taken from USDA databases ( https://doi.org/10.15482/USDA.ADC/1178142)
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Juha
commented on 30 March, 2020
I appreciate your approach. Traditional chinese medicines contains several plant derived compounds capable blocking the entry of CoV into the cells. FDA approval would be the key hurdle to get these medicines to the people in need urgently.
View 1 reply
Ron Brightmore
commented on 02 April, 2020
An excellent article. Have you seen the product Capsol-T which combines EGCG and capsaicin in a highly synergistic mixture? [researched by DR James Morre]. EGCG has also been shown to inhibit furin, inhibit the transport of furin to the cell membrane by a HIF-1 mechanism, potentially inhibit the thiol/disulide mechanism vital for COVID-19 spike entry and fusion, also inhibit caspase 1 which activates IL-1B cascade which has been managed by the COVID-19 E protein and inhibit angiotensin 2 which is set free by the COVI-19 interaction with ACE2 [angiotensin 2 will also activate IL-1B and the inflammatory cytokine cascade that attacks the lung cells. As you can see, I am very interested in the potential use of RGCG re this virus and see a potential for a combination in the use of Capsol-T, hydrocloroquine and curcumun, Hydrocchloroquine will act to inhibit the alternative entry mechanism via the endosomes and curcumin acts in a similar way to EGCG in inhibiting angiotensin 2 and activating NRF2 which controls the balance between proteases and antiproteases. I am sorry for that rush of ideas but I am very excited by your article. I can send you copies of e-mails that discuss all the above if you are interested. Thank you for your research Ron
View 2 replies
Dr M Faheem Khan
replied on 05 April, 2020
Thank you so much for appreciation and to give your valuable suggestions. Thanks are also due to providing us a details of other molecules having synergistic effect with EGCG. We will be happy if you share copies of your mails as per discussed by you.
Martha Whitehill
replied on 29 December, 2020
Second doorway (besides ACE2) is DPP4. Furin cleaves the toxin, PRRA (proline, arginine, arginine - THOSE 3 are FROM GLUTAMATE - AND alanine FROM PYRUVATE) between the two "R's" between 'SPIKES" S1 and S2. Furin was found to be involved in the posttranslational cleavage of syncytin 1 and 2... then demethylated? Look very closely at TUDCA also - very helpful from many respects.. The Chinese recommend UDCA, but conjugating taurine onto that bile salt helps it cross the "blood brain barrier'. Syncytium formation by SARS-CoV-2 is many times faster than in the 2002 SARS-CoV, and syncytium formation is highly responsible for the virulence factor and induction of a cytokine storm of any virus in general and SARS-CoV-2 especially (Matsuyama et al., 2020; Xia et al., 2020).
Zaw Ali Khan
commented on 05 April, 2020
Thank for your suggestions and encouragement. We'd be interested in reading more about this.
Michio Jibiki
commented on 05 April, 2020
I appreciate your screening approach. Japanese green tea is unfermented tea. Therefore, it contains cathecin components a lot. I believed that EGCG is effective for inactivate virus at the upper respiratory tract part due to its feature of easy binding to proteins and early coverage of infectious spikes.
Wasif Raza
commented on 06 April, 2020
A great research which could bring about a breakthrough amidst this fulminant pandemic. However, as agreed, more research is needed to establish a guideline. Best wishes.
Djoko Agus Purwanto
commented on 06 April, 2020
I really appreciate to this research. Compared to the chloroquine, EGCG is known as a non-toxic compound and has been used in daily drinks for hundreds of years. Therefore EGCG is not only used for the treatment of COVID-19 but also prevention. What is the dose of EGCG needed by adults to prevent corona infection?? Thank you so much for your attention.
View 1 reply
Tham
replied on 23 July, 2020
Try 400 ng twice a day. Combine with Daflon, two tablets daily.
Tukaram Pandharipande
commented on 12 April, 2020
The findings are very interesting and looks promising in the current situation of Covid19. However, the article do not have information about the grade or specification of EGCG and Curcumin used in the investigations. I request if you can send me some information about the grades/ specifications of EGCG and Curcumin used in the investigations.
Greg
commented on 17 April, 2020
EGCG is also a zinc ionophore like Quercetin and chloroquine analogues. Zinc gluconate, as a lozenge/powder ever 4 hours 15mg, should be combined with EGCG /Quercetin for maximal effect. Many modes of action, combination therapies usually more effective than single molecule interventions.
Hiroyuki Shibata
commented on 02 May, 2020
Thank you Drs. It's a very encouraging data. I know the death rate in India is 0.83/ 1,000,000 peoples, while in Italy, 462.56/1,000,000. We have developed new curcumin analogs, such as GO-Y030 and GO-Y022, published elsewhere. They have more potent activities. We want to check the possibility of them. GO-Y022 is a natural ingredient. Best regards.
Germán Gutierrez
commented on 28 May, 2020
Thank you the EGCG ACE2 interaction and zinc plus vitamin d. Sinergies with cafein
Martha Whitehill
commented on 19 October, 2020
COVID-19's main protease is a cysteine protease called 3CL or Mpro = Nsp#5 and is*inhibited by* Baicalin or the drug ebselen. TUDCA (taurine conjugated bile salt) also can help as it shares 2 actions similar to Baicalin - decreases inflammation and activates Nfr2. Not surprising GABAA receptors are involved. JSTX-3 (= a spider toxin shares an amino acid sequences with COVID-19) blocks specific glutamate receptors. I believe the horseshoe bat eats the Jaro spider (golden orb) that has a venom with a toxin that shares an amino acid sequence in COVID-19. The toxin/virus is transferred to the horseshoe bat and the virus is excreted in the guano. The reason why persons given antibodies fail to recover is because the neuro toxin has to be addressed. The toxin target is NaV1.7 and is linked to the loss of the sense of smell.
View 1 reply
MOHD FAHEEM KHAN
replied on 12 November, 2020
Thanks a lot "Martha Whitehill", your information is very much useful for us.
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Research Article
Identification of Dietary Molecules as Therapeutic Agents to Combat COVID-19 Using Molecular Docking Studies
Mohammad Faheem Khan
Era' Lucknow medical College, Era University, Lucknow-226003, India
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1943-7160
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Complete author information
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Recently, a new and fatal strain of coronavirus named as SARS-CoV-2 (Disease: COVID-19) appeared in Wuhan, China in December of 2019. Due to its fast growing human to human transmission and confirmed cases in nearly every country, it has been declared as pandemic by World Health Organisation (WHO) on 11 March 2020. Till now, there is no therapy such as vaccines and specific therapeutic agents available globally. Inspite of this, some protease inhibitors and antiviral agents namely lopinavir, ritonavir, remdisivir and chloroquine are under investigation and also implemented in several countries as therapeutic agents for the treatment of COVID-19. Seeing the health crisis across the world, it was our aim to find out a suitable drug candidate which could target SARS-CoV-2. For this purpose, molecular docking of 7 proteinsof SARS-CoV-2 was done with 18active constituents that have previously been reported to be antiviral or anti-SARS-CoV agents. The docking results of these 18 compounds were compared with 2 FDA approved drugs that have are currently being used in COVID 19, namely Remdesivir and Chloroquine. Our result revealed that among all, epigallocatechin gallate (EGCG), a major constituent of green tea, is the lead compound that could fit well into the binding sites of docked proteins of SARS-CoV-2. EGCG showed very strong molecular interactions with binding energies -9.30, -8.66, -8.38, -7.57, -7.26, -6.99 and -4.90 kcal/mole for6y2e, 6vw1, 6vww, 6lxt,6vsb, 6lu7 and 6lvnproteins of SARS-CoV-2, respectively.Therefore, EGCG as per our results, should be explored as a drug candidate for the treatment of COVID-19.
Figure 1
Figure 2
Figure 3
In the light of recent pandemic situation, there are two questions raised: first of which protein molecule of SARS-CoV–2 is responsible for their high virulence and replication processeswhile second is that which therapeutic agent can prevent or kill the SARS-CoV–2. For the answer of the first question, we searched the literatureand found out recently released structural and non-structural proteins of SARS-CoV–2 which are structured and repositioned on Protein Data Bank (PDB) site (https://www.rcsb.org/). Thus, based on database of PDB, we have selected seven different types of protein macromolecules which play a pivotal role in propagating the SARS-CoV–2 (table 1). Our intriguing protein targets include main protease covid–19 (6lu7), structure of the 2019-nCoV HR2 Domain (6lvn), structure of post fusion core of 2019-nCoV S2 subunit (6lxt), prefusion 2019-nCoV spike glycoprotein (6vsb), structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2 (6vw1), crystal structure of NSP15 endoribonuclease from SARS CoV–2 (6vww) and crystal structure of the free enzyme of the SARS-CoV–2 (2019-nCoV) main protease (6y2e).
Due to technical limitations, Table 1 is provided in the Supplementary Files section.
In search of the answer for the second question, we selected 18 dietary molecules namely allicin, alliin, apigenin, beta-glucan, curcumin, diadzein, EGCG, ferullic acid, genistein, gingerol-[6], glucosamine, alpha-lipoic acid, myricetin, phycocyanobillin, piperine, quercetin, resveratrol andsulphoraphanethat are abundantly present in commonly used herbs, spices, fruits and vegetables. All the dietary moleculesexhibited either antiviral or anti-SARS-CoV activities as reported in previous studies (table 2).Recent studies revealed that some drugs like remdisivir, chloroquine, lopinavir and ritonavir could be repurposed and studied to treat COVID–19. All these dietary molecules as well as selected drugs remdisivir and chloroquine as control to verify and compare our results were docked against SARS-CoV–2 3CL homology model. Based on our docking analysis, we recommend that theligands with the highest binding affinity and lowest inhibition constant be considered for further investigation.
Due to technical limitations, Table2 is provided in the Supplementary Files section.
Among these dietary molecules, epigallocatechin gallate (EGCG) which is found abundantly in green tea, was found as most active agent against COVID–19. EGCG showed highest binding affinity (–9.30kcal/mole) and lowest inhibition constant (0.152µM) for 6y2e protein. Moreover, EGCG exhibited a strong molecular interaction with 6vw1 which is an important target of this new CoV. It showed highest binding affinity and lowest inhibition constant with –8.66 kcal/mole and 0.152µM values respectively. Further, EGCG displayed excellent interactions with 6vww wherein it showed highest binding affinity (–8.38 kcal/mole) with lowest inhibition constant at 0.724 µM concentration. Additionally, EGCG also exhibited good molecular interactions with SARS-CoV–2 proteins 6lu7, 6lvn, 6lxt, and 6vsb with the values of binding energies and inhibition constant as –6.99, –4.90, –7.57, –7.26 kcal/mole and 7.57, 255.95, 2.84, 4.75 µM concentrations. The computed activity of EGCG was found to be higher than that of both reference drugs, Remdesivir and Chloroquine. All docked poses are depicted in figure 1 and 2 which showstrong interactions of EGCG with selected protein residues.
It has been established that the molecules having hydroxyl (-OH) and carbonyl (C = O) functionalities showed strong intermolecular interactions with amino acid residues at active sites of proteins through physical forces such as hydrogen bonds and hydrophobic bonds. Due to amount and types of these intermolecular interactions, they show druggable and druglikeness properties. In this study, we also identified eight more active phytochemicals namely curcumin, apigenin, beta-glucan, myricetin, piperine, genistein, diadzein and quercetin. Apigenin, myricetin, and quercetin are flavonoids while genistein and diadzein are isoflavonoids. On the other hand curcumin and piperineare phenolic compounds whereas beta-glucan is a polymer of sugar. They all have hydroxyl (-OH) and carbonyl (C = O) functionalitiesin their core structures and hence exhibited strong molecular interaction with all protein macromolecules chosen under this study. All values of binding affinities and inhibition constant of these dietary molecules are listed in table 3.
Table 3: Molecular docking values of phytochemicals against target protein macromolecules
|
Phytochemicals |
Targets Proteins; binding energy in kcal/mole (inhibition constant in µM) |
|
|
|
||||
|
|
|
6lu7 |
6lvn |
6lxt |
6vsb |
6vw1 |
6vww |
6y2e |
|
1 |
EGCG |
-6.99 (7.57) |
-4.90 (255.95) |
-7.57 (2.84) |
-7.26 (4.75) |
-8.66 (0.451) |
-8.38 (0.724) |
-9.30 (0.152) |
|
2 |
Curcumin |
-6.04 (37.57) |
-4.73 (340.89) |
-5.50 (92.90) |
-5.05 (197.96) |
-7.13 (5.91) |
-7.37 (3.96) |
-7.39 (3.83) |
|
3 |
Apigenin |
-5.96 (43.03) |
-3.71 (1.9x10-5) |
-5.13 (1.74x10-5) |
-5.98 (4.1x10-5) |
-6.02 (38.69) |
-6.48 (17.86) |
-7.05 (6.76) |
|
4 |
Beta Glucan |
-5.96 (42.79) |
-4.16 (889.95) |
-5.06 (195.39) |
-3.20 (4.4x10-5) |
-6.44 (19.09) |
-6.72 (11.86) |
-7.05 (6.83) |
|
5 |
Myricetin |
-5.38 (114.10) |
-3.70 (1.96x10-5) |
-5.74 (62.01) |
-6.14 (31.32) |
-6.50 (17.16) |
-6.57 (15.20) |
-7.15 (5.79) |
|
6 |
Quercetin |
-5.29 (132.27) |
-3.68 (2.02x10-5) |
-5.73 (63.52) |
-6.14 (31.32) |
-6.59 (14.73) |
-6.53 (16.36) |
-6.77 (10.86) |
|
7 |
Piperine |
-5.16 (165.72) |
-4.08 (1.02x10-5) |
-5.40 (109.87) |
-6.05 (36.85) |
-5.64 (73.80) |
-6.18 (29.44) |
-6.40 (20.37) |
|
8 |
Genistein |
-5.03 (204.91) |
-3.97 (1.24x10-5) |
-5.68 (69.09) |
-6.54 (16.04) |
-6.35 (22.18) |
-6.73 (11.70 ) |
-6.80 (10.32) |
|
9 |
Diadzein |
-4.86 (275.53) |
-3.72 (1.89x10-5) |
-5.21 (151.77) |
-6.16 (30.34) |
-5.96 (42.54) |
-6.43 (19.50) |
-6.05 (36.86) |
|
10 |
Ferulic acid |
-4.76 (322.26) |
-2.79 (9.00x10-5) |
-3.75 (1.80 x10-5) |
-5.44 (103.05) |
-3.74 (1.8x10-5) |
-3.90 (1.3 x10-5) |
-4.71 (355.68) |
|
11 |
Alliin |
-4.66 (385.74) |
-3.90 (1.37x10-5) |
-5.02 (210.26) |
-4.57 (447.67) |
-5.15 (168.32) |
-4.07 (1.0 x10-5) |
-5.68 (68.09) |
|
12 |
Lipoic acid |
-4.58 (439.80) |
-1.90 (40.6x10-5) |
-3.25 (4.16x10-5) |
-4.93 (243.60) |
-2.73 (9.9x10-5) |
-3.38 (3.3 x10-5) |
-3.59 (2.3x10-5) |
|
13 |
Resveratrol |
-4.20 (832.91) |
-3.58 (2.38x10-5) |
-4.32 (685.04) |
-5.57 (82.09) |
-5.26 (138.32) |
-5.57 (83.02) |
-5.54 (86.98) |
|
14 |
Glucosamine |
-4.06 (1.06x10-5) |
-3.59 (2.32x10-5) |
-5.26 (138.93) |
-4.89 (262.36) |
-6.77 (10.89) |
-4.18 (862.43) |
-4.70 (359.49) |
|
15 |
Gingerol-[6] |
-4.00 (1.16) |
-2.23 (23.38) |
-3.08 (50.56) |
-4.46 (537.58) |
-4.60 (425.87) |
-4.57 (449.30) |
-5.30 (130.87) |
|
16 |
Sulforaphane |
-3.74 (1.81x10-5) |
-2.25 (22.3x10-5) |
-3.11 (5.22x10-5) |
-3.43 (3.0x10-5) |
-3.46 (2.9x10-5) |
-3.21 (4.4x10-5) |
-4.21 (815.35) |
|
17 |
Allicin |
-3.46 (2.89x10-5) |
-2.09 (29.4x10-5) |
-3.20 (4.49x10-5) |
-3.46 (2.92) |
-3.07 (5.6x10-5) |
-3.14 (5.0x10-5) |
-3.63 (2.1x10-5) |
|
18 |
PCB |
+0.16, (Nil) |
-3.12 (5.14x10-5) |
-4.63 (4.05x10-5) |
+11.3 (Nil) |
-3.59 (2.3x10-5) |
-6.14 (3.1x10-5) |
-5.15 (1.6x10-5) |
|
19 |
Remdesvir |
-2.47 (15.4x10-5) |
-2.68 (10.7x10-5) |
-4.84 (281.48) |
-4.27 (745.64) |
-5.27 (136.97) |
-5.10 (183.96) |
-5.47 (97.23) |
|
20 |
Chloroquine |
-3.62 (2.2x10-5) |
-3.26 (4.0x10-5) |
-4.35 (651.5) |
-4.79 (309.3) |
-6.41 (19.9) |
-4.85 (277.5) |
-6.10 (33.5) |
6lu7: Main protease of covid-19; 6lvn: Structure of the 2019-nCoV-HR2 Domain; 6lxt: Structure of post fusion core of 2019-nCoV S2 subunit; 6vsb: Prefusion 2019-nCoV spike glycoprotein; 6vw1: Structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2; 6vww: Crystal structure of NSP15 endoribonuclease from SARS CoV-2; 6y2e: Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease. Remdesvir and Chloroquine are used as standard drugs to compare our results; EGCG: Epigallocatechin gallate; PCB: Phycocyanobillin
From docking results as well as analysis of binding affinity with binding pockets within active sites of proteins, we prepared a decreasing order of their potency against SARS-CoV–2.
- Orderof activityagainst main protease (6lu7) of SARS-CoV–2is EGCG > curcumin > apigenin > beta-glucan > myricetin
- Order of activity against HR2 domain of spike glycoprotein (6lvn) of SARS-CoV–2is EGCG > curcumin > beta-glucan > piperine > genistein.
- Order of activity against chimeric receptor-binding domain of spike glycoprotein (6vw1) of SARS-CoV–2 is EGCG > curcumin > glucosamine > quercetin > myricetin.
- Order of activity against single receptor binding domain of spike glycoprotein (6vsb) of SARS-CoV–2 is EGCG > genistein > myricetin > quercetin > curcumin > diadzein
- Order of activity against NSP15 endoribonuclease (6vww) of SARS-CoV–2 is EGCG > curcumin > genistein > beta-glucan > myricetin
- Order of activity against post fusion core S2 subunit (6lxt) of SARS-CoV–2is EGCG > myricetin > quercetin > genistein > curcumin
- Order of activity against free enzyme of (6y2e) of SARS-CoV–2 main protease is EGCG > curcumin > apigenin > myricetin > beta-glucan
We, thus, found EGCG, curcumin, myricetin, genistein, myricetin, beta-glucan, quercetin and diadzein as recommended compounds for the treatment of COVID–19 (figure 3). Finally, as a result of our study, we have discovered EGCG as potent SARS-CoV–2 inhibitor which might be a drug candidate in future to treat this dreadful disease
Diet Suggestions
In light of current findings, intake of the suggested foods (Table 4) as supplements in adequate doses could be helpful to prevent and control COVID–19 infection by suppression of propagation and pathogenesis of SARS-CoV–2.Since green tea is a rich source of EGCG, it may have a major role in combating the SARS-CoV–2. Our careful and extensive analysis revealed that other promising molecules that can be easily available to us, might also be expected to suppress the pathogenicity of this coronavirus. It might be helpful to include the suggested food substances in the diet of COVID 19 patients and healthcare workers to control and avoid the infection. Doing so may also prevent secondary infections, since these compounds have previously been reported to have antimicrobial activity. Hence, these dietary suggestions may also be implemented in case of influenza and common flu.
Table 4: Daily dose based diet suggestion for prevention and treatment of COVID-19
|
Dietary Molecules (DM) |
Recommen- dedDaily Intake |
Amount of DM present in Food Source (per 100g) |
Suggested Dose of Food Source Per Day (gm) |
t1/2(h) |
Suggested Frequency |
Suggested Preparation |
|
EGCG |
800 mg |
7.38 gin Green Tea |
16.67* |
4.5 |
3-4 times a day after every 4.5 h |
Brewed for 3 minutes in boiling water |
|
Curcumin |
500 mg |
3.2 gin Turmeric |
15.625 |
6-7 |
3 times a day every 6.5 h |
Mix with lukewarm milk |
|
Apigenin |
3-10 mg |
1.2 gin Chamomile Tea |
1.08** |
12 |
2 times a day every 12 h |
Brewed for 5-10 minutes in boiling water |
|
300 mg in Parsley |
2.16 |
|||||
|
Beta Glucan |
3-10 g |
5.5 g in Whole Grain Oats# |
118.18 |
19.5- 27.3 |
Once a day |
Boil in water or milk |
|
11 g in Whole Grain Barley## |
59 |
#average based on range 3-8%; ##average based on range 2-20%; *assuming 65% yield; **assuming 50% yield. All values of dietary molecules are taken from USDA databases ( https://doi.org/10.15482/USDA.ADC/1178142)
Juha
commented on 30 March, 2020
I appreciate your approach. Traditional chinese medicines contains several plant derived compounds capable blocking the entry of CoV into the cells. FDA approval would be the key hurdle to get these medicines to the people in need urgently.
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Dr M Faheem Khan
replied on 05 April, 2020
Thanks for your valuable appreciation
Ron Brightmore
commented on 02 April, 2020
An excellent article. Have you seen the product Capsol-T which combines EGCG and capsaicin in a highly synergistic mixture? [researched by DR James Morre]. EGCG has also been shown to inhibit furin, inhibit the transport of furin to the cell membrane by a HIF-1 mechanism, potentially inhibit the thiol/disulide mechanism vital for COVID-19 spike entry and fusion, also inhibit caspase 1 which activates IL-1B cascade which has been managed by the COVID-19 E protein and inhibit angiotensin 2 which is set free by the COVI-19 interaction with ACE2 [angiotensin 2 will also activate IL-1B and the inflammatory cytokine cascade that attacks the lung cells. As you can see, I am very interested in the potential use of RGCG re this virus and see a potential for a combination in the use of Capsol-T, hydrocloroquine and curcumun, Hydrocchloroquine will act to inhibit the alternative entry mechanism via the endosomes and curcumin acts in a similar way to EGCG in inhibiting angiotensin 2 and activating NRF2 which controls the balance between proteases and antiproteases. I am sorry for that rush of ideas but I am very excited by your article. I can send you copies of e-mails that discuss all the above if you are interested. Thank you for your research Ron
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Dr M Faheem Khan
replied on 05 April, 2020
Thank you so much for appreciation and to give your valuable suggestions. Thanks are also due to providing us a details of other molecules having synergistic effect with EGCG. We will be happy if you share copies of your mails as per discussed by you.
Martha Whitehill
replied on 29 December, 2020
Second doorway (besides ACE2) is DPP4. Furin cleaves the toxin, PRRA (proline, arginine, arginine - THOSE 3 are FROM GLUTAMATE - AND alanine FROM PYRUVATE) between the two "R's" between 'SPIKES" S1 and S2. Furin was found to be involved in the posttranslational cleavage of syncytin 1 and 2... then demethylated? Look very closely at TUDCA also - very helpful from many respects.. The Chinese recommend UDCA, but conjugating taurine onto that bile salt helps it cross the "blood brain barrier'. Syncytium formation by SARS-CoV-2 is many times faster than in the 2002 SARS-CoV, and syncytium formation is highly responsible for the virulence factor and induction of a cytokine storm of any virus in general and SARS-CoV-2 especially (Matsuyama et al., 2020; Xia et al., 2020).
Zaw Ali Khan
commented on 05 April, 2020
Thank for your suggestions and encouragement. We'd be interested in reading more about this.
Michio Jibiki
commented on 05 April, 2020
I appreciate your screening approach. Japanese green tea is unfermented tea. Therefore, it contains cathecin components a lot. I believed that EGCG is effective for inactivate virus at the upper respiratory tract part due to its feature of easy binding to proteins and early coverage of infectious spikes.
Wasif Raza
commented on 06 April, 2020
A great research which could bring about a breakthrough amidst this fulminant pandemic. However, as agreed, more research is needed to establish a guideline. Best wishes.
Djoko Agus Purwanto
commented on 06 April, 2020
I really appreciate to this research. Compared to the chloroquine, EGCG is known as a non-toxic compound and has been used in daily drinks for hundreds of years. Therefore EGCG is not only used for the treatment of COVID-19 but also prevention. What is the dose of EGCG needed by adults to prevent corona infection?? Thank you so much for your attention.
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Tham
replied on 23 July, 2020
Try 400 ng twice a day. Combine with Daflon, two tablets daily.
Tukaram Pandharipande
commented on 12 April, 2020
The findings are very interesting and looks promising in the current situation of Covid19. However, the article do not have information about the grade or specification of EGCG and Curcumin used in the investigations. I request if you can send me some information about the grades/ specifications of EGCG and Curcumin used in the investigations.
Greg
commented on 17 April, 2020
EGCG is also a zinc ionophore like Quercetin and chloroquine analogues. Zinc gluconate, as a lozenge/powder ever 4 hours 15mg, should be combined with EGCG /Quercetin for maximal effect. Many modes of action, combination therapies usually more effective than single molecule interventions.
Hiroyuki Shibata
commented on 02 May, 2020
Thank you Drs. It's a very encouraging data. I know the death rate in India is 0.83/ 1,000,000 peoples, while in Italy, 462.56/1,000,000. We have developed new curcumin analogs, such as GO-Y030 and GO-Y022, published elsewhere. They have more potent activities. We want to check the possibility of them. GO-Y022 is a natural ingredient. Best regards.
Germán Gutierrez
commented on 28 May, 2020
Thank you the EGCG ACE2 interaction and zinc plus vitamin d. Sinergies with cafein
Martha Whitehill
commented on 19 October, 2020
COVID-19's main protease is a cysteine protease called 3CL or Mpro = Nsp#5 and is*inhibited by* Baicalin or the drug ebselen. TUDCA (taurine conjugated bile salt) also can help as it shares 2 actions similar to Baicalin - decreases inflammation and activates Nfr2. Not surprising GABAA receptors are involved. JSTX-3 (= a spider toxin shares an amino acid sequences with COVID-19) blocks specific glutamate receptors. I believe the horseshoe bat eats the Jaro spider (golden orb) that has a venom with a toxin that shares an amino acid sequence in COVID-19. The toxin/virus is transferred to the horseshoe bat and the virus is excreted in the guano. The reason why persons given antibodies fail to recover is because the neuro toxin has to be addressed. The toxin target is NaV1.7 and is linked to the loss of the sense of smell.
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MOHD FAHEEM KHAN
replied on 12 November, 2020
Thanks a lot "Martha Whitehill", your information is very much useful for us.
Dr M Faheem Khan
replied on 05 April, 2020
Thanks for your valuable appreciation