Identification of Dietary Molecules as Therapeutic Agents to Combat COVID-19 Using Molecular Docking Studies CURRENT

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. 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


Introduction
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has emerged as a virus ofgrave concern due to its ability to cause the severe and life-threatening diseasecalledcoronavirus disease 2019 (COVID- 19) with high mortality rate worldwide [1]. World Health Organization (WHO) declared COVID-19 as a pandemic disease on 11 March 2020 [2]. As per "situation report-63"released by WHO on 23 March 2020, more than300,000 cases and 14510deaths have been confirmed globally.ByJanuary 12, 2020 the Chinese authorities had released the whole genome sequence of SARS-CoV-2 which has been hallmark for researchers worldwide to quickly identify and develop the potential candidates by using computational methods and other therapeutic techniques [3]. First publication along with other recent studies on current outbreak revealed that SARS-CoV-2 is a member of the coronavirus family and shared 96% similarity with previously identified genome of SARS-CoV that had emerged in China in November, 2002 [4].
Based on recent studies, this virus has a complex genomic organization consisting of single strandedpositive sense RNA which codes for several structural and non-structural proteins (nsps) including envelope protein (E) gene, spike protein (S) gene, membrane protein (M) gene, nucleocapsid protein (N) gene, replicase complex (orf1ab) gene along with 3' and 5'-untranslated region (UTR) [5,6]. As per study carried out by K. Anand et al. in 2003, coronaviruses make small polypeptide chains during transcription by proteolytic enzymes such as papain-like protease (PLpro) and 3-chymotrypsin-like protease (3CL pro ) to form several types of non-structural proteins which are responsible for viral replication [7]. Additionally, unique spike protein (S) has also been found to have a strong affinity with the human ACE2 receptor [8]. Thus, both main protease and spike protein complexed with human ACE2 receptor might be important targets to discover and develop vaccines and other therapeutic agents to control this new CoV.
Since the first reported case of COVID 19 on 31 December 2019, no specific medication is available to prevent or kill the SARS-CoV-2 so far. Preliminary treatment of COVID-19 depends upon the severity of infection which ranges from mild to strong including, if necessary administration of oxygen, maintaining the body fluids and administration of antibiotics and antiviral drugs to combat coinfections because of numerous types of bacteria and virus [9]. Recent studies suggested the use of remdisivir and chloroquine along with HIV-1 protease inhibitors like lopinavir and ritonavir as therapeutic agents for the treatment of COVID-19 [10]. Moreover, Xu et al. identified four tested drugs nelfinavir, praziquantel, perampanel and pitavestatin as potential candidates against SARS-CoV-2 using computational methods. Therefore, three approaches need to be urgently pursued, namely vaccines, post exposure prophylaxis and therapeutic agents that target virus-encoded functions, replication, infection as well as the respiratory symptoms in humans that exacerbate the disease.
In the last decade, dietary moleculesfrom edible herbs and vegetables have ofgreat interest amongresearchers worldwide because of their diversified and complex structures having health benefits with no or minimal side-effects [11]. These dietary molecules may be developed as herbal medicines or therapeutic agents in the prevention and treatment of current COVID-19 disease. In previous studies, numerous dietary molecules such as curcumin, savinin and betulinic acid have been found to show inhibition of SARS-CoV in the range of 3-10 μM concentrations [12]. Recently, kaempferol, quercetin, luteolin-7-glucoside, demethoxycurcumin, naringenin, apigenin-7-glucoside, oleuropein, curcumin, catechin, and epicatechin-gallate have been identified as significant anti-COVID-19 agents with the help of molecular docking study [13]. Seeing this terrible and deadly crisis, as yet, it is urgent and timely need to evaluate and develop more potent and reliable anti-COVID-19agents which are easy to reach us. In this study, we evaluated 18 dietary moleculesnamely epigallocatechin gallate (EGCG), piperine, apigenin, curcumin, gingerol- [6], beta glucan, resveratrol, myricetin, quercetin, genistein, diadzein, alliin, allicin, sulphoraphane, phycocyanobillin, ferulic acid and alpha lipoic acid by using molecular docking study. Our findings will provide valuable information to explore and develop dietary moleculesas novel anti-COVID-19 agents in the future.

Material And Methods
To obtain molecular interactions of selected dietary molecules with the binding pockets of different types of proteins of COVID-19, molecular docking analysis was carried out by using computer cluster system provided by Gigabyte Technology co., LTD, model-B365M DS3H running Intel Core i5-9400F CPU @2.90GHz Processor, 16 GB RAM, 1TB hard disk, and Intel HD Graphic card. The crystal structures of seven types of newly released proteins of COVID-19 were retrieved from protein data bank (PDB) site whose PDB IDs were 6lu7, 6lvn, 6lxt, 6vsb, 6vw1, 6vww and 6y2e.Prior to docking study, the retrieval of target protein binding sites was necessary to find the best docking result.
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 (-  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)   exhibited the strongest molecular interactions within pockets at active sites of all the proteins of SARS-CoV-2 which were taken under this study. EGCG was also far more active than the standard drugs remdesvir and chloroquine. Therefore, in our study we suggest EGCG as a potential inhibitor of SARS-CoV-2. However, further research is needed to investigate the mechanism and mode of action of these phytochemicals in future.

Conflict of interests
The author(s) declared no conflict of interest

Supplementary Files
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