WO2021229609A1 - Composition and method for prevention and treatment of conditions caused by sars-cov-2 (covid-19) - Google Patents

Abstract

The present invention relates to a composition and method for prevention and treatment of viral infection caused by SARS-CoV-2 (COVID-19) in humans. In particular, the present invention relates to a composition comprising omega-3 fatty acids Alpha-Linoleic Acid (ALA), Eicosapentaenoic Acid (EPA) or combinations thereof for the prevention and treatment of a symptom or condition associated with viral infection caused by SARS-CoV-2 (COVID-19) in humans. Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) are found to interfere with normal functions of SARS-CoV-2 proteins, Main protease, ADP ribose phosphatase and RNA dependent RNA polymerase, and inhibit the interactions of its spike protein with host ACE2 receptors, which are crucial for the establishment of infection. These omega-3 fatty acids also induces the host-directed response and acts as anti-inflammatory agents.

Description

TITLE OF THE INVENTION

Composition and Method for Prevention and Treatment of Conditions Caused by SARS- CoV-2 (COVID-19)

TECHNICAL FIELD

The present invention relates to a composition and method for prevention and treatment of symptoms and conditions associated with viral infection caused by SARS-CoV-2 (COVID- 19).

BACKGROUND ART

The entire globe is affected by pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome) virus, also known as COVID-19. Coronaviruses are a group of positive-sense single-strand RNA viruses in the family Coronaviridae in the order Nidovirales. Examples of coronaviruses include SARS-CoV [causing Severe Acute Respiratory Syndrome (SARS)], MERS-CoV [Middle East Respiratory Syndrome (MERS)], also sometimes called camel flu. Coronaviruses can cause a wide range of disease in both humans and animals, including the common cold. In some cases, coronavirus infection can be more severe. COVID-19 can have a long incubation period before symptoms appear, and the incubation period typically ranges between 1 to 14 days, but has been reported to be up to 27 days. The fatality rate of COVID- 19 varies by geographical location and age of the subject, but on average, it has been reported to be about 2% to about 3% with higher fatalities reported in older age groups. Currently, there are no approved specific therapies or drugs for COVID-19.

The genome of SARS-COV-2 is a polyadenylated positive strand RNA,~30 Kb in length, consisting of 12 ORF’s, coding for structural (spike, membrane and envelope) proteins, non- structural proteins and viral RNA-dependent RNA polymerase (RDRP) (Coronaviridae Study Group of the International Committee on Taxonomy of 2020).

Genomic and functional analysis of SARS-CoV-2 of 250+ genomes have highlighted the emergence of distinct clusters worldwide since the initial outbreak in Wuhan, China (Sheikh JA 2020). In the context of Indian sub-continent, analysis of 25 isolates sequenced in India and upon a comparison of 3500+ global strains, placed Indian isolates into three distinct clusters (Singh H 2020). Qualitative analysis of mutations in each ORF’s revealed that each type of amino acid had undergone mutations globally. At the same time, in Indian isolates, some of ORFs are conserved compared to first Wuhan-Hu-1 strain. The viral-host in humans (ACE2 receptor) interactions are initiated through spike protein of SARS-COV-2 followed by viral entry mediated by its S2 domain (Andersen, Rambaut et al. 2020). Post-endocytosis, viral RNA is released into cytoplasm followed by natural life cycle as observed in other coronaviruses (Weiss and Navas-Martin 2005). In the absence of specific drug against COVID-19, much of the research efforts are exploiting drug repurposing to treat infections. Remedesvir and combination of Hydroxychloroquine and azithromycin are one of the first US FDA approved drugs which are being clinically tested in COVID-19 affected patients (Cao, Deng et al. 2020, Gautret, Lagier et al. 2020, Grein, Ohmagari et al. 2020). In a total of 639 direct interventional clinical studies against COVID-19, 44 are in their phase-4 clinical trials worldwide (Source: clinicaltrials.gov/). Most of these studies involve the use of previously established anti-virals or their combination with other antibiotics. Some of the examples include Favipiravir, Lopinavir / Ritonavir, Sargramostim, Lenalidomide, Carrimycin, ACE inhibitors and their combinations with Hydroxychloroquine and azithromycin. Lack of sufficient evidence on toxicity or side effects in already infected COVID-19 patients poses a direct need for safer and equipotent alternatives in disease mitigation.

The COVID-19 pandemic may last for several more years in the absence of an effective vaccine(s) or therapeutic agent. Owing to the fact that any new drug or compound for prevention or treatment of a disease takes years in trials and approvals before reaching market, and since there is an urgency owing to the pandemic, the efforts are to find existing pharmaceuticals and nutraceuticals which may be effective against COVID-19. Particularly, any FDA approved nutraceutical, if found effective against the COVID-19, is likely to be most suitable candidate in the fight against the current pandemic. Therefore, since its outbreak, many studies have been undertaken to identify potential anti-viral agents while others have reviewed possible use of FDA approved and investigational agents against SARS-CoV-2 (Xue, Yu et al. 2008, Ciavarella, Motta et al. 2020, Jin, Zhao et al. 2020, Panda, Arul et al. 2020, Wang, Yang et al. 2020, Yin, Mao et al. 2020). In this direction, nutraceuticals could be a viable option due to their range of host-directed responses and better therapeutic to safety indices.

The present invention aims to obviate the problems associated with the prior art by providing a composition of nutraceuticals which is effective in prevention and treatment of symptoms and conditions associated with viral infection caused by SARS-CoV-2 (COVID-19). OBJECTS OF THE INVENTION

The main object of the present invention is to provide a composition for prevention and treatment of the symptoms and conditions caused by COVID-19 in humans.

Another object of the present invention is to provide a composition for prevention and treatment of the symptoms and conditions caused by COVID-19 in humans wherein the composition preferably contains compound(s) or nutraceutical(s) which are known and already approved for consumption or administration by regulators such as USFDA.

Yet another object of the present invention is to provide a composition for prevention and treatment of the symptoms and conditions caused by COVID-19 in humans wherein the composition inhibits the transmission, progression, proliferation and replication of COVID-19 virus in the host cells without causing any damage, temporary or permanent, to the host cells.

Another object of the present invention is to provide a composition for prevention and treatment of the symptoms and conditions caused by COVID-19 in humans wherein the composition also induces host-directed response to COVID-19.

Still another object of the present invention is to provide a method for prevention and treatment of the symptoms and conditions caused by COVID-19 in humans wherein the method involves administration of a composition which contains compound(s) or nutraceutical(s) which are known and already approved for consumption or administration by regulators such as USFDA.

The other objects, preferred embodiments and advantages of the present invention will become more apparent from the following detailed description of the present invention when read in conjunction with the accompanying claims, examples, figures and tables, which are not intended to limit scope of the present invention in any manner.

SUMMARY OF THE INVENTION

The present invention provides a composition comprising a pharmaceutically effective amount of omega-3 fatty acid selected from the group consisting of Alpha-Linoleic Acid (ALA), Eicosapentaenoic Acid (EPA) and combinations thereof, wherein the composition inhibits the transmission, replication, progression or proliferation of SARS-CoV-2 (COVID-19) virus in a host cell. The composition, when administered in pharmaceutically effective dosage into a subject, inhibits the interaction between SARS-CoV-2 (COVID-19) and host cells in the subject.

The present invention further provides a composition for use in the treatment or prevention of a symptom or condition associated with viral infection caused by SARS-CoV-2 (COVID-19), the composition comprising a pharmaceutically effective amount of omega-3 fatty acid selected from the group consisting of Alpha-Linoleic Acid (ALA), Eicosapentaenoic Acid (EPA) and combinations thereof. The composition, when administered in pharmaceutically effective dosage into a healthy subject, prevents or reduces the chances of infection of SARS- CoV-2 (COVID-19) by inhibiting the interaction between SARS-CoV-2 (COVID-19) and host cells in the subject. Further, the composition, when administered in pharmaceutically effective dosage into a subject infected with SARS-CoV-2 (COVID-19) and in the need of treatment, prevents transmission, replication, progression or proliferation of virus inside the subject by inhibiting the interaction between SARS-CoV-2 (COVID-19) and the host cells of the subject.

The present invention provides use of the composition comprising a pharmaceutically effective amount of omega-3 fatty acid selected from the group consisting of Alpha-Linoleic Acid (ALA), Eicosapentaenoic Acid (EPA) and combinations thereof to prevent or treat a symptom or condition associated with viral infection caused by SARS-CoV-2 (COVID-19) in humans.

The present invention also provides a method for treating a symptom or disorder associated with SARS-CoV-2 (COVID-19) in a subject, the method comprising the step of administering into the subject a composition comprising a pharmaceutically effective amount of omega-3 fatty acid selected from the group consisting of Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) and combinations thereof in a pharmaceutically effective dose. The dose is sufficient to inhibit the interaction between SARS-CoV-2 (COVID-19) and host cells in the subject.

BRIEF DESCRIPTION OF DRAWINGS

Figure 1. Mechanism of anti -viral effects exerted by Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) by direct interference with viral proliferation inside the host or by modulating host-directed responses. Figure 2. Schematic of nutraceutical collection screening against essential proteome of SARS-CoV-2.

(A) Initiation of host-viral contact and life cycle of SARS-CoV-2. Host-viral contacts are established through interactions of Receptor Binding Domains (RBDs) of S protein (Cyan) with host ACE2 receptor (Grey). Post-interactions the S protein mediates endocytosis of virus followed by release of genomic RNA and expression of polyproteins ppla and pplab. These further encode SARS-CoV-2 main protease (Mpro), RNA dependent RNA polymerase (RDRP) and ADP ribose phosphatase (ADRP) subunit of nsp3 which propagate viral infection inside hosts. Protein targets in current invention are highlighted as red.

(B) Virtual screening workflow for identification of potential viral inhibitory nutraceutical candidates. Structural representation of ADP ribose phosphatase subunit of nsp3 of SARS- CoV-2. Orange circle shows where ALA (Blue) and EPA (Yellow) are bound at ADP (Green) binding site. Zoomed-in image shows binding of ALA and EPA at the same site where ADP is bound. A Protein-ligand interaction map of EPA. Protein-ligand interaction map of ALA. The blue circles show ligand exposure points. Dotted arrows at carboxyl end show H-bond formation.

Figure 3. MD simulations and MM-PBSA analysis of ACE2-ligand complexes. (A-C) Variations in Ca-RMSD, Rg and Ligand RMSD for simulations of ACE2 alone (Black) and in presence of ALA (Red) and icosapent (Blue). (D) Free energy terms obtained from MM-PBSA calculations of four nutraceuticals, averaged over last 5 ns of respective simulations. (E) Protein-ligand interaction map extracted from ACE2 (Grey) bound ligands at defined screening site. 3D orientation of protein residues (grey sticks) with ALA (red), icosapent (blue) are showed as individual zoomed sub-panels. Blue lines represent H-bonds, Yellow lines as salt- bridges and dashed grey lines represent hydrophobic interactions.

Figure 4. ACE2-RBD interface interaction analysis from simulation outcomes. (A) Post simulation analysis of frequency of ACE2 (Grey)-RBD (Cyan) contacts in the presence ligands when bound only in the ACE2 cavity. (B) Global energy scoring obtained through FireDock analysis of ACE2-RBD complexes (where ligands were bound in ACE2 cavity), extracted at end of respective simulations. AttVdW: attractive Van der Waals, RepVdW: repulsive Van der Waals, ACE: atomic contact energy and HB: H-bond interaction energy. (C) Post simulation analysis of frequency of ACE2-RBD contacts in the presence ligands when bound at ACE2- RBD interface. (D) Global energy scoring obtained through FireDock analysis of ACE2-RBD complexes (where ligands were bound at ACE2-RBD interface), extracted at end of respective simulations. AttVdW: attractive Van der Waals, RepVdW: repulsive Van der Waals, ACE: atomic contact energy and HB: H-bond interaction energy. Contact frequency analysis and post simulation energy scoring shows potential of compounds to modulate ACE2-RBD interface.

Figure 5. MD simulations and MM-PBSA analysis of Mpro-ligand complexes. (A-C) Variations in Ca-RMSD, Rg and Ligand RMSD for simulations of Mpro alone (Black) and in presence of ALA (Red), icosapent (Blue), ankaflavin (pink) and monascin (green). (D) Free energy terms obtained from MM-PBSA calculations of four nutraceuticals and X77 inhibitor, averaged over last 5 ns of respective simulations. (E) Protein-ligand interaction map extracted from Mpro (Grey) bound ligands at defined screening site. 3D orientation of protein residues (grey sticks) with ALA (red), icosapent (blue) and a known inhibitor X77 (light purple) are showed as individual zoomed sub-panels. Blue lines represent H-bonds, Yellow lines as salt- bridges and dashed grey lines represent hydrophobic interactions.

Figure 6. MD simulations and MM-PBSA analysis of ADRP-ligand complexes. (A-C) Variations in Ca-RMSD, Rg and Ligand RMSD for simulations of ADPR (NCBI Accession No. QHD43415) alone (Black) and in presence of ALA (Red), icosapent (Blue) (D) Free energy terms obtained from MM-PBSA calculations of four nutraceuticals and its substrate, averaged over last 5 ns of respective simulations. (E) Protein-ligand interaction map extracted from ADPR (Grey) bound ligands at defined screening site. 3D orientation of protein residues (grey sticks) with ALA (red), icosapent (blue) and its substrate ADPr (light purple) are showed as individual zoomed sub-panels. Blue lines represent H-bonds, Yellow lines as salt-bridges and dashed grey lines represent hydrophobic interactions.

Figure 7. MD simulations and MM-PBSA analysis of E-protein pentamer-ligand complexes. (A-C) Variations in Ca-RMSD, Rg and Ligand RMSD for simulations of E-protein alone (Black) and in presence of ALA (Red), icosapent (Blue) and previously known inhibitor of closely related SARS-CoV E-protein pentamer (light purple). (D) Free energy terms obtained from MM-PBSA calculations of two nutraceuticals and a known inhibitor HMA, averaged over last 5 ns of respective simulations. (E) Protein-ligand interaction map extracted from E-protein (Grey) bound ligands at defined screening site. 3D orientation of protein residues (grey sticks) with ALA (red), icosapent (blue) and its inhibitor (light purple) are showed as individual zoomed sub-panels. Blue lines represent H-bonds, Yellow lines as salt- bridges and dashed grey lines represent hydrophobic interactions. Figure 8. MD simulations and MM-PBSA analysis of RDRP-ligand complexes. (A-C) Variations in Ca-RMSD, Rg and Ligand RMSD for simulations of RNA dependent RNA polymerase alone (Black) and in presence of ALA (Red), icosapent (Blue) and its known inhibitor remsdesivir (light purple). (D) Free energy terms obtained from MM-PBSA calculations of two nutraceuticals and remdesivir, averaged over last 5 ns of respective simulations. (E) Protein-ligand interaction map extracted from RDRP (Grey) bound ligands at defined screening site. 3D orientation of protein residues (grey sticks) with ALA (red), icosapent (blue) and remdesivir (Rem) (light purple) are showed as individual zoomed sub panels. Blue lines represent H-bonds, Yellow lines as salt-bridges and dashed grey lines represent hydrophobic interactions.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a composition and method for prevention and treatment of viral infection caused by SARS-CoV-2 (COVID-19).

The initial establishment of COVID-19 infection in a host requires protein-protein interactions (PPIs) between spike protein of SARS-CoV-2 and ACE2 receptor of hosts. Similar interactions were responsible for establishing infection of SARS-CoV and MERS-CoV epidemics and in viruses causing the common cold. It was found by the inventors of the present invention that by harnessing crucial interactions via available crystal structure of SARS-CoV-2 spike and ACE2 complex, it is possible to break the essential protein-protein interactions (PPIs). This is similarly applicable for other proteins such as main protease (Mpro), RDRP, ADP ribose phosphatase subunit of nsp3 which are crucial for the establishment of viral infection and propagation. Considering the crucial role of these proteins in the establishment of infection and viral progression, inventors adopted an extensive drug repositioning approach using more than 100 nutraceuticals from PubChem library (https://pubchem.ncbi.nlm.nih.gOv/T Selection of nutraceuticals was primarily based on two criteria: (i) Compounds that can directly interfere with normal functioning of target proteins in SARS-CoV-2, and (ii) Compounds may act on host directed therapeutics based on previously known history in related viral infections such as SARS-CoV, MERS-CoV and HCoV-229E.

Inventors screened approved/investigational nutraceuticals against structural and replication machinery components of SARS-CoV-2, which can potentially interfere with establishing early viral-host contacts and later its propagation inside hosts. Using a multi-layered screening and clustering protocol and after repeated screening runs inventors identified two essential omega-3 fatty acids - Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA). The binding of fatty acids were mediated only through polar carboxyl end while non-polar carbon chains participated in hydrophobic interactions with receptors. EPA has been shown to inhibit degradation of arachidonic acid to the thromboxane-2 and prostaglandin-2 families by preferentially binding to catalytic subunit of prostaglandin endoperoxide H synthase (Malkowski, Thuresson et al. 2001, Dong, Zou et al. 2016). ALA, however, competes for the linoleic acid binding site in D5, D6 desaturases which mediate conversion of linoleic acid (LA) to arachidonic acid (AA) (Balendiran, Schnutgen et al. 2000, Simonetto, Infante et al. 2019). Recent literature points towards role of essential fatty acids in mediating host lipid responses against coronavirus infections. Host lipidomics profiling on HCoV-229E coronavirus revealed perturbation of LA and AA metabolism axis in infected cells. Reverse supplementation of LA/AA to infected cells was observed to interfere with replication of HCoV-229E and also MERS-CoV (Yan, Chu et al. 2019). Inventors found that modulation of host lipid responses in SARS-CoV-2 infections acts as potential therapeutic strategy, and in this regard, both ALA and EPA act as modulators of LA-AA metabolism axis to stall viral replication and disease progression. ALA, being preferred substrate over LA for desaturases, directly interferes with SARS-CoV-2 replication in hosts. On the other hand, EPA mediated inhibition of AA conversion into the prostaglandin-2 and thromboxane-2 leads to balanced AA levels, thereby supressing viral replication (Malkowski, Thuresson et al. 2001, Dong, Zou et al. 2016).

Eicosapentaenoic Acid (EPA) or Icosapent has been shown to inhibit degradation of arachidonic acid to the thromboxane-2 and prostaglandin-2 families by preferentially binding to catalytic subunit of prostaglandin endoperoxide H synthase (Malkowski, Thuresson et al. 2001, Dong, Zou et al. 2016). Alpha-Linoleic Acid (ALA), however, competes for the linoleic acid binding site in D5, D6 desaturases which mediates conversion of linoleic acid (LA) to arachidonic acid (AA) (Balendiran, Schnutgen et al. 2000, Simonetto, Infante et al. 2019). Recently, it was observed that during MERS-CoV (Middle East Respiratory Syndrome) and HCoV 229E coronavirus infections, lipidomic pathways involving Linoleic to arachidonic acid metabolism was perturbed along with increased production of AA (Yan, Chu et al. 2019). The study also showed reduction in viral replication of both strains by exogenous supplementation of arachidonic acid, possibly by feedback inhibition of arachidonic acid on conversion from linoleic acid. This suggests that linoleic to arachidonic acid pathway is essential for viral replication. Based on previous anti-viral profiles of these fatty acids, the inventors surprisingly found that ALA and EPA are high affinity nutraceuticals which interferes with establishment of SARS-CoV-2 infection and its replication, by direct interference of function of target proteins or as host directed response by interfering with essential linoleic-arachidonic acid pathway. These nutraceuticals prevent transmission, progression and proliferation of the virus and acts as adjunct therapy in controlling COVID-19 infections.

Accordingly, it has been found that two essential omega-3 fatty acids inhibit interaction between SARS-CoV-2 spike protein and host ACE2 receptors. Further, the inventors also found that same fatty acids possess tendency to simultaneously interfere with other target proteins of SARS-CoV-2 and inhibit its replication and proliferation inside hosts. In accordance with one of the most preferred embodiment of the present invention, it is provided that:

1. Two essential omega-3 fatty acids - Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) inhibits interaction between SARS-CoV-2 (COVID-19) and hosts cells of humans. The Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) have prophylactic effect and prevents transmission of the SARS-CoV-2 (COVID-19) to a healthy host. Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) also have therapeutic effect and cures a subject infected with SARS-CoV-2 (COVID-19) by inhibiting replication, progression and proliferation of the virus inside the host cells.

2. A composition comprising the aforementioned omega-3 fatty acids Alpha-Linoleic Acid (ALA) or Eicosapentaenoic Acid (EPA) or combination thereof in a pharmaceutically effective amount is useful to inhibit COVID-19 infection and proliferation in a subject.

3. Method for treating COVID-19, which comprises the step of administering the composition comprising the omega-3 fatty acids Alpha-Linoleic Acid (ALA) or Eicosapentaenoic Acid (EPA) or combination thereof in a pharmaceutically effective amount in a dose sufficient to inhibit interaction between SARS-CoV-2 and host cells.

4. Use of omega-3 fatty acids Alpha-Linoleic Acid (ALA) or Eicosapentaenoic Acid (EPA) for treatment of COVID-19 in human hosts. Methodology

Virtual Screening

An In-house manually curated nutraceutical library was prepared using NCGC Pharmaceutical Collection database (Huang, Southall et al. 2011). Three separate virtual screens were run for each protein target with a flexible docking approach. One screen involved Autodock Vina scoring (Trott and Olson 2010) while other two screens involved PLANTS based PLANTSCHEMPLP and PLANTSPLP scoring methods (Korb, Stutzle et al. 2009). For Vina, exhaustiveness level was set to 12 in all screens. In PLANTS based screens, search speed was set to 1 along with cluster RMSD of 2.

Binding sites for screening

To identify interaction sites of ACE2 with spike protein (PDBid: 6m0j), the interface was first analysed using PDBPisa followed by identification of potential binding sites using AutoSite program of AGFR (Ravindranath, Forli et al. 2015). For SARS-CoV-2 3CL protease (PDB id: 6w63; NCBI Accession No. QHD43415 5), coordinates of a pre-bound inhibitor (X77) was used as docking site. For ADP ribose phosphatase subunit of nsp3, its ADP ribose (ADPr) binding pocket was used and for RDRP, remdesivir binding was used (PDB id: 7bv2). Full length model of SARS-CoV-2 E-protein was modelled with swiss-modelling server using pentameric ion channel homolog from SARS-CoV (PDB id: 5x29). Binding site radius of 7A was used for all dockings. Global ranking was done on the basis of number of docking hits in each run.

Selection of candidates

Top 10 candidates were selected on the basis of global clustering averaged using individual screening outcomes. These were classified into three different categories. Nutraceuticals which appeared in top 20 solutions in each docking run followed by compounds which appeared in consecutively lesser number of runs.

Molecular dynamics simulations of protein-ligand complexes

Molecular dynamics simulations of protein-ligand complexes were carried for 20 ns using Gromacs v2018.1 and charmm36-2019 all-atom force field (Van Der Spoel, Lindahl et al. 2005, Huang and MacKerell 2013). Ligand topologies were generated using SwissParam (Zoete, Cuendet et al. 2011). Periodic box containing ligand bound protein complexes were solvated using SPC/E water model at 0.1 M ionic concentration. Systems were minimized using steepest decent algorithm followed by equilibration run of 500 ps in NVT and NPT ensemble with restrains on the protein and ligand atoms. All systems were simulated at 310 K maintained by a Berendsen thermostat with a time constant of 1 ps. Pressure coupling was done employing a Parrinello-Rahman barostat using a 1 bar reference pressure and a time constant of 2.0 ps with compressibility of 4.5e^-5 bar using isotropic scaling scheme.

Trajectory analysis was done using in-built GROMACS tools. Images were created using PyMol. Lastly, polar and nonpolar solvation energies and binding energy of the protein- ligand complexes were calculated using MM-PBSA free energy calculations averaged over last 5 ns of individual trajectories (Kumari, Kumar et al. 2014). The general expression for binding free energy of protein and ligand in solvent system can be expressed by following terms:

D Gbinding ^— Gcomplex ^— (Gprotein t Gligand) where G_COmpiex : Total free energy of the protein-ligand complex Total free energies of isolated protein and ligand in solvent, respectively

Gx = (EMM) - TS + (G_soivation) where x: protein/ligand/protein-ligand

(E_MM): the average molecular mechanics potential energy in a vacuum.

TS: Entropic contribution to the free energy in a vacuum, T is temperature and S is entropy Gsoivation : Free energy of solvation

E Ebonded t Enonbonded Ebonded t ( E_vdW t Eelec) where E_bonded: Bonded interactions formed of bond, angle, dihedral, and improper interactions.

Enonbonded : Non-bonded interactions formed from contribution of electrostatic (E_eiec) and van der Waals (E_vdw) interactions.

Structures were extracted at the end of respective simulations (t=20 ns) and protein-ligand interactions map was constructed using PLIP (protein-ligand interaction profiler) (Salentin, Schreiber et al. 2015).

Protein-protein interactions

Prediction of ACE2 binding with spike protein post simulation in the presence of ligands was done by template modelling using complex of receptor binding domain of S protein (NCBI Accession No. QHD43416) and ACE2 (PDB id: 6m0j). The ternary complex was then simulated for 20 ns to check interference of bound ligands with ACE2-RBD interface. This was done by analysing global energy of ACE2-RBD interactions from structures extracted at the end of respective simulations (t=20 ns) and subjecting the complex to FireDock (Fast Interaction REfmement in molecular DOCKing) protein-protein interaction analysis software (Andrusier, Nussinov et al. 2007, Mashiach, Schneidman-Duhovny et al. 2008). In a restricted refinement protocol, 100 cycles for the rigid body optimization and an atomic scale radius of 0.85 for optimal final refinement of best candidates were used.

Outcomes of Screening and Simulations

Polypharmacological screening of nutraceuticals Targeting of protein-protein interaction(s) (PPI) has been long standing challenge owing to featureless conformations, flat and difficult surface topologies and shallow pockets comprising these PPI interfaces (Qiu, Li et al. 2020). SARS-CoV-2 also employs a similar PPI network involving receptor binding domains of its S protein and ACE2 receptors of hosts to establish initial contact. Analysis of crystal structure of receptor binding domain (RBD) of S protein and ACE2 receptor complex (PDB id: 6m0j) showed interaction interface, stabilized by 14 H-bonds and a salt bridge with solvation free energy gain of -2.1 kcal/mol. See Table 1 below:

Table 1: PDBpisa analysis of ACE2 (Chain A)-RBD of S protein of SARS-CoV-2 (ChainE) complex showing H-bond network.

It was, however, observed that flattened ACE2-RBD interaction interface (involved in protein- protein interactions) could obstruct targeting of small molecules through structure based screens. This prompted the inventors to look for druggable sites (cavities) in the vicinity of interaction interface of ACE2 and RBD of S protein. The objective was to identify sites where ligands could perturb local RBD-ACE2 interfacial interactions sparing major structural changes in host ACE2 receptors. The inventors found one such site in the vicinity of interaction interface. This was followed by high-throughput Vina and PLANTS structure-based screening of 106 nutraceuticals. For 3CL protease, ADP ribose phosphatase subunit of nsp3 and RDRP of SARS-CoV-2, screenings were carried using previously known substrate or inhibitor binding site coordinates from available crystal structures, as discussed above. For E-protein pentamer, its ion channel cavity was kept as screening site. In total 15 virtual screenings were carried out to arrive at best hits. The binding scores from all docking runs were normalized and clustered for obtaining average score for individual candidates. Top hits appearing as high average score candidates for all targets were retained for further analysis. Binding scores of nutraceuticals were further compared with known non-covalent substrates/inhibitors of protein targets (via crystal complexes) except for ACE2, for which inhibitors are yet undiscovered. Surprisingly, we observe wide range of docking scores for 106 nutraceuticals screened against ACE2, 3 CL protease, ADP ribose phosphatase subunit of nsp3, E-protein pentameric channel and RDRP of SARS-CoV-2. However, the inventors’ criteria for final selection of candidates yielded four nutraceuticals which could be capable of high affinity binding with >3 target proteins of SARS-CoV-2. The inventors have shown binding profiles of these four candidates with all targets under consideration. For convenience, only the binding affinities calculated in kcal/mol by Vina are mentioned. The results are presented as individual analysis of each target protein of SARS-CoV-2 with identified nutraceutical candidates.

Docking and MD simulations with free energy (MM-PBSA) calculations

ACE2

The identified ligand binding pocket in the ACE2 (NCBI Accession No. NP_001358344.1) was composed of Trp69, Leu73, Leul20, Trp271, Phe390, Leu392, Leu395 and Arg514 residues, which lied in the vicinity of residues forming polar contacts with RBD of S protein of SARS-CoV-2 (see Table 1). This pocket is distinct from active/inhibitor (MLN-4760) binding site formed of Arg273, His345, Pro346, Aspr368, His374, His378, His505 and Tyr515 (Towler, Staker et al. 2004). The interaction affinity (as calculated by Vina) was -6.7 kcal/mol for a-linolenic acid (ALA) and -6.5 kcal/mol for Icosapent (EPA). Further the inventors checked for binding confirmation of selected ligands/compounds and to assess if their atomic interactions with ACE2 could hamper its association with RBD of S protein and without inducing substantial structural changes in ACE2. To check this, the inventors first performed MD simulations of ACE2-ligand conjugates for 20 ns followed by simulations of ACE2-RBD-ligand conjugates for another 20 ns (Figure 3). The initial simulations of ACE2-ligand complexes showed comparable fluctuations in Ca RMSD (-0.1- 0.25 nm) and Ca gyration radius (-2.4-2.55 nm) with ACE2 alone (Figure 3A-B). This indicated absence of any major structural perturbations, otherwise induced by our screened ligands during whole simulation trajectory. Inventors observed substantial variations in ligand RMSD indicating their displacement from originally bound site (Figure 3C). To estimate binding energetics of the biomolecular interactions, all protein-ligand systems were subjected to MM-PBSA calculations which relies on conformational fluctuations and entropic contributions to the binding energy from MD simulations. Energy components; vander waals, electrostatic and polar solvation energies were calculated for last 5 ns of each production trajectory with 500 ps intervals. The binding energy AGbindmg calculated from MM-PBSA calculations are shown in Figure 3D. Inventors observed protein-ligand contacts of ALA with Asp350 (H-bond) and Phe40, Leu73, Phe390 (hydrophobic interactions) and Icosapent (EPA) with Leul20 (H-bond) and Phe504, Tyr510, Tyr515 (hydrophobic) of ACE2 protein; deduced from the structures extracted at the end of respective simulations (Figure 3E).

The highest scoring poses for the screened candidates lied in proximity to Glu37 and Lys353 which form part of a b-hairpin loop in ACE2 and involved in polar interactions with Tyr505 and Gly496, Gly502 of RBD of S protein. Inventors hypothesized that the candidate compounds by virtue of their own local interactions near this hairpin within receptor cavity could interfere with ACE2-RBD interaction network. Comparative interfacial contact analysis of ACE2-RBD alone and ACE2-RBD-ligand conjugates from simulation outcomes showed that the ligands had induced varying levels of perturbations at critical host-pathogen interface. Simulations of ACE2-RBD alone showed a persistent H-bond network over the entire simulation period with -9.2 average number of H-bonds per time frame (Figure 4A). However, in presence of compounds, inventors observed decrease H-bond contacts at interface; average number of H-bonds per time frame 9.1 for ALA and 5.2 for EPA (Figure 4A). Further inventors calculated global energy of PPI (using structures extracted at end of respective simulations, t=20 ns) for ACE2 and RBD alone and in presence of ligands. The observed global energy score for interaction of ACE2 with RBD of S protein was -57.3 (Figure 4B). Global energy of ACE2-RBD interactions decreased substantially in the presence of ALA (-37.3) and EPA (-35.2). Accordingly, as per one of the preferred embodiments of the present invention, EPA and ALA modulates ACE2-RBD interactions and disruption of protein-protein interactions at interface without inducing structural perturbations in host receptor.

In recent reports on targeting host-viral interactions, many diverse chemical collections have been screened against intact RBD-ACE2 interface (viral attached state) (Figure 4) (Panda, Arul et al. 2020). Inventors also checked capability of identified candidates to bind at this interface and possible modulation of PPIs. Both ALA and EPA showed moderate binding affinity at this interface (-5.5 and -5.7 kcal/mol respectively). PPI residues at interfaces generally involve polar amino acids, found in abundance at protein surfaces (Jayashree, Murugavel et al. 2019). The relative binding affinities in two different set of nutraceuticals is consistent with their constituent polar side chains.

Subsequently, MD simulations of RBD-ACE2-ligand conjugates (ligand bound atRBD-ACE2 interface) were carried to ascertain ligand interaction dynamics and modulatory potential. MM- PBSA analysis of MD simulations of these conjugates concurred with docking outcomes. ALA and EPA showed moderate binding affinities of -35.8±12.1 and -23.8±14.2 kJ/mol respectively. Analysis of protein-protein contact frequency showed substantial reduction in ACE2-RBD contacts in the presence of EPA (~4 contacts) while these remained similar in presence of ALA (10-13 contacts) (Figure 4C). Contact analysis shows interference in ACE2- RBD interaction network, predominantly by EPA. Further PPI energy scoring of final RBD- ACE2 conjugates (t=20 ns) showed weakened interfacial interactions in the presence of all compounds. The calculated global energy scores of interaction between RBD and ACE2 in the presence of ligands were -49.2 (ALA) and -30.5 (icosapent) compared to -57.4 for RBD-ACE2 alone (Figure 4D). Protein-ligand interaction analysis of these conjugates showed interactions of compounds with residues of both RBD and ACE2. ALA showed H-bonds with Ser494 and hydrophobic interaction with Lys417 of RBD of S protein, EPA showed strong hydrophobic interaction network with Glu35, Lys353 of ACE2 and Tyr449 of S protein (RBD). Estimates from contact and PPI interaction analysis shows potential of these compounds to interfere directly with host- viral interface.

3CL Protease

The main protease in SARS-CoV-2 and related coronaviruses aids in replication of virus via proteolytic processing of C-terminal of replicase polyprotein (Xue, Yu et al. 2008, Cherian, Agrawal et al. 2020). Inventors used crystal structure of Mpro complexed with its non-covalent inhibitor X77 (N-(4-tert-butylphenyl)-N-[(lR)-2-(cyclohexylamino)-2-oxo-l-(pyri din-3- yl)ethyl]-lH-imidazole-4-carboxamide) to screen and compare identified candidates. X77 forms polar H-bonds with Asnl42, Glyl43, Glul66 and hydrophobic interactions with His41, Metl65, Glul66 and Glnl89 which contributed to binding affinity of -9.1 kcal/mol with Mpro. The four candidate from our screening also showed comparable binding affinity with Mpro; - 8.2 for ALA and -7.6 for icosapent at X77 binding site.

Subsequently, unrestrained MD simulations of Mpro-ligand conjugates were carried out to understand behaviour of protein in presence of compounds and validate atomic interactions followed by MM-PBSA binding energy calculations. Ca-RMSD and gyration radius (Rg) analysis showed absence of any major structural perturbations in presence of compounds (Ca- RMSD~0.1-0.25 nm and Rg~2.2 nm, Figure 5A-B). Due to its strong interaction network with Mpro, X77 showed minimal ligand RMSD fluctuations while other compounds showed slight deviations (~0.1-0.4 nm) over the simulation period (Figure 5C). However, MM-PBSA analysis from all simulations showed comparable binding affinities of screened candidates with X77 (Figure 5D). The binding affinity calculated through contribution of electrostatic, van der waals and polar solvation energies for X77 was -96.1±4.6 kJ/mol and -69.2±7.6, -56.5±18.1, for ALA and EPA respectively (Figure 5D). The protein-ligand interaction network of all systems was analysed by extracting frames from end of respective simulations. ALA formed polar contacts with Asn691, Ser759; EPA showed hydrophobic interactions with Val557, Ala688, Tyr689 (Figure 5E).

ADP ribose phosphatase (ADRP) subunit of nsp3

ADRP, also known as macrodomain forms largest component of the replicase assembly protein, nsp3 and has been structurally characterized for numerous other CoV’ s as HCoV-229E (Human Coronavirus 229E), S ARS-CoV and MERS-CoV (Middle East Respiratory Syndrome virus) (Egloff, Malet et al. 2006). Kuri et al showed that the viruses with deactivated macrodomains were sensitive to interferon pre-treatment (Kuri, Eriksson et al. 2011). Recently, it was also shown that mutations in ADRP lowered viral replication in bone derived macrophages, thus indicating them as attractive targets (Grunewald, Chen et al. 2019). Inhibition of ADRP may reduce viral loads and foster recovery in affected individuals (Alhammad and Fehr 2020). In this case, inventors used ADP ribose (adenosine-5- diphosphoribose, ADPr) binding site in ADRP for screening and analysis. In its crystal structure (PDB id: 6w02), ADPr interacts with ADRP through H-bonds with its Asp22, Ile23, Asn40, Gly46, Gly48, Val49, Ala50, Serl28, Alal29, Glyl30, Ilel31, Phel32 and Phel56 and a binding affinity of -7.5 kcal/mol. The binding affinity calculated for ALA and EPA was -7.2 and -7.6 kcal/mol respectively.

MD simulations of conjugates showed absence of major structural changes (minimal variations in Ca-RMSD and Rg) in ADRP in the presence of ligands (Figure 6A-B). Ligand RMSD varied between 0.1-0.5 nm (Figure 6C). Here only ADPr showed minimal ligand fluctuations during simulation period. MM-PBSA analysis showed comparable binding affinities of all nutraceuticals with ADPr (Figure 6D). Binding affinity calculated for ADPr was -84.9±17.8 kJ/mol while ALA and iscopent showed binding affinities of -100.0±8.7, -82.3±15.5 kJ/mol respectively. Within the ADPr binding pocket of ADRP, protein-ligand interactions of (i) ALA with Asn40, Gly46, Gly47 (H-bond) and Val49, Prol25, lie 131, Phel32 and Phel56 (hydrophobic), (ii) icosapent with Ala38, Val49, Ala50, Prol25, Leul26, Ilel31, Phel32, Vall55, Phel56, Aspl57 and Leul60 (hydrophobic) were observed (Figure 6E).

E-protein

The smallest structural envelope (E) protein (NCBI Accession No. QHD43418), indispensable in viral production and maturation, is highly conserved among beta coronaviruses such as SARS-CoV and related animal coronaviruses as Beta-CoV (RaTG13) and Beta-CoV (Pangolins). The highly conserved SARS-CoV E-protein ion channel activity was reportedly blocked by hexamethylene amiloride (HMA) leading to impaired viral replication (Pervushin, Tan et al. 2009). The ion channel cavity of E-protein pentamer was used as screening/binding site (Figure 7). In the screening, inventors observed high binding affinities of ALA (-8.5 kcal/mol) and EPA (-7.9 kcal/mol) with E-protein. The reference drug HMA showed binding affinity of -7.6 kcal/mol.

MD simulations of E-protein alone showed large deviations in Ca-RMSD and Rg compared to starting pentameric model (Figure 7A-B). However, these deviations were similar for E- protein-ALA/icosapent complexes suggesting absence of major structural perturbations in presence of the fatty acids. Inventors obsevered minimal variations in ligand RMSD for HMA (~0.1 nm) compared to ALA and EPA (0.2-0.4 nm) during simulations (Figure 7C). Analysis of ligand binding energies by MM-PBSA analysis revealed higher binding affinities of ALA (-140.8+ 5.6 kJ/mol) and EPA (-157.7+ 8.1 kJ/mol) compared to HMA (119.1+ 15.6 kJ/mol) (Figure 7D). MM-PBSA calculations suggest that both ALA and EPA act as E-protein channel inhibitors. The apparently high affinity of fatty acids could be attributed to its strong protein- ligand interaction interface compared to that of HMA. ALA for H-bonds with Asnl5, Asnl5’ and hydrophobic interaction network with Leul9, Phe23’, Phe26, Phe26’. EPA only showed hydrophobic interactions with Phe26, Phe26’, Phe26” and Phe23’ (Figure 7E).

RNA dependent RNA polymerase (RDRP)

In CoVs, RDRP or nspl2 (NCBI Accession No. QHD43415 11) plays central role in replication and transcription machinery (Yin, Mao et al. 2020). RDRP acts as primary drug target for antiviral s-remdesivir and sofosbuvir in SARS-CoV-2 and Hepatitis C virus respectively (Appleby, Perry et al. 2015, Yin, Mao et al. 2020). The binding scores of ALA (- 6.5 kcal/mol) and EPA (-6.7 kcal/mol) were comparable to remdesivir (-7.5 kcal/mol in our screening and -7.6 kcal/mol from recent studies (Ahmed, Mahtarin et al. 2020). In the crystal structure (PDB id: 7bv2), remdesivir forms H-bond contacts with Arg555, Asp623, Asn691, Asp760 along with pi-cationic interaction with Arg555 of RDRP.

In protein-ligand MD simulations, remdesivir and other two compounds did not induce structural changes in RDRP protein (Figure 8A-B). Ligand RMSD variations for remsdesivir was singinifcantly lower than other two compounds (Figure 8C). Binding energy analysis from simulation outcomes were concordant with initial screening outcomes. ALA and EPA displayed lesser binding affinities than Remdesivir (Figure 8D). ALA showed only two H- bonds with Ser691, Ser759 while EPA displayed only hydrophobic interaction network with Val557, Ala688, Tyr689 of RDRP respectively (Figure 8E).

Furthermore, over activation of innate immune responses to SARS-COV-2 infection leading to abnormal production of inflammatory cytokine storm has been pivotal in COVID-19 mediated deaths globally. Many reports have surfaced suggesting use of anti-inflammatory agents in controlling cytokine production during COVID-19 infection. Many clinical trials are also being undertaken to manage chronic COVID-19 infections by using anti-inflammatory agents as naproxen, clarithromycin, radiotherapies and nutritional supplements as eicosapentaenoic acid, gamma-linolenic acid and antioxidants (clinicaltrials.gov/COVID-19). Besides possible role in direct interference with function of screened targets and already known protective/anti-inflammatory role of omega-3-fatty acids, these appear to be well suited candidates in treating/managing COVID-19 infections. Accordingly, in another embodiment, the omega-3 -fatty acids ALA and EPA also acts as inflammatory agents.

In another embodiment of the present invention is included the derivatives of omega-3 fatty acids ALA and EPA. Many types of derivatives are well known to one skilled in the art. Examples of suitable derivatives are esters, such as branched or unbranched and/or saturated or unsaturated C1C30 cycloalkyl esters, in particular C1-C6 alkyl esters. Their systemic potential has been recognized in the art. As used in this application and claims “omega-3 fatty acid” “Alpha-Linoleic Acid (ALA)”, and “Eicosapentaenoic Acid (EPA)” includes their derivatives. Linolenic acid and LA obtained in foods undergo oxidative conversion to many potent bioactive derivatives that optimize growth, development, and immunity in animals, and these bioactive derivatives also effective substitutes for ALA. Likewise, derivative of the omega-3 fatty acid EPA like Icosapent ethyl or ethyl eicosapentaenoic acid are also found to be effective.

In another embodiment, with respect to the quantity of the omega-3 fatty acid ALA and EPA or mixture of these omega-3 fatty acids, a minimum amount of about 0.5 wt. %, preferably above about 1.0 wt. %, or 2 wt. %, on a dry matter basis, as measured by quantity of daily diet composition should be administered. Generally no more than about 10 wt. %, preferably no more than about 7, 5, or 4 wt. % can be employed. The fatty acids can be administered in a diet such as canned (wet) or dry, in combination with a supplement such as a treat in liquid or solid form, or in the water supply or even as a separate dosage unit, for example a capsule or tablet containing the omega-3 fatty acid or mixture of omega-3 fatty acids.

In one of the embodiments of the present invention, the composition of the invention contains only Alpha-Linoleic Acid (ALA) as omega-3 fatty acid. In another embodiment of the present invention, the composition of the invention contains only Eicosapentaenoic Acid (EPA) as omega-3 fatty acid. In yet another embodiment of the present invention, composition of the invention contains a combination of Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA). In another preferred embodiment, the proportion of Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) in the composition is in the range of about 1:4 to about 4:1. In yet another embodiment, the composition of the present invention further comprises pharmaceutically acceptable form of supplements, carriers, excipients, diluents, vitamins, antioxidants, nutraceuticals, other fatty acids, oils, etc. In an embodiment, the composition of the present invention is a pharmaceutical composition or a nutraceutical composition in the form of capsule, soft capsule, tablet, pill, jelly, powder, granule, emulsion, solution, syrup, suspension, a food, a food supplement, a food ingredient, a food product, a functional food, a medicated food, a beverage, a medicament, etc.

In a preferred embodiment, the composition of the present invention when administered in pharmaceutically effective dosage into a subject, inhibits the interaction between SARS-CoV- 2 (COVID-19) and host cells in the subject. In yet another preferred embodiment, the composition of the present invention when administered in pharmaceutically effective dosage into a subject induces host-directed responses to prevent or treat the symptoms or conditions associated with the viral infection caused by SARS-CoV-2 (COVID-19) in the host. In another preferred embodiment, the composition also acts as inflammatory agents prevent or treat the symptoms or conditions associated with the viral infection caused by SARS-CoV-2 (COVID- 19) in the host. In a preferred embodiment, the composition of the present invention when administered in pharmaceutically effective dosage into a healthy subject, prevents or reduces the chances of infection of SARS-CoV-2 (COVID-19) in the subject. In another preferred embodiment, the composition of the present invention when administered in pharmaceutically effective dosage into a subject infected with SARS-CoV-2 (COVID-19) and in the need of treatment, prevents transmission, replication, progression or proliferation of virus inside the subject. In a preferred embodiment, the pharmaceutically effective dosage of the composition the present invention to prevent or treat the symptoms or conditions associated with the viral infection caused by SARS-CoV-2 (COVID-19) in a host is about 100-4000 mg and more preferably 500-2000 mg of the omega-3 fatty acids per adult per day. In accordance with the present invention, the composition is administered into the subject by way of oral administration, intravenous administration, or parenteral administration.

Another preferred embodiment of the present invention provides a method for treating a symptom or disorder associated with SARS-CoV-2 (COVID-19) in a subject, wherein the method comprises the step of administering into the subject a composition comprising a pharmaceutically effective amount of omega-3 fatty acid selected from the group consisting of Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) and combinations thereof in a dose sufficient to inhibit the interaction between SARS-CoV-2 (COVID-19) and host cells in the subject. Although the present invention has been described in considerable detail with reference to certain preferred embodiments and examples thereof, other embodiments and equivalents are very much possible. Even though numerous characteristics and advantages of the present invention have been set forth in the foregoing description, together with efficacy, functional and other details, the disclosure is illustrative only, and changes may be made in detail, especially in terms of non-essential ingredients to the composition or the procedural steps within the principles of the invention to the full extent indicated by the broad general meaning of the terms in which the appended claims are expressed. Thus various modifications are possible of the presently disclosed composition and method without deviating from the intended scope and spirit of the present invention. More particularly, the composition and method as depicted in the present invention, is simplified and generalized one and there are several trivial variations possible. Accordingly, in one embodiment, such modifications of the presently disclosed composition and method are included in the scope of the present invention. In addition to the method, there are functional variants of the presently disclosed composition, all of which are included in the scope of the present invention. Also, unless the context clearly dictates otherwise, it is understood that when a range of value is provided, the tenth of the unit of the lower limit as well as other stated or intervening values in that range shall be deemed to be encompassed within the disclosure. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the disclosure.

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Claims

1. A composition comprising a pharmaceutically effective amount of omega-3 fatty acid selected from the group consisting of Alpha-Linoleic Acid (ALA), Eicosapentaenoic Acid (EPA) and combinations thereof, wherein the composition inhibits the transmission, replication, progression or proliferation of SARS-CoV-2 (COVID-19) virus in a host cell.

2. The composition of claim 1 wherein the omega-3 fatty acid is Alpha-Linoleic Acid (ALA).

3. The composition of claim 1 wherein the omega-3 fatty acid is Eicosapentaenoic Acid (EPA).

4. The composition of claim 1 wherein the omega-3 fatty acid is a combination of Alpha- Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA).

5. The composition of claim 4 wherein the proportion of Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) in the said composition is in the range of about 1 :4 to about 4:1.

6. The composition of any of claims 1 to 5, wherein the composition is a pharmaceutical composition or a nutraceutical composition.

7. The composition of claims 6, wherein the said pharmaceutical composition or nutraceutical composition is in the form of capsule, soft capsule, tablet, pill, jelly, powder, granule, emulsion, solution, syrup, suspension, a food, a food supplement, a food ingredient, a food product, a functional food, a medicated food, a beverage, or a medicament.

8. The composition of any of the preceding claims, wherein the said composition further comprises pharmaceutically acceptable form of supplements, carriers, excipients, diluents, vitamins, antioxidants, nutraceuticals, fatty acids or additives.

9. The composition of any of the preceding claims, wherein the said composition, when administered in pharmaceutically effective dosage into a subject, inhibits the interaction between SARS-CoV-2 (COVID-19) spike protein and ACE2 receptors of host cells in the subject.

10. The composition of claims 9, wherein the said dosage unit is 100-4000 mg and more preferably 500-2000 mg of the omega-3 fatty acids per adult per day.

11. The composition of any of claims 9 or 10, wherein the administration of the composition into the subject is by way of oral administration, intravenous administration, or parenteral administration.

12. A composition for use in the treatment or prevention of a symptom or condition associated with viral infection caused by SARS-CoV-2 (COVID-19), the composition comprising a pharmaceutically effective amount of omega-3 fatty acid selected from the group consisting of Alpha-Linoleic Acid (ALA), Eicosapentaenoic Acid (EPA) and combinations thereof.

13. The composition of claim 12 wherein the omega-3 fatty acid is Alpha-Linoleic Acid (ALA).

14. The composition of claim 12 wherein the omega-3 fatty acid is Eicosapentaenoic Acid (EPA).

15. The composition of claim 12 wherein the omega-3 fatty acid is a combination of Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA).

16. The composition of claim 15 wherein the proportion of Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) in the said composition is in the range of about 1 :4 to about 4:1.

17. The composition of any of the claims 12 to 16, wherein the said composition, when administered in pharmaceutically effective dosage into a healthy subject, prevents or reduces the chances of infection of SARS-CoV-2 (COVID-19) by inhibiting the interaction between SARS-CoV-2 (COVID-19) and host cells in the subject.

18. The composition of any of the claims 12 to 16, wherein the said composition, when administered in pharmaceutically effective dosage into a subject infected with SARS- CoV-2 (COVID-19) and in the need of treatment, prevents transmission, replication, progression or proliferation of virus inside the subject by inhibiting the interaction between SARS-CoV-2 (COVID-19) and the host cells of the subject or interfering with the SARS-CoV-2 (COVID-19) proteins.

19. The composition of any of claims 17 or 18, wherein the said dosage unit is 100-4000 mg and more preferably 500-2000 mg of the omega-3 fatty acids per adult per day.

20. The composition of any of claims 17 or 18, wherein the said administration of the composition into the subject is by way of oral administration, intravenous administration, or parenteral administration.

21. Use of the composition as claimed in any of the claims 12 to 20 to prevent or treat a symptom or condition associated with viral infection caused by SARS-CoV-2 (COVID-19) in humans.

22. A method for treating a symptom or disorder associated with SARS-CoV-2 (COVID- 19) in a subject, the method comprising the step of administering into the subject a composition comprising a pharmaceutically effective amount of omega-3 fatty acid selected from the group consisting of Alpha-Linoleic Acid (ALA) and Eicosapentaenoic Acid (EPA) and combinations thereof in a pharmaceutically effective dose.

23. The method of claim 22 wherein the said composition is a pharmaceutical composition or a nutraceutical composition in the form of a capsule, soft capsule, tablet, pill, jelly, powder, granule, emulsion, solution, syrup, suspension, a food, a food supplement, a food ingredient, a food product, a functional food, a medicated food, a beverage, or a medicament.

24. The method of claim 22, wherein the said dosage unit is 100-4000 mg and more preferably 500-2000 mg of the said omega-3 fatty acid per adult per day.

25. The method of any of claims 22 to 24, wherein the said administration of the composition into the subject is by way of oral administration, intravenous administration, or parenteral administration.