1. INTRODUCTION:
Nidovirales is the order from which the family of coronaviridae are
classified they are further subdivided into four genera namely, α, β, γ
and δ. The virus SARS-CoV-2 which has caused global pandemic and havoc
is of the β genera of the coronaviridae family, which has four protein
constructs where its frame is made of Nucleocapsid protein (N) which
encompasses the single stranded viral RNA (ssRNA), Membrane protein (M),
Envelope protein (E) and spike protein (S) 1. These
proteins are replicated and multiple copies of the virus are produced
within the human cell as per the well-known mechanism as described: The
spike protein of the SARS-CoV-2 virus attaches to the Angiotensin
Converting Enzyme-2 (ACE-2) and with host factors as Cell Surface Serine
Protease (TMPRSS-2) and enters the cell resulting in the release of the
viral contents to the cell cytoplasm in which the viral ssRNA is
spontaneously translated as individual non- structural proteins which
act as regulatory proteins along with protective vesicles which contain
genomic RNA and subgenomic mRNA for viral replication and transcription.
And the resultant structural proteins move towards the endoplasmic
reticulum which in-turn produces newly replicated viral genomic RNA and
the viral structural construct when transporting through the Endoplasmic
Reticulum to Golgi Intermediate Compartment (ERGIC) and the newly made
viral constructs are released out of the cell via exocytosis2. SARS-CoV-2 infection causes COVID-19 which is an
upper respiratory infection emerged from Wuhan, China also it spread as
a pandemic leading to more than 208 million cases, 4.3 million deaths
and 186 million recoveries worldwide 3.
The production of more number of viral particles then results in the
increased infection and lysis of the alveolar epithelial cells, Type I
and II pneumocytes following cytokine storm and inflammatory reaction in
the lungs thereby leading to Acute Respiratory Distress Syndrome (ARDS).
The recoveries from COVID- 19 were made possible through treatment of
symptoms, repurposing drugs, convalescent plasma therapy, and artificial
oxygen supply to the patients. SARS-CoV-2 mainly causes damage in the
lungs due to high concentration of ACE-2 receptors and presents drastic
effects in the advanced stages of the disease progression as shock,
ARDS, hypoxemia, coagulation defects, encephalopathy, acute kidney
injury and heart failure resulting to the death of the affected person.
The patients with symptoms are diagnosed with Reverse Transcriptase
Polymerase Chain Reaction (RT-PCR), Basic blood work, Chest X ray, High
Resolution Computer Tomography Chest, Serology and classified into five
groups based on their severity of infection which are: Asymptomatic or
Pre-symptomatic infection, Mild infection, Moderate infection, severe
infection and Critical infection 4.
Treatments proposed according to the infection rate are: Mild infection
the treatment for the symptoms is given and for Moderate infection
treatment of symptoms is given individually or along with antibacterial
medication only if a bacterial infection can be seen. For treatment with
severe infection and critical infection the supplemental oxygen or
non-invasive ventilation along with treatment of symptoms and
interleukin 6 blockers (IL-6 Blockers), Ivermetcin, Hydroxychloroquine,
Lopinavir or Ritonavir, Remdesivir and systemic corticosteroids are
given according to the systemic evaluation or national health
guidelines. However, these drugs are advised to be used with extreme
caution as it may cause severe side effects and permanent damage the
major organs such as kidney, liver and heart 5.
Due to these reasons natural product scientists have turned to nature
for assistance to eradicate this dreadful disease. Natural products can
have potential therapeutic use for the emerging diseases and also enable
to eliminate them, it has been reported that 234 drugs for various
diseases have been isolated and were approved from natural products for
treating various diseases during the timeline of 1981 to 2014. About
antiviral 64 small molecules and 138 antiviral drugs have been approved
from the same time period 6. Mushrooms belong to the
separate Kingdom of Fungi and Phylum Basidiomycota. They are also an
excellent source of natural products and antivirals which expresses
antiviral activity in both enveloped and non-enveloped RNA viruses by
mechanisms which can prohibit the attachment and entry, replication,
assembly and release of the same. Such antiviral activity is possible
through compounds which are in different forms of like analogues,
derivatives, fraction or direct polysaccharides, triterpenoids,
proteoglycan, proteins, lectins, polyphenols and enzymes7. A recent study involving in silico approach
for Main Protease (MPro) inhibition through 36 compounds with edible and
medicinal mushrooms with anti-HIV activity 8 but they
fail to investigate and recognize compounds with wide antiviral activity
especially in the light of compounds which prohibit or totally eradicate
the upper respiratory viruses, they are only single targeted and they
are not validated by molecular dynamics which predicts the stability of
the docked molecule.
In this study our focus is on edible mushrooms which accessible in super
markets such as Lentinula edodes , Agaricus bisporus ,Pleutorus ostreatus and Hericium erinaceus . And we target
their main compounds such as Eritadenine, Gallic acid, Pleuran and
Ergosterol peroxide, these main compounds were chosen especially due to
their ability to inhibit upper respiratory infections which are
specifically caused by viruses from known existing literature. According
to the literature, Eritadenine is a main compound of L. edodesand has been synthesized synthetically and was found to have antiviral
activity against Poxviruses, Paramyxovirus, Rhabdovirus and Reovirus9, 10. A. bisporus has Gallic acid as its main
component was reported to have activity against early viral entry of
hepatitis C, Herpes Simplex Virus-1 (HSV-1), Human Immunodeficiency
Virus-1 (HIV-1) and Influenza-A virus 11. Pleuran a
main compound of P. ostreatus was studied to have activity
against Influenza –A virus, provided cellular immune response and
respiratory tract infections in athletes 12, 13, 14.
Ergosterol Peroxide a main component from H. erinaceus was
examined to have antiviral activity against porcine delta coronavirus
and other upper respiratory infections 15, 16, 17.
Due to these molecules has such antiviral activities, we target them
against the Main Protease (Mpro) and the spike protein (S) of the
SARS-CoV-2 virus in order to inhibit these targets and prohibit the
entry and replication of the virus within the cell by using molecular
docking tools and molecular dynamics simulation studies. We have also
undertaken studies to assess the target accuracy and pharmacokinetic
parameters by in silico analysis and compare them to the existing
antivirals proposed against the SARS-CoV-2 with the targets mentioned in
the literature.