about covid 19

1. Structure of SARS-CoV-2

2.  SARS CoV-2 virus is a betacoronavirus which was discovered in Wuhan City, Hubei
Province, China in December 2019.
 They are enveloped, positive-sense, single-stranded RNA viruses of zoonotic origin.
 They are spherical to pleomorphic particles, measuring between 80 and 160 nm in length.
SARS CoV-2 contains four structural proteins, namely envelope (E), spike (S), membrane (M),
and nucleocapsid (N).
 The S, M, and E proteins together form the envelope of the virus. The M protein is the most
abundant, mostly responsible for the shape of the envelope. The E protein is the smallest
structural protein.
 The S and M proteins are also the transmembrane proteins that are involved in virus
assembly during replication.
 N proteins remain associated with the RNA forming a nucleocapsid inside the envelope.
Although N protein is largely involved in processes relating to the viral genome, it is also
involved in other aspects of the CoV replication cycle (assembly and budding) and the host
cellular response to viral infection.
 Polymers of S proteins remain embedded in the envelope giving it a crown-like
appearance, thus the name coronavirus.

3. Spike glycoprotein
 As a first line of treatment, along with the antiviral drugs, clinicians are using SARS-CoV and
MERS-CoV neutralizing antibodies targeting the S1 domain of the COVID-19 spike glycoprotein
Very recently (25 January 2020) the first and complete genome sequence of COVID-19 was
deposited in the NCBI (GenBank: MN908947.3) providing the key to the likely structure and
glycosylationpattern of the viral proteins and consequent mode of interaction with the host cell.
Similar tomostother coronaviruses,the outer membrane spike glycoprotein, known for its
glycosylation , is the prime host interacting protein with host cell targets (such as ACE2, CD26,
Ezrin, cyclophilins and other cell adhesion factors) important for cell adhesion and virulence
[4,5]. However, the specific host cell factors or proteins that facilitate the novel COVID-19
remain elusive. The current study was thus undertaken to predict the COVID-19 spike
glycoprotein structure and glycan shield pattern that has great implications for understanding the
viral camouflage and mode of cell entry,potentially assisting the development of new vaccines,
antibodies, small-molecule drugs and screening of the human host targets.
 The spike protein ectodomain consists of the S1 and S2 domains. The S1 domain contains
the receptor binding domain and is responsible for recognition and binding to the host cell
receptor. The S2 domain, responsible for fusion, contains the putative fusion peptide and the
heptad repeat HR1 and HR2.

4. The Clustal-W sequence alignment of COVID-19 and SARS-CoV spike glycoproteins
(Figure S1) shows ∼91% identity in the S2 domain region (aa570– aa1278), however it
lacks similarity in three regions (aa677–690, wing), (aa877–884 and aa930–943, stalk). A
larger sequence difference (∼55% identity), was found in the S1 domain (aa01–aa550),
which is known for its host cell target interaction underlying cell adhesion and virulence
.Despitesequence dissimilarity in the S1 domains there are conserved residues involved in
ternary folding which were conserved. This suggests that the COVID-19 might interact
with some of the previously known host targets (ACE2, CD26, Ezrin, cyclophilins),
albeit via slightly varied molecular interactions.

5.  Angiotensin converting enzyme 2 (ACE2), a relatively new member of the RAS, has drawn
extensive attention since 2003, because of the findings that ACE2 is the receptor for SARS
Corona virus and that maintenance of normal ACE2 levels in the lung is beneficial for the host
to combat inflammatory lung disease. Nevertheless, the mechanism through which ACE2 plays
a role in inflammatory lung disease has not been clearly identified.
 In the lung, the ACE2 protein co-localizes with cholesterol and sphingolipid-rich lipid raft
microdomains in the plasma membrane and its expression level is positively correlated to the
state of airway epithelial differentiation. Interestingly, ACE2, as its homolog ACE, is released
from the surface of epithelia into airway surface liquid via cleavage by TACE (ADAM17) and
other sheddases. This soluble ACE2 (sACE2) is catalytically active in ASL. Release of soluble
ACE2 (sACE2) from airway epithelial cells is dynamic, occurring both constitutively and in
response to stimuli. Previous research indicated that a single mutation in human ACE2 gene at
residue 584 prevented ACE2 shedding from the cell membrane. In vitro studies on non-
sheddable ACE2 cell surface expression have demonstrated impaired enzymatic activity,
suggesting that releasing ACE2 from the cell membrane is a critical step in catalyzing substrates
andimplying that attenuation of ACE2 shedding might contribute to disease pathogenesis in
which ACE2 activity is crucial in disease initiation and progression.
ACE2
Angiotensin-converting enzyme 2 (ACE2

6. spike glycoprotein interaction with human ACE2 enzyme
Receptor recognition by SARS-CoV has been extensively studied. A virus-surface spike protein
mediates the entry of coronavirus into host cells. The spike protein of SARS-CoV contains a
RBD that specifically recognizes ACE2 as its receptor3,4. A series of crystal structures of the
SARS-CoV RBD from different strains in complex with ACE2 from different
hosts has previously been determined. These structures showed that SARS-CoV RBD contains
a core and a receptor-binding motif (RBM); the RBM mediates contacts with ACE2. The
surface of ACE2 contains two virus-binding hotspots that are essential for SARS-CoV binding.
Several naturally selected mutations in the SARS-CoV RBM surround these hotspots and
regulate the infectivity, pathogenesis, and cross-species and human-to-human transmissions of
SARS-CoV3,11,12. Because of the sequence similarity between the spike proteins of SARS-
CoV and SARS-CoV-2, it was recently predicted that SARS-CoV-2.

7. SARS-CoV-2 and bat coronavirus RaTG13 both contain a four-residue motif glycine-
valine/glutamine-glutamate/threonine-glycine; the two relatively bulky residues and two
flexible glycines enable the loop to take a different conformation.
an additional main-chain hydrogen bond forms between Asn487 and Ala475 in the SARS-
CoV-2 RBM, causing the ridge to take a more compact conformation and the loop
containing Ala475 to move closer to ACE2.

8. As a consequence, the ridge in the SARS-CoV-2 RBM forms more contacts with the N-
terminal helix of ACE2 (Extended Data Fig. 4b). For example, the N-terminal residue Ser19
of ACE2 forms a new hydrogen bond with the main chain of Ala475 of the SARS-CoV-2
RBM, and Gln24 in the N-terminal helix of ACE2 also forms a new contact with the SARS-
CoV-2 RBM.
virus-binding hotspots at the SARS-CoV-2 RBM–ACE2 interface At the SARS-CoV–ACE2
interface, two virus-binding hotspots were previously identified11,12: hotspot Lys31 (that is,
hotspot 31) consists of a salt bridge between Lys31 and Glu35, and hotspot Lys353 (that is,
hotspot 353) consists of a salt bridge between Lys353 and Asp38. Both salt bridges are weak,
as judged by the relatively long distance of these interactions. Burial of these weak salt
bridges in hydrophobic environments on virus binding would enhance their energy, owing to a
reduction in the dielectric constant. This process is facilitated by interactions between the
hotspots and nearby RBD residue.
SARS-CoV-2 RBM–ACE2 interface, Leu455 of the SARS-CoV-2 RBM has a less bulky
side chain, providing less support to Lys31 of ACE2. As a result, the structure of hotspot 31
has rearranged: the salt bridge between Lys31 and Glu35 breaks apart, and each of the
residues forms a hydrogen bond with Gln493 of the SARS-CoV-2 RBM.

9.  SARS-CoV-2 RBM has its conformation fixed through a hydrogen bond between its
side chain and the RBM main chain.
SARS-CoV-2 pseudovirus entry depends on ACE2, but its spike was cleaved to S2 on
the pseudovirus surface (probably because of a furin site insertion16). Moreover, we
performed a rotein pull-down assay using ACE2 as the bait and cell-associated RaTG13
spike as the target . We found that the RaTG13 spike was pulled down by ACE2.
Therefore, SARS-CoV-2, bat RaTG13 binds to human ACE2 and can use human ACE2
as its entry receptor.

10.  RDV is a phosphoramidate prodrug of a 1’-cyano-substituted nucleotide analogue. Its
triphosphate form (RDV-TP) resembles adenosine triphosphate (ATP) and is used as a
substrate of several viral RNA-dependent RNA polymerase (RdRp) enzymes or complexes.
The compound has shown broad-spectrum in vitro and in vivo antiviral activity against
nonsegmented negative-sense RNA viruses.
 Remdesivir is a broad-spectrum antiviral medication. The biopharmaceutical
developed by company Gilead Sciences, It is administered via injection into a vein.
Machanism of action
SARS-CoV-2 is a positive strand RNA virus. Its replication is mediated by a multi-
subunit replication/transcription complex of viral non-structural proteins (nsp) (11).
The core component of this complex is the catalytic subunit (nsp12) of an RNA-
dependent RNA polymerase (RdRp) . By itself, nsp12 has little activity and its
functions require accessory factors including nsp7 and nsp8 , which increase RdRp
template binding and processivity. RdRp is also proposed to be the target of a class of
antiviral drugs that are nucleotide analogs, including Remdesivir , which is a prodrug
that is converted to the active drug in the triphosphate form (RTP) within cells .
Drug used in covid 19

11.  nsp12 with nsp7 and nsp8 to form the core RdRp complex in insect cells.
The presence of nsp7 and nsp8 dramatically increased nsp12 binding to the template-
primer RNA .The nsp12-nsp7-nsp8 complex also showed RNA polymaerization activity
on a poly-U template addition of adenosine triphosphate (ATP). This rna polymerization
activity was effectively inhibited by the addition of the active triphosphate from of
Remdesivir.

12. SARS-CoV-2 RdRp is a relatively stable enzyme that is ready to function as a
replicase upon binding of RNA template. Viral RdRp is a highly processive enzyme
with a rate of replication up to 100 nucleotides per second . No significant
conformational changes between the apo and the active enzyme structures are
consistent with the high processivity of the viral RNA polymeras.
Remdesivir, these nucleotide analogs are proposed to inhibit the viral RdRp through
non-obligate RNA chain termination, a mechanism that requires the conversion of the
parent compound to the triphosphate active form . The structure of the template-RTP
RdRp complex provides an excellent model to rationalize drug inhibit the SARS-CoV-2
RdRp activity.
Pharmacokinetics
In non-human primates, the plasma half-life of the prodrug is 20 minutes, with the main
metabolite being the nucleoside, GS-441524. Two hours post injection, the main metabolite GS-
441524 is present at micromolar concentrations, whilst intact Remdesivir is nob longer
detectable. Because of this rapid extracellular conversion to the nucleoside GS-441524, some
researchers have questioned whether the active nucleotide triphosphate is truly derived from
Remdesivir pro-drug removal or whether it occurs by GS-441524 phosphorylation. The activated
nucleotide triphosphate form has sustained intracellular levels in PBMC and presumably in other
cells as well.

13. The most common adverse effects in studies of remdesivir for COVID-19 include respiratory
failure and organ impairment, including low albumin, low potassium, low count of red
blood cells, low count of platelets that help with clotting, and yellow discoloration of the skin.
Other reported side effects include gastrointestinal distress, elevated transaminase levels in the
blood (liver enzymes), and infusion site reactions.
Other possible side effects of remdesivir include:
Infusion‐related reactions. Infusion‐related reactions have been seen during a remdesivir
infusion or around the time remdesivir was given.[Signs and symptoms of infusion‐related
reactions may include: low blood pressure, nausea, vomiting, sweating, and shivering.
Increases in levels of liver enzymes, seen in abnormal liver blood tests. Increases in levels of
liver enzymes have been seen in people who have received remdesivir, which may be a sign of
inflammation or damage to cells in the liver.
Side effects
Interactions
Remdesivir is at least partially metabolized by the cytochrome P450 enzymes CYP2C8, CYP2D6,
and CYP3A4 . Blood plasma concentrations of remdesivir are expected to decrease if it is
administered together with cytochrome P450 inducers such as rifampicin , carbamazepin,
phenobarbital, phenytoin, primidone.

14. anti-malarial drugs chloroquine (CQ) and its analog hydroxychloroquine (HCQ), which
are among the most used drugs because they are easy to obtain and have a proven favorable
safety record at relatively low cost. CQ/HCQ are derivatives of 4-aminoquinolin. They are
lipophilic weak bases that quickly pass across cell membranes and accumulate in acidic
organelles, such as lysosomes, endoplasmic reticulum and Golgi . CQ/HCQ are used to
treat and prevent malaria attacks due to their anti-plasmodium activity and to treat
autoimmune diseases such as systemic lupus erythematosus (SLE) and rheumatoid arthritis
(RA) owing to their immunomodulatory activity . In addition, CQ/HCQ display
antibacterial, antifungal and antiviral activities.
Mechanisms of CQ/HCQ in treating COVID-19
The S protein of SARS-CoV-2 is cleaved by host proteases into two subunits, S1 and S2 .
The S1 subunit binds to the host cell surface receptor angiotensin-converting enzyme 2 (ACE2)
for virus attachment, and the S2 subunit fuses the virus and the host cell membrane . The
investigation of the effect of CQ on ACE2 in VeroE6 cells showed that effective anti-SARS-
CoV-2 concentrations of CQ had no significant effect on the synthesis and glycosylation of S
protein on the surface of SARS-CoV, and although it had no significant effect on the cell
surface expression of ACE2, CQ could destroy the glycosylation at the terminal glycosylation
site of ACE2 [13]. Therefore, the mechanism of anti-CoV activity of CQ/HCQ may be at least
partly related to the impairment of terminal glycosylation of ACE2, which may result in
reduced binding affinities between ACE2 and SARS CoV S protein, thereby blocking receptor
recognition.
chloroquine and hydroxychloroquine for the treatment of
COVID-19

15.  coVs are enveloped RNA viruses, and their cell entry processes involve a principal
route of receptor-mediated endocytosis . Membrane fusion takes place in the endosomal
compartment after endocytosis, which needs additional triggers such as pH acidification or
proteolytic activation . Multiple cellular proteases, such as trypsin, furin, proprotein
convertase (PC) family, cathepsins, transmembrane protease/serine (TMPRSS) proteases
and elastase, are involved in S protein activation, which can induce membrane fusion.
 SARS-CoV-2 enters 2ACE2 cells mainly through endocytosis, in which cathepsin L is critical
for priming of SARS-CoV-2 S protein [24]. A study investigated the detailed mechanism of
action of CQ/HCQ in inhibiting SARS-CoV-2 entry, and co-localization of SARS-CoV-2 with
early endosomes (EEs) or endolysosomes (ELs) in VeroE6 cells, and the results showed that
CQ/HCQ hampered the transport of SARS-CoV-2 from EEs to ELs, indicating that CQ/HCQ
might inhibit endosomal maturation . These studies revealed that the mechanism of anti-CoV
activity of CQ/HCQ may involve the inhibition of the endosome acidification process, which
might inactivate lysosomal proteases, thus interfering with the fusion of virus and host
membrane.
 The mitogen-activated protein kinase (MAPK) pathway transmits signals from the cell surface
to the nucleus involved in the infection of CoVs such as MHV [36] and SARS-CoV. CQ could
inhibit HCoV-229E replication in human embryonic lung epithelial cells (L132) through
suppressing the activation of p38 MAPK . Moreover, HCQ could markedly induce the production
of cellular reactive oxygen species (ROS), which play an important role in the activation of
innate immunity. HCQ also could trigger the host defense mechanism through the mitochondrial
antiviral signaling (MAVS) pathway, resulting in anti-dengue virus activity.
Interference of the membrane fusion process

17. Pharmacokinetics
Hydroxychloroquine has similar pharmacokinetis to chloroquine, with rapid gastrointestinal
absorption, large distribution volume, and elimination by the kidneys. Cytochrome P450 enzymes
(CYP2D6, 2C8, 3A4 and 3A5) metabolize hydroxychloroquine to N-
desethylhydroxychloroquin.both agents also inhibit CYP2D6 activity and may interact with other
medications that depend on this enzyme.
Contraindications
the drug label advises that hydroxychloroquine should not be prescribed to individuals with
known hypersensitivity to 4-aminoquinoline compound. There are other contraindication and
caution is required if the person considered for treatment has certain heart conditions, diabetes
or psoriasis.
Adverse effects
adverse effects of hydroxychloroquine use include agitation, , mani , difficulty sleeping
hallucinations, psychosis, catatonia, paranoia, depression. and suicidal thoughts.In rare
situations, hydroxychloroquine has been implicated in cases of serious skin reactions such
as Stevens-Johnson syndrome, toxic epidermal necrolysis, and Drug reaction with eosinophilia
and systemic symptoms. Reported blood abnormalities with it use lymphopenia, eosinophilia,
and atypical lymphocytosis.

18. Ivermectin [mixture of 22, 23-dihydroavermectin B1a (80%) and 22, 23-dihydroavermectin B1b
(20%)] (Fig. 1) is a macrocyclic lactone with a broad-spectrum antiparasitic pharmacological
activity (Gonzalez Canga et al. 2008). It is the safest and most effective semi-synthetic derivative
of the entire class of avermectins, discovered in 1975 by Professor Satoshi Ōmura as
fermentation product of the actinomycetebacterium Streptomyces avermitilis (Crump 2017)
(later reclassified in S. avermectiniu,)
Its main pharmacodynamics is to bind some channel proteins for chlorine controlled by
glutamate,typical of specific classes of invertebrates, causing a greater permeability to this
electrolyte: allthiscauses a hyperpolarization of the cell membrane, blocking inhibitory
neurotransmissioninneur on sandmyocytes,resulting in paralysis and death.
Ivermectin

19. Ivermectin is a versatile drug with unique characteristics, which make it interesting also for
basic and applied research (in particular for drug repurposing): it seems to reveal an antibacterial,
antiviral, and Anticancer activity, besides being potentially useful for the treatment of some
chronic pathologies, result of an action on a wide range of cellular targets.
The broad-spectrum antiviral potential of ivermectin against several RNA viruses is due to its
ability to specifically inhibit importin α/β-mediated nuclear transport, which in turn blocks the
nuclear trafficking of viral proteins . Several RNA viruses depend on Impα/β1 during the
process of infection . SARS-CoV-2, is an RNA virus, is expected to show a similar mechanism
of action. The proposed anti-SARS-CoV-2 action of ivermectin involves the binding of
ivermectin to the Impα/β1 heterodimer, leading to its destabilization and prevention of
Impα/β1binding to the viral proteins. This prevents viral proteins from entering the nucleus,
thereby reducing the inhibition of antiviral responses and leading to an efficient antiviral
response .
The antiviral activity of ivermectin is also found to be related to other mechanisms. Ivermectin
has been reported to suppress the replication of the pseudorabies virus by inhibiting the nuclear
import of UL42 (an accessory subunit of DNA polymerase) . A similar mechanism of inhibition
was reported for another DNA virus,

21. Pharmacokinetics
Ivermectin can be given by mouth, topically, or via injection. It does not readily cross the blood–
brain barrier of mammals due to the presence of P-glycoprotein (the MDR1 gene mutation
affects function of this protein). Crossing may still become significant if ivermectin is given at
high doses (in which case, brain levels peak 2–5 hours after administration). In contrast to
mammals, ivermectin can cross the blood–brain barrier in tortoises, often with fatal
consequences.
Adverse effects
The main concern is neurotoxicity, which in most mammalian species may manifest as central
nervous system depression, and consequent ataxia as might be expected from potentiation of
inhibitory GABA-ergic synapses.
Since drugs that inhibit the enzyme CYP3A4 often also inhibit P-glycoprotein transport, the
risk of increased absorption past the blood-brain barrier exists when ivermectin is administered
along with other CYP3A4 inhibitors. These drugs include statins, HIV protease inhibitors, many
calcium channel blockers, lidocaine, the benzodiazepines, and glucocorticoids such as
dexamethasone.[
For dogs, the insecticide spinosad may have the effect of increasing the toxicity of ivermectin.
Contraindications
Ivermectin is contraindicated in children under the age of five or those who weigh less than 15
kilograms (33 pounds), and individuals with liver or kidney disease. Ivermectin is secreted in
very low concentration in breast milk.It remains unclear if ivermectin is safe during pregnancy