Antiviral - Hepatitis C

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Table of Contents
The Nature of Hepatitis C and the Conditions that are treated by DAAs... Error! Bookmark
not defined.
Fig. 1: Specific Targets of the Direct Acting Antiviral Agents ........................................... 3
The History of the Development of DAAs .................................................................................. 4
The Mechanism of DAAs’ Action (NS3/4A Protease Inhibitors (PIs), telaprevir, Nucleotide
NS5B inhibitor, Sofosbuvir and NS5A inhibitor, Daclatasvir) Relating it to the Content of
the Nature of the Disease/Condition ............................................................................................ 6
Stereo-Chemical and Conformational Requirements of Drug-Target Interactions ........... 6
Telaprevir Mechanism of Action ......................................................................... 7
Sofosbuvir Mechanism of Action ......................................................................... 8
Daclatasvir Mechanism of Action........................................................................ 8
The Quantitative Structure-Activity Relationships Relevant to Telaprevir Illustrated with
its Chemical Structure .................................................................................................................. 9
Fig. 5: Chemical Structure of Telaprevir ......................................................................... 10
Fig. 6: QSAR Tables ......................................................................................................... 11
Works Cited .................................................................................................................................. 13
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Antiviral - Hepatitis C
The Nature of Hepatitis C
Hepatitis C refers to inflammation of the liver, and it is caused by Hepatitis C Virus
(HCV). HCV is a small positive-strand ribonucleic acid (RNA) virus in the Flaviviridae family.
There are several different HCV genotypes with the most common one in the U.S.A being HCV
genotype 1. The rate of new infection with HCV is estimated to be between 3-4 million
individuals each year (WHO 2017). Hepatitis C is the main cause of many deaths each year in
the U.S and other parts of the world. The human immune system cannot easily eliminate the
HCV from the body due to its rapid rate of replication hence the infection usually becomes
chronic (medicaleconomics). If left untreated, Hepatitis C can cause serious damages to the liver
and lead to liver failure. Nevertheless, modern treatments have made it possible to cure Hepatitis
C infection, thus giving most people with it the hope of a normal life expectancy. This paper will
hence dwell on antiviral drugs(NS3/4A Protease Inhibitors (PIs), telaprevir, Nucleotide NS5B
inhibitor, Sofosbuvirand NS5A inhibitor, Daclatasvir) which are used to cure the Hepatitis C
infection and the conditions that the drugs can be used to treat.
HCV is a blood borne virus, and one can be infected with it through exposure to infected
blood. Organ transplants, blood transfusions, and sharing of sharp objects are common ways
through which the virus can be spread. The infection may be short-lived in some people as their
body can clear the virus without treatment. Usually, there are no noticeable symptoms when the
virus first enters the body, and many people may have the infection without realizing it (NCBI).
The symptoms may develop gradually right from the acute stage of Hepatitis C. If the infection
lingers in the body for six months or longer, symptoms such as fever, appetite loss and tiredness
may be experienced by the infected person. The only way to be certain whether one has been
infected or not is through testing.
Since the discovery of Hepatitis C in 1989, many advances have been made in developing
safe and effective treatments. The development of Direct-Acting Antivirals (DAAs) has
significantly improved the efficacy of treatments for HCV infection. These drugs target HCV
and stop its replication at various stages of the virus life cycle (Halfon). By preventing HCV
from making copies of itself, the virus can eventually be eliminated from the body. DAAs stop
the virus from reproducing and can clear the HCV in a matter of two weeks. This way, the
danger of liver inflammation and liver failure after a severe attack by the virus is eliminated.
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HCV infection is likely the leading cause of chronic liver-related diseases such as hepatocellular
carcinoma, liver failure, and liver cirrhosis. DAAs stop the damage of the liver by getting rid of
the virus that is responsible for the damage.
The DAAs are categorized into four classes. They include NS3/4A Protease Inhibitors
(PIs), Nucleoside and Nucleotide NS5B Polymerase Inhibitors, NS5A Inhibitors, and Non-
Nucleoside NS5B Polymerase Inhibitors ( NS3/4A Protease Inhibitors (PIs) prevent
HCV from replicating in the host cell by blocking protease, a viral enzyme. Nucleoside and
Nucleotide NS5B Polymerase Inhibitors attach themselves onto RNA, thereby blocking the virus
from multiplying. NS5A Inhibitors block NS5A which is a protein that HCV needs to reproduce
and for the various stages of infection (Jakobsen et al.). Non-Nucleoside NS5B Polymerase
Inhibitors attach themselves to HCV so that other pieces cannot attach themselves to it. DAAs
work by inhibiting specific stages of the HCV replication cycle
Fig. 1: Specific Targets of the Direct Acting Antiviral Agents
Adopted from (Jakobsen).
The NS5B polymerase and NS3-4A protease target active sites of the viral enzyme which
are essential for replication (Gardner). The NS5A protein inhibits the activities of NS5A. DAAs
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have fewer side effects and relatively higher efficacy with shorter treatment times. These host-
targeting antivirals have Sustained Viral Reaction (SVR) rate of up to 95%. Before treatment
with DAA drugs, factors such as baseline viral load, HCV genotype and virological response to
treatment need to be considered (Delang). Eradication of HCV before a liver transplant can lead
to improved efficacy. DAAs treatment can take 8-12 weeks to eliminate the HCV from the body.
The History of the Development of DAAs
Unlike antibiotics which achieved an advanced therapeutic stage in 30 years, Antiviral
chemotherapy has advanced at a slow pace. Antiviral development took 60 years to reach its
current status of effectiveness (Bryan-Marrugo et al.). The evolution of Hepatitis C treatment has
shown how the development of Antiviral is a very complex process. Combined and specific
targeted antiviral therapy has proved to be the best approach for the treatment of a viral disease.
A thorough description of the development of specifically targeted antiviral therapy can be
useful for further research and treatment of viral diseases.
The number of new viruses that have been identified as causative agents of human
diseases since 1972 is more than 50. More sophisticated therapeutic agents are required to
combat these new viral diseases (Gane). Unfortunately, the development of these strategies has
been slow and full of hurdles. The development of DAAs has come a long way. A standard of
care (SOC) between 2001 and 2011 consisted a combination of ribavirin (RBV) and pegylated
interferon (PEG-IFN) (Strader and Seeff). The lingering response rates of HCV genotype 1 to
ribavirin (RBV) and pegylated interferon (PEG-IFN) treatment led to investigations to develop
therapies that focus on the virus itself. The first-generation NS3/4A protease inhibitors,
telaprevir, and boceprevir, were authorized for use in combination with RBV and PEG-IFN in
May 2011(Fung). The HCV genotype 1 treatment using these combinations was to take 24-48
In December 2013, a second-generation NS3/4A protease inhibitor, Simeprevir was
approved for use in combination with RBV and PEG-IFN for 12 weeks treatment course in HCV
genotype 1(Graham). An NS5B nucleotide polymerase inhibitor, Sofosbuvir was also approved
in 2013 for use in combination with RBV and PEG-IFN for 12-24 weeks treatment course in
HCV genotype 1 to 4 (Catherine). IFN free regimens were later found to be more effective and
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gave better results. A combination of simeprevir or NS5A replication complex inhibitor,
daclatasvir or ledipasvir with Sofosbuvir with or without RBV for a 12 weeks treatment course
in HCV genotype1 saw a sustained virological response (SVR) of more than 90% (Lin).
Additionally, regimens based on ritonavir-boosted NS3/4A protease inhibitor, ABT-450/r
combined with or without RBV for 12 weeks treatment course in HCV genotype 1 have also
produced similar results (Rosenquist).
Development of NS3/4A Protease Inhibitors (PIs), telaprevir faced a lot of hurdles as it
had to be put on hold due to its performance in a standard IC
assay. It took data from new
experiments and hypothesis to justify further investment in the development of telaprevir. The
drug was approved in Europe in 2011 for the treatment of HCV genotype 1. Nucleotide NS5B
inhibitor, Sofosbuvir, also known, as GS-7977 discovery revolutionized the management of
Hepatitis C Virus infection. It was used in the initial evaluation with RBV and PEG-IFN. The
valuable features of Sofosbuvir which include its excellent tolerability, pan genotypic activity,
and safety profile makes it a powerful weapon in the treatment of HCV infection (Zappulo). The
highly selective NS5A inhibitor, Daclatasvir (BMS790052) was developed by Bristol-Myers
Squibb. It has a broad coverage of HCV genotypes in vitro. Daclatasvir (BMS790052 was
approved in July 2015 for use in treatment of HCV genotype 1 and 3
Therapy for HCV infection was at the pace of snail as it remained nearly the same
between 2001 and 2011. The development of specific compounds against HCV took a very long
time. The hurdles that slowed the process include the limitation of animal models for
experimentation and in vitro systems. Also, there was a low rate of discovery of suitable
candidate molecules and the balance between resistance to the selected antiviral drugs, toxicity,
and efficacy. The development of an in vitro virus propagation system by Weller, Robbins, and
Enders in 1951 was a huge breakthrough in this field. This helped in the study of viruses. The
inception of 9-(2-hydroxy ethoxy methyl) guanine (Acyclovir) improved the understanding of
virus-host interaction. It was the first highly effective antiviral drug.
DAAs approval has substantially improved therapeutic options for treatment of HCV
infection. An era of development of new DAAs for HCV treatment is currently emerging.
Several other Direct-acting antivirals are being developed such as Protease inhibitors:
asunaprevir, faldaprevir, vaniprevir, danoprevir, GS-9451, MK5172, ABT-450-ritonavir; NS5A
inhibitors:daclatasvir, MK-8742, PPI-668, GS-5816, ombitasvir and ledipasvir; NS5b
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inhibitors:GS-9669, BMS-791325, dasabuvir, VX-135, and mericitabine. These have been
shown to reduce viral RNA levels with upto 95% SVR in treated patients (Clercq E). DAAs have
to overcome the main obstacles of drug resistance and HCV genetic variability.
Antiviral therapy is well established and shows a promising future. Depending on
medical, economic and scientific interest, development of antiviral drugs in the coming years
will majorly focus on HCV and HIV. The increase in knowledge about viruses, their lifecycle,
structure, pathogenesis, function, infection mechanism and rapid discovery of antiviral strategies
and techniques will speed up the development of antiviral drugs (Akimitsu). Antiviral drugs have
brought a dramatic paradigm shift in the space of a few years. HCV infection which was once
very difficult to cure has become easily curable with a short duration of oral antiviral therapy
with minimal side effects.
Mechanism of Action
Stereo-Chemical and Conformational Requirements of Drug-Target Interactions.
Stereochemistry has become a significant issue in recent years not only to the pharmaceutical
industry but also to the regulatory authorities. It is important for drug manufacturers to consider
stereo selectivity when designing small molecules to interact with the targets. The pharmacologic
basis of drug action majorly involves modulation of the physiological activities of
macromolecules such as ribosomes, receptors, and enzymes by binding them to the drug
molecules. The temporal persistence of target occupancy by the drug dictates the duration of
pharmacologic effect. Historically, the effectiveness of a drug's interaction with a target has often
been quantified by measuring the concentration of drug required to achieve a specific level of
target occupancy under equilibrium conditions (Mehnaz). In recent years, there has been
increased recognition that equilibrium conditions do not define drug-target interactions in vivo.
The binary drug-target complex is stabilized in vivo to achieve sustained pharmacologic effect.
The reaction of drugs with receptors as specific tissues is a very important goal when
designing drugs. Recent techniques such as molecular modeling can be used to search structures
that show specificity for the target receptor that will produce the desired pharmacological
response while decreasing the affinity for undesired receptors that produce adverse response
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(Rang). Additionally, biodistrubution can be altered by altering the molecule. Chemical
structures of any drugs profoundly affect both its pharmacokinetic and pharmacodynamic
Telaprevir Mechanism of Action
NS3/4A protease of HCV is an important target for the development of antiviral drugs.
NS3/4A Protease Inhibitors (PIs), telaprevir works by inhibiting protease enzymes activities in
the body. It directly interferes with the different steps of HCV life cycle by blocking the protease
enzyme that the virus must use for reproduction. The HCV NS3/4A is a multifunctional protein
that is made up of helicase domain and protease domain linked by a flexible linker (Kirkegaard).
Its activities are crucial in the production of viral nonstructural (NS) proteins which are involved
in RNA replication. Helicase activity is also required for replication of RNA. HCV useNS3/4A
protease to clip long protein strands into shorter strands that it then uses for replication. Protease
inhibitors block NS3-dependent polyprotein processing by binding to protease active sites. This
impacts other steps of the virus life cycle. Telaprevir exerts a direct effect on the synthesis of
RNA by engaging and blocking NS3 Synthesis and virus maturation (Li et al.). Additionally, it
inhibits polyprotein processing. Telaprevir rapidly inhibits production of viruses from infected
cells. The cure rate of Telaprevirtriple therapy is 75%, but it works better for certain groups than
others. The risks of long-term complications of hepatitis C such as liver cancer or needing a
liver transplant can be reduced after successful treatment.
Fig. 2: Chemical Structure of Telaprevir
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Sofosbuvir Mechanism of Action
Nucleotide NS5B inhibitor, Sofosbuvir prevents HCV from further replicating. RNA is
key for generation of new viruses. Upon infesting the liver, HCV produces billions of virus
clones every single day. The huge magnitude of billions of virus overwhelms the immune system
reducing its ability to eliminate the viruses. Sofosbuvir blocks viral RNA polymerase which is
the component that HCV uses to construct genetic material (Maraolo). It puts on hold
multiplication of the virus thereby allowing the immune system to come in and eradicate the
Fig. 3: Chemical Structure of Sofosbuvir
Molecular Formula: C
Sofosbuvir mechanism of action against HCV inhibits viral RNA polymerase by being a
defective substrate (Herbst Jr). It disguises itself as a nucleoside, a structural part of NS5B which
HCV uses to build new viruses. Sofosbuvir is very efficient since it is already activated and does
not require prior activation as was the case with previous antiviral drugs. Sofosbuvir mimics the
nucleoside, and attaches itself to the NS5B polymerase viral protein which is a vital component
virus replication, thus, preventing further construction of the viral protein.The number of HCV
stagnates as the immune system eliminates them resulting in healing of Hepatitis C virus
Daclatasvir Mechanism of Action
Daclatasvir (BMS790052) mechanism of action targets one of HCV proteins causing the
fastest viral decline ever seen with anti-HCV drugs. The drug is an NS5A replication complex
inhibitor that blocks two stages of the viral life cycle (Newsmedicals). The nonstructural protein
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NS5A encoded by the HCV is a specific target for drug development. The discovery of
Daclatasvir was a huge breakthrough since the drug produced one of the most potent effects in
combating HCV with a manifold decrease in the levels of the virus within about 12 hours
(Pawlotsky). Daclatasvir blocks two distinct processes in the viral life cycle namelythe release of
the virus from the infected cells and the synthesis of new viral genomes.The drug binds to the
domain I of NS5Aprotein and blocks both virion maturation and viral replication (Marko). The
interaction of daclatasvir with the NS5A terminus causes structural distortions that interfere with
the functions of NS5A. It prevents activation and formation of the HCV replication complex.
This helps to counter the buildup of HCV in the liver thereby reducing liver damage.
Fig. 4: Chemical Structure of Daclatasvir
Molecular Formula: C
The Quantitative Structure-Activity Relationships in drugs manufacture
Many lives are lost every year due to Severe Adverse Drug Reactions (ADR). The
quantitative structure-activity relationship (QSAR) can be utilized to predict the likelihood of
drug-drug interactions (DDI) which is believed to be the cause of many deaths world over
(Alexey). QSAR is one of the earliest approach that incorporated the use of computer in
screening a large data set of small molecules and categorizing them under certain features or
descriptors. It involves the analysis of the quantitative relationship between the biological
activity of a set of compounds and their three-dimensional properties using statistical correlation
methods. QSAR makes it possible to derive compounds with elevated desired property or mix of
few. It is useful in the exploration of small molecule activities and their relation on the basis of
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their structure relatedness. The structure relatedness between different molecules is quantified
and how similar structural parts govern their activities is searched.
QSAR of NS3/4A Protease Inhibitors Telaprevir helps to investigate the possibility of
improving biological activity of the drug (Zakharov et al.). The structure of Telaprevir is
modified, and then molecular modeling is used to calculate the QSAR properties of suggested
compounds and to select the best of the suggested compounds which are then compared with the
unmodified Telaprevir. This is useful in studying the biological activity of the new inhibitors and
the physical aspect of the interaction with the virus and selecting the possibly best compound to
synthesize (Saleh). In the study of the QSAR of Telaprevir, eleven different modifications are
suggested to the structure of Telaprevir. Molecular modeling software, SCIGRESS is then used
to carry out the calculations. The investigated compounds are built and calculations performed
with the help of SCIGRESS. Geometries optimization calculations are performed using MO-G at
the PM3 level of theory to refine the compounds' geometries. The comparison is then made
between the QSAR properties of the optimized structures and the unmodified Telaprevir. The
chemical structure of Telaprevir helps in determination of the chemical group that evokes the a
target biological effect in the organism.
Fig. 5: Chemical Structure of Telaprevir
Molecular formula: C
The suggested compounds, some QSAR, and biological activities of Telaprevir are
presented in Table II (Fig. 6: QSAR Tables). The PM3 method is used to carry out the QSAR
calculations. Dipole moment, log P and, polarizability, molar refractivity, surface area and
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volume are QSAR descriptors used in this study. The volume and surface area of the studied
modified compound and Telaprevir are shown in Table II. The results show that the volume and
surface area values of compound number 6 are closer to that of Telaprevir than the other
compounds. The surface areas of compound number 6 and Telaprevirare 720.22 Å2 and 706.6
Å2 respectively. Molar refractivity and polarizability related to the molecule are also listed in
Table II. From the table, the molar refractivity and polarizability of compound number 6 and
Telaprevir are close to each other. The values of dipole moment are very low compared to that of
Telaprevir. Compound number 6 has the highest dipole moment. This indicates that compound
number 6 is more reactive with the biological system compared to all other compounds including