Summary:
The aim of this dissertation was the in silico identification of new compounds
against hepatitis C and beta-thalassaemia diseases.
Hepatitis C, caused by hepatitis C virus (HCV), mainly affects the liver and
has spread worldwide in recent decades. To date, no vaccine has been discovered
against hepatitis C virus, while the current therapy is effective only in
limited cases. The HCV NS5B RNA-dependent RNA polymerase is the key function of
the replication of viral RNA, constituting a therapeutic target of disease.
Search of inhibitors of HCV NS5B RNA polymerase has led to the investigation of
the nucleoside (NIs) and non-nucleoside inhibitors (NNIs), targeting on the
catalytic site and allosteric sites (palm, thumb, fingers) of the enzyme,
respectively. NNIs have attracted the particular interest of researchers.
Molecular docking, 3D-QSAR CoMSIA and similarity search were combined in a
multi-step framework with the ultimate goal to identify potent indole analogs,
in the ChEMBL database, as inhibitors of HCV replication, in a virtual
screening procedure. Initially, 41 known inhibitors were docked into the enzyme
‘‘Palm II’’ active site. In a second step, the docking pose of each compound
was used in a receptor-based alignment for the generation of the CoMSIA fields.
A validated 3D-QSAR CoMSIA model was subsequently built to accurately estimate
the activity values. The proposed framework gave insight into the structural
characteristics that affect the binding and the inhibitory activity of these
derivatives on HCV polymerase. The obtained in silico model was used to predict
the activity of novel compounds prior to their synthesis and biological
testing, within a virtual screening procedure. The ChEMBL database was mined to
afford 18 compounds containing the indole scaffold that are predicted to
possess high activity and thus can be prioritized for biological screening.
A similar combination of the computational methods: (i) molecular docking, (ii)
3D-QSAR CoMFA, (iii) similarity search and (iv) virtual screening using PubChem
database was applied to identify new anthranilic acid-based inhibitors of HCV
replication. 53 known inhibitors were initially docked into the ‘‘Thumb Pocket
2’’ allosteric site of the crystal structure of the RNA polymerase. Then, the
CoMFA fields were generated through a receptor-based alignment of docking poses
to build a validated and stable 3D-QSAR CoMFA model. The proposed model was
utilized to get insight into the molecular features that promote bioactivity,
and then a virtual screening procedure was used to estimate the activity of
novel potential bioactive compounds.
Beta-thalassaemia is a common blood disorder spread worldwide, that reduces the
production of hemoglobin (Hb). Pharmacological reactivation of the γ-globin
gene for the production of fetal haemoglobin (HbF) is a very promising
therapeutic avenue for the disease. K562 human erythroleukemic cell line has
the potential to highly express the γ- but not the β-globin gene. Erythroid
differentiation of K562 cells is associated with an increase in the expression
of embryo-fetal globin genes such as ζ, ε, and γ-globin genes. This
characteristic makes K562 cells a widely useful model cell line for the study
of compounds that are potential γ-globin inducers for use β–thalassaemia
In an attempt to aid the design of new chemotypes with enhanced cytotoxicity
against K562 cells, 3D pharmacophore models were generated and 3D-QSAR CoMFA
and CoMSIA studies were carried out on the 33 novel ABL kinase inhibitors (E)-α-
benzylthio chalcones. BCR-ABL is a constitutively active tyrosine kinase that
is responsible for the malignant transformation and chronic myelogenous
leukemia (CML). A five-point pharmacophore (AHHRR) with a hydrogen bond
acceptor, two hydrophobic groups, and two aromatic rings as pharmacophore
features, and a statistically significant 3D-QSAR model with excellent
predictive power were developed. The pharmacophore model was also used for
alignment of 33 compounds in a CoMFA/CoMSIA analysis. The contour maps of the
fields of CoMFA and CoMSIA models were utilized to provide structural insight
into how these molecules promote their toxicity. The possibility of using this
model for the design of drugs for the treatment of β–thalassaemia since several
BCR-ABL inhibitors are able to promote erythroid differentiation and γ–globin
expression in CML cell lines and primary erythroid cells was discussed.
Keywords:
HCV, beta-thalassaemia, Molecular Modeling, 3D-QSAR, CoMFA/CoMSIA
