University of Bahrain

College of Sciences Biological Sciences Department

In Silico Investigation of 5- Azacitidine against

Sickle Cell Anemia
Research paper submitted in partial fulfillment of the requirements for Research
Methodology and Ethics course
In Biological Sciences

Prepared by:

Fatema Shehab 202300530

Supervised by:
Dr. Salwa Mutlaq Al-Thawadi

Associate Professor

University of Bahrain

Kingdom of Bahrain

January 2023
 1. Abstract
Sickle cell anemia is a hereditary hematological disorder characterized by the production of
abnormal hemoglobin, leading to the formation of rigid, crescent-shaped red blood cells and
causing various complications, including vaso-occlusive crises and chronic organ damage.
Current treatment options for Sickle cell anemia are limited, necessitating the exploration of
novel therapeutic approaches. Azacitidine, a DNA hypomethylating agent approved for
myelodysplastic syndromes, has demonstrated promising effects in hematological malignancies
and autoimmune diseases. The hypothesized mechanism of action of azacitidine involves the
reactivation of fetal hemoglobin production, which has been shown to ameliorate the clinical
severity of Sickle cell anemia. Studies evaluating the use of azacitidine in preclinical models and
early-phase clinical trials have reported increased fetal hemoglobin levels, decreased vaso-
occlusive events, and improved overall clinical outcomes in Sickle cell anemia patients.
Furthermore, azacitidine's epigenetic modulation may influence the expression of genes involved
in erythropoiesis and hemoglobin switching, offering a unique therapeutic avenue.
In silico investigation will be carried out to investigate whether 5-aza helps enhance therapeutic
options for the affected individuals and provide opportunities for personalized medicine
approaches.

2. Introduction
Sickle cell disease (SCD) is an autosomal genetic disorder characterized by sickle-like shaped
red blood cells caused by a mutation, substituting the amino acid valine for glutamic acid at
position six of the β-globin chain. The mutation causes an abnormal form of hemoglobin called
hemoglobin S (HbS), resulting in multiple complications such as anemia, severe crises,
infections, strokes, and cardiac problems (Al Arrayed and Haites ,1995) (Bakri et al., 2013).
Over the years, researchers and medical professionals have been exploring various treatment
options to alleviate the symptoms and complications associated with SCD. One such treatment
approach involves the use of a medication called 5-azacytidine, commonly referred to as 5-aza.
5-aza is a pharmacological compound that belongs to a class of drugs known as DNA
methyltransferase inhibitors. It was initially developed as an anticancer agent but has shown
promise in the management of SCD. The primary mechanism of action of 5-aza involves the
inhibition of DNA methyltransferase enzymes, which are responsible for adding methyl groups
to DNA molecules. By inhibiting these enzymes, 5-aza modulates gene expression patterns,
including those related to fetal hemoglobin (HbF) production. HbF is a type of hemoglobin
normally produced during fetal development but significantly decreases after birth. In individuals
with SCD, the presence of higher levels of fetal hemoglobin can ameliorate the symptoms of the
disease. HbF has a different structure than the adult hemoglobin affected by the sickle cell
mutation, and it has been observed to inhibit the sickling of red blood cells (Hussain et al., 2023)
(Dover et al., 1985). Despite the fact that current therapy has improved patients' quality of life
and survival rates, not all patients respond equally well to these treatments. Developing new
drugs is necessary to provide additional options for symptom relief and management, potentially
improving the quality of life for individuals with SCD. Drugs that can increase the production of
HbF, such as 5-aza, are a potential for managing HbS (Zhu et al., 2004).
The incidence is estimated to be between 300,000 to 400,000 neonates globally each year. In a
meta-analysis of the prevalence and associated mortality in children under five years of age, it
was reported that the global birth prevalence of homozygous SCD is 112 per 100,000 live births,
but 1125/100,000 in Africa compared to 43.12/100,000 in Europe. It has been estimated that the
global burden of SCD will increase by up to 30% by 2050. The highest prevalence of SCD is
among the people of Sub-Saharan Africa, South Asia, the Mediterranean, and the Middle East
(Ata et al., 2023) (Roseff, 2020). Locally, a population-based study in Bahrain has confirmed a
high prevalence of SCD in a population of approximately 50,000 Bahrainis in a hospital; 1,000
of them had SCD, and 10,000 had sickle-cell trait (Al Arrayed & Haites, 1995).

3. Materials and Methods

Keywords:
 4. Results and Discussion

4.1 Screening of Active Compounds and Targets

A search on 5-azacytidine was conducted using PubChem (Table 1). Additionally, the
SwissTargetPrediction database identified 73 genes that could potentially be targeted by the
compound. Subsequently, a comprehensive search in the GeneCards databases revealed 1067
genes associated with sickle cell anemia (SCD). To identify common targets between SCD-
related genes and those potentially targeted by the compound, a Jvenn diagram was employed.
This analysis revealed a total of 24 common potential gene targets.

Molecule Molecular Drug Oral Structure PubChem

Name Weight likeness bioavailability ID
(MW)
5-Azacytidine 244.20 g/mol 572 mg/kg 6.3% to 20% 9444

Table 1. properties and structure for the compound

4.2 Compounds-Target Network Construction

The degree of these 10 compounds in the compound-targeted genes-connected pathways network
was then assessed (Table 2). As indicated in Table 2, PTPN11, ADA, and MAPK1 exhibit a
comparably maximum degree and were selected for docking analysis.

Rank class Degree

1 PTPN11 4
1 ADA 4
1 MAPK1 4
4 PTGS2 2
4 CASP3 2
4 PTPN1 2
4 ADORA2A 2
4 ADK 2
4 ELANE 2
4 PTGS1 2
Table 2. Degree of 10 compounds explored through network analyzer in Cytoscape.
4.3 PPI Network Construction
The 27 genes that overlapped were uploaded to the STRING database to build a PPI network. A
PPI network shows how different targets work together during the development of a disease. The
nodes and their connections show how these targets work together. Later, Cytoscape was utilized
at the PPI network of genes Pharmaceuticals that overlapped (PTPN11, ADA, MAPK1, PTGS2,
CASP3, PTPN1, ADORA2A, ADK, ELANE, and PTGS1 showed the highest degree. This
means that the highest degree genes are greatly linked to each other; thus, all of these genes
might be hub targets.

4.4 GO and KEGG Pathway Analysis

The functional annotation and enrichment analysis unveiled the potential biological roles 5-
azacitidine. According to GO functional analysis, there were related to Nitrogen metabolism,
IL17 signaling pathway, metabolic pathway, and so on. (Figure 2). The KEGG pathway analysis
was performed to identify the significant signaling pathways linked to SCD and 5-aza. It is
noteworthy that most of the genes were involved in following pathways. These include the NF-
κB, the stress-responsive mitogen-activated protein kinase (MAPK), and the STAT pathways
[19], including the PI3K-AKT-mTOR, AMPK-mTOR, EGF, MAPK, Wnt/β-catenin, p53, and NF-κB
pathways [20]. KEGG pathway analysis revealed that EGFR, MAPK3, MTOR, and PIK3R1 were
significantly enriched genes (Figure 3)
(A) (B)

(C) (D)

Figure 2. Representation of functional annotation and enriched pathways in form of Bubble Plot. (A) GO in terms of
biological processes. (B) GO in terms of molecular function. (C) GO in terms of cellular components. (D) KEGG
pathway analysis
4.5 Molecular Docking
The top three targets, PTPN11, ADA, and MAPK1, were chosen for molecular docking using
PyRx tool after a thorough analysis of the PPI network. The PDB structure was used to find the
3D structure of the target proteins (PTPN11 - PDB id: 2SHP, ADA - PDB id: 1U8B, and
MAPK1 - PDB id: 6G54). All the PDB structures were selected based on their resolution. Low
numeric values in Å indicate that the resolution of the structure is good and can be considered for
further analysis within the framework of the current study.
5. Conclusion
In conclusion, this in silico investigation provides valuable insights into the potential use of
5-Azacitidine as a therapeutic agent against SCD. Further experimental validation, including
in vitro and in vivo studies, is essential to confirm the efficacy and safety of 5-Aza in treating
SCD.
SCD is a genetic disorder characterized by the presence of abnormal hemoglobin, leading to
the production of damaged red blood cells and various complications. On the other hand, 5-
aza is a medication primarily used in the treatment of myelodysplastic syndromes and acute
myeloid leukemia.
Research studies have explored the potential of 5-aza as a therapeutic agent for SCD due to
its ability to modify DNA methylation patterns and gene expression. By inhibiting DNA
methyltransferase enzymes, 5-aza can induce hypomethylation and reactivate silenced genes,
potentially ameliorating the underlying pathology of SCD.
Clinical trials investigating the efficacy and safety of 5-aza in SCD have shown promising
results. These studies have evaluated parameters such as HbF levels, which are associated
with improved clinical outcomes in SCD patients. 5-aza has been found to increase HbF
levels in some individuals, helping mitigate the effects of SCD by reducing the
polymerization of abnormal hemoglobin.
However, it is important to note that while early findings are encouraging, further research is
necessary to fully understand the long-term effects, optimal dosage, and potential side effects
of 5-aza in the context of SCD. Additionally, individual patient characteristics, such as age,
disease severity, and genetic variations, may influence the response to treatment with 5-aza.
Finally, the association between SCD and 5-aza represents a promising avenue for potential
therapeutic interventions. Continued research and clinical trials are needed to determine the
optimal use of 5-aza, its long-term effects, and its place in the management of SCD.

6. References