Int. J. Life. Sci. Scienti.
Res., 3(3): 1085-1088, May
2017
Computational
Analysis of BACE1 Involved in Alzheimer’s disease Using Zebrafish (Danio rerio) as A Model
Nilofer K Shaikh*,
Sana. A. Shaikh
Department of
Bioinformatics, Walchand College of Arts and Science Solapur, Maharashtra,
India
*Address for Correspondence: Dr.
Sana. A. Shaikh, Associate Professor, Department of
Bioinformatics, Walchand College of Arts and Science Solapur, Maharashtra, India
ABSTRACT-
Beta-site amyloid precursor protein cleaving enzyme
(BACE-1) is a single-membrane protein belongs to the aspartyl
protease class of catabolic enzymes. This enzyme involved in the processing of
the amyloid precursor protein (APP). The cleavage of
APP by BACE-1 is the rate-limiting step in the amyloid
cascade leading to the production of two peptide fragments Ab40 and Ab42.
Inhibition of BACE-1 is expected to stop amyloid
plaque formation and emerged as an interesting and attractive therapeutic
target for Alzheimer’s disease. The Zebrafish (Danio rerio) has been established as an
excellent vertebrate model for the study of developmental biology and gene
function. Zebrafish possess genes orthologous to
those mutated in familial Alzheimer’s disease and research using Zebrafish has
revealed unique characteristics of these genes that have been difficult to
observe in rodent models. We were identified and described the expression
of BACE-1, the Zebrafish otology of human BACE-1. Computational approach was
used to identify the molecular chemical features required for the inhibition of
BACE-1 enzyme. Despite its potential, only few compounds targeting BACE-1 have
entered the clinical trials. In this study, we investigated that Cibacron Blue functioned
as an inhibitor and was retrieved from Pubchem
database at NCBI. This paper also deals with the binding mechanism of Cibacron Blue with BACE-1 through
molecular docking coupled with molecular dynamics simulations. The
computational analyses revealed that hydrophobic contact is a
major contributing factor to the binding of Cibacron Blue with
BACE-1.
Keyword-
Amyloid precursor protein (APP), BACE-1, Molecular
Docking, Zebrafish, Cibacron Blue
INTRODUCTION- Alzheimer's
disease (AD) is the most common form of neurodegerative
disease [1]. .AD is characterized
by progressive memory loss and can include impairment of speech and motor
ability, depression, delusions, hallucinations, aggressive behavior and,
ultimately, increasing dependence upon others before death.BACE1 expression is
tightly regulated at the level of transcription and translation [2].
It was reported that a G/C polymorphism in exon 5 of
the BACE-1gene might be associated with some sporadic cases of AD .Although
genetic analyses from our and other laboratories have failed to uncover any mutation
in the BACE-1coding sequence or any disease-associated SNP in its promoter
region in AD patients, increased β-secretase
levels and activity have been reported in AD [3]. BACE-1 levels were
elevated in neurons around plaques. BACE-1mRNA levels tended to
increase as miR-107 levels decreased in the progression of AD [4].
We were reported that hypoxia, a common vascular component among AD risk
factors, increased BACE-1 expression, resulting in both increased Aβ deposition and memory deficits in AD transgenic
mice [5]. Recently we found that both NF-κB
and BACE-1 levels were increased in sporadic AD patients, and NF-κB facilitated BACE1 gene expression
and APP processing. Thus, increased BACE-1 expression by NF-κB
Pubchem database signaling in the brain could be one
of the mechanisms underlying AD development [6]. Together these
studies indicate that BACE-1 deregulation plays an important role in AD
pathogenesis [7]. Zebrafish as a model for AD has been use and of
the Zebrafish brain and a better characterization of the injury caused by
alterations in the major neurotransmitter systems are needed [8-9].
Despite the progress in this field, we still need a better understanding of AD,
which supports the growing importance of further innovative research using experimental
models of neuro-degeneration [10]. Alzheimer's disease is the major cause of senile
dementia, flewing out 10% of 65 years old and 50% of
85 years old global population [11-12]. The major fisiopathologic characteristics of Alzheimer's disease are
the deposition of extracellular neuritic plaques and
the presence of intracellular neurofibrillary tangles
in memory-related areas of the brain [13]. The plaques are composed
by the β-amyloid peptide with 40 or 42 residues,
result from hydrolysis of the amyloid precursor
protein by the β-secretase 1 (BACE-1) on the amyloidogenic pathway, that begins with the BACE-1 and
which inhibition is considered one of the most promising treatments available
of Alzheimer's disease[14-15].
MATERIALS AND
METHODS
Protein Sequence Retrieval:
National Center for Biotechnology Information(www.ncbi.nih.nlm.gov/) database provides a
protein sequence database for characterization and analysis of protein
sequences. The BACE1 protein sequences of Homosapiens
and Danio rerio were retrieved from protein database
at NCBI. The sequences were further prepared in FASTA format for the
characterization.
Characterization of the BACE1:
The two sequences were subjected to PROTPARAM tool at EXPASY server for the
predicting the physicochemical parameters of both sequences. The
physicochemical analysis were calculated by ProtParam
tool (http://web.expasy.org/protparam/), including pI,
total number of negatively and positively charged residues, the instability
index (II), aliphatic index, and grand average of hydrophilic (GRAVY).
Secondary
structure prediction: These condary structures were predicated by SOPMA tool of BACE1
in human and Zebrafish. Secondary structure prediction was performed by using
SOPMA [16] Server
(https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html).
SOPMA is using homologue method of Levin etal.According
to this method, short homologous sequence of amino
acids will tend to form similar secondary structure.
Protein and ligand
Preparation: The FASTA format protein sequence was
subjected to SWISS Model server (http://swiss-model.expasy.org/) for predicting
the templates for the BACE-1 sequence. The target template alignment and final
3D structure were predicted.
Molecular Docking studies:
The predicted 3D structure was docked with specific inhibitor retrieved from Pubchem database and the binding energies and efficiency
were studied using HEX software. The new version of HEX 8.2
server. It is offline and also online but we have done offline.
RESULTS AND DISCUSSION
Protein
Sequence Retrieval- Protein sequence of BACE1was retrieved
from NCBI database, it is 501aa long in human and 505aa long in Danio rerio.
Characterization of the BACE1- The
physicochemical
analysis of both the protein was performed using Protparam
and results were shown in Table 1.This
protein had amino acids with molecular weight. Protparamtool computed that the
Theoretical pi of protein nature and Instability index of the protein which
represents protein stability. The GRAVY, index protein the total number of
positively charged residues and the total number of negatively charged
residues.
Table
1: Physico-chemical analysis of both Human and Danio rerio
|
1 |
Number of amino acids |
505 |
501 |
|
2 |
Molecular weight |
55661.4 |
55823.8 |
|
3 |
Theoretical pI |
6.19 |
5.31 |
|
4 |
Total number of negatively charged
residues (Asp+Glu) |
46 |
55 |
|
5 |
Total number of positively charged
residues (Arg+Lys) |
41 |
42 |
|
6 |
Total number of atoms |
7743 |
7801 |
|
7 |
Instability index |
48.35 |
43.85 |
|
8 |
Aliphatic index |
86.32 |
88.14 |
|
9 |
GRAVY |
-0.015 |
-0.056 |
Secondary structure
prediction: The secondary structure of the protein was
predicted using SOPMA server Table 2 and Table 3. It was observed that random
coil, alpha helix, extended strand Random coils have important functions in
proteins for flexibility and conformational changes such as enzymatic turnover
as it is shown in the (Graph 1 and Graph 2) (Buxbaum,
2007)[12].
Table 2: Secondary structure prediction
|
1 |
Alpha helix (Hh) |
147 |
29.34% |
|
2 |
310 helix (Gg) |
0 |
0.00% |
|
3 |
Pi helix (Ii) |
0 |
0.00% |
|
4 |
Beta bridge (Bb) |
0 |
0.00% |
|
5 |
Extended strand (Ee) |
125 |
24.95% |
|
6 |
Beta turn (Tt) |
62 |
12.38% |
|
7 |
Bend region (Ss) |
0 |
0.00% |
|
8 |
Random coil (Cc) |
167 |
33.33% |
Table 3: Secondary structure prediction
|
1 |
Alpha
helix (Hh) |
133 |
26.34% |
|
2 |
310
helix (Gg) |
0 |
0.00% |
|
3 |
Pi
helix (Ii) |
0 |
0.00% |
|
4 |
Beta
bridge (Bb) |
0 |
0.00% |
|
5 |
Extended
strand (Ee) |
138 |
27.33% |
|
6 |
Beta
turn (Tt) |
49 |
9.70% |
|
7 |
Bend region (Ss) |
0 |
0.00% |
|
8 |
Random
coil (Cc) |
185 |
36.63% |
Secondary Structure Predication:
The Secondary Structure Predication of Homo
sapiens
Graph 1: Showing the number of Secondary structure of the protein
The Secondary Structure Predication of Danio
rerio
Graph 2: Showing the number ofSecondary structure
of the protein
Protein
and ligand Preparation: Protein and ligand werepreparedby
subjected to SWISS Model server for predicting the templates for the BACE1
sequence. The target template alignment and final 3D structure were predicted
by Hex 8.6 version.
Molecular
Docking studies: The predicate 3D structures were
docked with Cibacron Blue compound
and it show Binding Energy with respective to Homo sapiens in the "Fig. 1", "Fig. 2"
and -352.5 with respective Danio rerio as shown in the "Fig. 3", "Fig.4
".
Docking Studies:
CONCLUSIONS-
The sequence annotation of primary sequence of BACE1
in Homo sapiens and Danio rerio
was performed for further sequence analyses. According to literature conserding BACE-1 as a target some drugs were screened againsed targate using Pubchem. Cibacron Blue show
a potential inhibitor againsed BACE-1 the docking
analyzed revealed that hydrophobic contact is major contributing factor to
binding of Cibacron Blue with BACE-1.Hence,itis invested that Cibacron Blue functioned
as an inhibitor for BACE-1.
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