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Computational Analysis of BACE1 Involved in Alzheimer’s Disease Using Zebrafish (Daniorerio) as A Model

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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
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   Int. J. Life. Sci. Scienti. Res., 3(3): 1085-1088 MAY 2017   Copyright © 2015-2017| IJLSSR by Society for Scientific Research is under a CC BY-NC 4.0 International License   Page 1085   Computational Analysis of BACE-1 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 Received: 21 February  2017/Revised: 06 March 2017/Accepted: 20 April 2017 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 were 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. Key-words-   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-1 gene 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-1 coding sequence or any disease associated SNP in its promoter region in AD patients, Access this article online   Quick Response Code   Website: www.ijlssr.com   DOI:  10.21276/ijlssr.2017.3.3.20 increased β-secretase levels and activity have been reported in AD [3] . BACE-1 levels were elevated in neurons around  plaques. BACE-1 mRNA 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 BACE-1 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 neuro transmitter 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 ARTICLE   RESEARCH     Int. J. Life. Sci. Scienti. Res.  MAY 2017   Copyright © 2015-2017| IJLSSR by Society for Scientific Research is under a CC BY-NC 4.0 International License   Page 1086   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 neuro-fibrillary 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  Homo sapiens  and  Danio rerio were retrieved from protein database at NCBI. The sequences were further prepared in FASTA format for the characterization. Characterization of the BACE-1 : 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 secondary 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 et al. [17] . According to this method, short homologous sequences of amino acids 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, it is 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 BACE1 was 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   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). Table 2: Secondary structure prediction   Number of amino acids 505501 Molecular weight 55661.455823.8 Theoretical pI 6.195.31 Total number of negatively charged residues (Asp+Glu) 4655 Total number of positively charged residues (Arg+Lys) 4142 Total number of atoms 77437801 Instability index 48.3543.85 Aliphatic index 86.3288.14 GRAVY -0.015-0.056 Alpha helix (Hh) 147 29.34% 3 10 helix (Gg) 0 0.00%  Pi helix (Ii) 0 0.00%  Beta bridge (Bb) 0 0.00%  Extended strand (Ee) 125 24.95%  Beta turn (Tt) 62 12.38%  Bend region (Ss) 0 0.00%  Random coil (Cc) 167 33.33%     Int. J. Life. Sci. Scienti. Res.  MAY 2017   Copyright © 2015-2017| IJLSSR by Society for Scientific Research is under a CC BY-NC 4.0 International License   Page 1087   Table 3: Secondary structure prediction   Secondary Structure Predication   1)   The Secondary Structure Predication of  Homo sapiens Graph 1: Showing the number of Secondary structure of the protein 2) The Secondary Structure Predication of  Danio rerio   Graph 2: Showing the number of Secondary structure of the protein Protein and ligand Preparation:   Protein and ligand were prepared by 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 Docking studies of  Homo sapiens Fig. 1: Before docking Fig. 2: After docking   Docking studies of  Danio rerio Fig. 3: Before docking   Alpha helix (Hh) 133 26.34% 3 10 helix (Gg) 0 0.00%  Pi helix (Ii) 0 0.00%  Beta bridge (Bb) 0 0.00%  Extended strand (Ee) 138 27.33%  Beta turn (Tt) 49 9.70%  Bend region (Ss) 0 0.00%  Random coil (Cc) 185 36.63%     Int. J. Life. Sci. Scienti. Res.  MAY 2017   Copyright © 2015-2017| IJLSSR by Society for Scientific Research is under a CC BY-NC 4.0 International License   Page 1088   Fig. 4: After docking   CONCLUSIONS The sequence annotation of primary sequence of BACE-1 in  Homo sapiens  and  Danio rerio  was performed for further sequence analyses. According to this 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, it is invested that Cibacron Blue functioned as an inhibitor for BACE-1. REFERENCES [1]   T. Voisin, B. Vellas, Diagnosis and treatment of patients with severe Alzheimer's disease, Drugs Aging 26, 2009; 135–144. [2]   Mullane, K.; Williams, M. Alzheimer’s therapeutics: Continued clinical failures question the validity of the amyloid hypothesis-but what lies beyond? Biochem. Pharmacol. 2013;85:289–305. [3]   Venugopal, C.; Demos, C.M.; Rao, K.S.; Pappolla, M.A.; Sambamurti, K. β-Secretase: Structure, function, and evolution. CNS Neurol. Disord. Drug Targets 2008;7: 278–294. [4]   Limongelli, V.; Marinelli, L.; Cosconati, S. Braun, H.A.; Schmidt, B.; Novellino, E. Ensemble-docking approach on BACE-1: Pharmacophore perception and guidelines for drug design. Chem Med Chem 2007;2:667–678. [5]   Kandalepas, P.C.; Vassar, R. Identification and biology of β-secretase. J. Neurochem. 2012; 120:55–61. [6]   Zhang X,Current Development of the medicinal chemistry of temporary molecular target involved in nurological and central nervous system (CNS), Drug Target CNS and  Neurological Disorders, 2004;3:137-152. [7]   Cole, S.L.; Vassar, R. The Alzheimer’s disease β-secretase enzyme, BACE-1. Mol. Neurodegener. 2007;2:(22):1–22:25. [8]   Jeppsson, F.; Eketjall, S.; Janson, J.; Karlstrom, S.; Gustavsson, S.; Olsson, L.L.; Radesater, A.C.; Ploeger, B.; Cebers, G.; Kolmodin, K.; et al. Discovery of AZD3839, a  potent and selective BACE1 inhibitor clinical candidate for the treatment of alzheimer disease. J. Biol. Chem. 2012;287:41245–41257. [9]   Silvestri, R. Boom in the development of non-peptidic β-secretase (BACE1) inhibitors for the treatment of Alzheimer’s disease. Med. Res. Rev. 2009;29: 295–338. 38. [10]   Cole SL and Vassar R, S.L Cole, R. Vassar Intraneuronal ß-amyloid-induced neuro-degeneration and Alzheimer’s dementia , Current Alzheimer Research. 2008;5:100-120. [11]   Protein Data Bank. Available online: http://www.rcsb.org, accessed on 1 March, 2013. [12]   Chirapu, S.R.; Pachaiyappan, B.; Nural, H.F.; Cheng, X.; Yuan, H.; Lankin, D.C.; Abdul-Hay, S.O.; Thatcher, G.R.; Shen, Y.; Kozikowski, A.P.; et al. Molecular modeling, synthesis, and activity studies of novel biaryl and fused-ring BACE1 inhibitors. Bioorg. Med. Chem. Lett. 2009;19: 264–274. [13]   Mattson, M. P. Pathways towards and away from Alzheimer’s Disease, Nature, 2004; 430:631-639. [14]   Kandalepas, P.C.; Vassar, R. Identification and biology of β-secretase. J. Neurochem. 2012;120:55–61. [15]   Cole, S.L.; Vassar, R. The Alzheimer’s disease β-secretase enzyme, BACE-1. Mol. Neurodegener. 2007; 2:22:1–22:25. [16]   Geourjon C, Deléage G. SOPMA: Significant improvements in protein secondary structure prediction by consensus  prediction from multiple alignments.   Comput Appl Biosci. 1995;11(6):681-4. [17]   Levin JM, Robson B, Garnier J. An algorithm for secondary structure determination in proteins based on sequence similarity. FEBS Lett. 1986;205(2): 303–308. International Journal of Life-Sciences Scientific Research (IJLSSR) Open Access Policy Authors/Contributors are responsible for srcinality, contents, correct references, and ethical issues. IJLSSR publishes all articles under Creative Commons Attribution- Non-Commercial 4.0 International License (CC BY-NC). https://creativecommons.org/licenses/by-nc/4.0/legalcode How to cite this article: Shaikh NK, Shaikh SA, Karki J: Computational Analysis of BACE-1 Involved in Alzheimer’s disease Using Zebrafish (  Danio rerio ) as A Model.  Int. J. Life. Sci. Scienti. Res.,  2017;   3(3): 1085-1088. DOI:10.21276/ijlssr.2017.3.3.20  Source of Financial Support:  Nil, Conflict of interest:  Nil  
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