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Chowdhury FT, Shohan MU, Islam T, Mimu TT, Palit P. A Therapeutic Approach Against Leishmania donovani by Predicting RNAi Molecules Against the Surface Protein, gp63. Curr Bioinform 2019. [DOI: 10.2174/1574893613666180828095737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Background:
Leishmaniasis is a disease caused by the Leishmania sp. and can be
classified into two major types: cutaneous and visceral leismaniasis. Visceral leishmaniasis is the
deadlier type and is mediated by Leishmania donovani and involves the establishment of persistent
infection and causes damage to the liver, spleen and bone marrow. With no vaccine yet available
against leishmaniasis and the current therapeutic drugs of leishmaniasis being toxic and expensive;
an alternative treatment is necessary.
Objective:
Surface glycocalyx protein gp63, plays a major role in the virulence and resulting
pathogenicity associated with the disease. Henceforth, silencing the gp63 mRNA through the RNA
interference system was the aim of this study.
Methods:
In this study two competent siRNAs and three miRNAs have been designed against gp63
for five different strains of L. donovani by using various computational methods. Target specific
siRNAs were designed using siDirect 2.0 and to design possible miRNA, another tool named IDT
(IntegratedDNA Technology). Screening for off-target similarity was done by BLAST and the GC
contents and the secondary structures of the designed RNAs were determined. RNA-RNA
interaction was calculated by RNAcofold and IntraRNA, followed by the determination of heat
capacity and the concentration of duplex by DNAmelt web server.
Results:
The selected RNAi molecules; two siRNA and three miRNA had no off-target in human
genome and the ones with lower GC content were selected for efficient RNAi function. The
selected ones showed proper thermodynamic characteristics to suppress the expression of the
pathogenic gene of gp63.
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Affiliation(s)
- Farhana T. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Mohammad U.S. Shohan
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tasmia Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Taisha T. Mimu
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Parag Palit
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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