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Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development

This study aims to isolate the RNA-dependent RNA polymerase (RdRp) gene of the dengue virus (DENV) isolates from Indonesia, determine the serotype of the local DENV strain through homology modeling, and express the recombinant RdRp protein in Escherichia coli BL21 (DE3), as the target for anti-dengu...

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Main Authors: Subroto, Toto, Firdaus, Ade Rizqi Ridwan, Kusumawardani, Shinta, Tohari, Taufik Ramdani, Nababan, Theresia Adventina, Pertiwi, Wulan, Fadhlillah, Muhammad, Kusuma, Sri Agung Fitri, Rukayadi, Yaya
Format: Article
Language:English
Published: HH Publisher 2024
Online Access:http://psasir.upm.edu.my/id/eprint/114680/1/114680.pdf
http://psasir.upm.edu.my/id/eprint/114680/
https://journals.hh-publisher.com/index.php/pmmb/article/view/1031
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spelling my.upm.eprints.1146802025-01-23T01:58:59Z http://psasir.upm.edu.my/id/eprint/114680/ Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development Subroto, Toto Firdaus, Ade Rizqi Ridwan Kusumawardani, Shinta Tohari, Taufik Ramdani Nababan, Theresia Adventina Pertiwi, Wulan Fadhlillah, Muhammad Kusuma, Sri Agung Fitri Rukayadi, Yaya This study aims to isolate the RNA-dependent RNA polymerase (RdRp) gene of the dengue virus (DENV) isolates from Indonesia, determine the serotype of the local DENV strain through homology modeling, and express the recombinant RdRp protein in Escherichia coli BL21 (DE3), as the target for anti-dengue drug development. We utilize reverse transcription-polymerase chain reaction (RT-PCR) and nested PCR for serotyping the DENV isolates, obtained from Hasan Sadikin Hospital, Indonesia. Then, followed by the extraction and purification of the RdRp amplicon for gene sequencing. The resulting RdRp gene sequences are translated into amino acid sequences, which are then used for protein modeling and the construction of a recombinant plasmid for RdRp protein expression. As a result, the RdRp gene, which belongs to the non-structural protein 5 (NS5) of DENV, was successfully isolated and sequenced from DENV RNA samples. Based on serotyping results and homology modeling, the serotype of the isolate DENV was identified as serotype-3. The isolated NS5-RdRp gene from the local strain was then inserted into the pET28a(+) plasmid and transformed into E. coli BL21(DE3) as the host cell. Recombinant NS5-RdRp was predominantly found in the insoluble fraction with a molecular weight of 72 kDa. Future studies on the development of an anti-dengue drug model that confirms the inhibition of the binding domain in the recombinant RdRp protein structure will be required to provide more insight and expand the development of a universal anti-dengue strategy in Indonesia. HH Publisher 2024-09-10 Article PeerReviewed text en cc_by_nc_4 http://psasir.upm.edu.my/id/eprint/114680/1/114680.pdf Subroto, Toto and Firdaus, Ade Rizqi Ridwan and Kusumawardani, Shinta and Tohari, Taufik Ramdani and Nababan, Theresia Adventina and Pertiwi, Wulan and Fadhlillah, Muhammad and Kusuma, Sri Agung Fitri and Rukayadi, Yaya (2024) Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development. Progress in Microbes and Molecular Biology, 7 (1). art. no. a0000449. ISSN 2637-1049; eISSN: 2637-1049 https://journals.hh-publisher.com/index.php/pmmb/article/view/1031 10.36877/pmmb.a0000449
institution Universiti Putra Malaysia
building UPM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Putra Malaysia
content_source UPM Institutional Repository
url_provider http://psasir.upm.edu.my/
language English
description This study aims to isolate the RNA-dependent RNA polymerase (RdRp) gene of the dengue virus (DENV) isolates from Indonesia, determine the serotype of the local DENV strain through homology modeling, and express the recombinant RdRp protein in Escherichia coli BL21 (DE3), as the target for anti-dengue drug development. We utilize reverse transcription-polymerase chain reaction (RT-PCR) and nested PCR for serotyping the DENV isolates, obtained from Hasan Sadikin Hospital, Indonesia. Then, followed by the extraction and purification of the RdRp amplicon for gene sequencing. The resulting RdRp gene sequences are translated into amino acid sequences, which are then used for protein modeling and the construction of a recombinant plasmid for RdRp protein expression. As a result, the RdRp gene, which belongs to the non-structural protein 5 (NS5) of DENV, was successfully isolated and sequenced from DENV RNA samples. Based on serotyping results and homology modeling, the serotype of the isolate DENV was identified as serotype-3. The isolated NS5-RdRp gene from the local strain was then inserted into the pET28a(+) plasmid and transformed into E. coli BL21(DE3) as the host cell. Recombinant NS5-RdRp was predominantly found in the insoluble fraction with a molecular weight of 72 kDa. Future studies on the development of an anti-dengue drug model that confirms the inhibition of the binding domain in the recombinant RdRp protein structure will be required to provide more insight and expand the development of a universal anti-dengue strategy in Indonesia.
format Article
author Subroto, Toto
Firdaus, Ade Rizqi Ridwan
Kusumawardani, Shinta
Tohari, Taufik Ramdani
Nababan, Theresia Adventina
Pertiwi, Wulan
Fadhlillah, Muhammad
Kusuma, Sri Agung Fitri
Rukayadi, Yaya
spellingShingle Subroto, Toto
Firdaus, Ade Rizqi Ridwan
Kusumawardani, Shinta
Tohari, Taufik Ramdani
Nababan, Theresia Adventina
Pertiwi, Wulan
Fadhlillah, Muhammad
Kusuma, Sri Agung Fitri
Rukayadi, Yaya
Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development
author_facet Subroto, Toto
Firdaus, Ade Rizqi Ridwan
Kusumawardani, Shinta
Tohari, Taufik Ramdani
Nababan, Theresia Adventina
Pertiwi, Wulan
Fadhlillah, Muhammad
Kusuma, Sri Agung Fitri
Rukayadi, Yaya
author_sort Subroto, Toto
title Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development
title_short Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development
title_full Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development
title_fullStr Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development
title_full_unstemmed Homology modeling and expression of recombinant NS5-RDRP based on the Indonesian local strain of dengue virus for anti-dengue drug development
title_sort homology modeling and expression of recombinant ns5-rdrp based on the indonesian local strain of dengue virus for anti-dengue drug development
publisher HH Publisher
publishDate 2024
url http://psasir.upm.edu.my/id/eprint/114680/1/114680.pdf
http://psasir.upm.edu.my/id/eprint/114680/
https://journals.hh-publisher.com/index.php/pmmb/article/view/1031
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score 13.235362

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