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All Journal JURNAL PEMULIAAN TANAMAN HUTAN Indonesian Journal of Biotechnology Journal of Tropical Biodiversity and Biotechnology Agrin : Jurnal Penelitian Pertanian Journal of Tropical Crop Science Menara Perkebunan Nusantara Science and Technology Proceedings
Riza Arief Putranto
Unknown Affiliation
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Economics, Econometrics & Finance Engineering Environmental Science Immunology & microbiology Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Medicine & Pharmacology

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Journal : Nusantara Science and Technology Proceedings

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In Silico Design and Validation of CRISPR-Cas13a System as a Potential Antiviral for SARS-CoV-2 in Indonesia Alfero Putra Iryanto; Christy; Muhammad Farrel Ewaldo; Anggia Prasetyoputri; Ratih Asmana Ningrum; Riza Arief Putranto; Akhirta Atikana
Nusantara Science and Technology Proceedings 2nd Bioinformatics and Biodiversity Conference
Publisher : Future Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/nstp.2022.2107

Abstract

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic of coronavirus disease (COVID-19). Indonesia is one of the countries with large numbers of positive cases in Asia with certain dominant variants. Currently, there are no specific therapeutic agents against SARS-CoV-2. Therefore, the development of specific and effective therapeutic tools is urgently needed to overcome the pandemic. This study designed a CRISPR-Cas13a system strategy as a potential anti-SARS-CoV-2. We utilized comprehensive bioinformatics methods to identify a unique segment in the SARS-CoV-2 consensus sequence from Indonesia that is different from the related segment in the SARS-CoV. This unique segment was used as a specific target for SARS-CoV-2 Spike Protein to design a set of crRNA libraries. Off-target analysis and molecular docking simulation were performed to validate the specificity and to analyze interactions among the crRNA candidates, target RNA, and Cas13a. Our study identified a 17 amino acid unique segment on the Receptor Binding Domain (RBD) region. By using that unique segment, a total of 12 crRNA candidates were selected based on their GC content. Finally, based on the off-target and molecular docking validation, four crRNAs were selected as potential candidates for CRISPR-Cas13a-based antivirals. Although further validation with in vitro assays is important, the present study provides a comprehensive demonstration regarding the potential of CRISPR-Cas13a as a strategy for SARS-CoV-2 antiviral development. Considering the specific property of the CRISPR system, the present methodology can also be utilized to develop novel antiviral candidates for other RNA viruses.
Co-Authors . KUSWANHADI . NUHAIMI-HARIS . PRIYONO . SISWANTO . SUMARYONO Afandi, Dadang Agustin Sri MULYATNI Akhirta Atikana Aksa, Annisa Aulia Alfero Putra Iryanto Anggia Prasetyoputri Annisa A Aksa Asmini Budiani Asmini Budiani Asmini Budiani Asmini Budiani Asmini BUDIANI Asmini BUDIANI1 Barahima Abbas Christy Dewi Sukma Dini Astika Sari Dini Astika Sari Dini Astika Sari Ernayunita Ernayunita Ernayunita, Ernayunita Galuh Wening Permatasari Galuh Wening PERMATASARI Galuh Wening PERMATASARI Happy WIDIASTUTI Hayati Minarsih Hayati Minarsih Hayati Minarsih Hayati MINARSIH Imam Bagus Nugroho Imron RIYADI Imron Riyadi Imron Riyadi Imron Riyadi Indra Syahputra Inez Palupi Irfan MARTIANSYAH Irfan Martiansyah Iskandar, Hayati Minarsih Jembar PAMBUDI Julie LECLERCQ Lailia Zubaidah Larasati D Mahardhika Lutfi Anggadhania Mardhika, Larasati Dena MARTIANSYAH, Irfan Masna Maya Sinta Masna Maya Sinta Mose, Windi Muhammad Farrel Ewaldo Mukmin, Restu Prasetya Nurul Khumaida Nurul Khumaida Pambudi, Jembar Pascal MONTORO Pascal MONTORO Pascal MONTORO PERMATASARI, Galuh Wening pri yono Radite TISTAMA Ratih Asmana Ningrum Rizka Tamania Saptari Rizka Tamania SAPTARI Rizka Tamania Saptari Rokhana Faizah Rokhana Faizah Sapto Nugroho Hadi Sapto Nugroho Hadi Sari, Dini Astika Sekar WOELAN Sri Wening Sri Wening Sudarsono Sudarsono Suhandono, Sonny Sustiprijatno Sustiprijatno, Sustiprijatno TATI KRISTIANTI Turhadi Turhadi Vivi Restu Raharti Y.M.M Anita Nugraheni Yuli Setiawati Yuli Setiawati Yuli Setiawati, Yuli