Efektivitas Interaksi Antigen Protein N Termutasi Dengan Antibodi IgM Dalam Pengembangan Vaksin Covid-19 Secara In Silico

Nazila, Shafira Salzabilla (2025) Efektivitas Interaksi Antigen Protein N Termutasi Dengan Antibodi IgM Dalam Pengembangan Vaksin Covid-19 Secara In Silico. Other thesis, Institut Teknologi Sepuluh Nopember.

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Abstract

Pandemi COVID-19 yang berkepanjangan mendorong upaya berkelanjutan dalam pengembangan vaksin yang efektif, terutama dengan mempertimbangkan keberadaan varian varian virus yang mengalami mutasi. Salah satu strategi dalam pengembangan vaksin adalah dengan menargetkan interaksi antara antibodi manusia dan antigen protein virus. Dalam hal ini, antibodi IgM berperan penting dalam respons imun awal terhadap infeksi. Penelitian ini dilakukan untuk mengeksplorasi efektivitas interaksi antibodi IgM dengan antigen protein N termutasi SARS-CoV-2 yang dapat menjadi dasar pengembangan vaksin COVID-19 di Indonesia. Antigen protein N yang telah mengalami mutasi diidentifikasi dari beberapa daerah di Pulau Jawa, yakni Jawa Timur, Jawa Tengah, Jawa Barat dan wild type yang digunakan sebagai referensi. Daerah ini dipilih berdasarkan provinsi dengan penduduk terpadat di Pulau Jawa untuk mengetahui mutasi pada tiap daerah. Tujuan dari penelitian ini adalah untuk membandingkan efektivitas interaksi antara antibodi IgM dengan varian antigen protein N termutasi dari ketiga wilayah tersebut, berdasarkan kekuatan ikatan dan kestabilan kompleks yang terbentuk. Penelitian ini dilakukan secara in silico menggunakan metode molecular docking. Data sekuens antigen diperoleh dari GISAID (Global Initiative on Sharing All Influenza Data) dan NCBI (National Center for Biotechnology Information), sedangkan struktur antibodi IgM diperoleh dari RCSB PDB (Research Collaboratory for Structural Bioinformatics Protein Data Bank). Pemodelan struktur tiga dimensi antigen dan antibodi dilakukan dengan menggunakan web server I-TASSER, lalu dilakukan docking menggunakan web server ClusPro. Kompleks hasil docking dianalisis menggunakan web server PRODIGY untuk mengetahui energi ikatan (ΔG), konstanta disosiasi (Kd), dan Inter-Residu Contact (IC). Hasil analisis menunjukkan bahwa protein N termutasi varian Jawa Barat memiliki nilai afinitas paling tinggi terhadap antibodi IgM, dengan nilai ΔG sebesar -13,4 kkal/mol dan Kd sebesar 1,6×10⁻¹⁰, yang menunjukkan ikatan yang sangat kuat dan stabil. Nilai ΔΔG sebesar 0,31 kkal/mol dari mutasi G179S pada protein N varian Jawa Barat mengindikasikan bahwa mutasi tersebut meningkatkan stabilitas ikatan terhadap antibodi IgM. Protein N termutasi varian Jawa Barat menunjukkan potensi paling besar sebagai target dalam pengembangan vaksin COVID 19 berbasis antibodi IgM, dan pendekatan in silico seperti molecular docking dapat menjadi alat yang efektif dalam proses seleksi kandidat vaksin di daerah Jawa Barat. ========================================================================================================================================
The prolonged COVID-19 pandemic has prompted ongoing efforts to develop effective vaccines, especially considering the existence of mutated virus variants. One strategy in vaccine development is to target the interaction between human antibodies and viral protein antigens. In this case, IgM antibodies play an important role in the initial immune response to infection. This study was conducted to explore the effectiveness of IgM antibody interactions with mutated SARS-CoV-2 N protein antigens, which could serve as a basis for COVID-19 vaccine development in Indonesia. The mutated N protein antigen was identified from several regions in Java, namely East Java, Central Java, West Java, and the wild-type strain as a reference. These regions were selected based on the provinces with the highest population density in Java to determine mutations in each region. The objective of this study was to compare the effectiveness of interactions between IgM antibodies and the mutated N protein antigen variants from the three regions, based on the strength of the bond and the stability of the complex formed. This study was conducted in silico using molecular docking methods. Antigen sequence data were obtained from GISAID (Global Initiative on Sharing All Influenza Data) and NCBI (National Center for Biotechnology Information), while IgM antibody structures were obtained from RCSB PDB (Research Collaboratory for Structural Bioinformatics Protein Data Bank). Three-dimensional modeling of the antigen and antibody structures was performed using the I-TASSER web server, followed by docking using the ClusPro web server. The docking complexes were analyzed using PRODIGY web server to determine binding energy (ΔG), dissociation constant (Kd), and Inter-Residue Contact (IC). The analysis results showed that the mutated N protein of the West Java variant had the highest affinity for IgM antibodies, with a ΔG value of -13.4 kcal/mol and a Kd value of 1.6×10⁻¹⁰, indicating a very strong and stable bond. The ΔΔG value of 0,31 kcal/mol from the G179S mutation in the West Java variant N protein indicates that this mutation enhances the stability of the bond with IgM antibodies. The mutated N protein of the West Java variant showed the greatest potential as a target in the development of an IgM antibody-based COVID-19 vaccine, and in silico approaches such as molecular docking can be an effective tool in the selection of vaccine candidates in West Java.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	Interaksi Antigen-Antibodi, Imunoglobulin, Molecular docking, SARS-CoV-2, Antigen-Antibody Interaction, Immunoglobulin, Molecular docking, SARS CoV-2.
Subjects:	Q Science > QD Chemistry > QD251.2 Chemistry, Organic. Biochemistry Q Science > QR Microbiology > QR180 Immunology
Divisions:	Faculty of Science and Data Analytics (SCIENTICS) > Chemistry > 47201-(S1) Undergraduate Thesis
Depositing User:	Shafira Salzabilla Nazila
Date Deposited:	04 Aug 2025 04:04
Last Modified:	04 Aug 2025 04:04
URI:	http://repository.its.ac.id/id/eprint/125921

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