Efektivitas Interaksi Antigen Protein Membran dengan Antibodi IgM dalam Pengembangan Vaksin untuk COVID-19 secara In Silico

Rachman, Adinda Putri Aulia (2025) Efektivitas Interaksi Antigen Protein Membran dengan Antibodi IgM dalam Pengembangan Vaksin untuk COVID-19 secara In Silico. Other thesis, Institut Teknologi Sepuluh Nopember.

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Abstract

Coronavirus Disease 2019 (COVID-19) adalah pandemi penyakit jenis penyebab gangguan pernapasan akut yang telah mengakibatkan keadaan darurat kesehatan masyarakat, sehingga dalam upaya pengendaliannya, diciptakanlah vaksin. Pada enam bulan setelah mendapatkan vaksinasi COVID-19 berbasis protein spike dosis primer lengkap, terjadi penurunan antibodi, sehingga dibutuhkan booster. Oleh karena itu, penelitian ini mengeksplorasi potensi protein membrane (M) SARS-CoV-2 sebagai antigen alternatif melalui pendekatan in silico, sebab protein M dapat diekspresikan pada permukaan virion dan sel yang terinfeksi sehingga merupakan target yang mungkin untuk pengawasan imun antibodi. Penelitian ini bertujuan untuk mengetahui besar kecocokan interaksi antara IgM dan antigen membrane mutasi SARS-CoV-2 melalui molecular docking serta parameter afinitas pengikatan berupa ΔG (energi bebas Gibbs), Kd (konstanta disosiasi), dan inter-residue contact (IC) untuk memperkirakan efektivitas vaksin tersebut. Penelitian dilakukan melalui serangkaian proses komputasional, dimulai dari preparasi protein IgM dan modifikasi manual sekuens antigen protein M dengan empat tipe mutasi (I82T, V70L, I82T-V70F, I82T-V66M). Pemodelan struktur tiga dimensi dilakukan menggunakan I-TASSER, sedangkan simulasi interaksi dilakukan melalui ClusPro 2.0. Visualisasi dan identifikasi interaksi dilakukan dengan LigPlot+ dan pengukuran afinitas ikatan dihitung menggunakan PRODIGY. Didapatkan nilai terbaik dimiliki oleh antigen membran mutasi I82T-V70F, yakni 2×10-7 M dengan nilai ΔG -9,1 kcal/mol, yang mana berarti paling favorable diantara keempat antigen. Nilai afinitas pengikatan untuk kompleks antibodi IgG-antigen membrane SARS-CoV-2 wild type termasuk kedalam kategori nilai Kd tinggi yang mana berarti interaksi IgM-antigen membrane SARS-CoV-2 lebih lemah secara termodinamika.

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Coronavirus Disease 2019 (COVID-19) is an acute respiratory disease that has triggered a global public health emergency, leading to vaccine development. Six months after receiving a full dose of spike protein-based COVID-19 vaccines, antibody levels decline, requiring booster doses. This study explores the potential of the SARS-CoV-2 membrane (M) protein as an alternative antigen using an in silico approach, as the M protein is expressed on virions and infected cells, making it a possible target for antibody immune surveillance. The study aims to determine the interaction compatibility between IgM and mutated SARS-CoV-2 membrane antigens through molecular docking and assess binding affinity parameters, including ΔG (Gibbs free energy), Kd (dissociation constant), and inter-residue contact (IC), to estimate vaccine effectiveness. The research was conducted through computational processes, starting with IgM protein preparation and manual modification of the M protein sequence with four mutations (I82T, V70L, I82T-V70F, I82T-V66M). Three-dimensional structure modeling was performed using I-TASSER, while interaction simulations were conducted with ClusPro 2.0. Visualization and interaction identification were carried out using LigPlot+, and binding affinities were calculated with PRODIGY. The best result was observed for the I82T-V70F membrane antigen, with a Kd value of 2×10⁻⁷ M and ΔG of -9.1 kcal/mol, indicating the most favorable interaction among the four antigens. The binding affinity for the IgM–wild type membrane antigen complex falls into the high Kd category, indicating that the IgM–membrane antigen interaction is thermodynamically weaker.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	afinitas pengikatan, IgM, in silico, protein membrane SARS-CoV-2, vaksin COVID-19. binding affinity, COVID-19 vaccine, IgM, in silico, SARS-CoV-2 membrane protein.
Subjects:	Q Science > QD Chemistry > QD251.2 Chemistry, Organic. Biochemistry
Divisions:	Faculty of Science and Data Analytics (SCIENTICS) > Chemistry > 47201-(S1) Undergraduate Thesis
Depositing User:	Adinda Putri Aulia Rachman
Date Deposited:	04 Aug 2025 02:08
Last Modified:	04 Aug 2025 02:08
URI:	http://repository.its.ac.id/id/eprint/125257

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