Investigasi Interaksi Antibodi IgG dengan Antigen Vaksin COVID-19 dalam Pencarian Spesifisitas Kompleksnya melalui Studi In Silico

Abidiy, Syafri Izzat (2024) Investigasi Interaksi Antibodi IgG dengan Antigen Vaksin COVID-19 dalam Pencarian Spesifisitas Kompleksnya melalui Studi In Silico. Other thesis, Institut Teknologi Sepuluh Nopember.

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Abstract

Efikasi vaksin COVID-19 seringkali dikaitkan dengan efektivitas vaksin. Meski di dalam perhitungan efikasi vaksin membutuhkan berbagai faktor untuk mengetahui efektivitasnya, namun sebenarnya terdapat hal yang paling fundamental dari efektivitas vaksin, yaitu dengan menelusuri interaksi yang diperoleh dari kecocokan antara antibodi dengan antigen vaksin. Penelitian ini berfokus pada studi molecular docking antibodi-antigen dengan menggunakan ClusPro 2.0 untuk mengetahui seberapa besar kecocokan antigen vaksin COVID-19 serta memperoleh segala faktor interaksi yang mempengaruhi kompleks antibodi-antigen. Studi ini menggunakan antigen-binding fragment (Fab) antibodi IgG (PDB: 7CM4) sebagai protein reseptor dan protein antigen vaksin COVID-19. Hasil dari penelitian ini menunjukkan adanya interaksi antibodi-antigen yang divisualisasikan dengan LigPlot+. Selain itu, didapatkan juga data binding affinity yang diperoleh dengan menggunakan PRODIGY, berupa nilai ΔG yang dipengaruhi oleh jumlah dari inter-residue contact (IC) polar-apolar, charged-charged, charged-apolar, dan polar-polar serta nilai Kd dari semua kompleks antibodi-antigen yang tergolong bagus. Nilai ΔG dari setiap hasil docking kompleks antibodi IgG-antigen vaksin COVID-19 berturut-turut adalah -8,8 kkal.mol-1 (envelop CoronaVac), -10,3 kkal.mol-1 (spike glikoprotein CoronaVac), -10,7 kkal.mol-1 (BNT162b2), -11,1 kkal.mol-1 (nukleokapsid fosfoprotein CoronaVac), -11,7 kkal.mol-1 (mRNA-1273), -11,7 kkal.mol-1 (NVX-CoV2373), -13,3 kkal.mol-1 (Ad26.COV2. S), -14,3 kkal.mol-1 (membran CoronaVac). Sementara nilai Kd dari setiap hasil docking kompleks antibodi IgG-antigen vaksin COVID-19 berturut-turut adalah 3,3x10-7 M (envelop CoronaVac), 1,5x10-8 M (BNT162b2), 2,8x10-8 M (spike glikoprotein CoronaVac), 2,8x10-9 M (mRNA-1273), 2,8x10-9 M (NVX-CoV2373), 7,3x10-9 M (nukleokapisd fosfoprotein CoronaVac), 1,7x10-10 M (Ad26.COV2.S), 3,5x10-11 M (membran CoronaVac). Dari penelitian ini, dapat disimpulkan bahwa antigen vaksin COVID-19 yang berasal dari antigen membran CoronaVac tergolong memiliki interaksi yang paling kuat.
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The efficacy of the COVID-19 vaccine is often linked to the effectiveness of the vaccine. Although calculating vaccine efficacy requires various factors to determine its effectiveness, in fact there is the most fundamental aspect of vaccine effectiveness, namely tracing the interactions obtained from the match between antibodies and vaccine antigens. This research focuses on antibody-antigen molecular docking studies using ClusPro 2.0 to find out how much the COVID-19 vaccine antigen matches and to obtain all interaction factors that influence the antibody-antigen complex. This study uses the antigen-binding fragment (Fab) of IgG antibodies (PDB: 7CM4) as the receptor protein and antigen protein of the COVID-19 vaccine. The results of this study show the existence of antibody-antigen interactions which are visualized with LigPlot+. Apart from that, binding affinity data was also obtained using PRODIGY, in the form of ΔG values which were influenced by the number of polar-apolar, charged-charged, charged-apolar, and polar-polar inter-residue contacts (IC) as well as the Kd values of all relatively good antibody-antigen complex. The ΔG value from each docking result of the IgG antibody-antigen complexes for the COVID-19 vaccines are -8.8 kcal.mol-1 (envelop CoronaVac), -10.3 kcal.mol-1 (spike glycoprotein CoronaVac), -10.7 kcal.mol-1 (BNT162b2), -11.1 kcal.mol-1 (CoronaVac phosphoprotein nucleocapsid), -11.7 kcal.mol-1 (mRNA-1273), -11.7 kcal.mol-1 (NVX-CoV2373), -13.3 kcal.mol-1 (Ad26.COV2.S), -14.3 kcal.mol-1 (CoronaVac membrane). Meanwhile, the Kd value of each docking result of the IgG antibody-antigen complexes for the COVID-19 vaccines are respectively 3.3x10-7 M (CoronaVac envelope), 1.5x10-8 M (BNT162b2), 2.8x10-8 M (spike glycoprotein CoronaVac), 2.8x10-9 M (mRNA-1273), 2.8x10-9 M (NVX-CoV2373), 7.3x10-9 M (CoronaVac phosphoprotein nucleocapsid), 1.7x10-10 M (Ad26.COV2.S), 3.5x10-11 M (CoronaVac membrane). From this research, it can be concluded that the COVID-19 vaccine antigen derived from the CoronaVac membrane antigen is classified as having the strongest interaction.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	Interaksi Antibodi-Antigen, Vaksin COVID-19, Molecular Docking, SARS-COV-2, ClusPro2.0, Antibody-Antigen Interaction, COVID-19 Vaccine, Molecular Docking, SARS-COV-2, ClusPro2.0
Subjects:	Q Science > QD Chemistry > QD251.2 Chemistry, Organic. Biochemistry Q Science > QR Microbiology > QR180 Immunology
Divisions:	Faculty of Mathematics and Science > Chemistry > 47201-(S1) Undergraduate Thesis
Depositing User:	Syafri Izzat Abidiy
Date Deposited:	17 Jul 2024 02:37
Last Modified:	17 Jul 2024 02:37
URI:	http://repository.its.ac.id/id/eprint/108377

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