Efektivitas Vaksin Covid-19 Berbasis Protein Spike Terhadap Antibodi Igm Secara In Silico

Asyura, Genta Ihsa (2025) Efektivitas Vaksin Covid-19 Berbasis Protein Spike Terhadap Antibodi Igm Secara In Silico. Other thesis, Institut Teknologi Sepuluh Nopember.

Text 5004211023-Undergraduate_Thesis.pdf - Accepted Version Restricted to Repository staff only Download (3MB) | Request a copy

Abstract

Pandemi COVID-19 telah mendorong implementasi strategi mitigasi global melalui berbagai program, salah satunya adalah vaksinasi massal sebagai upaya pemutusan rantai penyebaran virus SARS-CoV-2. Namun, dalam perkembangannya, vaksin diduga masih kurang efektif dengan fakta bahwa masih diperlukan vaksin dengan tiga kali dosis beserta booster-nya. Dari permasalahan tersebut, dilakukan penelitian yang bertujuan untuk menganalisis efektivitas secara molekular dari tiga antigen vaksin COVID-19, yang dominan digunakan di Indonesia, terhadap pembentukan antibodi IgM sebagai indikator respons imunitas humoral primer melalui parameter binding affinity (ΔG dan Kd), serta membandingkan efektivitas antibodi IgM dan IgG dalam berinteraksi dengan antigen protein spike vaksin COVID-19. Penelitian dilakukan dengan mengkaji interaksi antibodi IgM dengan tiga jenis vaksin COVID-19 berbasis protein spike, yaitu jenis vaksin inactivated virus pada Spike 1 serta jenis vaksin mRNA pada Spike 2 dan spike 3. Metode yang dilakukan melibatkan pengambilan data protein antibodi IgM (Kode: 1IGM) dari RCSB PDB yang diproses dengan PDB-Tools. Sedangkan data sekuens antigen vaksin COVID-19 pada spike 1 dan spike 2 diambil dari penelitian sebelumnya serta dokumen WHO untuk pemodelan protein 3D, sementara antigen vaksin spike 3 dimodifikasi melalui substitusi asam amino secara manual yang ditemukan melalui literatur. Proses molecular docking dilakukan untuk setiap protein antigen dengan antibodi IgM menggunakan ClusPro 2.0. Setelah itu, visualisasi kompleks 2D antibodi-antigen dilakukan dengan software LigPlot+ untuk memetakan interaksi antar-residu. Prediksi binding affinity dilakukan menggunakan PRODIGY melalui parameter ΔG dan Kd. Hasil penelitian menunjukkan bahwa vaksin Spike 3 menunjukkan kinerja yang baik terhadap IgM dengan ΔG -14,5 kcal/mol dan Kd 2,3 x 10-11 M, dan juga paling optimal pada IgG dengan ΔG -11,7 kcal/mol, Kd 2,8x10-9 M. Vaksin Spike 2 paling baik pada IgM (ΔG -14,9 kcal/mol, Kd 1.2 x10-11 M), tetapi juga kurang efektif untuk IgG (ΔG -10,7 kcal/mol, Kd 1,5x10-8 M). Vaksin Spike 1 menunjukkan respons terendah untuk IgM (ΔG -12,4 kcal/mol, Kd 8.2 x10-10 M) serta IgG (ΔG -10,3 kcal/mol, Kd 2,8x10-8 M) dibandingkan vaksin lainnya. Urutan efektivitas ketiga vaksin adalah Spike 3 > Spike 2 > Spike 1 secara konsisten baik pada antibodi IgM maupun IgG.
=======================================================================================================================================
The COVID-19 pandemic has encouraged the implementation of global mitigation strategies through various programs, one of which is mass vaccination as an effort to break the chain of spread of the SARS-CoV-2 virus. However, in its development, the vaccine is still suspected to be less effective with the fact that a vaccine with three doses is still needed along with the booster. From these problems, a study was conducted that aimed to analyze the molecular effectiveness of three COVID-19 vaccine antigens, which are predominantly used in Indonesia, on the formation of IgM antibodies as an indicator of primary humoral immunity response through binding affinity parameters (ΔG and Kd), as well as compare the effectiveness of IgM and IgG antibodies in interacting with COVID-19 vaccine spike protein antigens. The study was conducted by examining the interaction of IgM antibodies with three types of spike protein-based COVID-19 vaccines, namely the inactivated virus vaccine type on Spike 1 and the mRNA vaccine type on Spike 2 and spike 3. The method involved taking IgM antibody protein data (Code: 1IGM) from RCSB PDB processed with PDB-Tools. Meanwhile, the COVID-19 vaccine antigen sequence data on spike 1 and spike 2 were taken from previous research as well as WHO documents for 3D protein modeling, while the spike 3 vaccine antigen was modified through manual amino acid substitution found through the literature. The molecular docking process is performed for each antigen protein with IgM antibodies using ClusPro 2.0. After that, the visualization of the 2D antibody-antigen complex was carried out with the LigPlot+ software to map the interaction between residues. The results showed that the Spike 3 vaccine showed good performance against IgM with ΔG -14.5 kcal/mol and Kd 2.3 x 10-11 M, and was also most optimal on IgG with ΔG -11.7 kcal/mol, Kd 2.8x10-9 M. Spike 2 vaccine performed best on IgM (ΔG -14.9 kcal/mol, Kd 1.2 x10-11 M), but also less effective for IgG (ΔG -10.7 kcal/mol, Kd 1.5x10-8 M). The Spike 1 vaccine showed the lowest response to IgM (ΔG -12.4 kcal/mol, Kd 8.2 x10-10 M) and IgG (ΔG -10.3 kcal/mol, Kd 2.8x10-8 M) compared to other vaccines. The sequence of effectiveness of the three vaccines is Spike 3 > Spike 2 > Spike 1 consistently on both IgM and IgG antibodies.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	Interaksi Antibodi-Antigen, Immunoglobulin M, Molecular docking, Vaksin COVID-19, SARS CoV-2. Interaxi Antibodi-Antigen, Immunoglobulin M, Molecular docking, Vaccine COVID-19, SARS CoV-2.
Subjects:	Q Science > QP Physiology > QP624 Molecular biology. Q Science > QR Microbiology > QR180 Immunology Q Science > QR Microbiology > QR355 Virology
Divisions:	Faculty of Science and Data Analytics (SCIENTICS) > Chemistry > 47201-(S1) Undergraduate Thesis
Depositing User:	Genta Ihsa Asyura
Date Deposited:	04 Aug 2025 11:21
Last Modified:	04 Aug 2025 11:21
URI:	http://repository.its.ac.id/id/eprint/126080

Actions (login required)

View Item