PENAMBATAN DAN SIMULASI DINAMIKA MOLEKULER ANTARA DESAIN VAKSIN DENGAN ADJUVAN RIBOSOMAL 50S L7/L12 DAN TOLL LIKE RECEPTOR 3 (TLR 3)

FIRMANSYAH, MOHAMAD AFRIZAL (2022) PENAMBATAN DAN SIMULASI DINAMIKA MOLEKULER ANTARA DESAIN VAKSIN DENGAN ADJUVAN RIBOSOMAL 50S L7/L12 DAN TOLL LIKE RECEPTOR 3 (TLR 3). Skripsi thesis, Universitas Setia Budi.

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Abstract

The new corona virus named SARS-CoV-2 has become a global pandemic which is still developing to this day. Several countries are racing to develop a safe and effective vaccine. The developing vaccine is ineffective because a booster dose is required. Some vaccines today are starting to lose their neutralization effectiveness because the virus continues to mutate. This study aims to determine the interaction of atomic vaccine design with Toll Like Receptor 3, so as to obtain an effective and stable design that is assessed by the RMSD and RMSF values from molecular dynamics simulations. Vaccine design is made using a webserver. The vaccine design was made using sequences obtained from Uniprot. Sequences with the highest antigenicity were identified with Epitope MHC-1, II, and B cells. Epitope was constructed in 3D by combining the obtained epitope with Ribosomal 50S L7/L12 adjuvants. Molecular anchoring was carried out using HADDOCK 2.4, as well as molecular dynamics simulation using YASARA. The vaccine design obtained has an antigenicity of 0.5114, the vaccine design is also predicted to be structurally stable with a molecular weight of 42.47 Kda, has a GRAVY value of -0.056, a Procheck value of 86.15%, and an ERRAT of 0 error. Molecular anchoring has a value of -104.867. Molecular dynamics simulation using YASARA obtained an average RMSD of 5.12 and RMSF of 2.01 Angstrom. The molecular anchoring value of HADDOCK 2.4 has a good value, so it can be concluded that the vaccine design with Ribosomal 50S L7/L12 and TLR 3 adjuvants is predicted to have effectiveness in responding to the immune system, while the average value of RMSD and RMSF resulting from molecular dynamics simulations also shows that the vaccine design withadjuvants 50S L7/L12 and TLR 3 can bind strongly to induce an immune response. Keywords: SARS-CoV-2, vaccine design, molecular tethering, molecular dynamics.

Item Type:	Thesis (Skripsi)
Uncontrolled Keywords:	SARS-CoV-2, vaccine design, molecular tethering, molecular dynamics.
Subjects:	R Medicine > RS Pharmacy and materia medica
Divisions:	Fakultas Farmasi > Prodi S1 Farmasi
Depositing User:	Tifany Nur Arfiana
Date Deposited:	30 Nov 2022 03:17
Last Modified:	30 Nov 2022 03:17
URI:	http://repo.setiabudi.ac.id/id/eprint/5553

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