Protein Modelling Insight to the Poor Sensitivity of Chikungunya Diagnostics on Indonesia’s Chikungunya Virus

Bevi Lidya (Doctoral Program of Biotechnology, Postgraduate School, Universitas Padjadjaran, Jl. Dipati Ukur No. 35, Bandung 40132, Indonesia Department of Chemical Engineering, Politeknik Negeri Bandung, Jl. Gegerkalong Hilir, Bandung 40559, Indonesia)
Muhammad Yusuf (Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km. 21, Jatinangor, Sumedang 45363, Indonesia Research Center of Molecular Biotechnology and Bioinformatics, Universitas Padjadj)
Umi Baroroh (Department of Biotechnology, Sekolah Tinggi Farmasi Indonesia, Jl. Soekarno Hatta No. 354, Bandung 40266, Indonesia)
Korry Novitriani (Department of Medical Laboratory Technology, Faculty of Health Science, Universitas Bakti Tunas Husada, Jl. Cilolohan No. 36, Tasikmalaya 46115, Indonesia)
Bachti Alisjahbana (Health Center Unit, Faculty of Medicine, Universitas Padjadjaran, Jl. Prof. Eyckman No.38, Bandung 40161, Indonesia)
Iman Rahayu (Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km. 21, Jatinangor, Sumedang 45363, Indonesia)
Toto Subroto (Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km. 21, Jatinangor, Sumedang 45363, Indonesia Research Center of Molecular Biotechnology and Bioinformatics, Universitas Padjadj)

Indonesian Journal of Chemistry
Vol 23, No 5 (2023)

Sensitive detection of infectious diseases is crucial for effective clinical care. However, commercial rapid tests may be limited in their ability to detect pathogen variants across different countries. It was found that the sensitivity of a chikungunya rapid test on local strain was only 20.5% as compared to the East, Central, and South Africa (ECSA) phylogroup. Therefore, the development of geographically specific diagnostics is essential. Investigating the distinctive structural properties of a locally sourced antigenic protein is an important initiative for the development of a specific antibody. This study utilized structural bioinformatics and molecular dynamics simulations to investigate the differences between the E1-E2 antigenic proteins of the Indonesian chikungunya virus (Ind-CHIKV) and that of ECSA. The results showed that some of the mutation points are located at the antibody binding sites of Ind-CHIKV. G194S and V318R mutations were proposed as distinctive features of Ind-CHIKV, leading to weaker antibody binding compared to ECSA. It suggests that modifying the antibody to accommodate bulkier side chains at positions 194 and 318 could improve its effectiveness against Ind-CHIKV. These insights are valuable for developing a highly sensitive immunoassay for Ind-CHIKV and other regional pathogens, ultimately enhancing diagnostic capabilities in Indonesia.