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

Bevi Lidya(1*), Muhammad Yusuf(2), Umi Baroroh(3), Korry Novitriani(4), Bachti Alisjahbana(5), Iman Rahayu(6), Toto Subroto(7)

(1) 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
(2) 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 Padjadjaran, Jl. Singaperbangsa No. 2, Bandung 40132, Indonesia
(3) Department of Biotechnology, Sekolah Tinggi Farmasi Indonesia, Jl. Soekarno Hatta No. 354, Bandung 40266, Indonesia
(4) Department of Medical Laboratory Technology, Faculty of Health Science, Universitas Bakti Tunas Husada, Jl. Cilolohan No. 36, Tasikmalaya 46115, Indonesia
(5) Health Center Unit, Faculty of Medicine, Universitas Padjadjaran, Jl. Prof. Eyckman No.38, Bandung 40161, Indonesia
(6) Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km. 21, Jatinangor, Sumedang 45363, Indonesia
(7) 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 Padjadjaran, Jl. Singaperbangsa No. 2, Bandung 40132, Indonesia
(*) Corresponding Author


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.


chikungunya; bioinformatics; diagnostics; Indonesia; molecular dynamics simulation


[1] Kosasih, H., Widjaja, S., Surya, E., Hadiwijaya, S.H., Butarbutar, D.P.R., Jaya, U.A., and Alisjahbana, B., 2012, Evaluation of two IgM rapid immunochromatographic tests during circulation of Asian lineage chikungunya virus, Southeast Asian J. Trop. Med. Public Health, 43 (1), 55–61.

[2] Burdino, E., Calleri, G., Caramello, P., and Ghisetti V., 2016, Unmet needs for a rapid diagnosis of chikungunya virus infection, Emerging Infect. Dis., 22 (10), 1837–1839.

[3] Kosasih, H., de Mast, Q., Widjaja, S., Sudjana, P., Antonjaya, U., Ma’roef, C., Riswari, S.F., Porter, K.R., Burgess, T.H., Alisjahbana, B., van der Ven, A., and Williams, M., 2013, Evidence for endemic chikungunya virus infections in Bandung, Indonesia, PLoS Neglected Trop. Dis., 7 (10), e2483.

[4] Harapan, H., Michie, A., Mudatsir, M., Nusa, R., Yohan, B., Wagner, A.L., Sasmono, R.T., and Imrie, A., 2019, Chikungunya virus infection in Indonesia: A systematic review and evolutionary analysis, BMC Infect. Dis., 19 (1), 243.

[5] Arif, M., Tauran, P., Kosasih, H., Pelupessy, N.M., Sennang, N., Mubin, R.H., Sudarmono, P., Tjitra, E., Murniati, D., Alam, A., Gasem, M.H., Aman, A.T., Lokida, D., Hadi, U., Parwati, K.T.M., Lau, C.Y., Neal, A., and Karyana, M., 2020, Chikungunya in Indonesia: Epidemiology and diagnostic challenges, PLoS Neglected Trop. Dis., 14 (6), e0008355.

[6] Sahoo, B., and Chowdary, T.K., 2019, Conformational changes in chikungunya virus E2 protein upon heparan sulfate receptor binding explain mechanism of E2–E1 dissociation during viral entry, Biosci. Rep., 39 (6), BSR20191077.

[7] Bissoyi, A., Pattanayak, S.K., Bit, A., Patel, A., Singh, A.K., Behera, S.S., and Satpathy, D., 2017, "Alphavirus Nonstructural Proteases and Their Inhibitors" in Viral Proteases and Their Inhibitors, Eds. Gupta, S.P., Academic Press, Cambridge, US, 77–104.

[8] Segato-Vendrameto, C.Z., Zanluca, C., Zucoloto, A.Z., Zaninelli, T.H., Bertozzi, M.M., Saraiva-Santos, T., Ferraz, C.R., Staurengo-Ferrari, L., Badaro-Garcia, S., Manchope, M.F., Dionisio, A.M., Pinho-Ribeiro, F.A., Borghi, S.M., Mosimann, A.L.P., Casagrande, R., Bordignon, J., Fattori, V., dos Santos, C.N.D., and Verri, W.A., 2023, Chikungunya virus and its envelope protein E2 induce hyperalgesia in mice: Inhibition by anti-E2 monoclonal antibodies and by targeting TRPV1, Cells, 12 (4), 556.

[9] Chen, R., Mukhopadhyay, S., Merits, A., Bolling, B., Nasar, F., Coffey, L.L., Powers, A., Weaver, S.C., and Consortium, I.R., 2018, ICTV Virus Taxonomy Profile: Togaviridae, J. Gen. Virol., 99 (6), 761–762.

[10] Rangel, M.V, McAllister, N., Dancel-Manning, K., Noval, M.G., Silva, L.A., and Stapleford, K.A., 2022, Emerging chikungunya virus variants at the E1-E1 interglycoprotein spike interface impact virus attachment and inflammation, J. Virol., 96 (4), e0158621.

[11] Yap, M.L., Klose, T., Urakami, A., Hasan, S.S., Akahata, W., and Rossmann, M.G., 2017, Structural studies of chikungunya virus maturation, Proc. Natl. Acad. Sci. U. S. A., 114 (52), 13703–13707.

[12] Xu, X., Zhang, R., and Chen, X., 2017, Application of a single-chain fragment variable (scFv) antibody for the confirmatory diagnosis of hydatid disease in non-endemic areas, Electron. J. Biotechnol., 29, 57–62.

[13] Kam, Y.W., Lee, W.W.L., Simarmata, D., Le Grand, R., Tolou, H., Merits, A., Roques, P., and Ng, L.F.P., 2014, Unique epitopes recognized by antibodies induced in chikungunya virus-infected non-human primates: Implications for the study of immunopathology and vaccine development, PLoS One, 9 (4), e95647.

[14] Dwivedi, S., Purohit, P., Misra, R., Pareek, P., Goel, A., Khattri, S., Pant, K.K., Misra, S., and Sharma, P., 2017, Diseases and molecular diagnostics: A step closer to precision medicine, Indian J. Clin. Biochem., 32 (4), 374–398.

[15] Gao, Y.P., Huang, K.J., Wang, F.T., Hou, Y.Y., Xu, J., and Li, G., 2022, Recent advances in biological detection with rolling circle amplification: Design strategy, biosensing mechanism, and practical applications, Analyst, 147 (15), 3396–3414.

[16] Tiller, K.E., and Tessier, P.M., 2015, Advances in antibody design, Annu. Rev. Biomed. Eng., 17 (1), 191–216.

[17] Holstein, C.A., Chevalier, A., Bennett, S., Anderson, C.E., Keniston, K., Olsen, C., Li, B., Bales, B., Moore, D.R., Fu, E., Baker, D., and Yager, P., 2015, Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers, Anal. Bioanal. Chem., 408 (5), 1335–1346.

[18] Voss, J.E., Vaney, M.C., Duquerroy, S., Vonrhein, C., Girard-Blanc, C., Crublet, E., Thompson, A., Bricogne, G., and Rey, F.A., 2010, Glycoprotein organization of chikungunya virus particles revealed by X-ray crystallography, Nature, 468 (7324), 709–714.

[19] Webb, B., and Sali, A., 2016, Comparative protein structure modeling using MODELLER, Curr. Protoc. Bioinf., 54 (1), 5.6.1–5.6.37.

[20] Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M., 1993, PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr., 26 (2), 283–291.

[21] Wiederstein, M., and Sippl, M.J., 2007, ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Res., 35 (Suppl. 2), W407–W410.

[22] Ouyang, J., Huang, N., and Jiang, Y., 2020, A single-model quality assessment method for poor quality protein structure, BMC Bioinf., 21 (1), 157.

[23] Case, D.A., Babin, V., Berryman, J.T., Betz, R.M., Cai, Q., Cerutti, D.S., Cheatham, III, T.E., Darden, T.A., Duke, R.E., Gohlke, H., Goetz, A.W., Gusarov, S., Homeyer, N., Janowski, P., Kaus, J., Kolossváry, I., Kovalenko, A., Lee, T.S., LeGrand, S., Luchko, T., Luo, R., Madej, B., Merz, K.M., Paesani, F., Roe, D.R., Roitberg, A., Sagui, C., Salomon-Ferrer, R., Seabra, G., Simmerling, C.L., Smith, W., Swails, J., Walker, R.C., Wang, J., Wolf, R.M., Wu, X., and Kollman, P.A., 2014, AMBER 14, University of California, San Francisco.

[24] Andrusier, N., Nussinov, R., and Wolfson, H.J., 2007, FireDock: Fast interaction refinement in molecular docking, Proteins: Struct., Funct., Bioinf., 69 (1), 139–159.

[25] Mashiach, E., Schneidman-Duhovny, D., Andrusier, N., Nussinov, R., and Wolfson, H.J., 2008, FireDock: A web server for fast interaction refinement in molecular docking, Nucleic Acids Res., 36 (Suppl. 2), W229–W232.

[26] Zhang, H., and Shen, Y., 2020, Template-based prediction of protein structure with deep learning, BMC Genomics, 21 (11), 878.

[27] Wu, F., and Xu, J., 2021, Deep template-based protein structure prediction, PLoS Comput. Biol., 17 (5), e1008954.

[28] Lüthy, R., Bowie, J.U., and Eisenberg, D., 1992, Assessment of protein models with three-dimensional profiles, Nature, 356 (6364), 83–85.

[29] Sun, S., Xiang, Y., Akahata, W., Holdaway, H., Pal, P., Zhang, X., Diamond, M.S., Nabel, G.J., and Rossmann, M.G., 2013, Structural analyses at pseudo atomic resolution of chikungunya virus and antibodies show mechanisms of neutralization, eLife, 2, e00435.

[30] Sobolev, O.V., Afonine, P.V., Moriarty, N.W., Hekkelman, M.L., Joosten, R.P., Perrakis, A., and Adams, P.D., 2020, A global Ramachandran score identifies protein structures with unlikely stereochemistry, Structure, 28 (11), 1249–1258.e2.

[31] Moulin, E., Selby, K., Cherpillod, P., Kaiser, L., and Boillat-Blanco, N., 2016, Simultaneous outbreaks of dengue, chikungunya and Zika virus infections: Diagnosis challenge in a returning traveller with nonspecific febrile illness, New Microbes New Infect., 11, 6–7.

[32] Liu, Y., Liu, Y., Mernaugh, R.L., and Zeng, X., 2009, Single chain fragment variable recombinant antibody functionalized gold nanoparticles for a highly sensitive colorimetric immunoassay, Biosens. Bioelectron., 24 (9), 2853–2857.

[33] Hurwitz, A.M., Huang, W., Kou, B., Estes, M.K., Atmar, R.L., and Palzkill, T., 2017, Identification and characterization of single-chain antibodies that specifically bind GI noroviruses, PLoS One, 12 (1), e0170162.

[34] Shashi Kumar, N., Moger, N., Rabinal, C.A., Krishnaraj, P.U., and Chandrashekara, K.N., 2017, Production of diagnostic kit to detect CRY2B antigen by use of scFv monoclonal antibody, Int. J. Curr. Microbiol. Appl. Sci., 6 (7), 4401–4411.

[35] Chakraborty, S., Connor, S., and Velagic, M., 2022, Development of a simple, rapid, and sensitive diagnostic assay for enterotoxigenic E. coli and Shigella spp applicable to endemic countries, PLoS Neglected Trop. Dis., 16 (1), e0010180.

[36] Leong, S.W., Lim, T.S., Ismail, A., and Choong, Y.S., 2017, Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein, J. Mol. Recognit., 31 (5), e2695.

[37] Hong, Z., Tian, C., Stewart, T., Aro, P., Soltys, D., Bercow, M., Sheng, L., Borden, K., Khrisat, T., Pan, C., Zabetian, C.P., Peskind, E.R., Quinn, J.F., Montine, T.J., Aasly, J., Shi, M., and Zhang, J., 2021, Development of a sensitive diagnostic assay for Parkinson disease quantifying α-synuclein–containing extracellular vesicles, Neurology, 96 (18), e2332–e2345.

[38] Bandehpour, M., Ahangarzadeh, S., Yarian, F., Lari, A., and Farnia, P., 2018, In silico evaluation of the interactions among two selected single chain variable fragments (scFvs) and ESAT-6 antigen of Mycobacterium tuberculosis, J. Theor. Comput. Chem., 16 (8), 1750069.

[39] Rao, V.S., Srinivas, K., Sujini, G.N., and Kumar, G.N.S., 2014, Protein-protein interaction detection: Methods and analysis, Int. J. Proteomics, 2014, 147648.

[40] Sela-Culang, I., Kunik, V., and Ofran, Y., 2013, The structural basis of antibody-antigen recognition, Front. Immunol., 4, 00302.


Article Metrics

Abstract views : 1003 | views : 398 | views : 211

Copyright (c) 2023 Indonesian Journal of Chemistry

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.


Indonesian Journal of Chemistry (ISSN 1411-9420 /e-ISSN 2460-1578) - Chemistry Department, Universitas Gadjah Mada, Indonesia.

Analytics View The Statistics of Indones. J. Chem.