AutoDock Vina 1.1.2 [60] was employed to execute docking simulations, with the inputs of both PDB files and docking parameters. Docking preparation was done in AutoDock Tools [61]. this study, a collection of Zika proteomes was used to find the best candidates for T- and B-cell epitopes using the immunoinformatics approach. The most promising T-cell epitopes were mapped using the MS023 selected human leukocyte antigen (HLA) alleles, and further molecular docking and dynamics studies showed a good peptide-HLA interaction for the best major histocompatibility complex-II (MHC-II) epitope. The most promising B-cell epitopes include four linear peptides predicted to be cross-reactive with T-cells, and conformational epitopes from two MS023 proteins accessible by antibodies in their native biological assembly. It is believed that the use of immunoinformatics methods is a promising strategy against the Zika viral infection in designing an efficacious multiepitope vaccine. strong class=”kwd-title” Keywords: Zika virus, peptide vaccine, epitope, immunoinformatics, molecular docking, molecular dynamics 1. Introduction Zika Virus is an arbovirus of the genus Flavivirus known for causing Zika disease/fever in humans. Zika virus originates from Africa [1,2], and it has been around for a long time in Africa and South Asia [3,4]. Since human infections only happened sporadically with minimal to no symptoms, Zika remained largely overlooked until the 2007 outbreak at Yap Island in the Pacific Ocean [3]. It then continued to spread eastward while accumulating mutations that gave rise to some serious health problems, including microcephaly and the GuillainCBarr syndrome [1,4,5,6,7]. In late 2014, Zika entered America through Brazil, and promptly caused a major outbreak, reaching many Mouse monoclonal antibody to MECT1 / Torc1 countries in South and Central America, the Caribbean and several states within the United States [3,4,8,9]. In 2016, there were 205,578 probable Zika cases in Brazil [10]. From January 2015 to November 2016, there were 304 cases of microcephaly with a confirmed link to the Zika infection [11]. Although Zika is a potentially serious disease, there has been no medication or vaccine for Zika. Current treatments like rest, administration of fluids, and analgesics [3,4] only deal with the resulting symptoms. To directly target the virus, several Zika vaccines are currently under development, using various parts of the virus as their basis [12]. Some of them have reached clinical or preclinical trial stages, with one DNA-based vaccine currently in its second phase clinical trial [12]. Safety becomes the main concern in creating a Zika vaccine, considering pregnant women and infants are in the vulnerable population and at risk of antibody-dependent enhancement (ADE) upon entry of a related Flavivirus. ADE is the immunogenic mechanism for more severe virus infection, for example, secondary Dengue virus infections. Antibodies targeted for the virus envelope proteins are supposed to neutralize the virion by blocking it from binding to the receptors of fragment-crystallizable (Fc) on the surface of certain cells. If the affinity of the antibody from a primary infection is too low for a different serotype of the virus, the virion is not neutralized, and the secondary infection is increased [13]. ADE might arise when the production of reactive, non-neutralizing antibodies help the propagation of a related virus strain by facilitating antigen entry [14], and it has been observed in the dengue infection [15]. The peptide vaccine is seen as a safer platform for vaccine development. By only using the parts of a protein that can elicit an immune response, unnecessary components that are potentially antigenic can be eliminated. In the case of Zika, the CD8+ T-cell activity, a target of this vaccine, has been shown to play a protective role against ADE in the dengue infection [16,17]. Immunoinformatics approaches have been proven suitable for accurately determining 18 peptides from the ZIKV envelope containing predicted HLA-I T-cell epitopes and investigated T-cell cross-reactivity between ZIKV-infected individuals and DENV-vaccinated subjects by IFN ELISPOT [18]. Several in silico studies have searched epitopes on Zika, MS023 but most tended to focus on finding CD8+ T-cell epitopes, with a limited amount of further analyses like molecular docking and molecular dynamics [16,19,20,21,22,23,24]. A part of the reason for the popularity of CD8+ T-cells as a target is the more developed MHC-I epitope prediction methods [25]. The overall design of this study was to use the Zika protein sequence data to obtain candidate epitopes for CD4+ T-cell, CD8+ T-cell, and B-cell (linear epitopes), and also Zika 3D protein structures to find conformational B-cell epitope candidates in silico. The findings were verified by molecular docking and molecular dynamics analyses. 2. Materials and Methods 2.1. Preparation of Zika Polyprotein Sequences Polyprotein sequences for Zika viruses were.