In Silico Prediction of Malayan Krait (Bungarus candidus) PLA2 Epitope

Abstract

Nia Kurniawan, Coni Anggie Kurniasari, Fatchiyah

Malayan krait or Bungarus candidus is one of the medically important venomous snake species category I in Indonesia but there is no antivenom to cover Bungarus candidus envenomation. PLA2 is one of dominant toxin protein in Bungarus candidus venom, it is a multifunctional toxin which has several pathological effects. One alternative way to solve this problem is by generating an epitope-based vaccine, toward the epitope of PLA2 protein. This research aims to identify the epitope region of Bungarus candidus PLA2 and evaluate the potency of inducing the immune response. PLA2 amino acid sequence retrieved from NCBI (accession number: BAD06270.1), then the T cell epitope (MHC-I and MHC-II) are predicted from this sequence using the IEDB tools. We selected the prediction results with IC50 value below 200 nM. The prediction result was then analyzed by epitope conservancy, immunogenicity, and population coverage analysis. The three most potential epitopes are “FAKAPYNEE”, “LSYFRYTEM”, and “RTAALCFAK”. The docking simulation is conducted between three epitope prediction results and four MHC molecules (PDB ID: 6EI2, 3LKO, 1DLH, 6DIG). The docking simulation result showed that the epitopes are interacting with MHC molecules inside the binding grooves, the binding energies are relatively low (epitope “FAKAPYNEE” with 3LKO, -151.37 kcal/mol; “LSYFRYTEM” with 6DIG, -188.06 kcal/mol; and “RTAALCFAK” with 3LKO, -104.5 kcal/mol). The docking simulation result showed that the epitopes are forming a complex with MHC molecules inside the binding grooves and the binding energies are relatively low, thus it indicates that three predicted epitopes are potent to induce the immune response.