In silico design of a novel antigen based on safe epitopes of epsilon toxin: avoidance of potential molecular mimicry involved in autoimmune responses

Background

Clostridium perfringens, a bacterium associated with various animal and human diseases, could produce several toxins, such as epsilon toxin (ETX). The economic importance of ETX is related to its ability to cause enterotoxemia in domestic ruminants, which causes sudden death. This neurotoxin is also a unique environmental triggering agent for multiple sclerosis (MS). Antibodies against the TGVSLTTSYSFANTN peptide of ETX had been found in clinically definite multiple sclerosis (CDMS). However, no similarity with human proteins was found by the conducted basic local alignment search tool (BLAST) search. Several studies revealed that similar epitopes shared between the infectious microorganisms and the human proteome could trigger autoimmune responses. Although several ETX-based antigens had been designed, this issue was not considered in the designs.

Methods

In the current study, the ETX sequence was analyzed to find any shared peptides with more than 5 residues in length in the human proteome. Then, a vaccine construct was designed based on specific peptides of ETX with no similarity to the human proteome. The obtained construct was analyzed regarding its antigenic and structural properties.

Results

No match was discovered for peptides longer than 7-meric. Hepta- and 6-meric peptides matched to a total of 4 and 83 identical peptides in the human proteome, respectively. A construct with a length of 110 amino acids (approximately 13 kDa with the estimated pI of 8.75) was obtained. This construct contains both alpha helical and extended regions linked by coiled regions. The extended and coiled regions were more frequent than the helical regions. The AlphaFold 3D model was consistent with the results obtained from the secondary structure prediction. The molecular dynamic (MD) simulation demonstrated that the designed construct maintains its structural compactness during the simulation, and after 50 ns of MD, the designed construct achieves an equilibrium and stabilized state.

Conclusions

A novel antigen was designed based on safe epitopes of epsilon toxin by which potential molecular mimicry involved in autoimmune responses could be avoided. The current study results require experimental verification in future investigations.