Mining Autoimmune-Disorder-Linked Molecular-Mimicry Candidates in Clostridioides difficile and Prospects of Mimic-Based Vaccine Design: An In Silico Approach

Abstract

Molecular mimicry, a phenomenon in which microbial or environmental antigens resemble host antigens, has been proposed as a potential trigger for autoimmune responses. In this study, we employed a bioinformatics approach to investigate the role of molecular mimicry in Clostridioides difficile-caused infections and the induction of autoimmune disorders due to this phenomenon. Comparing proteomes of host and pathogen, we identified 23 proteins that exhibited significant sequence homology and were linked to autoimmune disorders. The disorders included rheumatoid arthritis, psoriasis, Alzheimer's disease, etc., while infections included viral and bacterial infections like HIV, HCV, and tuberculosis. The structure of the homologous proteins was superposed, and RMSD was calculated to find the maximum deviation, while accounting for rigid and flexible regions. Two sequence mimics (antigenic, non-allergenic, and immunogenic) of ≥10 amino acids from these proteins were used to design a vaccine construct to explore the possibility of eliciting an immune response. Docking analysis of the top vaccine construct C2 showed favorable interactions with HLA and TLR-4 receptor, indicating potential efficacy. The B-cell and T-helper cell activity was also simulated, showing promising results for effective immunization against C. difficile infections. This study highlights the potential of C. difficile to trigger autoimmunity through molecular mimicry and vaccine design based on sequence mimics that trigger a defensive response.

Keywords: Clostridioides difficile; autoimmunity; bioinformatics; docking; immune response; molecular mimicry; pathogenesis; vaccine design.

Figure 1

Superposed structures of the C. difficile and human homologous proteins. (A) Molecular chaperone DnaK; (B) Translation elongation factor 4; (C) Uracil-DNA glycosylase; (D) Acetyl-CoA C-acetyltransferase; (E) 3-oxoacid CoA-transferase subunit B; (F) UDP-glucose 4-epimerase GalE; (G) V-type proton ATPase subunit B; (H) V-type ATP synthase catalytic unit A; (I) Phosphopyruvate hydratase; (J) ATP-dependent Clp endopeptidase proteolytic subunit ClpP; (K) ATP-dependent Clp endopeptidase proteolytic subunit ClpP; (L) F0F1 ATP synthase subunit beta. Due to space constraints, the first 12 (Table 1) of the 23 proteins are shown here. Human homologs are shown in brown and bacterial proteins are shown in blue.

Figure 2

Conservation of sequence mimics from (A) phosphoribosylaminoimidazolecarboxamide formyltransferase and (B) adenylosuccinate lyase used for vaccine design underlined by red (and star symbol). Yellow color indicates insufficient data for conservation inference.

Figure 3

The 5083 bp cloned vector of the vaccine construct.

Figure 4

Immune system cells released after the C2 vaccine and C. difficile protein (phosphoribosylaminoimidazolecarboxamide formyltransferase and adenylosuccinate lyase) stress, including (A) immunoglobulins, (B) B cells, (C) TH cells, (D) TC cells, and (E) NK cells.

Figure 5

Vaccine construct (shown in green) interaction with (A) HLA-A, (B) HLA-B, and (C) TLR-4. Receptors are shown in cyan. (D) Control Tumor necrosis factor ligand superfamily member 11 (RANK-L) and 11A (RANK) from Mus musculus.