Protective Antimicrobial Effect of the Potential Vaccine Created on the Basis of the Structure of the IgA1 Protease from Neisseria meningitidis

Abstract

Background/Objectives: IgA1 protease is one of the virulence factors of Neisseria meningitidis, Haemophilus influenzae and other pathogens causing bacterial meningitis. The aim of this research is to create recombinant proteins based on fragments of the mature IgA1 protease A²⁸-P¹⁰⁰⁴ from N. meningitidis serogroup B strain H44/76. These proteins are potential components of an antimeningococcal vaccine for protection against infections caused by pathogenic strains of N. meningitidis and other bacteria producing serine-type IgA1 proteases. Methods: To obtain promising antigens for creating a vaccine, we designed and obtained several recombinant proteins. These proteins consisted of single or directly connected fragments selected from various regions of the IgA1 protease A²⁸-P¹⁰⁰⁴. The choice of these fragments was based on our calculated data on the distribution of linear and conformational B-cell epitopes and MHC-II T-cell epitopes in the structure of IgA1 protease, taking into account the physicochemical properties of potential compounds and the results of a comparative analysis of the spatial structures of the original IgA1 protease and potential recombinant proteins. We studied the immunogenic and protective effects of the obtained proteins on the BALB/c mice against meningococci of serogroups A, B and C. Results: Proteins MA²⁸-P¹⁰⁰⁴-LEH₆, MW¹⁴⁰-K⁸³³-LEH₆, MW³²⁹-P¹⁰⁰⁴-LEH₆, M(W¹⁴⁰-H³²⁸)-(W⁴¹²-D⁶⁰⁴)-(Y⁸⁶⁶-P¹⁰⁰⁴)-LEH₆ and M(W¹⁴⁰-Q²⁹⁹)-(Y⁸⁶⁶-P¹⁰⁰⁴)-LEH₆ have shown the following antibody titers, 10³/titer: 11 ± 1, 6 ± 2, 6 ± 1, 9 ± 1 and 22 ± 3, respectively. Also, the last two proteins have shown the best average degree of protection from N. meningitidis serogroups A, B and C, %: 62 ± 6, 63 ± 5, 67 ± 4 respectively for M(W¹⁴⁰-H³²⁸)-(W⁴¹²-D⁶⁰⁴)-(Y⁸⁶⁶-P¹⁰⁰⁴)-LEH₆ and 70 ± 5, 66 ± 6, 83 ± 3 respectively for M(W¹⁴⁰-Q²⁹⁹)-(Y⁸⁶⁶-P¹⁰⁰⁴)-LEH₆. Conclusions: We selected two recombinant proteins consisting of two (M(W¹⁴⁰-Q²⁹⁹)-(Y⁸⁶⁶-P¹⁰⁰⁴)-LEH₆) or three (M(W¹⁴⁰-H³²⁸)-(W⁴¹²-D⁶⁰⁴)-(Y⁸⁶⁶-P¹⁰⁰⁴)-LEH₆) linked fragments of IgA1 protease A²⁸-P¹⁰⁰⁴ as candidate active component for an antimeningococcal vaccine.

Keywords: IgA1 protease; Neisseria meningitidis; epitopes; fused proteins; meningococcal vaccine; protein structure prediction.

Figure 1

(a) The number of hits for amino acid residues involved in the predicted combinations of MHC-II T-cell epitopes, located on the A²⁸–P¹⁰⁰⁴ chain, with alleles of BALB/c mouse; rank ≤ 20. (b) The average_hit value sums for amino acid residues involved in the predicted combinations of MHC-II T-cell epitopes, located on the A²⁸–P¹⁰⁰⁴ chain, with alleles of human worldwide populations; rank ≤ 20.

Figure 2

Distribution of amino acid residues included in the conformational B-cell epitopes, predicted in SEPPA 2.0 (for secreted antigen, with default thresholds) for the surface of the region A²⁸–P¹⁰⁰⁴ of IgA1 protease ADC80147.1, shown as 2D charts for mouse (a) and human (b) hosts, and selected on the model of the 3D structure (c). At the 3D model, amino acid residues that belong to the epitopes for both mouse and human hosts are colored yellow, other amino acid residues from epitopes for mouse host are colored blue, for human host—red, non-epitope residues—gray.

Figure 3

Two-level schematic representations of aligned proteins 1–5. The top halves of the schematic protein images are colored according to pLDDT values: blue for pLDDT ≥ 90 (high accuracy), light blue for 90 > pLDDT ≥ 70 (medium accuracy for side chains, good accuracy for backbone), yellow for 70 > pLDDT ≥ 50 (low accuracy), red for pLDDT < 50 (should not be interpreted: “is either unstructured in physiological conditions or only structured as part of a complex”, as stated AlphaFold FAQ at https://alphafold.ebi.ac.uk/faq, accession date 25 January 2024). The bottom halves are colored blue and orange, with the regions selected for RMSD-based matching being colored blue.

Figure 4

Immunogenic and protective properties of proteins 1–5. (a) Level of antibodies to protein 1, 1/titer; (b) degree of protection from N. meningitidis serogroups, %.

Figure 5

Simplified representation of recombinant proteins design based of sequence and epitope data for A²⁸–P¹⁰⁰⁴. (a) Sequence similarity (with IgA1 proteases from various strains of N. meningitidis) and low complexity regions data from [8]. Regions with low (see Table 2 of [8]) similarity are colored red. Low complexity regions are colored blue. In the catalytic triad of the serine IgA1 protease, Ser is shown as a part of VLGDSGSPLF sequence [7]. (b) T- and B-cell epitope prediction results for mouse and human hosts, based on Figure 1 and Figure 2. For T-cell epitopes, amino acid residues with corresponding epitope hit and average_hit for mouse and human hosts, respectively, are colored darker for higher values in a chart. For B-cell epitopes, amino acid residues with score above recommended threshold are colored black. (c) Schemes of recombinant proteins 2–5.