In silico Prediction of Immunogenic Sites on PMN Antigen and Design of Epitope Blocking Caps

Abstract

Autoimmune disorders (AD) are a type of disease in which an individual's immune system attacks the cells of its own body. Currently, AD are the 2nd leading cause of chronic long term illness. The primary method of treating AD is the use of non‐specific immunosuppressant drugs, suppressing the entire immune system and leaving the patient vulnerable to infections. Antigen specific therapies have been proposed in order to replace treatment with immunosuppressant drugs for AD. The work here focuses on developing a new approach to AD therapy which targets the epitope site (ES) on the antigen, with an emphasis on the kidney specific AD primary membranous nephropathy, which affects 10–12 million people worldwide. Using in silico mutagenesis the ES on the phospholipase A2 receptor (PLA2R) were predicted and epitope binding proteins (EBP) were developed to target these regions. Using Epitopia and EPCES two regions on the CTLD1 domain of PLA2R were identified as potential ES. These ES are characterized in terms of the number of residues, their electrostatic potential, and their hydrophobicity. In silico prediction of immunogenicity showed the single nucleotide polymorphisms M292V, H300D, and G1106S do not directly contribute to immunogenic sites on PLA2R. In silico mutagenesis of two protein templates (5IMK and 4JE4) was performed to design EBP structures. The Rosetta protein‐protein docking server was used to evaluate the interface score of designed EBP to the PLA2R antigen, and disruption of binding to their original binding partner via molecular mechanics calculations. In silico mutations to the 5IMK monobody increased the binding interface score from −4.259 rosetta energy units (REU) to −8.903 REU. Similarly, in silico mutations to the 4JE4 monobdy increased the interface score from −3.964 REU to −5.867 REU. Data shows the introduction of charged residues to the monobody contributes to the most significant gains in interface score. Further in silico mutations were introduced to disrupt the binding preference of 5IMK and 4JE4 to their original targets. Binding potency was reduced from −7.851 REU to −3.87 REU for 5IMK, and from −12.263 REU to −3.693 REU for 4JE4. This work could be used to develop a new antigen specific therapy approach for PMN and AD in general.Support or Funding InformationWilliam Randolph Hearst FoundationThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.