Innovative IgG Biomarkers Based on Phage Display Microbial Amyloid Mimotope for State and Stage Diagnosis in Alzheimer’s Disease

An innovative approach to identify new conformational antigens of Aβ1–42 recognized by IgG autoantibodies as biomarkers of state and stage in Alzheimer’s disease (AD) patients is described. In particular, through the use of bioinformatics modeling, conformational similarities between several Aβ1–42 forms and other amyloid-like proteins with F1 capsular antigen (Caf1) of Yersinia pestis were first found. pVIII M13 phage display libraries were then screened against YPF19, anti-Caf1 monoclonal antibody, and IgGs of AD patients, in alternate biopanning cycles of a so-called “double binding” selection. From the selected phage clones, one, termed 12III1, was found to be able to prevent in vitro Aβ1–42-induced cytotoxicity in SH-SY5Y cells, as well as to promote disaggregation of preformed fibrils, to a greater extent with respect to wild-type phage (pC89). IgG levels detected by 12III1 provided a significant level of discrimination between diseased and nondemented subjects, as well as a good correlation with the state progression of the disease. These results give significant impact in AD state and stage diagnosis, paving the way for the development not only for an innovative blood diagnostic assay for AD precise diagnosis, progressive clinical assessment, and screening but also for new effective treatments.


S1 PDBeFold analysis results
Results summary of PDBeFold alignments between Aβ Peptide (1-42) (PDB ID 1z0q) or amyloid fibril (PDB ID 2nao) and all the structures associated to F1 capsule antigen protein are shown below.
The following imagines show 3D structure of beta amyloid fibril (PDB ID 2nao) with the F1 capsule antigen (5 different PDB ID number) with highlighted amino acid positions involved in the homology.

Beta-amyloid protein 42
Subject: (cyan/light grey) To calculate the coordinates of chain 2 aligned on chain 1 apply the following tra nsformation:

Beta-amyloid protein 42
Subject: ( cyan/light grey) To calculate the coordinates of chain 2 aligned on chain 1 apply the following tra nsformation:

Beta-amyloid protein 42
Subject: ( cyan/light grey) To calculate the coordinates of chain 2 aligned on chain 1 apply the following tra nsformation:

F1 capsule antigen
Best cluster Residues number: 4

S3.3 Molecular docking prediction of 12III1 phage clone displayed peptide with Aß fibrils
The following imagines show 3D structural modeled interaction between engineered 12III1-pVIII protein in wireframe style with displayed amino acid side positions and beta amyloid fibril in electrostatic surface style (A) and in backbone style coupled to energy map (B). Colors legend of electrostatic and steric clouds: i) Steric favorable non-polar amino acids are included in green regions; ii) Electrostatic favorable, red regions correspond to a nearby negative electro-static charge of amino acids, blue regions correspond to a nearby positive charge of amino acids; iii) Hydrogen donor favorable are yellow; iv) Hydrogen acceptor favorable are light blue.

A B
The amino acids involved in the interaction are listed in the following tables. Table S2.12III1-pVIII amino acid residues involved in the interaction with beta amyloid fibril chains.