Strategies for Identification of Small Molecule Inhibitors of Ad2 E3-19K/HLA-A2 Binding Interaction
thesisposted on 01.11.2017 by Nikita Raymond Dsouza
In order to distinguish essays and pre-prints from academic theses, we have a separate category. These are often much longer text based documents than a paper.
Adenovirus (Ad) infections are widespread in the human population, and causes infections linked to many gastrointestinal, respiratory and ocular illnesses. In vitro and in vivo studies have shown that the binding of the adenovirus protein E3-19K of the adenovirus with the Major Histocompatibility Complex (MHC) class I molecules plays a role in infection as it retains these molecules in the endoplasmic reticulum (ER) of the Ad infected cells, thus inhibiting the lysis of the Ad infected cells by cytotoxic T-lymphocytes (CTLs). The goal of this research study is to evaluate the Ad2 E3-19K – HLA-A2 complex as a target for its potential to bind small molecule inhibitors. The knowledge of the crystal structure, and the interaction surface of the Ad2 E3-19K – HLA-A2 complex provides us a foundation to conduct Structure-Based Drug Design (SBDD). We aim to disrupt the binding of E3-19K protein of adenovirus with the HLA-A2 molecule, which could then sensitize the adenovirus infected cells to lysis by the CTLs. To achieve this, we used computational methods to determine potential binding sites for small molecules. Hence, we analyzed the crystal structure of the complex, including the binding surface of the proteins involved in the complex; we compared the Ad2 E3-19K – HLA-A2 and Ad4 E3-19K – HLA-A2 structures to determine whether the binding site selected varies between strains. A structure-based virtual screening (SBVS) protocol was designed to probe the Ad2 E3-19K – HLA-A2 interface for its potential to be targeted by small molecules. Per-residue decomposition of the interface interactions was obtained from the analysis of Molecular Dynamic (MD) trajectories which was used to determine residues in peptides that could also be used to target the protein. We shortlisted compounds to be tested experimentally, using the scoring functions of the molecular docking program; we found 7 compounds with binding affinity to HLA-A2 out of the 36 compounds tested. In addition, the peptide sequence obtained from per-residue decomposition has been used to synthesize peptides that can be tested for its binding potential through experiments.