Design, Synthesis and Binding of Hydrogen Bond Surrogate (HBS) stabilized Helicomimics with Biorelevant DNA Transcription Factor Domains and Proteins

Abstract

Although all cells share the same genome, their diverse functions arise from differential gene expression, which governs cell fate and activity. Dysregulation of this transcriptional machinery leads to diseases, highlighting the therapeutic potential of artificial transcription factors to modulate gene expression for precise disease control. This thesis introduces the ERG-TF influence on Prostate Cancer (PCa), where over 50% of cases feature the recurrent TMPRSS2-ERG gene fusion. We developed a method “Weak Interaction Identification method” to identify hotspot residues by scanning all weak non-covalent interactions per residue using boundary distances on ERG crystal structures (PDB: 4IRG and 6VGG). A helix wheel diagram guided the design of an HBS-constrained helicomimic targeting the DNA-interacting ERG sequence. These molecules were synthesized with the help of Hydrogen bond surrogate (HBS) method standardized in our lab, and with the help of standard solid phase synthesis by using the Rinkamide resin. The final ERG-molecules were characterized with the help of 1H, C13, 2D-NMR, CD-spectroscopy. Various binding methods such as UV, Fluorescence, MST, and ITC-methods were used to study its interaction with the ds-DNA, which showed binding in nanomolar range, which is quite high as compared to other methods, and remarkably high selectivity. Similar case is seen in case of HBS-constrained GATA-3 Helicomimics also. Similar approach is done and similar case is seen in case of HBS-constrained α1-ACE2-Helicomimics, which are successful in inhibiting the protein-protein interaction of SARS-CoV-2-RBD with the mammalian cell culture purified hACE2-Fc.