Designing Bcl-2 protein binding aptamers using screened Coulomb interaction method & regulate apoptosis.

Abstract

Cancer cells develop different physiological abnormalities. One of them is overexpression of Bcl-2 protein, an anti-apoptotic biomolecule helping cancer cells to sustain. We planned to regulate the apoptosis by inhibiting the Bcl-2 protein's functions in cancer cells. We used computer aided drug design techniques to make a nucleic acid-based aptamer drug that targets Bcl-2 proteins. We applied a theoretical biophysics technique ‘screened Coulomb interactions approach (SCIA)’ for designing aptamers. This technique was patented (US10916330B1) and found suitable for designing novel aptamers to target biomoleculesin physiological conditions. Physicochemical analysis of Bcl-2 protein helps detect drug binding site(s) and charge distribution inamino acid structures. We made a judicious choice to select amino acid arginine as our target molecule in Bcl-2 structure. We constructed a universal drug design platform by applying SCIA, developed our algorithms and applied in Mathematica 13 to perform numerical computations (NCs) addressing the drug-target binding energetics. The NC results show that nucleotide guanine has the lowest binding energy over other nucleotides while interacting with arginine. Selection of other subsequent nucleotides as aptamer building blocks at various screening order is being made using their preferred SCI binding energetics with arginine. Thus, the discovery of a few aptamers to target arginine (specifically) and Bcl-2 protein (in general) has been made. Based on target binding energetic preferences we rank the aptamers. We are now working on the following two things: (i) perform 100 nanosecond molecular dynamics (MD) simulations to address drug-target binding kinetics and (ii) perform in vitro protein binding assays using top selected aptamers. Thus, we shall be able to finalize a few candidate drugs as optimal therapeutic agents capable of binding with Bcl-2 proteins and thus inhibit the protein functions. This research will lead us to discovering a few aptamer candidates for future chemotherapy applications.