In Silico Design and Simulation of Aptamer-Mediated Enrichment Strategies for CD8αα+ CAR T-Cells

CAR T-cell therapy treats malignant tumors by extracting T-cells from the patient’s blood and modifying the receptors to kill cancer cells. Enrichment is the process in which CAR T-cells are separated from the unmodified T-cells. Aptamers are molecules of genetic information that connect the T-cell receptor to the B-cell receptor. Recently, Kacherovsky et al. have designed aptamers that specifically bind to the CD8αα+ CAR T-cells and can be used to enrich the receptor. We hypothesize that the aptamers can selectively bind to the CD8αα receptor on CAR T-cells and help their enrichment. The 3D structure and binding sites of CD8αα+ were identified by using the software AlphaFold3, P2Rank, and ChimeraX. To see which aptamer can bind best to CD8αα, aptamer structures were predicted using web servers VFold2d and VFold3D by using their respective DNA structures and the dot-and-bracket notations. Once all necessary structures were created, the docking process began to eliminate aptamers that don’t bind to the binding site of CD8αα by using HDOCK and PLIP. Aptamers can further be decided for CAR T-cell therapy if they have a great number of interactions of hydrogen bonds and less binding energy. The A3 aptamer was applied to all three criteria and was concluded to be the most suitable aptamer for CAR T-cell therapy. By identifying the most effective aptamer, CAR T-cell therapy can be advanced to enrich normal T-cells to have the most suitable receptor and bind to the identified aptamer to show success in cancer removal efficiency.