Publication: In silico development of dna aptamer-targeting breast cancer soluble pdl-1 (spdl-1) protein
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Date
2026-01
Authors
Yazid, Ahmad Arif Akmal
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Abstract
This study aimed to develop an aptamer-based bioassay, also known as enzyme-linked oligonucleotide assay (ELONA), for the detection of soluble programmed death-ligand 1 (sPD-L1) by integrating in-silico approaches with experimental validation. sPD-L1 is an important immune-related cancer biomarker; however, conventional antibody-based ELISA methods are limited by high cost, stability issues and batch-to-batch variability. In this work, multiple ssDNA aptamers were generated and systematically screened in- silico using secondary and three-dimensional structure prediction, molecular docking, protein–ligand interaction analysis and molecular dynamics simulations to identify a candidate with favourable binding affinity and complex stability toward PD-L1. The selected aptamer was subsequently validated experimentally using ELONA. The assay demonstrated concentration-dependent and saturable binding of the aptamer to immobilised PD-L1, with a moderate equilibrium dissociation constant (Kd), indicating functional and specific interaction. Overall, the findings confirm the feasibility of combining in-silico guided aptamer selection with experimental ELONA development and support the potential of aptamers as viable alternatives to antibodies in cancer biomarker detection.