Since the emergence of the COVID-19 pandemic, the SARS-CoV-2 virus has continued to evolve, leading to the emergence of many variants worldwide. The qRT-PCR test of respiratory samples is the current gold standard for detecting SARS-CoV-2; however, this test is costly, time-consuming, and requires highly qualified personnel and instruments, making it unsuitable for rapid on-site analysis. Given the population health risk and social factors in Mexico, it is crucial to detect and track the COVID-19 disease in the Mexican population accurately and in a fast manner. Enzyme-linked aptamer-based biosensors are a fast, inexpensive, and simple method for detecting various targets, including viruses. However, a biosensor based on this technology to detect the SARS-CoV-2 virus has not yet been designed. Therefore, this project aims to develop a lab-on-a-chip enzyme-linked optical aptasensor to detect the virus. As a first step, in this study, three toehold aptamer sequences targeting the Nucleocapsid protein gene were developed and studied in silico. This approach reduces experimental time and cost while providing insights into the binding mechanism, binding affinity, and specificity of aptamers. The assays performed involved obtaining the secondary structures of aptamers with the mFold online server, predicting the 3D modeling structures and potential binding sites with the RNAcomposer modeling server and PyMOL software, performing molecular docking simulations of the target and aptamer, evaluating aptamer stability, and determining binding energies with high accuracy. The results obtained from the in-silico assays suggest that these aptamers are a promising option for detecting the SARS-CoV-2 virus. Further experimental testing is needed to determine whether these sequences can be integrated into a biosensor technology and used to process and test patient samples.