The present work reports the synthesis and optimization of a molecularly imprinted polymer (MIP) for the selective recognition of troponin T. Troponin T is a cardiac protein found to be responsible for contraction and relaxation in the striated muscles; this protein acts as biomarker for the early diagnosis of acute myocardial infarction (AMI). This paper aims to present two aspects of a study conducted on the synthesis and application of MIP for troponin T detection. The first aspect focuses on the theoretical analysis conducted based on the application of Density Functional Theory (DFT) for the prior selection of the reaction solvent and functional monomers capable of interacting effectively with troponin T aiming at enhancing the efficiency of the synthesis. The second aspect of the study deals with the synthesis, optimization and characterization of the MIP for the analyte determination. Molecular dynamics simulations were made in order to have a better understanding of the analytical system. The findings from the computational simulations help elucidate why it is difficult to create biomimetic polymers for bio-macromolecules and point to solutions that can enhance the effectiveness of the proposed MIP. The results obtained from ELISA adsorption tests showed a greater adsorption of troponin T in the MIP than in the non-imprinted polymer (NIP); the proposed MIP presented limits of detection and quantification of 17.18 ng mL−1 and 52.07 ng mL−1, respectively, and a linear response range of 25 ng mL−1 to 100 ng mL−1.