Cardiovascular diseases (CVD), particularly stroke and ischemic heart disease, are the leading causes of death in Indonesia and globally. Cardiac troponin (cTn) has been established as a crucial biomarker for diagnosing CVD, particularly in suspected acute coronary syndrome (ACS). Prolonged ACS can result in myocardial ischemia, where insufficient blood supply due to partial or complete coronary artery occlusion from plaque rupture occurs. Extended ischemic episodes lead to permanent myocardial damage, culminating in acute myocardial infarction (AMI).
The Role of Cardiac Troponins
Cardiac troponin proteins regulate calcium-mediated interactions between thin filaments and cardiac muscle actin. Cardiac troponin T (cTnT) and troponin I (cTnI) are highly sensitive and specific indicators of myocardial injury. Clinical assessments for acute and chronic CVD patients now routinely use cTnT and cTnI tests as the gold standard biomarkers. These tests rely on monoclonal antibodies (MAbs) to detect the proteins, providing high specificity and sensitivity. However, MAbs present several limitations, including high production costs due to complex instruments, reagents, and processes; batch-to-batch quality variability; low stability at high temperatures; and challenges in chemical modification.
Molecular Dynamics Simulations
Figure 1 shows the structural comparison of aptamers and cTnI before and after structural relaxation through Molecular Dynamics (MD) simulations. Significant structural changes were observed in aptamers Tro1 and Tro5, while Tro2, Tro3, Tro4, and Tro6 exhibited minor compactness loss. The lowest-scoring aptamer-cTnI complexes from docking simulations underwent 100 ns MD simulations to analyze the stability and structural dynamics. Root Mean Square Deviation (RMSD) and hydrogen bond counts between the aptamer and cTnI were calculated to evaluate complex stability.
To understand the aptamer binding effects on cTnI, an additional 100 ns MD simulation was conducted on the relaxed cTnI structure. The Root Mean Square Fluctuation (RMSF) of individual cTnI was compared with the RMSF of cTnI within the aptamer-cTnI complex, as illustrated in Figure 2.
Conclusion
We performed molecular docking and dynamics simulations for six DNA aptamers binding to cTnI protein to elucidate their molecular interactions. The RMSD values indicated that Tro4 exhibited the highest stability, evidenced by the lowest RMSD values throughout the simulation. Hydrogen bonding significantly contributed to the stability of the aptamers. The sustained binding during the 100 ns MD simulation confirmed the aptamer-cTnI interaction stability, as shown by consistent RMSD values. All aptamers bound to similar regions of cTnI, including specific residues unique to this protein. Observations suggest that Tro1 and Tro4 may possess higher selectivity due to their binding to specific cTnI regions (residues 1–33). Molecular interactions involved hydrophobic interactions, hydrogen bonds, π-stacking, cation-π interactions, and salt bridge formation. The MMPB(GB)SA calculations yielded negative values, indicating favorable interactions, with electrostatic energy identified as the primary driving force. Notably, our study revealed that aptamers exhibit molecular interactions similar to antibodies but with stronger binding affinity, as indicated in previous studies. Consequently, these developed aptamers present a potential replacement for anti-cTnI antibodies, offering enhanced sensitivity for diagnosing AMI. This in-silico analysis can further explain in-vitro results from initial experiments. Future development of this in-silico analysis can enhance aptamer stability, one method being the modification of nucleic acid structures.
Source Article : https://unair.ac.id/interaksi-molekuler-dari-enam-aptamers-dna-untai-tunggal-pada-troponin-jantung-i/
Link Journal : https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0302475