Modulation of the tRNA Structure and Recognition by Spermine Mimetics

A huge percentage of anticancer therapeutics are small molecules that can dynamically bind and modify proteins and nucleic acids effectively. In this article, we have investigated the interaction of synthetic polyamine analogues 333 (C9H24N4·4HCl; 334 g/mol), compound BE333 (C13H32N4·4HCl; 390 g/mol), compound BE3333 (C16H34N5.5HCl; 478.5 g/mol), and compound BE343 (C14H34N4·4HCl; 404 g/mol) with tRNAPhe. The polyamine analogues have been prepared based on the structure of the natural polyamine spermine. In this investigation, we wanted to see how the structural features of the synthetic polyamine analogues, i.e., length of polyamines, presence of the N-ethyl group, the number of secondary amines, and the methylene spacing, affect the biophysical and thermodynamic binding interaction with tRNAPhe. Methods like differential scanning calorimetry (DSC) revealed strong stabilization of tRNAPhe, where the highest stabilization was shown by the analogue BE3333, followed by BE343, BE333, and 333, along with the enhancement in transition enthalpy. Isothermal titration calorimetry studies revealed that the binding affinity was in the order of BE3333 > BE343 > BE333 > 333. All of them reported substantial enthalpy-entropy compensation behavior encompassing strong entropy-driven interactions. Salt-dependent studies showed the significant importance of both electrostatic and hydrophobic interactions in the binding process, proving that the interaction is more than simply electrostatic. Circular dichroism experiments lead to structural perturbations in the structure of tRNA to some extent with increase in peak maxima without changing the nature of the peak. Molecular docking showed that the synthetic polyamines bound to the D-arm elbow region, which is also the D-arm-T-arm interface of tRNAPhe, and presented a progressive enhancement in both binding affinity and the breadth of interaction for 333, BE333, BE343, and BE3333 across key regions of the tRNAPhe molecule via electrostatic attractions, hydrogen bonds, π-cation interactions, and carbon-hydrogen bonds. Collectively, the data indicate that BE3333 is the most potent candidate, as its extended chain length and increased positive charge density confer a significant advantage over its structural counterparts. Further, the development of synthetic polyamine analogues as promising lead molecules for anticancer therapeutics is potentiated by this type of investigation.