Systematic investigations into the mechanisms by which anticancer drugs interact with their targets have long intrigued researchers. These studies aim to elucidate how these drugs exert their cytotoxic effects, which is crucial for the rational design of new pharmaceuticals. Historically, significant research has focused on the interactions between anticancer agents and DNA [[1], [2], [3], [4], [5]]. Various mechanisms, such as groove binding, intercalation, and the formation of crosslinks between DNA strands, have been identified [[6], [7], [8], [9], [10], [11]].

The interaction between therapeutic molecules and nucleic acids, particularly RNA, has become a significant focus in drug development, especially in the context of cancer therapeutics. RNA-targeted therapeutics present several advantages over traditional DNA-binding agents. Unlike the predominantly helical double-stranded structure of DNA, RNA is typically single-stranded, allowing it to fold into various complex structures akin to proteins. This folding is influenced by the presence of unique 2′-hydroxyl group, which stabilizes a C3’-endo sugar conformation, resulting in an A-form structure in regions where RNA exhibits double helical characteristics [[12], [13], [14], [15]]. The structural differences between RNA and DNA lead to unique binding properties. The major groove of RNA is deep and narrow, in contrast to its minor groove, which is wide and shallow. These features facilitate distinct ligand accessibility, allowing small molecules to interact with specific pockets formed by secondary structures such as stem-loops, hairpin loops, and three-stem junctions [16,17]. The binding of these ligands is mediated by non-covalent interactions, such as electrostatic forces, van der Waals interactions, hydrogen bonds, and surface groove binding. [[18], [19], [20], [21]].

Idarubicin, an anthracycline antitumor antibiotic marketed as Zavedos and Idamycin. It is a 4-demethoxy analogue of daunorubicin [[22], [23], [24]]. This modification enhances its lipophilicity, facilitating increased cellular uptake and membrane penetration [[25], [26], [27]]. Idarubicin is often utilized in treating a range of cancers, including non-Hodgkin's lymphoma [28,29], multiple myeloma [30,31], and breast cancer [32,33]. It is often used in combination with cytosine arabinoside for acute myeloid leukemia [34,35]. While anthracyclines primarily target nuclear DNA [[36], [37], [38]] and DNA topoisomerase II [38,39], their cytotoxic mechanisms also involve free radical generation, apoptosis induction, and inhibition of DNA helicase [[40], [41], [42], [43]]. Willmore et al. demonstrated that idarubicin leads to the formation of DNA topoisomerase II cleavable complexes in human leukemia cell lines [44].

However, the interaction between idarubicin and RNA, particularly transfer RNA (tRNA), remains largely unexplored. This study investigates the binding mechanism of idarubicin to tRNA, aiming to enhance our understanding of structure-based RNA-targeting therapeutics. tRNA is recognized as a promising therapeutic target due to its unique structure and critical role in protein synthesis. Unlike ribosomal RNA (rRNA) and messenger RNA (mRNA), tRNA directly interacts with mRNA and amino acids, ensuring the accurate translation of the genetic code. The conservation of RNA across species and the distinct structural features makes certain tRNAs attractive for pharmaceutical targeting [[45], [46], [47]]. Additionally, tRNA is involved in various cellular processes beyond protein synthesis, including RNA editing and gene expression regulation [[48], [49], [50], [51]]. With its multifaceted role, tRNA demonstrates significant potential as a therapeutic target, aiding the development of compounds designed to modulate its functions.

Studying the complexes of idarubicin with DNA and RNA is crucial for several reasons. It helps elucidate the mechanisms through which idarubicin exerts its therapeutic effects, which is essential for optimizing cancer treatment. Understanding its selective interactions with nucleic acids can lead to the development of targeted therapies that minimize off-target effects and enhance efficacy against specific cancers. Additionally, insights from these studies can inform the design of improved anticancer strategies, potentially leading to more effective drug combinations or modifications of idarubicin, especially for cancers dependent on RNA. This research also lays the groundwork for exploring other nucleic acid-targeting drugs, paving the way for novel treatments. Furthermore, understanding the binding dynamics and mechanisms of resistance associated with idarubicin could provide pathways to overcome drug resistance, a major challenge in cancer therapy. Overall, these findings highlight the importance of investigating idarubicin-DNA and idarubicin-RNA complexes in advancing cancer therapies and improving the effectiveness of existing treatments.

Based on our previous research on idarubicin-DNA complexes [52], which provided valuable insights into its interactions with DNA duplexes, we aimed to investigate whether idarubicin also binds to tRNA and contributes to its cytotoxic effects. We performed a comprehensive spectroscopic and computational analysis of tRNA-idarubicin complexes, followed by a comparative study of idarubicin's interactions with both DNA and tRNA.