Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

The iodination of pyrimidines is usually carried out by using toxic reagents under acidic conditions, such as with sulfuric acid and nitric acid. To avoid toxic reagents, we developed a simple and eco-friendly approach for the iodination of pyrimidine derivatives under solvent-free conditions using solid iodine and AgNO₃ as an electrophilic iodinating reagent. The advantages of this method are the relatively short reaction time (20–30 min), simple set-up procedure, high yields (70–98%), and environmentally friendly reaction conditions. Our novel approach for the iodination of pyrimidines, as well as a variety of their derivatives, will contribute to the development of nucleobase-related drug candidates.

Background: Cyclin-dependent kinase 2 (CDK2) is a key regulator of cell cycle progression and an important therapeutic target in cancer treatment. This study aims to identify novel CDK2 inhibitors using an integrated computational approach combining machine learning and structure-based methods. Methods: A computational pipeline was developed incorporating Lipinski’s Rule of Five filtering, machine learning (ML)-based activity prediction, molecular docking, and molecular dynamics simulations (MDs). A dataset of CDK2 inhibitors with IC50 values was retrieved from ChEMBL, and molecular fingerprints were generated using PaDEL. A 5-fold stratified cross-validation approach was applied to train multiple classifiers, with the random forest model showing the best performance. Predicted active compounds from the InterBioScreen database were subjected to docking against CDK2 (PDB ID: 2FVD) using PyRx, followed by 100 ns MDS for stability analysis. Results: The random forest classifier achieved an AUC-ROC of 0.90 and an accuracy of 0.84. A total of 187 compounds were predicted as active. Among these, two compounds, STOCK4S-00019 and STOCK4S-00025, demonstrated docking scores comparable to the co-crystallized reference ligand. Molecular dynamics simulations confirmed stable binding, consistent interaction patterns, and favorable conformational behavior throughout the simulation period. Conclusions: The identified compounds, STOCK4S-00019 (hit1) and STOCK4S-00025 (hit2), show strong potential as CDK2 inhibitors. These findings support their further investigation through experimental validation and highlight the effectiveness of integrated computational approaches in anticancer drug discovery.

Thanks to the rapid development of advanced analytical methods, researchers can now identify new, so far unknown applications for existing drugs. This expanding knowledge about the mechanisms of drug action, including interactions with various molecules and molecular pathways, not only enables more effective use of available therapies but also reduces both the time and cost of developing new therapeutic options. One of the proteins reported to interact with numerous drugs and chemicals is Translationally Controlled Tumor Protein (TCTP). Numerous studies have demonstrated that TCTP plays a crucial role in diverse biological processes, including cell growth, cell cycle regulation, cellular proliferation, allergic reactions, stress response, inhibition of apoptosis, calcium ion binding, interacting with microtubules and actin microfilaments, the progression of various cancers, and tumor reversion. Therefore, this review article aims to compile a list of drugs and substances shown to interact with TCTP and that, given TCTP’s numerous cellular functions, could be repurposed for other therapies.