Introduction: Histone deacetylases (HDACs) are a key group of enzymes that regulate chromatin compaction and gene expression by removing acetyl groups from histone and non-histone proteins. These enzymes are classified into four main classes: Class I, including HDAC1, HDAC2, HDAC3, and HDAC8, which are primarily nuclear and play roles in the cell cycle and proliferation; Class II, comprising HDAC4, HDAC5, HDAC6, and HDAC7, which shuttle between the cytoplasm and nucleus and are involved in signaling and differentiation; Class III, or sirtuins, which are NAD⁺-dependent and participate in metabolism and cellular aging; and Class IV, represented solely by HDAC11, which exhibits combined functional properties. The critical role of these enzymes in epigenetic dynamics has established them as important drug targets in cancer, neurological disorders, and cellular reprogramming.
HDAC inhibitors (HDACi) prevent the activity of these enzymes, increasing histone acetylation levels and activating previously silenced genes. This property underlies their application in treating cancer, inflammatory conditions, and neurological disorders. Class I HDAC inhibitors are particularly significant, as they directly influence the cell cycle and the maintenance of differentiated states and are also employed in cellular reprogramming and pluripotency induction. Class I HDACi include hydroxamic acid derivatives (e.g., Vorinostat and Panobinostat), benzamides (e.g., Entinostat), cyclic peptides, and simple fatty acids such as Valproic acid. Each compound exhibits distinct pharmacological properties and isoform selectivity; for example, Valproic acid is a weak inhibitor with low toxicity and a favorable safety profile, making it suitable for cellular reprogramming.
Recent studies indicate that HDACi can enhance the efficiency of pluripotency induction; for instance, combining Valproic acid with Yamanaka factors has significantly improved the conversion of fibroblasts into iPSCs. Nevertheless, the use of HDACi presents limitations, including off-target effects, potential toxicity, and suboptimal pharmacological characteristics such as nuclear penetration and isoform selectivity. In this study, we focused on comparing pharmacological profiles, ADME properties, and predicted protein targets to identify HDAC inhibitors that are more suitable for pluripotency induction while minimizing potential side effects.
Methods: In this study, all HDAC inhibitors listed in the DrugBank database were screened, and only FDA-approved compounds were selected for further analyses. The chemical structures of the selected drugs were obtained in SMILES format and used for subsequent protein target prediction and evaluation of drug-likeness properties. Potential molecular targets for each inhibitor were predicted using the SwissTargetPrediction platform (http://www.swisstargetprediction.ch/), which enabled identification of probable protein interactions and evaluation of selectivity toward HDAC enzymes. In addition, pharmacokinetic properties, including ADME parameters and drug-likeness criteria, were assessed using SwissADME (http://www.swissadme.ch/). The resulting data were compiled into comparative tables to facilitate cross-evaluation of HDAC inhibitors and to i dentify critical factors influencing their suitability for enhancing pluripotency induction.
Results: Evaluation of FDA-approved HDAC inhibitors based on ADME/Tox analyses, revealed that each compound possesses distinct advantages and limitations. Vorinostat complied with Lipinski’s and Veber’s rules, indicating favorable bioavailability and nuclear penetration. Its moderate Log Po/w and Log S values suggested a balanced profile between lipophilicity and aqueous solubility; however, prediction as a P-gp substrate may limit intracellular accumulation. Brenk alerts indicated potential structural risks, although no PAINS were detected. Belinostat also met Lipinski’s and Veber’s criteria but exhibited lower Log Po/w, restricted nuclear entry, and a Brenk alert suggesting possible metabolic instability. Romidepsin failed to comply with these rules due to high molecular weight and limited flexibility, and its high TPSA along with predicted P-gp substrate status constrained nuclear penetration; multiple Brenk alerts indicated structural complexity and potential toxicity. Panobinostat showed strong nuclear penetration and high Log Po/w, but poor solubility and P-gp substrate prediction limited intracellular retention, with Brenk alerts suggesting toxicity risks. In contrast, Valproic acid, despite weaker HDAC binding, demonstrated the most favorable pharmacokinetic profile, with rapid nuclear entry, high solubility, stable intracellular retention, and minimal toxicity concerns.
Conclusion: In conclusion, these findings indicate that Vorinostat and Panobinostat are potent candidates for enhancing pluripotency induction, although their toxicity risks and potential intracellular retention issues warrant careful experimental evaluation. Valproic acid, while less potent, represents a safer and more practical option, with optimal pharmacokinetic properties supporting its potential utility in combinatorial strategies to enhance pluripotency.
Keywords: HDAC inhibitors, Epigenetic modulation, Pluripotency induction, Drug repurposing, iPSCs