Exploring the selective inhibition of post-translational lysine modifier enzymes: toward new therapeutic approaches for rare disorders

In recent years, the realm of lysine post-translational modifications (PTMs) has provided promising avenues for therapeutic interventions, motivating the research community to conceive innovative strategies to counteract the aberrant activity of PTMs modifiers in a wide array of diseases. Much progress has been made in targeting lysine deacetylation, and demethylation, enabling the identification of small molecules endowed with high therapeutic potential against histone deacetylases (HDACs), and lysine specific demethylase 1 (LSD1). During my PhD, I had the opportunity to take part to an ongoing project aimed to develop new selective, and dual-acting small-molecule inhibitors targeting lysine deacetylation, and demethylation. In this context, I focused many efforts on the development of selective HDAC6 inhibitors (HDAC6is) and HDAC1is as potential pharmacological agents for the treatment of diverse pathologies including (i) rare diseases, such as idiopathic pulmonary fibrosis (IPF), and retinitis pigmentosa (RP,) (ii), inflammation-based pathologies and (iii) cancer. To identify new pharmacological tools against IPF, we developed three series of potential HDAC6is. Considering the exceptional antifibrotic properties of the reported inhibitor NF2376, we found tempting to explore the PROTAC technology to attain HDAC6 proteasomal degradation. To this purpose, a series of NF2376 analogues were developed to study the possible functionalisable site for the construction of new HDAC6-PROTAC degraders. Then, I was involved in the development of two class of HDAC6is based on tetrahydroisoquinoline (THIQ), a privileged scaffold in medicinal chemistry. The structure-activity relationship for the first series allowed to identify the best pharmacophoric features which were combined in the second class of HDAC6is, namely the spiro-THIQ-based derivatives. These latter contain different spiro-groups which were easily installed by exploiting the three-component Castagnoli-Cushman reaction. THIQ and spiro-THIQ analogues were revealed effective in attenuating IPF-related fibrosis in in vitro and ex vivo models, respectively, allowing to confirm the pivotal role exerted by HDAC6 in the progression of IPF. As a continuation of our efforts in the field of rare disease, I contributed to the preparation of a new class of selective HDAC6is based on tetrahydro-γ-carboline-based scaffold, which was proven to tackle photoreceptor degeneration in in vitro, and in vivo model of RP. Aiming at simultaneously interfering with more than one aberrant mechanism associated with RP, we pursued a multi-targeting approach to rationally design, and develop new dual-acting compounds targeting HDAC1, and other two enzymes, namely LSD1, and fatty acid amide hydrolase (FAAH). In this frame, I contributed to the development of the new hybrid compounds which are still under biological investigation. Aiming at exploiting new chemical spaces for the cap group, we embarked in the exploration of the indolizine scaffold for the development of new HDAC6is as promising tools for treating inflammatory conditions. Preliminary enzymatic assay disclosed the potentiality of these new chemical entities. Given the ascertained role of HDACs in the onset and progression of different cancer types, I focused my efforts in identifying new aryl piperazine-based HDAC6is which were revealed promising antiproliferative agents against hematological cancer. Furthermore, we explored the selective HDAC1 inhibition to counter colorectal disease by preparing new HDAC1is, which are currently under biological evaluation in both in vitro and in vivo model. Finally, I had the opportunity to work on the development of dual selective HDAC6/8 inhibitors which were rationally designed by merging the structural requirements for the binding to both targets. In vitro studies in leukemia and colorectal cell lines corroborated the potentiality of the new compounds as anticancer agents.