Caratteristiche strutturali dei PROTACs: il loro ruolo nella degradazione del recettore degli androgeni e linee guida per la loro sintesi

Proteolysis-targeting chimeras (PROTACs, also known as degraders) are heterobifunctional molecules of huge interest in drug discovery since they induce protein degradation through the hijacking of the ubiquitin-proteasome system (UPS), the physiological mechanism used by cells to degrade proteins. PROTAC chemical structure includes three building blocks: a) the warhead that binds the protein of interest (POI), b) the E3 ligand which recruits the E3 ubiquitin ligase and c) the linker that couples warhead and E3 ligand. Once inside the cell, the degrader binds both the specific E3 ligase and the target protein and forms the ternary complex that allows POI ubiquitination and degradation to occur. The complex PROTAC chemical structure makes the drug discovery process difficult and time-consuming and calls for a rational and efficient drug design strategy. One of the key concepts in medicinal chemistry is the “structure-activity relationship” (SAR) paradigm, which highlights the tight relation that elapses the structure of a molecule and its function. The main aim of this MD thesis project is the implementation of a SAR model to design degraders targeting the androgen receptor (AR) of potential application in the treatment of prostatic cancer. The dataset used in the study was built by retrieving 92 PROTAC structures and degradation data from three recent papers by Wang et al., who assessed AR degradation under the same experimental conditions. The dataset was firstly characterized with the Bemis-Murcko framework (MF) tool and the Similarity Analysis (SA). MF and SA were performed on both the whole degrader structures and the building blocks as well. Classifications provided by the two methods were compared and gave equivalent results. The second step of the study consisted in the application of the Activity Cliffs (ACs) analysis on the clusters obtained from the classification step. This computational strategy consists in finding the molecular features responsible for a significant variation in activity between a couple of similar compounds. The ACs analysis provided fifteen pairs and allowed to identify the structural features of any building block responsible for the increase/decrease degradation activity of the investigated PROTACs. For instance, one of the pairs highlighted that the stereochemistry in the E3 ligand moiety chiral centres needs to be verified in order to design active degraders. Notably, this in silico approach represents the first attempt to apply MF, SA and ACs to large (MW>500) molecules lying in the beyond-Rule-of-5 (bRo5) chemical space. Since these computational techniques have been designed for small molecules, some upgrade was introduced for their application to PROTACs and other bRo5 structures.