Investigations of the synthesis and properties of romodomain and extra-terminal domain proteolysis targeting chimeras

  • John Priestner

Student thesis: Doctoral Thesis


Hijacking a cell’s ubiquitin proteasome system using PROTAC technology has the potential to be a powerful new therapeutic strategy. Some of the main advantages of this technology include the potential for PROTACs to be catalytic in activity and elicit long-lasting therapeutic effects, offering the possibility of low clinical doses and infrequent dosing regimens. However, PROTACs are large molecules and generally exhibit low cell permeability, low aqueous solubility and ultimately low bioavailability. Due to the specific defined structures of the target protein and E3 ligase binding moieties, the linker provides a facile handle to modulate physicochemical properties. A linker library containing 66 diverse linkers that provide broad coverage of desirable physicochemical space was developed. From this library, a series of 63 BET PROTACs was rapidly synthesised in a plate-based format using the high-throughput, one-pot protocols developed for acid-ester and diacid linkers. The linker functionality had a profound effect on the degradation profile of the PROTACs, furnishing a 4 log unit range of pDC50 values, with a maximum of 8.99 achieved by the PROTAC containing the 2,6-disubstituted pyridyl linker. Changes in the linker functionality of the PROTAC series furnished an approximate 3 log unit range of ChromlogD (2.95-5.55) and PΔC (-0.66-2.08) values, as well as a range of CAD (1-516 μg/mL) and FaSSIF (2-1000 μg/mL) solubilities, that cover the spectrum from limited to high permeability, and negligible to high solubility. PCA/PLS analysis of the series identified effective lipophilicity as the key property driving the cell permeability and Brd4 degradation potency of the PROTACs, with CAD solubility exhibiting a negative correlation. The three-dimensional molecular shape of the PROTACs that manifest from the linker was found to be pertinent in determining the physicochemical properties and degradation profile of the PROTACs. The most potent PROTACs occupy elongated discoid shapes, common to the 1,3-disubstituted 5- and 6-membered aromatic linkers that exhibit the optimum linker length of four bonds. These shapes are also common to PROTACs exhibiting high permeability and low CAD solubility. Additionally, the position of functional groups in the linker was found to have a significant effect on these properties. This work highlights that the guidelines of generic descriptors (TPSA, RBc, Fsp3, ARc, HBA and HBD count) need to be used with caution when analysing the physicochemical properties of PROTACs, due to the increased complexity of the relationships between them as a result of the effects of molecular shape and conformational folding of these large molecules. It also emphasises the need to screen linkers with a range of geometric properties, and not to discount linkers that will furnish PROTACs with higher ChromlogD values than would be desirable for a classical small molecule drug.
Date of Award26 May 2020
Original languageEnglish
Awarding Institution
  • University Of Strathclyde
SponsorsUniversity of Strathclyde
SupervisorJohn Murphy (Supervisor) & William Kerr (Supervisor)

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