CASSMedChem Lab

The increasing understanding of biological systems is providing a range of new targets, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required in modern drug discovery and Targeted Protein Degradation (TPD) and macrocycles (MC) are two of the most promising. 

At the forefront of the TPD field is the small molecule bifunctional degrader (a general term commonly referred to as PROteolysis Targeting Chimeras [PROTACs]). A PROTAC (Fig. 1A) consists of a ligand (warhead) for a target protein of interest (POI), covalently bound via a linker to an E3 ligase complex ligand. TPD technology functions by initiating the formation of a ternary complex between the POI, the PROTAC (Fig. 1B) and the E3 ligase, resulting in polyubiquitination of the target protein and subsequent degradation by the 26S proteasome machinery. It is essential for the PROTAC to establish a stable ternary complex, whose stability affects the degradation potential. 

In practice, by harnessing the cell’s own disposal system to degrade proteins of choice, PROTACs can eliminate otherwise undruggable disease-causing proteins. PROTACs technology exhibits several advantages in a drug discovery context. For instance, it does not need to have a high affinity with the target to degrade. Moreover, because of the catalytic mechanism, a low dose is required, and thus off-target toxicity is reduced. PROTACs also limit drug resistance since they do not cause overexpression of target proteins and mutations of the target rarely affect the outcome. Overall, the potential of TPD as therapeutics is enormous and the number of heterobifunctional degraders in advanced development is rapidly growing. Although many disease areas stand to benefit from this modality, the greatest impact is for degraders against oncology targets, for instance, two PROTACs targeting the AR and ER are already in Phase 2 clinical trials, whereas other candidates targeting oncoproteins such as IRAK, BTK and BRD9 are in Phase1.

Macrocycles are generally defined as organic molecules which contain a ring of at least 12 heavy atoms. The benefits of macrocycles as drugs originate from the fact that they can provide functional diversity and stereochemical complexity in a semirigid, preorganized structure. As compared to ring-opened analogues, this can allow macrocycles to bind with higher affinity and selectivity to targets that are difficult to drug with more traditional small-molecule drugs.

PROTAC targets are intracellular proteins, and their mode of action requires them to be cell permeable. Moreover, PROTAC and MC oral administration offers convenience for patients and improves compliance. Notably, most PROTACs in clinical trials and some commercial macrocyclic drugs are oral available, supporting that obtaining oral bRo5 drugs is a reachable goal. However, achieving oral bioavailability includes efforts to adjust absorption and thus the optimization of physicochemical properties, such as lipophilicity and polarity and in vitro ADME properties like solubility and permeability.

Literature supports that there is a lack of understanding of the structure–property relationships of bRo5s and a need for structural, physicochemical and in vitro ADME descriptors impacting the bRo5 drug metabolism and pharmacokinetic (DMPK) profiles. The main reason is related to the large and often flexible structure of MCs and PROTACs which place restrictions on default optimization strategies implemented in the actual drug discovery pipelines optimized on small molecules.

The main aim of the CASSMedChem team is therefore to design and produce innovative high quality structural, physicochemical and in vitro ADME data (a detailed overview of the main topics of CASSMedChem interest is in Figure 2) and build guidelines to discover oral bioavailable MCs and PROTACs, i.e. molecules with a future as drugs.

A battery of computational and experimental tech niques (Fig. 2) are used and combined to reach the goal.

The computational part (Fig. 2) first includes the production of conformer ensembles in polar and nonpolar environments, mimicking the molecular behavior in water and membrane core, respectively. Conformational sampling and molecular dynamic techniques are applied in this phase. On the resulting conformer ensembles, we calculate a pool of key molecular descriptors, a few examples are: Polar Surface Area (3D PSA) to quantify polarity, Radius of gyration (Rgyr) to characterize molecular size and shape and Intramolecular Hydrogen Bonds (IMHBs) formation. Finally, the data matrix is analysed with infographic and machine learning tools to obtain computational models that predict physicochemical properties and in vitro ADME properties (solubility in Fig. 2) of MCs and PROTACs. All the models are then combined to obtain a ranking tool for oral bioavailability and identify structural features responsible for it.

The experimental part (Fig. 2) includes the physicochemical and in vitro ADME characterization of MC and PROTAC datasets with a pool of chromatographic descriptors previously reported by the CASSMedChem team and suitable for the bRo5 chemical space. Remarkably, we recently set-up a chameleonicity descriptor (Chamelogk) that quantifies the molecular skills to adapt to the environment. Chamelogk is therefore a unique and specific tool for bRo5 compounds. Experimental data are used to validate models obtained with computational strategies and as an input to generate more models.