Proteolysis Targeting Chimeric Molecules: Tuning Molecular Strategies for a Clinically Sound Listening

Abstract

From seminal evidence in the early 2000s, the opportunity to drive the specific knockdown of a protein of interest (POI) through pharmacological entities called Proteolysis Targeting Chimeric molecules, or PROTACs, has become a possible therapeutic option with the involvement of these compounds in clinical trials for cancers and autoimmune diseases. The fulcrum of PROTACs pharmacodynamics is to favor the juxtaposition between an E3 ligase activity and the POI, followed by the ubiquitination of the latter and its degradation by the proteasome system. In the face of an apparently modular design of these drugs, being constituted by an E3 ligase binding moiety and a POI-binding moiety connected by a linker, the final structure of an efficient PROTAC degradation enhancer often goes beyond the molecular descriptors known to influence the biological activity, specificity, and pharmacokinetics, requiring a rational improvement through appropriate molecular strategies. Starting from the description of the basic principles underlying the activity of the PROTACs to the evaluation of the strategies for the improvement of pharmacodynamics and pharmacokinetics and rational design, this review examines the molecular elements that have been shown to be effective in allowing the evolution of these compounds from interesting proof of concepts to potential aids of clinical interest.

Keywords: Lipinski rule of five; Von Hippel-Lindau; molecular glue; thalidomide; warhead.

Figure 1

(A) Prototypical structure of a Proteolysis Targeting Chimeric Molecules (PROTAC) based on the example of dBET23 PROTAC (Protein Data Bank number 6BN7). PROTACs favor the formation of a ternary complex involving the PROTAC itself (cyan structure), a protein of interest (POI) in the case of the DNA damage-binding protein 1 (green surface), and a cell E3 ligase in the case of the Protein cereblon (pink surface). This is made available by the coexistence, in the same molecule, of a POI-binding moiety and an E3 ligase-binding moiety (in the case of thalidomide) joined by a linker of suitable length. (B) A list of PROTACS involved in clinical trials. Abbreviations: AR—androgen receptor; ER—oestrogen receptor; BCL-xL—B cell lymphoma- extra-large; BRD9—bromodomain-containing protein 9; BTK—Bruton’s tyrosine kinase; EGFR-L585R—epidermal growth factor receptor harboring the exon point mutation L858R; ER—oestrogen receptor; HS—hidradenitis suppurativa; IND-e—IND- enabling preclinical studies; IRAK4—interleukin-1 receptor-associated kinase 4; STAT3—signal transducer and activator of transcription 3; TRK—tropomyosin receptor kinase. * Ingo Hartung su Twitter: “The plot thickens regarding the structure of IRAK4 PROTAC KT-474 @KymeraTx. 2 patents disclosing deuterated, crystalline & salt forms of a single PROTAC. Comprising a non-conventional CRBN binder the chemists at Kymera seem to like a lot. More common NH-linked IMiD in KT-413? https://t.co/O8JMRLZvpY”/Twitter (accessed on 1 March 2022).

Figure 2

Available chemical structures, identification codes, indication, and route of administration of Proteolysis Targeting Chimeric molecules (PROTACs) involved in clinical trials. The molecular portions underlined in orange, green, and blue represent the E3 ligase-binding moiety, the protein of interest-binding moiety, and the linker, respectively.

Figure 3

Structural characteristics of Proteolysis Targeting Chimeric molecules (PROTACs) currently in a clinical trial, distinguished by structural moiety and route of administration.