Selective targeting of non-centrosomal AURKA functions through use of a targeted protein degradation tool.

Targeted protein degradation tools are becoming a new therapeutic modality, allowing small molecule ligands to be reformulated as heterobifunctional molecules (PROteolysis Targeting Chimeras, PROTACs) that recruit ubiquitin ligases to targets of interest, leading to ubiquitination and destruction of the targets. Several PROTACs against targets of clinical interest have been described, but detailed descriptions of the cell biology modulated by PROTACs are missing from the literature. Here we describe the functional characterization of a PROTAC derived from AURKA inhibitor MLN8237 (alisertib). We demonstrate efficient and specific destruction of both endogenous and overexpressed AURKA by Cereblon-directed PROTACs. At the subcellular level, we find differential targeting of AURKA on the mitotic spindle compared to centrosomes. The phenotypic consequences of PROTAC treatment are therefore distinct from those mediated by alisertib, and in mitotic cells differentially regulate centrosome- and chromatin- based microtubule spindle assembly pathways. In interphase cells PROTAC-mediated clearance of non-centrosomal AURKA modulates the cytoplasmic role played by AURKA in mitochondrial dynamics, whilst the centrosomal pool is refractory to PROTAC-mediated clearance. Our results point to differential sensitivity of subcellular pools of substrate, governed by substrate conformation or localization-dependent accessibility to PROTAC action, a phenomenon not previously described for this new class of degrader compounds

Selective targeting of non-centrosomal AURKA functions through use of a targeted protein degradation tool.

Targeted protein degradation tools are becoming a new therapeutic modality, allowing small molecule ligands to be reformulated as heterobifunctional molecules (PROteolysis Targeting Chimeras, PROTACs) that recruit ubiquitin ligases to targets of interest, leading to ubiquitination and destruction of the targets. Several PROTACs against targets of clinical interest have been described, but detailed descriptions of the cell biology modulated by PROTACs are missing from the literature. Here we describe the functional characterization of a PROTAC derived from AURKA inhibitor MLN8237 (alisertib). We demonstrate efficient and specific destruction of both endogenous and overexpressed AURKA by Cereblon-directed PROTACs. At the subcellular level, we find differential targeting of AURKA on the mitotic spindle compared to centrosomes. The phenotypic consequences of PROTAC treatment are therefore distinct from those mediated by alisertib, and in mitotic cells differentially regulate centrosome- and chromatin- based microtubule spindle assembly pathways. In interphase cells PROTAC-mediated clearance of non-centrosomal AURKA modulates the cytoplasmic role played by AURKA in mitochondrial dynamics, whilst the centrosomal pool is refractory to PROTAC-mediated clearance. Our results point to differential sensitivity of subcellular pools of substrate, governed by substrate conformation or localization-dependent accessibility to PROTAC action, a phenomenon not previously described for this new class of degrader compounds

Selective targeting of non-centrosomal AURKA functions through use of a targeted protein degradation tool

Funder: AstraZeneca; doi: https://doi.org/10.13039/100004325Abstract: Targeted protein degradation tools are becoming a new therapeutic modality, allowing small molecule ligands to be reformulated as heterobifunctional molecules (PROteolysis Targeting Chimeras, PROTACs) that recruit ubiquitin ligases to targets of interest, leading to ubiquitination and destruction of the targets. Several PROTACs against targets of clinical interest have been described, but detailed descriptions of the cell biology modulated by PROTACs are missing from the literature. Here we describe the functional characterization of a PROTAC derived from AURKA inhibitor MLN8237 (alisertib). We demonstrate efficient and specific destruction of both endogenous and overexpressed AURKA by Cereblon-directed PROTACs. At the subcellular level, we find differential targeting of AURKA on the mitotic spindle compared to centrosomes. The phenotypic consequences of PROTAC treatment are therefore distinct from those mediated by alisertib, and in mitotic cells differentially regulate centrosome- and chromatin- based microtubule spindle assembly pathways. In interphase cells PROTAC-mediated clearance of non-centrosomal AURKA modulates the cytoplasmic role played by AURKA in mitochondrial dynamics, whilst the centrosomal pool is refractory to PROTAC-mediated clearance. Our results point to differential sensitivity of subcellular pools of substrate, governed by substrate conformation or localization-dependent accessibility to PROTAC action, a phenomenon not previously described for this new class of degrader compounds

Synthesis of RNA containing 5-hydroxymethyl-, 5-formyl-, and 5-carboxycytidine

5-Hydroxymethyl-, 5-formyl-, and 5-carboxycytidine are new epigenetic bases (hmdC, fdC, cadC) that were recently discovered in the DNA of higher eukaryotes. The same bases (hmC, fC and caC) have now also been detected in mammalian RNA with a high abundance in mRNA. While for the DNA bases phosphoramidites (PAs) are available that allow the synthesis of xdC-containing oligonucleotides for deeper biological studies, the corresponding silyl protected RNA PAs for fC and caC have not yet been disclosed. Here we report novel RNA PAs for hmC, fC and caC that can be used in routine RNA synthesis. The new building blocks are compatible with the canonical PAs and also with themselves, which enables even the synthesis of RNA strands containing all three of these bases. The study will pave the way for detailed physical, biochemical and biological studies to unravel the function of these non-canonical modifications in RNA

Towards the total synthesis of calyciphylline A-type Daphniphyllum alkaloids

This thesis details the studies towards the total synthesis of the calyciphylline A-type Daphniphyllum alkaloids, with a particular focus on daphniyunnine D (23). Chapter 1 introduces these biologically and synthetically interesting polycyclic natural products and describes our designed approach towards their synthesis. Separate studies targeting the construction of two tricyclic ring systems have been developed. These provide rapid entry to synthetically versatile intermediates, allowing for the potential synthesis of numerous members of the alkaloid family. Chapter 2 describes the first study which focuses on the construction of the main tricyclic [6‒5‒7] ACD core 172 via a proton transfer/IMDAF reaction cascade as the main step. Large scale synthesis of the precursor to this cascade 164 has allowed for the successful investigation of an asymmetric variant giving rise to an enantioenriched adduct 104. Chapter 3 describes a novel design for the construction of the [7‒5‒5] DEF tricycle common to 100+ Daphniphyllum alkaloids. An IMPKR, double-bond migration, allylic oxygenation protocol was first validated on a model system and later applied in combination with the synthetic route developed in chapter 2 to achieve the construction of the [6‒5‒7‒5‒5] ACDEF pentacycle 249. Chapter 4 focuses on the construction of the piperidine ring B via an intramolecular gold-catalysed 6-exo-trig hydroalkylation. During the development of the route to daphniyunnine D, various intermediates were afforded which were further elaborated to provide appropriate cyclisation substrates for this study. Their synthesis combined with proof of principle experiments for the desired cyclisation conclude this dissertation work.</p

Towards the total synthesis of calyciphylline A-type Daphniphyllum alkaloids

This thesis details the studies towards the total synthesis of the calyciphylline A-type Daphniphyllum alkaloids, with a particular focus on daphniyunnine D (23). Chapter 1 introduces these biologically and synthetically interesting polycyclic natural products and describes our designed approach towards their synthesis. Separate studies targeting the construction of two tricyclic ring systems have been developed. These provide rapid entry to synthetically versatile intermediates, allowing for the potential synthesis of numerous members of the alkaloid family. Chapter 2 describes the first study which focuses on the construction of the main tricyclic [6‒5‒7] ACD core 172 via a proton transfer/IMDAF reaction cascade as the main step. Large scale synthesis of the precursor to this cascade 164 has allowed for the successful investigation of an asymmetric variant giving rise to an enantioenriched adduct 104. Chapter 3 describes a novel design for the construction of the [7‒5‒5] DEF tricycle common to 100+ Daphniphyllum alkaloids. An IMPKR, double-bond migration, allylic oxygenation protocol was first validated on a model system and later applied in combination with the synthetic route developed in chapter 2 to achieve the construction of the [6‒5‒7‒5‒5] ACDEF pentacycle 249. Chapter 4 focuses on the construction of the piperidine ring B via an intramolecular gold-catalysed 6-exo-trig hydroalkylation. During the development of the route to daphniyunnine D, various intermediates were afforded which were further elaborated to provide appropriate cyclisation substrates for this study. Their synthesis combined with proof of principle experiments for the desired cyclisation conclude this dissertation work.This thesis is not currently available in ORA

Total Synthesis of (−)-Himalensine A

The first enantioselective synthesis of (−)-himalensine A has been achieved in 22 steps. The synthesis was enabled by a novel catalytic, enantioselective prototropic shift/furan Diels–Alder (IMDAF) cascade to construct the ACD tricyclic core. A reductive radical cyclization cascade was utilized to build the B ring, and end-game manipulations featuring a molecular oxygen mediated γ-CH oxidation, a Stetter cyclization to access the pendant cyclopentenone, and a highly chemoselective lactam reduction delivered the natural product target

Total Synthesis of (−)-Himalensine A

The first enantioselective synthesis of (−)-himalensine A has been achieved in 22 steps. The synthesis was enabled by a novel catalytic, enantioselective prototropic shift/furan Diels–Alder (IMDAF) cascade to construct the ACD tricyclic core. A reductive radical cyclization cascade was utilized to build the B ring, and end-game manipulations featuring a molecular oxygen mediated γ-CH oxidation, a Stetter cyclization to access the pendant cyclopentenone, and a highly chemoselective lactam reduction delivered the natural product target

Total Synthesis of (−)-Himalensine A

The first enantioselective synthesis of (−)-himalensine A has been achieved in 22 steps. The synthesis was enabled by a novel catalytic, enantioselective prototropic shift/furan Diels–Alder (IMDAF) cascade to construct the ACD tricyclic core. A reductive radical cyclization cascade was utilized to build the B ring, and end-game manipulations featuring a molecular oxygen mediated γ-CH oxidation, a Stetter cyclization to access the pendant cyclopentenone, and a highly chemoselective lactam reduction delivered the natural product target

Rapid PROTAC discovery platform: nanomole scale array synthesis and direct screening of reaction mixtures to facilitate the expedited discovery and follow-up of PROTAC hits.

Precise linker length, shape and linker attachment point are all integral components to designing efficacious PROTACs. Due to the increased synthetic complexity of these heterobifunctional degraders and the difficulty of computational modelling to aid PROTAC design, the exploration of structure-activity-relationship (SAR) remains mostly empirical, which requires a significant time and resource investment. To facilitate rapid hit finding we developed capabilities for PROTAC parallel synthesis and purification by harnessing an array of pre-formed E3-ligand linker intermediates. In the next iteration of this approach, we developed a rapid, nanomole-scale PROTAC synthesis methodology using amide coupling that enables direct screening of non-purified reaction mixtures in cell-based degradation assays, as well as logD and EPSA measurements. This approach greatly expands and accelerates PROTAC SAR exploration (5 days instead of several weeks) while using nanomole amounts of reagents. Lastly, it avoids laborious and solvent-demanding purification of the reaction mixtures, thus making it an economical and more sustainable methodology for PROTAC hit finding