RNA plays a myriad of roles in the body including the coding, decoding, regulation, and expression of genes. RNA oligonucleotides have garnered significant interest as therapeutics via antisense oligonucleotides or small interfering RNA strategies for the treatment of diseases ranging from hyperlipidemia, HCV, and others. Additionally, the recently developed CRISPR-Cas9 mediated gene editing strategy also relies on Cas9-associated RNA strands. However, RNA presents numerous challenges as both a synthetic target and a potential therapeutic. RNA is inherently unstable, difficult to deliver into cells, and potentially immunogenic by itself or upon modification. Despite these challenges, with the help of chemically modified oligonucleotides, multiple RNA-based drugs have been approved by the FDA. The progress is made possible due to the nature of chemically modified oligonucleotides bearing advantages of nuclease stability, stronger binding affinity, and some other unique properties. This review will focus on the chemical synthesis of RNA and its modified versions. How chemical modifications of the ribose units and of the phosphatediester backbone address the inherent issues with using native RNA for biological applications will be discussed along the way.

Proteolysis targeting chimeras (PROTACs) are molecules that induce protein degradation via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The rational design of PROTACs requires accurate knowledge of the native configuration of the PROTAC-induced ternary complex. This study demonstrates that native and non-native ternary complex poses can be distinguished based on the pose occupancy time in MD, where native poses exhibit longer occupancy times at both room and higher temperatures. Candidate poses are generated by MD sampling and pre-ranked by classic MM/GBSA. A specific heating scheme is then applied to accelerate ternary pose departure, with the pose occupancy time and fraction being measured. This scoring identifies the native pose in all systems tested. Its success is partially attributed to the dynamic nature of pose departure analyses, which accounts for entropic effects typically neglected in the faster static scoring methods, while entropy plays a greater role in protein–protein than in protein–ligand systems.

Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that can induce the ubiquitination of targeted proteins via the formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The poly-ubiquitinated target protein will be escorted to the proteasome for degradation. Rational design of PROTACs require knowledge of an accurate configuration of the PROTAC induced ternary complex. This study demonstrates that native ternary poses can be distinguished by scoring candidate poses based on the pose residence time. The scoring is essentially heat-and-dissociate trials of candidate poses sampled by MD and pre-ranked by the classic MM/GBSA method. It is practical, simple to use and self-intuitive, relying on the observation that the assumed more stable native crystal ternary poses maintained a longer residence time than non-native ones at both room and higher temperatures. A time score and temperature score were generated from multiple replicate trajectories. These scores were able to correctly identify the native pose from non-native ones in all the systems examined. The absolute numbers were comparable across different systems in all currently available VHL and CRBN-containing ternary crystal structures. Therefore, it is also possible to provide an empirical criteria for unresolved ternary structures that under the conditions of this study. If a ternary pose is stable up to over a certain threshold score, it is likely a native pose. The success of the method is in part attributed to the dynamic nature of the pose change analysis which naturally involves entropic effects, one that is intrinsically unavailable with faster static scoring methods that consider molecular mechanical energy only. Protein-protein binding entropy is much more significant than in protein-ligands binding. The success is also attributed to the fact that the protein structures themselves were all stable in the short heating trials.

No abstract

Glutarimides such as thalidomide, pomalidomide, and lenalidomide are the most frequently used ligands to recruit E3 ubiquitin ligase cereblon (CRBN) for the development of proteolysistargeting chimeras (PROTACs). Due to the rapid and spontaneous racemization of glutarimides, most CRBN-recruiting PROTACs are synthesized as a mixture of racemates or diastereomers. Since the (S)enantiomer is primarily responsible for binding to CRBN, the existence of the largely inactive (R)-enantiomer complicates the drug development process. Herein, we report that substituted achiral phenyl dihydrouracil (PDHU) can be used as a novel class of CRBN ligands for the development of PROTACs. Although the parent PDHU has a minimal binding affinity to CRBN, we found that some substituted PDHUs had a comparable binding affinity to lenalidomide. Structural modeling provided a further understanding of the molecular interactions between PDHU ligands and CRBN. PDHUs also have greater stability than lenalidomide. Finally, potent BRD4 degraders were developed by employing trisubstituted PDHUs.