Determination of key functional structures of an amorphous VHL-based SMARCA2 PROTAC

DOI

<div> <p><span><span lang="EN-US">PROTACs are of high interest because of their ability to target previously challenging disease-related proteins. PROTACs promote the degradation of targets by ensuring the proximity of the E3-ligase and the target. The relation between structure and function of the ternary complex is of great interest. Of equal importance is the delivery of these drugs and determining the key interactions that stabilize the solid drug forms. Here, we determine the complete atomic-level structure of an amorphous VHL-based SMARCA2 PROTAC (PROTAC 2). The structure is solved using ultra-fast MAS, and DNP enhanced, NMR crystallography. We found that PROTAC 2 is more disordered as compared to previously studied amorphous formulations, and that the three functional units of the molecule have three distinct structural types. Overall, </span></span><span lang="EN-US">in contrast to structures of smaller drug molecules, where intermolecular H-bonding interactions were found to be the main stabilization mechanism for the amorphous solid form, for PROTAC 2 we postulate that, in analogy to glassy polymers, the main stabilization mechanism of the amorphous form is the entropic contribution introduced by the overall flexibility, especially in the linker region of the molecule.</span><span><span lang="EN-US"> We also note that the most populated conformations found in the amorphous form differ from those of bound PROTAC 2 found in the ternary protein complex as determined via X-ray crystallography. Our results provide insight into key structural features that stabilize amorphous formulations, specifically for molecules that can </span></span><span lang="EN-US">target proteins previously considered undruggable.</span></p> </div>

Identifier
DOI https://doi.org/10.24435/materialscloud:d0-ck
Related Identifier https://doi.org/10.1038/s41467-025-65478-5
Related Identifier https://archive.materialscloud.org/communities/mcarchive
Related Identifier https://doi.org/10.24435/materialscloud:x1-v1
Metadata Access https://archive.materialscloud.org/oai2d?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:materialscloud.org:m17qc-y7350
Provenance
Creator Torodii, Daria; Holmes, Jacob; Cordova, Manuel; Moutzouri, Pinelopi; van Beek, Lotte; Edfeldt, Fredrik; Malmerberg, Erik; Johansson, Johan; Milbradt, Alexander; Nilsson Lil, Sten; Malfait, Benjamin; Schantz, Staffan; Emsley, Lyndon
Publisher Materials Cloud
Contributor Emsley, Lyndon
Publication Year 2025
Rights info:eu-repo/semantics/openAccess; Creative Commons Attribution 4.0 International; https://creativecommons.org/licenses/by/4.0/legalcode
OpenAccess true
Contact archive(at)materialscloud.org
Representation
Language English
Resource Type info:eu-repo/semantics/other
Format application/zip; text/plain
Discipline Materials Science and Engineering