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Impact of Linker Composition on VHL PROTAC Cell Permeability
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.ORCID iD: 0000-0003-4617-7605
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.ORCID iD: 0000-0002-8880-9247
Bayer AG, Drug Discovery Sci, D-42113 Wuppertal, Germany..
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2024 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 68, no 1, p. 638-657Article in journal (Refereed) Published
Abstract [en]

The discovery of cell permeable and orally bioavailable von Hippel-Lindau (VHL) proteolysis targeting chimeras (PROTACs) is challenging as their structures locates them at, or beyond, the outer limits of oral druggable space. We have designed a set of nine VHL PROTACs and found that the linker had a profound impact on passive cell permeability. Determination of the solution ensembles in a nonpolar solvent revealed that high permeability was correlated to the ability of the PROTACs to adopt folded conformations that have a low solvent accessible 3D polar surface area. Our results suggest that the design of cell permeable VHL PROTACs could focus on linkers that facilitate shielding of polar surface area in the VHL ligand in a nonpolar but not in a polar environment. In addition, we found that not only intramolecular hydrogen bonds, but also NH-pi and pi-pi interactions contribute to the stabilization of low-polarity conformations, and thereby to high cell permeability.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024. Vol. 68, no 1, p. 638-657
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Chemical Sciences
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URN: urn:nbn:se:uu:diva-554786DOI: 10.1021/acs.jmedchem.4c02492ISI: 001379956800001PubMedID: 39693386Scopus ID: 2-s2.0-85212537783OAI: oai:DiVA.org:uu-554786DiVA, id: diva2:1952759
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Swedish Research CouncilVinnovaAvailable from: 2025-04-16 Created: 2025-04-16 Last updated: 2025-04-16Bibliographically approved

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Wieske, Hermina H. E.Poongavanam, VasanthanathanAtilaw, YosephErdélyi, MátéMeibom, DanielKihlberg, Jan
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