Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs.

Autor:	Bai N; Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA. Electronic address: nbai@amgen.com., Riching KM; Research and Development Department, Promega Corporation, Madison, Wisconsin, USA. Electronic address: Kristin.Riching@promega.com., Makaju A; Discovery Attribute Science, Amgen Research, South San Francisco, California, USA., Wu H; Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA., Acker TM; Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA., Ou SC; Discovery Attribute Science, Amgen Research, Thousand Oaks, California, USA., Zhang Y; Oncology, Amgen Research, Thousand Oaks, California, USA., Shen X; Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA., Bulloch DN; Discovery Attribute Science, Amgen Research, South San Francisco, California, USA., Rui H; Discovery Attribute Science, Amgen Research, Thousand Oaks, California, USA., Gibson BW; Discovery Attribute Science, Amgen Research, South San Francisco, California, USA., Daniels DL; Research and Development Department, Promega Corporation, Madison, Wisconsin, USA., Urh M; Research and Development Department, Promega Corporation, Madison, Wisconsin, USA., Rock BM; Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA., Humphreys SC; Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA. Electronic address: shumph01@amgen.com.
Jazyk:	angličtina
Zdroj:	The Journal of biological chemistry [J Biol Chem] 2022 Apr; Vol. 298 (4), pp. 101653. Date of Electronic Publication: 2022 Jan 29.
DOI:	10.1016/j.jbc.2022.101653
Abstrakt:	PROteolysis TArgeting Chimeras (PROTACs) are hetero-bifunctional small molecules that can simultaneously recruit target proteins and E3 ligases to form a ternary complex, promoting target protein ubiquitination and degradation via the Ubiquitin-Proteasome System (UPS). PROTACs have gained increasing attention in recent years due to certain advantages over traditional therapeutic modalities and enabling targeting of previously "undruggable" proteins. To better understand the mechanism of PROTAC-induced Target Protein Degradation (TPD), several computational approaches have recently been developed to study and predict ternary complex formation. However, mounting evidence suggests that ubiquitination can also be a rate-limiting step in PROTAC-induced TPD. Here, we propose a structure-based computational approach to predict target protein ubiquitination induced by cereblon (CRBN)-based PROTACs by leveraging available structural information of the CRL4A ligase complex (CRBN/DDB1/CUL4A/Rbx1/NEDD8/E2/Ub). We generated ternary complex ensembles with Rosetta, modeled multiple CRL4A ligase complex conformations, and predicted ubiquitination efficiency by separating the ternary ensemble into productive and unproductive complexes based on the proximity of the ubiquitin to accessible lysines on the target protein. We validated our CRL4A ligase complex models with published ternary complex structures and additionally employed our modeling workflow to predict ubiquitination efficiencies and sites of a series of cyclin-dependent kinases (CDKs) after treatment with TL12-186, a pan-kinase PROTAC. Our predictions are consistent with CDK ubiquitination and site-directed mutagenesis of specific CDK lysine residues as measured using a NanoBRET ubiquitination assay in HEK293 cells. This work structurally links PROTAC-induced ternary formation and ubiquitination, representing an important step toward prediction of target "degradability." Competing Interests: Conflict of interest The authors declare the following competing financial interest(s): N. B., A. M., H. W., T. M. A., S.-C. O., Y. Z., X. S., D. N. B., H. R., B. W. G., B. M. R., and S. C. H. are employees and stockholders of Amgen. K. M. R., D. L. D., and M. U. are employees and stockholders of Promega Corporation. (Published by Elsevier Inc.)
Databáze:	MEDLINE
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