Structural basis of peptidomimetic agonism revealed by small molecule GLP-1R agonists Boc5 and WB4-24

Cong, Z.; Zhou, Q.; Li, Y.; Chen, L.-N.; Zhang, Z.-C.; Liang, A.; Liu, Q.; Wu, X.; Dai, A.; Xia, T.; Wu, W.; Zhang, Y.; Yang, D.; Wang, M.-W.

doi:10.1101/2022.01.05.475023

bioRxiv · 10.1101/2022.01.05.475023

Structural basis of peptidomimetic agonism revealed by small molecule GLP-1R agonists Boc5 and WB4-24

Cong, Z.·Zhou, Q.·Li, Y.·Chen, L.-N.·Zhang, Z.-C.·Liang, A.·Liu, Q.·Wu, X.·Dai, A.·Xia, T.·Wu, W.·Zhang, Y.·Yang, D.·Wang, M.-W.

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Abstract

Glucagon-like peptide-1 receptor (GLP-1R) agonists are effective in treating type 2 diabetes and obesity with proven cardiovascular benefits. However, most of them are peptides and require subcutaneous injection except for orally available semaglutide. Boc5 was identified as the first orthosteric non-peptidic agonist of GLP-1R that mimics a broad spectrum of bioactivities of GLP-1 in vitro and in vivo. Here, we report the cryo-electron microscopy structures of Boc5 and its analog WB4-24 in complex with the human GLP-1R and Gs protein. Bound to the extracellular domain, extracellular loop 2, and transmembrane (TM) helices 1, 2, 3 and 7, one arm of both compounds inserted deeply into the bottom of the orthosteric binding pocket that is usually accessible by peptidic agonists, thereby partially overlapping with the residues A8-D15 in GLP-1. The other three arms, meanwhile, extended to the TM1-TM7, TM1-TM2, and TM2-TM3 clefts showing an interaction feature substantially similar to a previously known small molecule agonist LY3502970. Such a unique binding mode creates a distinct conformation that confers both peptidomimetic agonism and biased signaling induced by non-peptidic modulators at GLP-1R. Further, the conformational difference between Boc5 and WB4-24, two closed related compounds, provides a structural framework for fine tuning of pharmacological efficacy in the development of future small molecule therapeutics targeting GLP-1R. SignificanceGLP-1R agonists are efficacious in the treatment of type 2 diabetes and obesity. While most clinically used agents require subcutaneous injection, Boc5, as the first orthosteric non-peptidic agonist of GLP-1R, suffers from poor oral bioavailability that hinders its therapeutic development. The cryo-electron microscopy structures of Boc5 and its closely related analog WB4-24 presented here reveal a previously unknown binding pocket located deeper in the transmembrane domain for non-peptidic GLP-1R agonists. Molecular interaction with this site may facilitate a broad spectrum of in vivo agonistic activities, in addition to that with the upper helical bundles presumably responsible for biased signaling. These findings deepen our understanding of peptidomimetic agonism at GLP-1R and may help design better drug leads against this important target.

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Cong, Z., Zhou, Q., Li, Y., Chen, L.-N., Zhang, Z.-C., Liang, A., Liu, Q., Wu, X., Dai, A., Xia, T., Wu, W., Zhang, Y., Yang, D., Wang, M.-W.. 2022-01-05. Structural basis of peptidomimetic agonism revealed by small molecule GLP-1R agonists Boc5 and WB4-24. https://doi.org/10.1101/2022.01.05.475023

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