Structural basis for chemotype diversity in small molecule GLP-1 receptor agonist drug discovery

The glucagon-like peptide-1 receptor (GLP-1R) is an established therapeutic target for treating obesity and related diseases with several approved injectable peptide agonists on the market. Small molecule GLP-1R agonists, which offer great potential in accessibility, patient compliance, and maintenance compared to their peptide counterparts, are now progressing into late-stage clinical trials. Four different GLP-1 small molecule agonist chemotypes are currently known and here we compare their diverse binding modes and receptor conformations and introduce a novel Class B GPCR binding pocket nomenclature. To further understand the binding pocket and structure-based drug discovery opportunities, five novel high resolution cryo-EM structures of GLP-1R bound to small molecule agonists with different biased signaling properties were determined (aleniglipron, lotiglipron, compound 73, compound 3b, and compound 355), together with a comparative structural analysis of other known GLP-1 small molecule structures. We demonstrate how complementary lipophilic hotspot and water network analyses of the multiple GLP-1R structures provide new insights into GLP-1R agonist structure-activity relationships (SAR) and receptor activation mechanism, enabling new GLP-1 small molecule drug design strategies.