The putative binding site and SAR rationalization of small molecules against glucagon-like peptide-1 receptor using homology model and crystal structures: a comparative study

Abstract

Glucagon-like peptide-1 (GLP-1) is involved in glucose-stimulated insulin secretion and weight regulating actions through the activation of the GLP-1 receptor (GLP-1R). Clinical effectiveness of GLP-1 mimetics is effective in improving glucose control in patients. Thus, identifying and developing orally active small-molecule agonists are highly desirable. This study summarizes the structure-function relationship of hGLP-1R through computational approaches and search of small molecule GLP-1R agonists. We carried out mutation guided data-driven study, for developing the GLP-1R model to explore and validate the putative site for quinoxaline analogues. The developed GLP-1R homology model was subjected to 500 ns MD simulation for validation. Various snapshots were considered to identify the best structure of GLP-1R based on correlation between experimental pEC₅₀ and various theoretical parameters (docking score, MM-GBSA ΔG bind, WM/MM ΔG bind). The putative binding site (Sitemap and WaterMap has been predicted and it matched well with the available data. Excellent correlation (R² =0.94), between pEC50 and WM/MM ΔG bind for the snapshot at 350 ns was observed after including induced-fit docking results of the most potent molecule. Enrichment calculation indicates better AUC (=0.75) for predicted complex structure. A comparison of the developed GLP-1R model with the available crystal structure shows excellent similarities and it was used for virtual screening to find small molecule agonists. The good correlation of our model with crystal structures of GLP-1R may help to understand the structure-function relationship of other secretin families.

Graphical Abstract

Communicated by Ramaswamy H. Sarma

Keywords:

• GLP-1R
• Class-B GPCRs family
• watermap
• docking studies
• virtual screening

Acknowledgements

We acknowledge NIPER-Hajipur, NIPER-Kolkata, and IIT-Guwahati for necessary facilities. VT is thankful to the Ministry of Chemicals and Fertilizers, Department of Pharmaceuticals, Govt. of India for providing fellowship. We are grateful to Dr. Sachchidanand and Dr. Hemant Kumar Srivastava for guidance, fruitful discussion and suggestions. Suyash Pant and Sohini Chakraborti are acknowledged for various help and support.

Disclosure statement

No potential conflict of interest was reported by the author(s).