Exploring GPR109A receptor interaction with hippuric acid using MD simulations and CD spectroscopy

Authors: BHANDARI, DIPENDRA - Arkansas Children'S Nutrition Research Center (ACNC); KACHHAP, SANGITA - Polish Academy Of Sciences; MADHUKAR, GEET - Arkansas Children'S Nutrition Research Center (ACNC); ADEPU, KIRAN KUMAR - Arkansas Children'S Nutrition Research Center (ACNC); ANISHKIN, ANDRIY - University Of Maryland; CHEN, JIN-RAN - Arkansas Children'S Nutrition Research Center (ACNC); CHINTAPALLI, SREE - Arkansas Children'S Nutrition Research Center (ACNC)

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2022
Publication Date: 11/26/2022
Citation: Bhandari, D., Kachhap, S., Madhukar, G., Adepu, K., Anishkin, A., Chen, J., Chintapalli, S.V. 2022. Exploring GPR109A receptor interaction with hippuric acid using MD simulations and CD spectroscopy. International Journal of Molecular Sciences. 23(23):14778. https://doi.org/10.3390/ijms232314778.
DOI: https://doi.org/10.3390/ijms232314778

Interpretive Summary: Blueberry supplemented diet has been previously shown to significantly stimulate bone formation in rapidly growing rodents of both males and females. Phenolic acids (PAs) are metabolites derived from polyphenols found majorly in fruits and vegetables due to the action of gut bacteria. As a result, PAs like Hippuric acid (HA) and 3-3-hydroxyphenyl propionic acid (3-3-H-PPA) are the products of gut microbiome in the serum of rats fed blueberry containing diet. It has been proposed that these HA resembles niacin in structural similarity and act via G-protein coupled receptor GPR109A, a transmembrane protein which mediates the antilipolytic effect of niacin. Thus, it is important to understand HA-GPR109A structural interactions. Based on the docking and molecular dynamics simulation studies, HA binds to GPR109A similarly to niacin. Computational structural analysis reveals the importance of critical basic residues in the crevice, which along with other hydrophobic residues in binding and residues R111, K166, S178, S179 and R251 play a significant role in the HA binding to GPR109A.

Technical Abstract: Previous research has indicated that various metabolites belonging to phenolic acids (PAs), produced by gut microflora through the breakdown of polyphenols, help in promoting bone development and protecting bone from degeneration. Results have also suggested that G-protein-coupled receptor 109A (GPR109A) functions as a receptor for those specific PAs such as hippuric acid (HA) and 3-(3-hydroxyphenyl) propionic acid (3-3-PPA). Indeed, HA has a molecular structural similarity with nicotinic acid (niacin) which has been shown previously to bind to GPR109A receptor and to mediate antilipolytic effects; however, the binding pocket and the structural nature of the interaction remain to be recognized. In the present study, we employed a computational strategy to elucidate the molecular structural determinants of HA binding to GPR109A and GPR109B homology models in understanding the regulation of osteoclastogenesis. Based on the docking and molecular dynamics simulation studies, HA binds to GPR109A similarly to niacin. Specifically, the transmembrane helices 3, 4 and 6 (TMH3, TMH4 and TMH6) and Extracellular loop 1 and 2 (ECL1 and ECL2) residues of GRP109A; R111 (TMH3), K166 (TMH4), ECL2 residues; S178 and S179, and R251 (TMH6), and residues of GPR109B; Y87, Y86, S91 (ECL1) and C177 (ECL2) contribute for HA binding. Simulations and Molecular Mechanics Poisson-Boltzmann solvent accessible area (MM-PBSA) calculations reveal that HA has higher affinity for GPR109A than for GPR109B. Additionally, in silico mutation analysis of key residues have disrupted the binding and HA exited out from the GPR109A protein. Furthermore, measurements of time-resolved circular dichroism spectra revealed that there are no major conformational changes in the protein secondary structure on HA binding. Taken together, our findings suggest a mechanism of interaction of HA with both GPR109A and GPR109B receptors.