P2Y6R small molecule antagonist as a potential drug for the treatment of inflammatory diseases in Journal of Medicinal Chemistry

Extracellularpurines and pyrimidines are important signaling molecules from most tissues or organs, and exert their effects to regulate the immuno-inflammatory responseviaactivating purinergic receptors.Purinergic P2Y₆receptor (P2Y₆R), a cysteine-rich andβ-arrestin insensitive GPCR, has strong ligand selectivity for uridine 5’-diphosphate (UDP) and shows a ubiquitous distribution in mammalian tissues. In humans, P2Y₆R contains significant pro-inflammatory and pro-atherogenic role in a wide range of immunecells, including macrophage and T cells. In recent years, the important role of P2Y₆R in the occurrence and development of acute and chronic inflammatory injury and cardiovascular diseases has received widespread attention, and the development of small molecule drugs targeting P2Y₆R for the treatment of inflammatory diseases has become a research hotspot.

In recent years, Huanqiu Li’s group at the College of Pharmaceutical Science of Soochow University has conducted a series of researches on the development of small molecule drugs targeting P2Y₆R and P2Y₁₄R. (J Adv Res 2020, 23, 133-142; Drug Discov Today. 2020, 25, 568-573; Front Immunol 2022, 13, 870183; Eur J Med Chem 2022, 227, 113933; Phytomedicine 2023, 115, 154851.) Based on the above researches, Li group, in collaboration with Assoc. Prof. Sheng Tian from the College of Pharmaceutical Science and Prof. Qinghua Hu from the China Pharmaceutical University, published an online research paper entitled Discovery of Selective P2Y₆R Antagonists with High Affinity and In Vivo Efficacy for Inflammatory Disease Therapy in the Journal of Medicinal Chemistry, a top journal in the field of medicinal chemistry. The College of Pharmaceutical Science of Soochow University is the first unit to complete this article. Zhu Yifan, a graduate student of the College of Pharmaceutical Science, and Dr. Zhou Mengze of China Pharmaceutical University are co-authors. Assoc. Prof. Huanqiu Li, Assoc. Prof. Sheng Tian from the College of Pharmaceutical Science of Soochow University and Prof. Qinghua Hu from China Pharmaceutical University are the cocorresponding authors.

Due to the unclear key characteristics and mechanisms of P2Y₆R binding to compounds, it not only limits further drug design and optimization based on structure, but also hinders the pharmacodynamic research and target confirmation of drug-forming small molecules. This study investigated residues that contribute significantly to the binding of P2Y₆R to small molecules through molecular dynamics (MD) simulations and binding free energy calculations, and predicted the most likely conformation of the P2Y₆R binding site. Then, through the strategy of virtual screening based on large-scale molecular docking and structural optimization of lead compound, we successfully found a new P2Y₆R small molecule antagonist at the nano molar level: compound50(IC₅₀= 5.914 nM).

Figure 1. Construction of virtual screening model and structure optimization strategy for P2Y₆R antagonists.

CETSA and GCI experiments have confirmed that compound50can directly bind to P2Y₆R and exhibits good binding affinity. Subsequently, this study designed a biotin probe for compound50and further explored the mechanism of binding between compound50and P2Y₆R using Chemical pulldown experiments. In addition, compound50exhibits excellent target selectivity and has no inhibitory effect on other subtypes of P2Y receptors at 500 nM, with no significant cytotoxicity. In vivo activity experiments have shown that compound50has good in vivo efficacy in DSS induced ulcerative colitis models and LPS induced acute lung injury models, providing potential drug leads for the development of therapeutic drugs for inflammatory diseases.

Figure 2. Affinity andin vivoactivity study of P2Y₆R antagonist

References:Yifan Zhu, Mengze Zhou, Xiangyu Cheng, Hui Wang, Yehong Li, Yueyue Guo, Yaxuan Wang, Sheng Tian*, Tianqi Mao, Zhoudong Zhang, Duxin Li, Qinghua Hu*, and Huanqiu Li*. Discovery of Selective P2Y₆R Antagonists with High Affinity and In Vivo Efficacy for Inflammatory Disease Therapy.J. Med. Chem.2023, 66, 6315-6332.https://doi.org/10.1021/acs.jmedchem.3c00210

Corresponding authors:

Huanqiu Li, Associate Professor and Master's Supervisor,College of Pharmaceutical Science, Soochow University. The research work of Li’s group mainly focuses on the design, synthesis, and target confirmation of anti-inflammatory and anti-tumor targeted small molecule drugs. Prof. Li has published ~60 academic papers in relevant fields, among which he is the first/co-first/corresponding author in some first-class journals, such as J Med Chem、Drug Discov Today、J Adv Res、Eur J Med Chem、Cell Death Discov、ACS Synth Biol; and authorized 12 Chinese invention patents. He has successively led 10 national and provincial natural science projects, as well as 2 horizontal scientific research projects. He guided the students to win the bronze prize in the 2021 China International Internet plus Innovation and Entrepreneurship Competition, and won the second prize of the Natural Science and Technology Award of the Ministry of Education as the second person to complete the excellent master's degree thesis in Jiangsu Province in 2022.

Sheng Tian, Associate Professor and Master's Supervisor,College of Pharmaceutical Science, Soochow University. He is mainly engaged in the methodology and application research of computer-aided drug molecular design, including the construction of novel virtual screening strategies, prediction of key drug forming parameters, and drug molecular design for important targets. So far, more than 50 papers have been published in SCI, and as the first author or corresponding author, he has published more than 20 papers in the related SCI journals in the pharmaceutical field (Advanced Drug Delivery Reviews, Journal of Medical Chemistry, European Journal of Medical Chemistry, Journal of Chemical Information and Modeling, Molecular Pharmaceutics, etc.), and cited by others for more than 2600 times, H factor 23. Led and concluded the National Natural Science Foundation Youth Fund and Suzhou Science and Technology Development Plan Project Fund, currently researching one Jiangsu Provincial Natural Science Foundation project and two enterprise commissioned horizontal projects.