Structures of human P2Y₁ receptor bring new excitement to GPCR research

SHANGHAI, CHINA – March 30, 2015 – A team of Chinese and US scientists has determined the high-resolution atomic structure of a cell-surface receptor that plays a critical role in thrombosis, or blood clot, formation. This research unexpectedly discloses many new structural features, which challenge the conventional concepts of drug action at G protein-coupled receptors (GPCRs) and open a new door for future drug discovery.

In a paper published in Nature on March 30, the researchers at Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, collaborating with research groups from National Institutes of Health (NIH, U.S.), Bridge Institute at University of Southern California (U.S.) and iHuman Institute of ShanghaiTech University (China), provide a detailed molecular map of the human P2Y₁ receptor (P2Y₁R), a GPCR, in complex with a nucleotide antagonist MRS2500 and a non-nucleotide antagonist BPTU.

Human purinergic receptors P2Y₁R and P2Y₁₂R play a major physiological role in adenosine 5′-diphosphate (ADP)-mediated platelet aggregation, an important component of thrombosis, which can subsequently result in life-threatening diseases, such as heart attack and stroke. While most of the available antithrombotic drugs act on P2Y₁₂R, P2Y₁R has been suggested as a new promising antithrombotic drug target and may offer a safety advantage over P2Y₁₂R inhibitors in terms of reduced bleeding liabilities. However, efforts to develop new drugs have been impeded by poor understanding of receptor-ligand interaction.

“The P2Y₁R structures help us understand how this receptor and different types of experimental drugs interact at the molecular level, and could enable further exploration to design new and safer antithrombotic drugs with reduced adverse effects,” said team leader Dr. Beili Wu, Professor of SIMM.

The new study provides many valuable insights into the structure of P2Y₁R. One very exciting finding is that the P2Y₁R structures reveal two completely distinct ligand-binding sites. The nucleotide ligand MRS2500 recognizes a binding site within the transmembrane bundle of P2Y₁R; however, it is different in shape and location from the nucleotide-binding site in P2Y₁₂R structure previously determined by the same collaboration. Although recognized by the same endogenous ligand ADP, P2Y₁R and P2Y₁₂R structures reveal very different features in binding their nucleotide ligands. “It is amazing to observe that two GPCRs recognize the same ligand in such different ways,” said Dr. Wu. “The finding highlights the diversity of signal recognition mechanisms in GPCRs, and this is of great value to drug design for each receptor with high selectivity.”

The most surprising finding of this research is that, instead of interacting within the transmembrane bundle, the non-nucleotide ligand BPTU binds to a pocket on the outer interface of the receptor that is embedded in the cell membrane. This is the first structurally characterized selective and high affinity GPCR ligand located entirely outside of the helical bundle, and it represents a new paradigm in ligand binding to alter signaling in GPCRs. The P2Y₁R structure opens new opportunities to broaden the scope of future GPCR drug discovery to target novel sites outside of the conventional GPCR ligand-binding pocket, which may greatly improve drug selectivity and reduce side effects, and will thus facilitate the development of new pharmaceuticals for treatment of many severe diseases.

“The new structures will allow drug designers to work more efficiently and with greater precision to build new molecules to modulate the function of this receptor and other closely related receptors, many of which have potential for treating cancer and inflammation,” said Dr. Kenneth Jacobson, Chief of the Laboratory of Bioorganic Chemistry in the National Institute of Diabetes and Digestive and Kidney Diseases at NIH. Jacobson coauthored the study and invented the antagonist MRS2500 that was crystallized with P2Y₁R.

In addition to Wu and Jacobson, the contributors to the study, “Two disparate ligand-binding sites in the human P2Y₁ receptor”, were lead author Dandan Zhang, Kaihua Zhang, Jiang Wang, Cuiying Yi, Limin Ma, Wenru Zhang, Hong Liu, Hualiang Jiang and Qiang Zhao, all of SIMM; Zhan-Guo Gao, Evgeny Kiselev, Steven Crane, and Silvia Paoletta of NIH; Gye Won Han, Vadim Cherezov, Vsevolod Katritch of the Bridge Institute at the University of Southern California.

The study was funded in part by the National Basic Research Program of China (grants 2012CB518000, 2014CB910400 and 2012CB910400), CAS Strategic Priority Research Program (XDB08020300), the National Science Foundation of China (grants 31422017, 31370729 and 91313000), the National Science and Technology Major Project (2013ZX09507001), ShanghaiTech University, Shanghai Municipal Government, the National Institutes of Health (grant Z01 DK031116-26), and the National Institutes of Health Protein Structure Initiative (grant U54 GM094618). To view the study, visit http://www.nature.com.

In the implementation of the “One-Three-Five” strategic plan, SIMM has identified “Significant progress in GPCRs as drug targets” as one of the “3-in-1” focuses of the institute. Since 2013, SIMM has achieved several breakthroughs in research on structure and function of drug targets. There is no doubt that the three dimensional structure determination of P2Y₁R is another breakthrough from SIMM’s “One-Three-Five” development layout. Currently SIMM is taking all strength to establish the Institutes for Drug Research Innovation with the related R&D capability of drug discovery within Chinese Academy of Sciences. As one of the development directions of the Institutes for Drug Research Innovation, basic research aiming at new targets, new biomarkers, new mechanism and novel molecular entities is critical to meet the needs of drug innovation. Therefore, the three dimensional structure determination of P2Y₁R and the discovery of the related drug candidates will definitely lay the foundation for the establishment of the Institutes for Drug Research Innovation.

Figure: The new Nature study reveals the structure of the human P2Y₁ receptor, which mediates thrombosis formation. The image shows that two different ligands that inhibit platelet aggregation interact with P2Y₁R by binding to two completely distinct sites of the receptor. The receptor structure is shown as grey ribbon and surface. The ligands MRS2500 and BPTU are shown as magenta and yellow spheres, respectively. (Image courtesy of Yekaterina Kadyshevskaya of the Bridge Institute at the University of Southern California.)

About Shanghai Institute of Materia Medica, Chinese Academy of Sciences

The Shanghai Institute of Materia Medica (SIMM) at the Chinese Academy of Sciences emerged from the Institute of Materia Medica of the Peking Academy of Sciences, founded in 1932. By combining basic and applied research in chemistry and biological disciplines, SIMM carries out modern drug discovery. SIMM is also involved in the discovery of new therapeutic targets and carries out comprehensive pre-clinical evaluation of drug candidates, while also promoting commercialization, thereby playing a key role in building China's drug innovation capabilities. For more information, visit http://www.simm.cas.cn.

About National Institutes of Health (NIH)

NIH, the U.S.’s medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical and translational medical research, and is investigating the causes, treatments and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.

About University of Southern California

Founded in 1879, the University of Southern California is one of the world’s leading private research universities. An anchor institution in Los Angeles, a global center for arts, technology and international business, USC's diverse curricular offerings provide extensive opportunities for interdisciplinary study, and collaboration with leading researchers in highly advanced learning environments. With a strong tradition of integrating liberal and professional education, USC fosters a vibrant culture of public service and encourages students to cross academic as well as geographic boundaries in their pursuit of knowledge.

About iHuman Institute at ShanghaiTech University

The iHuman Institute was founded in 2012 and is located on the campus of ShanghaiTech University in Shanghai, China. The institute is focused on the study of human cell signaling using a combination of state of the art integrative structural biology, cell biology, chemistry, computational chemistry and biology. For more information, see http://ihuman.shanghaitech.edu.cn/.

To request an interview with Dr. Beili Wu, please contact beiliwu@simm.ac.cn.

To request an interview with Dr. Kenneth Jacobson, please contact Krysten.carrera@nih.gov. The opinions and conclusions are those of the authors of the release and do not necessary reflect the official views of the NIH.