Embargoed by the journal Nature until March 30, 2015, 4PM (1600) London time /
11AM (1100) U.S. Eastern Time / March 31, 2015, 0AM (0000) Beijing time
New Molecular Structures Challenge Conventional Concepts of Drug Action at
Receptors
Structures of human P2Y1 receptor bring new excitement to GPCR research
SHANGHAI, CHINA – March 31, 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 London time, 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 and Raymond Stevens of the Bridge Institute at the University of Southern
California, and Raymond Stevens from the iHuman Institute, ShanghaiTech
University.
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.
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://www.shanghaitech.edu.cn/en/en_iHuman_Overview.asp.
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.
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.)